A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus.

PubMed

Livingston, B T; Killian, C E; Wilt, F; Cameron, A; Landrum, M J; Ermolaeva, O; Sapojnikov, V; Maglott, D R; Buchanan, A M; Ettensohn, C A

2006-12-01

Biomineralization, the biologically controlled formation of mineral deposits, is of widespread importance in biology, medicine, and engineering. Mineralized structures are found in most metazoan phyla and often have supportive, protective, or feeding functions. Among deuterostomes, only echinoderms and vertebrates produce extensive biomineralized structures. Although skeletons appeared independently in these two groups, ancestors of the vertebrates and echinoderms may have utilized similar components of a shared genetic "toolkit" to carry out biomineralization. The present study had two goals. First, we sought to expand our understanding of the proteins involved in biomineralization in the sea urchin, a powerful model system for analyzing the basic cellular and molecular mechanisms that underlie this process. Second, we sought to shed light on the possible evolutionary relationships between biomineralization in echinoderms and vertebrates. We used several computational methods to survey the genome of the purple sea urchin Strongylocentrotus purpuratus for gene products involved in biomineralization. Our analysis has greatly expanded the collection of biomineralization-related proteins. We have found that these proteins are often members of small families encoded by genes that are clustered in the genome. Most of the proteins are sea urchin-specific; that is, they have no apparent homologues in other invertebrate deuterostomes or vertebrates. Similarly, many of the vertebrate proteins that mediate mineral deposition do not have counterparts in the S. purpuratus genome. Our findings therefore reveal substantial differences in the primary sequences of proteins that mediate biomineral formation in echinoderms and vertebrates, possibly reflecting loose constraints on the primary structures of the proteins involved. On the other hand, certain cellular and molecular processes associated with earlier events in skeletogenesis appear similar in echinoderms and vertebrates, leaving open the possibility of deeper evolutionary relationships.

Patterning of anteroposterior body axis displayed in the expression of Hox genes in sea cucumber Apostichopus japonicus.

PubMed

Kikuchi, Mani; Omori, Akihito; Kurokawa, Daisuke; Akasaka, Koji

2015-09-01

The presence of an anteroposterior body axis is a fundamental feature of bilateria. Within this group, echinoderms have secondarily evolved pentameral symmetric body plans. Although all echinoderms present bilaterally symmetric larval stages, they dramatically rearrange their body axis and develop a pentaradial body plan during metamorphosis. Therefore, the location of their anteroposterior body axis in adult forms remains a contentious issue. Unlike other echinoderms, sea cucumbers present an obvious anteroposterior axis not rearranged during metamorphosis, thus representing an interesting group to study their anteroposterior axis patterning. Hox genes are known to play a broadly conserved role in anteroposterior axis patterning in deuterostomes. Here, we report the expression patterns of Hox genes from early development to pentactula stage in sea cucumber. In early larval stages, five Hox genes (AjHox1, AjHox7, AjHox8, AjHox11/13a, and AjHox11/13b) were expressed sequentially along the archenteron, suggesting that the role of anteroposterior patterning of the Hox genes is conserved in bilateral larvae of echinoderms. In doliolaria and pentactula stages, eight Hox genes (AjHox1, AjHox5, AjHox7, AjHox8, AjHox9/10, AjHox11/13a, AjHox11/13b, and AjHox11/13c) were expressed sequentially along the digestive tract, following a similar expression pattern to that found in the visceral mesoderm of other bilateria. Unlike other echinoderms, pentameral expression patterns of AjHox genes were not observed in sea cucumber. Altogether, we concluded that AjHox genes are involved in the patterning of the digestive tract in both larvae and metamorphosis of sea cucumbers. In addition, the anteroposterior axis in sea cucumbers might be patterned like that of other bilateria.

The A/P axis in echinoderm ontogeny and evolution: evidence from fossils and molecules

NASA Technical Reports Server (NTRS)

Peterson, K. J.; Arenas-Mena, C.; Davidson, E. H.

2000-01-01

Even though echinoderms are members of the Bilateria, the location of their anterior/posterior axis has remained enigmatic. Here we propose a novel solution to the problem employing three lines of evidence: the expression of a posterior class Hox gene in the coeloms of the nascent adult body plan within the larva; the anatomy of certain early fossil echinoderms; and finally the relation between endoskeletal plate morphology and the associated coelomic tissues. All three lines of evidence converge on the same answer, namely that the location of the adult mouth is anterior, and the anterior/posterior axis runs from the mouth through the adult coelomic compartments. This axis then orients the animal such that there is but a single plane of symmetry dividing the animal into left and right halves. We tentatively hypothesize that this plane of symmetry is positioned along the dorsal/ventral axis. These axis identifications lead to the conclusion that the five ambulacra are not primary body axes, but instead are outgrowths from the central anterior/posterior axis. These identifications also shed insight into several other evolutionary mysteries of various echinoderm clades such as the independent evolution of bilateral symmetry in irregular echinoids, but do not elucidate the underlying mechanisms of the adult coelomic architecture.

Motoric impairment following manganese exposure in asteroid echinoderms.

PubMed

Sköld, Helen Nilsson; Baden, Susanne P; Looström, Jakob; Eriksson, Susanne P; Hernroth, Bodil E

2015-10-01

In the oceans, naturally occurring manganese (Mn) is released from the sediments during events of hypoxia. While neuro- and immuno-toxic effects of bioavailable manganese are well documented for crustaceans, studies of similar effects of manganese on other marine invertebrates are comparatively few. Here, we developed a new functional test "the repeated turning assay" to investigate if manganese exposure at ∼12 mg L(-1) affected motoric behaviour of two asteroid echinoderms, the Common sea star, Asterias rubens, and the Black brittle star, Ophiocomina nigra. By measuring of the turning-over capacity, from dorsal to ventral position, after one and two weeks of manganese exposure, we showed that for both species Mn exposure significantly delayed the ability to turn. After a recovery period of two weeks, the capacity of turning-over was not restored to that of unexposed animals neither for A. rubens nor for O. nigra. Further investigation of sea stars showed that Mn accumulated ∼5 fold in the tube feet, organs involved in their turning-over activity, and the high concentration remained after the recovery period. In the tube feet we also recorded an increased activity of acetylcholinesterase (AChE), here used as a proxy for neuromuscular disturbances. The results indicated that Mn induces neuromuscular disturbance in echinoderms which is important news, given that previous studies have concluded that adult echinoderms are relatively tolerant to Mn. Copyright © 2015 Elsevier B.V. All rights reserved.

The inorganic constituents of echinoderms

USGS Publications Warehouse

Clarke, F.W.; Wheeler, W.C.

1915-01-01

In a recent paper on the composition of crinoid skeletons we showed that crinoids contain large quantities of magnesia, and that its proportion varies with the temperature of the water in which the creatures live. This result was so novel and surprising that it seemed desirable to examine other echinoderms and to ascertain whether they showed the same characteristics and regularity. A number of sea urchins and starfishes were therefore studied, their inorganic constituents being analyzed in the same manner as those of the crinoids

Development of the five primary podia from the coeloms of a sea star larva: homology with the echinoid echinoderms and other deuterostomes

PubMed Central

Morris, Valerie B.; Selvakumaraswamy, Paulina; Whan, Renée; Byrne, Maria

2009-01-01

Confocal laser scanning microscopy of larvae of the asteroid Parvulastra exigua was used to investigate the development of the five primary podia from the coeloms in the echinoderm phylum in an approach to the problem of morphological homology in the deuterostome phyla. The development is shown from an early brachiolaria larval stage to a pre-settlement late brachiolaria larval stage. In the early brachiolaria larva, a single enterocoele connected to the archenteron has formed into two lateral coeloms and an anterior coelom. The primary podia form from the coelomic regions on the left side of the brachiolaria larva, while on the right the coelomic regions connect with the exterior through the pore canal and hydropore. The anterior coelom forms the coelom of the brachia. Homology between the primary podia of the asteroid and the echinoid classes of echinoderms is described and extended to coeloms of other deuterostome phyla. PMID:19129140

Ependymin, a gene involved in regeneration and neuroplasticity in vertebrates, is overexpressed during regeneration in the echinoderm Holothuria glaberrima.

PubMed

Suárez-Castillo, Edna C; Medina-Ortíz, Wanda E; Roig-López, José L; García-Arrarás, José E

2004-06-09

We report the characterization of an ependymin-related gene (EpenHg) from a regenerating intestine cDNA library of the sea cucumber Holothuria glaberrima. This finding is remarkable because no ependymin sequence has ever been reported from invertebrates. Database comparisons of the conceptual translation of the EpenHg gene reveal 63% similarity (47% identity) with mammalian ependymin-related proteins (MERPs) and close relationship with the frog and piscine ependymins. We also report the partial sequences of ependymin representatives from another species of sea cucumber and from a sea urchin species. Conventional and real-time reverse transcriptase polymerase chain reaction (RT-PCRs) show that the gene is expressed in several echinoderm tissues, including esophagus, mesenteries, gonads, respiratory trees, hemal system, tentacles and body wall. Moreover, the ependymin product in the intestine is overexpressed during sea cucumber intestinal regeneration. The discovery of ependymins in echinoderms, a group well known for their regenerative capacities, can give us an insight on the evolution and roles of ependymin molecules.

The Biology of the Germ line in Echinoderms

PubMed Central

Wessel, Gary M.; Brayboy, Lynae; Fresques, Tara; Gustafson, Eric A.; Oulhen, Nathalie; Ramos, Isabela; Reich, Adrian; Swartz, S. Zachary; Yajima, Mamiko; Zazueta, Vanessa

2014-01-01

SUMMARY The formation of the germ line in an embryo marks a fresh round of reproductive potential. The developmental stage and location within the embryo where the primordial germ cells (PGCs) form, however, differs markedly among species. In many animals, the germ line is formed by an inherited mechanism, in which molecules made and selectively partitioned within the oocyte drive the early development of cells that acquire this material to a germ-line fate. In contrast, the germ line of other animals is fated by an inductive mechanism that involves signaling between cells that directs this specialized fate. In this review, we explore the mechanisms of germ-line determination in echinoderms, an early-branching sister group to the chordates. One member of the phylum, sea urchins, appears to use an inherited mechanism of germ-line formation, whereas their relatives, the sea stars, appear to use an inductive mechanism. We first integrate the experimental results currently available for germ line determination in the sea urchin, for which considerable new information is available, and then broaden the investigation to the lesser-known mechanisms in sea stars and other echinoderms. Even with this limited insight, it appears that sea stars, and perhaps the majority of the echinoderm taxon, rely on inductive mechanisms for germ-line fate determination. This enables a strongly contrasted picture for germ-line determination in this phylum, but one for which transitions between different modes of germ-line determination might now be experimentally addressed. PMID:23900765

Echinoderm adhesive secretions: from experimental characterization to biotechnological applications.

PubMed

Flammang, P; Santos, R; Haesaerts, D

2005-01-01

Adhesion is a way of life in echinoderms. Indeed, all the species belonging to this phylum use adhesive secretions extensively for various vital functions. According to the species or to the developmental stage considered, different adhesive systems may be recognized. (1) The tube feet or podia are organs involved in attachment to the substratum, locomotion, feeding or burrowing. Their temporary adhesion relies on a duo-gland adhesive system resorting to both adhesive and de-adhesive secretions. (2) The larval adhesive organs allow temporary attachment of larvae during settlement and strong fixation during metamorphosis. (3) The Cuvierian tubules are sticky defence organs occurring in some holothuroid species. Their efficacy is based on the instantaneous release of a quick-setting adhesive. All these systems rely on different types of adhesion and therefore differ in the way they operate, in their structure and in the composition of their adhesive. In addition to fundamental interests in echinoderm bioadhesives, a substantial impetus behind understanding these adhesives are the potential technological applications that can be derived from their knowledge. These applications cover two broad fields of applied research: design of water-resistant adhesives and development of new antifouling strategies. In this context, echinoderm adhesives could offer novel features or performance characteristics for biotechnological applications. For example, the rapidly attaching adhesive of Cuvierian tubules, the releasable adhesive of tube feet or the powerful adhesive of asteroid larvae could each be useful to address particular bioadhesion problems.

Studying the Relative Strengths of Environmental Factors that Influence Echinoderm Body Size Trends

NASA Astrophysics Data System (ADS)

Low, A.; Randhawa, S.; Heim, N. A.; Payne, J.

2013-12-01

Body size is often a useful metric in observing how a clade responds to environmental changes. Previous research has uncovered how environmental factors such as carbon dioxide and oxygen levels influence body size evolution. However, we wanted to look into how these natural factors interact and which factors seem to have a stronger relative influence on echinoderm body size. We analyzed carbon dioxide levels, a proxy for paleotemperature, oxygen levels, and sea level. Our research process involved measuring and calculating the volume of Phanerozoic echinoderm fossils recorded in the Treatise on Invertebrate Paleontology, plotting their mean volumes over various natural factors, and using statistical tools such as correlation tests and the PaleoTS statistical analysis software to compare the relative strengths of these factors. Furthermore, we divided our data into the following three subsets to uncover more specific relationships: 1) A set that included all data of the phylum Echinodermata 2) A set that focused on the two classes with the most recorded data, Echinoidea and Crinoidea 3) A set that focused on the crinoid specimens that originated in the Paleozoic and in the post-Paleozoic. In the first subset, echinoderms had the strongest correlation with carbon dioxide, a proxy for temperature, and possessed a weaker correlation with oxygen. In the second subset, we discovered that the echinoid data also possessed a strong correlation with carbon dioxide and a weaker correlation with oxygen. For crinoids, we found that the class as a whole showed no strong correlation with any measured environmental factors. However, when we divided the crinoids based on age, we found that both Paleozoic and post-Paleozoic crinoids individually correlated strongly with sea level. However, some uncertainty with this correlation arose as the comparison of the environmental correlate models suggested that an unbiased random walk was the best fit for the data. This stands as a sharp contrast to the strong evidence provided by the appropriate graphs and correlation tests that indicate strong, dominant relationships between body size and environmental factors. Thus, though further research is necessary to settle such uncertainty, we were able to identify, observe, and compare the diversity in body size responses to environmental factors within echinoderms.

Effects of long-term elevated temperature on covering, sheltering and righting behaviors of the sea urchin Strongylocentrotus intermedius

PubMed Central

Zhang, Lisheng; Zhang, Lingling; Shi, Dongtao; Wei, Jing; Chang, Yaqing

2017-01-01

Increases in ocean temperature due to climate change are predicted to change the behaviors of marine invertebrates. Altered behaviors of keystone ecosystem engineers such as echinoderms will have consequences for the fitness of individuals, which are expected to flow on to the local ecosystem. Relatively few studies have investigated the behavioral responses of echinoderms to long-term elevated temperature. We investigated the effects of exposure to long-term (∼31 weeks) elevated temperature (∼3 °C above the ambient water temperature) on covering, sheltering and righting behaviors of the sea urchin Strongylocentrotus intermedius. Long-term elevated temperature showed different effects on the three behaviors. It significantly decreased covering behavior, including both covering behavior reaction (time to first covering) and ability (number of covered sea urchins and number of shells used for covering). Conversely, exposure to long-term elevated temperature significantly increased sheltering behavior. Righting response in S. intermedius was not significantly different between temperature treatments. The results provide new information into behavioral responses of echinoderms to ocean warming. PMID:28348933

An astral simulacrum of the central spindle accounts for normal, spindle-less, and anucleate cytokinesis in echinoderm embryos

PubMed Central

Su, Kuan-Chung; Bement, William M.; Petronczki, Mark; von Dassow, George

2014-01-01

Cytokinesis in animal cells depends on spindle-derived spatial cues that culminate in Rho activation, and thereby actomyosin assembly, in a narrow equatorial band. Although the nature, origin, and variety of such cues have long been obscure, one component is certainly the Rho activator Ect2. Here we describe the behavior and function of Ect2 in echinoderm embryos, showing that Ect2 migrates from spindle midzone to astral microtubules in anaphase and that Ect2 shapes the pattern of Rho activation in incipient furrows. Our key finding is that Ect2 and its binding partner Cyk4 accumulate not only at normal furrows, but also at furrows that form in the absence of associated spindle, midzone, or chromosomes. In all these cases, the cell assembles essentially the same cytokinetic signaling ensemble—opposed astral microtubules decorated with Ect2 and Cyk4. We conclude that if multiple signals contribute to furrow induction in echinoderm embryos, they likely converge on the same signaling ensemble on an analogous cytoskeletal scaffold. PMID:25298401

A trans-Atlantic examination of haddock Melanogrammus aeglefinus food habits.

PubMed

Tam, J C; Link, J S; Large, S I; Bogstad, B; Bundy, A; Cook, A M; Dingsør, G E; Dolgov, A V; Howell, D; Kempf, A; Pinnegar, J K; Rindorf, A; Schückel, S; Sell, A F; Smith, B E

2016-06-01

The food habits of Melanogrammus aeglefinus were explored and contrasted across multiple north-eastern and north-western Atlantic Ocean ecosystems, using databases that span multiple decades. The results show that among all ecosystems, echinoderms are a consistent part of M. aeglefinus diet, but patterns emerge regarding where and when M. aeglefinus primarily eat fishes v. echinoderms. Melanogrammus aeglefinus does not regularly exhibit the increase in piscivory with ontogeny that other gadoids often show, and in several ecosystems there is a lower occurrence of piscivory. There is an apparent inverse relationship between the consumption of fishes and echinoderms in M. aeglefinus over time, where certain years show high levels of one prey item and low levels of the other. This apparent binary choice can be viewed as part of a gradient of prey options, contingent upon a suite of factors external to M. aeglefinus dynamics. The energetic consequences of this prey choice are discussed, noting that in some instances it may not be a choice at all. © 2016 The Fisheries Society of the British Isles.

Signal transduction at fertilization: the Ca2+ release pathway in echinoderms and other invertebrate deuterostomes.

PubMed

Townley, Ian K; Roux, Michelle M; Foltz, Kathy R

2006-04-01

Gamete interaction and fusion triggers a number of events that lead to egg activation and development of a new organism. A key event at fertilization is the rise in intracellular calcium. In deuterostomes, this calcium is released from the egg's endoplasmic reticulum and is necessary for proper activation. This article reviews recent data regarding how gamete interaction triggers the initial calcium release, focusing on the echinoderms (invertebrate deuterostomes) as model systems. In eggs of these animals, Src-type kinases and phospholipase C-gamma are required components of the initial calcium trigger pathway in eggs.

Mid-Pacific Marine Laboratory. Annual report for the period, 1 October 1977--30 September 1978

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reese, E.S.; Johnson, V.R. Jr.

1979-03-01

Studies on behavior included reproduction and sociobiology of reef fishes and aggression, hearing, and ultrasonic telemetry in sharks. Ecological studies included population, growth, and mortality studies on birds, corals, crustacea, echinoderms, fishes, molluscs, and rats. Geochemistry studies included biogeochemistry of reef organisms and hydrogeochemistry of groundwater. Geology studies included bioerosion of sea urchins, biology of endolithic processes, and survey of soils. Oceanography studies were conducted on lagoon circulation. Physiological studies were conducted on symbiosis in corals and utilization of organic material by Foraminifera. Studies on systematics of algae, echinoderms, and fishes were conducted. (HLW)

Sea urchin spine calcite forms via a transient amorphous calcium carbonate phase.

PubMed

Politi, Yael; Arad, Talmon; Klein, Eugenia; Weiner, Steve; Addadi, Lia

2004-11-12

The skeletons of adult echinoderms comprise large single crystals of calcite with smooth convoluted fenestrated morphologies, raising many questions about how they form. By using water etching, infrared spectroscopy, electron diffraction, and environmental scanning electron microscopy, we show that sea urchin spine regeneration proceeds via the initial deposition of amorphous calcium carbonate. Because most echinoderms produce the same type of skeletal material, they probably all use this same mechanism. Deposition of transient amorphous phases as a strategy for producing single crystals with complex morphology may have interesting implications for the development of sophisticated materials.

Oral Region Homologies in Paleozoic Crinoids and Other Plesiomorphic Pentaradial Echinoderms

PubMed Central

Kammer, Thomas W.; Sumrall, Colin D.; Zamora, Samuel; Ausich, William I.; Deline, Bradley

2013-01-01

The phylogenetic relationships between major groups of plesiomorphic pentaradial echinoderms, the Paleozoic crinoids, blastozoans, and edrioasteroids, are poorly understood because of a lack of widely recognized homologies. Here, we present newly recognized oral region homologies, based on the Universal Elemental Homology model for skeletal plates, in a wide range of fossil taxa. The oral region of echinoderms is mainly composed of the axial, or ambulacral, skeleton, which apparently evolved more slowly than the extraxial skeleton that forms the majority of the body. Recent phylogenetic hypotheses have focused on characters of the extraxial skeleton, which may have evolved too rapidly to preserve obvious homologies across all these groups. The axial skeleton conserved homologous suites of characters shared between various edrioasteroids and specific blastozoans, and between other blastozoans and crinoids. Although individual plates can be inferred as homologous, no directly overlapping suites of characters are shared between edrioasteroids and crinoids. Six different systems of mouth (peristome) plate organization (Peristomial Border Systems) are defined. These include four different systems based on the arrangement of the interradially-positioned oral plates and their peristomial cover plates, where PBS A1 occurs only in plesiomorphic edrioasteroids, PBS A2 occurs in plesiomorphic edrioasteroids and blastozoans, and PBS A3 and PBS A4 occur in blastozoans and crinoids. The other two systems have radially-positioned uniserial oral frame plates in construction of the mouth frame. PBS B1 has both orals and uniserial oral frame plates and occurs in edrioasterid and possibly edrioblastoid edrioasteroids, whereas PBS B2 has exclusively uniserial oral frame plates and is found in isorophid edrioasteroids and imbricate and gogiid blastozoans. These different types of mouth frame construction offer potential synapomorphies to aid in parsimony-based phylogenetics for exploring branching order among stem groups on the echinoderm tree of life. PMID:24244284

Mg and Sr in Arctic echinoderm calcite: Nature or nurture?

NASA Astrophysics Data System (ADS)

Iglikowska, A.; Borszcz, T.; Drewnik, A.; Grabowska, M.; Humphreys-Williams, E.; Kędra, M.; Krzemińska, M.; Piwoni-Piórewicz, A.; Kukliński, P.

2018-04-01

The Mg/Ca and Sr/Ca ratios in echinoderm skeletal calcite are used as a proxy for Phanerozoic seawater changes, since the skeletal concentrations are, to some extent, controlled by environmental factors. However, it remains unclear how the influence of environmental factors is modified by vital effects, especially in polar waters. Therefore, the goal of this study was to compare the ratios of Mg/Ca and Sr/Ca among the skeletal parts of 10 common Arctic echinoderm species belonging to three classes Echinoidea, Asteroidea and Ophiuroidea that contribute substantially to the carbon cycle in the Arctic benthic system. Significant differences were recorded in echinoid skeletal element concentrations among specific skeletal parts. The lowest Mg/Ca and Sr/Ca ratios were detected in the spines (mean Mg/Ca 37.5 ± 8.8 SD; Sr/Ca 1.8 ± 0.1). The components of the Aristotle's lantern (epiphyses, pyramids and rotulas) were characterised by the highest Mg levels (Mg/Ca 79.9 ± 6.0; 75.2 ± 9.1; 60.1 ± 3.8, respectively). It is likely that mouth parts experience greater mechanical pressure compared to other body parts, and the higher content of Mg in the Aristotle's lantern contributes to its robustness. We did not find any distinctive trends in the distribution of skeletal elements in the asteroid and ophiuroid skeletal parts. The heterogeneous concentrations of Mg and Sr in different skeleton parts of the echinoids suggest possible physiological regulation of the chemical composition rather than the composition only being influenced by the environment. We cannot recommend echinoderm skeletons as reliable indicators in palaeoenvironmental reconstructions due to the possible biological control of skeletal chemistry, which may interfere with the effect of environmental variables.

Every which way--nanos gene regulation in echinoderms.

PubMed

Oulhen, Nathalie; Wessel, Gary M

2014-03-01

Nanos is an essential factor of germ line success in all animals tested. This gene encodes a Zn-finger RNA-binding protein that in complex with its partner pumilio binds to and changes the fate of several known transcripts. We summarize here the documented functions of Nanos in several key organisms, and then emphasize echinoderms as a working model for how nanos expression is regulated. Nanos presence outside of the target cells is often detrimental to the animal, and in sea urchins, nanos expression appears to be regulated at every step of transcription, and post-transcriptional activity, making this gene product exciting, every which way. Copyright © 2013 Wiley Periodicals, Inc.

Every which way – nanos gene regulation in echinoderms

PubMed Central

Oulhen, Nathalie; Wessel, Gary M.

2014-01-01

Nanos is an essential factor of germ line success in all animals tested. This gene encodes a Zn-finger RNA-binding protein that in complex with its partner pumilio, binds to and changes the fate of several known transcripts. We summarize here the documented functions of nanos in several key organisms, and then emphasize echinoderms as a working model for how nanos expression is regulated. Nanos presence outside of the target cells is often detrimental to the animal, and in sea urchins, nanos expression appears to be regulated at every step of transcription, and post-transcriptional activity, making this gene product exciting, every which way. PMID:24376110

Hemichordate models.

PubMed

Tagawa, Kuni

2016-08-01

Hemichordates are marine animals with two different lifestyles. The solitary, free-living enteropneusts or acorn worms resemble polychaetes or earthworms, while the tiny, colonial, sessile pterobranchs are similar to bryozoans and phoronids. Hemichordates, together with echinoderms, comprise the clade Ambulacraria and are a sister group to the Chordata. As adults, they exhibit cardinal chordate characters, such as gill slits. Their embryogenesis and dipleurula-type (tornaria) larvae are very similar to those of echinoderms. Recent advances in comparative genomics and molecular developmental biology of hemichordates, especially the vermiform enteropneusts, have shed light on deuterostome ancestors. This paper briefly reviews the numerous recent studies on the Phylum Hemichordata. Copyright © 2016 Elsevier Ltd. All rights reserved.

Regeneration in bipinnaria larvae of the bat star Patiria miniata induces rapid and broad new gene expression.

PubMed

Oulhen, Nathalie; Heyland, Andreas; Carrier, Tyler J; Zazueta-Novoa, Vanesa; Fresques, Tara; Laird, Jessica; Onorato, Thomas M; Janies, Daniel; Wessel, Gary

2016-11-01

Some metazoa have the capacity to regenerate lost body parts. This phenomenon in adults has been classically described in echinoderms, especially in sea stars (Asteroidea). Sea star bipinnaria larvae can also rapidly and effectively regenerate a complete larva after surgical bisection. Understanding the capacity to reverse cell fates in the larva is important from both a developmental and biomedical perspective; yet, the mechanisms underlying regeneration in echinoderms are poorly understood. Here, we describe the process of bipinnaria regeneration after bisection in the bat star Patiria miniata. We tested transcriptional, translational, and cell proliferation activity after bisection in anterior and posterior bipinnaria halves as well as expression of SRAP, reported as a sea star regeneration associated protease (Vickery et al., 2001b). Moreover, we found several genes whose transcripts increased in abundance following bisection, including: Vasa, dysferlin, vitellogenin 1 and vitellogenin 2. These results show a transformation following bisection, especially in the anterior halves, of cell fate reassignment in all three germ layers, with clear and predictable changes. These results define molecular events that accompany the cell fate changes coincident to the regenerative response in echinoderm larvae. Crown Copyright © 2016. Published by Elsevier Ireland Ltd. All rights reserved.

How do changes in parental investment influence development in echinoid echinoderms?

PubMed

Alcorn, Nicholas J; Allen, Jonathan D

2009-01-01

Understanding the relationship between egg size, development time, and juvenile size is critical to explaining patterns of life-history evolution in marine invertebrates. Currently there is conflicting information about the effects of changes in egg size on the life histories of echinoid echinoderms. We sought to resolve this conflict by manipulating egg size and food level during the development of two planktotrophic echinoid echinoderms: the green sea urchin, Strongylocentrotus droebachiensis and the sand dollar, Echinarachnius parma. Based on comparative datasets, we predicted that decreasing food availability and egg size would increase development time and reduce juvenile size. To test our prediction, blastomere separations were performed in both species at the two-cell stage to reduce egg volume by 50%, producing whole- and half-size larvae that were reared to metamorphosis under high or low food levels. Upon settlement, age at metamorphosis, juvenile size, spine number, and spine length were measured. As predicted, reducing egg size and food availability significantly increased age at metamorphosis and reduced juvenile quality. Along with previous egg size manipulations in other echinoids, this study suggests that the relationship between egg size, development time, and juvenile size is strongly dependent upon the initial size of the egg.

Long-term change in benthopelagic fish abundance in the abyssal northeast Pacific Ocean.

PubMed

Bailey, D M; Ruhl, H A; Smith, K L

2006-03-01

Food web structure, particularly the relative importance of bottom-up and top-down control of animal abundances, is poorly known for the Earth's largest habitats: the abyssal plains. A unique 15-yr time series of climate, productivity, particulate flux, and abundance of primary consumers (primarily echinoderms) and secondary consumers (fish) was examined to elucidate the response of trophic levels to temporal variation in one another. Towed camera sled deployments in the abyssal northeast Pacific (4100 m water depth) showed that annual mean numbers of the dominant fish genus (Coryphaenoides spp.) more than doubled over the period 1989-2004. Coryphaenoides spp. abundance was significantly correlated with total abundance of mobile epibenthic megafauna (echinoderms), with changes in fish abundance lagging behind changes in the echinoderms. Direct correlations between surface climate and fish abundances, and particulate organic carbon (POC) flux and fish abundances, were insignificant, which may be related to the varied response of the potential prey taxa to climate and POC flux. This study provides a rare opportunity to study the long-term dynamics of an unexploited marine fish population and suggests a dominant role for bottom-up control in this system.

The echinoderm collagen fibril: a hero in the connective tissue research of the 1990s.

PubMed

Szulgit, Greg

2007-07-01

Collagen fibrils are some of the most-abundant and important extracellular structures in our bodies, yet we are unsure of their shape and size. This is largely due to an inherent difficulty in isolating them from their surrounding tissues. Echinoderms have collagenous tissues that are similar to ours in many ways, yet they can be manipulated to easily relinquish their collagen fibrils, providing an excellent opportunity to study native fibrillar structure. In the early 1990s, they were found to defy the commonly accepted fibrillar model of the time in that they were much shorter, they were shaped like double-ended spindles, and their centers exhibited a reversal in molecular polarity. Realization of these features helped to reform the questions that were being asked about vertebrate fibrils, shifting the focus toward shape and size. Since then, researchers working with both groups (echinoderms and vertebrates) have worked together to find the structure of native fibrils. This information will be fundamental in understanding what holds collagenous tissues together at the fibrillar level, and could have important implications for people with Ehlers-Danlos syndrome. (c) 2007 Wiley Periodicals, Inc.

Hox expression in the direct-type developing sand dollar Peronella japonica.

PubMed

Tsuchimoto, Jun; Yamaguchi, Masaaki

2014-08-01

Echinoderms are a curious group of deuterostomes that forms a clade with hemichordates but has a pentameral body plan. Hox complex plays a pivotal role in axial patterning in bilaterians and often occurs in a cluster on the chromosome. In contrast to hemichordates with an organized Hox cluster, the sea urchin Strongylocentrotus purpuratus has a Hox cluster with an atypical organization. However, the current data on hox expression in sea urchin rudiments are fragmentary. We report a comprehensive examination of hox expression in a sand dollar echinoid. Nine hox genes are expressed in the adult rudiment, which are classified into two groups, but hox11/13b belongs to both: one with linear expression in the coelomic mesoderm and another with radial expression around the adult mouth. The linear genes may endow the coelom/mesentery with axial information to direct postmetamorphic transformation of the digestive tract, whereas the radial genes developmentally correlate with the morphological novelties of echinoderms and/or sea urchins. Recruitment of the radial genes except hox11/13b appears to be accompanied by the loss of ancestral/axial roles. This in toto co-option of the hox genes provides insight into the molecular mechanisms underlying the evolution of echinoderms from a bilateral ancestor. © 2014 Wiley Periodicals, Inc.

Novel Insights into the Echinoderm Nervous System from Histaminergic and FMRFaminergic-Like Cells in the Sea Cucumber Leptosynapta clarki

PubMed Central

Hoekstra, Luke A.; Moroz, Leonid L.; Heyland, Andreas

2012-01-01

Understanding of the echinoderm nervous system is limited due to its distinct organization in comparison to other animal phyla and by the difficulty in accessing it. The transparent and accessible, apodid sea cucumber Leptosynapta clarki provides novel opportunities for detailed characterization of echinoderm neural systems. The present study used immunohistochemistry against FMRFamide and histamine to describe the neural organization in juvenile and adult sea cucumbers. Histaminergic- and FMRFaminergic-like immunoreactivity is reported in several distinct cell types throughout the body of L. clarki. FMRFamide-like immunoreactive cell bodies were found in the buccal tentacles, esophageal region and in proximity to the radial nerve cords. Sensory-like cells in the tentacles send processes toward the circumoral nerve ring, while unipolar and bipolar cells close to the radial nerve cords display extensive processes in close association with muscle and other cells of the body wall. Histamine-like immunoreactivity was identified in neuronal somatas located in the buccal tentacles, circumoral nerve ring and in papillae distributed across the body. The tentacular cells send processes into the nerve ring, while the processes of cells in the body wall papillae extend to the surface epithelium and radial nerve cords. Pharmacological application of histamine produced a strong coordinated, peristaltic response of the body wall suggesting the role of histamine in the feeding behavior. Our immunohistochemical data provide evidence for extensive connections between the hyponeural and ectoneural nervous system in the sea cucumber, challenging previously held views on a clear functional separation of the sub-components of the nervous system. Furthermore, our data indicate a potential function of histamine in coordinated, peristaltic movements; consistent with feeding patterns in this species. This study on L. clarki illustrates how using a broader range of neurotransmitter systems can provide better insight into the anatomy, function and evolution of echinoderm nervous sytems. PMID:22970182

Transcriptomic identification of starfish neuropeptide precursors yields new insights into neuropeptide evolution

PubMed Central

Semmens, Dean C.; Mirabeau, Olivier; Moghul, Ismail; Pancholi, Mahesh R.; Wurm, Yannick; Elphick, Maurice R.

2016-01-01

Neuropeptides are evolutionarily ancient mediators of neuronal signalling in nervous systems. With recent advances in genomics/transcriptomics, an increasingly wide range of species has become accessible for molecular analysis. The deuterostomian invertebrates are of particular interest in this regard because they occupy an ‘intermediate' position in animal phylogeny, bridging the gap between the well-studied model protostomian invertebrates (e.g. Drosophila melanogaster, Caenorhabditis elegans) and the vertebrates. Here we have identified 40 neuropeptide precursors in the starfish Asterias rubens, a deuterostomian invertebrate from the phylum Echinodermata. Importantly, these include kisspeptin-type and melanin-concentrating hormone-type precursors, which are the first to be discovered in a non-chordate species. Starfish tachykinin-type, somatostatin-type, pigment-dispersing factor-type and corticotropin-releasing hormone-type precursors are the first to be discovered in the echinoderm/ambulacrarian clade of the animal kingdom. Other precursors identified include vasopressin/oxytocin-type, gonadotropin-releasing hormone-type, thyrotropin-releasing hormone-type, calcitonin-type, cholecystokinin/gastrin-type, orexin-type, luqin-type, pedal peptide/orcokinin-type, glycoprotein hormone-type, bursicon-type, relaxin-type and insulin-like growth factor-type precursors. This is the most comprehensive identification of neuropeptide precursor proteins in an echinoderm to date, yielding new insights into the evolution of neuropeptide signalling systems. Furthermore, these data provide a basis for experimental analysis of neuropeptide function in the unique context of the decentralized, pentaradial echinoderm bauplan. PMID:26865025

Near future ocean acidification increases growth rate of the lecithotrophic larvae and juveniles of the sea star Crossaster papposus.

PubMed

Dupont, Sam; Lundve, Bengt; Thorndyke, Mike

2010-07-15

Ocean acidification (OA) is believed to be a major threat for near-future marine ecosystems, and that the most sensitive organisms will be calcifying organisms and the free-living larval stages produced by most benthic marine species. In this respect, echinoderms are one of the taxa most at risk. Earlier research on the impact of near-future OA on echinoderm larval stages showed negative effects, such as a decreased growth rate, increased mortality, and developmental abnormalities. However, all the long-term studies were performed on planktotrophic larvae while alternative life-history strategies, such as nonfeeding lecithotrophy, were largely ignored. Here, we show that lecithotrophic echinoderm larvae and juveniles are positively impacted by ocean acidification. When cultured at low pH, larvae and juveniles of the sea star Crossaster papposus grow faster with no visible affects on survival or skeletogenesis. This suggests that in future oceans, lecithotrophic species may be better adapted to deal with the threat of OA compared with planktotrophic ones with potentially important consequences at the ecosystem level. For example, an increase in populations of the top predator C. papposus will likely have huge consequences for community structure. Our results also highlight the importance of taking varying life-history strategies into account when assessing the impacts of climate change, an approach that also provides insight into understanding the evolution of life-history strategies.

Up in Arms: Immune and Nervous System Response to Sea Star Wasting Disease.

PubMed

Fuess, Lauren E; Eisenlord, Morgan E; Closek, Collin J; Tracy, Allison M; Mauntz, Ruth; Gignoux-Wolfsohn, Sarah; Moritsch, Monica M; Yoshioka, Reyn; Burge, Colleen A; Harvell, C Drew; Friedman, Carolyn S; Hewson, Ian; Hershberger, Paul K; Roberts, Steven B

2015-01-01

Echinoderms, positioned taxonomically at the base of deuterostomes, provide an important system for the study of the evolution of the immune system. However, there is little known about the cellular components and genes associated with echinoderm immunity. The 2013-2014 sea star wasting disease outbreak is an emergent, rapidly spreading disease, which has led to large population declines of asteroids in the North American Pacific. While evidence suggests that the signs of this disease, twisting arms and lesions, may be attributed to a viral infection, the host response to infection is still poorly understood. In order to examine transcriptional responses of the sea star Pycnopodia helianthoides to sea star wasting disease, we injected a viral sized fraction (0.2 μm) homogenate prepared from symptomatic P. helianthoides into apparently healthy stars. Nine days following injection, when all stars were displaying signs of the disease, specimens were sacrificed and coelomocytes were extracted for RNA-seq analyses. A number of immune genes, including those involved in Toll signaling pathways, complement cascade, melanization response, and arachidonic acid metabolism, were differentially expressed. Furthermore, genes involved in nervous system processes and tissue remodeling were also differentially expressed, pointing to transcriptional changes underlying the signs of sea star wasting disease. The genomic resources presented here not only increase understanding of host response to sea star wasting disease, but also provide greater insight into the mechanisms underlying immune function in echinoderms.

Molecular Phylogeny of the Animal Kingdom.

ERIC Educational Resources Information Center

Field, Katharine G.; And Others

1988-01-01

A rapid sequencing method for ribosomal RNA was applied to the resolution of evolutionary relationships among Metazoa. Describes the four groups (chordates, echinoderms, arthropods, and eucoelomate protostomes) that radiated from the coelomates. (TW)

Hurricane effects on backreef echinoderms of the Caribbean

NASA Astrophysics Data System (ADS)

Aronson, R. B.

1993-11-01

The impacts of Hurricanes Gilbert (1988) and Hugo (1989) on echinoderm assemblages were assessed in backreef habitats in Jamaica and St. Croix, respectively. One site on each island was censused before the hurricanes. Ophiuroids were monitored at the Jamaican site for three years following Hurricane Gilbert, and ophiuroids and echinoids were monitored at the site on St. Croix for two years following Hurricane Hugo. No hurricane-related changes in ophiuroid abundance were observed at either site. Likewise, there was no evidence that Hurricane Hugo altered echinoid abundance at St. Croix. These negative results correlated with an observed lack of hurricane-generated physical disturbance in the backreef areas, despite 6-m waves that broke on the reef crests at the two sites during the storms. Hurricane impacts on mobile faunas appear to depend directly on physical habitat alterations.

Up in arms: Immune and nervous system response to sea star wasting disease

USGS Publications Warehouse

Fuess, Lauren E; Eiselord, Morgan E.; Closek, Collin J.; Tracy, Allison M.; Mauntz, Ruth; Gignoux-Wolfsohn, Sarah; Moritsch, Monica M; Yoshioka, Reyn; Burge, Colleen A.; Harvell, Drew; Friedman, Carolyn S.; Hershberger, Paul K.; Roberts, Steven B.

2015-01-01

Echinoderms, positioned taxonomically at the base of deuterostomes, provide an important system for the study of the evolution of the immune system. However, there is little known about the cellular components and genes associated with echinoderm immunity. The 2013–2014 sea star wasting disease outbreak is an emergent, rapidly spreading disease, which has led to large population declines of asteroids in the North American Pacific. While evidence suggests that the signs of this disease, twisting arms and lesions, may be attributed to a viral infection, the host response to infection is still poorly understood. In order to examine transcriptional responses of the sea star Pycnopodia helianthoides to sea star wasting disease, we injected a viral sized fraction (0.2 μm) homogenate prepared from symptomatic P. helianthoides into apparently healthy stars. Nine days following injection, when all stars were displaying signs of the disease, specimens were sacrificed and coelomocytes were extracted for RNA-seq analyses. A number of immune genes, including those involved in Toll signaling pathways, complement cascade, melanization response, and arachidonic acid metabolism, were differentially expressed. Furthermore, genes involved in nervous system processes and tissue remodeling were also differentially expressed, pointing to transcriptional changes underlying the signs of sea star wasting disease. The genomic resources presented here not only increase understanding of host response to sea star wasting disease, but also provide greater insight into the mechanisms underlying immune function in echinoderms.

Calcium pathway machinery at fertilization in echinoderms

PubMed Central

Ramos, Isabela; Wessel, Gary M.

2016-01-01

Calcium signaling in cells directs diverse physiological processes. The calcium waves triggered by fertilization is a highly conserved calcium signaling event essential for egg activation, and has been documented in every egg tested. This activity is one of the few highly conserved events of egg activation through the course of evolution. Echinoderm eggs, as well as many other cell types, have three main intracellular Ca2+ mobilizing messengers – IP3, cADPR and NAADP. Both cADPR and NAADP were identified as Ca2+ mobilizing messengers using the sea urchin egg homogenate, and this experimental system, along with the intact urchin and starfish oocyte/egg, continues to be a vital tool for investigating the mechanism of action of calcium signals. While many of the major regulatory steps of the IP3 pathway are well resolved, both cADPR and NAADP remain understudied in terms of our understanding of the fundamental process of egg activation at fertilization. Recently, NAADP has been shown to trigger Ca2+ release from acidic vesicles, separately from the ER, and a new class of calcium channels, the two-pore channels (TPCs), was identified as the likely targets for this messenger. Moreover, it was found that both cADPR and NAADP can be synthesized by the same family of enzymes, the ADP-rybosyl cyclases (ARCs). In this context of increasing amount of information, the potential coupling and functional roles of different messengers, intracellular stores and channels in the formation of the fertilization calcium wave in echinoderms will be critically evaluated. PMID:23218671

Centralspindlin and Chromosomal Passenger Complex Behavior During Normal and Rappaport Furrow Specification in Echinoderm Embryos

PubMed Central

Argiros, Haroula; Henson, Lauren; Holguin, Christiana; Foe, Victoria; Shuster, Charles Bradley

2014-01-01

The chromosomal passenger (CPC) and Centralspindlin complexes are essential for organizing the anaphase central spindle and providing cues that position the cytokinetic furrow between daughter nuclei. However, echinoderm zygotes are also capable of forming “Rappaport furrows” between asters positioned back-to-back without intervening chromosomes. To understand how these complexes contribute to normal and Rappaport furrow formation, we studied the localization patterns of Survivin and mitotic-kinesin-like-protein1 (MKLP1), members respectively of the CPC and the Centralspindlin complex, and the effect of CPC inhibition on cleavage in mono- and binucleate echinoderm zygotes. In zygotes, Survivin initially localized to metaphase chromosomes, upon anaphase onset relocalized to the central spindle and then, together with MKLP1 spread towards the equatorial cortex in an Aurora-dependent manner. Inhibition of Aurora kinase activity resulted in disruption of central spindle organization and furrow regression, although astral microtubule elongation and furrow initiation were normal. In binucleate cells containing two parallel spindles MKLP1 and Survivin localized to the plane of the former metaphase plate, but were not observed in the secondary cleavage plane formed between unrelated spindle poles, except when chromosomes were abnormally present there. However, the secondary furrow was sensitive to Aurora inhibition, indicating that Aurora kinase may still contribute to furrow ingression without chromosomes nearby. Our results provide insights that reconcile classic micromanipulation studies with current molecular understanding of furrow specification in animal cells. PMID:22887753

Holothurian Nervous System Diversity Revealed by Neuroanatomical Analysis

PubMed Central

Díaz-Balzac, Carlos A.; Lázaro-Peña, María I.; Vázquez-Figueroa, Lionel D.; Díaz-Balzac, Roberto J.; García-Arrarás, José E.

2016-01-01

The Echinodermata comprise an interesting branch in the phylogenetic tree of deuterostomes. Their radial symmetry which is reflected in their nervous system anatomy makes them a target of interest in the study of nervous system evolution. Until recently, the study of the echinoderm nervous system has been hindered by a shortage of neuronal markers. However, in recent years several markers of neuronal and fiber subpopulations have been described. These have been used to identify subpopulations of neurons and fibers, but an integrative study of the anatomical relationship of these subpopulations is wanting. We have now used eight commercial antibodies, together with three antibodies produced by our group to provide a comprehensive and integrated description and new details of the echinoderm neuroanatomy using the holothurian Holothuria glaberrima (Selenka, 1867) as our model system. Immunoreactivity of the markers used showed: (1) specific labeling patterns by markers in the radial nerve cords, which suggest the presence of specific nerve tracts in holothurians. (2) Nerves directly innervate most muscle fibers in the longitudinal muscles. (3) Similar to other deuterostomes (mainly vertebrates), their enteric nervous system is composed of a large and diverse repertoire of neurons and fiber phenotypes. Our results provide a first blueprint of the anatomical organization of cells and fibers that form the holothurian neural circuitry, and highlight the fact that the echinoderm nervous system shows unexpected diversity in cell and fiber types and their distribution in both central and peripheral nervous components. PMID:26987052

Developmental gene regulatory network architecture across 500 million years of echinoderm evolution

NASA Technical Reports Server (NTRS)

Hinman, Veronica F.; Nguyen, Albert T.; Cameron, R. Andrew; Davidson, Eric H.

2003-01-01

Evolutionary change in morphological features must depend on architectural reorganization of developmental gene regulatory networks (GRNs), just as true conservation of morphological features must imply retention of ancestral developmental GRN features. Key elements of the provisional GRN for embryonic endomesoderm development in the sea urchin are here compared with those operating in embryos of a distantly related echinoderm, a starfish. These animals diverged from their common ancestor 520-480 million years ago. Their endomesodermal fate maps are similar, except that sea urchins generate a skeletogenic cell lineage that produces a prominent skeleton lacking entirely in starfish larvae. A relevant set of regulatory genes was isolated from the starfish Asterina miniata, their expression patterns determined, and effects on the other genes of perturbing the expression of each were demonstrated. A three-gene feedback loop that is a fundamental feature of the sea urchin GRN for endoderm specification is found in almost identical form in the starfish: a detailed element of GRN architecture has been retained since the Cambrian Period in both echinoderm lineages. The significance of this retention is highlighted by the observation of numerous specific differences in the GRN connections as well. A regulatory gene used to drive skeletogenesis in the sea urchin is used entirely differently in the starfish, where it responds to endomesodermal inputs that do not affect it in the sea urchin embryo. Evolutionary changes in the GRNs since divergence are limited sharply to certain cis-regulatory elements, whereas others have persisted unaltered.

Mass mortality of the West Indian echinoid diadema antillarum: a natural experiment in taphonomy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greenstein, B.J.; Meyer, D.L.

1985-01-01

During 1983, populations of the common long-spined echinoid Diadema antillarum were decimated by disease throughout the West Indies. Depending on the degree of recovery, this mass mortality could have profound effects on the coral reef ecosystem. The role of D. antillarum as a grazer of algae and agent of bioerosion is well documented. The hypothesis that the sudden incorporation of tests and spines of innumerable urchins into the reef sediments would leave a clear record of the mortality event was tested at Bonaire, Netherlands Antilles, where the mortality was witnessed in November, 1983. By August, 1984, there were every fewmore » live D. antillarum, no intact empty tests, but abundant broken up spines in the superficial sediments of the leeward fringing reefs. Sediment samples taken along a series of profiles from 6-36 m depth were analyzed for total echinoderm content and contribution of D. antillarum material. The echinoderm fraction shows a slight increase over pre-mortality levels as reported by Kobluk and Lysenko (1984), but it is not yet clear that this resulted from an increase in D. antillarum. Samples taken from cores 30 cm below the sediment surface show echinoderm fractions equal to or greater than surficial samples, suggesting that bioturbation and turbulence have rapidly disseminated any sharp record of the event. The lack of a strong signal of this event demonstrates the inadequacy of the reef sedimentary record to record many short-term although ecologically significant perturbations.« less

A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence.

PubMed

Delroisse, Jérôme; Ullrich-Lüter, Esther; Blaue, Stefanie; Ortega-Martinez, Olga; Eeckhaut, Igor; Flammang, Patrick; Mallefet, Jérôme

2017-04-01

Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid Amphiura filiformis Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy Renilla (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the Renilla and Amphiura luciferases allowed us to detect the latter using anti- Renilla luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs in vivo However, enzymes homologous to the Renilla luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence. © 2017 The Authors.

A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence

PubMed Central

Ullrich-Lüter, Esther; Blaue, Stefanie; Ortega-Martinez, Olga; Eeckhaut, Igor; Flammang, Patrick; Mallefet, Jérôme

2017-01-01

Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid Amphiura filiformis. Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy Renilla (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the Renilla and Amphiura luciferases allowed us to detect the latter using anti-Renilla luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs in vivo. However, enzymes homologous to the Renilla luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence. PMID:28381628

First echinoderm trehalase from a tropical sea cucumber (Holothuria leucospilota): Molecular cloning and mRNA expression in different tissues, embryonic and larval stages, and under a starvation challenge.

PubMed

Huo, Da; Jiang, Xiao; Wu, Xiaofen; Ren, Chunhua; Yu, Zonghe; Liu, Jinshang; Li, Hongmei; Ruan, Yao; Wen, Jin; Chen, Ting; Hu, Chaoqun

2018-04-29

Trehalases are a group of enzymes that catalyse the conversion of trehalose to glucose, and they are observed in most organisms. In this study, the first echinoderm trehalase, designated Hl-Tre, was identified from a tropical sea cucumber, Holothuria leucospilota. The full-length cDNA of H. leucospilota trehalase (Hl-Tre) is 2461 bp in length with an open reading frame (ORF) of 1788 bp that encodes a 595-amino-acid protein with a deduced molecular weight of 67.95 KDa. The Hl-Tre protein contains a signal peptide at the N-terminal and a functional trehalase domain, which includes the signature motifs 1 and 2. The mRNA expression of Hl-Tre was ubiquitously detected in all selected tissues, with the highest level being detected in the intestine. By in situ hybridization (ISH), the positive Hl-Tre signals were observed in the brush borders of the intestinal mucosa. In embryonic and larval stages, the transcript levels of Hl-Tre decreased during embryonic development and increased after the pentactula stage. After a challenge of starvation, the intestinal Hl-Tre mRNA levels were observed to be first decreased and partially recovered thereafter. Overall, our study provided the first evidence for trehalase in echinoderms and showed that this enzyme was potentially linked to a trehalose metabolic pathway in sea cucumbers. Copyright © 2017. Published by Elsevier B.V.

Carbonate-shelf depositional environments of the Ordovician Viola formation in South-Central Kansas

USGS Publications Warehouse

Newell, K.D.

2000-01-01

The Upper Ordovician Viola Formation, an important petroleum reservoir in the Midcontinent, is a carbonate unit present over much of the subsurface in Kansas. The Viola is composed of two fining-upward sedimentary packages that are separated from each other by a minor karstic surface representing a brief period of exposure. Each package represents a third-order sedimentary cycle and consists of an echinoderm-rich packstone overlain by a thicker lime mudstone. The echinoderm-rich packstone was deposited nearshore in agitated waters, but subsequently was bioturbated. The overlying lime mudstone was deposited in deeper, quiet waters, and locally contains storm-deposited carbonate sands. Subtle growth of the Central Kansas Arch and Pratt Anticline (structures transecting the depositional shelf) is indicated by packstones and grainstones being thicker over these arches, whereas finer grained lithologies dominate in basinal areas on the arch flanks. Structureless lime mudstones, probably intensely bioturbated, grade into laminated lime mudstones farther basinward.

Interfibrillar stiffening of echinoderm mutable collagenous tissue demonstrated at the nanoscale

PubMed Central

Mo, Jingyi; Blowes, Liisa M.; Egertová, Michaela; Terrill, Nicholas J.; Wang, Wen; Elphick, Maurice R.; Gupta, Himadri S.

2016-01-01

The mutable collagenous tissue (MCT) of echinoderms (e.g., sea cucumbers and starfish) is a remarkable example of a biological material that has the unique attribute, among collagenous tissues, of being able to rapidly change its stiffness and extensibility under neural control. However, the mechanisms of MCT have not been characterized at the nanoscale. Using synchrotron small-angle X-ray diffraction to probe time-dependent changes in fibrillar structure during in situ tensile testing of sea cucumber dermis, we investigate the ultrastructural mechanics of MCT by measuring fibril strain at different chemically induced mechanical states. By measuring a variable interfibrillar stiffness (EIF), the mechanism of mutability at the nanoscale can be demonstrated directly. A model of stiffness modulation via enhanced fibrillar recruitment is developed to explain the biophysical mechanisms of MCT. Understanding the mechanisms of MCT quantitatively may have applications in development of new types of mechanically tunable biomaterials. PMID:27708167

Interfibrillar stiffening of echinoderm mutable collagenous tissue demonstrated at the nanoscale.

PubMed

Mo, Jingyi; Prévost, Sylvain F; Blowes, Liisa M; Egertová, Michaela; Terrill, Nicholas J; Wang, Wen; Elphick, Maurice R; Gupta, Himadri S

2016-10-18

The mutable collagenous tissue (MCT) of echinoderms (e.g., sea cucumbers and starfish) is a remarkable example of a biological material that has the unique attribute, among collagenous tissues, of being able to rapidly change its stiffness and extensibility under neural control. However, the mechanisms of MCT have not been characterized at the nanoscale. Using synchrotron small-angle X-ray diffraction to probe time-dependent changes in fibrillar structure during in situ tensile testing of sea cucumber dermis, we investigate the ultrastructural mechanics of MCT by measuring fibril strain at different chemically induced mechanical states. By measuring a variable interfibrillar stiffness (E IF ), the mechanism of mutability at the nanoscale can be demonstrated directly. A model of stiffness modulation via enhanced fibrillar recruitment is developed to explain the biophysical mechanisms of MCT. Understanding the mechanisms of MCT quantitatively may have applications in development of new types of mechanically tunable biomaterials.

Anatomy of the grainstone shoal facies of the Salem Limestone (Mississippian) of southern Indiana

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dodd, J.R.; Petzold, D.D.; Thompson, T.A.

In 1990 M.A. Brown described the middle Mississippian (Valmeyeran) Salem Limestone exposed on the eastern side of the Illinois Basin as consisting of a massive grainstone shoal facies behind which developed a sand flat, an open lagoon, and a restricted lagoon facies. Smaller intrashoal channels provided limited exchange between lagoon and open ocean. The authors have made detailed studies of sedimentary structures and petrography of the shoal facies in three settings: the shoal proper, an intrashoal channel, and an intershoal channel. The shoal and channel facies consists of tabular-planar and trough cross-stratified beds of grainstone containing echinoderm and fenestrate bryozoanmore » grains as their primary constituents. Prominent hardgrounds that have up to 1 m of erosional relief occur in two of the sections. Despite the apparent uniformity of composition of the shoal, porosity and especially permeability varies over a wide range, suggesting a range of cementation patterns within the shoal. Most of the cement in the shoal consists of syntaxial overgrowths on echinoderm grains. Cementation is less and thus porosity and permeability greater, in portions of the shoals containing a lower concentration of echinoderm grains and grains with thick micrite envelopes. However, some portions of the intershoal channel facies that contain a high percentage of ooids have reduced porosity and permeability due to crushing of ooids, producing micrite that clogged the pores. Primary sedimentary features of the shoal facies were produced predominantly by storm reworking of carbonate grains produced in situ and perhaps in part washed in from surrounding environments.« less

The evolution of neuropeptide signalling: insights from echinoderms.

PubMed

Semmens, Dean C; Elphick, Maurice R

2017-09-01

Neuropeptides are evolutionarily ancient mediators of neuronal signalling that regulate a wide range of physiological processes and behaviours in animals. Neuropeptide signalling has been investigated extensively in vertebrates and protostomian invertebrates, which include the ecdysozoans Drosophila melanogaster (Phylum Arthropoda) and Caenorhabditis elegans (Phylum Nematoda). However, until recently, an understanding of evolutionary relationships between neuropeptide signalling systems in vertebrates and protostomes has been impaired by a lack of genome/transcriptome sequence data from non-ecdysozoan invertebrates. The echinoderms-a deuterostomian phylum that includes sea urchins, sea cucumbers and starfish-have been particularly important in providing new insights into neuropeptide evolution. Sequencing of the genome of the sea urchin Strongylocentrotus purpuratus (Class Echinoidea) enabled discovery of (i) the first invertebrate thyrotropin-releasing hormone-type precursor, (ii) the first deuterostomian pedal peptide/orcokinin-type precursors and (iii) NG peptides-the 'missing link' between neuropeptide S in tetrapod vertebrates and crustacean cardioactive peptide in protostomes. More recently, sequencing of the neural transcriptome of the starfish Asterias rubens (Class Asteroidea) enabled identification of 40 neuropeptide precursors, including the first kisspeptin and melanin-concentrating hormone-type precursors to be identified outside of the chordates. Furthermore, the characterization of a corazonin-type neuropeptide signalling system in A. rubens has provided important new insights into the evolution of gonadotropin-releasing hormone-related neuropeptides. Looking forward, the discovery of multiple neuropeptide signalling systems in echinoderms provides opportunities to investigate how these systems are used to regulate physiological and behavioural processes in the unique context of a decentralized, pentaradial bauplan. © The Author 2017. Published by Oxford University Press.

Iterative Calibration: A Novel Approach for Calibrating the Molecular Clock Using Complex Geological Events.

PubMed

Loeza-Quintana, Tzitziki; Adamowicz, Sarah J

2018-02-01

During the past 50 years, the molecular clock has become one of the main tools for providing a time scale for the history of life. In the era of robust molecular evolutionary analysis, clock calibration is still one of the most basic steps needing attention. When fossil records are limited, well-dated geological events are the main resource for calibration. However, biogeographic calibrations have often been used in a simplistic manner, for example assuming simultaneous vicariant divergence of multiple sister lineages. Here, we propose a novel iterative calibration approach to define the most appropriate calibration date by seeking congruence between the dates assigned to multiple allopatric divergences and the geological history. Exploring patterns of molecular divergence in 16 trans-Bering sister clades of echinoderms, we demonstrate that the iterative calibration is predominantly advantageous when using complex geological or climatological events-such as the opening/reclosure of the Bering Strait-providing a powerful tool for clock dating that can be applied to other biogeographic calibration systems and further taxa. Using Bayesian analysis, we observed that evolutionary rate variability in the COI-5P gene is generally distributed in a clock-like fashion for Northern echinoderms. The results reveal a large range of genetic divergences, consistent with multiple pulses of trans-Bering migrations. A resulting rate of 2.8% pairwise Kimura-2-parameter sequence divergence per million years is suggested for the COI-5P gene in Northern echinoderms. Given that molecular rates may vary across latitudes and taxa, this study provides a new context for dating the evolutionary history of Arctic marine life.

Invertebrate Gonadotropin-Releasing Hormone-Related Peptides and Their Receptors: An Update

PubMed Central

Sakai, Tsubasa; Shiraishi, Akira; Kawada, Tsuyoshi; Matsubara, Shin; Aoyama, Masato; Satake, Honoo

2017-01-01

Gonadotropin-releasing hormones (GnRHs) play pivotal roles in reproductive functions via the hypothalamus, pituitary, and gonad axis, namely, HPG axis in vertebrates. GnRHs and their receptors (GnRHRs) are likely to be conserved in invertebrate deuterostomes and lophotrochozoans. All vertebrate and urochordate GnRHs are composed of 10 amino acids, whereas protostome, echinoderm, and amphioxus GnRH-like peptides are 11- or 12-residue peptide containing two amino acids after an N-terminal pyro-Glu. In urochordates, Halocynthia roretzi GnRH gene encodes two GnRH peptide sequences, whereas two GnRH genes encode three different GnRH peptides in Ciona intestinalis. These findings indicate the species-specific diversification of GnRHs. Intriguingly, the major signaling pathway for GnRHRs is intracellular Ca2+ mobilization in chordates, echinoderms, and protostomes, whereas Ciona GnRHRs (Ci-GnRHRs) are endowed with multiple GnRHergic cAMP production pathways in a ligand-selective manner. Moreover, the ligand-specific modulation of signal transduction via heterodimerization among Ci-GnRHR paralogs suggests the species-specific development of fine-tuning of gonadal functions in ascidians. Echinoderm GnRH-like peptides show high sequence differences compared to those of protostome counterparts, leading to the difficulty in classification of peptides and receptors. These findings also show both the diversity and conservation of GnRH signaling systems in invertebrates. The lack of the HPG axis in invertebrates indicates that biological functions of GnRHs are not release of gonadotropins in current invertebrates and common ancestors of vertebrates and invertebrates. To date, authentic or putative GnRHRs have been characterized from various echinoderms and protostomes as well as chordates and the mRNAs have been found to be distributed not only reproductive organs but also other tissues. Collectively, these findings further support the notion that invertebrate GnRHs have biological roles other than the regulation of reproductive functions. Moreover, recent molecular phylogenetic analysis suggests that adipokinetic hormone (AKH), corazonin (CRZ), and AKH/CRZ-related peptide (ACP) belong to the GnRH superfamily but has led to the different classifications of these peptides and receptors using different datasets including the number of sequences and structural domains. In this review, we provide current knowledge of, and perspectives in, molecular basis and evolutionary aspects of the GnRH, AKH, CRZ, and ACP. PMID:28932208

Impact of diagenetic alteration on sea urchin (Echinodermata) magnesium isotope signatures: Comparison of experimental and fossil data

NASA Astrophysics Data System (ADS)

Riechelmann, Sylvia; Mavromatis, Vasileios; Buhl, Dieter; Dietzel, Martin; Hoffmann, René; Jöns, Niels; Eisenhauer, Anton; Immenhauser, Adrian

2017-04-01

Due to their thermodynamically instable high-Mg calcite mineralogy, the skeletal elements of echinoderms are often regarded as unreliable archives of Phanerozoic marine climate dynamics. Nevertheless, traditional and non-traditional isotope and elemental proxy data from echinoderms have been used to reconstruct global changes in palaeoseawater composition (Sandberg-cycles). Recently, these data and the interpretation have been controversially discussed in context with ancient seawater properties. This paper tests the sensitivity of echinoderm skeletal hardparts, specifically sea urchin spines to diagenetic alteration based on magnesium isotope data. We apply a dual approach by: (i) performing hydrothermal alteration experiments using meteoric, marine, and burial reactive fluids; and (ii) comparing these data with fossil sea urchin hardparts. The degree of alteration of experimentally altered and fossil sea urchin hardparts is assessed by a combination of optical (fluorescence, cathodoluminescence (CL), scanning electron microscopy (SEM)) and geochemical tools (elemental distribution, carbon, oxygen and magnesium isotopes). Although initial fluid chemistry of the experiments did not allow the detection of diagenetic overprint by elemental distribution (Fe, Mn) and cathodoluminescence, other tools such as fluorescence, SEM, delta18O, Mg concentration and delta26Mg display alteration effects, which respond to differential fluid temperature, chemistry, and experiment duration time. At experiments run under meteoric conditions with no Mg in the initial fluid, the solid is enriched in the heavier Mg isotopomer due to preferential dissolution of the lighter isotope. In contrast, initial burial and marine fluids have medium to high Mg concentrations. There, the Mg concentration and the delta26Mg values of the altered sea urchin spines increase. Fossil sea urchin hardparts display partly very strong diagenetic overprint as observed by their elemental distribution, cathodoluminescence, delta18O, Mg elemental concentration and delta26Mg. The absence of luminescence might indicate both well-preserved sea urchin spines, but also the secondary enrichment of quenching elements such as iron along diagenetic pathways. The relation between Mg concentration and delta26Mg of the experimentally altered sea urchin spines is in agreement with observations from fossil spines, which also display a 26Mg-enrichment of the solid phase. There, it seems that with increasing degree of alteration, an increase in Mg concentration and delta26Mg occurs. Hence, the experiments performed in this study seem to reflect diagenetic processes under natural conditions. However, the patterns observed are complicated by the interplay of kinetic and thermodynamic processes and the presence of variable amounts of water soluble and water insoluble organic matter within these biominerals. Due to (i) a natural inter- and intra-species variability of the Mg concentration and Mg isotopic composition throughout the echinoderm skeleton and (ii) the fractionation of Mg isotopes during the transformation of ACC as a precursor phase to calcite, the use of delta26Mg values of sea urchin hardparts as a proxy for past seawater delta26Mg is deemed unsuitable. In general, the data shown here are considered significant for those aiming to reconstruct palaeoenvironmental parameters based on echinoderm archives.

Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding.(SETAC)

EPA Science Inventory

Extensive collections of histopathology materials from studies of marine and freshwater mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine Fisheri...

Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding (NACSETAC)

EPA Science Inventory

Extensive collections of histopathology materials from studies of marine and freshwater mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine Fishe...

Treasures in Archived Histolopathology Collections: Preserving the Past for Future Understanding

EPA Science Inventory

Extensive collections of histopathology materials from studies of marine and freshwater mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine Fishe...

Discovering Fossils--A Hands-on Lab.

ERIC Educational Resources Information Center

Goldstein, Alan

2002-01-01

Describes fossil investigations developed and provided by the Falls of the Ohio State Park near Louisville, Kentucky. The Devonian shale beds contain representatives of over 600 species including corals, sponges, brachiopods, mollusks, and echinoderms. Rather than focusing on identification, the activities emphasize the past ecological…

Evidence for a trophic cascade on rocky reefs following sea star mass mortality in British Columbia

PubMed Central

Cloutier, Ryan N.; Côté, Isabelle M.

2016-01-01

Echinoderm population collapses, driven by disease outbreaks and climatic events, may be important drivers of population dynamics, ecological shifts and biodiversity. The northeast Pacific recently experienced a mass mortality of sea stars. In Howe Sound, British Columbia, the sunflower star Pycnopodia helianthoides—a previously abundant predator of bottom-dwelling invertebrates—began to show signs of a wasting syndrome in early September 2013, and dense aggregations disappeared from many sites in a matter of weeks. Here, we assess changes in subtidal community composition by comparing the abundance of fish, invertebrates and macroalgae at 20 sites in Howe Sound before and after the 2013 sea star mortality to evaluate evidence for a trophic cascade. We observed changes in the abundance of several species after the sea star mortality, most notably a four-fold increase in the number of green sea urchins, Strongylocentrotus droebachiensis, and a significant decline in kelp cover, which are together consistent with a trophic cascade. Qualitative data on the abundance of sunflower stars and green urchins from a citizen science database show that the patterns of echinoderm abundance detected at our study sites reflected wider local trends. The trophic cascade evident at the scale of Howe Sound was observed at half of the study sites. It remains unclear whether the urchin response was triggered directly, via a reduction in urchin mortality, or indirectly, via a shift in urchin distribution into areas previously occupied by the predatory sea stars. Understanding the ecological implications of sudden and extreme population declines may further elucidate the role of echinoderms in temperate seas, and provide insight into the resilience of marine ecosystems to biological disturbances. PMID:27168988

The skeleton of postmetamorphic echinoderms in a changing world.

PubMed

Dubois, Philippe

2014-06-01

Available evidence on the impact of acidification and its interaction with warming on the skeleton of postmetamorphic (juvenile and adult) echinoderms is reviewed. Data are available on sea urchins, starfish, and brittle stars in 33 studies. Skeleton growth of juveniles of all sea urchin species studied so far is affected from pH 7.8 to 7.6 in seawater, values that are expected to be reached during the 21st century. Growth in adult sea urchins (six species studied) is apparently only marginally affected at seawater pH relevant to this century. The interacting effect of temperature differed according to studies. Juvenile starfish as well as adults seem to be either not impacted or even boosted by acidification. Brittle stars show moderate effects at pH below or equal to 7.4. Dissolution of the body wall skeleton is unlikely to be a major threat to sea urchins. Spines, however, due to their exposed position, are more prone to this threat, but their regeneration abilities can probably ensure their maintenance, although this could have an energetic cost and induce changes in resource allocation. No information is available on skeleton dissolution in starfish, and the situation in brittle stars needs further assessment. Very preliminary evidence indicates that mechanical properties in sea urchins could be affected. So, although the impact of ocean acidification on the skeleton of echinoderms has been considered as a major threat from the first studies, we need a better understanding of the induced changes, in particular the functional consequences of growth modifications and dissolution related to mechanical properties. It is suggested to focus studies on these aspects. © 2014 Marine Biological Laboratory.

Correlation Between Echinoidea Size and Threat Level

NASA Astrophysics Data System (ADS)

Bakshi, S.; Lee, A.; Heim, N.; Payne, J.

2017-12-01

Echinoidea (or sea urchins), are small, spiny, globular, animals that populate the seafloors of nearly the entire planet. Echinoidea have existed on Earth since the Ordovician period, and from their archaic origin there is much to be learned about the relationship between Echinoidea body size and how it affects the survivability of the individual. The goal of this project is to determine how Echinoidea dimensions such as body volume, area, and length compare across extinct and extant species by plotting Echinoidea data in R. We will use stratigraphic data as a source to find which species of sea urchin from our data is extinct. We will then create three sets of three histograms of the size data for each type of measurement. One set will include histograms for sea urchin length, area, and volume. The other set will include histograms for extinct sea urchin length, area, and volume. The last set will include histograms for extant sea urchin length, area, and volume. Our data showed that extant sea urchins had a larger size, and extinct sea urchins were smaller. Our length data showed that the average length of all sea urchins were 54.95791 mm, the average length of extinct sea urchins were 51.0337 mm, and the average length of extant sea urchins were 66.12774 mm. There is a generally increasing trend of size over time, except for a small outlier about 350 million years ago, where echinoderm extinction selected towards larger species and biovolume was abnormally high. Our data also showed that over the past 200 million years, echinoderm extinction selectivity drove slightly smaller sea urchins towards extinction, further supporting the idea that a larger size was and still is advantageous for echinoderms.

Antifungal and antiviral products of marine organisms

PubMed Central

Cheung, Randy Chi Fai; Pan, Wen Liang; Chan, Yau Sang; Yin, Cui Ming; Dan, Xiu Li; Wang, He Xiang; Fang, Evandro Fei; Lam, Sze Kwan; Ngai, Patrick Hung Kui; Xia, Li Xin; Liu, Fang; Ye, Xiu Yun; Zhang, Guo Qing; Liu, Qing Hong; Sha, Ou; Lin, Peng; Ki, Chan; Bekhit, Adnan A; Bekhit, Alaa El-Din; Wan, David Chi Cheong

2017-01-01

Marine organisms including bacteria, fungi, algae, sponges, echinoderms, mollusks, and cephalochordates produce a variety of products with antifungal activity including bacterial chitinases, lipopeptides, and lactones; fungal (−)-sclerotiorin and peptaibols, purpurides B and C, berkedrimane B and purpuride; algal gambieric acids A and B, phlorotannins; 3,5-dibromo-2-(3,5-dibromo-2-methoxyphenoxy)phenol, spongistatin 1, eurysterols A and B, nortetillapyrone, bromotyrosine alkaloids, bis-indole alkaloid, ageloxime B and (−)-ageloxime D, haliscosamine, hamigeran G, hippolachnin A from sponges; echinoderm triterpene glycosides and alkene sulfates; molluscan kahalalide F and a 1485-Da peptide with a sequence SRSELIVHQR; and cepalochordate chitotriosidase and a 5026.9-Da antifungal peptide. The antiviral compounds from marine organisms include bacterial polysaccharide and furan-2-yl acetate; fungal macrolide, purpurester A, purpurquinone B, isoindolone derivatives, alterporriol Q, tetrahydroaltersolanol C and asperterrestide A, algal diterpenes, xylogalactofucan, alginic acid, glycolipid sulfoquinovosyldiacylglycerol, sulfated polysaccharide p-KG03, meroditerpenoids, methyl ester derivative of vatomaric acid, lectins, polysaccharides, tannins, cnidarian zoanthoxanthin alkaloids, norditerpenoid and capilloquinol; crustacean antilipopolysaccharide factors, molluscan hemocyanin; echinoderm triterpenoid glycosides; tunicate didemnin B, tamandarins A and B and; tilapia hepcidin 1–5 (TH 1–5), seabream SauMx1, SauMx2, and SauMx3, and orange-spotted grouper β-defensin. Although the mechanisms of antifungal and antiviral activities of only some of the afore-mentioned compounds have been elucidated, the possibility to use those known to have distinctly different mechanisms, good bioavailability, and minimal toxicity in combination therapy remains to be investigated. It is also worthwhile to test the marine antimicrobials for possible synergism with existing drugs. The prospects of employing them in clinical practice are promising in view of the wealth of these compounds from marine organisms. The compounds may also be used in agriculture and the food industry. PMID:24562325

IDENTIFYING CRITICAL CYSTEINE RESIDUES IN ARSENIC (+3 OXIDATION STATE) METHYLTRANSFERASE

EPA Science Inventory

Arsenic (+3 oxidation state) methyltransferase (AS3MT) catalyzes methylation of inorganic arsenic to mono, di, and trimethylated arsenicals. Orthologous AS3MT genes in genomes ranging from simple echinoderm to human predict a protein with five conserved cysteine (C) residues. In ...

Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding (Histologic)

EPA Science Inventory

Extensive collections of histopathology materials from studies of marine and freshwater fish, mollusks, crustaceans, echinoderms, and other organisms are archived at the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency (EPA), NOAA’s National Ma...

Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding (ISAAH-6)

EPA Science Inventory

Extensive collections of histopathology materials from studies of marine and freshwater fish, mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine F...

Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding (IMCC09)

EPA Science Inventory

Extensive collections of histopathology materials from studies of marine and freshwater fish, mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine...

Metal concentrations, sperm motility, and RNA/DNA ratio in two echinoderm species from a highly contaminated fjord (the Sørfjord, Norway).

PubMed

Catarino, Ana I; Cabral, Henrique N; Peeters, Kris; Pernet, Philippe; Punjabi, Usha; Dubois, Philippe

2008-07-01

The present study evaluated the effects of field metal contamination on sperm motility and the RNA/DNA ratio in echinoderms. Populations of Asterias rubens and Echinus acutus that occur naturally along a contamination gradient of sediments by cadmium, copper, lead, and zinc in a Norwegian fjord (the Sørfjord) were studied. Sperm motility, a measure of sperm quality, was quantified using a computer-assisted sperm analysis system. The RNA/DNA ratio, a measure of protein synthesis, was assessed by a one-dye (ethidium bromide)/one-enzyme (RNase), 96-well microplate fluorometric assay. Although both species accumulate metals at high concentrations, neither sperm motility parameters in A. rubens nor the RNA/DNA ratio in both species were affected. The Sørfjord is still one of the most metal-contaminated marine sites in Europe, but even so, populations of A. rubens and E. acutus are able to endure under these conditions.

Secondary EML4-ALK-positive lung adenocarcinoma in a patient previously treated for acute lymphoblastic leukemia in childhood: a case report.

PubMed

Nakamura, Yoichi; Taniguchi, Hirokazu; Mizoguchi, Kosuke; Ikeda, Takaya; Motoshima, Kohei; Yamaguchi, Hiroyuki; Nagashima, Seiji; Nakatomi, Katsumi; Soda, Manabu; Mano, Hiroyuki; Kohno, Shigeru

2014-06-01

It is widely recognized that the risk of secondary neoplasms increases as childhood cancer survivors progress through adulthood. These are mainly hematological malignancies, and recurrent chromosome translocations are commonly detected in such cases. On the other hand, while secondary epithelial malignancies have sometimes been reported, chromosome translocations in these epithelial malignancies have not. A 33-year-old man who had been diagnosed with acute lymphoblastic leukemia and treated with chemotherapy almost 20 years earlier was diagnosed with lung adenocarcinoma. After chromosomal rearrangement of echinoderm microtubule-associated protein-like 4 gene and the anaplastic lymphoma kinase gene was detected in this adenocarcinoma, he responded to treatment with crizotinib. It was therefore concluded that this echinoderm microtubule-associated protein-like 4 gene-anaplastic lymphoma kinase gene-positive lung adenocarcinoma was a secondary epithelial malignancy. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Ultrastructure of sea urchin calcified tissues after high-pressure freezing and freeze substitution.

PubMed

Ameye, L; Hermann, R; Dubois, P

2000-08-01

The improvements brought by high-pressure freezing/freeze substitution fixation methods to the ultrastructural preservation of echinoderm mineralized tissues are investigated in developing pedicellariae and teeth of the echinoid Paracentrotus lividus. Three freeze substitution (FS) protocols were tested: one in the presence of osmium tetroxide, one in the presence of uranyl acetate, and the last in the presence of gallic acid. FS in the presence of osmium tetroxide significantly improved cell ultrastructure preservation and should especially be used for ultrastructural studies involving vesicles and the Golgi apparatus. With all protocols, multivesicular bodies, suggested to contain Ca(2+), were evident for the first time in skeleton-forming cells. FS in the presence of gallic acid allowed us to confirm the structured and insoluble character of a part of the organic matrix of mineralization in the calcification sites of the tooth, an observation which modifies the current understanding of biomineralization control in echinoderms. Copyright 2000 Academic Press.

A Sea Creature Treasury. Project CAPE Teaching Module K-2b.

ERIC Educational Resources Information Center

Gray, Carmen P.; Forrest, Diane W.

Fifteen interdisciplinary lessons on marine invertebrates (mollusks, echinoderms, and jellyfish) are provided in this unit designed for students in kindergarten and in grades 1 and 2. Each lesson includes lesson concept, competency goals, objectives, materials needed, background information, teacher preparation, and activities suitable for use in…

Mg isotopes in biocarbonates: new insight into vital effects associated to echinoderms and bivalves calcification

NASA Astrophysics Data System (ADS)

Planchon, F.; Hermans, J.; Borremans, C.; Dubois, P.; Poulain, C.; Paulet, Y.; Andre, L.

2007-12-01

Mg isotopes can be helpful tracers to reveal the fundamental pathways of Mg incorporation during biomineralisation. We report in this study a detailed characterisation of the Mg isotopic signatures of different biominerals: high magnesium calcitic skeletons of selected echinoderms (sea urchins and starfish) and low magnesium aragonitic shells of a bivalve species (clam). State of the art analytical procedures were applied including sample purification step followed by high precision measurements using MC-ICP-MS (Nu instrument) in dry plasma conditions. 26Mg/24Mg and 25Mg/24Mg are expressed as per mil deviations from the DSM3 (Dead Sea Metal 3) reference standard in delta notation (d26Mg and d25Mg). For echinoderms, we considered: (a) adult specimens of six starfish species (Asteria r., Marthasterias g., Anseropoda p., Asterina g., Echinaster s. and Henricia o.), sampled in Brittany (France); (b) a sea urchin species (Paracentrotus lividus) with field samples (Mediterranean Sea, Marseille, France) and culture specimen under T and S controlled conditions. In vivo endoskeletons display negative, but different d26Mg values of -3.06 for starfish (with uniform interspecies signatures) and -2.65 for sea urchin. Relative to seawater signature (-0.82), all echinoderms favour the incorporation of light isotopes during biocalcification. The d26Mg depletion is lower than theoretically expected from a inorganic calcite precipitation from seawater (at -3.5). These differences suggest that on its route from seawater to the shell, Mg isotopes are partly biologically fractionationated through "vital effects" leaving heavier Mg isotopic signatures. Taken into account that calcification in echinoderms is an intra- cellular process involving transient amorphous calcium carbonate (ACC) phase, the observed bio-fractionation factors can be related to: (1) changes in the isotopic composition of the precipitating intracellular fluids due to active pumping in and out of the cell; (2) a specific control of isotopic exchange by ACC. For bivalves, we considered one clam species (Ruditapes Philippinarum) from two different sampling sites in the gulf of Morbihan (Brittany, France). One site (Locmariaquer, Loc) is coastal and marine while the other (Le bono, BO) located upstream in the Auray river. For each site and specimen, we considered all reservoirs involved in the shell build-up: seawater, internal fluids with hemolymph (H) and extrapaleal fluid (EPF), soft tissues with mantle, muscle and remaining part (R) and finally aragonitic shells. Water d26Mg are -0.82 at Loc and -0.79 at BO and appear to be highly similar to internal fluids values (EPF and H), -0.6 for Loc and -0.8 for BO. The soft tissues with mean values of -2.7 (Mantle), -2.1 (Muscle), -2.8 (R) at both sites, show pronounced enrichments in the light isotopic fraction of Mg. The shells display the widest range of Mg isotopic signatures with -1.9 at Loc and -4.2 at BO suggesting that different routes of fractionation are acting. The shell signature at Loc similar to aragonitic coral (-1.9) suggests that moderate biological effects have influenced the shell composition at this site. In contrast, at BO, the very light signature of the shell suggests that a significant fraction of Mg has been internally recycled by the clam and used for the building of the shell.

CA2+ AND ZN2+ ARE TRANSPORTED BY THE ELECTROGENIC 2NA+/1H+ ANTIPORTER IN ECHINODERM GASTROINTESTINAL EPITHELIUM. (R823068)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Faunas of Mississippian oolitic limestones: Evidence from Salem Limestone, southern Indiana

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feldman, H.R.

In the Salem Limestone of southern Indiana, a correlation exists between the faunal assemblage and abundance of grains with superficial oolitic coatings in grainstones. Coarse, poorly sorted fossiliferous grainstones are dominated by an echinoderm-bryozoan-brachiopod assemblage of fossils with few mollusks. The presence of large whole fossils, such as articulated crinoid calyces, suggest limited transport of skeletal components. Grainstones, dominated by grains with superficial coatings, and foraminifers tend to contain a diverse mollusk-dominated assemblage of gastropods, bivalves, rostroconchs, chitins, and scaphopods. These fossils are disarticulated, but generally are not fragmented even though many of them are thin and delicate. Echinoderms, brachiopods,more » and bryozoans are repsented in the mollusk-domdinated assemblage almost exclusively by well-rounded and coated fragments, suggesting that they are not in situ. The presence of similar molluscan assemblages in other Mississippian coated-grain grainstones from Alabama (the Monteagle Limestone) and Oklahoma (an unnamed limestone) indicates that the assemblage may have been wide-spread. Mississippian grainstones dominated by oolites (which are not prominent in the Salem) generally have very few fossils.« less

Cambrian cinctan echinoderms shed light on feeding in the ancestral deuterostome

PubMed Central

Rahman, Imran A.; Zamora, Samuel; Falkingham, Peter L.; Phillips, Jeremy C.

2015-01-01

Reconstructing the feeding mode of the latest common ancestor of deuterostomes is key to elucidating the early evolution of feeding in chordates and allied phyla; however, it is debated whether the ancestral deuterostome was a tentaculate feeder or a pharyngeal filter feeder. To address this, we evaluated the hydrodynamics of feeding in a group of fossil stem-group echinoderms (cinctans) using computational fluid dynamics. We simulated water flow past three-dimensional digital models of a Cambrian fossil cinctan in a range of possible life positions, adopting both passive tentacular feeding and active pharyngeal filter feeding. The results demonstrate that an orientation with the mouth facing downstream of the current was optimal for drag and lift reduction. Moreover, they show that there was almost no flow to the mouth and associated marginal groove under simulations of passive feeding, whereas considerable flow towards the animal was observed for active feeding, which would have enhanced the transport of suspended particles to the mouth. This strongly suggests that cinctans were active pharyngeal filter feeders, like modern enteropneust hemichordates and urochordates, indicating that the ancestral deuterostome employed a similar feeding strategy. PMID:26511049

Biomineral nanoparticles are space-filling

NASA Astrophysics Data System (ADS)

Yang, Li; Killian, Christopher E.; Kunz, Martin; Tamura, Nobumichi; Gilbert, P. U. P. A.

2011-02-01

Sea urchin biominerals have been shown to form from aggregating nanoparticles of amorphous calcium carbonate (ACC), which then crystallize into macroscopic single crystals of calcite. Here we measure the surface areas of these biominerals and find them to be comparable to those of space-filling macroscopic geologic calcite crystals. These biominerals differ from synthetic mesocrystals, which are invariably porous. We propose that space-filling ACC is the structural precursor for echinoderm biominerals.Sea urchin biominerals have been shown to form from aggregating nanoparticles of amorphous calcium carbonate (ACC), which then crystallize into macroscopic single crystals of calcite. Here we measure the surface areas of these biominerals and find them to be comparable to those of space-filling macroscopic geologic calcite crystals. These biominerals differ from synthetic mesocrystals, which are invariably porous. We propose that space-filling ACC is the structural precursor for echinoderm biominerals. This article was submitted as part of a Themed Issue on Crystallization and Formation Mechanisms of Nanostructures. Other papers on this topic can be found in issue 11 of vol. 2 (2010). This issue can be found from the Nanoscale homepage [http://www.rsc.org/nanoscale

Variation in the composition of corals, fishes, sponges, echinoderms, ascidians, molluscs, foraminifera and macroalgae across a pronounced in-to-offshore environmental gradient in the Jakarta Bay-Thousand Islands coral reef complex.

PubMed

Cleary, D F R; Polónia, A R M; Renema, W; Hoeksema, B W; Rachello-Dolmen, P G; Moolenbeek, R G; Budiyanto, A; Yahmantoro; Tuti, Y; Giyanto; Draisma, S G A; Prud'homme van Reine, W F; Hariyanto, R; Gittenberger, A; Rikoh, M S; de Voogd, N J

2016-09-30

Substrate cover, water quality parameters and assemblages of corals, fishes, sponges, echinoderms, ascidians, molluscs, benthic foraminifera and macroalgae were sampled across a pronounced environmental gradient in the Jakarta Bay-Thousand Islands reef complex. Inshore sites mainly consisted of sand, rubble and turf algae with elevated temperature, dissolved oxygen, pH and chlorophyll concentrations and depauperate assemblages of all taxa. Live coral cover was very low inshore and mainly consisted of sparse massive coral heads and a few encrusting species. Faunal assemblages were more speciose and compositionally distinct mid- and offshore compared to inshore. There were, however, small-scale differences among taxa. Certain midshore sites, for example, housed assemblages resembling those typical of the inshore environment but this differed depending on the taxon. Substrate, water quality and spatial variables together explained from 31% (molluscs) to 72% (foraminifera) of the variation in composition. In general, satellite-derived parameters outperformed locally measured parameters. Copyright © 2016 Elsevier Ltd. All rights reserved.

On Mellitella stokesii and Amphipholis geminata (Echinodermata), from an intertidal flat in the upper Gulf of Nicoya estuary, Pacific, Costa Rica.

PubMed

Vargas, José A; Solano, Sylvia

2011-03-01

Information on changes over time in the biodiversity and ecology of tropical systems is of increasing importance against the background of local, regional, and global dynamics. This study aimed to contribute with long-term data on the abundance fluctuations of two species of echinoderms from a tropical tidal flat. From February 1984 to December 1986, March 1985 to April 1987, and July 1994 to September 1996 (total: 76 dates), core samples (17.7 cm2, 15 cm deep) were collected at low tide at a mud-sand flat in the mid upper Gulf of Nicoya estuary, Costa Rica, as part of a survey of the benthic community. Among more than 100 taxa, the burrowing brittle star, Amphipholis geminata, and the sand dollar, Mellitella stokesii, consistently appeared in the samples over the study period. A total of 63 M. stokesii and 149 A. geminata were collected. The 43 sand dollars found during 1984-1985, give an approximate density of 35 ind./m2, which is within the range reported for this species. M. stokesii was almost absent from 1994 to 1996, while A. geminata had its peak of abundance at the end of 1995. Low abundances of the sand dollar during the rainy seasons (May-November) and slight increments in dry seasons (December-April) cores, also agrees with a report from the region. A. geminata also presented an irregular pattern of abundance, with slight increases at the end of the rainy seasons or during the dry seasons, when higher salinities are more suitable for echinoderms. The patchy spatial distribution of both species makes difficult the detection of patterns with a corer. Nevertheless, this information is unique due to its extensive time coverage and provides a baseline for future surveys designed specifically for the study of tropical intertidal estuarine echinoderms.

IDENTIFICATION OF NF-KAPPAB IN THE MARINE FISH STENOTOMUS CHRYSOPS AND EXAMINATION OF ITS ACTIVATION BY ARYL HYDROCARBON RECEPTOR AGONISTS. (R827102)

EPA Science Inventory

Abstract

Members of the Rel family of proteins have been identified in Drosophila, an echinoderm, Xenopus, birds and mammals. Dimers of Rel proteins form the transcription factor nuclear factor Annotated Bibliography of Bioassays Related to Sediment Toxicity Testing in Washington State

DTIC Science & Technology

1990-10-01

effects of sediments contaminated with heavy metals, petroleum hydrocarbons , synthetic organic compounds and radionuclides. It also provides an... molluscs (adults only), echinoderm larvae and fish), and bioassay procedures with selected toxicants (metals, petrochemicals, pesticides, contaminated...reference sediment + 15 mm test sediment. Bioaccumulation tests (with same organisms) are a’so discussed. EPA/COE (U.S. Environmental Protection Agency

The Transcriptome of an Amphioxus, Asymmetron lucayanum, from the Bahamas: A Window into Chordate Evolution

PubMed Central

Yue, Jia-Xing; Yu, Jr-Kai; Putnam, Nicholas H.; Holland, Linda Z.

2014-01-01

Cephalochordates, the sister group of tunicates plus vertebrates, have been called “living fossils” due to their resemblance to fossil chordates from Cambrian strata. The genome of the cephalochordate Branchiostoma floridae shares remarkable synteny with vertebrates and is free from whole-genome duplication. We performed RNA sequencing from larvae and adults of Asymmetron lucayanum, a cephalochordate distantly related to B. floridae. Comparisons of about 430 orthologous gene groups among both cephalochordates and 10 vertebrates using an echinoderm, a hemichordate, and a mollusk as outgroups showed that cephalochordates are evolving more slowly than the slowest evolving vertebrate known (the elephant shark), with A. lucayanum evolving even more slowly than B. floridae. Against this background of slow evolution, some genes, notably several involved in innate immunity, stand out as evolving relatively quickly. This may be due to the lack of an adaptive immune system and the relatively high levels of bacteria in the inshore waters cephalochordates inhabit. Molecular dating analysis including several time constraints revealed a divergence time of ∼120 Ma for A. lucayanum and B. floridae. The divisions between cephalochordates and vertebrates, and that between chordates and the hemichordate plus echinoderm clade likely occurred before the Cambrian. PMID:25240057

Evolutionary modification of T-brain (tbr) expression patterns in sand dollar.

PubMed

Minemura, Keiko; Yamaguchi, Masaaki; Minokawa, Takuya

2009-10-01

The sand dollars are a group of irregular echinoids that diverged from other regular sea urchins approximately 200 million years ago. We isolated two orthologs of T-brain (tbr), Smtbr and Pjtbr, from the indirect developing sand dollar Scaphechinus mirabilis and the direct developing sand dollar Peronella japonica, respectively. The expression patterns of Smtbr and Pjtbr during early development were examined by whole mount in situ hybridization. The expression of Smtbr was first detected in micromere descendants in early blastula stage, similar to tbr expression in regular sea urchins. However, unlike in regular sea urchin, Smtbr expression in middle blastula stage was detected in micromere-descendent cells and a subset of macromere-descendant cells. At gastrula stage, expression of Smtbr was detected in part of the archenteron as well as primary mesenchyme cells. A similar pattern of tbr expression was observed in early Peronella embryos. A comparison of tbr expression patterns between sand dollars and other echinoderm species suggested that broader expression in the endomesoderm is an ancestral character of echinoderms. In addition to the endomesoderm, Pjtbr expression was detected in the apical organ, the animal-most part of the ectoderm.

Pulmonary lymphoepithelioma-like carcinoma with echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) fusion gene.

PubMed

Ose, Naoko; Kawai, Teruka; Ishida, Daisuke; Kobori, Yuko; Takeuchi, Yukiyasu; Senba, Hidetoshi

2016-11-01

A pulmonary lymphoepithelioma-like carcinoma (PLELC) is similar to a lymphoepithelioma, a subtype of nasopharyngeal carcinoma and commonly associated with Epstein-Barr virus infection which is a rare tumour and classified in the group of "other and unclassified carcinoma" in the latest 2015 World Health Organization (WHO) classification. Some reports of lymphoepithelioma-like carcinoma (LELC) have noted an epidermal growth factor receptor (EGFR) mutation, whereas none have noted a mutation of the echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) fusion gene. This is the first reported case of PLELC with ALK rearrangement. A 76-year-old woman underwent a right lower lobectomy and complicated partial resection of the upper lobe with lymph node dissection under complete thoracoscopic approach. A histopathological diagnosis of PLELC was made and the stage was classified as T1aN1(#12l) M0, pl0, G2, Ly1, V1. The results of both ALK immunohistochemistry and EML4-ALK fusion gene on fluorescence in situ hybridization (FISH) examinations were positive; however, EGFR mutational analysis results showed wild-type mutation.

An updated checklist of Echinoderms from Indian waters.

PubMed

Samuel, Vijay Kumar Deepak; Krishnan, Pandian; Sreeraj, Chemmencheri Ramakrishnan; Chamundeeswari, Kanagaraj; Parthiban, Chermapandi; Sekar, Veeramuthu; Patro, Shesdev; Saravanan, Raju; Abhilash, Kottarathil Rajendran; Ramachandran, Purvaja; Ramesh, Ramachandran

2017-11-27

Species checklists enlist the species available within the defined geographical region and thus serve as essential input for developing conservation and management strategies. The fields of conservation biology and ecology confront the challenge of inflated biodiversity, attributed to non-recognition of taxonomic inconsistencies such as synonyms, alternate representation, emendations etc. Critical review of the checklists and distributional records of Phylum Echinodermata from Indian waters and subsequent validation of species names with World Register of Marine Species (WoRMS) database, revealed that the current literature included 236 incorrect entries comprising of 162 synonyms, 15 emendations, 5 nomina dubia, 1 nomen nudum, 40 species under alternate representation, 9 species with author misnomer, 1 subspecies and 1 unaccepted. The 226 species found to be mixed with valid names and a revised checklist was prepared. The revised and updated checklist holds 741 species of echinoderms comprising of 182 asteroids (24.56%), 70 crinoids (9.45%), 138 echinoids (18.62%), 179 holothuroids (24.16%) and 172 ophiuroids (23.21%), placed under 28 orders and 107 families. This paper discusses the cause for taxonomic inflation and argues that such taxonomic inconsistencies alter our interpretations of a species including its inaccurate distribution and, could possibly impede the country's conservation and management efforts.

Bathyal sea urchins of the Bahamas, with notes on covering behavior in deep sea echinoids (Echinodermata: Echinoidea)

NASA Astrophysics Data System (ADS)

Pawson, David L.; Pawson, Doris J.

2013-08-01

In a survey of the bathyal echinoderms of the Bahama Islands region using manned submersibles, approximately 200 species of echinoderms were encountered and documented; 33 species were echinoids, most of them widespread in the general Caribbean area. Three species were found to exhibit covering behavior, the piling of debris on the upper surface of the body. Active covering is common in at least 20 species of shallow-water echinoids, but it has been reliably documented previously only once in deep-sea habitats. Images of covered deep-sea species, and other species of related interest, are provided. Some of the reasons adduced in the past for covering in shallow-water species, such as reduction of incident light intensity, physical camouflage, ballast in turbulent water, protection from desiccation, presumably do not apply in bathyal species. The main reasons for covering in deep, dark, environments are as yet unknown. Some covering behavior in the deep sea may be related to protection of the genital pores, ocular plates, or madreporite. Covering in some deep-sea species may also be merely a tactile reflex action, as some authors have suggested for shallow-water species.

Determination of Gonyautoxin-4 in Echinoderms and Gastropod Matrices by Conversion to Neosaxitoxin Using 2-Mercaptoethanol and Post-Column Oxidation Liquid Chromatography with Fluorescence Detection

PubMed Central

Silva, Marisa; Rey, Verónica; Botana, Ana; Vasconcelos, Vitor; Botana, Luis

2015-01-01

Paralytic Shellfish Toxin blooms are common worldwide, which makes their monitoring crucial in the prevention of poisoning incidents. These toxins can be monitored by a variety of techniques, including mouse bioassay, receptor binding assay, and liquid chromatography with either mass spectrometric or pre- or post-column fluorescence detection. The post-column oxidation liquid chromatography with fluorescence detection method, used routinely in our laboratory, has been shown to be a reliable method for monitoring paralytic shellfish toxins in mussel, scallop, oyster and clam species. However, due to its high sensitivity to naturally fluorescent matrix interferences, when working with unconventional matrices, there may be problems in identifying toxins because of naturally fluorescent interferences that co-elute with the toxin peaks. This can lead to erroneous identification. In this study, in order to overcome this challenge in echinoderm and gastropod matrices, we optimized the conversion of Gonyautoxins 1 and 4 to Neosaxitoxin with 2-mercaptoethanol. We present a new and less time-consuming method with a good recovery (82.2%, RSD 1.1%, n = 3), requiring only a single reaction step. PMID:26729166

The expression of embryonic primary mesenchyme genes of the sea urchin, Strongylocentrotus purpuratus, in the adult skeletogenic tissues of this and other species of echinoderms.

PubMed

Drager, B J; Harkey, M A; Iwata, M; Whiteley, A H

1989-05-01

Adult tissues of the sea urchin, Strongylocentrotus purpuratus, were analyzed for the products of a set of genes whose expression, in the embryo, is restricted to the skeletogenic primary mesenchyme (PM). Three embryonic PM-specific mRNAs were found to be abundant in adult skeletal tissues (test and lantern), but not in a variety of soft tissues. Homologous mRNAs were also found in skeletal tissues of the congeneric sea urchin, S. droebachiensis, as well as a more distantly related echinoid, Dendraster excentricus, and an asteroid, Evasterias troschellii. The distributions of two of these RNAs were analyzed in regenerating spines of adult S. purpuratus using in situ hybridization. These gene products were localized primarily in the calcoblasts that accumulated at the regeneration site. In nonregenerating spines SpLM 18 RNAs, the most abundant of these gene products, were localized in a small population of noncalcoblast cells scattered through the spine shaft, and were absent from calcoblasts. These observations suggest that a program of gene expression associated with the process of calcification is conserved both developmentally through the period of metamorphosis and evolutionarily among the echinoderms.

Therapies from Fucoidan: An Update

PubMed Central

Fitton, Janet Helen; Stringer, Damien N.; Karpiniec, Samuel S.

2015-01-01

Fucoidans are a class of sulfated fucose-rich polysaccharides found in brown marine algae and echinoderms. Fucoidans have an attractive array of bioactivities and potential applications including immune modulation, cancer inhibition, and pathogen inhibition. Research into fucoidan has continued to gain pace over the last few years and point towards potential therapeutic or adjunct roles. The source, extraction, characterization and detection of fucoidan is discussed. PMID:26389927

Stable isotope trophic patterns in echinoderm megafauna in close proximity to and remote from Gulf of Mexico lower slope hydrocarbon seeps

NASA Astrophysics Data System (ADS)

Carney, Robert Spencer

2010-11-01

Hydrocarbon-seep communities in the Gulf of Mexico have a high biomass that is exploited as a food source to varying degrees by the photosynthesis-dependent fauna inhabiting the surrounding mud bottom. A decline concurrent with ocean depth in detritus influx to that background habitat results in a much lower background biomass. The biomass contrast between population-rich seeps and depauperate mud bottom leads to the prediction that seep utilization by the background fauna should be extensive at all depths and should increase with depth. Species depth zonation makes like-species comparisons over the full depth of the Gulf of Mexico impossible. Seeps and normal bottom above 1000 m have different fauna from those below 1000 m. Lower slope seeps are surrounded by a fauna rich in echinoderm species, especially asteroids, ophiuroids, and holothuroids. All three taxa have species that are abundant within seeps and are probably endemic to them. They also contain species found only in mud background or within mud and seeps backgrounds. Tissue analyses of δ13C and δ15N of echinoderms collected by ROV within seeps and trawling away from seeps indicate a pattern of utilization similar to that found in upper slope seeps exploited by different taxa. Seastar and ophiuroid species abundant in or endemic to seeps have tissue isotope values reflecting seep chemosynthetic input via a free-living microbial detritus or predation. A single seep-endemic deposit-feeding holothuroid showed distinct seep tissue values. Background deposit-feeding holothuroids collected within seeps showed either no or only minor incorporation of seep carbon, indicating either a lack of access to seep detritus or short feeding times within the seep. A predicted extensive utilization of seep productivity at the deeper seeps was not found. Seeps may be relatively closed systems that require special adaptations of species in order for them to enter, exploit, and survive. Alternately, the surrounding deep benthos may not be as food-poor as assumed from biomass measurements and flux estimates.

Establishment of a Conditional Transgenic Mouse Model Recapitulating EML4-ALK-Positive Human Non-Small Cell Lung Cancer.

PubMed

Pyo, Kyoung Ho; Lim, Sun Min; Kim, Hye Ryun; Sung, Young Hoon; Yun, Mi Ran; Kim, Sung-Moo; Kim, Hwan; Kang, Han Na; Lee, Ji Min; Kim, Sang Gyun; Park, Chae Won; Chang, Hyun; Shim, Hyo Sup; Lee, Han-Woong; Cho, Byoung Chul

2017-03-01

Anaplastic lymphoma receptor tyrosine kinase gene (ALK) fusion is a distinct molecular subclassification of NSCLC that is targeted by anaplastic lymphoma kinase (ALK) inhibitors. We established a transgenic mouse model that expresses tumors highly resembling human NSCLC harboring echinoderm microtubule associated protein like 4 gene (EML)-ALK fusion. We aimed to test an EML4-ALK transgenic mouse model as a platform for assessing the efficacy of ALK inhibitors and examining mechanisms of acquired resistance to ALK inhibitors. Transgenic mouse lines harboring LoxP-STOP-LoxP-FLAGS-tagged human EML4-ALK (variant 1) transgene was established by using C57BL/6N mice. The transgenic mouse model with highly lung-specific, inducible expression of echinoderm microtubule associated protein like 4-ALK fusion protein was established by crossing the EML4-ALK transgenic mice with mice expressing Cre-estrogen receptor fusion protein under the control of surfactant protein C gene (SPC). Expression of EML4-ALK transgene was induced by intraperitoneally injecting mice with tamoxifen. When the lung tumor of the mice treated with the ALK inhibitor crizotinib for 2 weeks was measured, tumor shrinkage was observed. EML4-ALK tumor developed after 1 week of tamoxifen treatment. Echinoderm microtubule associated protein like 4-ALK was strongly expressed in the lung but not in other organs. ALK and FLAGS expressions were observed by immunohistochemistry. Treatment of EML4-ALK tumor-bearing mice with crizotinib for 2 weeks induced dramatic shrinkage of tumors with no signs of toxicity. Furthermore, prolonged treatment with crizotinib led to acquired resistance in tumors, resulting in regrowth and disease progression. The resistant tumor nodules revealed acquired ALK G1202R mutations. An EML4-ALK transgenic mouse model for study of drug resistance was successfully established with short duration of tumorigenesis. This model should be a strong preclinical model for testing efficacy of ALK TKIs, providing a useful tool for investigating the mechanisms of acquired resistance and pursuing novel treatment strategies in ALK-positive lung cancer. Copyright © 2016 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Biomineral nanoparticles are space-filling.

PubMed

Yang, Li; Killian, Christopher E; Kunz, Martin; Tamura, Nobumichi; Gilbert, P U P A

2011-02-01

Sea urchin biominerals have been shown to form from aggregating nanoparticles of amorphous calcium carbonate (ACC), which then crystallize into macroscopic single crystals of calcite. Here we measure the surface areas of these biominerals and find them to be comparable to those of space-filling macroscopic geologic calcite crystals. These biominerals differ from synthetic mesocrystals, which are invariably porous. We propose that space-filling ACC is the structural precursor for echinoderm biominerals.

Using sea urchin gametes and zygotes to investigate centrosome duplication.

PubMed

Sluder, Greenfield

2016-01-01

Centriole structure and function in the sea urchin zygote parallel those in mammalian somatic cells. Here, I briefly introduce the properties and attributes of the sea urchin system that make it an attractive platform for the study of centrosome and centriole duplication. These attributes apply to all echinoderms readily available from commercial suppliers: sea urchins, sand dollars, and starfish. I list some of the practical aspects of the system that make it a cost- and time-effective system for experimental work and then list properties that are a "tool kit" that can be used to conduct studies that would not be practical, or in some cases not possible, with mammalian somatic cells. Since centrioles organize and localize the pericentriolar material that nucleates the astral arrays of microtubules (Bobinnec et al. in J Cell Biol 143(6):1575-1589, 1998), the pattern of aster duplication over several cell cycles can be used as a reliable measure for centriole duplication (Sluder and Rieder in J Cell Biol 100(3):887-896, 1985). Descriptions of the methods my laboratory has used to handle and image echinoderm zygotes are reviewed in Sluder et al. (Methods Cell Biol 61:439-472, 1999). Also included is a bibliography of papers that describe additional methods.

Tentaculate fossils from the Cambrian of Canada (British Columbia) and China (Yunnan) interpreted as primitive deuterostomes.

PubMed

Caron, Jean-Bernard; Conway Morris, Simon; Shu, Degan

2010-03-08

Molecular and morphological evidence unite the hemichordates and echinoderms as the Ambulacraria, but their earliest history remains almost entirely conjectural. This is on account of the morphological disparity of the ambulacrarians and a paucity of obvious stem-groups. We describe here a new taxon Herpetogaster collinsi gen. et sp. nov. from the Burgess Shale (Middle Cambrian) Lagerstätte. This soft-bodied vermiform animal has a pair of elongate dendritic oral tentacles, a flexible stolon with an attachment disc, and a re-curved trunk with at least 13 segments that is directed dextrally. A differentiated but un-looped gut is enclosed in a sac suspended by mesenteries. It consists of a short pharynx, a conspicuous lenticular stomach, followed by a narrow intestine sub-equal in length. This new taxon, together with the Lower Cambrian Phlogites and more intriguingly the hitherto enigmatic discoidal eldoniids (Cambrian-Devonian), form a distinctive clade (herein the cambroernids). Although one hypothesis of their relationships would look to the lophotrochozoans (specifically the entoprocts), we suggest that the evidence is more consistent with their being primitive deuterostomes, with specific comparisons being made to the pterobranch hemichordates and pre-radial echinoderms. On this basis some of the earliest ambulacrarians are interpreted as soft-bodied animals with a muscular stalk, and possessing prominent tentacles.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Killian, Christopher; Metzler, Rebecca; Gong, Y. U. T.

Sea urchin teeth are remarkable and complex calcite structures, continuously growing at the forming end and self-sharpening at the mature grinding tip. The calcite (CaCO{sub 3}) crystals of tooth components, plates, fibers, and a high-Mg polycrystalline matrix, have highly co-oriented crystallographic axes. This ability to co-orient calcite in a mineralized structure is shared by all echinoderms. However, the physico-chemical mechanism by which calcite crystals become co-oriented in echinoderms remains enigmatic. Here, we show differences in calcite c-axis orientations in the tooth of the purple sea urchin (Strongylocentrotus purpuratus), using high-resolution X-ray photoelectron emission spectromicroscopy (X-PEEM) and microbeam X-ray diffraction ({mu}XRD).more » All plates share one crystal orientation, propagated through pillar bridges, while fibers and polycrystalline matrix share another orientation. Furthermore, in the forming end of the tooth, we observe that CaCO{sub 3} is present as amorphous calcium carbonate (ACC). We demonstrate that co-orientation of the nanoparticles in the polycrystalline matrix occurs via solid-state secondary nucleation, propagating out from the previously formed fibers and plates, into the amorphous precursor nanoparticles. Because amorphous precursors were observed in diverse biominerals, solid-state secondary nucleation is likely to be a general mechanism for the co-orientation of biomineral components in organisms from different phyla.« less

Discovery of novel representatives of bilaterian neuropeptide families and reconstruction of neuropeptide precursor evolution in ophiuroid echinoderms

PubMed Central

Abylkassimova, Nikara; Hugall, Andrew F.; O'Hara, Timothy D.; Elphick, Maurice R.

2017-01-01

Neuropeptides are a diverse class of intercellular signalling molecules that mediate neuronal regulation of many physiological and behavioural processes. Recent advances in genome/transcriptome sequencing are enabling identification of neuropeptide precursor proteins in species from a growing variety of animal taxa, providing new insights into the evolution of neuropeptide signalling. Here, detailed analysis of transcriptome sequence data from three brittle star species, Ophionotus victoriae, Amphiura filiformis and Ophiopsila aranea, has enabled the first comprehensive identification of neuropeptide precursors in the class Ophiuroidea of the phylum Echinodermata. Representatives of over 30 bilaterian neuropeptide precursor families were identified, some of which occur as paralogues. Furthermore, homologues of endothelin/CCHamide, eclosion hormone, neuropeptide-F/Y and nucleobinin/nesfatin were discovered here in a deuterostome/echinoderm for the first time. The majority of ophiuroid neuropeptide precursors contain a single copy of a neuropeptide, but several precursors comprise multiple copies of identical or non-identical, but structurally related, neuropeptides. Here, we performed an unprecedented investigation of the evolution of neuropeptide copy number over a period of approximately 270 Myr by analysing sequence data from over 50 ophiuroid species, with reference to a robust phylogeny. Our analysis indicates that the composition of neuropeptide ‘cocktails’ is functionally important, but with plasticity over long evolutionary time scales. PMID:28878039

CASA in invertebrates.

PubMed

van der Horst, Gerhard; Bennett, Monique; Bishop, John D D

2018-04-09

Sperm movement has been described in several phyla of invertebrates. Yet, sperm motility has only been quantified using computer-aided sperm analysis (CASA-Mot) in externally fertilising species (broadcast spawners) of two phyla, molluscs and echinoderms. In the present study we quantified in detail the nature of the sperm tracks, percentage motility groupings and detailed kinematics of rapid-, medium- and slow-swimming spermatozoa in the oyster Crassostrea gigas and four species never previously studied by CASA-Mot, namely the molluscs Choromytilus meridionalis, Donax serra and Haliotis midae and the echinoderm Parechinus angulosus. A feature common to all these species are the helical tracks, the diameter of which seems to be species specific. Using CASA-Mot, the behaviour of spermatozoa was also studied over time and in the presence of egg water and Ca2+ modulators such as caffeine and procaine hydrochloride. For the first time, we show that hyperactivation can be induced in all species in the presence of egg water (sea water that was mixed with mature eggs and then centrifuged) and/or caffeine, and these hyperactivated sperm tracks were characterised using CASA-Mot. We relate the different patterns of sperm motility and behaviour to reproductive strategies such as broadcast spawning and spermcasting, and briefly review studies using CASA-Mot on other invertebrates.

Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus

PubMed Central

Gaitán-Espitia, Juan Diego; Sánchez, Roland; Bruning, Paulina; Cárdenas, Leyla

2016-01-01

The edible sea urchin Loxechinus albus (Molina, 1782) is a keystone species in the littoral benthic systems of the Pacific coast of South America. The international demand for high-quality gonads of this echinoderm has led to an extensive exploitation and decline of its natural populations. Consequently, a more thorough understanding of L. albus gonad development and gametogenesis could provide valuable resources for aquaculture applications, management, conservation and studies about the evolution of functional and structural pathways that underlie the reproductive toolkit of marine invertebrates. Using a high-throughput sequencing technology, we explored the male gonad transcriptome of this highly fecund sea urchin. Through a de novo assembly approach we obtained 42,530 transcripts of which 15,544 (36.6%) had significant alignments to known proteins in public databases. From these transcripts, approximately 73% were functionally annotated allowing the identification of several candidate genes that are likely to play a central role in developmental processes, nutrient reservoir activity, sexual reproduction, gamete generation, meiosis, sex differentiation, sperm motility, male courtship behavior and fertilization. Additionally, comparisons with the male gonad transcriptomes of other echinoderms revealed several conserved orthologous genes, suggesting that similar functional and structural pathways underlie the reproductive development in this group and other marine invertebrates. PMID:27805042

Mechanism of calcite co-orientation in the sea urchin tooth.

PubMed

Killian, Christopher E; Metzler, Rebecca A; Gong, Y U T; Olson, Ian C; Aizenberg, Joanna; Politi, Yael; Wilt, Fred H; Scholl, Andreas; Young, Anthony; Doran, Andrew; Kunz, Martin; Tamura, Nobumichi; Coppersmith, Susan N; Gilbert, P U P A

2009-12-30

Sea urchin teeth are remarkable and complex calcite structures, continuously growing at the forming end and self-sharpening at the mature grinding tip. The calcite (CaCO(3)) crystals of tooth components, plates, fibers, and a high-Mg polycrystalline matrix, have highly co-oriented crystallographic axes. This ability to co-orient calcite in a mineralized structure is shared by all echinoderms. However, the physico-chemical mechanism by which calcite crystals become co-oriented in echinoderms remains enigmatic. Here, we show differences in calcite c-axis orientations in the tooth of the purple sea urchin ( Strongylocentrotus purpuratus ), using high-resolution X-ray photoelectron emission spectromicroscopy (X-PEEM) and microbeam X-ray diffraction (muXRD). All plates share one crystal orientation, propagated through pillar bridges, while fibers and polycrystalline matrix share another orientation. Furthermore, in the forming end of the tooth, we observe that CaCO(3) is present as amorphous calcium carbonate (ACC). We demonstrate that co-orientation of the nanoparticles in the polycrystalline matrix occurs via solid-state secondary nucleation, propagating out from the previously formed fibers and plates, into the amorphous precursor nanoparticles. Because amorphous precursors were observed in diverse biominerals, solid-state secondary nucleation is likely to be a general mechanism for the co-orientation of biomineral components in organisms from different phyla.

Use of 16S Ribosomal RNA Sequences to Infer Relationships among Archaebacteria.

DTIC Science & Technology

1987-04-16

the rRNAs of one or both other kingdoms , and among the archaebacteria there are also substantial variations) (1), echinoderms (5, 11), major...Security Classification) Ln Use of 16S Ribosomal RNA Sequences to infer Relationships among Archaebacteria : Annual Report (U) q 12 PERSONAL AUTHOR(S...FIELD GROUP SUB-GROUP Archaebacteria ; Eubacteria; Eukaryotes; 16S Ribosomal RNA; 08 I Phylogeny; rRNA; RNA Sequencing; Molecular Clock; Urkingdoms; r

European Scientific Notes. Volume 34, Number 11,

DTIC Science & Technology

1980-11-30

assumed risk factor of 2 x 10-4 1 reason for the risk to the public from man-rem, coal and oil stems from the assumedwhich includes cancers plus genetic ... genetic make-up, increasing rate of mor- types would lead to indirect risks tality, formation of extremist groups, (police state, etc.), but were...biology and reproduction of echinoderms In 1957, the University of Paris and siphonophores , (5) The physiology established a second laboratory, the Sta

Buffer capacity of the coelomic fluid in echinoderms.

PubMed

Collard, Marie; Laitat, Kim; Moulin, Laure; Catarino, Ana I; Grosjean, Philippe; Dubois, Philippe

2013-09-01

The increase in atmospheric CO2 due to anthropogenic activity results in an acidification of the surface waters of the oceans. The impact of these chemical changes depends on the considered organisms. In particular, it depends on the ability of the organism to control the pH of its inner fluids. Among echinoderms, this ability seems to differ significantly according to species or taxa. In the present paper, we investigated the buffer capacity of the coelomic fluid in different echinoderm taxa as well as factors modifying this capacity. Euechinoidea (sea urchins except Cidaroidea) present a very high buffer capacity of the coelomic fluid (from 0.8 to 1.8mmolkg(-1) SW above that of seawater), while Cidaroidea (other sea urchins), starfish and holothurians have a significantly lower one (from -0.1 to 0.4mmolkg(-1) SW compared to seawater). We hypothesize that this is linked to the more efficient gas exchange structures present in the three last taxa, whereas Euechinoidea evolved specific buffer systems to compensate lower gas exchange abilities. The constituents of the buffer capacity and the factors influencing it were investigated in the sea urchin Paracentrotus lividus and the starfish Asterias rubens. Buffer capacity is primarily due to the bicarbonate buffer system of seawater (representing about 63% for sea urchins and 92% for starfish). It is also partly due to coelomocytes present in the coelomic fluid (around 8% for both) and, in P. lividus only, a compound of an apparent size larger than 3kDa is involved (about 15%). Feeding increased the buffer capacity in P. lividus (to a difference with seawater of about 2.3mmolkg(-1) SW compared to unfed ones who showed a difference of about 0.5mmolkg(-1) SW) but not in A. rubens (difference with seawater of about 0.2 for both conditions). In P. lividus, decreased seawater pH induced an increase of the buffer capacity of individuals maintained at pH7.7 to about twice that of the control individuals and, for those at pH7.4, about three times. This allowed a partial compensation of the coelomic fluid pH for individuals maintained at pH7.7 but not for those at pH7.4. Copyright © 2013 Elsevier Inc. All rights reserved.

Intact cluster and chordate-like expression of ParaHox genes in a sea star

PubMed Central

2013-01-01

Background The ParaHox genes are thought to be major players in patterning the gut of several bilaterian taxa. Though this is a fundamental role that these transcription factors play, their activities are not limited to the endoderm and extend to both ectodermal and mesodermal tissues. Three genes compose the ParaHox group: Gsx, Xlox and Cdx. In some taxa (mostly chordates but to some degree also in protostomes) the three genes are arranged into a genomic cluster, in a similar fashion to what has been shown for the better-known Hox genes. Sea urchins possess the full complement of ParaHox genes but they are all dispersed throughout the genome, an arrangement that, perhaps, represented the primitive condition for all echinoderms. In order to understand the evolutionary history of this group of genes we cloned and characterized all ParaHox genes, studied their expression patterns and identified their genomic loci in a member of an earlier branching group of echinoderms, the asteroid Patiria miniata. Results We identified the three ParaHox orthologs in the genome of P. miniata. While one of them, PmGsx is provided as maternal message, with no zygotic activation afterwards, the other two, PmLox and PmCdx are expressed during embryogenesis, within restricted domains of both endoderm and ectoderm. Screening of a Patiria bacterial artificial chromosome (BAC) library led to the identification of a clone containing the three genes. The transcriptional directions of PmGsx and PmLox are opposed to that of the PmCdx gene within the cluster. Conclusions The identification of P. miniata ParaHox genes has revealed the fact that these genes are clustered in the genome, in contrast to what has been reported for echinoids. Since the presence of an intact cluster, or at least a partial cluster, has been reported in chordates and polychaetes respectively, it becomes clear that within echinoderms, sea urchins have modified the original bilaterian arrangement. Moreover, the sea star ParaHox domains of expression show chordate-like features not found in the sea urchin, confirming that the dynamics of gene expression for the respective genes and their putative regulatory interactions have clearly changed over evolutionary time within the echinoid lineage. PMID:23803323

Skeletal Strength and Skeletogenetic Mechanisms Over Phanerozoic Time

NASA Astrophysics Data System (ADS)

Constantz, B. R.

2004-12-01

Mineralized skeletons have a remarkable range of mechanical properties with respect to strength and durability. Measurements of skeletal mechanical properties show that taxonomic groups with relatively simple, `physiochemically-dominated' modes of mineralization possess skeletal strengths and durabilities that are among the lowest of any known mineralized skeletons. Organisms with relatively sophisticated, `biologically-dominated' modes of mineralization have mechanical properties among the highest values known for any materials. These extraordinarily strong and durable skeletal materials are found in mollusks, echinoderms, vertebrates, and arthropods, which are groups with primarily mobile ecological habits. These skeletons are frequently lightweight, non-massive skeletons with little phenotypic variation. By contrast, dominant reef framework builders and reef sediment formers, with physiochemically-dominated modes of mineralization, have non-mobile ecological habits and construct massive, phenotypically plastic skeletons, possessing extremely poor mechanical properties. Endolithic organisms that further degrade the mechanical properties of the mineralized skeletons of reef builders frequently ravage their massive skeletons. As a result, the skeletons of these groups commonly fragment, and play a central role in reef establishment and maintenance, as they are incorporated in reefal, wave-resistant carbonate buildups. Scleractinian corals have a physiochemically-dominated mode of mineralization and are the dominant modern reef framework builders. Mechanical properties of modern aragonitic scleractinian coral skeletons, tested alive, demonstrate skeletal strengths that are orders of magnitude lower than those seen in mollusks, echinoderms, vertebrates, and arthropods. Rudist bivalves, the dominant reef framework-building group of the Cretaceous, show prolific, massive, highly variable, calcific skeletal elements with structures similar to some reef-forming modern, non-mobile mollusks and the skeletons of other organisms with physiochemically-dominated modes of mineralization. Many aspects of the ecological habits of reef-framework building scleractinians and rudsits are similar, including relatively high skeletal growth rates, which produce massive skeletons and wave-resistant structures with entrapped bioclastic sediments. The principal adaptive role of mineralization in reef framework building groups appears to be the rapid production of massive, brittle, wave-resistant mineralized skeletons. The physiochemically-dominated mode of mineralization of these reef framework builders appears to have made them susceptible to secular variations in Phanerozoic seawater during `calcite' and `aragonite' seas, favoring scleractinians in aragonite seas and rudists during the Cretaceous calcite episode. By contrast, most mobile mollusks, echinoderms, vertebrates, and arthropods appear relatively unaffected by secular variations in seawater chemistry over the Phanerozoic

Gene expression profiling of intestinal regeneration in the sea cucumber

PubMed Central

Ortiz-Pineda, Pablo A; Ramírez-Gómez, Francisco; Pérez-Ortiz, Judit; González-Díaz, Sebastián; Santiago-De Jesús, Francisco; Hernández-Pasos, Josue; Del Valle-Avila, Cristina; Rojas-Cartagena, Carmencita; Suárez-Castillo, Edna C; Tossas, Karen; Méndez-Merced, Ana T; Roig-López, José L; Ortiz-Zuazaga, Humberto; García-Arrarás, José E

2009-01-01

Background Among deuterostomes, the regenerative potential is maximally expressed in echinoderms, animals that can quickly replace most injured organs. In particular, sea cucumbers are excellent models for studying organ regeneration since they regenerate their digestive tract after evisceration. However, echinoderms have been sidelined in modern regeneration studies partially because of the lack of genome-wide profiling approaches afforded by modern genomic tools. For the last decade, our laboratory has been using the sea cucumber Holothuria glaberrima to dissect the cellular and molecular events that allow for such amazing regenerative processes. We have already established an EST database obtained from cDNA libraries of normal and regenerating intestine at two different regeneration stages. This database now has over 7000 sequences. Results In the present work we used a custom-made microchip from Agilent with 60-mer probes for these ESTs, to determine the gene expression profile during intestinal regeneration. Here we compared the expression profile of animals at three different intestinal regeneration stages (3-, 7- and 14-days post evisceration) against the profile from normal (uneviscerated) intestines. The number of differentially expressed probes ranged from 70% at p < 0.05 to 39% at p < 0.001. Clustering analyses show specific profiles of expression for early (first week) and late (second week) regeneration stages. We used semiquantitative reverse transcriptase polymerase chain reaction (RT-PCR) to validate the expression profile of fifteen microarray detected differentially expressed genes which resulted in over 86% concordance between both techniques. Most of the differentially expressed ESTs showed no clear similarity to sequences in the databases and might represent novel genes associated with regeneration. However, other ESTs were similar to genes known to be involved in regeneration-related processes, wound healing, cell proliferation, differentiation, morphological plasticity, cell survival, stress response, immune challenge, and neoplastic transformation. Among those that have been validated, cytoskeletal genes, such as actins, and developmental genes, such as Wnt and Hox genes, show interesting expression profiles during regeneration. Conclusion Our findings set the base for future studies into the molecular basis of intestinal regeneration. Moreover, it advances the use of echinoderms in regenerative biology, animals that because of their amazing properties and their key evolutionary position, might provide important clues to the genetic basis of regenerative processes. PMID:19505337

A case of lung adenocarcinoma harboring exon 19 EGFR deletion and EML4-ALK fusion gene.

PubMed

Chen, Xiaoxia; Zhang, Jie; Hu, Qiong; Li, Xuefei; Zhou, Caicun

2013-08-01

We report a man with advanced adenocarcinoma who harboring exon 19 (E746-A750del) epidermal growth factor receptor (EGFR) deletion and echinoderm microtubule-associated protein like 4-anaplastic lymphoma kinase (EML4-ALK) gene translocation in the re-biospy specimen. The patient was treated with erlotinib with a stable disease but progressed slowly, while crizotinib showed a complete response. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Tentaculate Fossils from the Cambrian of Canada (British Columbia) and China (Yunnan) Interpreted as Primitive Deuterostomes

PubMed Central

Caron, Jean-Bernard; Conway Morris, Simon; Shu, Degan

2010-01-01

Molecular and morphological evidence unite the hemichordates and echinoderms as the Ambulacraria, but their earliest history remains almost entirely conjectural. This is on account of the morphological disparity of the ambulacrarians and a paucity of obvious stem-groups. We describe here a new taxon Herpetogaster collinsi gen. et sp. nov. from the Burgess Shale (Middle Cambrian) Lagerstätte. This soft-bodied vermiform animal has a pair of elongate dendritic oral tentacles, a flexible stolon with an attachment disc, and a re-curved trunk with at least 13 segments that is directed dextrally. A differentiated but un-looped gut is enclosed in a sac suspended by mesenteries. It consists of a short pharynx, a conspicuous lenticular stomach, followed by a narrow intestine sub-equal in length. This new taxon, together with the Lower Cambrian Phlogites and more intriguingly the hitherto enigmatic discoidal eldoniids (Cambrian-Devonian), form a distinctive clade (herein the cambroernids). Although one hypothesis of their relationships would look to the lophotrochozoans (specifically the entoprocts), we suggest that the evidence is more consistent with their being primitive deuterostomes, with specific comparisons being made to the pterobranch hemichordates and pre-radial echinoderms. On this basis some of the earliest ambulacrarians are interpreted as soft-bodied animals with a muscular stalk, and possessing prominent tentacles. PMID:20221405

Pennsylvanian stratigraphic reefs in Kansas, some modern comparisons and implications

USGS Publications Warehouse

Heckel, P.H.

1972-01-01

Broad platformlike buildups in the Stanton Limestone in southeastern Kansas are composed primarily of lime mud and phylloid algae and are rimmed with skeletal calcarenite composed largely of echinoderm and algal debris. Bordering the buildups are large (1??30 km) channels, lined or filled with similar calcarenite, and a broader basin containing shaly skeletal calcilutite. Grain abrasion and spar cement in the rimming calcarenites indicate water agitation and suggest wave resistance of the buildups during growth. Wave resistance may have been provided by 1) stalked echinoderms, which are resilient when alive and bind sediment with their roots, and also by 2) early drusy cementation of loose sediment to a coherent mass. Comparison to modern channel-separated buildups in the Persian Gulf and the Great Barrier Reef complex brings out the relative significance of organic frameworks in these different geologic settings. Recognized organic frameworks range from absent or insignificant in the Pennsylvanian examples through locally present but insignificant in the Persian Gulf, to apparently important in maintaining the buildups in the Great Barrier Reef. All three examples, however, exhibit patterns of original hydrodynamic control over initiation and gross form of the buildups. Determining significance of organic frameworks to overall buildup growth involves examining both their positions relative to evidence of wave action and the nature of binding in contemporaneous talus produced by wave action on the buildup. ?? 1972 Ferdinand Enke Verlag Stuttgart.

Metabolic rates are significantly lower in abyssal Holothuroidea than in shallow-water Holothuroidea

PubMed Central

van Oevelen, Dick

2018-01-01

Recent analyses of metabolic rates in fishes, echinoderms, crustaceans and cephalopods have concluded that bathymetric declines in temperature- and mass-normalized metabolic rate do not result from resource-limitation (e.g. oxygen or food/chemical energy), decreasing temperature or increasing hydrostatic pressure. Instead, based on contrasting bathymetric patterns reported in the metabolic rates of visual and non-visual taxa, declining metabolic rate with depth is proposed to result from relaxation of selection for high locomotory capacity in visual predators as light diminishes. Here, we present metabolic rates of Holothuroidea, a non-visual benthic and benthopelagic echinoderm class, determined in situ at abyssal depths (greater than 4000 m depth). Mean temperature- and mass-normalized metabolic rate did not differ significantly between shallow-water (less than 200 m depth) and bathyal (200–4000 m depth) holothurians, but was significantly lower in abyssal (greater than 4000 m depth) holothurians than in shallow-water holothurians. These results support the dominance of the visual interactions hypothesis at bathyal depths, but indicate that ecological or evolutionary pressures other than biotic visual interactions contribute to bathymetric variation in holothurian metabolic rates. Multiple nonlinear regression assuming power or exponential models indicates that in situ hydrostatic pressure and/or food/chemical energy availability are responsible for variation in holothurian metabolic rates. Consequently, these results have implications for modelling deep-sea energetics and processes. PMID:29892403

Mineralogical characterization of the Shelburne marble and the Salem limestone

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGee, E.S.

Samples of Shelburne marble and Salem limestone were selected to represent marbles and limestones used in buildings and monuments. The Royal variety of Shelburne marble is a white marble predominantly composed of calcite but has heterogeneously distributed gray inclusions. The select buff Salem limestone is a beige, homogeneous, fossiliferous limestone, predominantly composed of fragments of echinoderms and bryozoans. The author reports that both samples are appropriate test stones for the National Acid Precipitation Assessment Program stone exposure studies.

Histopathological Effects of Black Rock Harbor Dredged Material on Marine Organisms: A Laboratory Investigation.

DTIC Science & Technology

1986-02-01

Firmness of tissue, (d) Changes in the color of the internal organs such as the digestive diverticula and gonadal tissue, and (e) Cyst and tumor...from the BRH/BRH treatment from the Experiment B had parapodia with extensive metaplasia of the epidermis and also some cyst formation. Two animals (18...Binyon, J. 1972. Physiology of Echinoderms. Pergamon Press. 6. Bird, A.F. 1971. The Structure of Nematodes . Academic Press. 7. Boolootian, R.A., ed

Early and middle(?) Cambrian metazoan and protistan fossils from West Africa

USGS Publications Warehouse

Culver, S.J.; Repetski, J.E.; Pojeta, J.; Hunt, D.

1996-01-01

Supposed Upper Proterozoic strata in the southwest Taoudeni Basin, Guinea and Senegal, and from the Mauritanide fold belt, Mauritania, have yielded mostly poorly preserved small skeletal fossils of metazoan and protistan origin. Problematic, but possible echinoderm material and spicules of the heteractinid sponge Eiffelia dominate the Taoudeni Basin assemblage. The age of the material is not certain but the paleontologic data suggest an Early Cambrian age for the stratigraphically lowest faunas, and a Middle Cambrian age is possible for the stratigraphically highest collections.

Stratigraphic and facies analysis of Ste. Genevieve Limestone, Putnam County, Indiana

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stevenson, G.M.

1987-05-01

The Ste. Genevieve Limestone (Mississippian) in Putnam County, Indiana, was deposited on a southwestward-sloping ramp in the northeastern portion of the Illinois basin. This portion of the Ste. Genevieve Limestone is divided into three members which, in ascending order, are the Fredonia, the Spar Mountain, and the Levias. The Fredonia Member appears to be homogeneous biomicrite on out-crop, but petrographic analysis reveals mottling and distinguishable pellets and is classified as pelbiosparite. Storm deposits are observed and typically are composed of fossil hash zones (biopelsparite) overlain by calcitic shale layers. Bioclasts consist of stenohaline forms with foraminifera, echinoderms, and bryozoans predominant.more » The gray-green shale layers represent punctuated terrigenous influx in this shallow restricted shelf. The Spar Mountain Member is commonly cross-bedded calcarenite but commonly lacks the quartz and is oolitic-pelbiosparite. The dominant particle types are quartz-centered ooids, peloids, and echinoderm fragments. Relatively high energy conditions and herringbone-cross-beds suggest deposition of a shoal with tidal current influence. The Levias Member is thin-bedded biopelsparite which represents shallow shelf deposition. The Bryantsville Breccia Bed varies in thickness across the study area and marks the top of the Levias Member. Oolitic-biopelsparite centimeter-sized clasts are contained in a matrix of similar material, suggesting an intraformational mode of origin, possibly a collapse breccia. Two incomplete shoaling-upward cycles are present in this Ste. Genevieve sequence. The lower portion of each cycle is pelbiosparite/biopelsparite overlain by oolitic-pelbiosparite and/or calcarenite.« less

Hunt for Palytoxins in a Wide Variety of Marine Organisms Harvested in 2010 on the French Mediterranean Coast

PubMed Central

Biré, Ronel; Trotereau, Sophie; Lemée, Rodolphe; Oregioni, Davide; Delpont, Christine; Krys, Sophie; Guérin, Thierry

2015-01-01

During the summer of 2010, 31 species including fish, echinoderms, gastropods, crustaceans, cephalopods and sponges were sampled in the Bay of Villefranche on the French Mediterranean coast and screened for the presence of PLTX-group toxins using the haemolytic assay. Liquid chromatography tandem mass spectrometry (LC-MS/MS) was used for confirmatory purposes and to determine the toxin profile. The mean toxin concentration in the whole flesh of all sampled marine organisms, determined using the lower- (LB) and upper-bound (UB) approach was 4.3 and 5.1 µg·kg−1, respectively, with less than 1% of the results exceeding the European Food Safety Authority (EFSA) threshold of 30 µg·kg−1 and the highest values being reported for sea urchins (107.6 and 108.0 µg·kg−1). Toxins accumulated almost exclusively in the digestive tube of the tested species, with the exception of octopus, in which there were detectable toxin amounts in the remaining tissues (RT). The mean toxin concentration in the RT of the sampled organisms (fishes, echinoderms and cephalopods) was 0.7 and 1.7 µg·kg−1 (LB and UB, respectively), with a maximum value of 19.9 µg·kg−1 for octopus RT. The herbivorous and omnivorous organisms were the most contaminated species, indicating that diet influences the contamination process, and the LC-MS/MS revealed that ovatoxin-a was the only toxin detected. PMID:26308009

Hunt for Palytoxins in a Wide Variety of Marine Organisms Harvested in 2010 on the French Mediterranean Coast.

PubMed

Biré, Ronel; Trotereau, Sophie; Lemée, Rodolphe; Oregioni, Davide; Delpont, Christine; Krys, Sophie; Guérin, Thierry

2015-08-21

During the summer of 2010, 31 species including fish, echinoderms, gastropods, crustaceans, cephalopods and sponges were sampled in the Bay of Villefranche on the French Mediterranean coast and screened for the presence of PLTX-group toxins using the haemolytic assay. Liquid chromatography tandem mass spectrometry (LC-MS/MS) was used for confirmatory purposes and to determine the toxin profile. The mean toxin concentration in the whole flesh of all sampled marine organisms, determined using the lower- (LB) and upper-bound (UB) approach was 4.3 and 5.1 µg·kg(-1), respectively, with less than 1% of the results exceeding the European Food Safety Authority (EFSA) threshold of 30 µg·kg(-1)and the highest values being reported for sea urchins (107.6 and 108.0 µg·kg(-1)). Toxins accumulated almost exclusively in the digestive tube of the tested species, with the exception of octopus, in which there were detectable toxin amounts in the remaining tissues (RT). The mean toxin concentration in the RT of the sampled organisms (fishes, echinoderms and cephalopods) was 0.7 and 1.7 µg·kg(-1) (LB and UB, respectively), with a maximum value of 19.9 µg·kg(-1) for octopus RT. The herbivorous and omnivorous organisms were the most contaminated species, indicating that diet influences the contamination process, and the LC-MS/MS revealed that ovatoxin-a was the only toxin detected.

Chemical fate and biological effects of several endocrine disrupters compounds in two echinoderm species.

PubMed

Sugni, Michela; Tremolada, Paolo; Porte, Cinta; Barbaglio, Alice; Bonasoro, Francesco; Carnevali, M Daniela Candia

2010-03-01

Two echinoderm species, the sea urchin Paracentrotus lividus and the feather star Antedon mediterranea, were exposed for 28 days to several EDCs: three putative androgenic compounds, triphenyltin (TPT), fenarimol (FEN), methyltestosterone (MET), and two putative antiandrogenic compounds, p,p'-DDE (DDE) and cyproterone acetate (CPA). The exposure nominal concentrations were from 10 to 3000 ng L(-1), depending on the compound. This paper is an attempt to join three different aspects coming from our ecotoxicological tests: (1) the chemical behaviour inside the experimental system; (2) the measured toxicological endpoints; (3) the biochemical responses, to which the measured endpoints may depend. The chemical fate of the different compounds was enquired by a modelling approach throughout the application of the 'Aquarium model'. An estimation of the day-to-day concentration levels in water and biota were obtained together with the amount assumed each day by each animal (uptake in microg animal(-1) d(-1) or ng g-wet weight(-1) d(-1)). The toxicological endpoints investigated deal with the reproductive potential (gonad maturation stage, gonad index and oocyte diameter) and with the regenerative potential (growth and histology). Almost all the compounds exerted some kind of effect at the tested concentrations, however TPT was the most effective in altering both reproductive and regenerative parameters (also at the concentration of few ng L(-1)). The biochemical analyses of testosterone (T) and 17beta-estradiol (E(2)) also showed the ability of the selected compounds to significantly alter endogenous steroid concentrations.

Earth-System Scales of Biodiversity Variability in Shallow Continental Margin Seafloor Ecosystems

NASA Astrophysics Data System (ADS)

Moffitt, S. E.; White, S. M.; Hill, T. M.; Kennett, J.

2015-12-01

High-resolution paleoceanographic sedimentary sequences allow for the description of ecosystem sensitivity to earth-system scales of climate and oceanographic change. Such archives from Santa Barbara Basin, California record the ecological consequences to seafloor ecosystems of climate-forced shifts in the California Current Oxygen Minimum Zone (OMZ). Here we use core MV0508-20JPC dated to 735,000±5,000 years ago (Marine Isotope Stage 18) as a "floating window" of millennial-scale ecological variability. For this investigation, previously published archives of planktonic δ18O (Globigerina bulloides) record stadial and interstadial oscillations in surface ocean temperature. Core MV0508-20JPC is an intermittently laminated archive, strongly influenced by the California Current OMZ, with continuously preserved benthic foraminifera and discontinuously preserved micro-invertebrates, including ophiuroids, echinoderms, ostracods, gastropods, bivalves and scaphopods. Multivariate statistical approaches, such as ordinations and cluster analyses, describe climate-driven changes in both foraminiferal and micro-invertebrate assemblages. Statistical ordinations illustrate that the shallow continental margin seafloor underwent predictable phase-shifts in oxygenation and biodiversity across stadial and interstadial events. A narrow suite of severely hypoxic taxa characterized foraminiferal communities from laminated intervals, including Bolivina tumida, Globobulimina spp., and Nonionella stella. Foraminiferal communities from bioturbated intervals are diverse and >60% similar to each other, and they are associated with echinoderm, ostracod and mollusc fossils. As with climate shifts in the latest Quaternary, there is a sensitive benthic ecosystem response in mid-Pleistocene continental margins to climatically related changes in OMZ strength.

The genome of the sea urchin Strongylocentrotus purpuratus.

PubMed

Sodergren, Erica; Weinstock, George M; Davidson, Eric H; Cameron, R Andrew; Gibbs, Richard A; Angerer, Robert C; Angerer, Lynne M; Arnone, Maria Ina; Burgess, David R; Burke, Robert D; Coffman, James A; Dean, Michael; Elphick, Maurice R; Ettensohn, Charles A; Foltz, Kathy R; Hamdoun, Amro; Hynes, Richard O; Klein, William H; Marzluff, William; McClay, David R; Morris, Robert L; Mushegian, Arcady; Rast, Jonathan P; Smith, L Courtney; Thorndyke, Michael C; Vacquier, Victor D; Wessel, Gary M; Wray, Greg; Zhang, Lan; Elsik, Christine G; Ermolaeva, Olga; Hlavina, Wratko; Hofmann, Gretchen; Kitts, Paul; Landrum, Melissa J; Mackey, Aaron J; Maglott, Donna; Panopoulou, Georgia; Poustka, Albert J; Pruitt, Kim; Sapojnikov, Victor; Song, Xingzhi; Souvorov, Alexandre; Solovyev, Victor; Wei, Zheng; Whittaker, Charles A; Worley, Kim; Durbin, K James; Shen, Yufeng; Fedrigo, Olivier; Garfield, David; Haygood, Ralph; Primus, Alexander; Satija, Rahul; Severson, Tonya; Gonzalez-Garay, Manuel L; Jackson, Andrew R; Milosavljevic, Aleksandar; Tong, Mark; Killian, Christopher E; Livingston, Brian T; Wilt, Fred H; Adams, Nikki; Bellé, Robert; Carbonneau, Seth; Cheung, Rocky; Cormier, Patrick; Cosson, Bertrand; Croce, Jenifer; Fernandez-Guerra, Antonio; Genevière, Anne-Marie; Goel, Manisha; Kelkar, Hemant; Morales, Julia; Mulner-Lorillon, Odile; Robertson, Anthony J; Goldstone, Jared V; Cole, Bryan; Epel, David; Gold, Bert; Hahn, Mark E; Howard-Ashby, Meredith; Scally, Mark; Stegeman, John J; Allgood, Erin L; Cool, Jonah; Judkins, Kyle M; McCafferty, Shawn S; Musante, Ashlan M; Obar, Robert A; Rawson, Amanda P; Rossetti, Blair J; Gibbons, Ian R; Hoffman, Matthew P; Leone, Andrew; Istrail, Sorin; Materna, Stefan C; Samanta, Manoj P; Stolc, Viktor; Tongprasit, Waraporn; Tu, Qiang; Bergeron, Karl-Frederik; Brandhorst, Bruce P; Whittle, James; Berney, Kevin; Bottjer, David J; Calestani, Cristina; Peterson, Kevin; Chow, Elly; Yuan, Qiu Autumn; Elhaik, Eran; Graur, Dan; Reese, Justin T; Bosdet, Ian; Heesun, Shin; Marra, Marco A; Schein, Jacqueline; Anderson, Michele K; Brockton, Virginia; Buckley, Katherine M; Cohen, Avis H; Fugmann, Sebastian D; Hibino, Taku; Loza-Coll, Mariano; Majeske, Audrey J; Messier, Cynthia; Nair, Sham V; Pancer, Zeev; Terwilliger, David P; Agca, Cavit; Arboleda, Enrique; Chen, Nansheng; Churcher, Allison M; Hallböök, F; Humphrey, Glen W; Idris, Mohammed M; Kiyama, Takae; Liang, Shuguang; Mellott, Dan; Mu, Xiuqian; Murray, Greg; Olinski, Robert P; Raible, Florian; Rowe, Matthew; Taylor, John S; Tessmar-Raible, Kristin; Wang, D; Wilson, Karen H; Yaguchi, Shunsuke; Gaasterland, Terry; Galindo, Blanca E; Gunaratne, Herath J; Juliano, Celina; Kinukawa, Masashi; Moy, Gary W; Neill, Anna T; Nomura, Mamoru; Raisch, Michael; Reade, Anna; Roux, Michelle M; Song, Jia L; Su, Yi-Hsien; Townley, Ian K; Voronina, Ekaterina; Wong, Julian L; Amore, Gabriele; Branno, Margherita; Brown, Euan R; Cavalieri, Vincenzo; Duboc, Véronique; Duloquin, Louise; Flytzanis, Constantin; Gache, Christian; Lapraz, François; Lepage, Thierry; Locascio, Annamaria; Martinez, Pedro; Matassi, Giorgio; Matranga, Valeria; Range, Ryan; Rizzo, Francesca; Röttinger, Eric; Beane, Wendy; Bradham, Cynthia; Byrum, Christine; Glenn, Tom; Hussain, Sofia; Manning, Gerard; Miranda, Esther; Thomason, Rebecca; Walton, Katherine; Wikramanayke, Athula; Wu, Shu-Yu; Xu, Ronghui; Brown, C Titus; Chen, Lili; Gray, Rachel F; Lee, Pei Yun; Nam, Jongmin; Oliveri, Paola; Smith, Joel; Muzny, Donna; Bell, Stephanie; Chacko, Joseph; Cree, Andrew; Curry, Stacey; Davis, Clay; Dinh, Huyen; Dugan-Rocha, Shannon; Fowler, Jerry; Gill, Rachel; Hamilton, Cerrissa; Hernandez, Judith; Hines, Sandra; Hume, Jennifer; Jackson, Laronda; Jolivet, Angela; Kovar, Christie; Lee, Sandra; Lewis, Lora; Miner, George; Morgan, Margaret; Nazareth, Lynne V; Okwuonu, Geoffrey; Parker, David; Pu, Ling-Ling; Thorn, Rachel; Wright, Rita

2006-11-10

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.

The occurrence of Ophiocnemis marmorata (Echinodermata: Ophiuroidea) associated with the rhizostome medusa Rhopilema hispidum (Cnidaria: Scyphozoa)

NASA Astrophysics Data System (ADS)

Kanagaraj, Govindan; Kumar, Pithchai Sampath; Morandini, André C.

2008-11-01

The association of scyphomedusae with invertebrates has been long known in the literature; especially with hyperiids amphipods. The association of echinoderms with jellyfish is not common and rarely recorded. We reported the association of the ophiuroid Ophiocnemis marmorata with the rhizostome scyphomedusa Rhopilema hispidum collected in Vellar estuary (on the southeast coast of India). O. marmorata is supposed to be a filter feeding ophiuroid, quite common in soft bottom of shallow waters. The brittle stars possibly seek for food supply, shelter and protection through the association.

Acidified seawater impacts sea urchin larvae pH regulatory systems relevant for calcification

PubMed Central

Stumpp, Meike; Hu, Marian Y.; Melzner, Frank; Gutowska, Magdalena A.; Dorey, Narimane; Himmerkus, Nina; Holtmann, Wiebke C.; Dupont, Sam T.; Thorndyke, Michael C.; Bleich, Markus

2012-01-01

Calcifying echinoid larvae respond to changes in seawater carbonate chemistry with reduced growth and developmental delay. To date, no information exists on how ocean acidification acts on pH homeostasis in echinoderm larvae. Understanding acid–base regulatory capacities is important because intracellular formation and maintenance of the calcium carbonate skeleton is dependent on pH homeostasis. Using H+-selective microelectrodes and the pH-sensitive fluorescent dye BCECF, we conducted in vivo measurements of extracellular and intracellular pH (pHe and pHi) in echinoderm larvae. We exposed pluteus larvae to a range of seawater CO2 conditions and demonstrated that the extracellular compartment surrounding the calcifying primary mesenchyme cells (PMCs) conforms to the surrounding seawater with respect to pH during exposure to elevated seawater pCO2. Using FITC dextran conjugates, we demonstrate that sea urchin larvae have a leaky integument. PMCs and spicules are therefore directly exposed to strong changes in pHe whenever seawater pH changes. However, measurements of pHi demonstrated that PMCs are able to fully compensate an induced intracellular acidosis. This was highly dependent on Na+ and HCO3−, suggesting a bicarbonate buffer mechanism involving secondary active Na+-dependent membrane transport proteins. We suggest that, under ocean acidification, maintained pHi enables calcification to proceed despite decreased pHe. However, this probably causes enhanced costs. Increased costs for calcification or cellular homeostasis can be one of the main factors leading to modifications in energy partitioning, which then impacts growth and, ultimately, results in increased mortality of echinoid larvae during the pelagic life stage. PMID:23077257

Tissue Regeneration and Biomineralization in Sea Urchins: Role of Notch Signaling and Presence of Stem Cell Markers

PubMed Central

Reinardy, Helena C.; Emerson, Chloe E.; Manley, Jason M.; Bodnar, Andrea G.

2015-01-01

Echinoderms represent a phylum with exceptional regenerative capabilities that can reconstruct both external appendages and internal organs. Mechanistic understanding of the cellular pathways involved in regeneration in these animals has been hampered by the limited genomic tools and limited ability to manipulate regenerative processes. We present a functional assay to investigate mechanisms of tissue regeneration and biomineralization by measuring the regrowth of amputated tube feet (sensory and motor appendages) and spines in the sea urchin, Lytechinus variegatus. The ability to manipulate regeneration was demonstrated by concentration-dependent inhibition of regrowth of spines and tube feet by treatment with the mitotic inhibitor, vincristine. Treatment with the gamma-secretase inhibitor DAPT resulted in a concentration-dependent inhibition of regrowth, indicating that both tube feet and spine regeneration require functional Notch signaling. Stem cell markers (Piwi and Vasa) were expressed in tube feet and spine tissue, and Vasa-positive cells were localized throughout the epidermis of tube feet by immunohistochemistry, suggesting the existence of multipotent progenitor cells in these highly regenerative appendages. The presence of Vasa protein in other somatic tissues (e.g. esophagus, radial nerve, and a sub-population of coelomocytes) suggests that multipotent cells are present throughout adult sea urchins and may contribute to normal homeostasis in addition to regeneration. Mechanistic insight into the cellular pathways governing the tremendous regenerative capacity of echinoderms may reveal processes that can be modulated for regenerative therapies, shed light on the evolution of regeneration, and enable the ability to predict how these processes will respond to changing environmental conditions. PMID:26267358

NGFFFamide and echinotocin: structurally unrelated myoactive neuropeptides derived from neurophysin-containing precursors in sea urchins.

PubMed

Elphick, Maurice R; Rowe, Matthew L

2009-04-01

The myoactive neuropeptide NGIWYamide was originally isolated from the holothurian (sea cucumber) Apostichopus japonicus but there is evidence that NGIWYamide-like peptides also occur in other echinoderms. Here we report the discovery of a gene in the sea urchin Strongylocentrotus purpuratus that encodes two copies of an NGIWYamide-like peptide: Asn-Gly-Phe-Phe-Phe-(NH(2)) or NGFFFamide. Interestingly, the C-terminal region of the NGFFFamide precursor shares sequence similarity with neurophysins, carrier proteins hitherto uniquely associated with precursors of vasopressin/oxytocin-like neuropeptides. Thus, the NGFFFamide precursor is the first neurophysin-containing neuropeptide precursor to be discovered that does not contain a vasopressin/oxytocin-like peptide. However, it remains to be determined whether neurophysin acts as a carrier protein for NGFFFamide. The S. purpuratus genome also contains a gene encoding a precursor comprising a neurophysin polypeptide and 'echinotocin' (CFISNCPKGamide) - the first vasopressin/oxytocin-like peptide to be identified in an echinoderm. Therefore, in S. purpuratus there are two genes encoding precursors that have a neurophysin domain but which encode neuropeptides that are structurally unrelated. Furthermore, both NGFFFamide and echinotocin cause contraction of tube foot and oesophagus preparations from the sea urchin Echinus esculentus, consistent with the myoactivity of NGIWYamide in sea cucumbers and the myoactivity of vasopressin/oxytocin-like peptides in other animal phyla. Presumably the NGFFFamide precursor acquired its neurophysin domain following partial or complete duplication of a gene encoding a vasopressin/oxytocin-like peptide, but it remains to be determined when in evolutionary history this occurred.

Perturbation of gut bacteria induces a coordinated cellular immune response in the purple sea urchin larva.

PubMed

Ch Ho, Eric; Buckley, Katherine M; Schrankel, Catherine S; Schuh, Nicholas W; Hibino, Taku; Solek, Cynthia M; Bae, Koeun; Wang, Guizhi; Rast, Jonathan P

2016-10-01

The purple sea urchin (Strongylocentrotus purpuratus) genome sequence contains a complex repertoire of genes encoding innate immune recognition proteins and homologs of important vertebrate immune regulatory factors. To characterize how this immune system is deployed within an experimentally tractable, intact animal, we investigate the immune capability of the larval stage. Sea urchin embryos and larvae are morphologically simple and transparent, providing an organism-wide model to view immune response at cellular resolution. Here we present evidence for immune function in five mesenchymal cell types based on morphology, behavior and gene expression. Two cell types are phagocytic; the others interact at sites of microbial detection or injury. We characterize immune-associated gene markers for three cell types, including a perforin-like molecule, a scavenger receptor, a complement-like thioester-containing protein and the echinoderm-specific immune response factor 185/333. We elicit larval immune responses by (1) bacterial injection into the blastocoel and (2) seawater exposure to the marine bacterium Vibrio diazotrophicus to perturb immune state in the gut. Exposure at the epithelium induces a strong response in which pigment cells (one type of immune cell) migrate from the ectoderm to interact with the gut epithelium. Bacteria that accumulate in the gut later invade the blastocoel, where they are cleared by phagocytic and granular immune cells. The complexity of this coordinated, dynamic inflammatory program within the simple larval morphology provides a system in which to characterize processes that direct both aspects of the echinoderm-specific immune response as well as those that are shared with other deuterostomes, including vertebrates.

EML proteins in microtubule regulation and human disease.

PubMed

Fry, Andrew M; O'Regan, Laura; Montgomery, Jessica; Adib, Rozita; Bayliss, Richard

2016-10-15

The EMLs are a conserved family of microtubule-associated proteins (MAPs). The founding member was discovered in sea urchins as a 77-kDa polypeptide that co-purified with microtubules. This protein, termed EMAP for echinoderm MAP, was the major non-tubulin component present in purified microtubule preparations made from unfertilized sea urchin eggs [J. Cell Sci. (1993) 104: , 445-450; J. Cell Sci. (1987) 87: (Pt 1), 71-84]. Orthologues of EMAP were subsequently identified in other echinoderms, such as starfish and sand dollar, and then in more distant eukaryotes, including flies, worms and vertebrates, where the name of ELP or EML (both for EMAP-like protein) has been adopted [BMC Dev. Biol. (2008) 8: , 110; Dev. Genes Evol. (2000) 210: , 2-10]. The common property of these proteins is their ability to decorate microtubules. However, whether they are associated with particular microtubule populations or exercise specific functions in different microtubule-dependent processes remains unknown. Furthermore, although there is limited evidence that they regulate microtubule dynamics, the biochemical mechanisms of their molecular activity have yet to be explored. Nevertheless, interest in these proteins has grown substantially because of the identification of EML mutations in neuronal disorders and oncogenic fusions in human cancers. Here, we summarize our current knowledge of the expression, localization and structure of what is proving to be an interesting and important class of MAPs. We also speculate about their function in microtubule regulation and highlight how the studies of EMLs in human diseases may open up novel avenues for patient therapy. © 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Ground-glass nodule in a patient with echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK)-positive lung cancer: a case report.

PubMed

Owada, Yuki; Yonechi, Atsushi; Higuchi, Mitsunori; Suzuki, Hiroyuki

2016-03-10

Grand-glass nodule for CT image has thought to be less aggressive tumor in lung cancer. Echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK)-positive lung cancer presenting with Ground-glass nodules (GGNs) is relatively rare, and few such cases have been reported. An asymptomatic 56-year-old woman exhibited a 1.1-cm GGN in the lower lobe of the left lung on computed tomography during a medical checkup. Positron emission tomography showed no difference in uptake by the nodule compared with other organs. We elected to perform surgery because the nodule included a solid component and had grown only slightly during the last 2 years according to thin-section computed tomography. Partial resection of the lower left lung was performed by video-assisted thoracic surgery. Pathological examination revealed mucus-producing high columnar epithelium forming an irregular tubular-acinar-like structure partly replacing the alveolar epithelium on hematoxylin and eosin staining. More than 50 % of the tumor demonstrated a lepidic growth pattern. The tumor was negative for epidermal growth factor receptor mutation but positive for the EML4-ALK fusion oncogene according to fluorescence in situ hybridization. We herein report a case of EML4-ALK-positive lung cancer presenting with a GGN along with a review of the relevant literature, including histopathological findings and imaging features. We consider that EML4-ALK-positive lung cancer is often highly progressive and that careful follow-up is therefore essential in these patients.

Long Non-Coding RNAs (lncRNAs) of Sea Cucumber: Large-Scale Prediction, Expression Profiling, Non-Coding Network Construction, and lncRNA-microRNA-Gene Interaction Analysis of lncRNAs in Apostichopus japonicus and Holothuria glaberrima During LPS Challenge and Radial Organ Complex Regeneration.

PubMed

Mu, Chuang; Wang, Ruijia; Li, Tianqi; Li, Yuqiang; Tian, Meilin; Jiao, Wenqian; Huang, Xiaoting; Zhang, Lingling; Hu, Xiaoli; Wang, Shi; Bao, Zhenmin

2016-08-01

Long non-coding RNA (lncRNA) structurally resembles mRNA but cannot be translated into protein. Although the systematic identification and characterization of lncRNAs have been increasingly reported in model species, information concerning non-model species is still lacking. Here, we report the first systematic identification and characterization of lncRNAs in two sea cucumber species: (1) Apostichopus japonicus during lipopolysaccharide (LPS) challenge and in heathy tissues and (2) Holothuria glaberrima during radial organ complex regeneration, using RNA-seq datasets and bioinformatics analysis. We identified A. japonicus and H. glaberrima lncRNAs that were differentially expressed during LPS challenge and radial organ complex regeneration, respectively. Notably, the predicted lncRNA-microRNA-gene trinities revealed that, in addition to targeting protein-coding transcripts, miRNAs might also target lncRNAs, thereby participating in a potential novel layer of regulatory interactions among non-coding RNA classes in echinoderms. Furthermore, the constructed coding-non-coding network implied the potential involvement of lncRNA-gene interactions during the regulation of several important genes (e.g., Toll-like receptor 1 [TLR1] and transglutaminase-1 [TGM1]) in response to LPS challenge and radial organ complex regeneration in sea cucumbers. Overall, this pioneer systematic identification, annotation, and characterization of lncRNAs in echinoderm pave the way for similar studies and future genetic, genomic, and evolutionary research in non-model species.

Video image processing greatly enhances contrast, quality, and speed in polarization-based microscopy

PubMed Central

1981-01-01

Video cameras with contrast and black level controls can yield polarized light and differential interference contrast microscope images with unprecedented image quality, resolution, and recording speed. The theoretical basis and practical aspects of video polarization and differential interference contrast microscopy are discussed and several applications in cell biology are illustrated. These include: birefringence of cortical structures and beating cilia in Stentor, birefringence of rotating flagella on a single bacterium, growth and morphogenesis of echinoderm skeletal spicules in culture, ciliary and electrical activity in a balancing organ of a nudibranch snail, and acrosomal reaction in activated sperm. PMID:6788777

Environmental dermatology: skin manifestations of injuries caused by invertebrate aquatic animals*

PubMed Central

Haddad Junior, Vidal

2013-01-01

Contact between humans and coastal areas has increased in recent decades, which has led to an increase in injuries from aquatic animals. The majority of these present dermatological manifestations, and some of them show typical lesions. The highest percentages of injuries that occur in marine environments are associated with invertebrates such as sea urchins, jellyfish and Portuguese men-of-war (echinoderms and cnidarians). In this review, we discuss the clinical, therapeutic and preventive aspects of injuries caused by marine and freshwater invertebrates, focusing on first aid measures and diagnosis for dermatologists and professionals in coastal areas. PMID:24068119

The Genome of the Sea Urchin Strongylocentrotus purpuratus

PubMed Central

2011-01-01

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes. PMID:17095691

[Problems caused by poisonous tropical marine animals].

PubMed

Lääveri, Tinja; Räisänen-Sokolowski, Anne; Jama, Timo

2014-01-01

A Finnish physician encounters problems caused by tropical marine animals either during her/his own travelling or while treating travelers who have returned home. Certain species of medusae and cone shells as well as the stings by some fish species are life-threateningly poisonous. A person stung or bitten by any of the most dangerous species must immediately be admitted to the hospital. Foreign material remaining in tissues after stings by echinoderms and spiky fish may cause problems months after the actual injury. The injuries become easily infected, and antimicrobial drug therapy must thus cover gram-negative rod-shaped bacteria as well.

Acidified seawater impacts sea urchin larvae pH regulatory systems relevant for calcification.

PubMed

Stumpp, Meike; Hu, Marian Y; Melzner, Frank; Gutowska, Magdalena A; Dorey, Narimane; Himmerkus, Nina; Holtmann, Wiebke C; Dupont, Sam T; Thorndyke, Michael C; Bleich, Markus

2012-10-30

Calcifying echinoid larvae respond to changes in seawater carbonate chemistry with reduced growth and developmental delay. To date, no information exists on how ocean acidification acts on pH homeostasis in echinoderm larvae. Understanding acid-base regulatory capacities is important because intracellular formation and maintenance of the calcium carbonate skeleton is dependent on pH homeostasis. Using H(+)-selective microelectrodes and the pH-sensitive fluorescent dye BCECF, we conducted in vivo measurements of extracellular and intracellular pH (pH(e) and pH(i)) in echinoderm larvae. We exposed pluteus larvae to a range of seawater CO(2) conditions and demonstrated that the extracellular compartment surrounding the calcifying primary mesenchyme cells (PMCs) conforms to the surrounding seawater with respect to pH during exposure to elevated seawater pCO(2). Using FITC dextran conjugates, we demonstrate that sea urchin larvae have a leaky integument. PMCs and spicules are therefore directly exposed to strong changes in pH(e) whenever seawater pH changes. However, measurements of pH(i) demonstrated that PMCs are able to fully compensate an induced intracellular acidosis. This was highly dependent on Na(+) and HCO(3)(-), suggesting a bicarbonate buffer mechanism involving secondary active Na(+)-dependent membrane transport proteins. We suggest that, under ocean acidification, maintained pH(i) enables calcification to proceed despite decreased pH(e). However, this probably causes enhanced costs. Increased costs for calcification or cellular homeostasis can be one of the main factors leading to modifications in energy partitioning, which then impacts growth and, ultimately, results in increased mortality of echinoid larvae during the pelagic life stage.

First Report of Ciguatoxins in Two Starfish Species: Ophidiaster ophidianus and Marthasterias glacialis

PubMed Central

Silva, Marisa; Rodriguez, Inés; Barreiro, Aldo; Kaufmann, Manfred; Neto, Ana Isabel; Hassouani, Meryem; Sabour, Brahim; Alfonso, Amparo; Botana, Luis M.; Vasconcelos, Vitor

2015-01-01

Ciguatera fish poisoning (CFP) is a syndrome caused by the ingestion of fish contaminated with Ciguatoxins (CTXs). These phycotoxins are produced mainly by dinoflagellates that belong to the genus Gambierdiscus that are transformed in more toxic forms in predatory fish guts, and are more present in the Indo-Pacific and Caribbean areas. It is estimated that CFP causes per year more than 10,000 intoxications worldwide. With the rise of water temperature and anthropogenic intervention, it is important to study the prevalence of CFP in more temperate waters. Through inter- and subtidal sampling, 22 species of organisms were collected, in Madeira and Azores archipelagos and in the northwestern Moroccan coast, during September of 2012 and June and July of 2013. A total of 94 samples of 22 different species of bivalves, gastropods, echinoderms and crustaceans where analyzed by Ultra Performance Liquid Chromatography-Mass Spectometry-Ion Trap-Time of Flight (UPLC-MS-IT-TOF) and Ultra Performance Chromatography- Mass Spectrometry (UPLC-MS). Our main aim was to detect new vectors and ascertain if there were some geographical differences. We detected for the first time putative CTXs in echinoderms, in two starfish species—M. glacialis and O. ophidianus. We detected differences regarding uptake values by organisms and geographical location. Toxin amounts were significant, showing the importance and the need for continuity of these studies to gain more knowledge about the prevalence of these toxins, in order to better access human health risk. In addition, we suggest monitoring of these toxins should be extended to other vectors, starfish being a good alternative for protecting and accessing human health risk. PMID:26402702

Optimizing preservation protocols to extract high-quality RNA from different tissues of echinoderms for next-generation sequencing.

PubMed

Pérez-Portela, Rocío; Riesgo, Ana

2013-09-01

Transcriptomic information provides fundamental insights into biological processes. Extraction of quality RNA is a challenging step, and preservation and extraction protocols need to be adjusted in many cases. Our objectives were to optimize preservation protocols for isolation of high-quality RNA from diverse echinoderm tissues and to compare the utility of parameters as absorbance ratios and RIN values to assess RNA quality. Three different tissues (gonad, oesophagus and coelomocytes) were selected from the sea urchin Arbacia lixula. Solid tissues were flash-frozen and stored at -80 °C until processed. Four preservation treatments were applied to coelomocytes: flash freezing and storage at -80 °C, RNAlater and storage at -20 °C, preservation in TRIzol reagent and storage at -80 °C and direct extraction with TRIzol from fresh cells. Extractions of total RNA were performed with a modified TRIzol protocol for all tissues. Our results showed high values of RNA quantity and quality for all tissues, showing nonsignificant differences among them. However, while flash freezing was effective for solid tissues, it was inadequate for coelomocytes because of the low quality of the RNA extractions. Coelomocytes preserved in RNAlater displayed large variability in RNA integrity and insufficient RNA amount for further isolation of mRNA. TRIzol was the most efficient system for stabilizing RNA which resulted on high RNA quality and quantity. We did not detect correlation between absorbance ratios and RNA integrity. The best strategies for assessing RNA integrity was the visualization of 18S rRNA and 28S rRNA bands in agarose gels and estimation of RIN values with Agilent Bioanalyzer chips. © 2013 John Wiley & Sons Ltd.

Exposure to 2,4-decadienal negatively impacts upon marine invertebrate larval fitness.

PubMed

Caldwell, Gary S; Lewis, Ceri; Olive, Peter J W; Bentley, Matthew G

2005-06-01

Diatoms liberate volatile, biologically active unsaturated aldehydes following cell damage, which negatively impact upon invertebrate reproductive processes such as fertilization, embryogenesis and larval survival. 2,4-Decadienal is frequently identified among the aldehydes produced and is one of the more biologically active. The majority of studies which have examined the toxic effects of diatom aldehydes to invertebrate reproduction have scored egg production and/or hatching success as indicators of biological impacts. There are very few studies which have dealt specifically with the impacts of diatom-derived aldehydes on larval fitness. Larval stages of the polychaetes Arenicola marina and Nereis virens and the echinoderms Asterias rubens and Psammechinus miliaris exposed to 2,4-decadienal at sub 1 microg ml(-1) concentrations suffered reduced survival over the incubation period (day 1-8 post fertilization) with detectable differences for the polychates at a concentration of 0.005 and 0.01-0.1 microg ml(-1) for the echinoderms. Susceptibility of larval N. virens was investigated using stage specific 24 h exposures at 2,4-decadienal concentrations up to 1.5 microg ml(-1). A clear stage specific effect was found, with earlier larval stages most vulnerable. Nectochaete larvae (9-10 d) showed no reduction in survival at the concentrations assayed. Fluctuating asymmetry (FA), defined as random deviations from perfect bilateral symmetry, was used to analyse fitness of larval P. miliaris exposed to 2,4-decadienal at concentrations of 0.1, 0.5 and 1 microg ml(-1). The degree and frequency of asymmetrical development increased with increasing 2,4-decadienal concentration. Equally, as FA increased larval survival decreased. These results provide further support for the teratogenic nature of 2,4-decadienal and its negative impact on invertebrate larval fitness.

The complex simplicity of the brittle star nervous system.

PubMed

Zueva, Olga; Khoury, Maleana; Heinzeller, Thomas; Mashanova, Daria; Mashanov, Vladimir

2018-01-01

Brittle stars (Ophiuroidea, Echinodermata) have been increasingly used in studies of animal behavior, locomotion, regeneration, physiology, and bioluminescence. The success of these studies directly depends on good working knowledge of the ophiuroid nervous system. Here, we describe the arm nervous system at different levels of organization, including the microanatomy of the radial nerve cord and peripheral nerves, ultrastructure of the neural tissue, and localization of different cell types using specific antibody markers. We standardize the nomenclature of nerves and ganglia, and provide an anatomically accurate digital 3D model of the arm nervous system as a reference for future studies. Our results helped identify several general features characteristic to the adult echinoderm nervous system, including the extensive anatomical interconnections between the ectoneural and hyponeural components, neuroepithelial organization of the central nervous system, and the supporting scaffold of the neuroepithelium formed by radial glial cells. In addition, we provide further support to the notion that the echinoderm radial glia is a complex and diverse cell population. We also tested the suitability of a range of specific cell-type markers for studies of the brittle star nervous system and established that the radial glial cells are reliably labeled with the ERG1 antibodies, whereas the best neuronal markers are acetylated tubulin, ELAV, and synaptotagmin B. The transcription factor Brn1/2/4 - a marker of neuronal progenitors - is expressed not only in neurons, but also in a subpopulation of radial glia. For the first time, we describe putative ophiuroid proprioceptors associated with the hyponeural part of the central nervous system. Together, our data help establish both the general principles of neural architecture common to the phylum Echinodermata and the specific ophiuroid features.

Ancient origin of the modern deep-sea fauna.

PubMed

Thuy, Ben; Gale, Andy S; Kroh, Andreas; Kucera, Michal; Numberger-Thuy, Lea D; Reich, Mike; Stöhr, Sabine

2012-01-01

The origin and possible antiquity of the spectacularly diverse modern deep-sea fauna has been debated since the beginning of deep-sea research in the mid-nineteenth century. Recent hypotheses, based on biogeographic patterns and molecular clock estimates, support a latest Mesozoic or early Cenozoic date for the origin of key groups of the present deep-sea fauna (echinoids, octopods). This relatively young age is consistent with hypotheses that argue for extensive extinction during Jurassic and Cretaceous Oceanic Anoxic Events (OAEs) and the mid-Cenozoic cooling of deep-water masses, implying repeated re-colonization by immigration of taxa from shallow-water habitats. Here we report on a well-preserved echinoderm assemblage from deep-sea (1000-1500 m paleodepth) sediments of the NE-Atlantic of Early Cretaceous age (114 Ma). The assemblage is strikingly similar to that of extant bathyal echinoderm communities in composition, including families and genera found exclusively in modern deep-sea habitats. A number of taxa found in the assemblage have no fossil record at shelf depths postdating the assemblage, which precludes the possibility of deep-sea recolonization from shallow habitats following episodic extinction at least for those groups. Our discovery provides the first key fossil evidence that a significant part of the modern deep-sea fauna is considerably older than previously assumed. As a consequence, most major paleoceanographic events had far less impact on the diversity of deep-sea faunas than has been implied. It also suggests that deep-sea biota are more resilient to extinction events than shallow-water forms, and that the unusual deep-sea environment, indeed, provides evolutionary stability which is very rarely punctuated on macroevolutionary time scales.

Observing Evolutionary Entropy in Relation to Body Size Over Time

NASA Astrophysics Data System (ADS)

Idgunji, S.; Zhang, H.; Payne, J.; Heim, N. A.

2015-12-01

The Second Law of Thermodynamics, according to Clausius, states that entropy will always increase in the universe, meaning systems will break down and become simple and chaotic. However, this is seemingly contradicted by the existence of living organisms, which can have highly complex and organized systems. Furthermore, there is a greater contradiction in the theory of evolution, which sees organisms growing larger and becoming more complex over time. Our research project revolved around whether organisms actually became more complex over time, and correlating these findings with the body size of these organisms. We analyzed the relationship between body size and cell types of five different marine phyla: arthropods, brachiopods, chordates, echinoderms, and mollusks. We attempted to find a relation between the biovolume of these different phyla and the number of specialized cell types that they had, which is a common measure of biocomplexity. In addition, we looked at the metabolic intensity, which is the mass-specific rate of energy processing applied to an organism's size, because it is also correlated to genetic complexity. Using R programming, we tested for correlations between these factors. After applying a Pearson correlation test, we discovered a generally positive correlation between the body sizes, number of cell types, and metabolic intensities of these phyla. However, one exception is that there is a negative correlation between the body size and metabolic intensity of echinoderms. Overall, we can see that marine organisms tend to evolve larger and more complex over time, and that is a very interesting find. Our discovery yielded many research questions and problems that we would like to solve, such as how the environment is thermodynamically affected by these organisms.

Heterochronic developmental shift caused by thyroid hormone in larval sand dollars and its implications for phenotypic plasticity and the evolution of nonfeeding development.

PubMed

Heyland, Andreas; Hodin, Jason

2004-03-01

Recent work on a diverse array of echinoderm species has demonstrated, as is true in amphibians, that thyroid hormone (TH) accelerates development to metamorphosis. Interestingly, the feeding larvae of several species of sea urchins seem to obtain TH through their diet of planktonic algae (exogenous source), whereas nonfeeding larvae of the sand dollar Peronella japonica produce TH themselves (endogenous source). Here we examine the effects of TH (thyroxine) and a TH synthesis inhibitor (thiourea) on the development of Dendraster excentricus, a sand dollar with a feeding larva. We report reduced larval skeleton lengths and more rapid development of the juvenile rudiment in the exogenous TH treatments when compared to controls. Also, larvae treated with exogenous TH reached metamorphic competence faster at a significantly reduced juvenile size, representing the greatest reduction in juvenile size ever reported for an echinoid species with feeding larvae. These effects of TH on D. excentricus larval development are strikingly similar to the phenotypically plastic response of D. excentricus larvae reared under high food conditions. We hypothesize that exogenous (algae-derived) TH is the plasticity cue in echinoid larvae, and that the larvae use ingested TH levels as an indicator for larval nutrition, ultimately signaling the attainment of metamorphic competence. Furthermore, our experiments with the TH synthesis inhibitor thiourea indicate that D. excentricus larvae can produce some TH endogenously. Endogenous TH production might, therefore, be a shared feature among sand dollars, facilitating the evolution of nonfeeding larval development in that group. Mounting evidence on the effects of thyroid hormones in echinoderm development suggests life-history models need to incorporate metamorphic hormone effects and the evolution of metamorphic hormone production.

Excellent amino acid racemization results from Holocene sand dollars

NASA Astrophysics Data System (ADS)

Kosnik, M.; Kaufman, D. S.; Kowalewski, M.; Whitacre, K.

2015-12-01

Amino acid racemization (AAR) is widely used as a cost-effective method to date molluscs in time-averaging and taphonomic studies, but it has not been attempted for echinoderms despite their paleobiological importance. Here we demonstrate the feasibility of AAR geochronology in Holocene aged Peronella peronii (Echinodermata: Echinoidea) collected from Sydney Harbour (Australia). Using standard HPLC methods we determined the extent of AAR in 74 Peronella tests and performed replicate analyses on 18 tests. We sampled multiple areas of two individuals and identified the outer edge as a good sampling location. Multiple replicate analyses from the outer edge of 18 tests spanning the observed range of D/Ls yielded median coefficients of variation < 4% for Asp, Phe, Ala, and Glu D/L values, which overlaps with the analytical precision. Correlations between D/L values across 155 HPLC injections sampled from 74 individuals are also very high (pearson r2 > 0.95) for these four amino acids. The ages of 11 individuals spanning the observed range of D/L values were determined using 14C analyses, and Bayesian model averaging was used to determine the best AAR age model. The averaged age model was mainly composed of time-dependent reaction kinetics models (TDK, 71%) based on phenylalanine (Phe, 94%). Modelled ages ranged from 14 to 5539 yrs, and the median 95% confidence interval for the 74 analysed individuals is ±28% of the modelled age. In comparison, the median 95% confidence interval for the 11 calibrated 14C ages was ±9% of the median age estimate. Overall Peronella yields exceptionally high-quality AAR D/L values and appears to be an excellent substrate for AAR geochronology. This work opens the way for time-averaging and taphonomic studies of echinoderms similar to those in molluscs.

Ultrastructural and biochemical characterization of mechanically adaptable collagenous structures in the edible sea urchin Paracentrotus lividus.

PubMed

Barbaglio, Alice; Tricarico, Serena; Ribeiro, Ana R; Di Benedetto, Cristiano; Barbato, Marta; Dessì, Desirèe; Fugnanesi, Valeria; Magni, Stefano; Mosca, Fabio; Sugni, Michela; Bonasoro, Francesco; Barbosa, Mario A; Wilkie, Iain C; Candia Carnevali, M Daniela

2015-06-01

The viscoelastic properties of vertebrate connective tissues rarely undergo significant changes within physiological timescales, the only major exception being the reversible destiffening of the mammalian uterine cervix at the end of pregnancy. In contrast to this, the connective tissues of echinoderms (sea urchins, starfish, sea cucumbers, etc.) can switch reversibly between stiff and compliant conditions in timescales of around a second to minutes. Elucidation of the molecular mechanism underlying such mutability has implications for the zoological, ecological and evolutionary field. Important information could also arise for veterinary and biomedical sciences, particularly regarding the pathological plasticization or stiffening of connective tissue structures. In the present investigation we analyzed aspects of the ultrastructure and biochemistry in two representative models, the compass depressor ligament and the peristomial membrane of the edible sea urchin Paracentrotus lividus, compared in three different mechanical states. The results provide further evidence that the mechanical adaptability of echinoderm connective tissues does not necessarily imply changes in the collagen fibrils themselves. The higher glycosaminoglycan (GAG) content registered in the peristomial membrane with respect to the compass depressor ligament suggests a diverse role of these molecules in the two mutable collagenous tissues. The possible involvement of GAG in the mutability phenomenon will need further clarification. During the shift from a compliant to a standard condition, significant changes in GAG content were detected only in the compass depressor ligament. Similarities in terms of ultrastructure (collagen fibrillar assembling) and biochemistry (two alpha chains) were found between the two models and mammalian collagen. Nevertheless, differences in collagen immunoreactivity, alpha chain migration on SDS-PAGE and BLAST alignment highlighted the uniqueness of sea urchin collagen with respect to mammalian collagen. Copyright © 2015 Elsevier GmbH. All rights reserved.

In situ respiration measurements of megafauna in the Kermadec Trench

NASA Astrophysics Data System (ADS)

Nunnally, Clifton C.; Friedman, Jason R.; Drazen, Jeffrey C.

2016-12-01

The aim of this paper is to measure metabolic rates of megafauna living in depths greater than 6000 m. Echinoderms, actinarians and a polychaete were captured by remotely operated vehicle (ROV) and inserted into respiration chambers in situ at depths of 4049 m, 7140 m and 8074 m in the region of the Kermadec Trench SW Pacific Ocean. Hadal research has moved into a new frontier as technological improvements now allow for a meticulous investigation of trench ecology in depths greater than 6000 m. The development of an in situ respirometer for use in these studies was deployed in the Kermadec Trench to obtain the first ever rates of basal metabolic rates of hadal megafauna. Typical deep-sea experiments of individual animal physiology must deal with covarying factors of pressure, temperature, light and food supply in this study investigated the effects of pressure and increased food supply on overall animal metabolism. In the Kermadec Trench, holothurian respiration rates (n=4), 0.079±0.011 (mean±SE) μmol-O2 g-1 h-1, were higher than those captured at abyssal depths (n=2), 0.018±0.002 μmol-O2 g-1h-1, in the same region (p<0.001). When Q10 adjusted to a common temperature of 2.5 °C trench holothurian respiration rates ranged between 0.068 and 0.119 μmol-O2 g-1 h-1. Anemone respiration rates were remarkably similar between abyssal and hadal specimens, 0.110 and 0.111 μmol-O2 g-1 h-1, respectively. Our results on echinoderm respiration when corrected for temperature and mass fall below the slope regression when compared with other in situ measurements at shallower ocean depths.

Bathymetric and interspecific variability in maternal reproductive investment and diet of eurybathic echinoderms

NASA Astrophysics Data System (ADS)

Ross, David A. N.; Hamel, Jean-François; Mercier, Annie

2013-10-01

While conditions in shallow-water and deep-sea environments differ markedly, it remains unclear how eurybathic species adapt their life histories to cope with these changes. The present study compared indicators of maternal reproductive investment of three common echinoderms collected shallower than 20 m and deeper than 850 m: Cucumaria frondosa (Holothuroidea), Solaster endeca and Henricia sanguinolenta (Asteroidea). Depth-specific and species-specific differences were found in gonad indices (GI), potential fecundity, oocyte size frequency, as well as lipid classes and fatty acids measured in gonad tissue and oocytes. The asteroids, S. endeca and H. sanguinolenta, exemplified the interspecific trade-off between size and number of oocytes: the former had fewer larger oocytes than the latter, with higher total lipid proportions in them. However, intraspecifically, larger oocytes found in deep specimens of S. endeca did not translate into lower fecundity but rather into a seemingly higher GI, indicating greater investment per oocyte without reducing fecundity. Oocytes were absent in specimens of C. frondosa sampled in deep water, suggesting delayed or impaired maturation at the limit of their depth tolerance. Analysis of S. endeca sterol proportions in gonads and oocytes across depths showed higher sterol input into oocytes in females from the deep. Gonads of S. endeca and H. sanguinolenta contained similar essential fatty acids, but showed significant differences in major fatty acids and some of the less dominant ones, indicating diet specificities. Analyses within S. endeca showed evidence of similar feeding mode (carnivory) at both depths, but suggested shifts in the diet or synthesis of fatty acids, presumably reflecting differences in available food sources and/or adaptations to their respective environments.

Distribution of epibenthic megafauna and lebensspuren on two central North Pacific seamounts

NASA Astrophysics Data System (ADS)

Kaufmann, Ronald S.; Wakefield, W. Waldo; Genin, Amatzia

1989-12-01

The abundance, composition and spatial distribution of megafaunal communities and lebensspuren assemblages at three sites on two deep seamounts in the central North Pacific were surveyed photographically using still cameras mounted on the research submersible Alvin. Photographic transects were made on the summit cap (˜1500 m depth) and summit perimeter (˜ 1800 m depth) of Horizon Guyot and on the summit cap (˜3100 m depth) of Magellan Rise. The summit caps of both seamounts were covered with foraminiferal sand, while the summit perimeter of Horizon Guyot was characterized by numerous rock outcroppings (basalt and chert encrusted with ferromanganese oxides) on which was situated a speciose assemblage of suspension-feeding organisms. The most abundant megafauna at all three sites were large, sediment-agglutinating protists belonging to the class Xenophyophorea. Among the three sites, the Horizon Guyot summit cap supported the highest densities of fishes and lebensspuren and the fewest echinoderms, while the Magellan Rise summit cap was populated by a diverse community of deposit-feeding echinoderms. Megafaunal abundances on Horizon Guyot were lower than those at equivalent depths on the western North Atlantic continental slope, while those on Magellan Rise were higher. The faunal differences observed between the two seamounts were attributed primarily to differences in hydrodynamic conditions, substrate availability and nutrient availability. Most of the lebensspuren on these seamounts appeared to be patchily distributed on spatial scales of 10-1000 m, while xenophyophore distributions were predominantly random on the same spatial scales. Biogeographically the species identified exhibited predominantly widespread to cosmopolitan distributions with Indo-West Pacific faunal affinities, typical of other seamounts in the same depth range and biogeographic province.

Multi-residue analysis of 36 priority and emerging pollutants in marine echinoderms (Holothuria tubulosa) and marine sediments by solid-liquid extraction followed by dispersive solid phase extraction and liquid chromatography-tandem mass spectrometry analysis.

PubMed

Martín, J; Zafra-Gómez, A; Hidalgo, F; Ibáñez-Yuste, A J; Alonso, E; Vilchez, J L

2017-05-01

Marine echinoderms are filter-feeding invertebrates widely distributed along the coasts, and which are therefore extensively exposed to anthropogenic xenobiotics. They can serve as good sentinels for monitoring a large variety of contaminants in marine ecosystems. In this context, a multi-residue analytical method has been validated and applied to Holothuria tubulosa specimens and marine sediments for the determination of 36 organic compounds, which belong to some of the most problematic groups of emerging and priority pollutants (perfluoroalkyl compounds, estrogens, parabens, benzophenones, plasticizers, surfactants, brominated flame retardants and alkylphenols). Lyophilization of samples prior to solvent extraction and clean-up of extracts with C18, followed by liquid chromatography-tandem mass spectrometry analysis, is proposed. A Box-Behnken design was used for optimization of the most influential variables affecting the extraction and clean-up steps. For validation, matrix-matched calibration and recovery assay were applied. Linearity (% r 2 ) higher than 99%, recoveries between 80% and 114% (except in LAS and NP1EO), RSD (precision) lower than 15% and limits of quantification between 0.03 and 12.5ngg -1 dry weight (d.w.) were achieved. The method was applied to nine samples of Holothuria collected along the coast of Granada (Spain), and to marine sediments around the animals. The results demonstrated high bioaccumulation of certain pollutants. A total of 25 out of the 36 studied compounds were quantified, being surfactants, alkylphenols, perfluoroalkyl compounds, triclocarban and parabens the most frequently detected. Nonylphenol was found in the highest concentration (340 and 323ngg -1 d.w. in sediment and Holothuria samples, respectively). Copyright © 2017 Elsevier B.V. All rights reserved.

Lithofacies, paleoenvironment and high-resolution stratigraphy of the D5 and D6 members of the Middle Jurassic carbonates Dhruma Formation, outcrop analog, central Saudi Arabia

NASA Astrophysics Data System (ADS)

Yousif, Ibrahim M.; Abdullatif, Osman M.; Makkawi, Mohammad H.; Bashri, Mazin A.; Abdulghani, Waleed M.

2018-03-01

This study characterizes the lithofacies, paleoenvironment and stratigraphic architecture of the D5 and D6 members of carbonates Dhruma Formation outcrops in central Saudi Arabia. The study integrates detailed lithofacies analysis based on vertical and lateral profiles, in addition to thin-sections petrography to reveal the high-resolution architecture framework. Nine lithofacies types (LFTs) were defined namely: (1) skeletal peletal spiculitic wackestone (15%), (2) peloidal echinoderm packstone (19%), (3) fissile shale (36%), (4) peloidal spiculitic echinoderm pack-grainstone (5%), (5) cross-bedded peloidal skeletal oolitic grainstone (7%), (6) oolitic grainstone (2%), (7) intraformational rudstone (<1%), (8) skeletal peloidal foraminiferal packstone (12%) and (9) skeletal foraminiferal wackestone (4%). These lithofacies types were grouped into five major carbonate paleoenvironments that range from distal-to-proximal carbonate ramp setting. The detailed stratigraphic analysis revealed around 53 cycles and cycle sets with 5th to 6th orders magnitude, and thickness ranges from a few centimeters up to 6 m with an average of 1.5 m. Those are stacked to form four high-frequency sequences with thickness range from 1 m up to 14 m. The latter were grouped into a single depositional sequence of 3rd order magnitude. The architectural analysis also shows that the potential reservoir units were intensively affected by muddy-textured rocks which act as reservoir seals. These variations in the stratigraphic sequences in Middle Jurassic Dhruma Formation and its equivalents could be attributed to the eustatic sea-level changes, climate, tectonics, and local paleoenvironments. This study attempts to provide detailed insight into reservoir heterogeneity and architecture. The analog may help to understand and predict lithofacies heterogeneity, architecture, and quality in the subsurface equivalent reservoirs.

Germ line mechanics – and unfinished business

PubMed Central

Wessel, Gary M.

2016-01-01

Primordial germ cells are usually made early in the development of an organism. These are the mother of all stem cells that are necessary for propagation of the species, yet use highly diverse mechanisms between organisms. How they are specified, and when and where they form, are central to developmental biology. Using diverse organisms to study this development is illuminating for understanding the mechanics these cells use in this essential function, and for identifying the breadth of evolutionary changes that have occurred between species. This essay emphasizes how echinoderms may contribute to the patch-work quilt of our understanding of germ line formation during embryogenesis. PMID:26970000

Some studies on the biosynthesis of ubiquinone, isoprenoid alcohols, squalene and sterols by marine invertebrates

PubMed Central

Walton, M. J.; Pennock, J. F.

1972-01-01

The ability of fourteen marine invertebrates to utilize [14C]mevalonate for the biosynthesis of isoprenoid compounds was investigated. Several of the animals, in particular crustaceans, bivalve molluscs, a coelenterate and a sponge, were unable to synthesize squalene and sterols, whereas gastropod molluscs, echinoderms, an annelid and a sponge could. Regardless of sterol-synthesizing ability the animals (with the exception of a sponge) always made dolichol and ubiquinone, and thus a specific block in squalene and sterol synthesis was indicated in some animals. Radioactivity accumulated in relatively large amounts in farnesol and geranylgeraniol in those animals incapable of making sterols. PMID:4403925

Troglomorphism in the middle Triassic crinoids from Poland.

PubMed

Brom, Krzysztof R; Brachaniec, Tomasz; Salamon, Mariusz A

2015-10-01

In this paper, we document the Middle Triassic marine fauna recovered from the fissure/cave system of Stare Gliny (southern Poland) developed in the Devonian host dolomite. The fossils are mostly represented by in situ preserved and small-sized holdfasts of crinoids (Crinoidea) that are attached to the cave walls. Other fossils found in the cave infills include articulated brittle stars and brachiopods. Our findings constitute the oldest Mesozoic evidence for troglophile crinoids. We suggest that troglomorphism in these echinoderms was likely related to protection against predation, which underscores the magnitude of anti-predatory adaptations to increased predation pressure that occurred during the Early Mesozoic Marine Revolution.

Germ Line Mechanics--And Unfinished Business.

PubMed

Wessel, Gary M

2016-01-01

Primordial germ cells are usually made early in the development of an organism. These are the mother of all stem cells that are necessary for propagation of the species, yet use highly diverse mechanisms between organisms. How they are specified, and when and where they form, are central to developmental biology. Using diverse organisms to study this development is illuminating for understanding the mechanics these cells use in this essential function and for identifying the breadth of evolutionary changes that have occurred between species. This essay emphasizes how echinoderms may contribute to the patchwork quilt of our understanding of germ line formation during embryogenesis. © 2016 Elsevier Inc. All rights reserved.

A new genus of endoparasitic copepods (Cyclopoida: Enterognathidae), forming a gall in the calyx of deep-sea crinoids.

PubMed

Ohtsuka, Susumu; Kitazawa, Kota; Boxshall, Geoffrey A

2010-08-01

A new genus and species of cyclopoid copepod belonging to the family Enterognathidae, Parenterognathus troglodytes, is described from a gall on the calyx of the deep-sea crinoid Glyptometra crassa (Clark, 1912) collected at depths of 775-787 m off Kumano-nada, middle Japan. The new genus can be distinguished from the three known genera of the family by body tagmosis and by the segmentation and armature of the appendages. This is the first record of this family from the Pacific Ocean. This family seems to be host-specific to relatively basal deuterostomes, such as echinoderms and hemichordates. The evolutionary transformation and history of the Enterognathidae are briefly discussed.

Analysis of clinicopathological features of the echinoderm microtubule-associated protein-like-4-anaplastic lymphoma kinase fusion gene in Chinese patients with advanced non-small-cell lung cancer

PubMed Central

Liu, Yu-Tao; Shi, Yuan-Kai; Hao, Xue-Zhi; Wang, Lin; Li, Jun-Ling; Han, Xiao-Hong; Li, Dan; Zhou, Yu-Jie; Tang, Le

2014-01-01

Background The echinoderm microtubule-associated protein-like-4-anaplastic lymphoma kinase (EML4-ALK) fusion gene defines a novel molecular subset of non-small-cell lung cancer (NSCLC). However, the clinicopathological features of patients with the EML4-ALK fusion gene have not been defined completely. Methods Clinicopathological data of 200 Chinese patients with advanced NSCLC were analyzed retrospectively to explore their possible correlations with EML4-ALK fusions. Results The EML4-ALK fusion gene was detected in 56 (28.0%) of the 200 NSCLC patients, and undetected in 22 (11.0%) patients because of an insufficient amount of pathological tissue. The median age of the patients with positive and negative EML4-ALK was 48 and 55 years, respectively. Patients with the EML4-ALK fusion gene were significantly younger (P< 0.001). The detection rate of the EML4-ALK fusion gene in patients who received primary tumor or metastatic lymph node resection was significantly higher than in patients who received fine-needle biopsy (P= 0.003). The detection rate of the EML4-ALK fusion gene in patients with a time lag from obtainment of the pathological tissue to EML4-ALK fusion gene detection ≤48 months was significantly higher than in patients >48 months (P= 0.020). The occurrence of the EML4-ALK fusion gene in patients with wild-type epidermal growth factor receptor (EGFR) was significantly higher than in patients with mutant-type EGFR (42.5% [37/87] vs. 6.3% [1/16], P= 0.005). Conclusions Younger age and wild-type EGFR were identified as clinicopathological characteristics of patients with advanced NSCLC who harbored the EML4-ALK fusion gene. The optimal time lag from the obtainment of the pathological tissue to the time of EML4-ALK fusion gene detection is ≤48 months. PMID:26767009

Interdecadal change in the deep Puget sound benthos

USGS Publications Warehouse

Nichols, F.H.

2003-01-01

Data from quantitative samples of the benthos at a 200-m site in central Puget Sound, collected twice yearly in most years between 1963 and 1992, were evaluated to determine the extent to which species composition in a continental-shelf depth community exhibits long-term persistence. Study results showed that the most abundant species were consistently present over the 30-year period. However, measures of species composition (e.g., similarity, diversity) reveal a subtle, gradual change in the community over time. Among the changes are (1) multi-year periods of greatly increased abundance of the common species; (2) an overall increase in the total abundance of the benthic community beginning in the mid-1970s; (3) periods of increased abundance, during the late 1970s and early 1980s, of two species that are tolerant of organic enrichment; and (4) the steady decline in abundance of the large burrowing echinoderm, Brisaster latifrons as a consequence of the lack of recruitment to the site since 1970. Despite the conspicuousness of these changes, there are no observed environmental factors that readily explain them. Circumstantial evidence suggests that climate-related change in Puget Sound circulation beginning in the mid-1970s, organic enrichment associated with a nearby large source of primary-treated sewage, and the influence of changes in the abundance of the large echinoderms on the smaller species are potential agents of change. The principle reasons for our inability to identify causes of long-term change in the Puget Sound benthos are (a) inconsistent long-term monitoring of environmental variables, (b) the lack of quantitative information about long-term changes in plankton and fish populations, (c) lack of knowledge of specific predator/prey and competitive interactions in soft bottom benthos, (d) unknown influence of moderate levels of contamination on biota; and (e) lack of understanding of possible linkages between climate regime shifts and fluctuations in local biological populations.

Studies on the in vivo sensitivity of spindle microtubules to calcium ions and evidence for a vesicular calcium-sequestering system

PubMed Central

1981-01-01

I microinjected calcium ions into echinoderm eggs during mitosis to determine the calcium sensitivity of microtubules (Mts) in vivo. Spindle birefringence (BR), a measure of the number of aligned Mts in the spindle, is locally, rapidly, and reversibly abolished by small volumes of microinjected CaCl2 (1 mM). Rapid return of BR is followed by anaphase, and subsequent divisions are normal. Similar doses of MgCl2, BaCl2, KCl, NaCl, pH buffers, distilled water, or vegetable oil have no effect on spindle BR, whereas large doses of such agents sometimes cause slow, uniform loss in BR over the course of a minute or more. Of the ions tested, only Sr++ causes effects comparable to Ca++. Ca-EGTA buffers, containing greater than micromolar free Ca++, abolishes BR in a manner similar to millimolar concentrations of injected CaCl2. Caffeine, a potent uncoupler of the Ca++-pump/ATPase of sarcoplasmic reticulum, causes a local, transient depression in spindle BR in the injected region. Finally, injection of potassium oxalate results in the formation of small, highly BR crystals, presumably CA- oxalate, in Triton-sensitive compartments in the cytoplasm. Taken together, these findings demonstrate that spindle Mts are sensitive to levels of free Ca++ in the physiological range, provide evidence for the existence of a strong cytoplasmic Ca++-sequestering system, and support the notion that Mt assembly and disassembly in local regions of the spindle may be orchestrated by local changes in the cytoplasmic free Ca++ concentration during mitosis. An appendix offers the design of a new chamber for immobilizing echinoderm eggs for injection, a new method for determining the volume of the injected solution, and a description of the microinjection technique, which was designed, but never fully described, by Hiramoto (Y. Hiramoto, Exp. Cell. Res., 1962, 27:416-426.). PMID:7194345

Monitoring release of disposable radionuclides in the Kara sea: Bioaccumulation of long-lived radionuclides in echinoderms and molluscs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fisher, N.S.

1994-01-01

The objective of the present proposal is to continue and extend our research on the trophic transfer of important radionuclides in benthic fauna of the Kara Sea. This project is assessing the extent to which select species of seastars, brittle stars, and clams typical of the Kara Sea concentrate and retain a variety of long-lived radionuclides known to be (or suspected to be) present in the disposed wastes in the Russian Arctic. The rates and routes of uptake and depuration of isotopes in the same or in closely related species are being quantified so that endemic benthic organisms can bemore » assessed as potential bioindicators of released radionuclides in Arctic waters.« less

Nuclear lamins during gametogenesis, fertilization and early development

NASA Technical Reports Server (NTRS)

Maul, G. G.; Schatten, G.

1986-01-01

The distribution of lamins (described by Gerace, 1978, as major proteins of nuclear envelope) during gametogenesis, fertilization, and early development was investigated in germ cells of a mouse (Mus musculus), an echinoderm (Lytechinus variegatus), and the surf clam (Spisula solidissima) was investigated in order to determine whether the differences detected could be correlated with differences in the function of cells in these stages of the germ cells. In order to monitor the behavior of lamins, the gametes and embryos were labeled with antibodies to lamins A, C, and B extracted from autoimmune sera of patients with scleroderma and Lupus erythematosus. Results indicated that lamin B could be identified in nuclear envelopes on only those nuclei where chromatin is attached and where RNA synthesis takes place.

Crizotinib-induced Rectal Perforation with Abscess.

PubMed

Yanagisawa, Asako; Hayama, Noriko; Amano, Hiroyuki; Nakamura, Makoto; Hirano, Satoshi; Nakamura, Sukeyuki; Tabeta, Hiroshi

2017-12-01

An 86-year-old Japanese man was diagnosed with stage IV lung adenocarcinoma. The patient was treated with crizotinib after echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) rearrangement was detected from his pleural effusion. He subsequently developed abdominal pain and rebound tenderness in the right lower abdomen. Contrast-enhanced abdominal CT showed a low-density area in the abdominal cavity. The size of the abscess was decreased by drainage and the administration of antibiotics. Fistulography revealed a fistula from the rectum to the abscess, and a diagnosis of lower intestinal tract perforation with abscess formation was made. Crizotinib was discontinued and treatment with alectinib was initiated. The patient remains under treatment as an outpatient at our department without adverse effects.

Crizotinib-induced Rectal Perforation with Abscess

PubMed Central

Yanagisawa, Asako; Hayama, Noriko; Amano, Hiroyuki; Nakamura, Makoto; Hirano, Satoshi; Nakamura, Sukeyuki; Tabeta, Hiroshi

2017-01-01

An 86-year-old Japanese man was diagnosed with stage IV lung adenocarcinoma. The patient was treated with crizotinib after echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) rearrangement was detected from his pleural effusion. He subsequently developed abdominal pain and rebound tenderness in the right lower abdomen. Contrast-enhanced abdominal CT showed a low-density area in the abdominal cavity. The size of the abscess was decreased by drainage and the administration of antibiotics. Fistulography revealed a fistula from the rectum to the abscess, and a diagnosis of lower intestinal tract perforation with abscess formation was made. Crizotinib was discontinued and treatment with alectinib was initiated. The patient remains under treatment as an outpatient at our department without adverse effects. PMID:29021430

Details of the evolutionary history from invertebrates to vertebrates, as deduced from the sequences of 18S rDNA.

PubMed Central

Wada, H; Satoh, N

1994-01-01

Almost the entire sequences of 18S rDNA were determined for two chaetognaths, five echinoderms, a hemichordate, and two urochordates (a larvacean and a salp). Phylogenetic comparisons of the sequences, together with those of other deuterostomes (an ascidian, a cephalochordate, and vertebrates) and protostomes (an arthropod and a mollusc), suggest the monophyly of the deuterostomes, with the exception of the chaetognaths. Chaetognaths may not be a group of deuterostomes. The deuterostome group closest to vertebrates was the group of cephalochordates. Ascidians, larvaceans, and salps seem to form a discrete group (urochordates), in which the early divergence of larvaceans is evident. These results support the hypothesis that chordates evolved from free-living ancestors. PMID:8127885

Water vascular system architecture in an Ordovician ophiuroid.

PubMed

Clark, Elizabeth G; Bhullar, Bhart-Anjan S; Darroch, Simon A F; Briggs, Derek E G

2017-12-01

Understanding the water vascular system (WVS) in early fossil echinoderms is critical to elucidating the evolution of this system in extant forms. Here we present the first report of the internal morphology of the water vascular system of a stem ophiuroid. The radial canals are internal to the arm, but protected dorsally by a plate separate to the ambulacrals. The canals zig-zag with no evidence of constrictions, corresponding to sphincters, which control pairs of tube feet in extant ophiuroids. The morphology suggests that the unpaired tube feet must have operated individually, and relied on the elasticity of the radial canals, lateral valves and tube foot musculature alone for extension and retraction. This arrangement differs radically from that in extant ophiuroids, revealing a previously unknown Palaeozoic configuration. © 2017 The Author(s).

Proteoglycan: collagen interactions in connective tissues. Ultrastructural, biochemical, functional and evolutionary aspects.

PubMed

Scott, J E

1991-06-01

Electron histochemical investigations of mammalian and echinoderm tissues, using cupromeronic blue to stain proteoglycans (PGs) specifically in critical electrolyte concentration methods, showed that collagen fibrils are associated with keratan sulphate and chondroitin (dermatan) sulphate ('tadpole') PGs at the a, c, d and e bands on the fibril surface, giving rise to the 'one proteoglycan: one binding site' hypothesis. Intra-fibrillar PGs have been observed, distributed in a regular way which suggests that collagen fibrils are aggregates of 'protofibrils', some of which carry PGs at their surfaces. A scheme for remodelling of collagen fibrils, based on recycling of these protofibrils, is outlined. The choice of which tadpole PG to use to carry out a given function is decided to a considerable extent by the availability of oxygen to the relevant tissue element.

Digestive kinetics determines bioavailability of pollutants. Final report, 1 June 1993--30 September 1998

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jumars, P.A.; Mayer, L.M.

1999-04-19

The authors assayed digestive capabilities of marine deposit feeders (animals that eat sediments) by using fluorescently tagged substrates and contact-angle measurements of surfactancy. Polychaetes on average showed higher enzyme activities and surfactancy than echinoderms. They found that surfactants produced by deposit feeders substantially enhance their abilities to solubilize hydrophobic pollutants such as polycyclic aromatic hydrocarbons (PAHs). Amounts solubilized were consistent with incorporation into micelles of the surfactant. Kinetics of PAH uptake could be explained by passive diffusion. The authors also found that the digestive strategies of deposit feeders often produce concentrations of proteins (digestive enzymes plus products of protein digestion)more » that are sufficient to solubilize metals. Histidine residues in these proteins were found to be critical for copper binding.« less

Bioinspired, dynamic, structured surfaces for biofilm prevention

NASA Astrophysics Data System (ADS)

Epstein, Alexander K.

Bacteria primarily exist in robust, surface-associated communities known as biofilms, ubiquitous in both natural and anthropogenic environments. Mature biofilms resist a wide range of biocidal treatments and pose persistent pathogenic threats. Treatment of adherent biofilm is difficult, costly, and, in medical systems such as catheters, frequently impossible. Adding to the challenge, we have discovered that biofilm can be both impenetrable to vapors and extremely nonwetting, repelling even low surface tension commercial antimicrobials. Our study shows multiple contributing factors, including biochemical components and multiscale reentrant topography. Reliant on surface chemistry, conventional strategies for preventing biofilm only transiently affect attachment and/or are environmentally toxic. In this work, we look to Nature's antifouling solutions, such as the dynamic spiny skin of the echinoderm, and we develop a versatile surface nanofabrication platform. Our benchtop approach unites soft lithography, electrodeposition, mold deformation, and material selection to enable many degrees of freedom—material, geometric, mechanical, dynamic—that can be programmed starting from a single master structure. The mechanical properties of the bio-inspired nanostructures, verified by AFM, are precisely and rationally tunable. We examine how synthetic dynamic nanostructured surfaces control the attachment of pathogenic biofilms. The parameters governing long-range patterning of bacteria on high-aspect-ratio (HAR) nanoarrays are combinatorially elucidated, and we discover that sufficiently low effective stiffness of these HAR arrays mechanoselectively inhibits ˜40% of Pseudomonas aeruginosa biofilm attachment. Inspired by the active echinoderm skin, we design and fabricate externally actuated dynamic elastomer surfaces with active surface microtopography. We extract from a large parameter space the critical topographic length scales and actuation time scales for achieving nearly ˜80% attachment reduction. We furthermore investigate an atomically mobile, slippery liquid infused porous surface (SLIPS) inspired by the pitcher plant. We show up to 99.6% reduction of multiple pathogenic biofilms over a 7-day period under both static and physiologically realistic flow conditions—a ˜35x improvement over state-of-the-art surface chemistry, and over a far longer timeframe. Moreover, SLIPS is shown to be nontoxic: bacteria simply cannot attach to the smooth liquid interface. These bio-inspired strategies significantly advance biofilm attachment prevention and promise a tremendous range of industrial, clinical, and consumer applications.

Intrinsic and Extrinsic Regulation of PD-L2 Expression in Oncogene-Driven Non-Small Cell Lung Cancer.

PubMed

Shibahara, Daisuke; Tanaka, Kentaro; Iwama, Eiji; Kubo, Naoki; Ota, Keiichi; Azuma, Koichi; Harada, Taishi; Fujita, Jiro; Nakanishi, Yoichi; Okamoto, Isamu

2018-03-27

The interaction of programmed cell death ligand 2 (PD-L2) with programmed cell death 1 is implicated in tumor immune escape. The regulation of PD-L2 expression in tumor cells has remained unclear, however. We here examined intrinsic and extrinsic regulation of PD-L2 expression in NSCLC. PD-L2 expression was evaluated by reverse transcription and real-time polymerase chain reaction analysis and by flow cytometry. BEAS-2B cells stably expressing an activated mutant form of EGFR or the echinoderm microtubule associated protein like 4 (EML4)-ALK receptor tyrosine kinase fusion oncoprotein manifested increased expression of PD-L2 at both the mRNA and protein levels. Furthermore, treatment of NSCLC cell lines that harbor such driver oncogenes with corresponding EGFR or ALK tyrosine kinase inhibitors or depletion of EGFR or ALK by small interfering RNA transfection suppressed expression of PD-L2, demonstrating that activating EGFR mutations or echinoderm microtubule associated protein like 4 gene (EML4)-ALK receptor tyrosine kinase gene (ALK) fusion intrinsically induce PD-L2 expression. We also found that interferon gamma (IFN-γ) extrinsically induced expression of PD-L2 through signal transducer and activator of transcription 1 signaling in NSCLC cells. Oncogene-driven expression of PD-L2 in NSCLC cells was inhibited by knockdown of the transcription factors signal transducer and activator of transcription 3 (STAT3) or c-FOS. IFN-γ also activated STAT3 and c-FOS, suggesting that these proteins may also contribute to the extrinsic induction of PD-L2 expression. Expression of PD-L2 is induced intrinsically by activating EGFR mutations or EML4-ALK fusion and extrinsically by IFN-γ, with STAT3 and c-FOS possibly contributing to both intrinsic and extrinsic pathways. Our results thus provide insight into the complexity of tumor immune escape in NSCLC. Copyright © 2018 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Detection of Echinoderm Microtubule Associated Protein Like 4-Anaplastic Lymphoma Kinase Fusion Genes in Non-small Cell Lung Cancer Clinical Samples by a Real-time Quantitative Reverse Transcription Polymerase Chain Reaction Method.

PubMed

Zhao, Jing; Zhao, Jin-Yin; Chen, Zhi-Xia; Zhong, Wei; Li, Long-Yun; Liu, Li-Cheng; Hu, Xiao-Xu; Chen, Wei-Jun; Wang, Meng-Zhao

2016-12-20

Objective To establish a real-time quantitative reverse transcription polymerase chain reaction assay (qRT-PCR) for the rapid, sensitive, and specific detection of echinoderm microtubule associated protein like 4-anaplastic lymphoma kinase (EML4-ALK) fusion genes in non-small cell lung cancer. Methods The specific primers for the four variants of EML4-ALK fusion genes (V1, V2, V3a, and V3b) and Taqman fluorescence probes for the detection of the target sequences were carefully designed by the Primer Premier 5.0 software. Then, using pseudovirus containing EML4-ALK fusion genes variants (V1, V2, V3a, and V3b) as the study objects, we further analyzed the lower limit, sensitivity, and specificity of this method. Finally, 50 clinical samples, including 3 ALK-fluorescence in situ hybridization (FISH) positive specimens, were collected and used to detect EML4-ALK fusion genes using this method. Results The lower limit of this method for the detection of EML4-ALK fusion genes was 10 copies/μl if no interference of background RNA existed. Regarding the method's sensitivity, the detection resolution was as high as 1% and 0.5% in the background of 500 and 5000 copies/μl wild-type ALK gene, respectively. Regarding the method's specificity, no non-specific amplification was found when it was used to detect EML4-ALK fusion genes in leukocyte and plasma RNA samples from healthy volunteers. Among the 50 clinical samples, 47 ALK-FISH negative samples were also negative. Among 3 ALK-FISH positive samples, 2 cases were detected positive using this method, but another was not detected because of the failure of RNA extraction. Conclusion The proposed qRT-PCR assay for the detection of EML4-ALK fusion genes is rapid, simple, sensitive, and specific, which is deserved to be validated and widely used in clinical settings.

A lone biodetrital mound in the Chesterian (Carboniferous) of Alabama?

USGS Publications Warehouse

Kopaska-Merkel, D. C.; Haywick, D.W.

2001-01-01

A carbonate mound in the Chesterian Bangor Limestone of Lawrence County, Alabama, consists chiefly of packstone and grainstone dominated by echinoderm ossicles and fragments of fenestrate bryozoans. In-situ colonies of the rugose coral Caninia flaccida comprise about 8% of the mound by volume. The exposed portion of the mound is approximately 25 m wide, 1.6 m thick at the thickest point and roughly circular in plan. The mound developed on top of a shallow ooid shoal that had been cemented and stabilised during an earlier episode of sub-aerial exposure. Subsequent flooding of the exposed shoal surface permitted establishment of the mound biota. Lateral and vertical facies relationships suggest that the mound possessed about 45 cm of synoptic relief when fully developed. Rugose corals, fenestrate and ramose bryozoans, stalked echinoderms, and sessile soft-bodied organisms encrusted by foraminifera colonised the shoal, forming a mound. Baffling resulted in deposition of mixed-fossil packstone containing locally derived debris and coated grains from the surrounding sea floor. Strong currents within the mound are indicated by preferred orientation of corals and by coarse, commonly cross-stratified grainstone in channels between neighboring coral colonies. Corals are most abundant on the windward side of the mound, where they account for about 13% of the mound compared to 6- 10% in the central part of the mound, and 2-4% on the leeward flank. Biodetrital mounds such as the one described here are uncommon in upper Paleozoic strata and previously unknown in the Bangor Limestone. Of 10 carbonate buildups we examined in the Bangor in Alabama and Tennessee, only one is a biodetrital mound. Two are rugose coral-microbial reefs, one is a coral biostrome, and six are dominated by microbialite. The Bangor shelf, previously interpreted as sedimentologically simple, appears to contain many small mounds of quite varied characteristics. Also, the discovery of a biodetrital mound in the Chesterian of Alabama suggests that there may be more kinds of upper Paleozoic mounds than commonly acknowledged. ?? 2001 Elsevier Science B.V. All rights reserved.

Ocean acidification has little effect on developmental thermal windows of echinoderms from Antarctica to the tropics.

PubMed

Karelitz, Sam E; Uthicke, Sven; Foo, Shawna A; Barker, Mike F; Byrne, Maria; Pecorino, Danilo; Lamare, Miles D

2017-02-01

As the ocean warms, thermal tolerance of developmental stages may be a key driver of changes in the geographical distributions and abundance of marine invertebrates. Additional stressors such as ocean acidification may influence developmental thermal windows and are therefore important considerations for predicting distributions of species under climate change scenarios. The effects of reduced seawater pH on the thermal windows of fertilization, embryology and larval morphology were examined using five echinoderm species: two polar (Sterechinus neumayeri and Odontaster validus), two temperate (Fellaster zelandiae and Patiriella regularis) and one tropical (Arachnoides placenta). Responses were examined across 12-13 temperatures ranging from -1.1 °C to 5.7 °C (S. neumayeri), -0.5 °C to 10.7 °C (O. validus), 5.8 °C to 27 °C (F. zelandiae), 6.0 °C to 27.1 °C (P. regularis) and 13.9 °C to 34.8 °C (A. placenta) under present-day and near-future (2100+) ocean acidification conditions (-0.3 pH units) and for three important early developmental stages 1) fertilization, 2) embryo (prehatching) and 3) larval development. Thermal windows for fertilization were broad and were not influenced by a pH decrease. Embryological development was less thermotolerant. For O. validus, P. regularis and A. placenta, low pH reduced normal development, albeit with no effect on thermal windows. Larval development in all five species was affected by both temperature and pH; however, thermal tolerance was not reduced by pH. Results of this study suggest that in terms of fertilization and development, temperature will remain as the most important factor influencing species' latitudinal distributions as the ocean continues to warm and decrease in pH, and that there is little evidence of a synergistic effect of temperature and ocean acidification on the thermal control of species ranges. © 2016 John Wiley & Sons Ltd.

De Novo Adult Transcriptomes of Two European Brittle Stars: Spotlight on Opsin-Based Photoreception

PubMed Central

Mallefet, Jérôme; Flammang, Patrick

2016-01-01

Next generation sequencing (NGS) technology allows to obtain a deeper and more complete view of transcriptomes. For non-model or emerging model marine organisms, NGS technologies offer a great opportunity for rapid access to genetic information. In this study, paired-end Illumina HiSeqTM technology has been employed to analyse transcriptomes from the arm tissues of two European brittle star species, Amphiura filiformis and Ophiopsila aranea. About 48 million Illumina reads were generated and 136,387 total unigenes were predicted from A. filiformis arm tissues. For O. aranea arm tissues, about 47 million reads were generated and 123,324 total unigenes were obtained. Twenty-four percent of the total unigenes from A. filiformis show significant matches with sequences present in reference online databases, whereas, for O. aranea, this percentage amounts to 23%. In both species, around 50% of the predicted annotated unigenes were significantly similar to transcripts from the purple sea urchin, the closest species to date that has undergone complete genome sequencing and annotation. GO, COG and KEGG analyses were performed on predicted brittle star unigenes. We focused our analyses on the phototransduction actors involved in light perception. Firstly, two new echinoderm opsins were identified in O. aranea: one rhabdomeric opsin (homologous to vertebrate melanopsin) and one RGR opsin. The RGR-opsin is supposed to be involved in retinal regeneration while the r-opsin is suspected to play a role in visual-like behaviour. Secondly, potential phototransduction actors were identified in both transcriptomes using the fly (rhabdomeric) and mammal (ciliary) classical phototransduction pathways as references. Finally, the sensitivity of O.aranea to monochromatic light was investigated to complement data available for A. filiformis. The presence of microlens-like structures at the surface of dorsal arm plate of O. aranea could potentially explain phototactic behaviour differences between the two species. The results confirm (i) the ability of these brittle stars to perceive light using opsin-based photoreception, (ii) suggest the co-occurrence of both rhabdomeric and ciliary photoreceptors, and (iii) emphasise the complexity of light perception in this echinoderm class. PMID:27119739

Characterization and expression analysis of Galnts in developing Strongylocentrotus purpuratus embryos

PubMed Central

Famiglietti, Amber L.; Wei, Zheng; Beres, Thomas M.; Milac, Adina L.; Tran, Duy T.; Patel, Divya; Angerer, Robert C.; Angerer, Lynne M.

2017-01-01

Mucin-type O-glycosylation is a ubiquitous posttranslational modification in which N-Acetylgalactosamine (GalNAc) is added to the hydroxyl group of select serine or threonine residues of a protein by the family of UDP-GalNAc:Polypeptide N-Acetylgalactosaminyltransferases (GalNAc-Ts; EC 2.4.1.41). Previous studies demonstrate that O-glycosylation plays essential roles in protein function, cell-cell interactions, cell polarity and differentiation in developing mouse and Drosophila embryos. Although this type of protein modification is highly conserved among higher eukaryotes, little is known about this family of enzymes in echinoderms, basal deuterostome relatives of the chordates. To investigate the potential role of GalNAc-Ts in echinoderms, we have begun the characterization of this enzyme family in the purple sea urchin, S. purpuratus. We have fully or partially cloned a total of 13 genes (SpGalnts) encoding putative sea urchin SpGalNAc-Ts, and have confirmed enzymatic activity of five recombinant proteins. Amino acid alignments revealed high sequence similarity among sea urchin and mammalian glycosyltransferases, suggesting the presence of putative orthologues. Structural models underscored these similarities and helped reconcile some of the substrate preferences observed. Temporal and spatial expression of SpGalnt transcripts, was studied by whole-mount in situ hybridization. We found that many of these genes are transcribed early in developing embryos, often with restricted expression to the endomesodermal region. Multicolor fluorescent in situ hybridization (FISH) demonstrated that transcripts encoding SpGalnt7-2 co-localized with both Endo16 (a gene expressed in the endoderm), and Gcm (a gene expressed in secondary mesenchyme cells) at the early blastula stage, 20 hours post fertilization (hpf). At late blastula stage (28 hpf), SpGalnt7-2 message co-expresses with Gcm, suggesting that it may play a role in secondary mesenchyme development. We also discovered that morpholino-mediated knockdown of SpGalnt13 transcripts, results in a deficiency of embryonic skeleton and neurons, suggesting that mucin-type O-glycans play essential roles during embryonic development in S. purpuratus. PMID:28448610

Functional Characterization of Paralogous Gonadotropin-Releasing Hormone-Type and Corazonin-Type Neuropeptides in an Echinoderm

PubMed Central

Tian, Shi; Egertová, Michaela; Elphick, Maurice R.

2017-01-01

Homologs of the vertebrate neuropeptide gonadotropin-releasing hormone (GnRH) have been identified in invertebrates, including the insect neuropeptide corazonin (CRZ). Recently, we reported the discovery of GnRH-type and CRZ-type signaling systems in an echinoderm, the starfish Asterias rubens, demonstrating that the evolutionary origin of paralogous GnRH-type and CRZ-type neuropeptides can be traced back to the common ancestor of protostomes and deuterostomes. Here, we have investigated the physiological roles of the GnRH-type (ArGnRH) and the CRZ-type (ArCRZ) neuropeptides in A. rubens, using mRNA in situ hybridization, immunohistochemistry and in vitro pharmacology. ArGnRH precursor (ArGnRHP)-expressing cells and ArGnRH-immunoreactive cells and/or processes are present in the radial nerve cords, circumoral nerve ring, digestive system (e.g., cardiac stomach and pyloric stomach), body wall-associated muscle (apical muscle), and appendages (tube feet, terminal tentacle). The general distribution of ArCRZ precursor (ArCRZP)-expressing cells is similar to that of ArGnRHP, but with specific local differences. For example, cells expressing ArGnRHP are present in both the ectoneural and hyponeural regions of the radial nerve cords and circumoral nerve ring, whereas cells expressing ArCRZP were only observed in the ectoneural region. In vitro pharmacological experiments revealed that both ArGnRH and ArCRZ cause contraction of cardiac stomach, apical muscle, and tube foot preparations. However, ArGnRH was more potent/effective than ArCRZ as a contractant of the cardiac stomach, whereas ArCRZ was more potent/effective than ArGnRH as a contractant of the apical muscle. These findings demonstrate that both ArGnRH and ArCRZ are myoexcitatory neuropeptides in starfish, but differences in their expression patterns and pharmacological activities are indicative of distinct physiological roles. This is the first study to investigate the physiological roles of both GnRH-type and CRZ-type neuropeptides in a deuterostome, providing new insights into the evolution and comparative physiology of these paralogous neuropeptide signaling systems in the Bilateria. PMID:29033898

The attachment of collagenous ligament to stereom in primary spines of the sea-urchin, Eucidaris tribuloides.

PubMed

Smith, D S; Del Castillo, J; Morales, M; Luke, B

1990-01-01

The similar proximal and distal attachments to the stereom of primary spine ligament in the echinoid Eucidaris tribuloides are described, from thin sections and SEM studies on frozen and fractured spine articulations and ligaments from decalcified material. The orthogonal structure of the general stereom is modified on the attachment zones where bundles of collagen cylinders enter approximately hexagonally arranged channels. Straps of collagen extend in parallel series between adjacent bundles via regularly placed ports and collagen loops rather than non-striated 'tendons' pass over skeletal trabeculae. The regular pattern of collagen straps is most evident on the proximal and distal attachment zones. Mechanical features of the non-adhesive mode of attachment are considered, together with similarities and differences between insertion of muscle cells and mutable collagenous tissue (ligament) in echinoderms.

Unexpected link between polyketide synthase and calcium carbonate biomineralization.

PubMed

Hojo, Motoki; Omi, Ai; Hamanaka, Gen; Shindo, Kazutoshi; Shimada, Atsuko; Kondo, Mariko; Narita, Takanori; Kiyomoto, Masato; Katsuyama, Yohei; Ohnishi, Yasuo; Irie, Naoki; Takeda, Hiroyuki

2015-01-01

Calcium carbonate biominerals participate in diverse physiological functions. Despite intensive studies, little is known about how mineralization is initiated in organisms. We analyzed the medaka spontaneous mutant, ha, defective in otolith (calcareous ear stone) formation. ha lacks a trigger for otolith mineralization, and the causative gene was found to encode polyketide synthase (pks), a multifunctional enzyme mainly found in bacteria, fungi, and plant. Subsequent experiments demonstrate that the products of medaka PKS, most likely polyketides or their derivatives, act as nucleation facilitators in otolith mineralization. The generality of this novel PKS function is supported by the essential role of echinoderm PKS in calcareous skeleton formation together with the presence of PKSs in a much wider range of animals from coral to vertebrates. The present study first links PKS to biomineralization and provides a genetic cue for biogeochemistry of carbon and calcium cycles.

The Middle Miocene of the Fore-Carpathian Basin (Poland, Ukraine and Moldova)

NASA Astrophysics Data System (ADS)

Wysocka, Anna; Radwański, Andrzej; Górka, Marcin; Bąbel, Maciej; Radwańska, Urszula; Złotnik, Michał

2016-09-01

Studies of Miocene sediments in the Fore-Carpathian Basin, conducted by geologists from the University of Warsaw have provided new insights on the distribution of the facies infilling the basin, particularly in the forebulge and back-bulge zones. The origin of the large-scale sand bodies, evaporitic deposits and large-scale organic buildups is discussed, described and verified. These deposits originated in variable, shallow marine settings, differing in their water chemistry and the dynamics of sedimentary processes, and are unique with regard to the fossil assemblages they yield. Many years of taxonomic, biostratigraphic, palaeoecologic and ecotaphonomic investigations have resulted in the identification of the fossil assemblages of these sediments, their age, sedimentary settings and post-mortem conditions. Detailed studies were focused on corals, polychaetes, most classes of molluscs, crustaceans, echinoderms, and fishes.

Evidence for marine microfossils from amber.

PubMed

Girard, Vincent; Schmidt, Alexander R; Saint Martin, Simona; Struwe, Steffi; Perrichot, Vincent; Saint Martin, Jean-Paul; Grosheny, Danièle; Breton, Gérard; Néraudeau, Didier

2008-11-11

Amber usually contains inclusions of terrestrial and rarely limnetic organisms that were embedded in the places were they lived in the amber forests. Therefore, it has been supposed that amber could not have preserved marine organisms. Here, we report the discovery amber-preserved marine microfossils. Diverse marine diatoms as well as radiolarians, sponge spicules, a foraminifer, and a spine of a larval echinoderm were found in Late Albian and Early Cenomanian amber samples of southwestern France. The highly fossiliferous resin samples solidified approximately 100 million years ago on the floor of coastal mixed forests dominated by conifers. The amber forests of southwestern France grew directly along the coast of the Atlantic Ocean and were influenced by the nearby sea: shells and remnants of marine organisms were probably introduced by wind, spray, or high tide from the beach or the sea onto the resin flows.

The rising tide of ocean diseases: Unsolved problems and research priorities

USGS Publications Warehouse

Harvell, Drew; Aronson, Richard; Baron, Nancy; Connell, Joseph; Dobson, Andrew P.; Ellner, Steve; Gerber, Leah R.; Kim, Kiho; Kuris, Armand M.; McCallum, Hamish; Lafferty, Kevin D.; McKay, Bruce; Porter, James; Pascual, Mercedes; Smith, Garriett; Sutherland, Katherine; Ward, Jessica

2004-01-01

New studies have detected a rising number of reports of diseases in marine organisms such as corals, molluscs, turtles, mammals, and echinoderms over the past three decades. Despite the increasing disease load, microbiological, molecular, and theoretical tools for managing disease in the world's oceans are under-developed. Review of the new developments in the study of these diseases identifies five major unsolved problems and priorities for future research: (1) detecting origins and reservoirs for marine diseases and tracing the flow of some new pathogens from land to sea; (2) documenting the longevity and host range of infectious stages; (3) evaluating the effect of greater taxonomic diversity of marine relative to terrestrial hosts and pathogens; (4) pinpointing the facilitating role of anthropogenic agents as incubators and conveyors of marine pathogens; (5) adapting epidemiological models to analysis of marine disease.

Phylogenomics of caspase-activated DNA fragmentation factor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eckhart, Leopold; Fischer, Heinz; Tschachler, Erwin

2007-04-27

The degradation of nuclear DNA by DNA fragmentation factor (DFF) is a key step in apoptosis of mammalian cells. Using comparative genomics, we have here determined the evolutionary history of the genes encoding the two DFF subunits, DFFA (also known as ICAD) and DFFB (CAD). Orthologs of DFFA and DFFB were identified in Nematostella vectensis, a representative of the primitive metazoan clade cnidarians, and in various vertebrates and insects, but not in representatives of urochordates, echinoderms, and nematodes. The domains mediating the interaction of DFFA and DFFB, a caspase cleavage site in DFFA, and the amino acid residues critical formore » endonuclease activity of DFFB were conserved in Nematostella. These findings suggest that DFF has been a part of the primordial apoptosis system of the eumetazoan common ancestor and that the ancient cell death machinery has degenerated in several evolutionary lineages, including the one leading to the prototypical apoptosis model, Caenorhabditis elegans.« less

The Sea Urchin Arbacia lixula: A Novel Natural Source of Astaxanthin

PubMed Central

Cirino, Paola; Brunet, Christophe; Ciaravolo, Martina; Galasso, Christian; Musco, Luigi; Vega Fernández, Tomás; Sansone, Clementina; Toscano, Alfonso

2017-01-01

Several echinoderms, including sea urchins, are valuable sources of bioactive compounds but their nutraceutical potential is largely unexplored. In fact, the gonads of some sea urchin species contain antioxidants including carotenoids and polyhydroxylated naphthoquinones (PHNQ’s), such as echinochrome A. Astaxanthin is known to have particular bioactivity for the prevention of neurodegenerative diseases. This carotenoid is produced by microalgae, while several marine invertebrates can bioaccumulate or synthetize it from metabolic precursors. We determined the carotenoid content and analyzed the bioactivity potential of non-harvested Atlantic-Mediterranean sea urchin Arbacia lixula. The comparison of methanol crude extracts obtained from eggs of farmed and wild specimens revealed a higher bioactivity in farmed individuals fed with a customized fodder. HPLC-analysis revealed a high concentration of astaxanthin (27.0 μg/mg), which was the only pigment observed. This study highlights the potential of farmed A. lixula as a new source of the active stereoisomer of astaxanthin. PMID:28635649

Transgenerational effects of ocean warming on the sea urchin Strongylocentrotus intermedius.

PubMed

Zhao, Chong; Zhang, Lisheng; Shi, Dongtao; Ding, Jingyun; Yin, Donghong; Sun, Jiangnan; Zhang, Baojing; Zhang, Lingling; Chang, Yaqing

2018-04-30

Transgenerational effects, which involve both selection and plasticity, are important for the evolutionary adaptation of echinoderms in the changing ocean. Here, we investigated the effects of breeding design and water temperature for offspring on fertilization, hatchability, larval survival, size, abnormality and metamorphosis of the sea urchin Strongylocentrotus intermedius, whose dams and sires were exposed to long-term (~15 months) elevated temperature (~3°C above ambient) or ambient temperature. There was no transgenerational effect on fertilization and metamorphosis of S. intermedius, while negative transgenerational effects were found in hatchability and most traits of larval size. Dam and sire effects were highly trait and developmental stage dependent. Interestingly, we found S. intermedius probably cannot achieve transgenerational acclimation to long-term elevated temperature for survival provided their offspring were exposed to an elevated temperature. The present study enriches our understanding of transgenerational effects of ocean warming on sea urchins. Copyright © 2018 Elsevier Inc. All rights reserved.

Molecular mechanisms that underpin EML4-ALK driven cancers and their response to targeted drugs.

PubMed

Bayliss, Richard; Choi, Jene; Fennell, Dean A; Fry, Andrew M; Richards, Mark W

2016-03-01

A fusion between the EML4 (echinoderm microtubule-associated protein-like) and ALK (anaplastic lymphoma kinase) genes was identified in non-small cell lung cancer (NSCLC) in 2007 and there has been rapid progress in applying this knowledge to the benefit of patients. However, we have a poor understanding of EML4 and ALK biology and there are many challenges to devising the optimal strategy for treating EML4-ALK NSCLC patients. In this review, we describe the biology of EML4 and ALK, explain the main features of EML4-ALK fusion proteins and outline the therapies that target EML4-ALK. In particular, we highlight the recent advances in our understanding of the structures of EML proteins, describe the molecular mechanisms of resistance to ALK inhibitors and assess current thinking about combinations of ALK drugs with inhibitors that target other kinases or Hsp90.

[A case report: an EML4-ALK positive lung adenocarcinoma diagnosed 
with lymphoma previously].

PubMed

Liu, Li; Heng, Wei

2015-02-01

In recent years, with the deepening of the research of molecular biology, targeted therapy has become one of the trend of lung cancer treatment. The individualized treatment of lung cancer is attached great importance at present. Echinoderm microtubule associated protein like 4 anaplastic lymphoma kinase (EML4-ALK) as a new biological marker is a hot topic in the field of lung cancer treatment. Meanwhile, with the improvement of anticancer treatment and survival, the incidence of multiple primary carcinomas (MPC) has become increasingly. But the report that malignant lymphoma complicated with lung adenocarcinoma harboring EML4-ALK fusion gene in one individual is rare. Here, we report an EML4-ALK positive non-small cell lung cancer (NSCLC) in a patient previously diagnosed with T cell lymphoma and review literature on metachronous lung cancer complicating with lymphoma.

Concordance of IHC, FISH and RT-PCR for EML4-ALK rearrangements.

PubMed

Teixidó, Cristina; Karachaliou, Niki; Peg, Vicente; Gimenez-Capitan, Ana; Rosell, Rafael

2014-04-01

The echinoderm microtubule-associated protein-like 4 anaplastic lymphoma kinase (EML4-ALK) has emerged as the second most important driver oncogene in lung cancer and the first targetable fusion oncokinase to be identified in 4-6% of lung adenocarcinomas. Crizotinib, along with a diagnostic test-the Vysis ALK Break Apart fluorescence in situ hybridization (FISH) Probe Kit-is approved for the treatment of ALK positive advanced non-small cell lung cancer (NSCLC). However, the success of a targeted drug is critically dependent on a sensitive and specific screening assay to detect the molecular drug target. In our experience, reverse transcription polymerase chain reaction (RT-PCR)-based detection of EML4-ALK is a more sensitive and reliable approach compared to FISH and immunohistochemistry (IHC). Although ALK FISH is clinically validated, the assay can be technically challenging and other diagnostic modalities, including IHC and RT-PCR should be further explored.

Activator-inhibitor coupling between Rho signaling and actin assembly make the cell cortex an excitable medium

PubMed Central

Bement, William M.; Leda, Marcin; Moe, Alison M.; Kita, Angela M.; Larson, Matthew E.; Golding, Adriana E.; Pfeuti, Courtney; Su, Kuan-Chung; Miller, Ann L.; Goryachev, Andrew B.; von Dassow, George

2016-01-01

Animal cell cytokinesis results from patterned activation of the small GTPase Rho, which directs assembly of actomyosin in the equatorial cortex. Cytokinesis is restricted to a portion of the cell cycle following anaphase onset in which the cortex is responsive to signals from the spindle. We show that shortly after anaphase onset oocytes and embryonic cells of frogs and echinoderms exhibit cortical waves of Rho activity and F-actin polymerization. The waves are modulated by cyclin-dependent kinase 1 (Cdk1) activity and require the Rho GEF (guanine nucleotide exchange factor), Ect2. Surprisingly, during wave propagation, while Rho activity elicits F-actin assembly, F-actin subsequently inactivates Rho. Experimental and modeling results show that waves represent excitable dynamics of a reaction diffusion system with Rho as the activator and F-actin the inhibitor. We propose that cortical excitability explains fundamental features of cytokinesis including its cell cycle regulation. PMID:26479320

Physical Principles of Skeletal Minerals Revealed with Spectromicroscopy

ScienceCinema

Gilbert, Pupa [U of Wisconsin-Madison, Wisconsin, United States

2017-12-09

Skeletal elements of marine and terrestrial organisms have the most fascinating nano-to-macro-structures, attracting the attention of physicists, biologists, chemists, and materials scientists. Using X-PEEM spectromicroscopy we revealed some of the fundamental mechanisms leading to the formation of these biominerals. Specifically, we addressed the following questions and provided the answers: 1Q) How do teeth, bones, and echinoderm and mollusk shells acquire their unusual, curved and complex morphology, if they are composed of single crystals? 1A) Via amorphous precursor phases; 2Q) How does crystallinity propagate through the amorophous precursor phases in sea urchin spicules and teeth? 2A) By secondary nucleation, following random walk patterns; 3Q) How does iridescent mother-of-pearl become ordered? 3A) Gradually, through a kinetic mechanisms in which fastest growing single-crystals win the competition for space, thus end up being approximately co-oriented.

Biomineralization of the spicules of sea urchin embryos.

PubMed

Wilt, Fred H

2002-03-01

The formation of calcareous skeletal elements by various echinoderms, especially sea urchins, offers a splendid opportunity to learn more about some processes involved in the formation of biominerals. The spicules of larvae of euechinoids have been the focus of considerable work, including their developmental origins. The spicules are composed of a single optical crystal of high magnesium calcite and variable amounts of amorphous calcium carbonate. Occluded within the spicule is a proteinaceous matrix, most of which is soluble; this matrix constitutes about 0.1% of the mass. The spicules are also enclosed by an extracellular matrix and are almost completely surrounded by cytoplasmic cords. The spicules are deposited by primary mesenchyme cells (PMCs), which accumulate calcium and secrete calcium carbonate. A number of proteins specific, or highly enriched, in PMCs, have been cloned and studied. Recent work supports the hypothesis that proteins found in the extracellular matrix of the spicule are important for biomineralization.

Marine organisms as a therapeutic source against herpes simplex virus infection.

PubMed

Vo, Thanh-Sang; Ngo, Dai-Hung; Ta, Quang Van; Kim, Se-Kwon

2011-09-18

Herpes simplex virus (HSV) is a member of the Herpesviridae family that causes general communicable infections in human populations throughout the world, the most common being genital and orolabial disease. The current treatments for HSV infections are nucleoside analogs such as acyclovir, valacyclovir and famciclovir. Despite the safety and efficacy, extensive clinical use of these drugs has led to the emergence of resistant viral strains, mainly in immunocompromised patients. To counteract these problems, alternative anti-HSV agents from natural products have been reported. Recently, a great deal of interest has been expressed regarding marine organisms such as algae, sponges, tunicates, echinoderms, mollusks, shrimp, bacteria, and fungus as promising anti-HSV agents. This contribution presents an overview of potential anti-HSV agents derived from marine organisms and their promising application in HSV therapy. Copyright © 2011 Elsevier B.V. All rights reserved.

Evidence for gill slits and a pharynx in Cambrian vetulicolians: implications for the early evolution of deuterostomes

PubMed Central

2012-01-01

Background Vetulicolians are a group of Cambrian metazoans whose distinctive bodyplan continues to present a major phylogenetic challenge. Thus, we see vetulicolians assigned to groups as disparate as deuterostomes and ecdysozoans. This divergence of opinions revolves around a strikingly arthropod-like body, but one that also bears complex lateral structures on its anterior section interpreted as pharyngeal openings. Establishing the homology of these structures is central to resolving where vetulicolians sit in metazoan phylogeny. Results New material from the Chengjiang Lagerstätte helps to resolve this issue. Here, we demonstrate that these controversial structures comprise grooves with a series of openings. The latter are oval in shape and associated with a complex anatomy consistent with control of their opening and closure. Remains of what we interpret to be a musculature, combined with the capacity for the grooves to contract, indicate vetulicolians possessed a pumping mechanism that could process considerable volumes of seawater. Our observations suggest that food captured in the anterior cavity was transported to dorsal and ventral gutters, which then channeled material to the intestine. This arrangement appears to find no counterpart in any known fossil or extant arthropod (or any other ecdysozoan). Anterior lateral perforations, however, are diagnostic of deuterostomes. Conclusions If the evidence is against vetulicolians belonging to one or other group of ecdysozoan, then two phylogenetic options seem to remain. The first is that such features as vetulicolians possess are indicative of either a position among the bilaterians or deuterostomes but apart from the observation that they themselves form a distinctive and recognizable clade current evidence can permit no greater precision as to their phylogenetic placement. We argue that this is too pessimistic a view, and conclude that evidence points towards vetulicolians being members of the stem-group deuterostomes; a group best known as the chordates (amphioxus, tunicates, vertebrates), but also including the ambulacrarians (echinoderms, hemichordates), and xenoturbellids. If the latter, first they demonstrate that these members of the stem group show few similarities to the descendant crown group representatives. Second, of the key innovations that underpinned deuterostome success, the earliest and arguably most seminal was the evolution of openings that define the pharyngeal gill slits of hemichordates (and some extinct echinoderms) and chordates. PMID:23031545

Sea Cucumber Glycosides: Chemical Structures, Producing Species and Important Biological Properties.

PubMed

Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Rahman, M Aminur; Islam, Mohamad Tofazzal

2017-10-17

Sea cucumbers belonging to echinoderm are traditionally used as tonic food in China and other Asian countries. They produce abundant biologically active triterpene glycosides. More than 300 triterpene glycosides have been isolated and characterized from various species of sea cucumbers, which are classified as holostane and nonholostane depending on the presence or absence of a specific structural unit γ(18,20)-lactone in the aglycone. Triterpene glycosides contain a carbohydrate chain up to six monosaccharide units mainly consisting of d-xylose, 3-O-methy-d-xylose, d-glucose, 3-O-methyl-d-glucose, and d-quinovose. Cytotoxicity is the common biological property of triterpene glycosides isolated from sea cucumbers. Besides cytotoxicity, triterpene glycosides also exhibit antifungal, antiviral and hemolytic activities. This review updates and summarizes our understanding on diverse chemical structures of triterpene glycosides from various species of sea cucumbers and their important biological activities. Mechanisms of action and structural-activity relationships (SARs) of sea cucumber glycosides are also discussed briefly.

[Oropharyngeal morphology and food habits of Micropogonias furnieri (Pisces: Sciaenidae) in the North coast of Estado Sucre, Venezuela].

PubMed

Ruiz, L J; Prieto, A; Lemus, M

2001-01-01

Morphology of the mandibular and pharyngeal region, and the feeding habits of Micropogonias furnieri were examined in 256 male and female specimens, between 28.7 and 54.3 cm total length, collected around Morro Puerto Santo, in northeast Sucre State, Venezuela (10 degrees 45'00" N-63 degrees 8'0" W), from May 1989 to April 1990. Micropogonias furnieri has a small ventral mouth; protrusible premaxillary and dentary; first branchial arches with 21 to 27 gill rakers, generally 24 to 25; and 7 to 11 pyloric caecae. The index of vacuity was low, with mean value of 7.00%. The mean intestinal index was 0.72, indicative of carnivorous species. Analysis of frequency of occurrence, indicates preference for crustaceans (45.70%), mainly crabs (34.90%), followed by polychaetes (28.00%), fishes (11.41%) and occasionally mollusks and echinoderms (4.0 and 3.9%, respectively). The diet of this species did not vary with sex.

An occurence records database of Irregular Echinoids (Echinodermata: Echinoidea) in Mexico.

PubMed

Martínez-Melo, Alejandra; Solís-Marín, Francisco Alonso; Buitrón-Sánchez, Blanca Estela; Laguarda-Figueras, Alfredo

2016-01-01

Research on echinoderms in Mexico began in the late nineteenth century. We present a dataset that includes the taxonomic and geographic information of irregular echinoids from Mexico, housed in four collections: 1) Colección Nacional de Equinodermos "Ma. Elena Caso Muñoz" from the Instituto de Ciencias del Mar y Limnología (ICML), Universidad Nacional Autónoma de México (UNAM); 2) Invertebrate Zoology Collection, Smithsonian Museum of Natural History, Washington, D.C., United States of America (USA); 3) Invertebrate Collection, Museum of Comparative Zoology, University of Harvard, Boston, Massachusetts, USA and 4) Invertebrate Zoology, Peabody Museum, Yale University, New Haven, Connecticut, USA. A total of six orders, 17 families, 35 genera and 68 species are reported, 37 distributed in the Pacific coast and 31 in the Atlantic coast, none of them was found in both coasts. The most diverse region is the Gulf of California (S=32); the most diverse order is Spatangoida with 31 species reported in mexican waters.

Weighted gene co-expression network analysis reveals potential genes involved in early metamorphosis process in sea cucumber Apostichopus japonicus.

PubMed

Li, Yongxin; Kikuchi, Mani; Li, Xueyan; Gao, Qionghua; Xiong, Zijun; Ren, Yandong; Zhao, Ruoping; Mao, Bingyu; Kondo, Mariko; Irie, Naoki; Wang, Wen

2018-01-01

Sea cucumbers, one main class of Echinoderms, have a very fast and drastic metamorphosis process during their development. However, the molecular basis under this process remains largely unknown. Here we systematically examined the gene expression profiles of Japanese common sea cucumber (Apostichopus japonicus) for the first time by RNA sequencing across 16 developmental time points from fertilized egg to juvenile stage. Based on the weighted gene co-expression network analysis (WGCNA), we identified 21 modules. Among them, MEdarkmagenta was highly expressed and correlated with the early metamorphosis process from late auricularia to doliolaria larva. Furthermore, gene enrichment and differentially expressed gene analysis identified several genes in the module that may play key roles in the metamorphosis process. Our results not only provide a molecular basis for experimentally studying the development and morphological complexity of sea cucumber, but also lay a foundation for improving its emergence rate. Copyright © 2017 Elsevier Inc. All rights reserved.

[Clinical Advanced in Early-stage ALK-positive Non-small Cell Lung Cancer Patients].

PubMed

Gao, Qiongqiong; Jiang, Xiangli; Huang, Chun

2017-02-20

Lung cancer is the leading cause of cancer death in China. Non-small cell lung cancer (NSCLC) accounts for 85% of lung cancer cases, with the majority of the cases diagnosed at the advanced stage. Molecular targeted therapy is becoming the focus attention for advanced NSCLC. Echinoderm microtubule-associated protein-like 4 gene and the anaplastic lymphoma kinase gene (EML4-ALK) is among the most common molecular targets of NSCLC; its specific small-molecule tyrosine kinase inhibitors (TKIs) are approved for use in advanced NSCLC cases of ALK-positive. However, the influence of EML4-ALK fusion gene on the outcome of early-stage NSCLC cases and the necessity of application of TKIs for early-stage ALK-positive NSCLC patients are still uncertain. In this paper, we summarized the progression of testing methods for ALK-positive NSCLC patients as well as clinicopathological implication, outcome, and necessity of application of TKIs for early-stage ALK-positive NSCLC patients.

Stable and dynamic microtubules coordinately shape the myosin activation zone during cytokinetic furrow formation

PubMed Central

Foe, Victoria E.; von Dassow, George

2008-01-01

The cytokinetic furrow arises from spatial and temporal regulation of cortical contractility. To test the role microtubules play in furrow specification, we studied myosin II activation in echinoderm zygotes by assessing serine19-phosphorylated regulatory light chain (pRLC) localization after precisely timed drug treatments. Cortical pRLC was globally depressed before cytokinesis, then elevated only at the equator. We implicated cell cycle biochemistry (not microtubules) in pRLC depression, and differential microtubule stability in localizing the subsequent myosin activation. With no microtubules, pRLC accumulation occurred globally instead of equatorially, and loss of just dynamic microtubules increased equatorial pRLC recruitment. Nocodazole treatment revealed a population of stable astral microtubules that formed during anaphase; among these, those aimed toward the equator grew longer, and their tips coincided with cortical pRLC accumulation. Shrinking the mitotic apparatus with colchicine revealed pRLC suppression near dynamic microtubule arrays. We conclude that opposite effects of stable versus dynamic microtubules focuses myosin activation to the cell equator during cytokinesis. PMID:18955555

A novel method for determination of aragonite saturation state on the continental shelf of central Oregon using multi-parameter relationships with hydrographic data

NASA Astrophysics Data System (ADS)

Juranek, L. W.; Feely, R. A.; Peterson, W. T.; Alin, S. R.; Hales, B.; Lee, K.; Sabine, C. L.; Peterson, J.

2009-12-01

We developed a multiple linear regression model to robustly determine aragonite saturation state (Ωarag) from observations of temperature and oxygen (R2 = 0.987, RMS error 0.053), using data collected in the Pacific Northwest region in late May 2007. The seasonal evolution of Ωarag near central Oregon was evaluated by applying the regression model to a monthly (winter)/bi-weekly (summer) water-column hydrographic time-series collected over the shelf and slope in 2007. The Ωarag predicted by the regression model was less than 1, the thermodynamic calcification/dissolution threshold, over shelf/slope bottom waters throughout the entire 2007 upwelling season (May-November), with the Ωarag = 1 horizon shoaling to 30 m by late summer. The persistence of water with Ωarag < 1 on the continental shelf has not been previously noted and could have notable ecological consequences for benthic and pelagic calcifying organisms such as mussels, oysters, abalone, echinoderms, and pteropods.

Full allogeneic fusion of embryos in a holothuroid echinoderm.

PubMed

Gianasi, Bruno L; Hamel, Jean-François; Mercier, Annie

2018-05-30

Whole-body chimaeras (organisms composed of genetically distinct cells) have been directly observed in modular/colonial organisms (e.g. corals, sponges, ascidians); whereas in unitary deuterostosmes (including mammals) they have only been detected indirectly through molecular analysis. Here, we document for the first time the step-by-step development of whole-body chimaeras in the holothuroid Cucumaria frondosa , a unitary deuterostome belonging to the phylum Echinodermata. To the best of our knowledge, this is the most derived unitary metazoan in which direct investigation of zygote fusibility has been undertaken. Fusion occurred among hatched blastulae, never during earlier (unhatched) or later (larval) stages. The fully fused chimaeric propagules were two to five times larger than non-chimaeric embryos. Fusion was positively correlated with propagule density and facilitated by the natural tendency of early embryos to agglomerate. The discovery of natural chimaerism in a unitary deuterostome that possesses large externally fertilized eggs provides a framework to explore key aspects of evolutionary biology, histocompatibility and cell transplantation in biomedical research. © 2018 The Author(s).

A Waterborne Pursuit-Deterrent Signal Deployed by a Sea Urchin.

PubMed

Sheppard-Brennand, Hannah; Poore, Alistair G B; Dworjanyn, Symon A

2017-06-01

Selection by consumers has led to the evolution of a vast array of defenses in animals and plants. These defenses include physical structures, behaviors, and chemical signals that mediate interactions with predators. Some of the strangest defensive structures in nature are the globiferous pedicellariae of the echinoderms. These are small venomous appendages with jaws and teeth that cover the test of many sea urchins and sea stars. In this study, we report a unique use of these defensive structures by the collector sea urchin Tripneustes gratilla. In both the laboratory and the field, globiferous pedicellariae were unpalatable to fish consumers. When subject to simulated predator attack, sea urchins released a cloud of pedicellaria heads into the water column. Flume experiments established the presence of a waterborne cue associated with this release of pedicellariae that is deterrent to predatory fish. These novel results add to our understanding of how the ecosystem-shaping sea urchin T. gratilla is able to reach high densities in many reef habitats, with subsequent impacts on algal cover.

The potential for crizotinib in non-small cell lung cancer: a perspective review

PubMed Central

Bang, Yung-Jue

2011-01-01

Tyrosine kinases have a crucial role as key regulators of signaling pathways that influence cell differentiation and growth. Dysregulation of tyrosine kinase-mediated signaling is understood to be an important oncogenic driver. Genetic rearrangements involving the tyrosine kinase anaplastic lymphoma kinase (ALK) gene occur in non-small cell lung cancer (NSCLC), anaplastic large cell lymphomoas, inflammatory myofibroblastic tumors, and other cancers. Cells with abnormal ALK signaling are sensitive to ALK inhibitors such as crizotinib. This review will highlight the discovery of the fusion between echinoderm microtubule-associated protein-like 4 (EML4) and ALK as an oncogenic driver, recognition of other ALK gene rearrangements in NSCLC, and the confirmation that crizotinib is an effective treatment for patients with ALK-positive NSCLC. Work is underway to further define the role for crizotinib in the treatment of ALK-positive lung cancer and other cancers and to investigate the molecular mechanisms for resistance to ALK inhibition with crizotinib. PMID:22084642

Idiosyncratic species effects confound size-based predictions of responses to climate change.

PubMed

Twomey, Marion; Brodte, Eva; Jacob, Ute; Brose, Ulrich; Crowe, Tasman P; Emmerson, Mark C

2012-11-05

Understanding and predicting the consequences of warming for complex ecosystems and indeed individual species remains a major ecological challenge. Here, we investigated the effect of increased seawater temperatures on the metabolic and consumption rates of five distinct marine species. The experimental species reflected different trophic positions within a typical benthic East Atlantic food web, and included a herbivorous gastropod, a scavenging decapod, a predatory echinoderm, a decapod and a benthic-feeding fish. We examined the metabolism-body mass and consumption-body mass scaling for each species, and assessed changes in their consumption efficiencies. Our results indicate that body mass and temperature effects on metabolism were inconsistent across species and that some species were unable to meet metabolic demand at higher temperatures, thus highlighting the vulnerability of individual species to warming. While body size explains a large proportion of the variation in species' physiological responses to warming, it is clear that idiosyncratic species responses, irrespective of body size, complicate predictions of population and ecosystem level response to future scenarios of climate change.

A vertical wall in the Whittard Canyon with a novel community assemblage

NASA Astrophysics Data System (ADS)

Johnson, Mark; White, Martin; Wilson, Annette; Wuerzberg, Laura; Schwabe, Enrico; Folch, Helka; Allcock, Louise

2013-04-01

We describe a hitherto unreported community from a vertical wall in the Whittard Canyon system on the Atlantic Margin. The wall extended vertically for about 100 m from approximately 750 m depth. We explored the wall with an ROV and discovered an assemblage cominated by large limid bivalves Acesta excavata and deep-water oysters Neopycnodonte zibrowii at very high densities, particularly at overhangs. The assemblage also contained deep-water corals (including solitary corals). It had high numbers of flytrap anemones and had many mobile species associated with it including crustaceans such as Paramola cuvieri and Bathynectes longispina, echinoderms and fishes. We took CTD transects in the area of the wall and beam attenuation indicated nepheloid layers present in the water column. The greatest densities of suspended material at the ROV dive site were at the depth of the wall. We hypothesise that internal waves concentrate suspended sediment at the foot of the vertical wall. This may provide the resources to support the high density of large filter feeders at these depths.

EML4-ALK Variants: Biological and Molecular Properties, and the Implications for Patients

PubMed Central

Yeoh, Sharon; Jackson, George

2017-01-01

Since the discovery of the fusion between EML4 (echinoderm microtubule associated protein-like 4) and ALK (anaplastic lymphoma kinase), EML4-ALK, in lung adenocarcinomas in 2007, and the subsequent identification of at least 15 different variants in lung cancers, there has been a revolution in molecular-targeted therapy that has transformed the outlook for these patients. Our recent focus has been on understanding how and why the expression of particular variants can affect biological and molecular properties of cancer cells, as well as identifying the key signalling pathways triggered, as a result. In the clinical setting, this understanding led to the discovery that the type of variant influences the response of patients to ALK therapy. Here, we discuss what we know so far about the EML4-ALK variants in molecular signalling pathways and what questions remain to be answered. In the longer term, this analysis may uncover ways to specifically treat patients for a better outcome. PMID:28872581

EML4-ALK Variants: Biological and Molecular Properties, and the Implications for Patients.

PubMed

Sabir, Sarah R; Yeoh, Sharon; Jackson, George; Bayliss, Richard

2017-09-05

Since the discovery of the fusion between EML4 (echinoderm microtubule associated protein-like 4) and ALK (anaplastic lymphoma kinase), EML4-ALK, in lung adenocarcinomas in 2007, and the subsequent identification of at least 15 different variants in lung cancers, there has been a revolution in molecular-targeted therapy that has transformed the outlook for these patients. Our recent focus has been on understanding how and why the expression of particular variants can affect biological and molecular properties of cancer cells, as well as identifying the key signalling pathways triggered, as a result. In the clinical setting, this understanding led to the discovery that the type of variant influences the response of patients to ALK therapy. Here, we discuss what we know so far about the EML4-ALK variants in molecular signalling pathways and what questions remain to be answered. In the longer term, this analysis may uncover ways to specifically treat patients for a better outcome.

The Ciona intestinalis genome: when the constraints are off

NASA Technical Reports Server (NTRS)

Holland, Linda Z.; Gibson-Brown, Jeremy J.

2003-01-01

The recent genome sequencing of a non-vertebrate deuterostome, the ascidian tunicate Ciona intestinalis, makes a substantial contribution to the fields of evolutionary and developmental biology.1 Tunicates have some of the smallest bilaterian genomes, embryos with relatively few cells, fixed lineages and early determination of cell fates. Initial analyses of the C. intestinalis genome indicate that it has been evolving rapidly. Comparisons with other bilaterians show that C. intestinalis has lost a number of genes, and that many genes linked together in most other bilaterians have become uncoupled. In addition, a number of independent, lineage-specific gene duplications have been detected. These new results, although interesting in themselves, will take on a deeper significance once the genomes of additional invertebrate deuterostomes (e.g. echinoderms, hemichordates and amphioxus) have been sequenced. With such a broadened database, comparative genomics can begin to ask pointed questions about the relationship between the evolution of genomes and the evolution of body plans. Copyright 2003 Wiley Periodicals, Inc.

A new genus of Asterocheridae (Copepoda: Siphonostomatoida) ectoassociate of the ascidian Eudistoma vannamei Millar, 1977 (Polycitoridae) from Brazil.

PubMed

Johnsson, Rodrigo; Bahia, Cristiano; Neves, Elizabeth

2016-05-23

Asterocheres Boeck, 1860 is the largest genus of the siphonostomatoid copepod family Asterocheridae, containing 63 valid species. The genus is known for its symbiotic relationships with many marine invertebrate taxa, especially sponges, cnidarians, bryozoans, and echinoderms. Recent studies have restricted the diagnosis of this genus. Consequently, many species are now considered as species inquirendae. The present paper describes a new species living externally on the tunic of Eudistoma vannamei Millar, 1977, an endemic ascidian from Brazil. As the new species does not fit Asterocheres in the strict sense, a new genus is erected to accommodate it. Setacheres gen. nov. is characterized by its possession of two distal setae on the third endopodal segment of P3, thus differing from the distal seta and spine pattern that is deemed as diagnostic of Asterocheres. A revision and comparison of Asterocheres´ species inquirendae revealed eight species sharing the same generic characteristics and were thus reallocated as members of the new genus.

Ocean acidification: the other CO2 problem.

PubMed

Doney, Scott C; Fabry, Victoria J; Feely, Richard A; Kleypas, Joan A

2009-01-01

Rising atmospheric carbon dioxide (CO2), primarily from human fossil fuel combustion, reduces ocean pH and causes wholesale shifts in seawater carbonate chemistry. The process of ocean acidification is well documented in field data, and the rate will accelerate over this century unless future CO2 emissions are curbed dramatically. Acidification alters seawater chemical speciation and biogeochemical cycles of many elements and compounds. One well-known effect is the lowering of calcium carbonate saturation states, which impacts shell-forming marine organisms from plankton to benthic molluscs, echinoderms, and corals. Many calcifying species exhibit reduced calcification and growth rates in laboratory experiments under high-CO2 conditions. Ocean acidification also causes an increase in carbon fixation rates in some photosynthetic organisms (both calcifying and noncalcifying). The potential for marine organisms to adapt to increasing CO2 and broader implications for ocean ecosystems are not well known; both are high priorities for future research. Although ocean pH has varied in the geological past, paleo-events may be only imperfect analogs to current conditions.

The Oldest Jurassic Dinosaur: A Basal Neotheropod from the Hettangian of Great Britain.

PubMed

Martill, David M; Vidovic, Steven U; Howells, Cindy; Nudds, John R

2016-01-01

Approximately 40% of a skeleton including cranial and postcranial remains representing a new genus and species of basal neotheropod dinosaur is described. It was collected from fallen blocks from a sea cliff that exposes Late Triassic and Early Jurassic marine and quasi marine strata on the south Wales coast near the city of Cardiff. Matrix comparisons indicate that the specimen is from the lithological Jurassic part of the sequence, below the first occurrence of the index ammonite Psiloceras planorbis and above the last occurrence of the Rhaetian conodont Chirodella verecunda. Associated fauna of echinoderms and bivalves indicate that the specimen had drifted out to sea, presumably from the nearby Welsh Massif and associated islands (St David's Archipelago). Its occurrence close to the base of the Blue Lias Formation (Lower Jurassic, Hettangian) makes it the oldest known Jurassic dinosaur and it represents the first dinosaur skeleton from the Jurassic of Wales. A cladistic analysis indicates basal neotheropodan affinities, but the specimen retains plesiomorphic characters which it shares with Tawa and Daemonosaurus.

Receptor ligand-triggered resistance to alectinib and its circumvention by Hsp90 inhibition in EML4-ALK lung cancer cells.

PubMed

Tanimoto, Azusa; Yamada, Tadaaki; Nanjo, Shigeki; Takeuchi, Shinji; Ebi, Hiromichi; Kita, Kenji; Matsumoto, Kunio; Yano, Seiji

2014-07-15

Alectinib is a new generation ALK inhibitor with activity against the gatekeeper L1196M mutation that showed remarkable activity in a phase I/II study with echinoderm microtubule associated protein-like 4 (EML4)--anaplastic lymphoma kinase (ALK) non-small cell lung cancer (NSCLC) patients. However, alectinib resistance may eventually develop. Here, we found that EGFR ligands and HGF, a ligand of the MET receptor, activate EGFR and MET, respectively, as alternative pathways, and thereby induce resistance to alectinib. Additionally, the heat shock protein 90 (Hsp90) inhibitor suppressed protein expression of ALK, MET, EGFR, and AKT, and thereby induced apoptosis in EML4-ALK NSCLC cells, even in the presence of EGFR ligands or HGF. These results suggest that Hsp90 inhibitors may overcome ligand-triggered resistance to new generation ALK inhibitors and may result in more successful treatment of NSCLC patients with EML4-ALK.

Receptor ligand-triggered resistance to alectinib and its circumvention by Hsp90 inhibition in EML4-ALK lung cancer cells

PubMed Central

Tanimoto, Azusa; Yamada, Tadaaki; Nanjo, Shigeki; Takeuchi, Shinji; Ebi, Hiromichi; Kita, Kenji; Matsumoto, Kunio; Yano, Seiji

2014-01-01

Alectinib is a new generation ALK inhibitor with activity against the gatekeeper L1196M mutation that showed remarkable activity in a phase I/II study with echinoderm microtubule associated protein-like 4 (EML4) - anaplastic lymphoma kinase (ALK) non-small cell lung cancer (NSCLC) patients. However, alectinib resistance may eventually develop. Here, we found that EGFR ligands and HGF, a ligand of the MET receptor, activate EGFR and MET, respectively, as alternative pathways, and thereby induce resistance to alectinib. Additionally, the heat shock protein 90 (Hsp90) inhibitor suppressed protein expression of ALK, MET, EGFR, and AKT, and thereby induced apoptosis in EML4-ALK NSCLC cells, even in the presence of EGFR ligands or HGF. These results suggest that Hsp90 inhibitors may overcome ligand-triggered resistance to new generation ALK inhibitors and may result in more successful treatment of NSCLC patients with EML4-ALK. PMID:24952482

TRANSIENT AMORPHOUS CALCIUM PHOSPHATE IN FORMING ENAMEL

PubMed Central

Beniash, Elia; Metzler, Rebecca A.; Lam, Raymond S.K.; Gilbert, P.U.P.A.

2009-01-01

Enamel, the hardest tissue in the body, begins as a three-dimensional network of nanometer size mineral particles, suspended in a protein gel. This mineral network serves as a template for mature enamel formation. To further understand the mechanisms of enamel formation we characterized the forming enamel mineral at an early secretory stage using x-ray absorption near-edge structure (XANES) spectromicroscopy, transmission electron microscopy (TEM), FTIR microspectroscopy and polarized light microscopy. We show that the newly formed enamel mineral is amorphous calcium phosphate (ACP), which eventually transforms into apatitic crystals. Interestingly, the size, shape and spatial organization of these amorphous mineral particles and older crystals are essentially the same, indicating that the mineral morphology and organization in enamel is determined prior to its crystallization. Mineralization via transient amorphous phases has been previously reported in chiton teeth, mollusk shells, echinoderm spicules and spines, and recent reports strongly suggest the presence transient amorphous mineral in forming vertebrate bones. The present finding of transient ACP in murine tooth enamel suggests that this strategy might be universal. PMID:19217943

Organic matrix-related mineralization of sea urchin spicules, spines, test and teeth.

PubMed

Veis, Arthur

2011-06-01

The camarodont echinoderms have five distinct mineralized skeletal elements: embryonic spicules, mature test, spines, lantern stereom and teeth. The spicules are transient structural elements whereas the spines, and test plates are permanent. The teeth grow continuously. The mineral is a high magnesium calcite, but the magnesium content is different in each type of skeletal element, varying from 5 to 40 mole% Mg. The organic matrix creates the spaces and environments for crystal initiation and growth. The detailed mechanisms of crystal regulation are not known, but acidic and phosphorylated matrix proteins may be of special importance. Biochemical studies, sequencing of the complete genome, and high-throughput proteomic analysis have not yet provided insight into the mechanisms of crystallization, calcite composition, and orientation applicable to all skeletal elements. The embryonic spicules are not representative of the mature skeletal elements. The next phase of research will have to focus on the specific localization of the proteins and individual biochemistries of each system with regard to mineral content and placement.

Effects of bottom fishing on the benthic megafauna of Georges Bank

USGS Publications Warehouse

Collie, J.S.; Escanero, G.A.; Valentine, P.C.

1997-01-01

This study addresses ongoing concerns ever the effects of mobile fishing gear on benthic communities. Using side-scan sonar, bottom photographs and fishing records, we identified a set of disturbed and undisturbed sites on the gravel pavement area of northern Georges Bank in the northwest Atlantic. Replicate samples of the megofauna were collected with a 1 m Naturalists' dredge on 2 cruises in 1994. Compared with the disturbed sites, the undisturbed sites had higher numbers of organisms, biomass, species richness and species diversity; evenness was higher at the disturbed sites. Undisturbed sites were characterized by an abundance of bushy epifaunal taxa (bryozoans, hydroids, worm tubes) that provide a complex habitat for shrimps, polychaetes, brittle stars, mussels and small fish. Disturbed sites were dominated by larger, hard-shelled molluscs, and scavenging crabs and echinoderms. Many of the megafaunal species in our samples have also been identified in stomach contents of demersal fish on Georges Bank; the abundances of at feast some of these species were reduced at the disturbed sites.

Sea Cucumber Glycosides: Chemical Structures, Producing Species and Important Biological Properties

PubMed Central

Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Rahman, M. Aminur; Islam, Mohamad Tofazzal

2017-01-01

Sea cucumbers belonging to echinoderm are traditionally used as tonic food in China and other Asian countries. They produce abundant biologically active triterpene glycosides. More than 300 triterpene glycosides have been isolated and characterized from various species of sea cucumbers, which are classified as holostane and nonholostane depending on the presence or absence of a specific structural unit γ(18,20)-lactone in the aglycone. Triterpene glycosides contain a carbohydrate chain up to six monosaccharide units mainly consisting of d-xylose, 3-O-methy-d-xylose, d-glucose, 3-O-methyl-d-glucose, and d-quinovose. Cytotoxicity is the common biological property of triterpene glycosides isolated from sea cucumbers. Besides cytotoxicity, triterpene glycosides also exhibit antifungal, antiviral and hemolytic activities. This review updates and summarizes our understanding on diverse chemical structures of triterpene glycosides from various species of sea cucumbers and their important biological activities. Mechanisms of action and structural–activity relationships (SARs) of sea cucumber glycosides are also discussed briefly. PMID:29039760

Structural analysis and anticoagulant activities of two sulfated polysaccharides from the sea cucumber Holothuria coluber.

PubMed

Yang, Wenjiao; Cai, Ying; Yin, Ronghua; Lin, Lisha; Li, Zhongkun; Wu, Mingyi; Zhao, Jinhua

2018-05-01

Sulfated polysaccharides such as fucosylated glycosaminoglycan and fucan sulfate from echinoderm possess complex chemical structure and various biological activities. The two sulfated polysaccharides were purified from the low-value sea cucumber Holothuria coluber. Their physicochemical properties and chemical structures were analyzed and characterized by chemical and instrumental methods. Structural analysis clarified that the sea cucumber fucosylated glycosaminoglycan contains a chondroitin sulfate-like backbone and fucosyl branches with four various sulfation patterns. The fucan sulfate with molecular weight of 64.6 kDa comprises a central core of regular α(1 → 4)-linked tetrasaccharide repeating units, each of which is linked by a 4-O-sulfated fucose residue. Anticoagulant assays indicated that these sulfated polysaccharides possessed strong APTT prolonging activities and intrinsic factor Xase inhibitory activities, both of which decreased with the reduction of their molecular weights. Our results expand knowledge on the structural types of sulfated polysaccharides from sea cucumbers and further illustrate their functionality. Copyright © 2018. Published by Elsevier B.V.

Sea cucumber species identification of family Caudinidae from Surabaya based on morphological and mitochondrial DNA evidence

NASA Astrophysics Data System (ADS)

Amin, Muhammad Hilman Fu'adil; Pidada, Ida Bagus Rai; Sugiharto, Widyatmoko, Johan Nuari; Irawan, Bambang

2016-03-01

Species identification and taxonomy of sea cucumber remains a challenge problem in some taxa. Caudinidae family of sea cucumber was comerciallized in Surabaya, and it was used as sea cucumber chips. Members of Caudinid sea cucumber have similiar morphology, so it is hard to identify this sea cucumber only from morphological appearance. DNA barcoding is useful method to overcome this problem. The aim of this study was to determine Caudinid specimen of sea cucumber in East Java by morphological and molecular approach. Sample was collected from east coast of Surabaya, then preserved in absolute ethanol. After DNA isolation, Cytochrome Oxydase I (COI) gene amplification was performed using Echinoderm universal primer and PCR product was sequenced. Sequencing result was analyzed and identified in NCBI database using BLAST. Results showed that Caudinid specimen in have closely related to Acaudina molpadioides sequence in GenBank with 86% identity. Morphological data, especially based on ossicle, also showed that the specimen is Acaudina molpadioides.

Mississippian carbonate buildups and development of cool-waterlike carbonate platforms in the Illinois Basin, Midcontinent U.S.A.

USGS Publications Warehouse

Lasemi, Z.; Norby, R.D.; Utgaard, J.E.; Ferry, W.R.; Cuffey, R.J.; Dever, G.R.

2005-01-01

Numerous biohermal buildups occur in Mississippian (Lower Carboniferous) strata in the Illinois Basin and adjacent regions. They developed as mud mounds, biodetrital calcisiltite mounds, and bryozoan frame thickets (fenestrate-frame coquina or rudstone) during the Kinderhookian and early Meramecian (Tournaisian and early Visean), and as microbial mud mounds, microbial- serpulidbryozoanboundstones, and solenoporoid (red algal) boundstones during the Chesterian (late Visean and Serpukhovian). True Waulsortian mounds did not develop in the Illinois Basin, but echinoderm (primarily crinoids)-bryozoan carbonate banks and bryozoan frame thickets generally occupied the same niche during the Kinderhookian-early Meramecian. Nutrient availability and the resulting increase in the productivity of echinoderms and bryozoans were apparently detrimental to Waulsortian mound development. Deposition of crinoidal-bryozoan carbonates during the Kinderhookian-Osagean initially occurred on a ramp setting that later evolved into a platform with a relatively steep margin through sediment aggradation and progradation. By mid-Osagean-early Meramecian, two such platforms, namely the Burlington Shelf and the Ullin Platform, developed adjacent to a deep, initially starved basin. Sedimentologic and petrographic characteristics of the Kinderhookian-earliest Meramecian carbonates resemble the modern cool-water Heterozoan Association. This is in contrast with post-earliest Meramecian carbonates, which are typically oolitic and peloidal with common peri tidal facies. The post-earliest Meramecian carbonates, therefore, resemble those of the warm-water Photozoan Association. The prevalence of Heterozoan carbonates in the Illinois Basin correlates with a rapid increase in the rate of subsidence and a major second-order eustatic sea-level rise that resulted in deep-water starved basins at this time. In the starved Illinois Basin, deposition was initially limited to a thin phosphatic shale that was followed later by deposition of up to 200 m of siliceous, spiculitic, and radiolarianbearing limestone. The starved basin was connected to the deep open ocean through a bathymetric depression, which was centered over the failed late Precambrian-Early Cambrian Reelfoot Rift, which extended from the deep-water Ouachita Trough in central Arkansas to southern Illinois, approximately parallel to the trend of the modern Mississippi River. We believe that upwelling of cool, nutrient- and silica-rich deep oceanic water, which entered the basin through this bathymetric depression, resulted in proliferation of pelmatozoans and bryozoans. The subsequent change from cool-water-like carbonates to warm-water-like carbonates appears to be related to decreased subsidence and gradual shallowing of the basin.

Diagenetic comparisons between non-tropical Cenozoic limestones of New Zealand and tropical Mississippian limestones from Indiana, USA: Is the non-tropical model better than the tropical model?

NASA Astrophysics Data System (ADS)

Dodd, J. Robert; Nelson, Campbell S.

1998-10-01

Mississippian limestones exposed in Indiana, U.S.A., were deposited in a shallow tropical ocean. However, many properties of these limestones are more like those of modern and Cenozoic non-tropical limestones such as those found in New Zealand. The dominant skeletal grains in the Indiana limestones are calcitic echinoderms, bryozoans, and brachiopods. The dominant skeletal grains in most Cenozoic limestones of New Zealand are calcitic bryozoans, echinoderms, bivalve molluscs, and foraminifera. In contrast, modern and Cenozoic tropical limestones contain an abundance of aragonitic green algae, corals, and molluscs. Early in diagenesis the metastable aragonite dissolves and reprecipitates as calcite, causing early cementation of the sediments. Originally aragonitic fossils that have dissolved can be identified as molds that are commonly filled with secondary calcite. Because they contained little aragonite, most of the Indiana and New Zealand limestones did not have an abundant source of early cement. Except for local cases in which grains were cemented in contact with carbonate supersaturated seawater, grainstones were relatively deeply buried with little cement between the grains. This resulted in mechanical and chemical compaction of skeletal grains, producing a `fitted fabric' with greatly reduced pore space, either open or filled with cement between the grains. Cement in these aragonite-poor grainstones comes largely from pressure dissolution between grains and along stylolitic seams in the rock, features that are common only after burial beyond a few hundred meters. The final product of deeply buried (up to 2000 m) Cenozoic New Zealand grainstones is similar to the Mississippian grainstones of Indiana. In the Indiana limestones we have only the final product of this extensive burial diagenesis. However, the New Zealand sediments and rocks reveal all steps of formation of the final deeply buried limestone. The reason for the scarcity of originally aragonitic fossil grains in Paleozoic rocks worldwide is unknown. Organisms with aragonitic skeletons such as some molluscan groups and calcareous green algae were present, but seldom in much abundance. The aragonitic scleractinian corals had not yet evolved. Previous researchers have noted that non-skeletal precipitates such as ooids and cements have at times during the Paleozoic been predominantly aragonite and at other times calcite. They have attributed this difference to secular variation in seawater chemistry (icehouse vs. greenhouse seas). Abundance of aragonitic and calcitic skeletal grains does not follow this pattern.

Schaben field, Kansas: Improving performance in a Mississippian shallow-shelf carbonate

USGS Publications Warehouse

Montgomery, S.L.; Franseen, E.K.; Bhattacharya, S.; Gerlach, P.; Byrnes, A.; Guy, W.; Carr, T.R.

2000-01-01

Schaben field (Kansas), located along the northeastern shelf of the Hugoton embayment, produces from Mississippian carbonates in erosional highs immediately beneath a regional unconformity. Production comes from depths of around 4400 ft (1342 m) in partially dolomitized shelf deposits. A detailed reservoir characterization/simulation study, recently performed as part of a Department of Energy Reservoir Class Oil Field Demonstration Project, has led to important revision in explanations for observed patterns of production. Cores recovered from three new data wells identify three main facies: Spicule-rich wackestone-packstone, echinoderm wackestone/packstone/grainstone, and dolomitic mudstone-wackestone. Reservoir quality is highest in spicule-rich wackestone/packstones but is subject to a very high degree of vertical heterogeneity due to facies interbedding, silification, and variable natural fracturing. The oil reservoir is underlain by an active aquifer, which helps maintain reservoir pressure but supports significant water production. Reservoir simulation, using public-domain, PC-based software, suggests that infill drilling is an efficient approach to enhanced recovery. Recent drilling directed by simulation results has shown considerable success in improving field production rates. Results from the Schaben field demonstration project are likely to have wide application for independent oil and exploration companies in western Kansas.Schaben field (Kansas), located along the northeastern shelf of the Hugoton embayment, produces from Mississippian carbonates in erosional highs immediately beneath a regional unconformity. Production comes from depths of around 4400 ft (1342 m) in partially dolomitized shelf deposits. A detailed reservoir characterization/simulation study, recently performed as part of a Department of Energy Reservoir Class Oil Field Demonstration Project, has led to important revision in explanations for observed patterns of production. Cores recovered from three new data wells identify three main facies: spicule-rich wackestone-packstone, echinoderm wackestone/packstone/grainstone, and dolomitic mudstone-wackestone. Reservoir quality is highest in spicule-rich wackestone/packstones but is subject to a very high degree of vertical heterogeneity due to facies interbedding, silification, and variable natural fracturing. The oil reservoir is underlain by an active aquifer, which helps maintain reservoir pressure but supports significant water production. Reservoir simulation, using public-domain, PC-based software, suggests that infill drilling is an efficient approach to enhanced recovery. Recent drilling directed by simulation results has shown considerable success in improving field production rates. Results from the Schaben field demonstration project are likely to have wide application for independent oil and exploration companies in western Kansas.

A detailed description of the development of the hemichordate Saccoglossus kowalevskii using SEM, TEM, Histology and 3D-reconstructions

PubMed Central

2013-01-01

Introduction Traditionally, the origin of the third germ layer and its special formation of coelomic cavities by enterocoely is regarded to be an informative character in phylogenetic analyses. In early deuterostomes such as sea urchins, the mesoderm forms through a single evagination pinching off from the apical end of the archenteron which then gives off mesocoela and metacoela on each side. This echinoid-type coelom formation has conventionally been assumed to be ancestral for Deuterostomia. However, recent phylogenetic analyses show that Echinodermata hold a more derived position within Deuterostomia. In this regard a subgroup of Hemichordata, namely enteropneusts, seem to host promising candidates, because they are supposed to have retained many ancestral deuterostome features on the one hand, and furthermore share some characteristics with chordates on the other hand. In enteropneusts a wide range of different modes of coelom formation has been reported and in many cases authors of the original observations carefully detailed the limitations of their descriptions, while these doubts disappeared in subsequent reviews. In the present study, we investigated the development of all tissues in an enteropneust, Saccoglossus kowalevskii by using modern morphological techniques such as complete serial sectioning for LM and TEM, and 3D-reconstructions, in order to contribute new data to the elucidation of deuterostome evolution. Results Our data show that in the enteropneust S. kowalevskii all main coelomic cavities (single protocoel, paired mesocoela and metacoela) derive from the endoderm via enterocoely as separate evaginations, in contrast to the aforementioned echinoid-type. The anlagen of the first pair of gill slits emerge at the late kink stage (~96 h pf). From that time onwards, we documented a temporal left-first development of the gill slits and skeletal gill rods in S. kowalevskii until the 2 gill slit juvenile stage. Conclusions The condition of coelom formation from separate evaginations is recapitulated in the larva of amphioxus and can be observed in crinoid echinoderms in a similar way. Therefore, coelom formation from separated pouches, rather than from a single apical pouch with eventual subdivision is suggested as the ancestral type of coelom formation for Deuterostomia. Left-right asymmetries are also present in echinoderms (rudiment formation), cephalochordates (larval development), tunicates (gut coiling) and vertebrates (visceral organs), and it is known from other studies applying molecular genetic analyses that genes such as nodal, lefty and pitx are involved during development. We discuss our findings in S. kowalevskii in the light of morphological as well as molecular genetic data. PMID:24010725

Reciprocal Signaling between the Ectoderm and a Mesendodermal Left-Right Organizer Directs Left-Right Determination in the Sea Urchin Embryo

PubMed Central

Bessodes, Nathalie; Haillot, Emmanuel; Duboc, Véronique; Röttinger, Eric; Lahaye, François; Lepage, Thierry

2012-01-01

During echinoderm development, expression of nodal on the right side plays a crucial role in positioning of the rudiment on the left side, but the mechanisms that restrict nodal expression to the right side are not known. Here we show that establishment of left-right asymmetry in the sea urchin embryo relies on reciprocal signaling between the ectoderm and a left-right organizer located in the endomesoderm. FGF/ERK and BMP2/4 signaling are required to initiate nodal expression in this organizer, while Delta/Notch signaling is required to suppress formation of this organizer on the left side of the archenteron. Furthermore, we report that the H+/K+-ATPase is critically required in the Notch signaling pathway upstream of the S3 cleavage of Notch. Our results identify several novel players and key early steps responsible for initiation, restriction, and propagation of left-right asymmetry during embryogenesis of a non-chordate deuterostome and uncover a functional link between the H+/K+-ATPase and the Notch signaling pathway. PMID:23271979

Badenian (Middle Miocene) echinoids and starfish from western Ukraine, and their biogeographic and stratigraphic significance

NASA Astrophysics Data System (ADS)

Radwański, Andrzej; Górka, Marcin; Wysocka, Anna

2014-06-01

Echinoderms from the Badenian (Middle Miocene) of the Fore-Carpathian Basin of western Ukraine are facies restricted. The Mykolaiv Beds, stratigraphically older, yielded the starfish Astropecten forbesi (complete skeletons), two genera of sand dollars (Parascutella, Parmulechinus), and numerous other echinoids of the genera Psammechinus , Echinocyamus, Spatangus, Hemipatagus, Echinocardium, Clypeaster, Echinolampas, and Conolampas. The stratigraphically younger, calcareous Ternopil Beds yielded Eucidaris (complete coronae, isolated spines), Arbacina , Brissus, and Rhabdobrissus. Sixteen species of echinoids are distinguished and/or commented. A new brissid, Rhabdobrissus tarnopolensis sp. nov., is established. A mass occurrence of some species (Psammechinus dubius and Hemipatagus ocellatus) contrasts with that of mass aggregations (sand dollars and Echinocardium leopolitanum) by dynamic events in selected layers of proximal tempestites. Of special note is the occurrence of very small specimens, interpreted as juveniles (`babies') having been swept out of their restricted biotopes (`nurseries'). Some species hitherto regarded as of Early Miocene age, and the problem of their persistence beyond the Fore-Carpathian Basin and/or migration into that basin during the Middle Miocene transgression are discussed.

Nicotinic Acid Adenine Dinucleotide Phosphate Analogs Substituted on the Nicotinic Acid and Adenine Ribosides. Effects on Receptor-Mediated Ca2+ release

PubMed Central

Trabbic, Christopher J.; Zhang, Fan; Walseth, Timothy F.; Slama, James T.

2015-01-01

Nicotinic acid adenine dinucleotide phosphate (NAADP) is a Ca2+ releasing intracellular second messenger in both mammals and echinoderms. We report that large functionalized substituents introduced at the nicotinic acid 5-position are recognized by the sea urchin receptor, albeit with a 20–500 fold loss in agonist potency. 5-(3-Azidopropyl)-NAADP was shown to release Ca2+ with an EC50 of 31 µM and to compete with NAADP for receptor binding with an IC50 of 56 nM. Attachment of charged groups to the nicotinic acid of NAADP is associated with loss of activity, suggesting that the nicotinate riboside moiety is recognized as a neutral zwitterion. Substituents (Br- and N3-) can be introduced at the 8-adenosyl position of NAADP while preserving high potency and agonist efficacy and an NAADP derivative substituted at both the 5-position of the nicotinic acid and at the 8-adenosyl position was also recognized although the agonist potency was significantly reduced. PMID:25826221

The extent of ocean acidification on aragonite saturation state along the Washington-Oregon continental shelf margin in late summer 2012

NASA Astrophysics Data System (ADS)

Feely, R. A.; Alin, S. R.; Hales, B. R.; Juranek, L.; Greeley, D.

2012-12-01

The Washington-Oregon continental shelf region is exposed to conditions of low aragonite saturation state during the late spring/early summer upwelling season. However, the extent of its evolution in late summer/early fall has been largely unknown. Along this continental margin, ocean acidification, upwelling, biological productivity, and respiration processes in subsurface waters are major contributors to the variability in dissolved inorganic carbon (DIC), pH and aragonite saturation state. The persistence of water with aragonite saturation state <1 on the continental shelf off Washington and Oregon has been previously identified and could have profound ecological consequences for benthic and pelagic calcifying organisms such as mussels, oysters, abalone, echinoderms, and pteropods. In the late summer of 2012 we studied the extent of acidification conditions employing shipboard cruises and profiling gliders. We conducted several large-scale chemical and hydrographic surveys of the region in order to better understand the interrelationships between these natural and human-induced processes and their effects on aragonite saturation. We will compare the results of these new surveys with our previous work in 2011 and 2007.

Subtidal benthic megafauna in a productive and highly urbanised semi-enclosed bay (Ría de Vigo, NW Iberian Peninsula)

NASA Astrophysics Data System (ADS)

Aneiros, Fernando; Rubal, Marcos; Troncoso, Jesús S.; Bañón, Rafael

2015-11-01

The Ría de Vigo is a semi-enclosed bay with high primary productivity due to the influence of coastal upwelling-downwelling dynamics. The area is heavily populated and affected by numerous human activities, which lead to sediment modification. Epibenthic megafauna from the non-estuarine zones of this bay has been studied in order to describe its spatial distribution, testing possible differences between inner and outer areas. With that purpose, 75 sites have been sampled by means of a towing dredge. Megafauna was identified to the lowest taxonomic level possible, and each taxon counted and weighted. 113 different taxa were identified and a high spatial heterogeneity was observed in terms of abundance, biomass, taxa richness, diversity and evenness. Suspension-feeding molluscs dominated the innermost part of the studied area, and were substituted by echinoderms towards the external zones; this spatial pattern was also reflected in the results of multivariate analyses. These shifts in taxonomic and trophic guild composition of the assemblages have been tentatively related to differences in pollution levels and primary productivity along the main axis of the bay.

Non-small cell lung cancer patients with EML4-ALK fusion gene are insensitive to cytotoxic chemotherapy.

PubMed

Morodomi, Yosuke; Takenoyama, Mitsuhiro; Inamasu, Eiko; Toyozawa, Ryo; Kojo, Miyako; Toyokawa, Gouji; Shiraishi, Yoshimasa; Takenaka, Tomoyoshi; Hirai, Fumihiko; Yamaguchi, Masafumi; Taguchi, Kenichi; Seto, Takashi; Sugio, Kenji; Ichinose, Yukito

2014-07-01

Although patients with the echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase gene (EML4-ALK) re-arrangement and epidermal growth factor gene EGFR mutations have proven sensitive to specific inhibitors, there is currently no consensus regarding the sensitivity of non-small cell lung cancer (NSCLC) patients with such mutations to cytotoxic chemotherapy. The responses to first-line cytotoxic chemotherapy were retrospectively compared between advanced or postoperative recurrent patients with non-squamous NSCLC who harbor the EML4-ALK fusion gene (ALK+), EGFR mutation (EGFR+), or neither abnormality (wild-type). Data for 22 ALK+, 30 EGFR+, and 60 wild-type patients were analyzed. The ALK+ group had a significantly lower response rate than the other two groups. Progression-free survival was significantly shorter in the ALK+ cohort compared to the EGFR+ (p<0.001) and wild-type cohorts (p=0.0121). NSCLC patients with the EML4-ALK fusion gene might be relatively insensitivite to cytotoxic chemotherapy. Copyright© 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

An extremely rare case of small-cell lung cancer harboring variant 2 of the EML4-ALK fusion gene.

PubMed

Toyokawa, Gouji; Takenoyama, Mitsuhiro; Taguchi, Kenichi; Toyozawa, Ryo; Inamasu, Eiko; Kojo, Miyako; Shiraishi, Yoshimasa; Morodomi, Yosuke; Takenaka, Tomoyoshi; Hirai, Fumihiko; Yamaguchi, Masafumi; Seto, Takashi; Shimokawa, Mototsugu; Ichinose, Yukito

2013-09-01

Anaplastic lymphoma kinase (ALK) fuses echinoderm microtubule-associated protein-like 4 (EML4) to acquire a transforming activity in lung adenocarcinomas. However, the presence of an EML4-ALK fusion gene in other lung cancer histologies is an extremely rare phenomenon. A 43-year-old female was referred to our department due to dyspnea on effort and left back pain. Computed tomography (CT) showed a large mass in the upper lobe of the left lung and a massive left pleural effusion, while a CT-guided needle biopsy confirmed a diagnosis of small-cell lung cancer (SCLC). Surprisingly, the tumor was genetically considered to harbor the EML4-ALK fusion gene (variant 2). Although the patient underwent two regimens of cytotoxic chemotherapy for SCLC, she died approximately seven months after the administration of first-line chemotherapy. Our analysis of 30 consecutive patients with SCLC for EML4-ALK revealed that two patients, including the current patient and a patient we previously reported, harbored the EML4-ALK fusion gene. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

EML4-ALK-positive lung adenocarcinoma presenting an unusual metastatic pattern in a 29-year-old woman who is alive and well in her third year follow up:A case report.

PubMed

Tokat, Fatma; Zeren, Handan; Barut, Pinar; Tansan, Sualp; Ince, Umit

2017-01-01

Non-small cell lung cancer (NSCLC) is a frequent tumor entity with high mortality. Although several newly discovered chromosomal translocations and mutations opened new horizons for targeted therapy, literature still lacks large series of NSCLC with chromosomal abberations and their correlations with histological and clinical features. We present a case of echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) translocation positive adenocarcinoma of the lung with an unusual metastatic pattern in a 29-year-old young woman. Young adult non-smoker female patients with an unexplained pleural effusion and signs of metastatic disease should alert the physicians straight away for all types of malignancies including lung cancer. Any skin lesions should be evaluated carefully, biopsies should be done to exclude metastasis in urgency. On the other hand, an uncommon clinical presentation of a lung cancer requires corresponding molecular testing rapidly in order to offer the best treatment option.

EML4-ALK induces epithelial-mesenchymal transition consistent with cancer stem cell properties in H1299 non-small cell lung cancer cells.

PubMed

Guo, Fuchun; Liu, Xiaoke; Qing, Qin; Sang, Yaxiong; Feng, Chengjun; Li, Xiaoyu; Jiang, Li; Su, Pei; Wang, Yongsheng

2015-04-10

The echinoderm microtubule-associated protein-like 4(EML4)--anaplastic lymphoma kinase (ALK) fusion gene has been identified as a driver mutation in non-small-cell lung cancer (NSCLC). However, the role of EML4-ALK in malignant transformation is not entirely clear. Here, for the first time, we showed that H1299 NSCLC cells stably expressing EML4-ALK acquire EMT phenotype, associated with enhanced invasive migration and increased expression of EMT-inducing transcription factors. H1299-EML4-ALK cells also displayed cancer stem cell-like properties with a concomitant up-regulation of CD133 and enhanced ability of mammospheres formation. Moreover, we found that inhibition of ERK1/2 reversed EMT induced by EML4-ALK in H1299 cells. Taken together, these results suggested that EML4-ALK induced ERK activation is mechanistically associated with EMT phenotype. Thus, inhibition of ERK signaling pathway could be a potential strategy in treatment of NSCLC patients with EML4-ALK translocation. Copyright © 2015 Elsevier Inc. All rights reserved.

Lesions of Copper Toxicosis in Captive Marine Invertebrates With Comparisons to Normal Histology.

PubMed

LaDouceur, E E B; Wynne, J; Garner, M M; Nyaoke, A; Keel, M K

2016-05-01

Despite increasing concern for coral reef ecosystem health within the last decade, there is scant literature concerning the histopathology of diseases affecting the major constituents of coral reef ecosystems, particularly marine invertebrates. This study describes histologic findings in 6 species of marine invertebrates (California sea hare [Aplysia californica], purple sea urchin [Strongylocentrotus purpuratus], sunburst anemone [Anthopleura sola], knobby star [Pisaster giganteus], bat star [Asterina miniata], and brittle star [Ophiopteris papillosa]) with spontaneous copper toxicosis, 4 purple sea urchins with experimentally induced copper toxicosis, and 1 unexposed control of each species listed. The primary lesions in the California sea hare with copper toxicosis were branchial and nephridial necrosis. Affected echinoderms shared several histologic lesions, including epidermal necrosis and ulceration and increased numbers of coelomocytes within the water-vascular system. The sunburst anemone with copper toxicosis had necrosis of both epidermis and gastrodermis, as well as expulsion of zooxanthellae from the gastrodermis. In addition to the lesions attributed to copper toxicosis, our results describe normal microscopic features of these animals that may be useful for histopathologic assessment of marine invertebrates. © The Author(s) 2015.

Discovery of Brigatinib (AP26113), a Phosphine Oxide-Containing, Potent, Orally Active Inhibitor of Anaplastic Lymphoma Kinase.

PubMed

Huang, Wei-Sheng; Liu, Shuangying; Zou, Dong; Thomas, Mathew; Wang, Yihan; Zhou, Tianjun; Romero, Jan; Kohlmann, Anna; Li, Feng; Qi, Jiwei; Cai, Lisi; Dwight, Timothy A; Xu, Yongjin; Xu, Rongsong; Dodd, Rory; Toms, Angela; Parillon, Lois; Lu, Xiaohui; Anjum, Rana; Zhang, Sen; Wang, Frank; Keats, Jeffrey; Wardwell, Scott D; Ning, Yaoyu; Xu, Qihong; Moran, Lauren E; Mohemmad, Qurish K; Jang, Hyun Gyung; Clackson, Tim; Narasimhan, Narayana I; Rivera, Victor M; Zhu, Xiaotian; Dalgarno, David; Shakespeare, William C

2016-05-26

In the treatment of echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase positive (ALK+) non-small-cell lung cancer (NSCLC), secondary mutations within the ALK kinase domain have emerged as a major resistance mechanism to both first- and second-generation ALK inhibitors. This report describes the design and synthesis of a series of 2,4-diarylaminopyrimidine-based potent and selective ALK inhibitors culminating in identification of the investigational clinical candidate brigatinib. A unique structural feature of brigatinib is a phosphine oxide, an overlooked but novel hydrogen-bond acceptor that drives potency and selectivity in addition to favorable ADME properties. Brigatinib displayed low nanomolar IC50s against native ALK and all tested clinically relevant ALK mutants in both enzyme-based biochemical and cell-based viability assays and demonstrated efficacy in multiple ALK+ xenografts in mice, including Karpas-299 (anaplastic large-cell lymphomas [ALCL]) and H3122 (NSCLC). Brigatinib represents the most clinically advanced phosphine oxide-containing drug candidate to date and is currently being evaluated in a global phase 2 registration trial.

Spatial expression of Hox cluster genes in the ontogeny of a sea urchin

NASA Technical Reports Server (NTRS)

Arenas-Mena, C.; Cameron, A. R.; Davidson, E. H.

2000-01-01

The Hox cluster of the sea urchin Strongylocentrous purpuratus contains ten genes in a 500 kb span of the genome. Only two of these genes are expressed during embryogenesis, while all of eight genes tested are expressed during development of the adult body plan in the larval stage. We report the spatial expression during larval development of the five 'posterior' genes of the cluster: SpHox7, SpHox8, SpHox9/10, SpHox11/13a and SpHox11/13b. The five genes exhibit a dynamic, largely mesodermal program of expression. Only SpHox7 displays extensive expression within the pentameral rudiment itself. A spatially sequential and colinear arrangement of expression domains is found in the somatocoels, the paired posterior mesodermal structures that will become the adult perivisceral coeloms. No such sequential expression pattern is observed in endodermal, epidermal or neural tissues of either the larva or the presumptive juvenile sea urchin. The spatial expression patterns of the Hox genes illuminate the evolutionary process by which the pentameral echinoderm body plan emerged from a bilateral ancestor.

Assignment of polarization-dependent peaks in carbon K-edge spectra from biogenic and geologic aragonite.

PubMed

Zhou, Dong; Metzler, Rebecca A; Tyliszczak, Tolek; Guo, Jinghua; Abrecht, Mike; Coppersmith, Susan N; Gilbert, P U P A

2008-10-16

Many biominerals, including mollusk and echinoderm shells, avian eggshells, modern and fossil bacterial sediments, planktonic coccolithophores, and foraminifera, contain carbonates in the form of biogenic aragonite or calcite. Here we analyze biogenic and geologic aragonite using different kinds of surface- and bulk-sensitive X-ray absorption near-edge structure (XANES) spectroscopy at the carbon K-edge, as well as high-resolution scanning transmission X-ray microscopy (STXM). Besides the well-known main pi* and sigma* carbonate peaks, we observed and fully characterized four minor peaks, at energies between the main pi* and sigma* peaks. As expected, the main peaks are similar in geologic and biogenic aragonite, while the minor peaks differ in relative intensity. In this and previous work, the minor peaks appear to be the ones most affected in biomineralization processes, hence the interest in characterizing them. Peak assignment was achieved by correlation of polarization-dependent behavior of the minor peaks with that of the main pi* and sigma* peaks. The present characterization provides the background for future studies of aragonitic biominerals.

ELECTRIC IMPEDANCE OF HIPPONOË EGGS

PubMed Central

Cole, Kenneth S.

1935-01-01

Alternating current resistance and capacity measurements have been made from 1.08 103 to 2.32 106 cycles per second on suspensions of unfertilized, fertilized, and swollen unfertilized eggs of the echinoderm Hipponoë esculenta. A simple method has been developed for measuring the volume concentration of eggs in a suspension. The membrane of the unfertilized egg is practically non-conducting at low frequencies and shows a static capacity of 0.87 µf/cm.2 except perhaps at the highest frequencies. The equivalent specific resistance of the egg interior is 11 times that of sea water. The membrane of the fertilized egg is practically non-conducting at low frequencies and shows a static capacity 2.5 times that of the unfertilized egg except at the higher frequencies where another reactive element produces a marked effect. The internal resistance is apparently higher than that of the unfertilized egg. The static capacity per unit area of the membrane decreases as a linear function of the surface area when the eggs are swollen in dilute sea water. In 40 per cent sea water, the capacity falls to about 75 per cent of normal. PMID:19872897

Abrupt change in food environment induces cloning in plutei of Dendraster excentricus.

PubMed

McDonald, Kathryn A; Vaughn, Dawn

2010-08-01

Asexual reproduction, or cloning, of planktonic echinoderm larvae has been observed in the laboratory and in nature, but little is known about its ecology. Here we examine the effects of algal food density and of a change in food density on the incidence of cloning in larvae of the sand dollar Dendraster excentricus. Results indicate that a change in food concentration can induce cloning in plutei. Cultures transferred from a low to a high algal ration at the time when primary larvae were developing the third (posterodorsal) pair of larval arms showed decreased postoral arm length, unusual morphologies, and increased larval density in culture. These dense cultures of smaller plutei were produced within 48 h of the food pulse. The result is consistent with the occurrence of a burst of cloning, possibly through anterior autotomization. A second feeding experiment demonstrated that anterior autotomization does occur in 4- to 6-arm plutei. Rather than constituting a developmental rarity, cloning may happen early and often in D. excentricus cohorts when environmental conditions favor rapid growth.

The effect of TBT on the structure of a marine sediment comunity--a Boxcosm study.

PubMed

Dahllöf, I; Agrenius, S; Blanck, H; Hall, P; Magnusson, K; Molander, S

2001-08-01

The effect of tri-n-butyl tin (TBT) on an intact marine sediment community after five months exposure was investigated. Changes in the structure of macro- and meiofauna communities were determined, as well as the functional diversity of the microbial community using BIOLOG microplates for Gram negative bacteria. Development of tolerance in the microbial community was investigated using Pollution Induced Community Tolerance (PICT) experiments with fluxes of nutrients as effect indicators. TBT affected the structure and recruitment of the macro- and meiofauna at nominal additions of 30-137 micromol TBT/m2 sediment. Number of species, diversity, biomass and community similarity was reduced at these concentrations compared to control. Species that molt seemed to be the most tolerant since they were predominant in boxes that had received the highest TBT addition and echinoderms were the most sensitive species. Renewed addition of TBT in PICT experiments with sediment from each boxcosm showed that TBT had an effect on individual nutrient fluxes from all sediments. Analyses of the flux patterns revealed a memory of previous TBT exposure, either due to induced tolerance or other community conditioning.

Activated MET acts as a salvage signal after treatment with alectinib, a selective ALK inhibitor, in ALK-positive non-small cell lung cancer.

PubMed

Kogita, Akihiro; Togashi, Yosuke; Hayashi, Hidetoshi; Banno, Eri; Terashima, Masato; De Velasco, Marco A; Sakai, Kazuko; Fujita, Yoshihiko; Tomida, Shuta; Takeyama, Yoshifumi; Okuno, Kiyotaka; Nakagawa, Kazuhiko; Nishio, Kazuto

2015-03-01

Non-small cell lung cancer (NSCLC) carrying echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) rearrangements is hypersensitive to ALK inhibitors, including crizotinib and alectinib. Crizotinib was initially designed as a MET inhibitor, whereas alectinib is a selective ALK inhibitor. The MET signal, which is inhibited by crizotinib but not by alectinib, is dysregulated in many human cancers. However, the role of the MET signal in ALK-positive NSCLC remains unclear. In this study, we found that hepatocyte growth factor (HGF), ligand of MET, mediated the resistance to alectinib, but not to crizotinib, via the MET signal in ALK-positive NSCLC cell lines (H3122 and H2228 cell lines). In addition, alectinib activated the MET signal even in the absence of HGF and the inhibition of the MET signal enhanced the efficacy of alectinib. These findings suggest that activated MET acts as a salvage signal in ALK-positive NSCLC. This novel role of the MET signal in ALK-positive NSCLC may pave the way for further clinical trials examining MET inhibitors.

Dramatic response to alectinib in a patient of ALK-rearranged lung cancer with poor performance status.

PubMed

Tanaka, Hisashi; Taima, Kageaki; Morimoto, Takeshi; Nakamura, Kunihiko; Tanaka, Yoshihito; Itoga, Masamichi; Takanashi, Shingo; Okumura, Ken

2016-03-17

Lung cancers with anaplastic lymphoma kinase rearrangements are highly sensitive to anaplastic lymphoma kinase tyrosine kinase inhibition, underscoring the notion that such cancers are addicted to anaplastic lymphoma kinase activity. Several anaplastic lymphoma kinase inhibitors have been identified and are being evaluated in clinical trials. However patients with poor performance status (3 or 4) were not involved in these clinical trials, it has been unclear to use anaplastic lymphoma kinase-tyrosine kinase inhibitors for these patients. Here, we report an anaplastic lymphoma kinase-positive non small cell lung cancer patient with performance status 4, who was successfully treated with alectinib. We report on a 52-year-old patient diagnosed as non small cell lung cancer harboring echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase fusion gene. His performance status was 4 because of severe respiratory failure. We treated this patient with alectinib as the first line therapy. Dramatic response was obtained and his performance status improved from 4 to 1 without severe adverse events. Alectinib is a therapeutic option for the anaplastic lymphoma kinase positive patients with poor performance status.

IL17 factors are early regulators in the gut epithelium during inflammatory response to Vibrio in the sea urchin larva

PubMed Central

Buckley, Katherine M; Ho, Eric Chun Hei; Hibino, Taku; Schrankel, Catherine S; Schuh, Nicholas W; Wang, Guizhi; Rast, Jonathan P

2017-01-01

IL17 cytokines are central mediators of mammalian immunity. In vertebrates, these factors derive from diverse cellular sources. Sea urchins share a molecular heritage with chordates that includes the IL17 system. Here, we characterize the role of epithelial expression of IL17 in the larval gut-associated immune response. The purple sea urchin genome encodes 10 IL17 subfamilies (35 genes) and 2 IL17 receptors. Most of these subfamilies are conserved throughout echinoderms. Two IL17 subfamilies are sequentially strongly upregulated and attenuated in the gut epithelium in response to bacterial disturbance. IL17R1 signal perturbation results in reduced expression of several response genes including an IL17 subtype, indicating a potential feedback. A third IL17 subfamily is activated in adult immune cells indicating that expression in immune cells and epithelia is divided among families. The larva provides a tractable model to investigate the regulation and consequences of gut epithelial IL17 expression across the organism. DOI: http://dx.doi.org/10.7554/eLife.23481.001 PMID:28447937

Treating patients with ALK-positive non-small cell lung cancer: latest evidence and management strategy

PubMed Central

Liao, Bin-Chi; Shih, Jin-Yuan; Yang, James Chih-Hsin

2015-01-01

Rearrangements in anaplastic lymphoma kinase (ALK) gene and echinoderm microtubule-associated protein-like 4 (EML4) gene were first described in a small portion of patients with non-small cell lung cancer (NSCLC) in 2007. Fluorescence in situ hybridization is used as the diagnostic test for detecting an EML4–ALK rearrangement. Crizotinib, an ALK inhibitor, is effective in treating advanced ALK-positive NSCLC, and the US Food and Drug Administration approved it for treating ALK-positive NSCLC in 2011. Several mechanisms of acquired resistance to crizotinib have recently been reported. Second-generation ALK inhibitors were designed to overcome these resistance mechanisms. Two of them, ceritinib and alectinib, were approved in 2014 for advanced ALK-positive NSCLC in the US and Japan, respectively. Heat shock protein 90 (Hsp90) inhibitors also showed activity against ALK-positive NSCLC. Here we review the recent development of crizotinib, ceritinib, alectinib and other second-generation ALK inhibitors as well as Hsp90 inhibitors. We also discuss management strategies for advanced ALK-positive NSCLC. PMID:26327925

Evolution of the chordate body plan: New insights from phylogenetic analyses of deuterostome phyla

PubMed Central

Cameron, Chris B.; Garey, James R.; Swalla, Billie J.

2000-01-01

The deuterostome phyla include Echinodermata, Hemichordata, and Chordata. Chordata is composed of three subphyla, Vertebrata, Cephalochordata (Branchiostoma), and Urochordata (Tunicata). Careful analysis of a new 18S rDNA data set indicates that deuterostomes are composed of two major clades: chordates and echinoderms + hemichordates. This analysis strongly supports the monophyly of each of the four major deuterostome taxa: Vertebrata + Cephalochordata, Urochordata, Hemichordata, and Echinodermata. Hemichordates include two distinct classes, the enteropneust worms and the colonial pterobranchs. Most previous hypotheses of deuterostome origins have assumed that the morphology of extant colonial pterobranchs resembles the ancestral deuterostome. We present a molecular phylogenetic analysis of hemichordates that challenges this long-held view. We used 18S rRNA to infer evolutionary relationships of the hemichordate classes Pterobranchia and Enteropneusta. Our data show that pterobranchs may be derived within enteropneust worms rather than being a sister clade to the enteropneusts. The nesting of the pterobranchs within the enteropneusts dramatically alters our view of the evolution of the chordate body plan and suggests that the ancestral deuterostome more closely resembled a mobile worm-like enteropneust than a sessile colonial pterobranch. PMID:10781046

Anticancer and cancer preventive compounds from edible marine organisms.

PubMed

Correia-da-Silva, Marta; Sousa, Emília; Pinto, Madalena M M; Kijjoa, Anake

2017-10-01

A direct impact of food on health, which demonstrates that dietary habit is one of the most important determinants of chronic diseases such as cancers, has led to an increased interest of the consumers toward natural bioactive compounds as functional ingredients or nutraceuticals. Epidemiological studies revealed that the populations of many Asian countries with high consumption of fish and seafood have low prevalence of particular type of cancers such as lung, breast, colorectal and prostate cancers. This observation has led to extensive investigations of the benefits of compounds present in edible marine organisms such as fish, marine invertebrates (mollusks, echinoderms) and marine algae as cancer chemopreventive agents. Interestingly, many of these marine organisms not only constitute as seafood delicacy but also as ingredients used in folk medicine of some East and Southeast Asian countries. The results of the investigations on extracts and compounds from fish (cods, anchovy, eel and also fish protein hydrolysates), mollusks (mussel, oyster, clams and abalone), as well as from sea cucumbers on the in vivo/in vitro anticancer/antitumor activities can, in part, support the health benefits of these edible marine organisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Calcitic microlenses as part of the photoreceptor system in brittlestars

NASA Astrophysics Data System (ADS)

Aizenberg, Joanna; Tkachenko, Alexei; Weiner, Steve; Addadi, Lia; Hendler, Gordon

2001-08-01

Photosensitivity in most echinoderms has been attributed to `diffuse' dermal receptors. Here we report that certain single calcite crystals used by brittlestars for skeletal construction are also a component of specialized photosensory organs, conceivably with the function of a compound eye. The analysis of arm ossicles in Ophiocoma showed that in light-sensitive species, the periphery of the labyrinthic calcitic skeleton extends into a regular array of spherical microstructures that have a characteristic double-lens design. These structures are absent in light-indifferent species. Photolithographic experiments in which a photoresist film was illuminated through the lens array showed selective exposure of the photoresist under the lens centres. These results provide experimental evidence that the microlenses are optical elements that guide and focus the light inside the tissue. The estimated focal distance (4-7µm below the lenses) coincides with the location of nerve bundles-the presumed primary photoreceptors. The lens array is designed to minimize spherical aberration and birefringence and to detect light from a particular direction. The optical performance is further optimized by phototropic chromatophores that regulate the dose of illumination reaching the receptors. These structures represent an example of a multifunctional biomaterial that fulfills both mechanical and optical functions.

The emerging role of ALK inhibitors in the treatment of advanced non-small cell lung cancer.

PubMed

Galetta, Domenico; Rossi, Antonio; Pisconti, Salvatore; Colucci, Giuseppe

2012-04-01

Most NSCLC patients are diagnosed in the advanced stage of the disease. Recently, chemotherapeutic agents have reached a plateau of effectiveness. Increased understanding of cancer biology has revealed several potential therapeutic strategies that have led to marketing of new biologic agents. The echinoderm microtubule-associated protein like-4-anaplastic lymphoma kinase (EML4-ALK) fusion oncogene represents one of the newest molecular targets in NSCLC, identifying a subset of NSCLC patients characterized by distinct clinicopathological features. The available results concerning ALK inhibitors for the treatment of advanced NSCLC patients. An electronic search was used to retrieve the articles addressing this topic. In a pivotal Phase I clinical trial, crizotinib (PF-02341066), a small-molecule ALK inhibitor, demonstrated impressive antitumor activity in the majority of NSCLC patients with ALK fusions. Phase III randomized trials investigating crizotinib in this subgroup of patients are ongoing. If the results from these large international trials confirm the efficacy of crizotinib in the subset of patients, the next few years could see the treatment of advanced NSCLC patients with ALK fusions. Specific inhibitors would realize the so called personalized medicine in subsets of this disease.

Cell mediated immune response of the Mediterranean sea urchin Paracentrotus lividus after PAMPs stimulation.

PubMed

Romero, A; Novoa, B; Figueras, A

2016-09-01

The Mediterranean sea urchin (Paracentrotus lividus) is of great ecological and economic importance for the European aquaculture. Yet, most of the studies regarding echinoderm's immunological defense mechanisms reported so far have used the sea urchin Strongylocentrotus purpuratus as a model, and information on the immunological defense mechanisms of Paracentrotus lividus and other sea urchins, is scarce. To remedy this gap in information, in this study, flow cytometry was used to evaluate several cellular immune mechanisms, such as phagocytosis, cell cooperation, and ROS production in P. lividus coelomocytes after PAMP stimulation. Two cell populations were described. Of the two, the amoeboid-phagocytes were responsible for the phagocytosis and ROS production. Cooperation between amoeboid-phagocytes and non-adherent cells resulted in an increased phagocytic response. Stimulation with several PAMPs modified the phagocytic activity and the production of ROS. The premise that the coelomocytes were activated by the bacterial components was confirmed by the expression levels of two cell mediated immune genes: LPS-Induced TNF-alpha Factor (LITAF) and macrophage migration inhibitory factor (MIF). These results have helped us understand the cellular immune mechanisms in P. lividus and their modulation after PAMP stimulation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of theophylline on expression of the long cilia phenotype in sand dollar blastulae.

PubMed

Riederer-Henderson, M A

1988-04-01

Previously, increases in ciliary length have only been obtained through genetic mutation in Chlamydomonas or by incubation of swimming echinoderm blastulae in trypsin or elastase. We have found that the phenotypic switch from short to long cilia on sand dollar blastulae can also be effected by incubation in theophylline. Cilia detached from control blastulae have a mean length of 21 +/- 7 microns with 10% of the cilia being greater than 30 microns. Upon incubation in 10 mM theophylline additional long cilia appeared after 10 hours and by 24-32 hours 1/2-3/4 of the embryo was covered with long cilia. The percentage of long cilia increased to 65% with a mean length of 40.0 +/- 17.6 microns. Incubation in other methylxanthines, such as aminophylline, caffeine, or isobutylmethylxanthine, inhibited development but had no effect on ciliary length distribution. Dibutyryl cAMP, 8-bromoadenosine, and calcium ionophore also had no effect on ciliary length. Cyclic AMP levels were measured and showed only slight differences among controls and embryos incubated in trypsin, caffeine, or theophylline. These data suggest that theophylline may be altering ciliary length control through some mechanism other than elevations in cAMP.

The role of molecular pathology in non-small-cell lung carcinoma—now and in the future

PubMed Central

Brandao, G.D.A.; Brega, E.F.; Spatz, A.

2012-01-01

In recent years, better understanding of the molecular biology of non-small-cell lung carcinoma (nsclc) has led to a revolution in the work-up of these neoplasms. As a pathology diagnosis, “nsclc” without further attempt at subclassification is no longer accepted as a standard of care; separating squamous cell carcinoma from adenocarcinoma and large-cell carcinoma carries implications for prognosis and treatment decisions. Currently, detection of the presence in nsclc of mutations involving the epidermal growth factor receptor (EGFR) gene and fusion of the N-terminal portion of the protein encoded by EML4 (echinoderm microtubule-associated protein-like 4 gene) with the intracellular signaling portion of the receptor tyrosine kinase encoded by ALK (anaplastic lymphoma kinase gene)—that is, EML4–ALK—and variants has become routine in many centres because patients having tumours harbouring such alterations might benefit from tyrosine kinase inhibitors as part of their treatment regimen. The purpose of the present review is to highlight important aspects of the screening for molecular derangements in nsclc and to briefly discuss the emergence of possible future biomarkers. PMID:22787408

Meiofaunal deuterostomes from the basal Cambrian of Shaanxi (China).

PubMed

Han, Jian; Morris, Simon Conway; Ou, Qiang; Shu, Degan; Huang, Hai

2017-02-09

Deuterostomes include the group we belong to (vertebrates) as well as an array of disparate forms that include echinoderms, hemichordates and more problematic groups such as vetulicolians and vetulocystids. The Cambrian fossil record is well-populated with representative examples, but possible intermediates are controversial and the nature of the original deuterostome remains idealized. Here we report millimetric fossils, Saccorhytus coronarius nov. gen., nov. sp., from an Orsten-like Lagerstätte from the earliest Cambrian period of South China, which stratigraphically are amongst the earliest of deuterostomes. The bag-like body bears a prominent mouth and associated folds, and behind them up to four conical openings on either side of the body as well as possible sensory structures. An anus may have been absent, and correspondingly the lateral openings probably served to expel water and waste material. This new form has similarities to both the vetulicolians and vetulocystids and collectively these findings suggest that a key step in deuterostome evolution was the development of lateral openings that subsequently were co-opted as pharyngeal gills. Depending on its exact phylogenetic position, the meiofaunal habit of Saccorhytus may help to explain the major gap between divergence times seen in the fossil record and estimates based on molecular clocks.

Management of Resistance to Crizotinib in Anaplastic Lymphoma Kinase-Positive Non-Small-cell Lung Cancer.

PubMed

Matikas, Alexios; Kentepozidis, Nikolaos; Georgoulias, Vassilis; Kotsakis, Athanasios

2016-11-01

During the past decade, the recognition of an ever-expanding list of driver oncogenic mutations in non-small-cell lung cancer has resulted in rapid therapeutic advances. Since the first description of the echinoderm microtubule-associated protein-like 4 anaplastic lymphoma kinase (EML4-ALK) rearrangement in 4% of cases of non-small-cell lung cancer in 2007, a highly potent and selective ALK inhibitor, crizotinib, was developed and approved in record time. However, it soon became apparent that although the responses can be dramatic and durable and primary intrinsic resistance to crizotinib is uncommon, the emergence of secondary resistance is inevitable. Efforts to elucidate the specific mechanisms that confer acquired resistance to crizotinib are underway. These have led to the recognition of the role of secondary resistance mutations, of ALK amplification, and of activation of bypass signaling, all of which contribute to resistance to crizotinib. Moreover, the rapid preclinical and clinical development of multiple second-generation ALK inhibitors that exhibit significant clinical activity against crizotinib-resistant disease has provided multiple options to treating physicians, with the ultimate goal the delivery of tailored medicine. Copyright © 2016 Elsevier Inc. All rights reserved.

Variability in larval gut pH regulation defines sensitivity to ocean acidification in six species of the Ambulacraria superphylum.

PubMed

Hu, Marian; Tseng, Yung-Che; Su, Yi-Hsien; Lein, Etienne; Lee, Hae-Gyeong; Lee, Jay-Ron; Dupont, Sam; Stumpp, Meike

2017-10-11

The unusual rate and extent of environmental changes due to human activities may exceed the capacity of marine organisms to deal with this phenomenon. The identification of physiological systems that set the tolerance limits and their potential for phenotypic buffering in the most vulnerable ontogenetic stages become increasingly important to make large-scale projections. Here, we demonstrate that the differential sensitivity of non-calcifying Ambulacraria (echinoderms and hemichordates) larvae towards simulated ocean acidification is dictated by the physiology of their digestive systems. Gastric pH regulation upon experimental ocean acidification was compared in six species of the superphylum Ambulacraria. We observed a strong correlation between sensitivity to ocean acidification and the ability to regulate gut pH. Surprisingly, species with tightly regulated gastric pH were more sensitive to ocean acidification. This study provides evidence that strict maintenance of highly alkaline conditions in the larval gut of Ambulacraria early life stages may dictate their sensitivity to decreases in seawater pH. These findings highlight the importance of identifying and understanding pH regulatory systems in marine larval stages that may contribute to substantial energetic challenges under near-future ocean acidification scenarios. © 2017 The Author(s).

Association between EML4-ALK fusion gene and thymidylate synthase mRNA expression in non-small cell lung cancer tissues

PubMed Central

XU, CHUN-WEI; WANG, GANG; WANG, WU-LONG; GAO, WEN-BIN; HAN, CHUAN-JUN; GAO, JING-SHAN; ZHANG, LI-YING; LI, YANG; WANG, LIN; ZHANG, YU-PING; TIAN, YU-WANG; QI, DONG-DONG

2015-01-01

This study aimed to investigate the association of the mRNA expression of the echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) fusion gene with that of thymidylate synthase (TYMS) in non-small cell lung cancer (NSCLC) tissues. Quantitative polymerase chain reaction was used to detect the expression of EML4-ALK fusion gene and TYMS mRNA in 257 cases of NSCLC. The positive rate of EML4-ALK fusion gene was 4.28% in the NSCLC tissues (11/257), and was higher in nonsmokers than in smokers (P<0.05); TYMS mRNA expression was detected in 63.42% (163/257) of cases. An association of the EML4-ALK fusion gene with TYMS expression was detected; a low expression level of TYMS mRNA was observed more frequently when the EML4-ALK fusion gene was present than when it was not detected (P<0.05). In conclusion, patients positive for the EML4-ALK fusion gene in NSCLC tissues are likely to have a low expression level of TYMS, and may benefit from the first-line chemotherapy drug pemetrexed. PMID:26136951

Association between EML4-ALK fusion gene and thymidylate synthase mRNA expression in non-small cell lung cancer tissues.

PubMed

Xu, Chun-Wei; Wang, Gang; Wang, Wu-Long; Gao, Wen-Bin; Han, Chuan-Jun; Gao, Jing-Shan; Zhang, Li-Ying; Li, Yang; Wang, Lin; Zhang, Yu-Ping; Tian, Yu-Wang; Qi, Dong-Dong

2015-06-01

This study aimed to investigate the association of the mRNA expression of the echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) fusion gene with that of thymidylate synthase (TYMS) in non-small cell lung cancer (NSCLC) tissues. Quantitative polymerase chain reaction was used to detect the expression of EML4-ALK fusion gene and TYMS mRNA in 257 cases of NSCLC. The positive rate of EML4-ALK fusion gene was 4.28% in the NSCLC tissues (11/257), and was higher in nonsmokers than in smokers (P<0.05); TYMS mRNA expression was detected in 63.42% (163/257) of cases. An association of the EML4-ALK fusion gene with TYMS expression was detected; a low expression level of TYMS mRNA was observed more frequently when the EML4-ALK fusion gene was present than when it was not detected (P<0.05). In conclusion, patients positive for the EML4-ALK fusion gene in NSCLC tissues are likely to have a low expression level of TYMS, and may benefit from the first-line chemotherapy drug pemetrexed.

Reassessing the improbability of a muscular crinoid stem

PubMed Central

Gorzelak, Przemysław; Głuchowski, Edward; Salamon, Mariusz A.

2014-01-01

Muscular articulations in modern stalked crinoids are only present in the arms. Although it has been suggested that certain coiled-stemmed fossil taxa may have been functionally adapted to utilize muscles, evidence supporting this interpretation is lacking. Here, we use cathodoluminescence and SEM to reveal the skeletal microstructure of the enigmatic coiled-stemmed taxon Ammonicrinus (Flexibilia). Based on the well-established link between skeletal microstructure and the nature of infilling soft tissues in modern echinoderms, we reconstructed the palaeoanatomy of the Middle Devonian ammonicrinids. We show that their median columnals with elongated lateral columnal enclosure extensions (LCEE) have stereom microstructure unexpectedly resembling that in the crinoid muscular arm plates. In particular, large ligamentary facets, that are present on each side of a transverse ridge, are mainly comprised of fine galleried stereom that is indicative of the mutable collagenous tissues. In contrast, fine labyrinthic stereom, commonly associated with muscles, is situated in the periphery on each side of the surface of elongated LCEE. Our findings thus strongly suggest that the muscles may have also been present in the stem of ammonicrinids. These results reassess the previous hypotheses about evolution of muscles in crinoids and provide new insights into the mode of life of Ammonicrinus. PMID:25116414

Ocean acidification and its potential effects on marine ecosystems.

PubMed

Guinotte, John M; Fabry, Victoria J

2008-01-01

Ocean acidification is rapidly changing the carbonate system of the world oceans. Past mass extinction events have been linked to ocean acidification, and the current rate of change in seawater chemistry is unprecedented. Evidence suggests that these changes will have significant consequences for marine taxa, particularly those that build skeletons, shells, and tests of biogenic calcium carbonate. Potential changes in species distributions and abundances could propagate through multiple trophic levels of marine food webs, though research into the long-term ecosystem impacts of ocean acidification is in its infancy. This review attempts to provide a general synthesis of known and/or hypothesized biological and ecosystem responses to increasing ocean acidification. Marine taxa covered in this review include tropical reef-building corals, cold-water corals, crustose coralline algae, Halimeda, benthic mollusks, echinoderms, coccolithophores, foraminifera, pteropods, seagrasses, jellyfishes, and fishes. The risk of irreversible ecosystem changes due to ocean acidification should enlighten the ongoing CO(2) emissions debate and make it clear that the human dependence on fossil fuels must end quickly. Political will and significant large-scale investment in clean-energy technologies are essential if we are to avoid the most damaging effects of human-induced climate change, including ocean acidification.

Reassessing the improbability of a muscular crinoid stem

NASA Astrophysics Data System (ADS)

Gorzelak, Przemysław; Głuchowski, Edward; Salamon, Mariusz A.

2014-08-01

Muscular articulations in modern stalked crinoids are only present in the arms. Although it has been suggested that certain coiled-stemmed fossil taxa may have been functionally adapted to utilize muscles, evidence supporting this interpretation is lacking. Here, we use cathodoluminescence and SEM to reveal the skeletal microstructure of the enigmatic coiled-stemmed taxon Ammonicrinus (Flexibilia). Based on the well-established link between skeletal microstructure and the nature of infilling soft tissues in modern echinoderms, we reconstructed the palaeoanatomy of the Middle Devonian ammonicrinids. We show that their median columnals with elongated lateral columnal enclosure extensions (LCEE) have stereom microstructure unexpectedly resembling that in the crinoid muscular arm plates. In particular, large ligamentary facets, that are present on each side of a transverse ridge, are mainly comprised of fine galleried stereom that is indicative of the mutable collagenous tissues. In contrast, fine labyrinthic stereom, commonly associated with muscles, is situated in the periphery on each side of the surface of elongated LCEE. Our findings thus strongly suggest that the muscles may have also been present in the stem of ammonicrinids. These results reassess the previous hypotheses about evolution of muscles in crinoids and provide new insights into the mode of life of Ammonicrinus.

Quo Vadis Venomics? A Roadmap to Neglected Venomous Invertebrates

PubMed Central

von Reumont, Bjoern Marcus; Campbell, Lahcen I.; Jenner, Ronald A.

2014-01-01

Venomics research is being revolutionized by the increased use of sensitive -omics techniques to identify venom toxins and their transcripts in both well studied and neglected venomous taxa. The study of neglected venomous taxa is necessary both for understanding the full diversity of venom systems that have evolved in the animal kingdom, and to robustly answer fundamental questions about the biology and evolution of venoms without the distorting effect that can result from the current bias introduced by some heavily studied taxa. In this review we draw the outlines of a roadmap into the diversity of poorly studied and understood venomous and putatively venomous invertebrates, which together represent tens of thousands of unique venoms. The main groups we discuss are crustaceans, flies, centipedes, non-spider and non-scorpion arachnids, annelids, molluscs, platyhelminths, nemerteans, and echinoderms. We review what is known about the morphology of the venom systems in these groups, the composition of their venoms, and the bioactivities of the venoms to provide researchers with an entry into a large and scattered literature. We conclude with a short discussion of some important methodological aspects that have come to light with the recent use of new -omics techniques in the study of venoms. PMID:25533518

Characterization of Circular ssDNA Viruses within the Echinoderm Nanobiome

NASA Astrophysics Data System (ADS)

Jackson, E.; Bistolas, K. S.; Hewson, I.

2016-02-01

Viral metagenomics has revealed a great diversity and presence of circular single-stranded(ss) DNA viruses most similar to the viral family Circoviridae in various environments both ambient and host. These viruses are an emerging paradigm in viral discovery amongst aquatic invertebrates mainly from the sub-phlya Crustacea and to a lesser extent the phylum Echinodermata. This parasite-host relationship is furthered here with the discovery of circo-like viruses extracted from the tissue of members from the family Holothuroidea (sea cucumbers). Verification and presence of these viruses within the tissue of the host was confirmed through rigorous genome architecture screening and PCR amplification of the rep gene from unamplified viral DNA extracts. Phylogenetic analysis of the rep gene reveals high similarity to circular ssDNA viruses from environmental metagenomic surveys of marine habitats. The significance of these findings is changing the perception and understanding of circular ssDNA viruses by broadening the known host range and blurring certain defining characteristics established by their pathogenic counterparts. Aside from discover and characterization, the potential ecological impacts of ssDNA viruses upon their host remains relatively unknown and further investigations should aim to determine the pathology, route of infection, and ecological implications of viral infection.

The evolution of genes encoding for green fluorescent proteins: insights from cephalochordates (amphioxus)

NASA Astrophysics Data System (ADS)

Yue, Jia-Xing; Holland, Nicholas D.; Holland, Linda Z.; Deheyn, Dimitri D.

2016-06-01

Green Fluorescent Protein (GFP) was originally found in cnidarians, and later in copepods and cephalochordates (amphioxus) (Branchiostoma spp). Here, we looked for GFP-encoding genes in Asymmetron, an early-diverged cephalochordate lineage, and found two such genes closely related to some of the Branchiostoma GFPs. Dim fluorescence was found throughout the body in adults of Asymmetron lucayanum, and, as in Branchiostoma floridae, was especially intense in the ripe ovaries. Spectra of the fluorescence were similar between Asymmetron and Branchiostoma. Lineage-specific expansion of GFP-encoding genes in the genus Branchiostoma was observed, largely driven by tandem duplications. Despite such expansion, purifying selection has strongly shaped the evolution of GFP-encoding genes in cephalochordates, with apparent relaxation for highly duplicated clades. All cephalochordate GFP-encoding genes are quite different from those of copepods and cnidarians. Thus, the ancestral cephalochordates probably had GFP, but since GFP appears to be lacking in more early-diverged deuterostomes (echinoderms, hemichordates), it is uncertain whether the ancestral cephalochordates (i.e. the common ancestor of Asymmetron and Branchiostoma) acquired GFP by horizontal gene transfer (HGT) from copepods or cnidarians or inherited it from the common ancestor of copepods and deuterostomes, i.e. the ancestral bilaterians.

The role of the actin cytoskeleton in calcium signaling in starfish oocytes.

PubMed

Santella, Luigia; Puppo, Agostina; Chun, Jong Tai

2008-01-01

Ca2+ is the most universal second messenger in cells from the very first moment of fertilization. In all animal species, fertilized eggs exhibit massive mobilization of intracellular Ca2+ to orchestrate the initial events of development. Echinoderm eggs have been an excellent model system for studying fertilization and the cell cycle due to their large size and abundance. In preparation for fertilization, the cell cycle-arrested oocytes must undergo meiotic maturation. Studies of starfish oocytes have shown that Ca2+ signaling is intimately involved in this process. Our knowledge of the molecular mechanism of meiotic maturation and fertilization has expanded greatly in the past two decades due to the discovery of cell cycle-related kinases and Ca2+-mobilizing second messengers. However, the molecular details of their actions await elucidation of other cellular elements that assist in the creation and transduction of Ca2+ signals. In this regard, the actin cytoskeleton, the receptors for second messengers and the Ca2+-binding proteins also require more attention. This article reviews the physiological significance and the mechanism of intracellular Ca2+ mobilization in starfish oocytes during maturation and fertilization.

Brief Exposure to Turbulence Permanently Alters Development of Sand Dollar Larvae

NASA Astrophysics Data System (ADS)

Ferner, M. C.; Hodin, J.; Ng, G.; Lowe, C. J.; Gaylord, B.

2016-02-01

Fluid motion underlies interactions between animals and their environment through effects on locomotion, food capture, respiration, information transfer, and other processes. Recent studies of marine invertebrates indicate that metamorphosis and settlement can be altered when swimming larvae experience a change in turbulence intensity, possibly increasing the likelihood that larvae will settle in appropriate habitat. For example, brief exposure to levels of turbulence characteristic of wave-swept coasts causes echinoderm larvae to quickly transition from a non-responsive "pre-competent" stage into a "competent" stage, thereby allowing the larvae to respond to local cues and settle. However, responding to one's entry into the nearshore environment isn't enough, as many such species live as adults in a narrower range of highly specific benthic habitat that is even more rarely encountered. Here we provide an account for this apparent mismatch between larval responses to broadly distributed cues and their need for more specialized settlement locations: turbulence exposure seems to cause larval sand dollars (Dendraster excentricus) to permanently shift from pre-competence to competence. This observation suggests a scenario where turbulence can activate a temporally extensive search image in larvae over a broad habitat range, a seemingly adaptive feature for larvae entering dynamic coastal environments.

Snake oil and venoms for medical research

NASA Astrophysics Data System (ADS)

Wolpert, H. D.

2011-04-01

Some think that using derivatives of snake venom for medical purposes is the modern version of snake oil but they are seriously misjudging the research potentials of some of these toxins in medicines of the 2000's. Medical trials, using some of the compounds has proven their usefulness. Several venoms have shown the possibilities that could lead to anticoagulants, helpful in heart disease. The blood clotting protein from the taipan snake has been shown to rapidly stop excessive bleeding. The venom from the copperhead may hold an answer to breast cancer. The Malaysian pit viper shows promise in breaking blood clots. Cobra venom may hold keys to finding cures for Parkinson's disease and Alzheimer's. Rattlesnake proteins from certain species have produced blood pressure medicines. Besides snake venoms, venom from the South American dart frog, mollusks (i.e. Cone Shell Snail), lizards (i.e. Gila Monster & Komodo Dragon), some species of spiders and tarantulas, Cephalopods, mammals (i.e. Platypus & Shrews), fish (i.e. sting rays, stone fish, puffer fish, blue bottle fish & box jelly fish), intertidal marine animals (echinoderms)(i.e. Crown of Thorn Star Fish & Flower Urchin) and the Honeybee are being investigated for potential medical benefits.

Shallow-water reef ophiuroids (Echinodermata: Ophiuroidea) of Réunion (Mascarene Islands), with biogeographic considerations.

PubMed

Boissin, Emilie; Hoareau, Thierry B; Paulay, Gustav; Bruggemann, J Henrich

2016-04-06

Despite their importance in marine biodiversity, invertebrates are far less studied than vertebrates. Given the current global biodiversity crisis and insufficient taxonomic resources, sustained efforts need to be undertaken to assess species diversity, especially in the highly threatened 'biodiversity hotspots'. Réunion is a young volcanic island lying in the Mascarene Islands (south-western Indian Ocean, SWIO), a marine biodiversity hotspot. A substantial sampling effort was conducted around Réunion Island to document shallow water reef-associated ophiuroid (brittle-stars) diversity, a class recognised as the most diverse among echinoderms. A total of 33 species were documented, increasing the known species richness of the island by 56%. Findings include 15 new records for Réunion, 11 for the Mascarene Islands and 8 for the Indian Ocean. The most diverse family was Ophiocomidae, a family of large, abundant and conspicuous tropical species. Even in this well studied family, a new species was revealed by this survey. Morphological variants together with DNA sequence variations within several species revealed cryptic species. We compared our results with the known fauna of other Mascarene Islands and discuss biogeographic implications for the region.

Durophagous Predation by King Crabs on the Continental Slope off Antarctica

NASA Astrophysics Data System (ADS)

Smith, K.; Aronson, R. B.; Steffel, B. V.; McClintock, J. B.; Amsler, M.; Thatje, S.

2016-02-01

For perhaps tens of millions of years, marine communities in Antarctica have been essentially devoid of durophagous (shell-crushing) predators, which have been excluded by low temperatures. In their absence, the resident species have evolved in isolation and are slow-moving with limited defenses. Rapidly rising sea temperatures around Antarctica are now relaxing the cold-thermal barrier and appear to be allowing deep-water king crabs (Lithodidae) to move up the continental slope, into shallower water. Their potential to emerge on the continental shelf could drastically restructure the endemic communities that live there; in other areas of the world, lithodids are typically generalist predators of invertebrates. Their diet in Antarctic waters remains unknown and it has been speculated that they are opportunistic scavengers. We report the findings of a trapping study conducted in deep water off the western Antarctic Peninsula in 2015. Stomach contents were analyzed for 18 adult Paralomis birsteini trapped on the continental slope. P. birsteini feed primarily on invertebrates such as echinoderms, gastropods and polychaetes. By understanding the prey species targeted by slope-dwelling lithodids, we can begin to project the future impact of an expansion of king crabs onto the Antarctic continental shelf.

Evidence for a Saponin Biosynthesis Pathway in the Body Wall of the Commercially Significant Sea Cucumber Holothuria scabra.

PubMed

Mitu, Shahida Akter; Bose, Utpal; Suwansa-Ard, Saowaros; Turner, Luke H; Zhao, Min; Elizur, Abigail; Ogbourne, Steven M; Shaw, Paul Nicholas; Cummins, Scott F

2017-11-07

The sea cucumber (phylum Echinodermata) body wall is the first line of defense and is well known for its production of secondary metabolites; including vitamins and triterpenoid glycoside saponins that have important ecological functions and potential benefits to human health. The genes involved in the various biosynthetic pathways are unknown. To gain insight into these pathways in an echinoderm, we performed a comparative transcriptome analysis and functional annotation of the body wall and the radial nerve of the sea cucumber Holothuria scabra ; to define genes associated with body wall metabolic functioning and secondary metabolite biosynthesis. We show that genes related to signal transduction mechanisms were more highly represented in the H. scabra body wall, including genes encoding enzymes involved in energy production. Eight of the core triterpenoid biosynthesis enzymes were found, however, the identity of the saponin specific biosynthetic pathway enzymes remains unknown. We confirm the body wall release of at least three different triterpenoid saponins using solid phase extraction followed by ultra-high-pressure liquid chromatography-quadrupole time of flight-mass spectrometry. The resource we have established will help to guide future research to explore secondary metabolite biosynthesis in the sea cucumber.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saller, A.H.; Schlanger, S.O.

Two wells drilled along the margin of Enewetak Atoll penetrated approximately 1,000 m of upper eocene, Oligocene, and lower Miocene carbonates. STrontium isotope stratigraphy indicates relatively continuous deposition of carbonate from 40 Ma to 20 Ma. Depositional environments show a gradual basinward progradation of facies with slope carbonates passing upward into fore-reef, reef, back-reef, and lagoonal carbonates. Slope strata contain wackestones and packstones with submarine-cemented lithoclasts, coral, coralline algae fragments, benthic rotaline forams, planktonic forams, and echinoderm fragments. Fore-reef strata are dominantly packstones and boundstones containing large pieces of coral, abundant benthic forams, coralline algae fragments, stromatoporoids(.), and minor planktonicmore » forams. Reef and near-reef sediments include coralgal boundstones and grainstones with abundant benthic forams. Halimeda and miliolid forams are common in lagoonward parts of the back reef. Sponge borings, geopetal structures, and fractures are common in reef and fore-reef strata. Lagoonal strata are wackestones and packstones with common mollusks, coral, coralline algae, and benthic forams (rotaline and miliolid). Diagenesis has extensively altered strata near the atoll margin. Aragonite dissolution and calcite cements (radiaxial and cloudy prismatic are abundant in fore-reef, reef, and some back-reef strata). Petrographic and geochemical data indicate arogonite dissolution and calcite cementation in seawater at burial depths of 100 to 300 m. Dolomite occurs in slope and deeply buried reefal carbonates.« less

New Invertebrate Vectors of Okadaic Acid from the North Atlantic Waters--Portugal (Azores and Madeira) and Morocco.

PubMed

Silva, Marisa; Rodriguez, Inés; Barreiro, Aldo; Kaufmann, Manfred; Isabel Neto, Ana; Hassouani, Meryem; Sabour, Brahim; Alfonso, Amparo; Botana, Luis M; Vasconcelos, Vitor

2015-12-08

Okadaic acid and its analogues are potent phosphatase inhibitors that cause Diarrheic Shellfish Poisoning (DSP) through the ingestion of contaminated shellfish by humans. This group of toxins is transmitted worldwide but the number of poisoning incidents has declined over the last 20 years due to legislation and monitoring programs that were implemented for bivalves. In the summer of 2012 and 2013, we collected a total of 101 samples of 22 different species that were made up of benthic and subtidal organisms such echinoderms, crustaceans, bivalves and gastropods from Madeira, São Miguel Island (Azores archipelago) and the northwestern coast of Morocco. The samples were analyzed by UPLC-MS/MS. Our main objective was to detect new vectors for these biotoxins. We can report nine new vectors for these toxins in the North Atlantic: Astropecten aranciacus, Arbacia lixula, Echinaster sepositus, Holothuria sanctori, Ophidiaster ophidianus, Onchidella celtica, Aplysia depilans, Patella spp., and Stramonita haemostoma. Differences in toxin contents among the species were found. Even though low concentrations were detected, the levels of toxins that were present, especially in edible species, indicate the importance of these types of studies. Routine monitoring should be extended to comprise a wider number of vectors other than for bivalves of okadaic acid and its analogues.

Metallothionein Gene Family in the Sea Urchin Paracentrotus lividus: Gene Structure, Differential Expression and Phylogenetic Analysis

PubMed Central

Ragusa, Maria Antonietta; Nicosia, Aldo; Costa, Salvatore; Cuttitta, Angela; Gianguzza, Fabrizio

2017-01-01

Metallothioneins (MT) are small and cysteine-rich proteins that bind metal ions such as zinc, copper, cadmium, and nickel. In order to shed some light on MT gene structure and evolution, we cloned seven Paracentrotus lividus MT genes, comparing them to Echinodermata and Chordata genes. Moreover, we performed a phylogenetic analysis of 32 MTs from different classes of echinoderms and 13 MTs from the most ancient chordates, highlighting the relationships between them. Since MTs have multiple roles in the cells, we performed RT-qPCR and in situ hybridization experiments to understand better MT functions in sea urchin embryos. Results showed that the expression of MTs is regulated throughout development in a cell type-specific manner and in response to various metals. The MT7 transcript is expressed in all tissues, especially in the stomach and in the intestine of the larva, but it is less metal-responsive. In contrast, MT8 is ectodermic and rises only at relatively high metal doses. MT5 and MT6 expression is highly stimulated by metals in the mesenchyme cells. Our results suggest that the P. lividus MT family originated after the speciation events by gene duplications, evolving developmental and environmental sub-functionalization. PMID:28417916

Chordate evolution and the three-phylum system

PubMed Central

Satoh, Noriyuki; Rokhsar, Daniel; Nishikawa, Teruaki

2014-01-01

Traditional metazoan phylogeny classifies the Vertebrata as a subphylum of the phylum Chordata, together with two other subphyla, the Urochordata (Tunicata) and the Cephalochordata. The Chordata, together with the phyla Echinodermata and Hemichordata, comprise a major group, the Deuterostomia. Chordates invariably possess a notochord and a dorsal neural tube. Although the origin and evolution of chordates has been studied for more than a century, few authors have intimately discussed taxonomic ranking of the three chordate groups themselves. Accumulating evidence shows that echinoderms and hemichordates form a clade (the Ambulacraria), and that within the Chordata, cephalochordates diverged first, with tunicates and vertebrates forming a sister group. Chordates share tadpole-type larvae containing a notochord and hollow nerve cord, whereas ambulacrarians have dipleurula-type larvae containing a hydrocoel. We propose that an evolutionary occurrence of tadpole-type larvae is fundamental to understanding mechanisms of chordate origin. Protostomes have now been reclassified into two major taxa, the Ecdysozoa and Lophotrochozoa, whose developmental pathways are characterized by ecdysis and trochophore larvae, respectively. Consistent with this classification, the profound dipleurula versus tadpole larval differences merit a category higher than the phylum. Thus, it is recommended that the Ecdysozoa, Lophotrochozoa, Ambulacraria and Chordata be classified at the superphylum level, with the Chordata further subdivided into three phyla, on the basis of their distinctive characteristics. PMID:25232138

Comparative analysis of sediments from the coast of southern California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, J.W.; Tjeerdema, R.; Newman, J.

1995-12-31

Sediment samples were collected in the summer of 1994 along the coast of the Southern California Bight, from Point Conception to the boarder with Mexico. Agencies involved in the program included EPA (EMAP), NOAA (ORCA), the state of California (State Water Board, California Dept. of Fish and Game, the University of Calif., Santa Cruz), major municipal waste dischargers (cities of Los Angeles and San Diego, Los Angeles and Orange Counties), and their research organization, SCCWRP. The level of effort in certain regions (bays) was more intensive than on the open coast, since there was an attempt to find ``hot spots``.more » For some of these sites the sediments were analyzed for inorganic and organic contaminants, toxicity to amphipods and echinoderm larvae, and a biomarker (P450 reporter gene system; RGS). The findings from chemical and biological testing on sediments from Orange County to San Diego Bay will be presented to demonstrate the range of contamination and the responses of the test species. Further comparisons between the concentrations of key contaminants and biological measures of toxicity will describe the correlations found, and the likelihood of identifying hot spots with toxicological endpoints. A strong correlation was found for the relationship between PAHs in sediments and the induction of P450 in a screening test system (RGS).« less

Structural analysis of the starfish SALMFamide neuropeptides S1 and S2: the N-terminal region of S2 facilitates self-association.

PubMed

Otara, Claire B; Jones, Christopher E; Younan, Nadine D; Viles, John H; Elphick, Maurice R

2014-02-01

The neuropeptides S1 (GFNSALMFamide) and S2 (SGPYSFNSGLTFamide), which share sequence similarity, were discovered in the starfish Asterias rubens and are prototypical members of the SALMFamide family of neuropeptides in echinoderms. SALMFamide neuropeptides act as muscle relaxants and both S1 and S2 cause relaxation of cardiac stomach and tube foot preparations in vitro but S2 is an order of magnitude more potent than S1. Here we investigated a structural basis for this difference in potency using spectroscopic techniques. Circular dichroism spectroscopy showed that S1 does not have a defined structure in aqueous solution and this was supported by 2D nuclear magnetic resonance experiments. In contrast, we found that S2 has a well-defined conformation in aqueous solution. However, the conformation of S2 was concentration dependent, with increasing concentration inducing a transition from an unstructured to a structured conformation. Interestingly, this property of S2 was not observed in an N-terminally truncated analogue of S2 (short S2 or SS2; SFNSGLTFamide). Collectively, the data obtained indicate that the N-terminal region of S2 facilitates peptide self-association at high concentrations, which may have relevance to the biosynthesis and/or bioactivity of S2 in vivo. © 2013.

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

PubMed Central

Brozovic, Matija; Dantec, Christelle; Dardaillon, Justine; Dauga, Delphine; Faure, Emmanuel; Gineste, Mathieu; Louis, Alexandra; Naville, Magali; Nitta, Kazuhiro R; Piette, Jacques; Reeves, Wendy; Scornavacca, Céline; Simion, Paul; Vincentelli, Renaud; Bellec, Maelle; Aicha, Sameh Ben; Fagotto, Marie; Guéroult-Bellone, Marion; Haeussler, Maximilian; Jacox, Edwin; Lowe, Elijah K; Mendez, Mickael; Roberge, Alexis; Stolfi, Alberto; Yokomori, Rui; Cambillau, Christian; Christiaen, Lionel; Delsuc, Frédéric; Douzery, Emmanuel; Dumollard, Rémi; Kusakabe, Takehiro; Nakai, Kenta; Nishida, Hiroki; Satou, Yutaka; Swalla, Billie; Veeman, Michael; Volff, Jean-Nicolas

2018-01-01

Abstract ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates. PMID:29149270

Ichnofabrics of the Capdevila Formation (early Eocene) in the Los Palacios Basin (western Cuba): Paleoenvironmental and paleoecological implications

NASA Astrophysics Data System (ADS)

Villegas-Martín, Jorge; Netto, Renata Guimarães; Lavina, Ernesto Luis Correa; Rojas-Consuegra, Reinaldo

2014-12-01

The ichnofabrics present in the early Eocene siliciclastic deposits of the Capdevila Formation exposed in the Pinar del Rio area (Los Palacios Basin, western Cuba) are analyzed in this paper and their paleoecological and paleoenvironmental significance are discussed. Nine ichnofabrics were recognized in the dominantly sandy sedimentary succession: Ophiomorpha, Asterosoma, Thalassinoides, Palaeophycus, Scolicia, Bichordites-Thalassinoides, Rhizocorallium, Scolicia-Thalassinoides and rhizobioturbation. Diversity of ichnofauna is low and burrows made by detritus-feeding organisms in well oxygenated and stenohaline waters predominate. Suites of the Cruziana and Skolithos Ichnofacies lacking their archetypical characteristics were recognized, being impoverished in diversity and presenting dominance of echinoderm and decapods crustacean burrows as a response to the environmental stress caused by the high frequency of deposition. The ichnofabric distribution in the studied succession, its recurrence in the sandstone beds and the presence of a Glossifungites Ichnofacies suite with rhizobioturbation associated reflect a shoaling-upward event with subaerial exposure of the substrate. The integrated analysis of the ichnology and the sedimentary facies suggests deposition in a shallow slope frequently impacted by gravitational flows and high-energy events. The evidence of substrate exposure indicates the occurrence of a forced regression and suggests the existence of a sequence boundary at the top of the Capdevila Formation.

The Origin and Fate of Annulate Lamellae in Maturing Sand Dollar Eggs

PubMed Central

Merriam, R. W.

1959-01-01

Electron micrograph evidence is presented that the nuclear envelope of the mature ovum of Dendraster excentricus is implicated in a proliferation of what appear as nuclear envelope replicas in the cytoplasm. The proliferation is associated with intranuclear vesicles which apparently coalesce to form comparatively simple replicas of the nuclear envelope closely applied to the inside of the nuclear envelope. The envelope itself may become disorganized at the time when fully formed annulate lamellae appear on the cytoplasmic side and parallel with it. The concept of interconvertibility of general cytoplasmic vesicles with most of the membrane systems of the cytoplasm is presented. The structure of the annuli in the annulate lamellae is shown to include small spheres or vesicles of variable size embedded in a dense matrix. Dense particles which are about 150 A in diameter are often found closely associated with annulate lamellae in the cytoplasm. Similar structures in other echinoderm eggs are basophilic. In this species, unlike other published examples, the association apparently takes place in the cytoplasm only after the lamellae have separated from the nucleus. If 150 A particles are synthesized by annulate lamellae, as their close physical relationship suggests, then in this species at least the necessary synthetic mechanisms and specificity must reside in the structure of annulate lamellae. PMID:13630942

Inter- and intra-organ spatial distributions of sea star saponins by MALDI imaging.

PubMed

Demeyer, Marie; Wisztorski, Maxence; Decroo, Corentin; De Winter, Julien; Caulier, Guillaume; Hennebert, Elise; Eeckhaut, Igor; Fournier, Isabelle; Flammang, Patrick; Gerbaux, Pascal

2015-11-01

Saponins are secondary metabolites that are abundant and diversified in echinoderms. Mass spectrometry is increasingly used not only to identify saponin congeners within animal extracts but also to decipher the structure/biological activity relationships of these molecules by determining their inter-organ and inter-individual variability. The usual method requires extensive purification procedures to prepare saponin extracts compatible with mass spectrometry analysis. Here, we selected the sea star Asterias rubens as a model animal to prove that direct analysis of saponins can be performed on tissue sections. We also demonstrated that carboxymethyl cellulose can be used as an embedding medium to facilitate the cryosectioning procedure. Matrix-assisted laser desorption/ionization (MALDI) imaging was also revealed to afford interesting data on the distribution of saponin molecules within the tissues. We indeed highlight that saponins are located not only inside the body wall of the animals but also within the mucus layer that probably protects the animal against external aggressions. Graphical Abstract Saponins are the most abundant secondary metabolites in sea stars. They should therefore participate in important biological activities. Here, MALDI imaging is presented as a powerful method to determine the spatial distribution of saponins within the animal tissues. The inhomogeneity of the intra-organ saponin distribution is highlighted, paving the way for future elegant structure/activity relationship investigations.

Lipid, sterols and fatty acid composition of abyssal holothurians and ophiuroids from the North-East Pacific Ocean: food web implications.

PubMed

Drazen, Jeffrey C; Phleger, Charles F; Guest, Michaela A; Nichols, Peter D

2008-09-01

The lipid, fatty acid (FA), and sterol composition of two ophiuroids and four holothurians from the abyssal eastern North Pacific were analysed to assess their feeding habits and to ascertain their composition for use in a larger study to examine food web dynamics and trophic ecology. Holothurians were rich in phytosterols and algal derived FA such as docosahexaenoic acid and eicosapentaenoic suggesting tight trophic coupling to phytodetritus. Large proportions of stanols were found, probably a result of enteric bacteria but they may come from sterol metabolism in the holothurians themselves. Oneirophanta mutabilis was distinct with much higher levels of stanols and bacterially derived FA suggesting specific selection of bacteria rich detrital particles or the activity of enteric and integumental bacteria. The ophiuroids sterol and FA compositions differed greatly from the holothurians and reflected consumption of animal material in addition to phytodetritus. Large proportions of energy storage lipids suggested a sporadic food supply. Several unusual fatty acids were found in these abyssal echinoderms. Tetracosahexaenoic acid, 24:6omega3, in ophiuroids and 23:1 in holothurians may be good biomarkers for food web studies. We report the first occurrence of alphaOH 24:1 in holothurians with none detected in ophiuroids. Its function is presently unknown.

Long-Term Trends in Calcifying Plankton and pH in the North Sea

PubMed Central

Beare, Doug; McQuatters-Gollop, Abigail; van der Hammen, Tessa; Machiels, Marcel; Teoh, Shwu Jiau; Hall-Spencer, Jason M.

2013-01-01

Relationships between six calcifying plankton groups and pH are explored in a highly biologically productive and data-rich area of the central North Sea using time-series datasets. The long-term trends show that abundances of foraminiferans, coccolithophores, and echinoderm larvae have risen over the last few decades while the abundances of bivalves and pteropods have declined. Despite good coverage of pH data for the study area there is uncertainty over the quality of this historical dataset; pH appears to have been declining since the mid 1990s but there was no statistical connection between the abundance of the calcifying plankton and the pH trends. If there are any effects of pH on calcifying plankton in the North Sea they appear to be masked by the combined effects of other climatic (e.g. temperature), chemical (nutrient concentrations) and biotic (predation) drivers. Certain calcified plankton have proliferated in the central North Sea, and are tolerant of changes in pH that have occurred since the 1950s but bivalve larvae and pteropods have declined. An improved monitoring programme is required as ocean acidification may be occurring at a rate that will exceed the environmental niches of numerous planktonic taxa, testing their capacities for acclimation and genetic adaptation. PMID:23658686

Ecological effects of ocean acidification and habitat complexity on reef-associated macroinvertebrate communities.

PubMed

Fabricius, K E; De'ath, G; Noonan, S; Uthicke, S

2014-01-22

The ecological effects of ocean acidification (OA) from rising atmospheric carbon dioxide (CO2) on benthic marine communities are largely unknown. We investigated in situ the consequences of long-term exposure to high CO2 on coral-reef-associated macroinvertebrate communities around three shallow volcanic CO2 seeps in Papua New Guinea. The densities of many groups and the number of taxa (classes and phyla) of macroinvertebrates were significantly reduced at elevated CO2 (425-1100 µatm) compared with control sites. However, sensitivities of some groups, including decapod crustaceans, ascidians and several echinoderms, contrasted with predictions of their physiological CO2 tolerances derived from laboratory experiments. High CO2 reduced the availability of structurally complex corals that are essential refugia for many reef-associated macroinvertebrates. This loss of habitat complexity was also associated with losses in many macroinvertebrate groups, especially predation-prone mobile taxa, including crustaceans and crinoids. The transition from living to dead coral as substratum and habitat further altered macroinvertebrate communities, with far more taxa losing than gaining in numbers. Our study shows that indirect ecological effects of OA (reduced habitat complexity) will complement its direct physiological effects and together with the loss of coral cover through climate change will severely affect macroinvertebrate communities in coral reefs.

Ecological effects of ocean acidification and habitat complexity on reef-associated macroinvertebrate communities

PubMed Central

Fabricius, K. E.; De'ath, G.; Noonan, S.; Uthicke, S.

2014-01-01

The ecological effects of ocean acidification (OA) from rising atmospheric carbon dioxide (CO2) on benthic marine communities are largely unknown. We investigated in situ the consequences of long-term exposure to high CO2 on coral-reef-associated macroinvertebrate communities around three shallow volcanic CO2 seeps in Papua New Guinea. The densities of many groups and the number of taxa (classes and phyla) of macroinvertebrates were significantly reduced at elevated CO2 (425–1100 µatm) compared with control sites. However, sensitivities of some groups, including decapod crustaceans, ascidians and several echinoderms, contrasted with predictions of their physiological CO2 tolerances derived from laboratory experiments. High CO2 reduced the availability of structurally complex corals that are essential refugia for many reef-associated macroinvertebrates. This loss of habitat complexity was also associated with losses in many macroinvertebrate groups, especially predation-prone mobile taxa, including crustaceans and crinoids. The transition from living to dead coral as substratum and habitat further altered macroinvertebrate communities, with far more taxa losing than gaining in numbers. Our study shows that indirect ecological effects of OA (reduced habitat complexity) will complement its direct physiological effects and together with the loss of coral cover through climate change will severely affect macroinvertebrate communities in coral reefs. PMID:24307670

First glimpse into Lower Jurassic deep-sea biodiversity: in situ diversification and resilience against extinction

PubMed Central

Thuy, Ben; Kiel, Steffen; Dulai, Alfréd; Gale, Andy S.; Kroh, Andreas; Lord, Alan R.; Numberger-Thuy, Lea D.; Stöhr, Sabine; Wisshak, Max

2014-01-01

Owing to the assumed lack of deep-sea macrofossils older than the Late Cretaceous, very little is known about the geological history of deep-sea communities, and most inference-based hypotheses argue for repeated recolonizations of the deep sea from shelf habitats following major palaeoceanographic perturbations. We present a fossil deep-sea assemblage of echinoderms, gastropods, brachiopods and ostracods, from the Early Jurassic of the Glasenbach Gorge, Austria, which includes the oldest known representatives of a number of extant deep-sea groups, and thus implies that in situ diversification, in contrast to immigration from shelf habitats, played a much greater role in shaping modern deep-sea biodiversity than previously thought. A comparison with coeval shelf assemblages reveals that, at least in some of the analysed groups, significantly more extant families/superfamilies have endured in the deep sea since the Early Jurassic than in the shelf seas, which suggests that deep-sea biota are more resilient against extinction than shallow-water ones. In addition, a number of extant deep-sea families/superfamilies found in the Glasenbach assemblage lack post-Jurassic shelf occurrences, implying that if there was a complete extinction of the deep-sea fauna followed by replacement from the shelf, it must have happened before the Late Jurassic. PMID:24850917

Densovirus associated with sea-star wasting disease and mass mortality

USGS Publications Warehouse

Hewson, Ian; Button, Jason B.; Gudenkauf, Brent M.; Miner, Benjamin; Newton, Alisa L.; Gaydos, Joseph K.; Wynne, Janna; Groves, Cathy L.; Hendler, Gordon; Murray, Michael; Fradkin, Steven; Breitbart, Mya; Fahsbender, Elizabeth; Lafferty, Kevin D.; Kilpatrick, A. Marm; Miner, C. Melissa; Raimondi, Peter T.; Lahner, Lesanna L.; Friedman, Carolyn S.; Danielson, Stephen D.; Haulena, Martin; Marliave, Jeffrey; Burge, Colleen A.; Eisenlord, Morgan E.; Harvell, C. Drew

2015-01-01

Populations of at least 20 asteroid species on the Northeast Pacific Coast have recently experienced an extensive outbreak of sea-star (asteroid) wasting disease (SSWD). The disease leads to behavioral changes, lesions, loss of turgor, limb autotomy, and death characterized by rapid degradation (“melting”). Here, we present evidence from experimental challenge studies and field observations that link the mass mortalities to a densovirus (Parvoviridae). Virus-sized material (i.e., <0.2 μm) from symptomatic tissues that was inoculated into asymptomatic asteroids consistently resulted in SSWD signs whereas animals receiving heat-killed (i.e., control) virus-sized inoculum remained asymptomatic. Viral metagenomic investigations revealed the sea star-associated densovirus (SSaDV) as the most likely candidate virus associated with tissues from symptomatic asteroids. Quantification of SSaDV during transmission trials indicated that progression of SSWD paralleled increased SSaDV load. In field surveys, SSaDV loads were more abundant in symptomatic than in asymptomatic asteroids. SSaDV could be detected in plankton, sediments and in nonasteroid echinoderms, providing a possible mechanism for viral spread. SSaDV was detected in museum specimens of asteroids from 1942, suggesting that it has been present on the North American Pacific Coast for at least 72 y. SSaDV is therefore the most promising candidate disease agent responsible for asteroid mass mortality.

Blocking the PI3K pathway enhances the efficacy of ALK-targeted therapy in EML4-ALK-positive nonsmall-cell lung cancer.

PubMed

Yang, Lin; Li, Guangchao; Zhao, Likun; Pan, Fei; Qiang, Jiankun; Han, Siqi

2014-10-01

Targeted therapy based on ALK tyrosine kinase inhibitors (ALK-TKIs) has made significant achievements in individuals with EML4-ALK (echinoderm microtubule-associated protein-like 4 gene and the anaplastic lymphoma kinase gene) fusion positive nonsmall-cell lung cancer (NSCLC). However, a high fraction of patients receive inferior clinical response to such treatment in the initial therapy, and the exact mechanisms underlying this process need to be further investigated. In this study, we revealed a persistently activated PI3K/AKT signaling that mediates the drug ineffectiveness. We found that genetic or pharmacological inhibition of ALK markedly abrogated phosphorylated STAT3 and ERK, but it failed to suppress AKT activity or induce apoptosis, in EML4-ALK-positive H2228 cells. Furthermore, targeted RNA interference of PI3K pathway components restored sensitivity to TAE684 treatment at least partially due to increased apoptosis. Combined TAE684 with PI3K inhibitor synergistically inhibited the proliferation of EML4-ALK-positive cells in vitro and significantly suppressed the growth of H2228 xenografts in vivo, suggesting the potential clinical application of such combinatorial therapy regimens in patients with EML4-ALK positive lung cancer.

Analytical electron microscopy of biogenic and inorganic carbonates

NASA Technical Reports Server (NTRS)

Blake, David F.

1989-01-01

In the terrestrial sedimentary environment, the mineralogically predominant carbonates are calcite-type minerals (rhombohedral carbonates) and aragonite-type minerals (orthorhombic carbonates). Most common minerals precipitating either inorganically or biogenically are high magnesium calcite and aragonite. High magnesium calcite (with magnesium carbonate substituting for more than 7 mole percent of the calcium carbonate) is stable only at temperatures greater than 700 C or thereabouts, and aragonite is stable only at pressures exceeding several kilobars of confining pressure. Therefore, these carbonates are expected to undergo chemical stabilization in the diagenetic environment to ultimately form stable calcite and dolomite. Because of the strong organic control of carbonate deposition in organisms during biomineralization, the microchemistry and microstructure of invertebrate skeletal material is much different than that present in inorganic carbonate cements. The style of preservation of microstructural features in skeletal material is therefore often quite distinctive when compared to that of inorganic carbonate even though wholesale recrystallization of the sediment has taken place. Microstructural and microchemical comparisons are made between high magnesium calcite echinoderm skeletal material and modern inorganic high magnesium calcite inorganic cements, using analytical electron microscopy and related techniques. Similar comparisons are made between analogous materials which have undergone stabilization in the diagenetic environment. Similar analysis schemes may prove useful in distinguishing between biogenic and inorganic carbonates in returned Martian carbonate samples.

The elusive baseline of marine disease: Are diseases in ocean ecosystems increasing?

USGS Publications Warehouse

Ward, Jessica R.; Lafferty, Kevin D.

2004-01-01

Disease outbreaks alter the structure and function of marine ecosystems, directly affecting vertebrates (mammals, turtles, fish), invertebrates (corals, crustaceans, echinoderms), and plants (seagrasses). Previous studies suggest a recent increase in marine disease. However, lack of baseline data in most communities prevents a direct test of this hypothesis. We developed a proxy to evaluate a prediction of the increasing disease hypothesis: the proportion of scientific publications reporting disease increased in recent decades. This represents, to our knowledge, the first quantitative use of normalized trends in the literature to investigate an ecological hypothesis. We searched a literature database for reports of parasites and disease (hereafter “disease”) in nine marine taxonomic groups from 1970 to 2001. Reports, normalized for research effort, increased in turtles, corals, mammals, urchins, and molluscs. No significant trends were detected for seagrasses, decapods, or sharks/rays (though disease occurred in these groups). Counter to the prediction, disease reports decreased in fishes. Formulating effective resource management policy requires understanding the basis and timing of marine disease events. Why disease outbreaks increased in some groups but not in others should be a priority for future investigation. The increase in several groups lends urgency to understanding disease dynamics, particularly since few viable options currently exist to mitigate disease in the oceans.

New Invertebrate Vectors of Okadaic Acid from the North Atlantic Waters—Portugal (Azores and Madeira) and Morocco

PubMed Central

Silva, Marisa; Rodriguez, Inés; Barreiro, Aldo; Kaufmann, Manfred; Neto, Ana Isabel; Hassouani, Meryem; Sabour, Brahim; Alfonso, Amparo; Botana, Luis M.; Vasconcelos, Vitor

2015-01-01

Okadaic acid and its analogues are potent phosphatase inhibitors that cause Diarrheic Shellfish Poisoning (DSP) through the ingestion of contaminated shellfish by humans. This group of toxins is transmitted worldwide but the number of poisoning incidents has declined over the last 20 years due to legislation and monitoring programs that were implemented for bivalves. In the summer of 2012 and 2013, we collected a total of 101 samples of 22 different species that were made up of benthic and subtidal organisms such echinoderms, crustaceans, bivalves and gastropods from Madeira, São Miguel Island (Azores archipelago) and the northwestern coast of Morocco. The samples were analyzed by UPLC-MS/MS. Our main objective was to detect new vectors for these biotoxins. We can report nine new vectors for these toxins in the North Atlantic: Astropecten aranciacus, Arbacia lixula, Echinaster sepositus, Holothuria sanctori, Ophidiaster ophidianus, Onchidella celtica, Aplysia depilans, Patella spp., and Stramonita haemostoma. Differences in toxin contents among the species were found. Even though low concentrations were detected, the levels of toxins that were present, especially in edible species, indicate the importance of these types of studies. Routine monitoring should be extended to comprise a wider number of vectors other than for bivalves of okadaic acid and its analogues. PMID:26670254

Defining thresholds of sustainable impact on benthic communities in relation to fishing disturbance.

PubMed

Lambert, G I; Murray, L G; Hiddink, J G; Hinz, H; Lincoln, H; Hold, N; Cambiè, G; Kaiser, M J

2017-07-14

While the direct physical impact on seabed biota is well understood, no studies have defined thresholds to inform an ecosystem-based approach to managing fishing impacts. We addressed this knowledge gap using a large-scale experiment that created a controlled gradient of fishing intensity and assessed the immediate impacts and short-term recovery. We observed a mosaic of taxon-specific responses at various thresholds. The lowest threshold of significant lasting impact occurred between 1 and 3 times fished and elicited a decrease in abundance of 39 to 70% for some sessile epifaunal organisms (cnidarians, bryozoans). This contrasted with significant increases in abundance and/or biomass of scavenging species (epifaunal echinoderms, infaunal crustaceans) by two to four-fold in areas fished twice and more. In spite of these significant specific responses, the benthic community structure, biomass and abundance at the population level appeared resilient to fishing. Overall, natural temporal variation in community metrics exceeded the effects of fishing in this highly dynamic study site, suggesting that an acute level of disturbance (fished over six times) would match the level of natural variation. We discuss the implications of our findings for natural resources management with respect to context-specific human disturbance and provide guidance for best fishing practices.

Natural genomic amplification of cholinesterase genes in animals.

PubMed

Chatonnet, Arnaud; Lenfant, Nicolas; Marchot, Pascale; Selkirk, Murray E

2017-08-01

Tight control of the concentration of acetylcholine at cholinergic synapses requires precise regulation of the number and state of the acetylcholine receptors, and of the synthesis and degradation of the neurotransmitter. In particular, the cholinesterase activity has to be controlled exquisitely. In the genome of the first experimental models used (man, mouse, zebrafish and drosophila), there are only one or two genes coding for cholinesterases, whereas there are more genes for their closest relatives the carboxylesterases. Natural amplification of cholinesterase genes was first found to occur in some cancer cells and in insect species subjected to evolutionary pressure by insecticides. Analysis of the complete genome sequences of numerous representatives of the various metazoan phyla show that moderate amplification of cholinesterase genes is not uncommon in molluscs, echinoderms, hemichordates, prochordates or lepidosauria. Amplification of acetylcholinesterase genes is also a feature of parasitic nematodes or ticks. In these parasites, over-production of cholinesterase-like proteins in secreted products and the saliva are presumed to have effector roles related to host infection. These amplification events raise questions about the role of the amplified gene products, and the adaptation processes necessary to preserve efficient cholinergic transmission. This is an article for the special issue XVth International Symposium on Cholinergic Mechanisms. © 2017 International Society for Neurochemistry.

In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system

PubMed Central

Maddalo, Danilo; Manchado, Eusebio; Concepcion, Carla P.; Bonetti, Ciro; Vidigal, Joana A.; Han, Yoon-Chi; Ogrodowski, Paul; Crippa, Alessandra; Rekhtman, Natasha; de Stanchina, Elisa; Lowe, Scott W.; Ventura, Andrea

2014-01-01

Chromosomal rearrangements play a central role in the pathogenesis of human cancers and often result in the expression of therapeutically actionable gene fusions1. A recently discovered example is a fusion between the Echinoderm Microtubule-associated Protein-like 4 (EML4) and the Anaplastic Lymphoma Kinase (ALK) genes, generated by an inversion on the short arm of chromosome 2: inv(2)(p21p23). The EML4-ALK oncogene is detected in a subset of human non-small cell lung cancers (NSCLC)2 and is clinically relevant because it confers sensitivity to ALK inhibitors3. Despite their importance, modeling such genetic events in mice has proven challenging and requires complex manipulation of the germline. Here we describe an efficient method to induce specific chromosomal rearrangements in vivo using viral-mediated delivery of the CRISPR/Cas9 system to somatic cells of adult animals. We apply it to generate a mouse model of Eml4-Alk-driven lung cancer. The resulting tumors invariably harbor the Eml4-Alkinversion, express the Eml4-Alk fusion gene, display histo-pathologic and molecular features typical of ALK+ human NSCLCs, and respond to treatment with ALK-inhibitors. The general strategy described here substantially expands our ability to model human cancers in mice and potentially in other organisms. PMID:25337876

Evolution of the SOUL Heme-Binding Protein Superfamily Across Eukarya.

PubMed

Fortunato, Antonio Emidio; Sordino, Paolo; Andreakis, Nikos

2016-06-01

SOUL homologs constitute a heme-binding protein superfamily putatively involved in heme and tetrapyrrole metabolisms associated with a number of physiological processes. Despite their omnipresence across the tree of life and the biochemical characterization of many SOUL members, their functional role and the evolutionary events leading to such remarkable protein repertoire still remain cryptic. To explore SOUL evolution, we apply a computational phylogenetic approach, including a relevant number of SOUL homologs, to identify paralog forms and reconstruct their genealogy across the tree of life and within species. In animal lineages, multiple gene duplication or loss events and paralog functional specializations underlie SOUL evolution from the dawn of ancestral echinoderm and mollusc SOUL forms. In photosynthetic organisms, SOUL evolution is linked to the endosymbiosis events leading to plastid acquisition in eukaryotes. Derivative features, such as the F2L peptide and BH3 domain, evolved in vertebrates and provided innovative functionality to support immune response and apoptosis. The evolution of elements such as the N-terminal protein domain DUF2358, the His42 residue, or the tetrapyrrole heme-binding site is modern, and their functional implications still unresolved. This study represents the first in-depth analysis of SOUL protein evolution and provides novel insights in the understanding of their obscure physiological role.

Densovirus associated with sea-star wasting disease and mass mortality

PubMed Central

Hewson, Ian; Button, Jason B.; Gudenkauf, Brent M.; Miner, Benjamin; Newton, Alisa L.; Gaydos, Joseph K.; Wynne, Janna; Groves, Cathy L.; Hendler, Gordon; Murray, Michael; Fradkin, Steven; Breitbart, Mya; Fahsbender, Elizabeth; Lafferty, Kevin D.; Kilpatrick, A. Marm; Miner, C. Melissa; Raimondi, Peter; Lahner, Lesanna; Friedman, Carolyn S.; Daniels, Stephen; Haulena, Martin; Marliave, Jeffrey; Burge, Colleen A.; Eisenlord, Morgan E.; Harvell, C. Drew

2014-01-01

Populations of at least 20 asteroid species on the Northeast Pacific Coast have recently experienced an extensive outbreak of sea-star (asteroid) wasting disease (SSWD). The disease leads to behavioral changes, lesions, loss of turgor, limb autotomy, and death characterized by rapid degradation (“melting”). Here, we present evidence from experimental challenge studies and field observations that link the mass mortalities to a densovirus (Parvoviridae). Virus-sized material (i.e., <0.2 μm) from symptomatic tissues that was inoculated into asymptomatic asteroids consistently resulted in SSWD signs whereas animals receiving heat-killed (i.e., control) virus-sized inoculum remained asymptomatic. Viral metagenomic investigations revealed the sea star-associated densovirus (SSaDV) as the most likely candidate virus associated with tissues from symptomatic asteroids. Quantification of SSaDV during transmission trials indicated that progression of SSWD paralleled increased SSaDV load. In field surveys, SSaDV loads were more abundant in symptomatic than in asymptomatic asteroids. SSaDV could be detected in plankton, sediments and in nonasteroid echinoderms, providing a possible mechanism for viral spread. SSaDV was detected in museum specimens of asteroids from 1942, suggesting that it has been present on the North American Pacific Coast for at least 72 y. SSaDV is therefore the most promising candidate disease agent responsible for asteroid mass mortality. PMID:25404293

Densovirus associated with sea-star wasting disease and mass mortality.

PubMed

Hewson, Ian; Button, Jason B; Gudenkauf, Brent M; Miner, Benjamin; Newton, Alisa L; Gaydos, Joseph K; Wynne, Janna; Groves, Cathy L; Hendler, Gordon; Murray, Michael; Fradkin, Steven; Breitbart, Mya; Fahsbender, Elizabeth; Lafferty, Kevin D; Kilpatrick, A Marm; Miner, C Melissa; Raimondi, Peter; Lahner, Lesanna; Friedman, Carolyn S; Daniels, Stephen; Haulena, Martin; Marliave, Jeffrey; Burge, Colleen A; Eisenlord, Morgan E; Harvell, C Drew

2014-12-02

Populations of at least 20 asteroid species on the Northeast Pacific Coast have recently experienced an extensive outbreak of sea-star (asteroid) wasting disease (SSWD). The disease leads to behavioral changes, lesions, loss of turgor, limb autotomy, and death characterized by rapid degradation ("melting"). Here, we present evidence from experimental challenge studies and field observations that link the mass mortalities to a densovirus (Parvoviridae). Virus-sized material (i.e., <0.2 μm) from symptomatic tissues that was inoculated into asymptomatic asteroids consistently resulted in SSWD signs whereas animals receiving heat-killed (i.e., control) virus-sized inoculum remained asymptomatic. Viral metagenomic investigations revealed the sea star-associated densovirus (SSaDV) as the most likely candidate virus associated with tissues from symptomatic asteroids. Quantification of SSaDV during transmission trials indicated that progression of SSWD paralleled increased SSaDV load. In field surveys, SSaDV loads were more abundant in symptomatic than in asymptomatic asteroids. SSaDV could be detected in plankton, sediments and in nonasteroid echinoderms, providing a possible mechanism for viral spread. SSaDV was detected in museum specimens of asteroids from 1942, suggesting that it has been present on the North American Pacific Coast for at least 72 y. SSaDV is therefore the most promising candidate disease agent responsible for asteroid mass mortality.

Late Ordovician (post-Sardic) rifting branches in the North Gondwanan Montagne Noire and Mouthoumet massifs of southern France

NASA Astrophysics Data System (ADS)

Javier Álvaro, J.; Colmenar, Jorge; Monceret, Eric; Pouclet, André; Vizcaïno, Daniel

2016-06-01

Upper Ordovician-Lower Devonian rocks of the Cabrières klippes (southern Montagne Noire) and the Mouthoumet massif in southern France rest paraconformably or with angular discordance on Cambrian-Lower Ordovician strata. Neither Middle-Ordovician volcanism nor associated metamorphism is recorded, and the subsequent Middle-Ordovician stratigraphic gap is related to the Sardic phase. Upper Ordovician sedimentation started in the rifting branches of Cabrières and Mouthoumet with deposition of basaltic lava flows and lahar deposits (Roque de Bandies and Villerouge formations) of continental tholeiite signature (CT), indicative of continental fracturing. The infill of both rifting branches followed with the onset of (1) Katian (Ka1-Ka2) conglomerates and sandstones (Glauzy and Gascagne formations), which have yielded a new brachiopod assemblage representative of the Svobodaina havliceki Community; (2) Katian (Ka2-Ka4) limestones, marlstones, and shales with carbonate nodules, reflecting development of bryozoan-echinoderm meadows with elements of the Nicolella Community (Gabian and Montjoi formations); and (3) the Hirnantian Marmairane Formation in the Mouthoumet massif that has yielded a rich and diverse fossil association representative of the pandemic Hirnantia Fauna. The sealing of the subaerial palaeorelief generated during the Sardic phase is related to Silurian and Early Devonian transgressions leading to onlapping patterns and the record of high-angle discordances.

Alectinib-Induced Erythema Multiforme and Successful Rechallenge with Alectinib in a Patient with Anaplastic Lymphoma Kinase-Rearranged Lung Cancer.

PubMed

Kimura, Tatsuo; Sowa-Osako, Junko; Nakai, Toshiyuki; Ohyama, Ayako; Kawaguchi, Tomoya; Tsuruta, Daisuke; Ohsawa, Masahiko; Hirata, Kazuto

2016-01-01

Alectinib is an oral drug developed for the treatment of patients with fusion gene encoding echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase ( EML4-ALK )-rearranged non-small cell lung cancer (NSCLC). Here, we present the case of a patient treated with alectinib who developed a hypersensitivity reaction with successful rechallenge treatment. A 39-year-old woman who was a passive smoker was referred to Osaka City University Hospital for the evaluation of a skin event caused by treatment for NSCLC with the fusion gene EML4-ALK . The skin reaction was observed on the anterior chest, upper arms, and ear auricles on day 11 of treatment with oral alectinib. The skin event presented as widely distributed erythematous macules that were confluent, indicating a severe and life-threatening form. The skin lesions started to resolve after the initiation of treatment with 40 mg prednisolone. After regrowth of the tumor, she received a rechallenge program for alectinib for 2 weeks; thereafter, alectinib treatment was successfully reinitiated. To the best of our knowledge, we present the first case in which alectinib, which binds to the adenosine triphosphate site of EML4-ALK , induced erythema multiforme. Moreover, successful readministration of alectinib through our rechallenge program has not been reported so far.

[Benthic macrofauna associated to Thalassia testudinum in Bahía de Mochima, Sucre, Venezuela].

PubMed

Jiménez Prieto, M; Liñero-Arana, I; Blanco-Rambla, J P; Fermín, J

2000-12-01

Diversity and abundance of benthic macrofauna associated to Thalassia testudinum were studied at Ensenada de Reyes, Mochima Bay, in the northeastern coast of Venezuela. Samples were taken monthly in six stations, three at 1 m in depth and three at 6 m, between December 1992 and February 1994, using a quadrat of 0.25 m2 for collecting plants and sediment; each sample was washed with seawater through a 1 mm sieve. The specimens were fixed in 6% formaldehyde. A total of 1722 organisms (6 888 ind x m2) and 127 species of macroinvertebrates were collected. Mollusks dominated with 53 species, followed by polychaetes (40), crustaceans (18) and echinoderms (8). Remaining groups were represented by 1-2 species. The highest abundance was in October (214 specimens), and the lowest in December 1993 (79 specimens). Specific richness was between 47 species in October and 18 in May 1993. Mean species diversity was 2.79-1.36 bits/ind. There were differences (ANOVA p<0.01) in number of specimens at the two depths but not throughout the 15 month study period (p>0.05). There were more specimens and species at the lowest depth and in stations with higher Thalassia testudinum biomass.

Proteins and saccharides of the sea urchin organic matrix of mineralization: characterization and localization in the spine skeleton.

PubMed

Ameye, L; De Becker, G; Killian, C; Wilt, F; Kemps, R; Kuypers, S; Dubois, P

2001-04-01

Properties of the echinoderm skeleton are under biological control, which is exerted in part by the organic matrix embedded in the mineralized part of the skeleton. This organic matrix consists of proteins and glycoproteins whose carbohydrate component is specifically involved in the control mechanisms. The saccharide moiety of the organic matrix of the spines of the echinoid Paracentrotus lividus was characterized using enzyme-linked lectin assays (ELLAs). O-glycoproteins, different types of complex N-glycoproteins, and terminal sialic acids were detected. Sialic acids are known to interact with Ca ions and could play an important role in the mineralization process. Some of the carbohydrate components detected by ELLAs as well as two organic matrix proteins (SM30 and SM50) were localized within different subregions of the spine skeleton using field-emission scanning electron microscopy. The mappings show that some of these components are not homogeneously distributed in the different skeletal subregions. For example, some N-glycoproteins were preferentially located in the putative amorphous subregion of the skeleton, whereas some O-glycoproteins were localized in the subregion where skeletal growth is inhibited. These results suggest that the biological control exerted on the skeletal properties can be partly modulated by local differences in the organic matrix composition. Copyright 2001 Academic Press.

Changes in mitochondrial genetic codes as phylogenetic characters: Two examples from the flatworms

PubMed Central

Telford, Maximilian J.; Herniou, Elisabeth A.; Russell, Robert B.; Littlewood, D. Timothy J.

2000-01-01

Shared molecular genetic characteristics other than DNA and protein sequences can provide excellent sources of phylogenetic information, particularly if they are complex and rare and are consequently unlikely to have arisen by chance convergence. We have used two such characters, arising from changes in mitochondrial genetic code, to define a clade within the Platyhelminthes (flatworms), the Rhabditophora. We have sampled 10 distinct classes within the Rhabditophora and find that all have the codon AAA coding for the amino acid Asn rather than the usual Lys and AUA for Ile rather than the usual Met. We find no evidence to support claims that the codon UAA codes for Tyr in the Platyhelminthes rather than the standard stop codon. The Rhabditophora are a very diverse group comprising the majority of the free-living turbellarian taxa and the parasitic Neodermata. In contrast, three other classes of turbellarian flatworm, the Acoela, Nemertodermatida, and Catenulida, have the standard invertebrate assignments for these codons and so are convincingly excluded from the rhabditophoran clade. We have developed a rapid computerized method for analyzing genetic codes and demonstrate the wide phylogenetic distribution of the standard invertebrate code as well as confirming already known metazoan deviations from it (ascidian, vertebrate, echinoderm/hemichordate). PMID:11027335

Endocrine interactions between plants and animals: Implications of exogenous hormone sources for the evolution of hormone signaling.

PubMed

Miller, Ashley E M; Heyland, Andreas

2010-05-01

Hormones are central to animal physiology, metabolism and development. Details on signal transduction systems and regulation of hormone synthesis, activation and release have only been studied for a small number of animal groups, notably arthropods and chordates. However, a significant body of literature suggests that hormonal signaling systems are not restricted to these phyla. For example, work on several echinoderm species shows that exogenous thyroid hormones (THs) affect larval development and metamorphosis and our new data provide strong evidence for endogenous synthesis of THs in sea urchin larvae. In addition to these endogenous sources, these larvae obtain THs when they consume phytoplankton. Another example of an exogenously acquired hormone or their precursors is in insect and arthropod signaling. Sterols from plants are essential for the synthesis of ecdysteroids, a crucial group of insect morphogenic steroids. The availability of a hormone or hormone precursor from food has implications for understanding hormone function and the evolution of hormonal signaling in animals. For hormone function, it creates an important link between the environment and the regulation of internal homeostatic systems. For the evolution of hormonal signaling it helps us to better understand how complex endocrine mechanisms may have evolved. Copyright 2009 Elsevier Inc. All rights reserved.

Ecological adaptations and commensal evolution of the Polynoidae (Polychaeta) in the Southwest Indian Ocean Ridge: A phylogenetic approach

NASA Astrophysics Data System (ADS)

Serpetti, Natalia; Taylor, M. L.; Brennan, D.; Green, D. H.; Rogers, A. D.; Paterson, G. L. J.; Narayanaswamy, B. E.

2017-03-01

The polychaete family polynoid is very large and includes a high diversity of behaviours, including numerous examples of commensal species. The comparison between free-living and commensal behaviours and the evolution of the relationships between commensal species and their hosts are valuable case studies of ecological adaptations. Deep-sea species of Polynoidae were sampled at four seamounts in the Southwest Indian Ridge and twenty specimens from seven species were selected to be analysed. Among them, there were free-living species, living within the three-dimensional framework of cold-water coral reefs, on coral rubble and on mobile sediments, and commensal species, associated with octocorals, hydrocorals (stylasterids), antipatharians and echinoderms (holothurian and ophiuroids). We analysed two mitochondrial (COI, 16S) and two nuclear (18S, 28S) ribosomal genetic markers and their combined sequences were compared with other Genbank sequences to assess the taxonomic relationships within the species under study, and the potential role of hosts in speciation processes. Most basal species of the sub-family Polynoinae are obligate symbionts showing specific morphological adaptations. Obligate and facultative commensal species and free-living species have evolved a number of times, although, according to our results, the obligate coral commensal species appear to be monophyletic.

Understanding processes at the origin of species flocks with a focus on the marine Antarctic fauna.

PubMed

Chenuil, Anne; Saucède, Thomas; Hemery, Lenaïg G; Eléaume, Marc; Féral, Jean-Pierre; Améziane, Nadia; David, Bruno; Lecointre, Guillaume; Havermans, Charlotte

2018-02-01

Species flocks (SFs) fascinate evolutionary biologists who wonder whether such striking diversification can be driven by normal evolutionary processes. Multiple definitions of SFs have hindered the study of their origins. Previous studies identified a monophyletic taxon as a SF if it displays high speciosity in an area in which it is endemic (criterion 1), high ecological diversity among species (criterion 2), and if it dominates the habitat in terms of biomass (criterion 3); we used these criteria in our analyses. Our starting hypothesis is that normal evolutionary processes may provide a sufficient explanation for most SFs. We thus clearly separate each criterion and identify which biological (intrinsic) and environmental (extrinsic) traits are most favourable to their realization. The first part focuses on evolutionary processes. We highlight that some popular putative causes of SFs, such as key innovations or ecological speciation, are neither necessary nor sufficient to fulfill some or all of the three criteria. Initial differentiation mechanisms are diverse and difficult to identify a posteriori because a primary differentiation of one type (genetic, ecological or geographical) often promotes other types of differentiation. Furthermore, the criteria are not independent: positive feedbacks between speciosity and ecological diversity among species are expected whatever the initial cause of differentiation, and ecological diversity should enhance habitat dominance at the clade level. We then identify intrinsic and extrinsic factors that favour each criterion. Low dispersal emerges as a convincing driver of speciosity. Except for a genomic architecture favouring ecological speciation, for which assessment is difficult, high effective population sizes are the single intrinsic factor that directly enhances speciosity, ecological diversity and habitat dominance. No extrinsic factor appeared to enhance all criteria simultaneously but a combination of factors (insularity, fragmentation and environmental stability) may favour the three criteria, although the effect is indirect for habitat dominance. We then apply this analytical framework to Antarctic marine environments by analysing data from 18 speciose clades belonging to echinoderms (five unrelated clades), notothenioid fishes (five clades) and peracarid crustaceans (eight clades). Antarctic shelf environments and history appear favourable to endemicity and speciosity, but not to ecological specialization. Two main patterns are distinguished among taxa. (i) In echinoderms, many brooding, species-rich and endemic clades are reported, but without remarkable ecological diversity or habitat dominance. In these taxa, loss of the larval stage is probably a consequence of past Antarctic environmental factors, and brooding is suggested to be responsible for enhanced allopatric speciation (via dispersal limitation). (ii) In notothenioids and peracarids, many clades fulfill all three SF criteria. This could result from unusual features in fish and crustaceans: chromosome instability and key innovations (antifreeze proteins) in notothenioids, ecological opportunity in peracarids, and a genomic architecture favouring ecological speciation in both groups. Therefore, the data do not support our starting point that normal evolutionary factors or processes drive SFs because in these two groups uncommon intrinsic features or ecological opportunity provide the best explanation. The utility of the three-criterion SF concept is therefore questioned and guidelines are given for future studies. © 2017 Cambridge Philosophical Society.

New Insights into Mutable Collagenous Tissue: Correlations between the Microstructure and Mechanical State of a Sea-Urchin Ligament

PubMed Central

Ribeiro, Ana R.; Barbaglio, Alice; Benedetto, Cristiano D.; Ribeiro, Cristina C.; Wilkie, Iain C.; Carnevali, Maria D. C.; Barbosa, Mário A.

2011-01-01

The mutable collagenous tissue (MCT) of echinoderms has the ability to undergo rapid and reversible changes in passive mechanical properties that are initiated and modulated by the nervous system. Since the mechanism of MCT mutability is poorly understood, the aim of this work was to provide a detailed morphological analysis of a typical mutable collagenous structure in its different mechanical states. The model studied was the compass depressor ligament (CDL) of a sea urchin (Paracentrotus lividus), which was characterized in different functional states mimicking MCT mutability. Transmission electron microscopy, histochemistry, cryo-scanning electron microscopy, focused ion beam/scanning electron microscopy, and field emission gun-environmental scanning electron microscopy were used to visualize CDLs at the micro- and nano-scales. This investigation has revealed previously unreported differences in both extracellular and cellular constituents, expanding the current knowledge of the relationship between the organization of the CDL and its mechanical state. Scanning electron microscopies in particular provided a three-dimensional overview of CDL architecture at the micro- and nano-scales, and clarified the micro-organization of the ECM components that are involved in mutability. Further evidence that the juxtaligamental cells are the effectors of these changes in mechanical properties was provided by a correlation between their cytology and the tensile state of the CDLs. PMID:21935473

Sea urchin tube feet are photosensory organs that express a rhabdomeric-like opsin and PAX6

PubMed Central

Lesser, Michael P.; Carleton, Karen L.; Böttger, Stefanie A.; Barry, Thomas M.; Walker, Charles W.

2011-01-01

All echinoderms have unique hydraulic structures called tube feet, known for their roles in light sensitivity, respiration, chemoreception and locomotion. In the green sea urchin, the most distal portion of these tube feet contain five ossicles arranged as a light collector with its concave surface facing towards the ambient light. These ossicles are perforated and lined with pigment cells that express a PAX6 protein that is universally involved in the development of eyes and sensory organs in other bilaterians. Polymerase chain reaction (PCR)-based sequencing and real time quantitative PCR (qPCR) also demonstrate the presence and differential expression of a rhabdomeric-like opsin within these tube feet. Morphologically, nerves that could serve to transmit information to the test innervate the tube feet, and the differential expression of opsin transcripts in the tube feet is inversely, and significantly, related to the amount of light that tube feet are exposed to depending on their location on the test. The expression of these genes, the differential expression of opsin based on light exposure and the unique morphological features at the distal portion of the tube foot strongly support the hypothesis that in addition to previously identified functional roles of tube feet they are also photosensory organs that detect and respond to changes in the underwater light field. PMID:21450733

Chordate evolution and the three-phylum system.

PubMed

Satoh, Noriyuki; Rokhsar, Daniel; Nishikawa, Teruaki

2014-11-07

Traditional metazoan phylogeny classifies the Vertebrata as a subphylum of the phylum Chordata, together with two other subphyla, the Urochordata (Tunicata) and the Cephalochordata. The Chordata, together with the phyla Echinodermata and Hemichordata, comprise a major group, the Deuterostomia. Chordates invariably possess a notochord and a dorsal neural tube. Although the origin and evolution of chordates has been studied for more than a century, few authors have intimately discussed taxonomic ranking of the three chordate groups themselves. Accumulating evidence shows that echinoderms and hemichordates form a clade (the Ambulacraria), and that within the Chordata, cephalochordates diverged first, with tunicates and vertebrates forming a sister group. Chordates share tadpole-type larvae containing a notochord and hollow nerve cord, whereas ambulacrarians have dipleurula-type larvae containing a hydrocoel. We propose that an evolutionary occurrence of tadpole-type larvae is fundamental to understanding mechanisms of chordate origin. Protostomes have now been reclassified into two major taxa, the Ecdysozoa and Lophotrochozoa, whose developmental pathways are characterized by ecdysis and trochophore larvae, respectively. Consistent with this classification, the profound dipleurula versus tadpole larval differences merit a category higher than the phylum. Thus, it is recommended that the Ecdysozoa, Lophotrochozoa, Ambulacraria and Chordata be classified at the superphylum level, with the Chordata further subdivided into three phyla, on the basis of their distinctive characteristics. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Postembryonic Organogenesis of the Digestive Tube: Why Does It Occur in Worms and Sea Cucumbers but Fail in Humans?

PubMed Central

Mashanov, Vladimir S.; Zueva, Olga; García-Arrarás, José E.

2017-01-01

We provide an integrative view of mechanisms that enable regeneration of the digestive tube in various animal models, including vertebrates, tunicates, echinoderms, insects, and flatworms. Two main strategies of regeneration of the endodermal luminal (mucosal) epithelium have evolved in metazoans. One of them involves proliferation of resident epithelial cells, while the other relies on recruitment of cells from extramucosal sources. In any of these two scenarios, either pluri-/multipotent stem cells or specialized differentiated cells can be used as the starting material. Posttraumatic visceral regeneration shares some common mechanisms with normal embryonic development as well as with organ homeostatic maintenance, but there are signaling pathways and/or cellular pools that are specific to the regenerative phenomena. Comparative analysis of the literature suggests that mammals share with spontaneously regenerating animals many of the regeneration-related adaptations and are able to efficiently repair components of their digestive tube at the level of individual tissues, but fail to do so at the whole-organ scale. We review what might cause this failure in the context of the current state of knowledge about various regenerative models. If the latent capacity for regeneration persists […], then the restoration of its overt expression should be possible if the mechanisms of its inhibition could be discovered and eventually rendered ineffectualRichard Goss (1992) PMID:24512710

Sperm nuclear basic proteins of tunicates and the origin of protamines.

PubMed

Saperas, Núria; Ausió, Juan

2013-08-01

Sperm nuclear basic proteins (SNBPs) are the chromosomal proteins that are found associated with DNA in sperm nuclei at the end of spermiogenesis. These highly specialized proteins can be classified into three major types: histone type (H-type), protamine-like type (PL-type), and protamine type (P-type). A hypothesis from early studies on the characterization of SNBPs proposed a mechanism for the vertical evolution of these proteins that involved an H1 → PL → P transition. However, the processes and mechanisms involved in such a transition were not understood. In particular, it was not clear how a molecular transition from a lysine-rich protein precursor (H1 histone) to the arginine-rich protamines might have taken place. In deuterostomes, the presence of SNBPs of the H-type in echinoderms and of protamines in the higher phylogenetic groups of vertebrates had long been known. The initial work on the characterization of tunicate SNBPs attempted to define the types and range of SNBPs that characterize this phylogenetically intermediate group. It was found that tunicate SNBPs belong to the PL-type. In this work we discuss how the study of SNBPs in the tunicates has been key to providing support to the H1 → PL → P transition. Most significantly, it was in tunicates that a potential molecular mechanism to explain the lysine-to-arginine transition was first reported.

Endogenous thyroid hormone synthesis in facultative planktotrophic larvae of the sand dollar Clypeaster rosaceus: implications for the evolutionary loss of larval feeding.

PubMed

Heyland, Andreas; Reitzel, Adam M; Price, David A; Moroz, Leonid L

2006-01-01

Critical roles of hormones in metamorphic life history transitions are well documented in amphibians, lampreys, insects, and many plant species. Recent evidence suggests that thyroid hormones (TH) or TH-like compounds can regulate development to metamorphosis in echinoids (sea urchins, sand dollars, and their relatives). Moreover, previous research has provided evidence for endogenous hormone synthesis in both feeding and nonfeeding echinoderm larvae. However, the mechanisms for endogenous synthesis remain largely unknown. Here, we show that facultatively planktotrophic larvae (larvae that reach metamorphosis in the absence of food but have the ability to feed) from the subtropical sea biscuit Clypeaster rosaceus can synthesize thyroxine endogenously from incorporated iodine (I(125)). When treated with the goitrogen thiourea (a peroxidase inhibitor), iodine incorporation, thyroxine synthesis, and metamorphosis are all blocked in a dose-dependent manner. The inhibitory effect on metamorphosis can be rescued by administration of exogenous thyroxine. Finally, we demonstrate that thiourea induces morphological changes in feeding structures comparable to the phenotypic plastic response of larval structures to low food conditions, further supporting a signaling role of thyroxine in regulating larval morphogenesis and phenotypic plasticity. We conclude that upregulation of endogenous hormone synthesis might have been associated with the evolution of nonfeeding development, subsequently leading to morphological changes characteristic of nonfeeding development.

Endogenous thyroid hormone synthesis in facultative planktotrophic larvae of the sand dollar Clypeaster rosaceus: implications for the evolutionary loss of larval feeding

PubMed Central

Heyland, Andreas; Reitzel, Adam M.; Price, David A.; Moroz, Leonid L.

2014-01-01

SUMMARY Critical roles of hormones in metamorphic life history transitions are well documented in amphibians, lampreys, insects, and many plant species. Recent evidence suggests that thyroid hormones (TH) or TH-like compounds can regulate development to metamorphosis in echinoids (sea urchins, sand dollars, and their relatives). Moreover, previous research has provided evidence for endogenous hormone synthesis in both feeding and nonfeeding echinoderm larvae. However, the mechanisms for endogenous synthesis remain largely unknown. Here, we show that facultatively planktotrophic larvae (larvae that reach metamorphosis in the absence of food but have the ability to feed) from the subtropical sea biscuit Clypeaster rosaceus can synthesize thyroxine endogenously from incorporated iodine (I125). When treated with the goitrogen thiourea (a peroxidase inhibitor), iodine incorporation, thyroxine synthesis, and metamorphosis are all blocked in a dose-dependent manner. The inhibitory effect on metamorphosis can be rescued by administration of exogenous thyroxine. Finally, we demonstrate that thiourea induces morphological changes in feeding structures comparable to the phenotypic plastic response of larval structures to low food conditions, further supporting a signaling role of thyroxine in regulating larval morphogenesis and phenotypic plasticity. We conclude that upregulation of endogenous hormone synthesis might have been associated with the evolution of nonfeeding development, subsequently leading to morphological changes characteristic of nonfeeding development. PMID:17073939

Liquid biopsy for monitoring anaplastic lymphoma kinase inhibitors in non-small cell lung cancer: two cases compared.

PubMed

Manicone, Mariangela; Scaini, Maria Chiara; Rodriquenz, Maria Grazia; Facchinetti, Antonella; Tartarone, Alfredo; Aieta, Michele; Zamarchi, Rita; Rossi, Elisabetta

2017-10-01

Three to seven percent of non-small cell lung cancer (NSCLC) patients show anaplastic lymphoma kinase (ALK)-translocation and could be treated with ALK-inhibitors. However, under crizotinib, a first-generation ALK-inhibitor, patients develop drug resistance after a median of 12 months. To overcome crizotinib resistance, several next-generation ALK inhibitors have been developed. In NSCLC, liquid biopsy allowed important improvements in the detection of the epidermal growth factor receptor (EGFR) mutation. The ability of liquid biopsy to detect oncogenic gene/protein fusions is a newly investigated field, and is not routinely applied yet. We here present two NSCLC patients, both rearranged for echinoderm microtubule associated-protein like 4-anaplastic lymphoma kinase (EML4-ALK) and treated accordingly, who differed in the clinical outcome. We analyzed the predictive value of the liquid biopsy components, namely epithelial cellular adhesion molecule (EpCAM)+ circulating tumor cells (CTCs), EpCAM low/neg CTCs, EML4-ALK rearranged CTCs, and cell-free mRNA (cfmRNA), during ALK-inhibitors treatment. This analysis showed a potential association between the liquid biopsy biomarkers, patients' outcome and response to treatment, thus suggesting their combined use in the clinical practice, as proposed here. This approach would allow longitudinal monitoring and consequent identification of putative drug-resistance mechanisms, in the light of improving high-risk patient management.

Getting around when you're round: quantitative analysis of the locomotion of the blunt-spined brittle star, Ophiocoma echinata.

PubMed

Astley, Henry C

2012-06-01

Brittle stars (Ophiuroidea, Echinodermata) are pentaradially symmetrical echinoderms that use five multi-jointed limbs to locomote along the seafloor. Prior qualitative descriptions have claimed coordinated movements of the limbs in a manner similar to tetrapod vertebrates, but this has not been evaluated quantitatively. It is uncertain whether the ring-shaped nervous system, which lacks an anatomically defined anterior, is capable of generating rhythmic coordinated movements of multiple limbs. This study tested whether brittle stars possess distinct locomotor modes with strong inter-limb coordination as seen in limbed animals in other phyla (e.g. tetrapods and arthropods), or instead move each limb independently according to local sensory feedback. Limb tips and the body disk were digitized for 56 cycles from 13 individuals moving across sand. Despite their pentaradial anatomy, all individuals were functionally bilateral, moving along the axis of a central limb via synchronous motions of contralateral limbs (±~13% phase lag). Two locomotor modes were observed, distinguishable mainly by whether the central limb was directed forwards or backwards. Turning was accomplished without rotation of the body disk by defining a different limb as the center limb and shifting other limb identities correspondingly, and then continuing locomotion in the direction of the newly defined anterior. These observations support the hypothesis that, in spite of their radial body plan, brittle stars employ coordinated, bilaterally symmetrical locomotion.

A novel EML4-ALK variant: exon 6 of EML4 fused to exon 19 of ALK.

PubMed

Penzel, Roland; Schirmacher, Peter; Warth, Arne

2012-07-01

Cytotoxic chemotherapy remains the mainstay of treatment for most patients with advanced disease. Recently, anaplastic lymphoma kinase (ALK) expression as a major target for successful treatment with ALK inhibitors was detected in a subset of non-small-cell lung carcinomas, usually as a result of echinoderm microtubule-associated protein-like 4 (EML4)-ALK rearrangements. Although the chromosomal breakpoint within the EML4 gene varied, the breakpoint within ALK was most frequently reported within intron 19 or rarely in exon 20. Therefore, the different EML4-ALK variants so far contain the same 3' portion of ALK starting with exon 20. Here, we report a novel EML4-ALK variant detected by reverse transcription polymerase chain reaction analysis. Subsequent sequencing revealed an EML4-ALK fusion variant in which exon 6 of EML4 was fused to exon 19 of ALK. It occurred in a predominant solid pulmonary adenocarcinoma of a 65-year-old woman with a clear split signal of ALK in fluorescence in situ hybridization analysis and a weakly homogeneous ALK expression in immunohistochemical staining. Because of the growing number of fusion variants a primary reverse transcription polymerase chain reaction-based screening for ALK-positive non-small-cell lung carcinoma patients may not be sufficient for predictive diagnostics but transcript-based approaches and sequencing of ALK fusion variants might finally contribute to an optimized selection of patients.

The other ocean acidification problem: CO2 as a resource among competitors for ecosystem dominance

PubMed Central

Connell, Sean D.; Kroeker, Kristy J.; Fabricius, Katharina E.; Kline, David I.; Russell, Bayden D.

2013-01-01

Predictions concerning the consequences of the oceanic uptake of increasing atmospheric carbon dioxide (CO2) have been primarily occupied with the effects of ocean acidification on calcifying organisms, particularly those critical to the formation of habitats (e.g. coral reefs) or their maintenance (e.g. grazing echinoderms). This focus overlooks direct and indirect effects of CO2 on non-calcareous taxa that play critical roles in ecosystem shifts (e.g. competitors). We present the model that future atmospheric [CO2] may act as a resource for mat-forming algae, a diverse and widespread group known to reduce the resilience of kelp forests and coral reefs. We test this hypothesis by combining laboratory and field CO2 experiments and data from ‘natural’ volcanic CO2 vents. We show that mats have enhanced productivity in experiments and more expansive covers in situ under projected near-future CO2 conditions both in temperate and tropical conditions. The benefits of CO2 are likely to vary among species of producers, potentially leading to shifts in species dominance in a high CO2 world. We explore how ocean acidification combines with other environmental changes across a number of scales, and raise awareness of CO2 as a resource whose change in availability could have wide-ranging community consequences beyond its direct effects. PMID:23980244

Characterization of Spindle Checkpoint Kinase Mps1 Reveals Domain with Functional and Structural Similarities to Tetratricopeptide Repeat Motifs of Bub1 and BubR1 Checkpoint Kinases*

PubMed Central

Lee, Semin; Thebault, Philippe; Freschi, Luca; Beaufils, Sylvie; Blundell, Tom L.; Landry, Christian R.; Bolanos-Garcia, Victor M.; Elowe, Sabine

2012-01-01

Kinetochore targeting of the mitotic kinases Bub1, BubR1, and Mps1 has been implicated in efficient execution of their functions in the spindle checkpoint, the self-monitoring system of the eukaryotic cell cycle that ensures chromosome segregation occurs with high fidelity. In all three kinases, kinetochore docking is mediated by the N-terminal region of the protein. Deletions within this region result in checkpoint failure and chromosome segregation defects. Here, we use an interdisciplinary approach that includes biophysical, biochemical, cell biological, and bioinformatics methods to study the N-terminal region of human Mps1. We report the identification of a tandem repeat of the tetratricopeptide repeat (TPR) motif in the N-terminal kinetochore binding region of Mps1, with close homology to the tandem TPR motif of Bub1 and BubR1. Phylogenetic analysis indicates that TPR Mps1 was acquired after the split between deutorostomes and protostomes, as it is distinguishable in chordates and echinoderms. Overexpression of TPR Mps1 resulted in decreased efficiency of both chromosome alignment and mitotic arrest, likely through displacement of endogenous Mps1 from the kinetochore and decreased Mps1 catalytic activity. Taken together, our multidisciplinary strategy provides new insights into the evolution, structural organization, and function of Mps1 N-terminal region. PMID:22187426

Characterization of spindle checkpoint kinase Mps1 reveals domain with functional and structural similarities to tetratricopeptide repeat motifs of Bub1 and BubR1 checkpoint kinases.

PubMed

Lee, Semin; Thebault, Philippe; Freschi, Luca; Beaufils, Sylvie; Blundell, Tom L; Landry, Christian R; Bolanos-Garcia, Victor M; Elowe, Sabine

2012-02-17

Kinetochore targeting of the mitotic kinases Bub1, BubR1, and Mps1 has been implicated in efficient execution of their functions in the spindle checkpoint, the self-monitoring system of the eukaryotic cell cycle that ensures chromosome segregation occurs with high fidelity. In all three kinases, kinetochore docking is mediated by the N-terminal region of the protein. Deletions within this region result in checkpoint failure and chromosome segregation defects. Here, we use an interdisciplinary approach that includes biophysical, biochemical, cell biological, and bioinformatics methods to study the N-terminal region of human Mps1. We report the identification of a tandem repeat of the tetratricopeptide repeat (TPR) motif in the N-terminal kinetochore binding region of Mps1, with close homology to the tandem TPR motif of Bub1 and BubR1. Phylogenetic analysis indicates that TPR Mps1 was acquired after the split between deutorostomes and protostomes, as it is distinguishable in chordates and echinoderms. Overexpression of TPR Mps1 resulted in decreased efficiency of both chromosome alignment and mitotic arrest, likely through displacement of endogenous Mps1 from the kinetochore and decreased Mps1 catalytic activity. Taken together, our multidisciplinary strategy provides new insights into the evolution, structural organization, and function of Mps1 N-terminal region.

Unusual organic osmolytes in deep-sea animals: adaptations to hydrostatic pressure and other perturbants.

PubMed

Yancey, Paul H; Blake, Wendy R; Conley, James

2002-11-01

Shallow-living marine invertebrates use free amino acids as cellular osmolytes, while most teleosts use almost no organic osmolytes. Recently we found unusual osmolyte compositions in deep-sea animals. Trimethylamine N-oxide (TMAO) increases with depth in muscles of some teleosts, skates, and crustaceans (up to 300 mmol/kg at 2900 m). Other deep-sea animals had high levels of (1). scyllo-inositol in echinoderms, gastropods, and polychaetes, (2). that polyol plus beta-alanine and betaine in octopods, (3). hypotaurine, N-methyltaurine, and unidentified methylamines in vestimentiferans from hydrothermal vents and cold seeps, and (4). a depth-correlated serine-phosphate osmolyte in vesicomyid clams from trench seeps. We hypothesize that some of these solutes counteract effects of hydrostatic pressure. With lactate dehydrogenase, actin, and pyruvate kinase, 250 mM TMAO (but not glycine) protected both ligand binding and protein stability against pressure. To test TMAO in living cells, we grew yeast under pressure. After 1 h at 71 MPa, 3.5 h at 71 MPa, and 17 h at 30 MPa, 150 mM TMAO generally doubled the number of cells that formed colonies. Sulfur-based osmolytes which are not correlated with depth, such as hypotaurine and thiotaurine, are probably involved in sulfide metabolism and detoxification. Thus deep-sea osmolytes may have at least two other roles beyond acting as simple compatible osmotica.

Stratigraphy and facies development of the marine Late Devonian near the Boulongour Reservoir, northwest Xinjiang, China

NASA Astrophysics Data System (ADS)

Suttner, Thomas J.; Kido, Erika; Chen, Xiuqin; Mawson, Ruth; Waters, Johnny A.; Frýda, Jiří; Mathieson, David; Molloy, Peter D.; Pickett, John; Webster, Gary D.; Frýdová, Barbora

2014-02-01

Late Devonian to Early Carboniferous stratigraphic units within the 'Zhulumute' Formation, Hongguleleng Formation (stratotype), 'Hebukehe' Formation and the Heishantou Formation near the Boulongour Reservoir in northwestern Xinjiang are fossil-rich. The Hongguleleng and 'Hebukehe' formations are biostratigraphically well constrained by microfossils from the latest Frasnian linguiformis to mid-Famennian trachytera conodont biozones. The Hongguleleng Formation (96.8 m) is characterized by bioclastic argillaceous limestones and marls (the dominant facies) intercalated with green spiculitic calcareous shales. It yields abundant and highly diverse faunas of bryozoans, brachiopods and crinoids with subordinate solitary rugose corals, ostracods, trilobites, conodonts and other fish teeth. The succeeding 'Hebukehe' Formation (95.7 m) consists of siltstones, mudstones, arenites and intervals of bioclastic limestone (e.g. 'Blastoid Hill') and cherts with radiolarians. A diverse ichnofauna, phacopid trilobites, echinoderms (crinoids and blastoids) together with brachiopods, ostracods, bryozoans and rare cephalopods have been collected from this interval. Analysis of geochemical data, microfacies and especially the distribution of marine organisms, which are not described in detail here, but used for facies analysis, indicate a deepening of the depositional environment at the Boulongour Reservoir section. Results presented here concern mainly the sedimentological and stratigraphical context of the investigated section. Additionally, one Late Devonian palaeo-oceanic and biotic event, the Upper Kellwasser Event is recognized near the section base.

The evolution of mollusc shells.

PubMed

McDougall, Carmel; Degnan, Bernard M

2018-05-01

Molluscan shells are externally fabricated by specialized epithelial cells on the dorsal mantle. Although a conserved set of regulatory genes appears to underlie specification of mantle progenitor cells, the genes that contribute to the formation of the mature shell are incredibly diverse. Recent comparative analyses of mantle transcriptomes and shell proteomes of gastropods and bivalves are consistent with shell diversity being underpinned by a rapidly evolving mantle secretome (suite of genes expressed in the mantle that encode secreted proteins) that is the product of (a) high rates of gene co-option into and loss from the mantle gene regulatory network, and (b) the rapid evolution of coding sequences, particular those encoding repetitive low complexity domains. Outside a few conserved genes, such as carbonic anhydrase, a so-called "biomineralization toolkit" has yet to be discovered. Despite this, a common suite of protein domains, which are often associated with the extracellular matrix and immunity, appear to have been independently and often uniquely co-opted into the mantle secretomes of different species. The evolvability of the mantle secretome provides a molecular explanation for the evolution and diversity of molluscan shells. These genomic processes are likely to underlie the evolution of other animal biominerals, including coral and echinoderm skeletons. This article is categorized under: Comparative Development and Evolution > Regulation of Organ Diversity Comparative Development and Evolution > Evolutionary Novelties. © 2018 Wiley Periodicals, Inc.

Experimental strategies for the identification and characterization of adhesive proteins in animals: a review

PubMed Central

Hennebert, Elise; Maldonado, Barbara; Ladurner, Peter; Flammang, Patrick; Santos, Romana

2015-01-01

Adhesive secretions occur in both aquatic and terrestrial animals, in which they perform diverse functions. Biological adhesives can therefore be remarkably complex and involve a large range of components with different functions and interactions. However, being mainly protein based, biological adhesives can be characterized by classical molecular methods. This review compiles experimental strategies that were successfully used to identify, characterize and obtain the full-length sequence of adhesive proteins from nine biological models: echinoderms, barnacles, tubeworms, mussels, sticklebacks, slugs, velvet worms, spiders and ticks. A brief description and practical examples are given for a variety of tools used to study adhesive molecules at different levels from genes to secreted proteins. In most studies, proteins, extracted from secreted materials or from adhesive organs, are analysed for the presence of post-translational modifications and submitted to peptide sequencing. The peptide sequences are then used directly for a BLAST search in genomic or transcriptomic databases, or to design degenerate primers to perform RT-PCR, both allowing the recovery of the sequence of the cDNA coding for the investigated protein. These sequences can then be used for functional validation and recombinant production. In recent years, the dual proteomic and transcriptomic approach has emerged as the best way leading to the identification of novel adhesive proteins and retrieval of their complete sequences. PMID:25657842

EML4-ALK induces epithelial–mesenchymal transition consistent with cancer stem cell properties in H1299 non-small cell lung cancer cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Fuchun; Liu, Xiaoke, E-mail: liuxk57@163.com; Qing, Qin, E-mail: qinqingscu@126.com

2015-04-10

The echinoderm microtubule-associated protein-like 4(EML4) – anaplastic lymphoma kinase (ALK) fusion gene has been identified as a driver mutation in non-small-cell lung cancer (NSCLC). However, the role of EML4-ALK in malignant transformation is not entirely clear. Here, for the first time, we showed that H1299 NSCLC cells stably expressing EML4-ALK acquire EMT phenotype, associated with enhanced invasive migration and increased expression of EMT-inducing transcription factors. H1299-EML4-ALK cells also displayed cancer stem cell-like properties with a concomitant up-regulation of CD133 and enhanced ability of mammospheres formation. Moreover, we found that inhibition of ERK1/2 reversed EMT induced by EML4-ALK in H1299 cells.more » Taken together, these results suggested that EML4-ALK induced ERK activation is mechanistically associated with EMT phenotype. Thus, inhibition of ERK signaling pathway could be a potential strategy in treatment of NSCLC patients with EML4-ALK translocation. - Highlights: • EML4-ALK induced epithelial–mesenchymal transition in H1299 cells. • Expression of EML4-ALK promotes invasion and migration in vitro. • EML4-ALK enhanced sphere formation and stem cell-like properties in H1299 cells. • Blockage of ERK1/2 reverse Epithelial–Mesenchymal transition induced by EML4-ALK.« less

Micro- to nanostructure and geochemistry of extant crinoidal echinoderm skeletons.

PubMed

Gorzelak, P; Stolarski, J; Mazur, M; Meibom, A

2013-01-01

This paper reports the results of micro- to nanostructural and geochemical analyses of calcitic skeletons from extant deep-sea stalked crinoids. Fine-scale (SEM, FESEM, AFM) observations show that the crinoid skeleton is composed of carbonate nanograins, about 20-100 nm in diameter, which are partly separated by what appears to be a few nm thick organic layers. Sub-micrometre-scale geochemical mapping of crinoid ossicles using a NanoSIMS ion microprobe, combined with synchrotron high-spatial-resolution X-ray micro-fluorescence (μ-XRF) maps and X-ray absorption near-edge structure spectroscopy (XANES) show that high Mg concentration in the central region of the stereom bars correlates with the distribution of S-sulphate, which is often associated with sulphated polysaccharides in biocarbonates. These data are consistent with biomineralization models suggesting a close association between organic components (including sulphated polysaccharides) and Mg ions. Additionally, geochemical analyses (NanoSIMS, energy dispersive spectroscopy) reveal that significant variations in Mg occur at many levels: within a single stereom trabecula, within a single ossicle and within a skeleton of a single animal. Together, these data suggest that physiological factors play an important role in controlling Mg content in crinoid skeletons and that great care should be taken when using their skeletons to reconstruct, for example, palaeotemperatures and Mg/Ca palaeo-variations of the ocean. © 2012 Blackwell Publishing Ltd.

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

PubMed

Brozovic, Matija; Dantec, Christelle; Dardaillon, Justine; Dauga, Delphine; Faure, Emmanuel; Gineste, Mathieu; Louis, Alexandra; Naville, Magali; Nitta, Kazuhiro R; Piette, Jacques; Reeves, Wendy; Scornavacca, Céline; Simion, Paul; Vincentelli, Renaud; Bellec, Maelle; Aicha, Sameh Ben; Fagotto, Marie; Guéroult-Bellone, Marion; Haeussler, Maximilian; Jacox, Edwin; Lowe, Elijah K; Mendez, Mickael; Roberge, Alexis; Stolfi, Alberto; Yokomori, Rui; Brown, C Titus; Cambillau, Christian; Christiaen, Lionel; Delsuc, Frédéric; Douzery, Emmanuel; Dumollard, Rémi; Kusakabe, Takehiro; Nakai, Kenta; Nishida, Hiroki; Satou, Yutaka; Swalla, Billie; Veeman, Michael; Volff, Jean-Nicolas; Lemaire, Patrick

2018-01-04

ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Assessment of hydrocarbons concentration in marine fauna due to Tasman Spirit oil spill along the Clifton beach at Karachi coast.

PubMed

Siddiqi, Hina A; Ansari, Fayyaz A; Munshi, Alia B

2009-01-01

On 27 July 2003, Tasman Spirit spilled 31,000 tonnes of crude oil into the sea at the Karachi coast. This disaster badly affected the marine life (Flora and Fauna.) Present research has been proposed to ascertain the level of Polycyclic Aromatic hydrocarbons (PAHs) contamination in different fisheries including Fishes, Crustaceans; Crabs and Shrimps, Mollusks and Echinoderms along with passing time. Heavier components of crude oil such as Polycyclic Aromatic Hydrocarbons (PAHs) appear to cause most damages as these are relatively unreactive and persist in water. High concentrations of toxic PAHs were observed in all the fisheries and shellfishes caught form oil-impacted area. In this study fishes were found most contaminated than shellfishes i.e. summation operator 16 PAH = 1821.24 microg/g and summation operator 1164.34 microg/g, respectively. Naphthalene was found in the range of 0.042-602.23 microg/g. Acenaphthylene, acenaphthene, fluorene, phenanthrene and anthracene were detected in the range 0.008-80.03 microg/g, fluoranthene, pyrene, benzo(a)anthracene and chrysene 0.0008-221.32 microg/g, benzo(b) fluoranthene, benzo(k)fluoranthene and benzo(a) pyrene 0.0005-7.71 microg/g, benzo(g,h,i)perylene and indeno(1,2,3-c,d)pyrene 0.02-503.7 microg/g. Dibenzo(a,h)anthracenre was not detected in any specie.

The sea cucumber genome provides insights into morphological evolution and visceral regeneration

PubMed Central

Dai, Hui; Hamel, Jean-François; Liu, Chengzhang; Yu, Yang; Liu, Shilin; Lin, Wenchao; Guo, Kaimin; Jin, Songjun; Xu, Peng; Storey, Kenneth B.; Huan, Pin; Zhang, Tao; Zhou, Yi; Zhang, Jiquan; Lin, Chenggang; Li, Xiaoni; Xing, Lili; Huo, Da; Sun, Mingzhe; Wang, Lei; Mercier, Annie; Li, Fuhua; Yang, Hongsheng

2017-01-01

Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs. PMID:29023486

Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents

PubMed Central

2009-01-01

Olfaction is essential for the survival of animals. Versatile odour molecules in the environment are received by olfactory receptors (ORs), which form the largest multigene family in vertebrates. Identification of the entire repertories of OR genes using bioinformatics methods from the whole-genome sequences of diverse organisms revealed that the numbers of OR genes vary enormously, ranging from ~1,200 in rats and ~400 in humans to ~150 in zebrafish and ~15 in pufferfish. Most species have a considerable fraction of pseudogenes. Extensive phylogenetic analyses have suggested that the numbers of gene gains and losses are extremely large in the OR gene family, which is a striking example of the birth-and-death evolution. It appears that OR gene repertoires change dynamically, depending on each organism's living environment. For example, higher primates equipped with a well-developed vision system have lost a large number of OR genes. Moreover, two groups of OR genes for detecting airborne odorants greatly expanded after the time of terrestrial adaption in the tetrapod lineage, whereas fishes retain diverse repertoires of genes that were present in aquatic ancestral species. The origin of vertebrate OR genes can be traced back to the common ancestor of all chordate species, but insects, nematodes and echinoderms utilise distinctive families of chemoreceptors, suggesting that chemoreceptor genes have evolved many times independently in animal evolution. PMID:20038498

Arsenate (As V) in water: quantitative sensitivity relationships among biomarker, ecotoxicity and genotoxicity endpoints.

PubMed

Silva, Valéria C; Almeida, Sônia M; Resgalla, Charrid; Masfaraud, Jean-François; Cotelle, Sylvie; Radetski, Claudemir M

2013-06-01

It is useful to test ecotoxicity and genotoxicity endpoints in the environmental impact assessment. Here, we compare and discuss ecotoxicity and genotoxicity effects in organisms in response to exposure to arsenate (As V) in solution. Eco(geno)toxicity responses in Aliivibrio fischeri, Lytechinus variegatus, Daphnia magna, Skeletonema costatum and Vicia faba were analyzed by assessing different endpoints: biomass growth, peroxidase activity, mitotic index, micronucleus frequency, and lethality in accordance with the international protocols. Quantitative sensitivity relationships (QSR) between these endpoints were established in order to rank endpoint sensitivity. The results for the QSR values based on the lowest observed effect concentration (LOEC) ratios varied from 2 (for ratio of root peroxidase activity to leaf peroxidase activity) to 2286 (for ratio of higher plant biomass growth to root peroxidase activity). The QSR values allowed the following sensitivity ranking to be established: higher plant enzymatic activity>daphnids≈echinoderms>bacteria≈algae>higher plant biomass growth. The LOEC values for the mitotic index and micronucleus frequency (LOEC=0.25mgAsL(-1)) were similar to the lowest LOEC values observed in aquatic organisms. This approach to the QSR of different endpoints could form the basis for monitoring and predicting early effects of pollutants before they give rise to significant changes in natural community structures. Copyright © 2013 Elsevier Inc. All rights reserved.

First-line treatment of advanced ALK-positive non-small-cell lung cancer

PubMed Central

Gandhi, Shipra; Chen, Hongbin; Zhao, Yujie; Dy, Grace K

2015-01-01

Non-small-cell lung cancer (NSCLC) is one of the leading causes of cancer deaths, both within the US and worldwide. There have been major treatment advances in NSCLC over the past decade with the discovery of molecular drivers of NSCLC, which has ushered in an era of personalized medicine. There are several actionable genetic aberrations in NSCLC, such as epidermal growth factor receptor and anaplastic lymphoma kinase (ALK). In 3%–7% of NSCLC, a chromosomal inversion event in chromosome 2 leads to fusion of a portion of the ALK gene with the echinoderm microtubule–associated protein-like 4 (EML4) gene. The constitutive activation of the ALK fusion oncogene renders it vulnerable to therapeutic intervention. This review focuses on the first-line treatment of advanced ALK-positive NSCLC using ALK inhibitors. Crizotinib was the first agent proven to be efficacious as first-line treatment for ALK-positive NSCLC. However, acquired resistance inevitably develops. The central nervous system is a sanctuary site that represents a common site for disease progression as well. Hence, more potent, selective next-generation ALK inhibitors that are able to cross the blood–brain barrier have been developed for treatment against crizotinib-resistant ALK-positive NSCLC and are also currently being evaluated for first-line therapy as well. In this review, we provide summary of the clinical experience with these drugs in the treatment of ALK-positive NSCLC. PMID:28210152

The sea cucumber genome provides insights into morphological evolution and visceral regeneration.

PubMed

Zhang, Xiaojun; Sun, Lina; Yuan, Jianbo; Sun, Yamin; Gao, Yi; Zhang, Libin; Li, Shihao; Dai, Hui; Hamel, Jean-François; Liu, Chengzhang; Yu, Yang; Liu, Shilin; Lin, Wenchao; Guo, Kaimin; Jin, Songjun; Xu, Peng; Storey, Kenneth B; Huan, Pin; Zhang, Tao; Zhou, Yi; Zhang, Jiquan; Lin, Chenggang; Li, Xiaoni; Xing, Lili; Huo, Da; Sun, Mingzhe; Wang, Lei; Mercier, Annie; Li, Fuhua; Yang, Hongsheng; Xiang, Jianhai

2017-10-01

Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs.

A new species of Monocheres Stock (Copepoda, Siphonostomatoida, Asterocheridae) from shallow waters off Florida, USA: an unexpected discovery.

PubMed

Suárez-Morales, Eduardo

2016-01-01

The rare asterocherid copepod genus Monocheres, ectosymbionts of corals and sponges, contains only two species, one from Mauritius (Indian Ocean) and the other one from Brazil (western Atlantic). From the analysis of the digestive caecum contents of the benthic hesionid polychaete Hesione picta Müller, 1858, an adult female of an undescribed species of Monocheres was unexpectedly recovered; it is the third species of this rare asterocherid genus. The new species, Monocheres sergioi sp. n., has the distinctive reduction of the fifth leg as a process with a single seta. It differs from its two other congeners by several characters including the presence of an inner basipodal spine, the armature details of the third exopodal segment of leg 1, the shape of the cephalosome and pedigerous somites 3 and 4, and the ornamentation of the postero-lateral corners of the genital double-somite. The main synapomorphies include the presence of spinules along the posterior margin of the first leg coxal sclerite and the reduced, spiniform coxal seta on leg 4. The biology and feeding habits of the polychaete containing this specimen suggests that the copepod was ingested as an ectosymbiont from sponges or coral but it is also possible that it was consumed from an ophiurid echinoderm. This finding allows an expansion of the genus geographical distribution in the northwestern Atlantic. A key to the species of Monocheres is also provided.

A new species of Monocheres Stock (Copepoda, Siphonostomatoida, Asterocheridae) from shallow waters off Florida, USA: an unexpected discovery

PubMed Central

Suárez-Morales, Eduardo

2016-01-01

Abstract The rare asterocherid copepod genus Monocheres, ectosymbionts of corals and sponges, contains only two species, one from Mauritius (Indian Ocean) and the other one from Brazil (western Atlantic). From the analysis of the digestive caecum contents of the benthic hesionid polychaete Hesione picta Müller, 1858, an adult female of an undescribed species of Monocheres was unexpectedly recovered; it is the third species of this rare asterocherid genus. The new species, Monocheres sergioi sp. n., has the distinctive reduction of the fifth leg as a process with a single seta. It differs from its two other congeners by several characters including the presence of an inner basipodal spine, the armature details of the third exopodal segment of leg 1, the shape of the cephalosome and pedigerous somites 3 and 4, and the ornamentation of the postero-lateral corners of the genital double-somite. The main synapomorphies include the presence of spinules along the posterior margin of the first leg coxal sclerite and the reduced, spiniform coxal seta on leg 4. The biology and feeding habits of the polychaete containing this specimen suggests that the copepod was ingested as an ectosymbiont from sponges or coral but it is also possible that it was consumed from an ophiurid echinoderm. This finding allows an expansion of the genus geographical distribution in the northwestern Atlantic. A key to the species of Monocheres is also provided. PMID:27551233

The Last Common Ancestor of Most Bilaterian Animals Possessed at Least Nine Opsins

PubMed Central

Pairett, Autum N.; Pankey, M. Sabrina; Serb, Jeanne M.; Speiser, Daniel I.; Swafford, Andrew J.

2016-01-01

Abstract The opsin gene family encodes key proteins animals use to sense light and has expanded dramatically as it originated early in animal evolution. Understanding the origins of opsin diversity can offer clues to how separate lineages of animals have repurposed different opsin paralogs for different light-detecting functions. However, the more we look for opsins outside of eyes and from additional animal phyla, the more opsins we uncover, suggesting we still do not know the true extent of opsin diversity, nor the ancestry of opsin diversity in animals. To estimate the number of opsin paralogs present in both the last common ancestor of the Nephrozoa (bilaterians excluding Xenoacoelomorpha), and the ancestor of Cnidaria + Bilateria, we reconstructed a reconciled opsin phylogeny using sequences from 14 animal phyla, especially the traditionally poorly-sampled echinoderms and molluscs. Our analysis strongly supports a repertoire of at least nine opsin paralogs in the bilaterian ancestor and at least four opsin paralogs in the last common ancestor of Cnidaria + Bilateria. Thus, the kernels of extant opsin diversity arose much earlier in animal history than previously known. Further, opsins likely duplicated and were lost many times, with different lineages of animals maintaining different repertoires of opsin paralogs. This phylogenetic information can inform hypotheses about the functions of different opsin paralogs and can be used to understand how and when opsins were incorporated into complex traits like eyes and extraocular sensors. PMID:28172965

Production, characterization and application of monoclonal antibodies to the coelomocytes of sea urchin Strongylocentrotus intermedius.

PubMed

Wang, Yinan; Meng, Shaodong; Zhang, Jialin; Ding, Jun; Li, Qiang

2018-04-01

Sea urchin is one of marine animals with high economic and great scientific research values. Axial organ is a glandular organ that has been presumed as coelomocytes origin site. In this paper, two monoclonal antibodies (3G10 and 6B3) against coelomocytes of sea urchin Strongylocentrotus intermedius were developed by hybridoma technique. The mAbs were characterized by indirect immunofluorescence assay test (IIFAT), flow cytometry (FCM) and western blot assay. Results showed that mAb 3G10 recognized a protein of a molecular weight of 17 kDa in the spherule cells, while mAb 6B3 reacted with a protein of a molecular weight of 35 kDa in the phagocytes. Furthermore, specificity analysis revealed that the two mAbs could react with the coelomocytes of sea urchin S. nudus and Hemicentrotus pulcherrimus, but not with those of other common echinoderms including sea cucumber Apostichopus japonicus and starfish Asterias rollestoni. To determine whether the coelomocytes exist in the axial organ of sea urchin, the IIFAT assays were carried out based on the two mAbs. Result showed that positive fluorescence signals were distributed in the organ. It was revealed that the axial organ was rich in coelomocytes, which suggests that the organ may play as a producing source or reservoir in the ontogenesis of coelomocytes of sea urchin. Copyright © 2018 Elsevier Ltd. All rights reserved.

Identification and expression characterization of WntA during intestinal regeneration in the sea cucumber Apostichopus japonicus.

PubMed

Li, Xiaoni; Sun, Lina; Yang, Hongsheng; Zhang, Libin; Miao, Ting; Xing, Lili; Huo, Da

2017-08-01

Wnt genes encode secreted glycoproteins that act as signaling molecules; these molecules direct cell proliferation, migration, differentiation and survival during animal development, maintenance of homeostasis and regeneration. At present, although the regeneration mechanism in Apostichopus japonicus has been studied, there is a little research on the Wnt signaling pathway in A. japonicus. To understand the potential role of the Wnt signaling pathway in A. japonicus, we cloned and sequenced the WntA gene in A. japonicus. Protein localization analysis showed that WntA protein was ubiquitously expressed in epidermal cells, the muscle and submucosa of the intestinal tissue. After stimulation and evisceration, the dynamic changes in expression of the WntA gene and protein showed that WntA was constitutively expressed during different stages of intestine regeneration in A. japonicus, with higher levels during the early wound healing stage and late lumen formation in the residual and nascent intestinal tissues, indicating its response to intestinal regeneration. Simultaneously, cell proliferation and apoptosis analysis showed that the patterns of cell proliferation were similar to the patterns of WntA protein expression during different intestinal regeneration stages in this organism. Taken together, these results suggested that WntA might participate in intestinal regeneration and may be connected with cell proliferation, apoptosis in different intestinal layers. This research could establish a basis for further examination of WntA functions in A. japonicus and Wnt genes in other echinoderms. Copyright © 2017 Elsevier Inc. All rights reserved.

Regulatory heterochronies and loose temporal scaling between sea star and sea urchin regulatory circuits.

PubMed

Gildor, Tsvia; Hinman, Veronica; Ben-Tabou-De-Leon, Smadar

2017-01-01

It has long been argued that heterochrony, a change in relative timing of a developmental process, is a major source of evolutionary innovation. Heterochronic changes of regulatory gene activation could be the underlying molecular mechanism driving heterochronic changes through evolution. Here, we compare the temporal expression profiles of key regulatory circuits between sea urchin and sea star, representative of two classes of Echinoderms that shared a common ancestor about 500 million years ago. The morphologies of the sea urchin and sea star embryos are largely comparable, yet, differences in certain mesodermal cell types and ectodermal patterning result in distinct larval body plans. We generated high resolution temporal profiles of 17 mesodermally-, endodermally- and ectodermally-expressed regulatory genes in the sea star, Patiria miniata, and compared these to their orthologs in the Mediterranean sea urchin, Paracentrotus lividus. We found that the maternal to zygotic transition is delayed in the sea star compared to the sea urchin, in agreement with the longer cleavage stage in the sea star. Interestingly, the order of gene activation shows the highest variation in the relatively diverged mesodermal circuit, while the correlations of expression dynamics are the highest in the strongly conserved endodermal circuit. We detected loose scaling of the developmental rates of these species and observed interspecies heterochronies within all studied regulatory circuits. Thus, after 500 million years of parallel evolution, mild heterochronies between the species are frequently observed and the tight temporal scaling observed for closely related species no longer holds.

Detection of EML4-ALK fusion gene and features associated with EGFR mutations in Chinese patients with non-small-cell lung cancer.

PubMed

Wen, Miaomiao; Wang, Xuejiao; Sun, Ying; Xia, Jinghua; Fan, Liangbo; Xing, Hao; Zhang, Zhipei; Li, Xiaofei

2016-01-01

Echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) and epidermal growth factor receptor (EGFR) define specific molecular subsets of lung cancer with distinct clinical features. We aimed at revealing the clinical features of EML4-ALK fusion gene and EGFR mutation in non-small-cell lung cancer (NSCLC). We enrolled 694 Chinese patients with NSCLC for analysis. EML4-ALK fusion gene was analyzed by real-time polymerase chain reaction, and EGFR mutations were analyzed by amplified refractory mutation system. Among the 694 patients, 60 (8.65%) patients had EML4-ALK fusions. In continuity correction χ (2) test analysis, EML4-ALK fusion gene was correlated with sex, age, smoking status, and histology, but no significant association was observed between EML4-ALK fusion gene and clinical stage. A total of 147 (21.18%) patients had EGFR mutations. In concordance with previous reports, EGFR mutation was correlated with age, smoking status, histology, and clinical stage, whereas patient age was not significantly associated with EGFR mutation. Meanwhile, to our surprise, six (0.86%) patients had coexisting EML4-ALK fusions and EGFR mutations. EML4-ALK fusion gene defines a new molecular subset in patients with NSCLC. Six patients who harbored both EML4-ALK fusion genes and EGFR mutations were identified in our study. The EGFR mutations and the EML4-ALK fusion genes are coexistent.

High resolution cathodoluminescence spectroscopy of carbonate cementation in Khurmala Formation (Paleocene-L. Eocene) from Iraqi Kurdistan Region, Northern Iraq

NASA Astrophysics Data System (ADS)

Omer, Muhamed F.; Omer, Dilshad; Zebari, Bahroz Gh.

2014-12-01

A combination of high resolution cathodoluminsecnce-spectroscopy (HRS-CL) with spatial electron microprobe analysis and optical microscopy is used to determine paragenesis and history of cementation in the limestones and dolostones of Khurmala Formation which is exposed in many parts of Northern Iraq. Khurmala Formation was subjected to different diagenetic processes such as micritization, compaction, dissolution, neomorphism, pyritization and cementation that occurred during marine to shallow burial stages and culminated during intermediate to deep burial later stages. Five dolomite textures are recognized and classified according to crystal size distribution and crystal-boundary shape. Dolomitization is closely associated with the development of secondary porosity that pre-and postdates dissolution and corrosion; meanwhile such porosity was not noticed in the associated limestones. Microprobe analysis revealed three types of cement, calcite, dolomite and ankerite which range in their luminescence from dull to bright. Cathodoluminescence study indicated four main texture generations. These are (1) unzoned microdolomite of planar and subhedral shape, with syntaxial rim cement of echinoderm that show dull to red luminescence, (2) equant calcite cements filling interparticle pores which shows dull luminescence and weak zonal growth, (3.1) homogenous intrinsic blue stoichiometric calcite with dull luminescence and without activators, (3.2) coarse blocky calcite cement with strong oscillatory zoning and bright orange luminescence which postdates other calcite cements, (4) ankerite cement with red to orange, non-luminescence growth zonation which is the last formed cement.

Effects of an artificial oyster shell reef on macrobenthic communities in Rongcheng Bay, East China

NASA Astrophysics Data System (ADS)

Xu, Qinzeng; Zhang, Libin; Zhang, Tao; Zhou, Yi; Xia, Sudong; Liu, Hui; Yang, Hongsheng

2014-01-01

An artificial oyster shell reef was deployed in Rongcheng Bay, East China. However, the effects of this reef on the surrounding macrobenthic communities were unknown. We compared sedimentary factors, macrobenthic biomass, abundance, and community composition and ecological indicators between the reef and non-reef areas over a one year period. The mean values for chlorophyll a (Chl a), total organic matter (TOM), total organic carbon (TOC), and total nitrogen (TN) content in surface sediments in the reef area were slightly higher than those in the non-reef area. The Chl a levels differed significantly between the two areas, but the TOM, TOC, and TN were not significantly different. The abundance of crustaceans was significantly different between the two areas, but the abundance and biomass of polychaetes, echinoderms, mollusk did not differ significantly. The permutational multivariate analysis of variance (PERMANOVA) revealed that the macrobenthic community differed significantly through time and analysis of similarity multivariate analyses (ANOSIM) revealed that the macrobenthic community differed significantly in some months. The ecological indicators revealed that the environmental quality of the reef area was slightly better than that of the non-reef area. Overall, our results suggest that the artificial oyster shell reef may change the macrobenthic community and the quality of the environment. Despite the lack of an effect in the short term, long-term monitoring is still needed to evaluate the effects of artificial oyster shell reefs on macrobenthic communities.

Effects of seawater acidification on the early development of sea urchin Glyptocidaris crenularis

NASA Astrophysics Data System (ADS)

Zhan, Yaoyao; Hu, Wanbin; Duan, Lizhu; Liu, Minbo; Zhang, Weijie; Chang, Yaqing; Li, Cong

2017-10-01

In this study, we evaluated the effects of CO2-induced seawater acidification on fertilization, embryogenesis and early larval development in the sea urchin Glyptocidaris crenularis, that inhabits subtidal coastal areas in northern China. The range in seawater pH used in experiments was based on the projections of the Intergovernmental Panel on Climate Change (IPCC), to the year 2100. A natural seawater treatment (pHnbs=7.98±0.03) and three laboratory-controlled acidified treatments (OA1, ΔpHnbs=-0.3 units; OA2, ΔpHnbs=-0.4 units; OA3, ΔpHnbs=-0.5 units) were used in experiments. Results show that: (1) there was a negative effect of seawater acidification on fertilization and on the percentage of abnormal fertilized eggs; (2) the size of early cleavage stage embryos decreased in a dose-dependent manner with decreasing pH; (3) both the hatching rate of blastulae and the survival rate of four-armed pluteus larvae decreased as pH declined; (4) larval abnormalities including asymmetrical development, changes in the length of skeletal elements, and corroded spicules were observed in all seawater acidified-treatments compared with the control. These data indicate that seawater acidification has a negative impact on the early development of G. crenularis, and supports the hypothesis that the response of echinoderms to ocean acidification (OA) varies among species. Further research is required to clarify the specific cellular mechanisms involved.

Metabolic flexibility: the key to long-term evolutionary success in Bryozoa?

PubMed

Peck, Lloyd S; Barnes, David K A

2004-02-07

Oxygen consumption (MO2) and activity were evaluated in Antarctic Bryozoa. Three species representing two different morphologies, flat sheet, laminar forms, Isoseculiflustra tenuis and Kymella polaris, and the bush form Camptoplites bicornis were used. In Bryozoa, activity is measured as the proportion of colony zooids with their lophophores extended. In I. tenuis and K. polaris, residual analysis showed that the percentage of zooids with extended lophophores was not correlated with colony MO2. Lophophore extension is, therefore, a poor measure of activity, and other costs (e.g. growth, reproduction, storage) probably form the major metabolic costs. MO2 per unit of ash-free dry mass (AFDM) in the laminar forms was low compared with other Antarctic marine invertebrates, but not lower than brachiopods and echinoderms. However, the lowest rate here, 16.8 microg O2 g AFDM(-1) h(-1) for a K. polaris colony, is (to our knowledge) the lowest for any animal so far reported. MO2 per unit of AFDM for C. bicornis, however, is among the highest reported for sessile or slow moving Antarctic marine ectotherms, with values similar to those for bivalve and gastropod molluscs. The highest rate, 527 microg O2 g AFDM(-1) h(-1) for one colony is (to our knowledge) the highest reported for polar animals of this type. Extreme diversity in metabolic strategy may explain the bryozoan long evolutionary record and great success in shallow marine environments worldwide.

Reliability Assurance of Detection of EML4-ALK Rearrangement in Non-Small Cell Lung Cancer: The Results of Proficiency Testing in China.

PubMed

Li, Yulong; Zhang, Rui; Peng, Rongxue; Ding, Jiansheng; Han, Yanxi; Wang, Guojing; Zhang, Kuo; Lin, Guigao; Li, Jinming

2016-06-01

Currently, several approaches are being used to detect echinoderm microtubule associated protein like 4 gene (EML4)-anaplastic lymphoma receptor tyrosine kinase gene (ALK) rearrangement, but the performance of laboratories in China is unknown. To evaluate the proficiency of different laboratories in detecting EML4-ALK rearrangement, we organized a proficiency test (PT). We prepared formalin-fixed, paraffin-embedded samples derived from the xenograft tumor tissue of three non-small cell lung cancer cell lines with different EML4-ALK rearrangements and used PTs to evaluate the detection performance of laboratories in China. We received results from 94 laboratories that used different methods. Of the participants, 75.53% correctly identified all samples in the PT panel. Among the errors made by participants, false-negative errors were likely to occur. According to the methodology applied, 82.86%, 76.67%, 77.78%, and 66.67% of laboratories using reverse transcriptase polymerase chain reaction, fluorescence in situ hybridization, next-generation sequencing, and immunohistochemical analysis, respectively, could analyze all the samples correctly. Moreover, we have found that the laboratories' genotyping capacity is high, especially for variant 3. Our PT survey revealed that the performance and methodological problems of laboratories must be addressed to further increase the reproducibility and accuracy of detection of EML4-ALK rearrangement to ensure reliable results for selection of appropriate patients. Copyright © 2016 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Detection of EML4-ALK in Lung Adenocarcinoma Using Pleural Effusion with FISH, IHC, and RT-PCR Methods

PubMed Central

Zhou, Xiaodie; Song, Yong; Zhou, Xiaojun; Yu, Like; Wang, Jiandong

2015-01-01

Anaplastic lymphoma kinase (ALK) and echinoderm microtubule-associated protein-like 4 (EML4) gene rearrangements occur in approximately 5% of non-small-cell lung cancers (NSCLC), leading to the overexpression of anaplastic lymphoma kinase and predicting a response to the targeted inhibitor, crizotinib. Malignant pleural effusion occurs in most patients with advanced lung cancer, especially adenocarcinoma, and tissue samples are not always available from these patients. We attempted to clarify the feasibility of detecting the EML4-ALK fusion gene in pleural effusion cells using different methods. We obtained 66 samples of pleural effusion from NSCLC patients. The pleural effusion fluid was centrifuged, and the cellular components obtained were formalin fixed and paraffin embedded. The EML4-ALK fusion gene status was determined with fluorescent in situ hybridization (FISH), reverse transcription—polymerase chain reaction (RT-PCR), and immunohistochemistry (IHC). EML4-ALK was detected in three of 66 patient samples (4.5%) with RT-PCR. When the RT-PCR data were used as the standard, one false positive and one false negative samples were identified with IHC; and one false negative sample was identified with FISH. These results suggest that a block of pleural effusion cells can be used to detect the EML4-ALK fusion gene. IHC had good sensitivity, but low specificity. FISH had low sensitivity, but high specificity. RT-PCR is a good candidate method for detecting EML4-ALK in blocks of pleural effusion cells from lung cancer patients. PMID:25785456

Detection of EML4-ALK in lung adenocarcinoma using pleural effusion with FISH, IHC, and RT-PCR methods.

PubMed

Liu, Leilei; Zhan, Ping; Zhou, Xiaodie; Song, Yong; Zhou, Xiaojun; Yu, Like; Wang, Jiandong

2015-01-01

Anaplastic lymphoma kinase (ALK) and echinoderm microtubule-associated protein-like 4 (EML4) gene rearrangements occur in approximately 5% of non-small-cell lung cancers (NSCLC), leading to the overexpression of anaplastic lymphoma kinase and predicting a response to the targeted inhibitor, crizotinib. Malignant pleural effusion occurs in most patients with advanced lung cancer, especially adenocarcinoma, and tissue samples are not always available from these patients. We attempted to clarify the feasibility of detecting the EML4-ALK fusion gene in pleural effusion cells using different methods. We obtained 66 samples of pleural effusion from NSCLC patients. The pleural effusion fluid was centrifuged, and the cellular components obtained were formalin fixed and paraffin embedded. The EML4-ALK fusion gene status was determined with fluorescent in situ hybridization (FISH), reverse transcription-polymerase chain reaction (RT-PCR), and immunohistochemistry (IHC). EML4-ALK was detected in three of 66 patient samples (4.5%) with RT-PCR. When the RT-PCR data were used as the standard, one false positive and one false negative samples were identified with IHC; and one false negative sample was identified with FISH. These results suggest that a block of pleural effusion cells can be used to detect the EML4-ALK fusion gene. IHC had good sensitivity, but low specificity. FISH had low sensitivity, but high specificity. RT-PCR is a good candidate method for detecting EML4-ALK in blocks of pleural effusion cells from lung cancer patients.

Detection of EML4-ALK fusion gene and features associated with EGFR mutations in Chinese patients with non-small-cell lung cancer

PubMed Central

Wen, Miaomiao; Wang, Xuejiao; Sun, Ying; Xia, Jinghua; Fan, Liangbo; Xing, Hao; Zhang, Zhipei; Li, Xiaofei

2016-01-01

Purpose Echinoderm microtubule-associated protein-like 4–anaplastic lymphoma kinase (EML4-ALK) and epidermal growth factor receptor (EGFR) define specific molecular subsets of lung cancer with distinct clinical features. We aimed at revealing the clinical features of EML4-ALK fusion gene and EGFR mutation in non-small-cell lung cancer (NSCLC). Methods We enrolled 694 Chinese patients with NSCLC for analysis. EML4-ALK fusion gene was analyzed by real-time polymerase chain reaction, and EGFR mutations were analyzed by amplified refractory mutation system. Results Among the 694 patients, 60 (8.65%) patients had EML4-ALK fusions. In continuity correction χ2 test analysis, EML4-ALK fusion gene was correlated with sex, age, smoking status, and histology, but no significant association was observed between EML4-ALK fusion gene and clinical stage. A total of 147 (21.18%) patients had EGFR mutations. In concordance with previous reports, EGFR mutation was correlated with age, smoking status, histology, and clinical stage, whereas patient age was not significantly associated with EGFR mutation. Meanwhile, to our surprise, six (0.86%) patients had coexisting EML4-ALK fusions and EGFR mutations. Conclusion EML4-ALK fusion gene defines a new molecular subset in patients with NSCLC. Six patients who harbored both EML4-ALK fusion genes and EGFR mutations were identified in our study. The EGFR mutations and the EML4-ALK fusion genes are coexistent. PMID:27103824

Targeting stemness is an effective strategy to control EML4-ALK+ non-small cell lung cancer cells

PubMed Central

Oh, Se Jin; Noh, Kyung Hee; Lee, Young-Ho; Hong, Soon-Oh; Song, Kwon-Ho; Lee, Hyo-Jung; Kim, Soyeon; Kim, Tae Min; Jeon, Ju-Hong; Seo, Jae Hong; Kim, Dong-Wan; Kim, Tae Woo

2015-01-01

The fusion between anaplastic lymphoma kinase (ALK) and echinoderm microtubule-associated protein-like 4 (EML4) is a causative factor in a unique subset of patients with non-small cell lung carcinoma (NSCLC). Although the inhibitor crizotinib, as it blocks the kinase activity of the resulting EML4-ALK fusion protein, displays remarkable initial responses, a fraction of NSCLC cases eventually become resistant to crizotinib by acquiring mutations in the ALK domain or activating bypass pathways via EGFR, KIT, or KRAS. Cancer stem cell (CSC) theory provides a plausible explanation for acquisition of tumorigenesis and resistance. However, the question as to whether EML4-ALK-driven tumorigenesis is linked with the stem-like property and whether the stemness is an effective target in controlling EML4-ALK+ NSCLC including crizotinib-resistant NSCLC cells has not been addressed. Here, we report that stem-like properties stem from ALK activity in EML4-ALK+ NSCLC cells. Notably, treatment with rapamycin, a CSC targeting agent, attenuates stem-like phenotypes of the EML4-ALK+ cells, which increased capability of tumor formation and higher expression of stemness-associated molecules such as ALDH, NANOG, and OCT4. Importantly, combinational treatment with rapamycin and crizotinib leads to synergistic anti-tumor effects on EML4-ALK+ NSCLC cells as well as on those resistant to crizotinib. Thus, we provide a proof of principle that targeting stemness would be a novel strategy to control intractable EML4-ALK+ NSCLC. PMID:26517679

Comparative morphology of the axial complex and interdependence of internal organ systems in sea urchins (Echinodermata: Echinoidea).

PubMed

Ziegler, Alexander; Faber, Cornelius; Bartolomaeus, Thomas

2009-06-09

The axial complex of echinoderms (Echinodermata) is composed of various primary and secondary body cavities that interact with each other. In sea urchins (Echinoidea), structural differences of the axial complex in "regular" and irregular species have been observed, but the reasons underlying these differences are not fully understood. In addition, a better knowledge of axial complex diversity could not only be useful for phylogenetic inferences, but improve also an understanding of the function of this enigmatic structure. We therefore analyzed numerous species of almost all sea urchin orders by magnetic resonance imaging, dissection, histology, and transmission electron microscopy and compared the results with findings from published studies spanning almost two centuries. These combined analyses demonstrate that the axial complex is present in all sea urchin orders and has remained structurally conserved for a long time, at least in the "regular" species. Within the Irregularia, a considerable morphological variation of the axial complex can be observed with gradual changes in topography, size, and internal architecture. These modifications are related to the growing size of the gastric caecum as well as to the rearrangement of the morphology of the digestive tract as a whole. The structurally most divergent axial complex can be observed in the highly derived Atelostomata in which the reorganization of the digestive tract is most pronounced. Our findings demonstrate a structural interdependence of various internal organs, including digestive tract, mesenteries, and the axial complex.

Macrobenthic patterns at the shallow marine waters in the caldera of the active volcano of Deception Island, Antarctica

NASA Astrophysics Data System (ADS)

Angulo-Preckler, Carlos; Figuerola, Blanca; Núñez-Pons, Laura; Moles, Juan; Martín-Martín, Rafael; Rull-Lluch, Jordi; Gómez-Garreta, Amelia; Avila, Conxita

2018-04-01

Deception Island is an active volcano located at the southern end of the South Shetland Archipelago, in the Antarctic Ocean. After the last eruption in 1970, benthic recolonization took place within the bay, with echinoderms being the dominant epifauna (e.g., the ophiuroid Ophionotus victoriae, the echinoid Sterechinus neumayeri and the sea star Odontaster validus), together with dense infaunal communities (mostly composed by oligochaetes, polychaetes, and bivalves). Here, we aim to describe the actual status of the marine benthic ecosystems inhabiting the shallow subtidal areas of this volcanic island. Benthic species were qualitatively scored as presence versus absence, considering the different sampling effort between localities done over the years. A total of 139 species of macroorganisms, belonging to 16 phyla were found, including fauna and flora, increasing the species richness values previously reported in all sites surveyed within the volcano caldera. Moreover, a dramatic increase in biodiversity was found towards the entrance of the bay. We suggest, however, that recolonization from external waters may not be the only reason for this pattern. In fact, sediment flux rates and substrate instability are common disturbances within the bay, probably being among the major factors determining benthic community assemblages. These processes probably favour deposit feeding communities at the innermost locations of the bay. This study provides a remarkably increased and updated species inventory from previous reports, altogether with a description of the main communities inhabiting the bay and the abiotic factors regulating this, mainly the bottom type.

GEMINI-TITAN (GT)-3 - WEIGHTLESSNESS EXPERIMENT - AMES RESEARCH CENTER (ARC), CA

NASA Image and Video Library

1965-03-01

S65-18762 (March 1965) --- Effects of the weightless environment on cell division, the basic growth process for living tissue, will be studied during the Gemini-Titan 3 flight scheduled for March 23, 1965. A spiny black sea urchin (upper left) is stimulated by mild electric shock or potassium chloride. As a result it sheds many thousands of eggs. When fertilized, these eggs become actively dividing cells very similar in basic processes to cells of other animals, including humans. These pictures show stages of cell division. At upper right is a single cell; at lower right cell divisions have produced many cells. Cell photos are magnified about 700 times, and all cells shown are too small to be seen by the naked eye. (Photos at upper right and lower left are of sea urchin eggs. Group of cells at lower right are from a sand dollar, which like the sea urchin, is an Echinoderm. Its eggs are virtually identical and are used interchangeably with those of the sea urchin in NASA Ames Center weightlessness experiments.) The Gemini experiment will involve cell division like that shown here. This will take place during several hours of weightlessness aboard the Gemini spacecraft. The experiment will be flown back to laboratories at Cape Kennedy after spacecraft recovery. It has been designed so that any abnormal cell division found by postflight analysis should suggest that the weightless environment has effects on individual cells. This might mean hazards for prolonged periods of manned spaceflight.

Cytotoxicity and Physiological Effects of Silver Nanoparticles on Marine Invertebrates.

PubMed

Magesky, Adriano; Pelletier, Émilien

2018-01-01

Silver nanoparticles (AgNPs) incorporation in commercial products is increasing due to their remarkable physical and chemical properties and their low cost on the market. Silver has been known for a long time to be highly toxic to bacterial communities, aquatic organisms, and particularly to marine biota. Strong chloro-complexes dominate Ag speciation in seawater and facilitate its persistence in dissolved form. It has a great impact on marine organisms because low concentration of silver can lead to strong bioaccumulation, partly because the neutral silver chloro complex (AgCl 0 ) is highly bioavailable. Owing to the fact that estuaries and coastal areas are considered as the ultimate fate for AgNPs, the study of their toxic effects on marine invertebrates can reveal some environmental risks related to nanosilver exposure. In an attempt to reach this goal, many invertebrate taxa including mollusks, crustaceans, echinoderms and polychaetes have been used as biological models. The main findings related to AgNP toxicity and marine invertebrates are summarized hereafter. Some cellular mechanisms involving nano-internalization (cellular uptake, distribution and elimination), DNA damaging, antioxidant cellular defenses and protein expression are discussed. Physiological effects on early stage development, silver metabolic speciation, immune response, tissue damaging, anti-oxidant effects and nano-depuration are also described. Finally, we paid attention to some recent interesting findings using sea urchin developmental stages and their cells as models for nanotoxicity investigation. Cellular and physiological processes characterizing sea urchin development revealed new and multiple toxicity mechanisms of both soluble and nano forms of silver.

Deep questions about the nature of early-life signals: a commentary on Lister (1673) ‘A description of certain stones figured like plants’

PubMed Central

Brasier, Martin

2015-01-01

In 1673, Martin Lister explored the preservation of ‘St Cuthbert's beads’ plus other fossil crinoid remains from approximately 350 Ma Carboniferous limestone in northern England. He used taphonomic evidence (transport, disarticulation, burial and cementation) to infer an origin as petrified plant remains, in contrast with his views expressed elsewhere that fossil mollusc shells could have formed abiogenically, by ‘plastic forces’ within rock. Lister also observed pentagonal symmetry, now seen as characteristic of living echinoderm skeletons. A postscript from John Ray supports Lister's ‘taphonomic’ observations and accepts the biogenicity of these fossil ‘vegetables’. Ray then concluded with a prophecy, predicting the discovery of comparable living fossils in remote ocean waters. These early discussions compare with current debates about the character of candidate microfossils from the early Earth and Mars. Interesting biomorphs are now tested against the abiogenic null hypotheses, making use of features such as those pioneered by Lister, including evidence for geological context, rules for growth and taphonomy. Advanced techniques now allow us to extend this list of criteria to include the nanoscale mapping of biology-like behaviour patterns plus metabolic pathways. Whereas the science of palaeobiology once began with tests for biogenicity, the same is now true for geobiology and astrobiology. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society. PMID:25750150

Evidence of low molecular weight components in the organic matrix of the reef building coral, Stylophora pistillata.

PubMed

Puverel, S; Houlbrèque, F; Tambutté, E; Zoccola, D; Payan, P; Caminiti, N; Tambutté, S; Allemand, D

2007-08-01

Biominerals contain both inorganic and organic components. Organic components are collectively termed the organic matrix, and this matrix has been reported to play a crucial role in mineralization. Several matrix proteins have been characterized in vertebrates, but only a few in invertebrates, primarily in Molluscs and Echinoderms. Methods classically used to extract organic matrix proteins eliminate potential low molecular weight matrix components, since cut-offs ranging from 3.5 to 10 kDa are used to desalt matrix extracts. Consequently, the presence of such components remains unknown and these are never subjected to further analyses. In the present study, we have used microcolonies from the Scleractinian coral Stylophora pistillata to study newly synthesized matrix components by labelling them with 14C-labelled amino acids. Radioactive matrix components were investigated by a method in which both total organic matrix and fractions of matrix below and above 5 kDa were analyzed. Using this method and SDS-PAGE analyses, we were able to detect the presence of low molecular mass matrix components (<3.5 kDa), but no free amino acids in the skeletal organic matrix. Since more than 98% of the 14C-labelled amino acids were incorporated into low molecular weight molecules, these probably form the bulk of newly synthesized organic matrix components. Our results suggest that these low molecular weight components may be peptides, which can be involved in the regulation of coral skeleton mineralization.

Dynamic depositional and early diagenetic processes in a deep-water shelf setting, upper cretaceous Austin Chalk, North Texas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hovorka, S.D.; Nance, H.S.

1994-12-31

The Austin Chalk of north Texas was deposited on a deep-water shelf north of the Sea Marcos Platform during a worldwide Coniacian and Santonian sea-level highstand. Transgressive (lowermost lower Austin Chalk), highstand (uppermost lower Austin Chalk), and regressive (middle and upper Austin Chalk) phases of cyclic chalk and marl sedimentation are recognized in excavations and tunnels created in Ellis County for the Superconducting Super Collider provide new evidence of sediment transport during Austin Chalk deposition. During transgression, bottom currents syndepositionally reworked nannoplankton oozes, incising channels as much as 120 ft across and 8 ft deep. Weakly burrowed channel fills havingmore » preservation of fine lamination document rapid infilling. Channel fills are composed of pyritized and carbonized wood and Inoceramus lag deposits, pellets, echinoderm fragments, and globigerinid grainstones, and coccolith ooze. During maximum highstand, bottom reworking was suppressed. Detrital content of highstand marls is low (>20 percent); organic content is high (1.4 to 3.5 percent). Coccolith preservation is excellent because of minimal diagenetic alteration. Regression is marked by resumed channel cutting and storm-bed winnowing in the middle and upper Austin Chalk. Suppressed resistivity log response and recessive weathering characteristics of the middle Austin Chalk are not primarily related to depositional environment but rather to increased input of volcanic ash during the accumulation of this interval. Early stabilization of ash produced clay-coated microfabrics in sediments that are otherwise similar to the transgressive deposits.« less

An Organismal Model for Gene Regulatory Networks in the Gut-Associated Immune Response

PubMed Central

Buckley, Katherine M.; Rast, Jonathan P.

2017-01-01

The gut epithelium is an ancient site of complex communication between the animal immune system and the microbial world. While elements of self-non-self receptors and effector mechanisms differ greatly among animal phyla, some aspects of recognition, regulation, and response are broadly conserved. A gene regulatory network (GRN) approach provides a means to investigate the nature of this conservation and divergence even as more peripheral functional details remain incompletely understood. The sea urchin embryo is an unparalleled experimental model for detangling the GRNs that govern embryonic development. By applying this theoretical framework to the free swimming, feeding larval stage of the purple sea urchin, it is possible to delineate the conserved regulatory circuitry that regulates the gut-associated immune response. This model provides a morphologically simple system in which to efficiently unravel regulatory connections that are phylogenetically relevant to immunity in vertebrates. Here, we review the organism-wide cellular and transcriptional immune response of the sea urchin larva. A large set of transcription factors and signal systems, including epithelial expression of interleukin 17 (IL17), are important mediators in the activation of the early gut-associated response. Many of these have homologs that are active in vertebrate immunity, while others are ancient in animals but absent in vertebrates or specific to echinoderms. This larval model provides a means to experimentally characterize immune function encoded in the sea urchin genome and the regulatory interconnections that control immune response and resolution across the tissues of the organism. PMID:29109720

Warming influences Mg2+ content, while warming and acidification influence calcification and test strength of a sea urchin.

PubMed

Byrne, Maria; Smith, Abigail M; West, Samantha; Collard, Marie; Dubois, Philippe; Graba-landry, Alexia; Dworjanyn, Symon A

2014-11-04

We examined the long-term effects of near-future changes in temperature and acidification on skeletal mineralogy, thickness, and strength in the sea urchin Tripneustes gratilla reared in all combinations of three pH (pH 8.1, 7.8, 7.6) and three temperatures (22 °C, 25 °C, 28 °C) from the early juvenile to adult, over 146 days. As the high-magnesium calcite of the echinoderm skeleton is a biomineral form highly sensitive to acidification, and influenced by temperature, we documented the MgCO3 content of the spines, test plates, and teeth. The percentage of MgCO3 varied systematically, with more Mg2+ in the test and spines. The percentage of MgCO3 in the test and teeth, but not the spines increased with temperature. Acidification did not change the percentage MgCO3. Test thickness increased with warming and decreased at pH 7.6, with no interaction between these factors. In crushing tests live urchins mostly ruptured at sutures between the plates. The force required to crush a live urchin was reduced in animals reared in low pH conditions but increased in those reared in warm conditions, a result driven by differences in urchin size. It appears that the interactive effects of warming and acidification on the Mg2+ content and protective function of the sea urchin skeleton will play out in a complex way as global climatic change unfolds.

²⁶Mg labeling of the sea urchin regenerating spine: Insights into echinoderm biomineralization process.

PubMed

Gorzelak, Przemysław; Stolarski, Jarosław; Dubois, Philippe; Kopp, Christophe; Meibom, Anders

2011-10-01

This paper reports the results of the first dynamic labeling experiment with regenerating spines of sea urchins Paracentrotus lividus using the stable isotope ²⁶Mg and NanoSIMS high-resolution isotopic imaging, which provide a direct information about the growth process. Growing spines were labeled twice (for 72 and 24 h, respectively) by increasing the abundance of ²⁶Mg in seawater. The incorporation of ²⁶Mg into the growing spines was subsequently imaged with the NanoSIMS ion microprobe. Stereom trabeculae initially grow as conical micro-spines, which form within less than 1 day. These micro-spines fuse together by lateral outgrowths and form a thin, open meshwork (inner stereom), which is subsequently reinforced by addition of layered thickening deposits (outer stereom). The (longitudinal) growth rate of the inner stereom is ca. 125 μm/day. A single (ca. 1 μm) thickening layer in the stereom trabeculae is deposited during 24h. The thickening process is contemporaneous with the formation micro-spines and involves both longitudinal trabeculae and transverse bridges to a similar degree. Furthermore, the skeleton-forming cells remain active in the previously formed open stereom for at least 10 days, and do not migrate upwards until the end of the thickening process. The experimental capability presented here provides a new way to obtain detailed information about the skeleton formation of a multitude of marine, calcite producing organisms. Copyright © 2011 Elsevier Inc. All rights reserved.

Crystalline order of a water/glycine film coadsorbed on the (104) calcite surface.

PubMed

Magdans, Uta; Torrelles, Xavier; Angermund, Klaus; Gies, Hermann; Rius, Jordi

2007-04-24

For biomineralization processes, the interaction of the surface of calcite crystals with organic molecules is of particular importance. Especially, biologically controlled biomineralization as in exoskeletons of mollusks and echinoderms, e.g., sea urchin with single-crystal-like spines and shells,1-3 requires molecular control of seed formation and growth process. So far, experiments showing the obvious influence of organic molecules on the morphology and habit of calcite crystals have demonstrated the molecular dimension of the interaction.4-7 Details of the kinetics of growth and dissolution of mineral surfaces influenced by additives are available,8,9 but other experimental data about the structure of the organic/inorganic interface on the atomic scale are rare. On the other hand, complicated organic macromolecules which are involved in biomineralization are numerous, with only a small fraction solved in structure and function so far.10-13 Therefore, model systems have to be designed to provide a basic understanding for the interaction process.14 Using grazing incidence X-ray diffraction combined with molecular modeling techniques, we show that glycine molecules order periodically on the calcite (104) face in competition with the solvent water when exposed to an aqueous solution of the most simple amino acid. In contrast to the general concept of the charge-matching fit of organic molecules on mineral surfaces,4,14 glycine is not attached to the calcite surface directly but substitutes for water molecules in the second hydration layer.

Using computational fluid dynamics to test functional and ecological hypotheses in fossil taxa

NASA Astrophysics Data System (ADS)

Rahman, Imran

2016-04-01

Reconstructing how ancient organisms moved and fed is a major focus of study in palaeontology. Traditionally, this has been hampered by a lack of objective data on the functional morphology of extinct species, especially those without a clear modern analogue. However, cutting-edge techniques for characterizing specimens digitally and in three dimensions, coupled with state-of-the-art computer models, now provide a robust framework for testing functional and ecological hypotheses even in problematic fossil taxa. One such approach is computational fluid dynamics (CFD), a method for simulating fluid flows around objects that has primarily been applied to complex engineering-design problems. Here, I will present three case studies of CFD applied to fossil taxa, spanning a range of specimen sizes, taxonomic groups and geological ages. First, I will show how CFD enabled a rigorous test of hypothesized feeding modes in an enigmatic Ediacaran organism with three-fold symmetry, revealing previously unappreciated complexity of pre-Cambrian ecosystems. Second, I will show how CFD was used to evaluate hydrodynamic performance and feeding in Cambrian stem-group echinoderms, shedding light on the probable feeding strategy of the latest common ancestor of all deuterostomes. Third, I will show how CFD allowed us to explore the link between form and function in Mesozoic ichthyosaurs. These case studies serve to demonstrate the enormous potential of CFD for addressing long-standing hypotheses for a variety of fossil taxa, opening up an exciting new avenue in palaeontological studies of functional morphology.

Targeting stemness is an effective strategy to control EML4-ALK+ non-small cell lung cancer cells.

PubMed

Oh, Se Jin; Noh, Kyung Hee; Lee, Young-Ho; Hong, Soon-Oh; Song, Kwon-Ho; Lee, Hyo-Jung; Kim, Soyeon; Kim, Tae Min; Jeon, Ju-Hong; Seo, Jae Hong; Kim, Dong-Wan; Kim, Tae Woo

2015-11-24

The fusion between anaplastic lymphoma kinase (ALK) and echinoderm microtubule-associated protein-like 4 (EML4) is a causative factor in a unique subset of patients with non-small cell lung carcinoma (NSCLC). Although the inhibitor crizotinib, as it blocks the kinase activity of the resulting EML4-ALK fusion protein, displays remarkable initial responses, a fraction of NSCLC cases eventually become resistant to crizotinib by acquiring mutations in the ALK domain or activating bypass pathways via EGFR, KIT, or KRAS. Cancer stem cell (CSC) theory provides a plausible explanation for acquisition of tumorigenesis and resistance. However, the question as to whether EML4-ALK-driven tumorigenesis is linked with the stem-like property and whether the stemness is an effective target in controlling EML4-ALK+ NSCLC including crizotinib-resistant NSCLC cells has not been addressed. Here, we report that stem-like properties stem from ALK activity in EML4-ALK+ NSCLC cells. Notably, treatment with rapamycin, a CSC targeting agent, attenuates stem-like phenotypes of the EML4-ALK+ cells, which increased capability of tumor formation and higher expression of stemness-associated molecules such as ALDH, NANOG, and OCT4. Importantly, combinational treatment with rapamycin and crizotinib leads to synergistic anti-tumor effects on EML4-ALK+ NSCLC cells as well as on those resistant to crizotinib. Thus, we provide a proof of principle that targeting stemness would be a novel strategy to control intractable EML4-ALK+ NSCLC.

Tropical dermatology: marine and aquatic dermatology.

PubMed

Haddad, Vidal; Lupi, Omar; Lonza, Juan Pedro; Tyring, Stephen K

2009-11-01

Dermatoses caused by marine organisms are frequently seen in dermatology clinics worldwide. Cutaneous injuries after exposure to marine environments include bacterial and fungal infections and lesions caused by aquatic plants and protists. Some of these diseases are well known by dermatologists, such as Vibrio vulnificus septicemia and erysipeloid, but others are uncommon, such as envenomation caused by ingestion or contact with certain dinoflagellates or cyanobacteria, which are associated with rashes that can begin within minutes after exposure. Many marine/aquatic invertebrates, such as sponges, cnidarians, echinoderms, crustaceans, and mollusks, are associated with different kinds of dermatologic lesions that can vary from irritant or allergic contact dermatitis to physical trauma and envenomations. These cutaneous lesions may result in mild local reactions or can be associated with severe systemic reactions. Invertebrate animals, such as cnidarians, sea urchins, and worms, and aquatic vertebrates, such as venomous fishes and stingrays, are commonly associated with skin lesions in many countries, where they can constitute occupational dermatoses among fishermen and scuba divers, but they can also be observed among persons who contact these animals in kitchens or beaches. The presence of unusual lesions, a recent travel history, and/or a report of contact with an aquatic environment (including ownership of a marine or freshwater aquarium) should alert the dermatologist to the etiology of the cutaneous problems. After completing this learning activity, participants should be able to recognize the cutaneous manifestations of marine/aquatic infections, bites, stings, and wounds, etc., treat the cutaneous manifestations of marine/aquatic injuries, and help prevent marine/aquatic injuries.

Depositional environments and sequence architecture of the Raha and Abu Qada formations (Cenomanian-Turonian), west central Sinai, Egypt

NASA Astrophysics Data System (ADS)

Anan, Tarek I.; El-Shahat, Adam; Genedi, Adel; Grammer, Michael

2013-06-01

Cenomanian-Turonian deposits are important reservoirs for many oil fields in the Western Desert and the Gulf of Suez region of Egypt. Study of the Raha and Abu Qada formations (Cenomanian-Turonian), from five dip-oriented outcrop locations in west central Sinai; indicates deposition of a mixed siliciclastic-carbonate system on a ramp setting. The inner ramp facies (bivalve and benthonic foraminiferal wackestone) grades northward to the mid ramp facies (echinoderm calcisphere packstone, and oyster floatstone), and outer ramp facies (planktonic foraminiferal wackestone and calcisphere wackestone). The two studied formations comprise one second-order depositional sequence (duration of approximately 10 Million years). This large scale sequence includes four third-order depositional sequences, three of which are observed in the Raha Formation, with the other one recorded in the Abu Qada Formation. Because west central Sinai was tectonically stable during the Cenomanian and Turonian, the main factor controlling the lateral and vertical distribution of facies tracts is likely due to changes in the relative sea level. The Cenomanian-Turonian boundary event is known as the largest oceanic anoxic event during the Cretaceous. This global event has been documented in three of the studied sections. The recorded δ13C excursions range from +3.04‰ to +5.24‰. These high positive excursions in δ13C are associated with highly negative values of δ18O (values range from -6.01‰ to -1.38‰).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saller, A.H.; Schlanger, S.O.

Two wells drilled along the margin of Enewetak Atoll penetrated approximately 1000 m of upper Eocene, Oligocene, and lower Miocene carbonates. Strontium isotope stratigraphy indicates relatively continuous deposition of carbonate from 40 Ma to 20 Ma. Depositional environments show a gradual basinward progradation of facies with slope carbonates passing upward into fore-reef, reef, back-reef, and lagoonal carbonates. Slope strata contain wackestones and packstones with submarine-cemented lithoclasts, coral, coralline algae fragments, benthic rotaline forams, planktonic forams, and echinoderm fragments. Fore-reef strata are dominantly packstones and boundstones containing large pieces of coral, abundant benthic forams, coralline algae fragments, stromatoporoids( ), and minormore » planktonic forams. Reef and near-reef sediments include coralgal boundstones and grainstones with abundant benthic forams. Halimeda and miliolid forams are common in lagoonward parts of the back reef. Sponge borings, geopetal structures, and fractures are common in reef and fore-reef strata. Lagoonal strata are wackestones and packstones with common mollusks, coral, coralline algae, and benthic forams (rotaline and miliolid). Diagenesis has extensively altered strata near the atoll margin. Aragonite dissolution and calcite cements (radiaxial and cloudy prismatic) are abundant in fore-reef, reef, and some back-reef strata. Petrographic and geochemical data indicate aragonite dissolution and calcite cementation in seawater at burial depths of 100 to 300 m. Dolomite occurs in slope and deeply buried reefal carbonates. Most dolomitization occurred at burial depths of more than 1000 m in cool marine waters circulating through the atoll. lagoonal strata are not significantly altered by marine diagenesis and still contain abundant primary aragonite and magnesium calcite.« less

Unique system of photoreceptors in sea urchin tube feet

PubMed Central

Ullrich-Lüter, Esther M; Dupont, Sam; Arboleda, Enrique; Hausen, Harald; Arnone, Maria Ina

2011-01-01

Different sea urchin species show a vast variety of responses to variations in light intensity; however, despite this behavioral evidence for photosensitivity, light sensing in these animals has remained an enigma. Genome information of the recently sequenced purple sea urchin (Strongylocentrotus purpuratus) allowed us to address this question from a previously unexplored molecular perspective by localizing expression of the rhabdomeric opsin Sp-opsin4 and Sp-pax6, two genes essential for photoreceptor function and development, respectively. Using a specifically designed antibody against Sp-Opsin4 and in situ hybridization for both genes, we detected expression in two distinct groups of photoreceptor cells (PRCs) located in the animal's numerous tube feet. Specific reactivity of the Sp-Opsin4 antibody with sea star optic cushions, which regulate phototaxis, suggests a similar visual function in sea urchins. Ultrastructural characterization of the sea urchin PRCs revealed them to be of a microvillar receptor type. Our data suggest that echinoderms, in contrast to chordates, deploy a microvillar, r-opsin–expressing PRC type for vision, a feature that has been so far documented only in protostome animals. Surprisingly, sea urchin PRCs lack any associated screening pigment. Indeed, one of the tube foot PRC clusters may account for directional vision by being shaded through the opaque calcite skeleton. The PRC axons connect to the animal internal nervous system, suggesting an integrative function beyond local short circuits. Because juveniles display no phototaxis until skeleton completion, we suggest a model in which the entire sea urchin, deploying its skeleton as PRC screening device, functions as a huge compound eye. PMID:21536888

Evidence for the evolution of tenascin and fibronectin early in the chordate lineage.

PubMed

Tucker, Richard P; Chiquet-Ehrismann, Ruth

2009-02-01

Fibronectin and tenascin are extracellular matrix glycoproteins that play important roles in cell adhesion and motility. In a previous study we provided evidence that tenascin first appeared early in the chordate lineage. As tenascin has been proposed to act, in part, through modulation of cell-fibronectin interactions, we sought here to identify fibronectin genes in non-vertebrate chordates and other invertebrates to determine if tenascin and fibronectin evolved separately or together, and to identify phylogenetically conserved features of both proteins. We found that the genome of the urochordate Ciona savignyi contains both a tenascin gene and a gene encoding a fibronectin-like protein with fibronectin type 1, 2 and 3 repeats. The genome of the cephalochordate Branchiostoma floridae (amphioxus) also has a tenascin gene. However, we could not identify a fibronectin-like gene in B. floridae, nor could we identify fibronectin or tenascin genes in echinoderms, protostomes or cnidarians. If urochordates are more closely related to vertebrates, tenascin may have evolved before fibronectin in an ancestor common to tunicates and amphioxus. Alternatively, tenascin and fibronectin may have evolved in an ancestor common to B. floridae and C. savignyi and the fibronectin gene was subsequently lost in the cephalochordate lineage. The fibronectin-like gene from C. savignyi does not encode the RGD motif for integrin binding found in all vertebrate fibronectins, and it lacks most of the fibronectin type 1 domains believed to be critical for fibrillogenesis. In contrast, the tenascin gene in B. floridae encodes multiple RGD motifs, suggesting that integrin binding is fundamental to tenascin function.

Time-lapse camera studies of sea-disposed chemical munitions in Hawaii

NASA Astrophysics Data System (ADS)

Edwards, Margo H.; Fornari, Daniel J.; Rognstad, Mark R.; Kelley, Christopher D.; Mah, Christopher L.; Davis, Logan K.; Flores, Kyle R. M.; Main, Erin L.; Bruso, Natalie L.

2016-06-01

The interactions between fauna and sea-disposed munitions provide important evidence regarding whether munitions constituents affect the health of the ocean environment and its inhabitants. To date few studies of these interactions have been conducted at deep-water disposal sites; typically observations of fauna in the vicinity of sea-disposed munitions are limited to the few minutes or hours required to collect physical samples at a specific location. During the 2012 Hawaii Undersea Military Munitions Assessment (HUMMA) field program we deployed two deep-sea time-lapse camera systems with the objectives of cataloging the diversity of fauna visiting sea-disposed chemical munitions and observing faunal behavior and physiology. Over the 1- and 3-day deployments we recorded 28 different species of fishes, crustaceans, mollusks, cnidarians, and echinoderms at the two sites. Both cameras captured the previously undocumented behavior of brisingid sea stars repositioning themselves along chemical munitions casings. Despite the fact that brisingid sea stars are able to move, for the duration of both time-lapse experiments they remained on chemical munitions casings. We interpret this result to indicate that the advantages of residing on a hard substrate slightly elevated above the seafloor outweigh the effects of chemical munitions constituents for brisingid sea stars. One type of physiological anomaly observed on several arms of the brisingid sea stars at the time-lapse sites led to the collection and examination of six specimens. As reported by Mah (2015. Deep Sea Res. II, 2015, XX-XX), these physiological features are the result of parasitic crustaceans and are not caused by chemical munitions constituents.

Apoptosis inducing capacity of Holothuria arenicola in CT26 colon carcinoma cells in vitro and in vivo

PubMed Central

Baharara, Javad; Amini, Elaheh; Afzali, Mahbubeh; Nikdel, Najme; Mostafapour, Asma; Kerachian, Mohammad Amin

2016-01-01

Objective(s): Sea cucumber is one of the classes of echinoderms, which is considered as a health marine product and possess various biological characteristics with therapeutic application. The present investigation attempted to evaluate the potential of anti-cancer Persian Gulf sea cucumber species Holothuria arenicola (H. arenicola) aqueous extract on mice colon carcinoma cells in vitro and in vivo. Materials and Methods: The CT26 carcinoma cells were treated with various concentrations of extract in 24 and 48 hr, and then its anti-proliferative effect was measured by MTT assay and morphological observations. The apoptotic effect was examined by fluorescence microscopy (DNA fragmentation assay), Flow cytometry, caspase-3 and -9 colorimetric assays. The in vivo anti-tumor efficacy of sea cucumber extract on CT26 tumor cells transplanted in BALB/c mice was also investigated. Results: The results showed that the water extract of sea cucumber revealed remarkable anti-proliferative effect on CT26 tumor cells with IC50= 31 µg/ml with recruitment of intrinsic apoptotic pathway in vitro. In addition, the colon tumor volume in treated groups remarkably reduced in homozygous mice. Histopathological examination elucidated that sea cucumber extract attenuated tumor size and volume along with apoptosis characteristics. Moreover, RT-PCR analysis revealed that sea cucumber extract induced intrinsic apoptosis in vivo through suppression of Bcl-2 expression. Conclusion: Our data confirmed this notion that sea cucumber administrates anti-cancer effect that can be used as complementary in preclinical experiments, so further characterization are recommended for detection sea cucumber metabolites and clinical application. PMID:27279978

Megafauna of the UKSRL exploration contract area and eastern Clarion-Clipperton Zone in the Pacific Ocean: Echinodermata

PubMed Central

Ziegler, Amanda F; Kremenetskaia, Antonina; Mah, Christopher L; Mooi, Rich; O'Hara, Tim; Pawson, David L; Roux, Michel; Smith, Craig R

2017-01-01

Abstract Background There is growing interest in mining polymetallic nodules from the abyssal Clarion-Clipperton Zone (CCZ) in the tropical Pacific Ocean. Despite being the focus of environmental studies for decades, the benthic megafauna of the CCZ remain poorly known. In order to predict and manage the environmental impacts of mining in the CCZ, baseline knowledge of the megafauna is essential. The ABYSSLINE Project has conducted benthic biological baseline surveys in the UK Seabed Resources Ltd polymetallic-nodule exploration contract area (UK-1). Prior to these research cruises in 2013 and 2015, no biological studies had been done in this area of the eastern CCZ. New information Using a Remotely Operated Vehicle and Autonomous Underwater Vehicle, the megafauna within the UKSRL exploration contract area (UK-1) and at a site ~250 km east of the UK-1 area were surveyed, allowing us to make the first estimates of megafaunal morphospecies richness from the imagery collected. Here, we present an atlas of the abyssal echinoderm megafauna observed and collected during the ABYSSLINE cruises to the UK-1 polymetallic-nodule exploration contract area in the CCZ. There appear to be at least 62 distinct morphospecies (13 Asteroidea, 5 Crinoidea, 9 Echinoidea, 29 Holothuroidea and 6 Ophiuroidea) identified mostly by imagery but also using molecular barcoding for a limited number of animals that were collected. This atlas will aid the synthesis of megafaunal presence/absence data collected by contractors, scientists and other stakeholders undertaking work in the CCZ, ultimately helping to decipher the biogeography of the megafauna in this threatened habitat. PMID:28765722

Megafauna of the UKSRL exploration contract area and eastern Clarion-Clipperton Zone in the Pacific Ocean: Echinodermata.

PubMed

Amon, Diva J; Ziegler, Amanda F; Kremenetskaia, Antonina; Mah, Christopher L; Mooi, Rich; O'Hara, Tim; Pawson, David L; Roux, Michel; Smith, Craig R

2017-01-01

There is growing interest in mining polymetallic nodules from the abyssal Clarion-Clipperton Zone (CCZ) in the tropical Pacific Ocean. Despite being the focus of environmental studies for decades, the benthic megafauna of the CCZ remain poorly known. In order to predict and manage the environmental impacts of mining in the CCZ, baseline knowledge of the megafauna is essential. The ABYSSLINE Project has conducted benthic biological baseline surveys in the UK Seabed Resources Ltd polymetallic-nodule exploration contract area (UK-1). Prior to these research cruises in 2013 and 2015, no biological studies had been done in this area of the eastern CCZ. Using a Remotely Operated Vehicle and Autonomous Underwater Vehicle, the megafauna within the UKSRL exploration contract area (UK-1) and at a site ~250 km east of the UK-1 area were surveyed, allowing us to make the first estimates of megafaunal morphospecies richness from the imagery collected. Here, we present an atlas of the abyssal echinoderm megafauna observed and collected during the ABYSSLINE cruises to the UK-1 polymetallic-nodule exploration contract area in the CCZ. There appear to be at least 62 distinct morphospecies (13 Asteroidea, 5 Crinoidea, 9 Echinoidea, 29 Holothuroidea and 6 Ophiuroidea) identified mostly by imagery but also using molecular barcoding for a limited number of animals that were collected. This atlas will aid the synthesis of megafaunal presence/absence data collected by contractors, scientists and other stakeholders undertaking work in the CCZ, ultimately helping to decipher the biogeography of the megafauna in this threatened habitat.

Relationships among Egg Size, Composition, and Energy: A Comparative Study of Geminate Sea Urchins

PubMed Central

McAlister, Justin S.; Moran, Amy L.

2012-01-01

Egg size is one of the fundamental parameters in the life histories of marine organisms. However, few studies have examined the relationships among egg size, composition, and energetic content in a phylogenetically controlled context. We investigated the associations among egg size, composition, and energy using a comparative system, geminate species formed by the closure of the Central American Seaway. We examined western Atlantic (WA) and eastern Pacific (EP) species in three echinoid genera, Echinometra, Eucidaris, and Diadema. In the genus with the largest difference in egg size between geminates (Echinometra), the eggs of WA species were larger, lipid rich and protein poor compared to the smaller eggs of their EP geminate. In addition, the larger WA eggs had significantly greater total egg energy and summed biochemical constituents yet significantly lower egg energy density (energy-per-unit-volume). However, the genera with smaller (Eucidaris) or no (Diadema) differences in egg size were not significantly different in summed biochemical constituents, total egg energy, or energy density. Theoretical models generally assume a strong tradeoff between egg size and fecundity that limits energetic investment and constrains life history evolution. We show that even among closely-related taxa, large eggs cannot be assumed to be scaled-up small eggs either in terms of energy or composition. Although our data comes exclusively from echinoid echinoderms, this pattern may be generalizable to other marine invertebrate taxa. Because egg composition and egg size do not necessarily evolve in lockstep, selective factors such as sperm limitation could act on egg volume without necessarily affecting maternal or larval energetics. PMID:22911821

Marine environmental risk assessment and acute water quality criterion for pentachlorophenol in coastal waters.

PubMed

Beiras, R; Tato, T

2018-04-07

Pentachlorophenol (PCP) is a organochlorine biocide that, unlike most other organochlorines, is still in use as timber preservative. Its water solubility, high toxicity, bioaccumulation potential, and the concentrations reported in estuarine waters (up to 0.1 µg L -1 ) indicate it may pose a risk in coastal environments. Aquatic environrmental regulations are commonly based on standard freshwater organisms that may not represent the sensitivity of marine species. The present study consists of a water quality criteira reevalutation of PCP in coastal waters based on toxicity tests conducted recording sensitive endpoints of marine species representative of coastal ecosystems, following QA/QC standard procedures. The toxicity thresholds (EC 10 ) found were 4.69 µg L -1 for Paracentrotus lividus sea-urchin embryos, 6.47 µg L -1 for Mytilus galloprovincialis mussel larvae, and 78.4 µg L -1 for Isochrysis galbana cells. Therefore, there is only one order of magnitude between the predicted no-effect concentration (PNEC) for early life stages of bivalves and echinoderms and the maximum concentrations actually recorded in coastal water, which yields a remarkable risk quotient for PCP in these highly productive marine habitats. In addition, we have reviewed the ecotoxicological data on PCP toxicity on marine species representative of the main systematic groups, from algae to chordates, and derived a probabilistic acute saltwater quality criterion of 2.66 µg L -1 , intended to protect 95% of the marine species. Lack of adequate protection for marine ecosystems in some current PCP national guidelines has been identified.

Sedimentology and diagenesis of Miocene Lirio Limestone, Isla de Mona, Puerto Rico

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruiz, H.; Gonzalez, L.A.; Budd, A.F.

1991-03-01

Isla de Mona is a carbonate plateau, 50 mi west of Puerto Rico. The island lies on the southern portion of the Mona Platform. It is composed mostly of two Miocene carbonate units: Isla de Mona Dolomite overlain by Lirio Limestone. The Lirio Limestone was deposited on a sloping erosional surface over the Isla de Mona Dolomite. The Miocene Lirio Limestone consists mostly of backreef sands (packstones) with a reefal sequence (boundstones and grainstones) present in the southwestern portion of the island. The reefal sequence is made up mostly of Stylophora, Porites, and Millepora. Thin, discreet pockets of carbonate mud,more » rich in planktonic foraminifera and radiolarians and mixed with shallow benthic fauna/flora (foraminifera, echinoderms, red algae, and corals) interpreted as storm deposits, are found throughout the unit. An extensive reefal zone can be inferred to be present throughout the southwestern to southern portions of the Mona Platform. The Lirio Limestone is heavily karstified and is riddled with sinkholes on the plateau surfaces and caves around the periphery of the island. Caves are exposed around the periphery of the island, radiating from a depression in the central portions of the Lirio Limestone, near contacts with the Isla de Mona Dolomite, are partially dolomitized. The southwestern outcrops exhibit partial dolomitization throughout. The distribution of sinkholes, seaward caverns, and partial dolomitization of the lowermost Lirio Limestone suggests diagenetic modifications by meteoric fluids in central exposed portions of the island and by marine-meteoric fluids in the lowermost portions of the phreatic lens.« less

Mixed siliciclastic and carbonate sedimentation within Spar Mountain Member of Ste. Genevieve Limestone, Hamilton County, Illinois

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roberts, M.J.; Pryor, W.A.

1985-02-01

The Spar Mountain Member of the Ste. Genevieve Limestone (middle Mississippian) in Hamilton County, Illinois, consists of 40-60 ft (12-18 m) of interbedded limestones, shales, and sandstones. Five cores and 1400 electric logs were used to delineate two shallowing-upward carbonate cycles and 2 major clastic pulses within the Spar Mountain. Eight lithofacies representing 6 depositional environments were identified. They are: (A) echinoderm-brachiopod dolostone to packstone (outer ramp), (B) ooid-peloidal grainstone (intermediate ramp), (C) skeletal grainstone (intermediate ramp), (D) ooid-molluscan-intraclastic wackestone to grainstone (inner ramp), (E) pelletal-skeletal wackestone (inner ramp), (F) quartzarenite (channelized nearshore), (G) quartz-sublithic arenite to wacke (delta platform),more » and (H) quartz mudstone (prodelta, delta platform). Deposition occurred on a southwest-dipping carbonate ramp, with siliciclastic sediments originating from the northeast. The sequence of facies and their inferred depositional environments record 2 major progradational episodes. Oolitic facies are interpreted to be of tidal-bar belt origin and quartzarenite facies are interpreted to be of delta-distributary channel origin. Their distribution is partially controlled by antecedent and syndepositional topography. Many of these paleotopographic highes are positive features today and yield pinch-out stratigraphic relationships. Paleogeographic reconstructions demonstrate that the primary control on facies distribution was the position of the delta proper along strike. However, depositional topography also influenced sedimentation, particularly in the sand-sized fraction. Using this concept, better prediction of underlying porous buildups (ooid shoals) is possible if thickness of the overlying siliciclastic is known. Within buildups, a complex diagenetic history complicates the distribution of porosity.« less

Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity.

PubMed

Krishnan, Arunkumar; Iyer, Lakshminarayan M; Holland, Stephen J; Boehm, Thomas; Aravind, L

2018-04-03

AID/APOBEC deaminases (AADs) convert cytidine to uridine in single-stranded nucleic acids. They are involved in numerous mutagenic processes, including those underpinning vertebrate innate and adaptive immunity. Using a multipronged sequence analysis strategy, we uncover several AADs across metazoa, dictyosteliida, and algae, including multiple previously unreported vertebrate clades, and versions from urochordates, nematodes, echinoderms, arthropods, lophotrochozoans, cnidarians, and porifera. Evolutionary analysis suggests a fundamental division of AADs early in metazoan evolution into secreted deaminases (SNADs) and classical AADs, followed by diversification into several clades driven by rapid-sequence evolution, gene loss, lineage-specific expansions, and lateral transfer to various algae. Most vertebrate AADs, including AID and APOBECs1-3, diversified in the vertebrates, whereas the APOBEC4-like clade has a deeper origin in metazoa. Positional entropy analysis suggests that several AAD clades are diversifying rapidly, especially in the positions predicted to interact with the nucleic acid target motif, and with potential viral inhibitors. Further, several AADs have evolved neomorphic metal-binding inserts, especially within loops predicted to interact with the target nucleic acid. We also observe polymorphisms, driven by alternative splicing, gene loss, and possibly intergenic recombination between paralogs. We propose that biological conflicts of AADs with viruses and genomic retroelements are drivers of rapid AAD evolution, suggesting a widespread presence of mutagenesis-based immune-defense systems. Deaminases like AID represent versions "institutionalized" from the broader array of AADs pitted in such arms races for mutagenesis of self-DNA, and similar recruitment might have independently occurred elsewhere in metazoa. Copyright © 2018 the Author(s). Published by PNAS.

RNA Deep Sequencing Reveals Differential MicroRNA Expression during Development of Sea Urchin and Sea Star

PubMed Central

Kadri, Sabah; Hinman, Veronica F.; Benos, Panayiotis V.

2011-01-01

microRNAs (miRNAs) are small (20–23 nt), non-coding single stranded RNA molecules that act as post-transcriptional regulators of mRNA gene expression. They have been implicated in regulation of developmental processes in diverse organisms. The echinoderms, Strongylocentrotus purpuratus (sea urchin) and Patiria miniata (sea star) are excellent model organisms for studying development with well-characterized transcriptional networks. However, to date, nothing is known about the role of miRNAs during development in these organisms, except that the genes that are involved in the miRNA biogenesis pathway are expressed during their developmental stages. In this paper, we used Illumina Genome Analyzer (Illumina, Inc.) to sequence small RNA libraries in mixed stage population of embryos from one to three days after fertilization of sea urchin and sea star (total of 22,670,000 reads). Analysis of these data revealed the miRNA populations in these two species. We found that 47 and 38 known miRNAs are expressed in sea urchin and sea star, respectively, during early development (32 in common). We also found 13 potentially novel miRNAs in the sea urchin embryonic library. miRNA expression is generally conserved between the two species during development, but 7 miRNAs are highly expressed in only one species. We expect that our two datasets will be a valuable resource for everyone working in the field of developmental biology and the regulatory networks that affect it. The computational pipeline to analyze Illumina reads is available at http://www.benoslab.pitt.edu/services.html. PMID:22216218

Different routes lead to apoptosis in unfertilized sea urchin eggs.

PubMed

Philippe, Laetitia; Tosca, Lucie; Zhang, Wen Ling; Piquemal, Marion; Ciapa, Brigitte

2014-03-01

Results obtained in various species, from mammals to invertebrates, show that arrest in the cell cycle of mature oocytes is due to a high ERK activity. Apoptosis is stimulated in these oocytes if fertilization does not occur. Our previous data suggest that apoptosis of unfertilized sea urchin eggs is the consequence of an aberrant short attempt of development that occurs if ERK is inactivated. They contradict those obtained in starfish, another echinoderm, where inactivation of ERK delays apoptosis of aging mature oocytes that are nevertheless arrested at G1 of the cell cycle as in the sea urchin. This suggests that the cell death pathway that can be activated in unfertilized eggs is not the same in sea urchin and in starfish. In the present study, we find that protein synthesis is necessary for the survival of unfertilized sea urchin eggs, contrary to starfish. We also compare the effects induced by Emetine, an inhibitor of protein synthesis, with those triggered by Staurosporine, a non specific inhibitor of protein kinase that is widely used to induce apoptosis in many types of cells. Our results indicate that the unfertilized sea urchin egg contain different mechanisms capable of leading to apoptosis and that rely or not on changes in ERK activity, acidity of intracellular organelles or intracellular Ca and pH. We discuss the validity of some methods to investigate cell death such as measurements of caspase activation with the fluorescent caspase indicator FITC-VAD-fmk or acidification of intracellular organelles, methods that may lead to erroneous conclusions at least in the sea urchin model.

An efficient method to find potentially universal population genetic markers, applied to metazoans

PubMed Central

2010-01-01

Background Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing) loci are restricted to vertebrates or belong to multigenic families. Results In order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the Homolens databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians). The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals. Conclusions Our new method now makes it possible to (i) rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii) compare genetic diversity at potentially homologous polymorphic loci between divergent taxa. PMID:20836842

Sperm proteasome and fertilization.

PubMed

Sutovsky, Peter

2011-07-01

The omnipresent ubiquitin-proteasome system (UPS) is an ATP-dependent enzymatic machinery that targets substrate proteins for degradation by the 26S proteasome by tagging them with an isopeptide chain composed of covalently linked molecules of ubiquitin, a small chaperone protein. The current knowledge of UPS involvement in the process of sperm penetration through vitelline coat (VC) during human and animal fertilization is reviewed in this study, with attention also being given to sperm capacitation and acrosome reaction/exocytosis. In ascidians, spermatozoa release ubiquitin-activating and conjugating enzymes, proteasomes, and unconjugated ubiquitin to first ubiquitinate and then degrade the sperm receptor on the VC; in echinoderms and mammals, the VC (zona pellucida/ZP in mammals) is ubiquitinated during oogenesis and the sperm receptor degraded during fertilization. Various proteasomal subunits and associated enzymes have been detected in spermatozoa and localized to sperm acrosome and other sperm structures. By using specific fluorometric substrates, proteasome-specific proteolytic and deubiquitinating activities can be measured in live, intact spermatozoa and in sperm protein extracts. The requirement of proteasomal proteolysis during fertilization has been documented by the application of various proteasome-specific inhibitors and antibodies. A similar effect was achieved by depletion of sperm-surface ATP. Degradation of VC/ZP-associated sperm receptor proteins by sperm-borne proteasomes has been demonstrated in ascidians and sea urchins. On the applied side, polyspermy has been ameliorated by modulating sperm-associated deubiquitinating enzymes. Diagnostic and therapeutic applications could emerge in human reproductive medicine. Altogether, the studies on sperm proteasome indicate that animal fertilization is controlled in part by a unique, gamete associated, extracellular UPS.

Evaluation of EML4-ALK Fusion Proteins in Non-Small Cell Lung Cancer Using Small Molecule Inhibitors12

PubMed Central

Li, Yongjun; Ye, Xiaofen; Liu, Jinfeng; Zha, Jiping; Pei, Lin

2011-01-01

The echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) fusion gene resulting from an inversion within chromosome 2p occurs in approximately 5% of non-small cell lung cancer and is mutually exclusive with Ras and EGFR mutations. In this study, we have used a potent and selective ALK small molecule inhibitor, NPV-TAE684, to assess the oncogenic role of EML4-ALK in non-small cell lung cancer (NSCLC). We show here that TAE684 inhibits proliferation and induces cell cycle arrest, apoptosis, and tumor regression in two NSCLC models that harbor EML4-ALK fusions. TAE684 inhibits EML4-ALK activation and its downstream signaling including ERK, AKT, and STAT3. We used microarray analysis to carry out targeted pathway studies of gene expression changes in H2228 NSCLC xenograft model after TAE684 treatment and identified a gene signature of EML4-ALK inhibition. The gene signature represents 1210 known human genes, and the top biologic processes represented by these genes are cell cycle, DNA synthesis, cell proliferation, and cell death. We also compared the effect of TAE684 with PF2341066, a c-Met and ALK small molecule inhibitor currently in clinical trial in cancers harboring ALK fusions, and demonstrated that TAE684 is a much more potent inhibitor of EML4-ALK. Our data demonstrate that EML4-ALK plays an important role in the pathogenesis of a subset of NSCLC and provides insight into the mechanism of EML4-ALK inhibition by a small molecule inhibitor. PMID:21245935

Response to crizotinib in a non-small-cell lung cancer patient harboring an EML4-ALK fusion with an atypical LTBP1 insertion.

PubMed

Aguado, Cristina; Gil, Maria-de-Los-Llanos; Yeste, Zaira; Giménez-Capitán, Ana; Teixidó, Cristina; Karachaliou, Niki; Viteri, Santiago; Rosell, Rafael; Molina-Vila, Miguel A

2018-01-01

Fusion of the anaplastic lymphoma receptor tyrosine kinase gene ( ALK ) with the echinoderm microtubule-associated protein 4 gene ( EML4 ) is the second most common actionable alteration in non-small-cell lung cancer, with a frequency of 5%. Here, we present a case of an EML4-ALK-positive patient with an atypical in-frame insertion from the LTBP1 gene in the canonical junction of variant 1 . The patient was a 39-year-old never-smoker female diagnosed with Stage IV lung adenocarcinoma. A core biopsy was negative for EGFR and KRAS mutations but positive for ALK immunohistochemistry and fluorescence in situ hybridization. When submitted to nCounter, the sample showed a 3'/5' imbalance indicative of an ALK rearrangement, but failed to give a positive signal for any of the variants tested. Finally, a band with a molecular weight higher than expected appeared after reverse transcriptase-polymerase chain reaction analysis. When Sanger sequencing was performed, the band revealed an atypical EML4-ALK fusion gene with an in-frame 129 bp insertion. A 115 bp segment of the insertion corresponded to an intronic region of LTBP1 , a gene located in the short arm of chromosome 2, between ALK and EML4 . The patient received crizotinib and showed a good therapeutic response that is still ongoing after 12 months. Our result suggests that short in-frame insertions of other genes in the EML4-ALK junction do not affect the sensitivity of the EML4-ALK fusion protein to crizotinib.

Prevalence, Variability and Bioconcentration of Saxitoxin-Group in Different Marine Species Present in the Food Chain

PubMed Central

Oyaneder Terrazas, Javiera; Contreras, Héctor R.; García, Carlos

2017-01-01

The saxitoxin-group (STX-group) corresponds to toxic metabolites produced by cyanobacteria and dinoflagellates of the genera Alexandrium, Gymnodinium, and Pyrodinium. Over the last decade, it has been possible to extrapolate the areas contaminated with the STX-group worldwide, including Chile, a phenomenon that has affected ≈35% of the Southern Pacific coast territory, generating a high economic impact. The objective of this research was to study the toxicity of the STX-group in all aquatic organisms (bivalves, algae, echinoderms, crustaceans, tunicates, cephalopods, gastropods, and fish) present in areas with a variable presence of harmful algal blooms (HABs). Then, the toxic profiles of each species and dose of STX equivalents ingested by a 60 kg person from 400 g of shellfish were determined to establish the health risk assessment. The toxins with the highest prevalence detected were gonyautoxin-4/1 (GTX4/GTX1), gonyautoxin-3/2 (GTX3/GTX2), neosaxitoxin (neoSTX), decarbamoylsaxitoxin (dcSTX), and saxitoxin (STX), with average concentrations of 400, 2800, 280, 200, and 2000 µg kg−1 respectively, a species-specific variability, dependent on the evaluated tissue, which demonstrates the biotransformation of the analogues in the trophic transfer with a predominance of α-epimers in all toxic profiles. The identification in multiple vectors, as well as in unregulated species, suggests that a risk assessment and risk management update are required; also, chemical and specific analyses for the detection of all analogues associated with the STX-group need to be established. PMID:28604648

Recent evidence for evolution of the genetic code

NASA Technical Reports Server (NTRS)

Osawa, S.; Jukes, T. H.; Watanabe, K.; Muto, A.

1992-01-01

The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.

Diversity, Abundance and Community Structure of Benthic Macro- and Megafauna on the Beaufort Shelf and Slope

PubMed Central

Nephin, Jessica; Juniper, S. Kim; Archambault, Philippe

2014-01-01

Diversity and community patterns of macro- and megafauna were compared on the Canadian Beaufort shelf and slope. Faunal sampling collected 247 taxa from 48 stations with box core and trawl gear over the summers of 2009–2011 between 50 and 1,000 m in depth. Of the 80 macrofaunal and 167 megafaunal taxa, 23% were uniques, present at only one station. Rare taxa were found to increase proportional to total taxa richness and differ between the shelf ( 100 m) where they tended to be sparse and the slope where they were relatively abundant. The macrofauna principally comprised polychaetes with nephtyid polychaetes dominant on the shelf and maldanid polychaetes (up to 92% in relative abundance/station) dominant on the slope. The megafauna principally comprised echinoderms with Ophiocten sp. (up to 90% in relative abundance/station) dominant on the shelf and Ophiopleura sp. dominant on the slope. Macro- and megafauna had divergent patterns of abundance, taxa richness ( diversity) and diversity. A greater degree of macrofaunal than megafaunal variation in abundance, richness and diversity was explained by confounding factors: location (east-west), sampling year and the timing of sampling with respect to sea-ice conditions. Change in megafaunal abundance, richness and diversity was greatest across the depth gradient, with total abundance and richness elevated on the shelf compared to the slope. We conclude that megafaunal slope taxa were differentiated from shelf taxa, as faunal replacement not nestedness appears to be the main driver of megafaunal diversity across the depth gradient. PMID:25007347

Diversity, abundance and community structure of benthic macro- and megafauna on the Beaufort shelf and slope.

PubMed

Nephin, Jessica; Juniper, S Kim; Archambault, Philippe

2014-01-01

Diversity and community patterns of macro- and megafauna were compared on the Canadian Beaufort shelf and slope. Faunal sampling collected 247 taxa from 48 stations with box core and trawl gear over the summers of 2009-2011 between 50 and 1,000 m in depth. Of the 80 macrofaunal and 167 megafaunal taxa, 23% were uniques, present at only one station. Rare taxa were found to increase proportional to total taxa richness and differ between the shelf (< 100 m) where they tended to be sparse and the slope where they were relatively abundant. The macrofauna principally comprised polychaetes with nephtyid polychaetes dominant on the shelf and maldanid polychaetes (up to 92% in relative abundance/station) dominant on the slope. The megafauna principally comprised echinoderms with Ophiocten sp. (up to 90% in relative abundance/station) dominant on the shelf and Ophiopleura sp. dominant on the slope. Macro- and megafauna had divergent patterns of abundance, taxa richness (α diversity) and β diversity. A greater degree of macrofaunal than megafaunal variation in abundance, richness and β diversity was explained by confounding factors: location (east-west), sampling year and the timing of sampling with respect to sea-ice conditions. Change in megafaunal abundance, richness and β diversity was greatest across the depth gradient, with total abundance and richness elevated on the shelf compared to the slope. We conclude that megafaunal slope taxa were differentiated from shelf taxa, as faunal replacement not nestedness appears to be the main driver of megafaunal β diversity across the depth gradient.

Zooplankton seasonality across a latitudinal gradient in the Northeast Atlantic Shelves Province

NASA Astrophysics Data System (ADS)

Fanjul, Alvaro; Iriarte, Arantza; Villate, Fernando; Uriarte, Ibon; Atkinson, Angus; Cook, Kathryn

2018-05-01

Zooplankton seasonality and its environmental drivers were studied at four coastal sites within the Northeast Atlantic Shelves Province (Bilbao35 (B35) and Urdaibai35 (U35) in the Bay of Biscay, Plymouth L4 (L4) in the English Channel and Stonehaven (SH) in the North Sea) using time series spanning 1999-2013. Seasonal community patterns were extracted at the level of broad zooplankton groups and copepod and cladoceran genera using redundancy analysis. Temperature was generally the environmental factor that explained most of the taxa seasonal variations at the four sites. However, between-site differences related to latitude and trophic status (i.e. from oligotrophic to mesotrophic) were observed in the seasonality of zooplankton community, mainly in the pattern of taxa that peaked in spring-summer as opposed to late autumn-winter zooplankton, which were linked primarily to differences in the seasonal pattern of phytoplankton. The percentage of taxa variations explained by environmental factors increased with latitude and trophic status likely related to the increase in the co-variation of temperature and chlorophyll a, as well as in the increase in regularity of the seasonal patterns of both temperature and chlorophyll a from south to north, and of chlorophyll a with trophic status. Cladocerans and cirripede larvae at B35 and U35, echinoderm larvae at L4 and decapod larvae at SH made the highest contribution to shape the main mode of seasonal pattern of zooplankton community, which showed a seasonal delay with latitude, as well as with the increase in trophic status.

Shedding genomic light on Aristotle's lantern.

PubMed

Sodergren, Erica; Shen, Yufeng; Song, Xingzhi; Zhang, Lan; Gibbs, Richard A; Weinstock, George M

2006-12-01

Sea urchins have proved fascinating to biologists since the time of Aristotle who compared the appearance of their bony mouth structure to a lantern in The History of Animals. Throughout modern times it has been a model system for research in developmental biology. Now, the genome of the sea urchin Strongylocentrotus purpuratus is the first echinoderm genome to be sequenced. A high quality draft sequence assembly was produced using the Atlas assembler to combine whole genome shotgun sequences with sequences from a collection of BACs selected to form a minimal tiling path along the genome. A formidable challenge was presented by the high degree of heterozygosity between the two haplotypes of the selected male representative of this marine organism. This was overcome by use of the BAC tiling path backbone, in which each BAC represents a single haplotype, as well as by improvements in the Atlas software. Another innovation introduced in this project was the sequencing of pools of tiling path BACs rather than individual BAC sequencing. The Clone-Array Pooled Shotgun Strategy greatly reduced the cost and time devoted to preparing shotgun libraries from BAC clones. The genome sequence was analyzed with several gene prediction methods to produce a comprehensive gene list that was then manually refined and annotated by a volunteer team of sea urchin experts. This latter annotation community edited over 9000 gene models and uncovered many unexpected aspects of the sea urchin genetic content impacting transcriptional regulation, immunology, sensory perception, and an organism's development. Analysis of the basic deuterostome genetic complement supports the sea urchin's role as a model system for deuterostome and, by extension, chordate development.

Progression-Free and Overall Survival of Patients With ALK Rearrangement-Positive Non-Small Cell Lung Cancer Treated Sequentially With Crizotinib and Alectinib.

PubMed

Watanabe, Satomi; Hayashi, Hidetoshi; Okamoto, Kunio; Fujiwara, Kimiko; Hasegawa, Yoshikazu; Kaneda, Hiroyasu; Tanaka, Kaoru; Takeda, Masayuki; Nakagawa, Kazuhiko

2016-11-01

Anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors (TKIs) show marked therapeutic efficacy in patients with non-small cell lung cancer (NSCLC) harboring the echinoderm microtubule-associated protein-like 4-ALK fusion gene. The effect on overall survival (OS) of sequential treatment with the first- and second-generation ALK-TKIs crizotinib and alectinib, respectively, has remained unknown. We have examined the clinical outcome of such sequential treatment in a retrospective analysis of patients with ALK-rearranged NSCLC. Eleven patients with ALK-rearranged NSCLC treated with crizotinib followed by alectinib were identified. The progression-free survival (PFS) and OS for these patients were determined from a retrospective review of their medical records. The median PFS on crizotinib or alectinib was 6.1 months (range, 1.0-15.4 months) and 15.2 months (range, 1.0-28.3 months), respectively. The median combined PFS for both crizotinib and alectinib was 18.2 months (range, 10.4-43.7 months). Crizotinib was continued beyond radiographic evidence of progressive disease in 6 of the 11 patients, with a median duration of postprogression crizotinib treatment of 9.4 months (range, 0-20.5 months). The OS period from the diagnosis of metastatic disease or the initiation of crizotinib treatment was 51.1 months (range, 20.9-69.5 months) and 48.6 months (range, 19.8-50.1 months), respectively. Our retrospective study has revealed durable survival for alectinib treatment after crizotinib failure in patients with ALK-rearranged NSCLC. Copyright © 2016 Elsevier Inc. All rights reserved.

Biofilm attachment reduction on bioinspired, dynamic, micro-wrinkling surfaces

NASA Astrophysics Data System (ADS)

Epstein, Alexander K.; Hong, Donggyoon; Kim, Philseok; Aizenberg, Joanna

2013-09-01

Most bacteria live in multicellular communities known as biofilms that are adherent to surfaces in our environment, from sea beds to plumbing systems. Biofilms are often associated with clinical infections, nosocomial deaths and industrial damage such as bio-corrosion and clogging of pipes. As mature biofilms are extremely challenging to eradicate once formed, prevention is advantageous over treatment. However, conventional surface chemistry strategies are either generally transient, due to chemical masking, or toxic, as in the case of leaching marine antifouling paints. Inspired by the nonfouling skins of echinoderms and other marine organisms, which possess highly dynamic surface structures that mechanically frustrate bio-attachment, we have developed and tested a synthetic platform based on both uniaxial mechanical strain and buckling-induced elastomer microtopography. Bacterial biofilm attachment to the dynamic substrates was studied under an array of parameters, including strain amplitude and timescale (1-100 mm s-1), surface wrinkle length scale, bacterial species and cell geometry, and growth time. The optimal conditions for achieving up to ˜ 80% Pseudomonas aeruginosa biofilm reduction after 24 h growth and ˜ 60% reduction after 48 h were combinatorially elucidated to occur at 20% strain amplitude, a timescale of less than ˜ 5 min between strain cycles and a topography length scale corresponding to the cell dimension of ˜ 1 μm. Divergent effects on the attachment of P. aeruginosa, Staphylococcus aureus and Escherichia coli biofilms showed that the dynamic substrate also provides a new means of species-specific biofilm inhibition, or inversely, selection for a desired type of bacteria, without reliance on any toxic or transient surface chemical treatments.

Larval spicules, cilia, and symmetry as remnants of indirect development in the direct developing sea urchin Heliocidaris erythrogramma.

PubMed

Emlet, R B

1995-02-01

Nonfeeding larvae of the echinoid Heliocidaris erythrogramma were raised in culture and examined for expression of a larval skeleton and for the arrangement of the ciliated band. Opaque larvae were fixed, cleared, and examined under polarized light for evidence of calcification. By 35 hr after fertilization (at 22 degrees C), a pair of triradiate spicules was present at the posterior end of the larvae. Each member of this pair formed a fenestrated spicule as it grew laterally. This pair and another pair which formed subsequently, were arranged across a plane of bilateral symmetry orthagonal to the juvenile oral aboral axis. These paired larval spicules can be identified as reduced expressions of postoral and posterodorsal rods found in plutei, and their expression indicates that the juvenile rudiment of H. erythrogramma forms on the left side and that larval body axes are conserved in this modified larva. By 44 hr the ciliated band formed as an incomplete transverse loop of three segments at the posterior end and on the dorsal surface of the ovoid larva. Cilia in these segments grew to lengths of 45-50 microns, longer than other swimming and feeding cilia reported for echinoderm larvae. Band segments are interpreted as expressions of epaulettes (specialized swimming bands) rather than the feeding ciliated band of the pluteus. The ciliated band segments and the larval spicules are both bilaterally symmetrical with respect to the same plane and indicate conserved larval bilateral symmetry despite the major asymmetry of the fates of cells on either side of this plane in their contribution to juvenile development.

Physical processes dominate in shaping invertebrate assemblages in reef-associated sediments of an exposed Hawaiian coast

USGS Publications Warehouse

DeFelice, R.C.; Parrish, J.D.

2001-01-01

The invertebrate assemblages in sediments bordering exposed fringing reefs at Hanalei Bay, Kauai, Hawaii, were examined during July to September 1994. Densities of invertebrate animals larger than 0.5 mm in sediments of the bay ranged from counts of 10 260 m-2 in the fine carbonate sands of the central bay to 870 m-2 in the habitat dominated by terrigenous silt near the reef edge close to the Hanalei river mouth. Similar sediment types supported broadly similar infaunal communities. Within the primarily carbonate sediments, mean grain size and wave exposure appear to have an important influence on the community. Taxonomic richness, number of individuals, and diversity showed significant negative relationships with exposure to wave energy (as estimated by sand ripple wavelength). The number of individuals was also significantly correlated with mean grain size. Overall, polychaetes and small crustaceans were numerically dominant among the major taxonomic groups investigated. Macrophagous and microphagous polychaetes had significant, but opposite, associations with grain size. In addition, microphagous polychaetes were significantly negatively correlated with wave exposure. No habitat variable measured could explain the variation in percent composition of crustaceans or echinoderms in the sedimentary habitats. The percentage of gastropods in the community was significantly negatively correlated with grain size, grain-size standard deviation and exposure, and positively with percent organic carbon. Bivalves were significantly positively associated with depth and grain size. These strong relationships imply that, in Hanalei Bay, physical processes are especially important in influencing assemblage structure, and that community structure and composition vary continuously along environmental gradients.

Drug Resistance Mechanisms in Non-Small Cell Lung Carcinoma

PubMed Central

Wangari-Talbot, Janet; Hopper-Borge, Elizabeth

2014-01-01

Lung cancer is the most commonly diagnosed cancer in the world. “Driver” and “passenger” mutations identified in lung cancer indicate that genetics play a major role in the development of the disease, progression, metastasis and response to therapy. Survival rates for lung cancer treatment have remained stagnant at ~15% over the past 40 years in patients with disseminated disease despite advances in surgical techniques, radiotherapy and chemotherapy. Resistance to therapy; either intrinsic or acquired has been a major hindrance to treatment leading to great interest in studies seeking to understand and overcome resistance. Genetic information gained from molecular analyses has been critical in identifying druggable targets and tumor profiles that may be predictors of therapeutic response and mediators of resistance. Mutated or overexpressed epidermal growth factor receptor (EGFR) and translocations in the echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) genes (EML4-ALK) are examples of genetic aberrations resulting in targeted therapies for both localized and metastatic disease. Positive clinical responses have been noted in patients harboring these genetic mutations when treated with targeted therapies compared to patients lacking these mutations. Resistance is nonetheless a major factor contributing to the failure of targeted agents and standard cytotoxic agents. In this review, we examine molecular mechanisms that are potential drivers of resistance in non-small cell lung carcinoma, the most frequently diagnosed form of lung cancer. The mechanisms addressed include resistance to molecular targeted therapies as well as conventional chemotherapeutics through the activity of multidrug resistance proteins. PMID:24634705

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosen, M.R.; Collins, L.B.; Wyrwoll, K.H.

The Houtman Abrolhos reefs are located 80 km off the west coast of Australia between latitudes 28 and 29{degree} south. The islands are situated on three Pleistocene carbonate reef platforms which rise above the surrounding shelf. The modern coral reefs are close to the geographic limit for coral growth in the southern hemisphere and survive due to the presence of the Leeuwin current (a poleward-flowing warm stream). Two major shallow-water benthic communities coexist in the Abrolhos: a macroalgal-dominated community on the windward platform margins and a coral-dominated community on the leeward margins. These communities overlap-particularly in the platform lagoons, wheremore » competition between macroalgae and corals is intense. This interaction has been suggested as a major factor controlling the growth of cord reefs at high latitudes. The Holocene carbonate sediments lack nonskeletal components and are dominated by coral and coralline algal fragments with subordinate molluskan and echinoderm debris. The accumulations can be grouped into the following major facies: (1) coral framestone and coralline algal/serpulid boundstone, (2) submarine sand sheets, (3) subaerial coral storm ridges, (4-) peritidal to subtidal shingle and rubble veneers composed of dominantly coral debris, and (5) eolian dunes and beach sand. The Holocene sediment is a thin (< 2 m) veneer on the Pleistocene reef platform, which is emergent as small islands. The Pleistocene platform is composed of reef facies that can be directly related to the Holocene sediments. The platform is composed of framestone and boundstone facies (corals and coralline algal/serpulid facies), rudstones (submarine coral rubble facies), planar-bedded skeletal grainstones dipping 12-13{degree} (submarine sand sheet and peritidal shingle facies), and large 15-m-high eolianite dunes (eolian dune facies).« less

Petrology and dolomitization of the C' zone, Red River Formation (Ordovician), in a deep core, Williston basin, Richland County, eastern Montana

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zenger, D.H.

Unocal's Superior [number sign]1 Vanderhoof 97-foot (29.6 m) core consists of 63 feet (19.2 m) of the upper part of the C' burrowed member (BM) overlain by 34 feet (10.4 m) of the C' laminated member (LM) of the productive Red River Formation. The LM is mainly laminated, anhydritic, stylolitic, essentially unfossiliferous dolomudstone to calcareous dolomudstone with more minor dolomitic lime mudstone. The unit represents a restricted, hypersaline, inner shelf environment. The BM is burrow-mottled (Thalassinoides ), skeletal, dolomitic wackestone to grainstone matrix to calcareous dolowackestone (burrow fills) and represents near-normal salinity, inner shelf conditions. Dolomite is primarily replacive andmore » in the LM occurs as 25--50 [mu]m rhombs floating in mudstone or associated with stylolites, and as nonplanar, polymodal (5--50 [mu]m) crystals in totally dolomitized intervals. Most BM dolomite consists of 20--160 [mu]m, primarily nonplanar crystals in the largely replaced burrow fills; it also occurs as crystals that are disseminated or focused along stylolites (as in LM), as large crystals selectively and pseudomorphically replacing echinoderm fragments, and more rarely as late-stage, void-filling saddle dolomite. Previous theories of dolomitization have invoked descending brines. Geochemical data, in particular depleted [delta][sup 18]O and relatively low amounts of trace elements Sr and Na, but high Fe and Mn content, reveal that if brines were responsible for early diagenetic replacement, the dolomite has not retained such geochemical memory; rather it has undergone modification, acquiring later diagenetic, burial signatures. Possibly more of the replacement itself was later and deeper than previously thought.« less

Organic Matrix-related mineralization of sea urchin spicules, spines, test and teeth

PubMed Central

Veis, Arthur

2012-01-01

The camarodont echinoderms have five distinct mineralized skeletal elements: the embryonic spicules and mature test; spines, lantern stereom and teeth. The embryonic spicules are transient structural elements of the larval skeleton whereas the spines and test plates are permanent structural elements. The teeth are continuously growing structures, matching wear at the incisal adoral end to the rate of new production at the aboral plumula. The mineral in all cases is a high magnesium calcite, but the magnesium content, crystal shape and growth pattern is different in each type of skeletal element. The crystal shape and organization into macro structures depends on the presence of an organic matrix which creates the spaces and controls the environments for crystal initiation and growth. The detailed mechanisms of crystal regulation are not known, but much work has been done on defining the proteins which appear to be involved. Phosphorylated matrix proteins may be of special importance. Biochemical isolation of proteins, construction and analysis of cDNA libraries, and most recently high-throughput proteomic analysis in conjunction with the sequencing of the complete genome have yielded a detailed list of protein components likely to be involved in the mineralization processes. However, the proteome-genome analyses have not yet provided insight into the mechanisms of crystallization, calcite composition, and orientation applicable to all skeletal elements. Although the embryonic pluteus and their spicules are the best studied system, it appears that spicule is not representative of the mature skeletal elements. Now armed with the compositions of most of the proteins involved, the next phase of research will have to focus on the specific localization of the proteins and individual biochemistries of each system with regard to mineral content and placement. PMID:21622194

Early development and molecular plasticity in the Mediterranean sea urchin Paracentrotus lividus exposed to CO2-driven acidification.

PubMed

Martin, Sophie; Richier, Sophie; Pedrotti, Maria-Luiza; Dupont, Sam; Castejon, Charlotte; Gerakis, Yannis; Kerros, Marie-Emmanuelle; Oberhänsli, François; Teyssié, Jean-Louis; Jeffree, Ross; Gattuso, Jean-Pierre

2011-04-15

Ocean acidification is predicted to have significant effects on benthic calcifying invertebrates, in particular on their early developmental stages. Echinoderm larvae could be particularly vulnerable to decreased pH, with major consequences for adult populations. The objective of this study was to understand how ocean acidification would affect the initial life stages of the sea urchin Paracentrotus lividus, a common species that is widely distributed in the Mediterranean Sea and the NE Atlantic. The effects of decreased pH (elevated P(CO(2))) were investigated through physiological and molecular analyses on both embryonic and larval stages. Eggs and larvae were reared in Mediterranean seawater at six pH levels, i.e. pH(T) 8.1, 7.9, 7.7, 7.5, 7.25 and 7.0. Fertilization success, survival, growth and calcification rates were monitored over a 3 day period. The expression of genes coding for key proteins involved in development and biomineralization was also monitored. Paracentrotus lividus appears to be extremely resistant to low pH, with no effect on fertilization success or larval survival. Larval growth was slowed when exposed to low pH but with no direct impact on relative larval morphology or calcification down to pH(T) 7.25. Consequently, at a given time, larvae exposed to low pH were present at a normal but delayed larval stage. More surprisingly, candidate genes involved in development and biomineralization were upregulated by factors of up to 26 at low pH. Our results revealed plasticity at the gene expression level that allows a normal, but delayed, development under low pH conditions.

Three-dimensional facies architecture of the Salem Limestone (middle Mississippian), Eastern Margin of Illinois basin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nadeem, A.; Keith, B.D.; Thompson, T.A.

Mapping of sedimentary surfaces in the Middle Mississippian Salem Limestone exposed on sawed quarry walls in south-central Indiana has revealed a hierarchy of depositional units representative of the extremely dynamic hydrographic regime of the upper shoreface zone. The depositional units on the scale of microform and mesoform are represented by the microfacies and the facies respectively. Based on their hierarchy, genetically related depositional units and associated bounding surfaces were grouped together to construct four architectural packages (APs) of the scale of mesoforms. AP-I is dominantly an echinoderm- and bryozoan-rich grainstone and consists of bedforms ranging from small ripples bounded bymore » first-order surfaces to two- and three- dimensional megaripples bounded by the second-order surfaces. It formed as part of a giant ramp (asymmetric wavefield) within the intrashoal channel setting. AP-II, also a skeletal grainstone, is a complex of giant sandwaves that moved into the area under the infulence of a storm and partly filled the basal channel form of AP-I. Large avalanche foresets with tangential toesets prevail. AP-III is a dark-gray spatially discontinuous skeletal grainstone to packstone that laterally grades into a skeletal packstone to wackestone. It locally developed overhangs, rips-ups, and hardground on its upper surface. AP-IV is a skeletal and oolitic grainstone formed of tabular two-dimensional megaripples (planar cross-beds) and three-dimensional oscillatory megaripples (trough cross-beds). These architectural packages based on the bedform architecture and micro-and mesoscale compositional changes can be used to characterize micro-, meso, and macroscale heterogeneities. Models of facies architecture from this and similar outcrop studies can be applied to the subsurface Salem reservoirs in the Illinois Basin using cores.« less

Feasibility of computed tomography-guided core needle biopsy in producing state-of-the-art clinical management in Chinese lung cancer.

PubMed

Chen, Hua-Jun; Yang, Jin-Ji; Fang, Liang-Yi; Huang, Min-Min; Yan, Hong-Hong; Zhang, Xu-Chao; Xu, Chong-Rui; Wu, Yi-Long

2014-03-01

A satisfactory biopsy determines the state-of-the-art management of lung cancer in this era of personalized medicine. This study aimed to investigate the suitability and efficacy of computed tomography (CT)-guided core needle biopsy in clinical management. A cohort of 353 patients with clinically suspected lung cancer was enrolled in the study. Patient factors and biopsy variables were recorded. Epidermal growth factor receptor (EGFR) gene mutations and echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) rearrangement were detected in tumor specimens. Adequacy of biopsic obtainment for clinical trial screening and tissue bank establishment were reviewed. Overall diagnostic accuracy of malignancy achieved 98.5%. The median biopsy time of the cohort was 20 minutes. In patients with non-small cell lung cancer (NSCLC), 99.3% (287/289) were diagnosed as specific histologic subtypes, and two patients (0.7%) were determined as NSCLC not otherwise specified (NOS). EGFR mutations were analyzed in 81.7% (236/289) of patients with NSCLC, and 98.7% (233/236) showed conclusive results. EML4-ALK gene fusion was tested in 43.9% (127/289) of NSCLC patients, and 98.4% (125/127) showed conclusive results: 6.4% (8/125) of those had gene fusion. Ninety-six NSCLC patients participated in clinical trial screening and provided mandatory tumor slides for molecular profiling. Pathological evaluation was fulfilled in 90 patients (93.8%); 99.4% (320/322) of patients with malignancy provided extra tissue for the establishment of a tumor bank. CT-guided core needle biopsy provided optimal clinical management in this era of translational medicine. The biopsic modality should be prioritized in selected lung cancer patients.

Feasibility of computed tomography-guided core needle biopsy in producing state-of-the-art clinical management in Chinese lung cancer

PubMed Central

Chen, Hua-Jun; Yang, Jin-Ji; Fang, Liang-Yi; Huang, Min-Min; Yan, Hong-Hong; Zhang, Xu-Chao; Xu, Chong-Rui; Wu, Yi-Long

2014-01-01

Background A satisfactory biopsy determines the state-of-the-art management of lung cancer in this era of personalized medicine. This study aimed to investigate the suitability and efficacy of computed tomography (CT)-guided core needle biopsy in clinical management. Methods A cohort of 353 patients with clinically suspected lung cancer was enrolled in the study. Patient factors and biopsy variables were recorded. Epidermal growth factor receptor (EGFR) gene mutations and echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) rearrangement were detected in tumor specimens. Adequacy of biopsic obtainment for clinical trial screening and tissue bank establishment were reviewed. Results Overall diagnostic accuracy of malignancy achieved 98.5%. The median biopsy time of the cohort was 20 minutes. In patients with non-small cell lung cancer (NSCLC), 99.3% (287/289) were diagnosed as specific histologic subtypes, and two patients (0.7%) were determined as NSCLC not otherwise specified (NOS). EGFR mutations were analyzed in 81.7% (236/289) of patients with NSCLC, and 98.7% (233/236) showed conclusive results. EML4-ALK gene fusion was tested in 43.9% (127/289) of NSCLC patients, and 98.4% (125/127) showed conclusive results: 6.4% (8/125) of those had gene fusion. Ninety-six NSCLC patients participated in clinical trial screening and provided mandatory tumor slides for molecular profiling. Pathological evaluation was fulfilled in 90 patients (93.8%); 99.4% (320/322) of patients with malignancy provided extra tissue for the establishment of a tumor bank. Conclusions CT-guided core needle biopsy provided optimal clinical management in this era of translational medicine. The biopsic modality should be prioritized in selected lung cancer patients. PMID:26766993

Diversity as Opportunity: Insights from 600 Million Years of AHR Evolution.

PubMed

Hahn, Mark E; Karchner, Sibel I; Merson, Rebeka R

2017-02-01

The aryl hydrocarbon receptor (AHR) was for many years of interest only to pharmacologists and toxicologists. However, this protein has fundamental roles in biology that are being revealed through studies in diverse animal species. The AHR is an ancient protein. AHR homologs exist in most major groups of modern bilaterian animals, including deuterostomes (chordates, hemichordates, echinoderms) and the two major clades of protostome invertebrates [ecdysozoans (e.g. arthropods and nematodes) and lophotrochozoans (e.g. molluscs and annelids)]. AHR homologs also have been identified in cnidarians such as the sea anemone Nematostella and in the genome of Trichoplax , a placozoan. Bilaterians, cnidarians, and placozoans form the clade Eumetazoa , whose last common ancestor lived approximately 600 million years ago (MYA). The presence of AHR homologs in modern representatives of all these groups indicates that the original eumetazoan animal possessed an AHR homolog. Studies in invertebrates and vertebrates reveal parallel functions of AHR in the development and function of sensory neural systems, suggesting that these may be ancestral roles. Vertebrate animals are characterized by the expansion and diversification of AHRs, via gene and genome duplications, from the ancestral protoAHR into at least five classes of AHR-like proteins: AHR, AHR1, AHR2, AHR3, and AHRR. The evolution of multiple AHRs in vertebrates coincided with the acquisition of high-affinity binding of halogenated and polynuclear aromatic hydrocarbons and the emergence of adaptive functions involving regulation of xenobiotic-metabolizing enzymes and roles in adaptive immunity. The existence of multiple AHRs may have facilitated subfunction partitioning and specialization of specific AHR types in some taxa. Additional research in diverse model and non-model species will continue to enrich our understanding of AHR and its pleiotropic roles in biology and toxicology.

Diversity as Opportunity: Insights from 600 Million Years of AHR Evolution

PubMed Central

Hahn, Mark E.; Karchner, Sibel I.; Merson, Rebeka R.

2017-01-01

The aryl hydrocarbon receptor (AHR) was for many years of interest only to pharmacologists and toxicologists. However, this protein has fundamental roles in biology that are being revealed through studies in diverse animal species. The AHR is an ancient protein. AHR homologs exist in most major groups of modern bilaterian animals, including deuterostomes (chordates, hemichordates, echinoderms) and the two major clades of protostome invertebrates [ecdysozoans (e.g. arthropods and nematodes) and lophotrochozoans (e.g. molluscs and annelids)]. AHR homologs also have been identified in cnidarians such as the sea anemone Nematostella and in the genome of Trichoplax, a placozoan. Bilaterians, cnidarians, and placozoans form the clade Eumetazoa, whose last common ancestor lived approximately 600 million years ago (MYA). The presence of AHR homologs in modern representatives of all these groups indicates that the original eumetazoan animal possessed an AHR homolog. Studies in invertebrates and vertebrates reveal parallel functions of AHR in the development and function of sensory neural systems, suggesting that these may be ancestral roles. Vertebrate animals are characterized by the expansion and diversification of AHRs, via gene and genome duplications, from the ancestral protoAHR into at least five classes of AHR-like proteins: AHR, AHR1, AHR2, AHR3, and AHRR. The evolution of multiple AHRs in vertebrates coincided with the acquisition of high-affinity binding of halogenated and polynuclear aromatic hydrocarbons and the emergence of adaptive functions involving regulation of xenobiotic-metabolizing enzymes and roles in adaptive immunity. The existence of multiple AHRs may have facilitated subfunction partitioning and specialization of specific AHR types in some taxa. Additional research in diverse model and non-model species will continue to enrich our understanding of AHR and its pleiotropic roles in biology and toxicology. PMID:28286876

Testing putative hemichordate homologues of the chordate dorsal nervous system and endostyle: expression of NK2.1 (TTF-1) in the acorn worm Ptychodera flava (Hemichordata, Ptychoderidae)

NASA Technical Reports Server (NTRS)

Takacs, Carter M.; Moy, Vanessa N.; Peterson, Kevin J.

2002-01-01

Recent phylogenetic investigations have confirmed that hemichordates and echinoderms are sister taxa. However, hemichordates share several cardinal characterstics with chordates and are thus an important taxon for testing hypotheses of homology between key chordate characters and their putative hemichordate antecedents. The chordate dorsal nervous system (DNS) and endostyle are intriguing characters because both hemichordate larval and adult structures have been hypothesized as homologues. This study attempts to test these purported homologies through examination of the expression pattem of a Ptychodera flava NK2 gene, PfNK2.1, because this gene is expressed both in the DNS and endostyle/thyroid in a wide range of chordate taxa. We found that PfNK2.1 is expressed in both neuronal and pharyngeal structures, but its expression pattem is broken up into distinct embryonic and juvenile phases. During embryogenesis, PfNK2.1 is expressed in the apical ectoderm, with transcripts later detected in presumable neuronal structures, including the apical organ and ciliated feeding band. In the developing juvenile we detected PfNK2.1 signal throughout the pharynx, including the stomochord, and later in the hindgut. We conclude that the similar utilization of NK2.1 in apical organ development and chordate DNS is probably due to a more general role for NK2.1 in neurogenesis and that hemichordates do not possess a homologue of the chordate DNS. In addition, we conclude that P. flava most likely does not possess a true endostyle; rather during the evolution of the endostyle NK2.1 was recruited from its more general role in pharynx development.

The response of abyssal organisms to low pH conditions during a series of CO2-release experiments simulating deep-sea carbon sequestration

NASA Astrophysics Data System (ADS)

Barry, J. P.; Buck, K. R.; Lovera, C.; Brewer, P. G.; Seibel, B. A.; Drazen, J. C.; Tamburri, M. N.; Whaling, P. J.; Kuhnz, L.; Pane, E. F.

2013-08-01

The effects of low-pH, high-pCO2 conditions on deep-sea organisms were examined during four deep-sea CO2 release experiments simulating deep-ocean C sequestration by the direct injection of CO2 into the deep sea. We examined the survival of common deep-sea, benthic organisms (microbes; macrofauna, dominated by Polychaeta, Nematoda, Crustacea, Mollusca; megafauna, Echinodermata, Mollusca, Pisces) exposed to low-pH waters emanating as a dissolution plume from pools of liquid carbon dioxide released on the seabed during four abyssal CO2-release experiments. Microbial abundance in deep-sea sediments was unchanged in one experiment, but increased under environmental hypercapnia during another, where the microbial assemblage may have benefited indirectly from the negative impact of low-pH conditions on other taxa. Lower abyssal metazoans exhibited low survival rates near CO2 pools. No urchins or holothurians survived during 30-42 days of exposure to episodic, but severe environmental hypercapnia during one experiment (E1; pH reduced by as much as ca. 1.4 units). These large pH reductions also caused 75% mortality for the deep-sea amphipod, Haploops lodo, near CO2 pools. Survival under smaller pH reductions (ΔpH<0.4 units) in other experiments (E2, E3, E5) was higher for all taxa, including echinoderms. Gastropods, cephalopods, and fish were more tolerant than most other taxa. The gastropod Retimohnia sp. and octopus Benthoctopus sp. survived exposure to pH reductions that episodically reached -0.3 pH units. Ninety percent of abyssal zoarcids (Pachycara bulbiceps) survived exposure to pH changes reaching ca. -0.3 pH units during 30-42 day-long experiments.

β-Catenin specifies the endomesoderm and defines the posterior organizer of the hemichordate Saccoglossus kowalevskii

PubMed Central

Darras, Sébastien; Gerhart, John; Terasaki, Mark; Kirschner, Marc; Lowe, Christopher J.

2011-01-01

The canonical Wnt/β-catenin pathway is a key regulator of body plan organization and axis formation in metazoans, being involved in germ layer specification, posterior growth and patterning of the anteroposterior axis. Results from animals spanning a wide phylogenetic range suggest that a unifying function of β-catenin in metazoans is to define the posterior/vegetal part of the embryo. Although the specification of vegetal territories (endoderm) by β-catenin has been demonstrated in distantly related animals (cnidarians, a protostome, echinoderms and ascidians), the definition of the posterior part of the embryo is well supported only for vertebrates and planarians. To gain insights into β-catenin functions during deuterostome evolution, we have studied the early development of the direct developing hemichordate Saccoglossus kowalevskii. We show that the zygote is polarized after fertilization along the animal-vegetal axis by cytoplasmic rearrangements resembling the ascidian vegetal contraction. This early asymmetry is translated into nuclear accumulation of β-catenin at the vegetal pole, which is necessary and sufficient to specify endomesoderm. We show that endomesoderm specification is crucial for anteroposterior axis establishment in the ectoderm. The endomesoderm secretes as yet unidentified signals that posteriorize the ectoderm, which would otherwise adopt an anterior fate. Our results point to a conserved function at the base of deuterostomes for β-catenin in germ layer specification and to a causal link in the definition of the posterior part of the embryonic ectoderm by way of activating posteriorizing endomesodermal factors. Consequently, the definition of the vegetal and the posterior regions of the embryo by β-catenin should be distinguished and carefully re-examined. PMID:21303849

ALK rearrangement in a large series of consecutive non-small cell lung cancers: comparison between a new immunohistochemical approach and fluorescence in situ hybridization for the screening of patients eligible for crizotinib treatment.

PubMed

Alì, Greta; Proietti, Agnese; Pelliccioni, Serena; Niccoli, Cristina; Lupi, Cristiana; Sensi, Elisa; Giannini, Riccardo; Borrelli, Nicla; Menghi, Maura; Chella, Antonio; Ribechini, Alessandro; Cappuzzo, Federico; Melfi, Franca; Lucchi, Marco; Mussi, Alfredo; Fontanini, Gabriella

2014-11-01

Echinoderm microtubule associated proteinlike 4-anaplastic lymphoma receptor tyrosine kinase (EML4-ALK) translocation has been described in a subset of patients with non-small cell lung cancer (NSCLC) and has been shown to have oncogenic activity. Fluorescence in situ hybridization (FISH) is used to detect ALK-positive NSCLC, but it is expensive, time-consuming, and difficult for routine application. To evaluate the potential role of immunohistochemistry (IHC) as a screening tool to identify candidate cases for FISH analysis and for ALK inhibitor therapy in NSCLC. We performed FISH and IHC for ALK and mutational analysis for epidermal growth factor receptor (EGFR) and KRAS in 523 NSCLC specimens. We conducted IHC analysis with the monoclonal antibody D5F3 (Ventana Medical Systems, Tucson, Arizona) and a highly sensitive detection system. We also performed a MassARRAY-based analysis (Sequenom, San Diego, California) in a small subset of 11 samples to detect EML4-ALK rearrangement. Of the 523 NSCLC specimens, 20 (3.8%) were positive for ALK rearrangement by FISH analysis. EGFR and KRAS mutations were identified in 70 (13.4%) and 124 (23.7%) of the 523 tumor samples, respectively. ALK rearrangement and EGFR and KRAS mutations were mutually exclusive. Of 523 tumor samples analyzed, 18 (3.4%) were ALK(+) by IHC, 18 samples (3.4%) had concordant IHC and FISH results, and 2 ALK(+) cases (0.3%) by FISH failed to show ALK protein expression. In the 2 discrepant cases, we did not detect any mass peaks for the EML4-ALK variants by MassARRAY. Our results show that IHC may be a useful technique for selecting NSCLC cases to undergo ALK FISH analysis.

The origin and paleoecologic significance of the trace fossil Asteriadtes in the Pennsylvanian of Kansas and Missouri

USGS Publications Warehouse

Mángano, M. Gabriela; Buatois, L.A.; West, R.R.; Maples, C.G.

1999-01-01

The trace fossil Asteriacites, recorded in Cambrian to Recent shallow- and deep-marine facie??s, is traditionally interpreted as the resting trace of asterozoans. Well-preserved specimens of A. lumbricalis are abundant in Pennsylvanian (Upper Carboniferous) shallow- and marginalmarine siliciclastic deposits of eastern Kansas and western Missouri. Detailed morphologic analysis of these specimens suggests that they record the activities of mobile epifaunal ophiuroids. Evidence of a brittle star (ophiuroid) producer rather than sea star (asteroid) is provided by (1) trace-fossil morphologic features reflecting the anatomy of the producer (e.g., well-differentiated central structure, slender vermiform arms) and ophiuroid burrowing technique (e.g., proximal arm expansion, arm branching), and (2) mode of occurrence (e.g., gregarious behavior, horizontal and vertical repetition). Vertical and horizontal repetition produces complex aggregates of A. lumbricalis that are interpreted either as escape structures (fugichnia) or as feeding structures, respectively. Ophiura texturata is proposed.as a modern analogue for the A. lumbricalis producer, based on inferred life habit and feeding behavior. Asteriacites lumbricalis is present in two different intertidal trace-fossil assemblages. The first assemblage is characterized by high diversity and records tidal flats developed outside of embayments under normal marine conditions. The second assemblage consists of A. lumbricalis together with a few other ichnotaxa and represents a depauperate association that developed in restricted tidal flats within an embayment or estuarine setting. This challenges the conventional view of Asteriacites as a normal-marine salinity indicator. Some echinoderms, and particularly asterozoans, penetrate and inhabit modern environments of depressed salinity. The presence of Asteriacites in Pennsylvanian marginal-marine facie??s of Kansas and Missouri provides evidence that ophiuroids had adapted to brackish-water conditions by the late Paleozoic.

Fauna and Predator-Prey Relationships of Ettling, an Actinopterygian Fish-Dominated Konservat-Lagerstätte from the Late Jurassic of Southern Germany

PubMed Central

Ebert, Martin; Kölbl-Ebert, Martina; Lane, Jennifer A.

2015-01-01

The newly recognized Konservat-Lagerstätte of Ettling (Bavaria), field site of the Jura-Museum Eichstätt (JME), is unique among Late Jurassic plattenkalk basins (Solnhofen region) in its abundant, extremely well preserved fossil vertebrates, almost exclusively fishes. We report actinopterygians (ginglymodins, pycnodontiforms, halecomorphs, aspidorynchiforms, “pholidophoriforms,” teleosts); turtles; and non-vertebrates (echinoderms, arthropods, brachiopods, mollusks, jellyfish, sponges, biomats, plants) in a current faunal list. Ettling has yielded several new fish species (Bavarichthys incognitus; Orthogonikleithrus hoelli; Aspidorhynchus sanzenbacheri; Macrosemimimus fegerti). Upper and lower Ettling strata differ in faunal content, with the lower dominated by the small teleost Orthogonikleithrus hoelli (absent from the upper layers, where other prey fishes, Leptolepides sp. and Tharsis sp., occur instead). Pharyngeal and stomach contents of Ettling fishes provide direct evidence that Orthogonikleithrus hoelli was a primary food source during early Ettling times. Scarcity of ammonites and absence of vampyromorph coleoids at Ettling differ markedly from the situation at other nearby localities in the region (e.g., Eichstätt, Painten, Schamhaupten, the Mörnsheim beds), where they are more common. Although the exact biochronological age of Ettling remains uncertain (lack of suitable index fossils), many Ettling fishes occur in other plattenkalk basins of Germany (e.g., Kelheim) and France (Cerin) dated as Late Kimmeridgian to Early Tithonian (eigeltingense horizon), suggesting a comparable geologic age. The Ettling deposits represent an independent basin within the larger Upper Jurassic “Solnhofen Archipelago”, a shallow subtropical sea containing scattered islands, sponge-microbial and coral reefs, sandbars, and deeper basins on a vast carbonate platform along the northern margin of the Tethys Ocean. PMID:25629970

Unraveling estradiol metabolism and involvement in the reproductive cycle of non-vertebrate animals: The sea urchin model.

PubMed

Silvia, Mercurio; Paolo, Tremolada; Nobile, Maria; Denise, Fernandes; Cinta, Porte; Michela, Sugni

2015-12-01

Estradiol (E2) is a well-known hormone in vertebrates whereas in invertebrates its unambiguous presence was verified only in some species. Weather this presence is also associated to similarly conserved roles in animal phylogeny is similarly uncertain. Due to their phylogenetic position, echinoderms represent ideal experimental models to provide evolutionary insights into estrogen appearance and function. Therefore, in this research, we investigated if E2 is truly present and has a role in the reproductive biology of the sea urchin Paracentrotus lividus. Presence of 17β estradiol in body fluids was confirmed by liquid chromatography-mass spectrometry. By immunological methods (RIA) we evaluated the physiological circulating E2 levels of adult specimens and, on the basis of these, we directly administered E2 to study its metabolism and its putative effects on gonad development at physiological doses. Although different E2 tested concentrations, a correspondent dose-dependent increase of hormone levels was not found in both body fluids and gonads, suggesting the presence of potent homeostatic/detoxification mechanisms. These latter do not involve enzymes such as aromatase-like, sulfotransferase-like and acyltransferase-like, whose activities were not affected by E2 administration. Despite the increase of endogenous E2, the treatment did not induce significant variations in none of the considered reproductive parameters. Overall, this research (1) provides definitive evidence of E2 presence in sea urchin tissues and (2) demonstrate that, differently from vertebrates and starfish, E2 does not play a key role in sea urchins reproductive processes. Intra-phylum differences suggest the existence of class-specific hormonal mechanisms and highlight the risk of Phylum generalization. Copyright © 2015 Elsevier Inc. All rights reserved.

HpBase: A genome database of a sea urchin, Hemicentrotus pulcherrimus.

PubMed

Kinjo, Sonoko; Kiyomoto, Masato; Yamamoto, Takashi; Ikeo, Kazuho; Yaguchi, Shunsuke

2018-04-01

To understand the mystery of life, it is important to accumulate genomic information for various organisms because the whole genome encodes the commands for all the genes. Since the genome of Strongylocentrotus purpratus was sequenced in 2006 as the first sequenced genome in echinoderms, the genomic resources of other North American sea urchins have gradually been accumulated, but no sea urchin genomes are available in other areas, where many scientists have used the local species and reported important results. In this manuscript, we report a draft genome of the sea urchin Hemincentrotus pulcherrimus because this species has a long history as the target of developmental and cell biology in East Asia. The genome of H. pulcherrimus was assembled into 16,251 scaffold sequences with an N50 length of 143 kbp, and approximately 25,000 genes were identified in the genome. The size of the genome and the sequencing coverage were estimated to be approximately 800 Mbp and 100×, respectively. To provide these data and information of annotation, we constructed a database, HpBase (http://cell-innovation.nig.ac.jp/Hpul/). In HpBase, gene searches, genome browsing, and blast searches are available. In addition, HpBase includes the "recipes" for experiments from each lab using H. pulcherrimus. These recipes will continue to be updated according to the circumstances of individual scientists and can be powerful tools for experimental biologists and for the community. HpBase is a suitable dataset for evolutionary, developmental, and cell biologists to compare H. pulcherrimus genomic information with that of other species and to isolate gene information. © 2018 Japanese Society of Developmental Biologists.

A review of nickel toxicity to marine and estuarine tropical biota with particular reference to the South East Asian and Melanesian region.

PubMed

Gissi, Francesca; Stauber, Jennifer L; Binet, Monique T; Golding, Lisa A; Adams, Merrin S; Schlekat, Christian E; Garman, Emily R; Jolley, Dianne F

2016-11-01

The South East Asian Melanesian (SEAM) region contains the world's largest deposits of nickel lateritic ores. Environmental impacts may occur if mining operations are not adequately managed. Effects data for tropical ecosystems are required to assess risks of contaminant exposure and to derive water quality guidelines (WQG) to manage these risks. Currently, risk assessment tools and WQGs for the tropics are limited due to the sparse research on how contaminants impact tropical biota. As part of a larger project to develop appropriate risk assessment tools to ensure sustainable nickel production in SEAM, nickel effects data were required. The aim of this review was to compile data on the effects of nickel on tropical marine, estuarine, pelagic and benthic species, with a particular focus on SEAM. There were limited high quality chronic nickel toxicity data for tropical marine species, and even fewer for those relevant to SEAM. Of the data available, the most sensitive SEAM species to nickel were a sea urchin, copepod and anemone. There is a significant lack of high quality chronic data for several ecologically important taxonomic groups including cnidarians, molluscs, crustaceans, echinoderms, macroalgae and fish. No high quality chronic nickel toxicity data were available for estuarine waters or marine and estuarine sediments. The very sparse toxicity data for tropical species limits our ability to conduct robust ecological risk assessment and may require additional data generation or read-across from similar species in other databases (e.g. temperate) to fill data gaps. Recommendations on testing priorities to fill these data gaps are presented. Copyright © 2016 Elsevier Ltd. All rights reserved.

Activation of HER family signaling as a mechanism of acquired resistance to ALK inhibitors in EML4-ALK-positive non-small cell lung cancer.

PubMed

Tanizaki, Junko; Okamoto, Isamu; Okabe, Takafumi; Sakai, Kazuko; Tanaka, Kaoru; Hayashi, Hidetoshi; Kaneda, Hiroyasu; Takezawa, Ken; Kuwata, Kiyoko; Yamaguchi, Haruka; Hatashita, Erina; Nishio, Kazuto; Nakagawa, Kazuhiko

2012-11-15

Anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors (TKI) such as crizotinib show marked efficacy in patients with non-small cell lung cancer positive for the echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusion protein. However, acquired resistance to these agents has already been described in treated patients, and the mechanisms of such resistance remain largely unknown. We established lines of EML4-ALK-positive H3122 lung cancer cells that are resistant to the ALK inhibitor TAE684 (H3122/TR cells) and investigated their resistance mechanism with the use of immunoblot analysis, ELISA, reverse transcription and real-time PCR analysis, and an annexin V binding assay. We isolated EML4-ALK-positive lung cancer cells (K-3) from a patient who developed resistance to crizotinib and investigated their characteristics. The expression of EML4-ALK was reduced at the transcriptional level, whereas phosphorylation of epidermal growth factor receptor (EGFR), HER2, and HER3 was upregulated, in H3122/TR cells compared with those in H3122 cells. This activation of HER family proteins was accompanied by increased secretion of EGF. Treatment with an EGFR-TKI induced apoptosis in H3122/TR cells, but not in H3122 cells. The TAE684-induced inhibition of extracellular signal-regulated kinase (ERK) and STAT3 phosphorylation observed in parental cells was prevented by exposure of these cells to exogenous EGF, resulting in a reduced sensitivity of cell growth to TAE684. K-3 cells also manifested HER family activation accompanied by increased EGF secretion. EGF-mediated activation of HER family signaling is associated with ALK-TKI resistance in lung cancer positive for EML4-ALK. ©2012 AACR.

A potential role for chondroitin sulfate/dermatan sulfate in arm regeneration in Amphiura filiformis.

PubMed

Ramachandra, Rashmi; Namburi, Ramesh B; Dupont, Sam T; Ortega-Martinez, Olga; van Kuppevelt, Toin H; Lindahl, Ulf; Spillmann, Dorothe

2017-05-01

Glycosaminoglycans (GAGs), such as chondroitin sulfate (CS) and dermatan sulfate (DS) from various vertebrate and invertebrate sources are known to be involved in diverse cellular mechanisms during repair and regenerative processes. Recently, we have identified CS/DS as the major GAG in the brittlestar Amphiura filiformis, with high proportions of di- and tri-O-sulfated disaccharide units. As this echinoderm is known for its exceptional regeneration capacity, we aimed to explore the role of these GAG chains during A. filiformis arm regeneration. Analysis of CS/DS chains during the regeneration process revealed an increase in the proportion of the tri-O-sulfated disaccharides. Conversely, treatment of A. filiformis with sodium chlorate, a potent inhibitor of sulfation reactions in GAG biosynthesis, resulted in a significant reduction in arm growth rates with total inhibition at concentrations higher than 5 mM. Differentiation was less impacted by sodium chlorate exposure or even slightly increased at 1-2 mM. Based on the structural changes observed during arm regeneration we identified chondroitin synthase, chondroitin-4-O-sulfotransferase 2 and dermatan-4-O-sulfotransferase as candidate genes and sought to correlate their expression with the expression of the A. filiformis orthologue of bone morphogenetic factors, AfBMP2/4. Quantitative amplification by real-time PCR indicated increased expression of chondroitin synthase and chondroitin-4-O-sulfotransferase 2, with a corresponding increase in AfBMP2/4 during regeneration relative to nonregenerating controls. Our findings suggest that proper sulfation of GAGs is important for A. filiformis arm regeneration and that these molecules may participate in mechanisms controlling cell proliferation. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Carbonate mud bodies in middle Mississippian strata of southern Indiana and northern Kentucky: End members of a middle Mississippian mud mound spectrum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, M.A.; Dodd, J.R.

1990-06-01

Relatively small, lens-shaped carbonate mud bodies are common features in the Ramp Creek Formation and Harrodsburg Limestone (Mississippian) of southern Indiana and northern Kentucky. The outcrop dimensions of the lenses range from approximately 10 cm thick and 3 m wide to as much as 2 m thick and in excess of 100 m wide; their three-dimensional geometry is unknown. The lens cores consist of dolomitic mudstone that grades laterally and vertically into increasingly more fossiliferous wackestone to grainstone with fenestrate bryozoans and echinoderms being the dominant fossils. The great abundance of fenestrate bryozoan fragments surrounding the lenses suggests that lensmore » evolution was controlled by the trapping of carbonate mud by the baffling action of bryozoans. Wisps of organic material preserved in the lens cores may be remnants of some form of non-calcareous algae that also baffled and trapped carbonate mud. These mud lenses are end members of a spectrum of Mississippian carbonate mud bodies ranging in size from these small lenses to the classical Waulsortian mounds that may be hundreds of meters thick and a kilometer or more broad. All of these carbonate mud bodies may have in part formed by baffling and localizing of carbonate mud by organisms and in part by local production of carbonate mud. The major difference between large and small bodies is the water depth in which each formed. The Ramp Creek-Harrodsburg mud lenses may be miniature Waulsortian mounds that developed at or above fair-weather wave base on a relatively shallow carbonate platform rather than on shelf-to-basin slopes as proposed for the classical Waulsortian mounds.« less

Changes in deep-sea carbonate-hosted microbial communities associated with high and low methane flux

NASA Astrophysics Data System (ADS)

Case, D. H.; Steele, J. A.; Chadwick, G.; Mendoza, G. F.; Levin, L. A.; Orphan, V. J.

2012-12-01

Methane seeps on continental shelves are rich in authigenic carbonates built of methane-derived carbon. These authigenic carbonates are home to micro- and macroscopic communities whose compositions are thus far poorly constrained but are known to broadly depend on local methane flux. The formation of authigenic carbonates is itself a result of microbial metabolic activity, as associations of anaerobic methane oxidizing archaea (ANME) and sulfate reducing bacteria (SRB) in the sediment subsurface increase both dissolved inorganic carbon (DIC) and alkalinity in pore waters. This 1:1 increase in DIC and alkalinity promotes the precipitation of authigenic carbonates. In this study, we performed in situ manipulations to test the response of micro- and macrofaunal communities to a change in methane flux. Methane-derived authigenic carbonates from two locations at Hydrate Ridge, OR, USA (depth range 595-604 mbsl), were transplanted from "active" cold seep sites (high methane flux) to "inactive" background sites (low methane flux), and vise versa, for one year. Community diversity surveys using T-RFLP and 16S rRNA clone libraries revealed how both bacterial and archaeal assemblages respond to this change in local environment, specifically demonstrating reproducible shifts in different ANME groups (ANME-1 vs. ANME-2). Animal assemblage composition also shifted during transplantation; gastropod representation increased (relative to control rocks) when substrates were moved from inactive to active sites and polychaete, crustacean and echinoderm representation increased when substrates were moved from active to inactive sites. Combined with organic and inorganic carbon δ13C measurements and mineralogy, this unique in situ experiment demonstrates that authigenic carbonates are viable habitats, hosting microbial and macrofaunal communities capable of responding to changes in external environment over relatively short time periods.

Inhibition of 19S proteasomal regulatory complex subunit PSMD8 increases polyspermy during porcine fertilization in vitro.

PubMed

Yi, Young-Joo; Manandhar, Gaurishankar; Sutovsky, Miriam; Jonáková, Vera; Park, Chang-Sik; Sutovsky, Peter

2010-03-01

The 26S proteoasome is a multi-subunit protease specific to ubiquitinated substrate proteins. It is composed of a 20S proteasomal core with substrate degradation activity, and a 19S regulatory complex that acts in substrate recognition, deubiquitination, priming and transport to the 20S core. Inhibition of proteolytic activities associated with the sperm acrosome-borne 20S core prevents fertilization in mammals, ascidians and echinoderms. Less is known about the function of the proteasomal 19S complex during fertilization. The present study examined the role of PSMD8, an essential non-ATPase subunit of the 19S complex, in sperm-ZP penetration during porcine fertilization in vitro (IVF). Immunofluorescence localized PSMD8 to the outer acrosomal membrane, acrosomal matrix and the inner acrosomal membrane. Colloidal gold transmission electron microscopy detected PSMD8 on the surface of vesicles in the acrosomal shroud, formed as a result of zona pellucida-induced acrosomal exocytosis. Contrary to the inhibition of fertilization by blocking of the 20S core activities, fertilization and polyspermy rates were increased by adding anti-PSMD8 antibody to fertilization medium. This observation is consistent with a possible role of PSMD8 in substrate deubiquitination, a process which when blocked, may actually accelerate substrate proteolysis by the 26S proteasome. Subunit PSMD8 co-immunoprecipitated with acrosomal surface-associated spermadhesin AQN1. This association indicates that the sperm acrosome-borne proteasomes become exposed onto the sperm surface following the acrosomal exocytosis. Since immunological blocking of subunit PSMD8 increases the rate of polyspermy during porcine fertilization, the activity of the 19S complex may be a rate-limiting factor contributing to anti-polyspermy defense during porcine fertilization. Copyright 2009. Published by Elsevier Ireland Ltd.

Crystal structure of EML1 reveals the basis for Hsp90 dependence of oncogenic EML4-ALK by disruption of an atypical β-propeller domain

PubMed Central

Richards, Mark W.; Law, Edward W. P.; Rennalls, La’Verne P.; Busacca, Sara; O’Regan, Laura; Fry, Andrew M.; Fennell, Dean A.; Bayliss, Richard

2014-01-01

Proteins of the echinoderm microtubule-associated protein (EMAP)-like (EML) family contribute to formation of the mitotic spindle and interphase microtubule network. They contain a unique hydrophobic EML protein (HELP) motif and a variable number of WD40 repeats. Recurrent gene rearrangements in nonsmall cell lung cancer fuse EML4 to anaplastic lymphoma kinase (ALK), causing expression of several fusion oncoprotein variants. We have determined a 2.6-Å crystal structure of the representative ∼70-kDa core of EML1, revealing an intimately associated pair of β-propellers, which we term a TAPE (tandem atypical propeller in EMLs) domain. One propeller is highly atypical, having a discontinuous subdomain unrelated to a WD40 motif in place of one of its blades. This unexpected feature shows how a propeller structure can be assembled from subdomains with distinct folds. The HELP motif is not an independent domain but forms part of the hydrophobic core that joins the two β-propellers. The TAPE domain binds α/β-tubulin via its conserved, concave surface, including part of the atypical blade. Mapping the characteristic breakpoints of each EML4-ALK variant onto our structure indicates that the EML4 TAPE domain is truncated in many variants in a manner likely to make the fusion protein structurally unstable. We found that the heat shock protein 90 (Hsp90) inhibitor ganetespib induced degradation of these variants whereas others lacking a partial TAPE domain were resistant in both overexpression models and patient-derived cell lines. The Hsp90-sensitive EML4-ALK variants are exceptions to the rule that oncogenic fusion proteins involve breakpoints in disordered regions of both partners. PMID:24706829

[Value of Immunohistochemical Methods in Detecting EML4-ALK Fusion Mutations: A Meta-analysis].

PubMed

Liu, Chang; Cai, Lu; Zhong, Diansheng; Wang, Jing

2016-01-01

The fusion between echinoderm microtubule-associated protein 4 (EML4) and anaplastic lymphatic tumor kinase (ALK) rearrangement is present in approximately 5% of non-small cell lung cancer (NSCLC) patients. It has been regarded as another new target gene after epidermal growth factor receptor (EGFR) and K-ras. Figures showed that the disease control rate could reach up to 80% in NSCLC patients with EML4-ALK fusion gene after treated with ALK inhibitors. Thus, exploring an accurate and rapid detecting method is the key in screening NSCLC patients with EML4-ALK expressions. The aim of this study is to analyze the specificity and sensitivity of IHC in detecting EML4-ALK fusion mutations. To evaluate the accuracy and clinical value of this method, and then provide basis for individual molecular therapy of NSCLC patients. Using Pubmed database to search all documents required. The deadline of retrieval was February 25, 2015. Then further screening the articles according to the inclusion and exclusion criteria. Using diagnostic test meta-analysis methods to analyze the sensitivity and specificity of the immunohistochemistry (IHC) method compared with fluorescence in situ hybridization (FISH) method. Eleven literatures were added into the meta analysis, there were 3,234 of total cases. The diagnostic odds ratio (DOR) was 1,135.00 (95%CI: 337.10-3,821.46); the area under curve (AUC) of summary receiver operating characteristic curve (SROC) curve was 0.992,3 (SEAUC=0.003,2), the Q* was 0.964,4 (SEQ*=0.008,7). Immunohistochemical detection of EML4-ALK fusion gene mutation with specific antibody is feasible. It has high sensitivity and specificity. IHC can be a simple and rapid way in screening EML4-ALK fusion gene mutation and exhibits important clinical values.

A causal link from ALK to hexokinase II overexpression and hyperactive glycolysis in EML4-ALK-positive lung cancer

PubMed Central

Ma, Yibao; Yu, Chunrong; Mohamed, Esraa M.; Shao, Huanjie; Wang, Li; Sundaresan, Gobalakrishnan; Zweit, Jamal; Idowu, Michael; Fang, Xianjun

2016-01-01

A high rate of aerobic glycolysis is a hallmark of malignant transformation. Accumulating evidence suggests that diverse regulatory mechanisms mediate this cancer-associated metabolic change seen in a wide spectrum of cancer. The echinoderm microtubule associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) fusion protein is found in approximately 3-7% of non-small cell lung carcinomas (NSCLC). Molecular evidence and therapeutic effectiveness of FDA-approved ALK inhibitors indicated that EML4-ALK is a driving factor of lung tumorigenesis. A recent clinical study showed that NSCLC harboring EML4-ALK rearrangements displayed higher glucose metabolism compared to EML4-ALK-negative NSCLC. In the current work, we presented evidence that EML4-ALK is coupled to overexpression of hexokinase II (HK2), one of the rate-limiting enzymes of the glycolytic pathway. The link from EML4-ALK to HK2 upregulation is essential for a high rate of glycolysis and proliferation of EML4-ALK-rearranged NSCLC cells. We identified hypoxia-inducible factor 1α (HIF1α) as a key transcription factor to drive HK2 gene expression in normoxia in these cells. EML4-ALK induced hypoxia-independent but glucose-dependent accumulation of HIF1α protein via both transcriptional activation of HIF1α mRNA and the PI3K-AKT pathway to enhance HIF1α protein synthesis. The EML4-ALK-mediated upregulation of HIF1α, HK2 and glycolytic metabolism was also highly active in vivo as demonstrated by FDG-PET imaging of xenografts grown from EML4-ALK-positive NSCLC cells. Our data reveal a novel EML4-ALK-HIF1α-HK2 cascade to enhance glucose metabolism in EML4-ALK-positive NSCLC. PMID:27132509

Crystal structure of EML1 reveals the basis for Hsp90 dependence of oncogenic EML4-ALK by disruption of an atypical β-propeller domain.

PubMed

Richards, Mark W; Law, Edward W P; Rennalls, La'Verne P; Busacca, Sara; O'Regan, Laura; Fry, Andrew M; Fennell, Dean A; Bayliss, Richard

2014-04-08

Proteins of the echinoderm microtubule-associated protein (EMAP)-like (EML) family contribute to formation of the mitotic spindle and interphase microtubule network. They contain a unique hydrophobic EML protein (HELP) motif and a variable number of WD40 repeats. Recurrent gene rearrangements in nonsmall cell lung cancer fuse EML4 to anaplastic lymphoma kinase (ALK), causing expression of several fusion oncoprotein variants. We have determined a 2.6-Å crystal structure of the representative ∼70-kDa core of EML1, revealing an intimately associated pair of β-propellers, which we term a TAPE (tandem atypical propeller in EMLs) domain. One propeller is highly atypical, having a discontinuous subdomain unrelated to a WD40 motif in place of one of its blades. This unexpected feature shows how a propeller structure can be assembled from subdomains with distinct folds. The HELP motif is not an independent domain but forms part of the hydrophobic core that joins the two β-propellers. The TAPE domain binds α/β-tubulin via its conserved, concave surface, including part of the atypical blade. Mapping the characteristic breakpoints of each EML4-ALK variant onto our structure indicates that the EML4 TAPE domain is truncated in many variants in a manner likely to make the fusion protein structurally unstable. We found that the heat shock protein 90 (Hsp90) inhibitor ganetespib induced degradation of these variants whereas others lacking a partial TAPE domain were resistant in both overexpression models and patient-derived cell lines. The Hsp90-sensitive EML4-ALK variants are exceptions to the rule that oncogenic fusion proteins involve breakpoints in disordered regions of both partners.

Recurrence of lung adenocarcinoma after an interval of 15 years revealed by demonstration of the same type of EML4-ALK fusion gene.

PubMed

Tsukamoto, Yoshitane; Kanamori, Kiyonobu; Watanabe, Takahiro; Mikami, Koji; Ieki, Ryuji; Nakano, Takashi; Kajimoto, Kazuyoshi; Hirota, Seiichi

2014-12-01

We carried out an experiment on a 58-year-old man with multiple left lung tumors and swelling of multiple lymph nodes. For clinical staging and therapeutic purposes, bronchoalveolar lavage (BAL) cytology and lung biopsy were performed. The biopsy specimen revealed the left lower lung mass to be immunohistochemically ALK (anaplastic lymphoma kinase)-positive adenocarcinoma. Using the BAL specimen from the left lower lung, EML4 (echinoderm microtubule-associated protein-like 4)-ALK variant 1 fusion gene was detected by reverse transcription-polymerase chain reaction (RT-PCR). His past history showed that he had undergone an operation for lung adenocarcinoma of the right lower lobe 15 years before, and the pathological specimen at that time revealed that the lung adenocarcinoma with pleural invasion and single metastasis of mediastinal lymph node showed a mucinous cribriform pattern and/or signet-ring cell pattern. The typical histology led us to examine the ALK rearrangement in the primary lung cancer and mediastinal metastatic tumor. Immunohistochemistry (IHC) for ALK was positive, and ALK break apart fluorescence in situ hybridization (FISH) showed a positive result. Moreover, RT-PCR using formalin-fixed, paraffin-embedded tissue from the right lung cancer also demonstrated EML4-ALK variant 1 fusion gene. Although there is a possibility that the left lung cancer is de novo one with multiple metastases, detection of the same fusion gene of the very rare EML4-ALK variant 1 in both tumors suggests that the left cancer is a recurrence of the right lung cancer after an interval of 15 years. Copyright © 2014 Elsevier GmbH. All rights reserved.

Whole-genome sequencing of an aggressive BRAF wild-type papillary thyroid cancer identified EML4-ALK translocation as a therapeutic target.

PubMed

Demeure, Michael J; Aziz, Meraj; Rosenberg, Richard; Gurley, Steven D; Bussey, Kimberly J; Carpten, John D

2014-06-01

Recent advances in the treatment of cancer have focused on targeting genomic aberrations with selective therapeutic agents. In radioiodine resistant aggressive papillary thyroid cancers, there remain few effective therapeutic options. A 62-year-old man who underwent multiple operations for papillary thyroid cancer and whose metastases progressed despite standard treatments provided tumor tissue. We analyzed tumor and whole blood DNA by whole genome sequencing, achieving 80× or greater coverage over 94 % of the exome and 90 % of the genome. We determined somatic mutations and structural alterations. We found a total of 57 somatic mutations in 55 genes of the cancer genome. There was notably a lack of mutations in NRAS and BRAF, and no RET/PTC rearrangement. There was a mutation in the TRAPP oncogene and a loss of heterozygosity of the p16, p18, and RB1 tumor suppressor genes. The oncogenic driver for this tumor is a translocation involving the genes for anaplastic lymphoma receptor tyrosine kinase (ALK) and echinoderm microtubule associated protein like 4 (EML4). The EML4-ALK translocation has been reported in approximately 5 % of lung cancers, as well as in pediatric neuroblastoma, and is a therapeutic target for crizotinib. This is the first report of the whole genomic sequencing of a papillary thyroid cancer in which we identified an EML4-ALK translocation of a TRAPP oncogene mutation. These findings suggest that this tumor has a more distinct oncogenesis than BRAF mutant papillary thyroid cancer. Whole genome sequencing can elucidate an oncogenic context and expose potential therapeutic vulnerabilities in rare cancers.

Response to erlotinib in a patient with lung adenocarcinoma harbouring the EML4-ALK translocation: A case report.

PubMed

Alì, Greta; Chella, Antonio; Lupi, Cristiana; Proietti, Agnese; Niccoli, Cristina; Boldrini, Laura; Davini, Federico; Mussi, Alfredo; Fontanini, Gabriella

2015-04-01

Lung cancer is the leading cause of cancer-associated mortality worldwide, and the mainstay of treatment remains to be personalised therapy. Tyrosine kinase inhibitors of the epidermal growth factor receptor (EGFR-TKIs) have been reported to exert a significant impact in the treatment of non-small cell lung cancer (NSCLC), particularly in patients harbouring mutations in the EGFR gene. The echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase ( EML4-ALK ) gene translocation has been described in a subset of patients with NSCLC and possesses potent oncogenic activity. This translocation represents one of the most novel molecular targets in the treatment of NSCLC. Patients who harbour the EML4-ALK rearrangement possess lung tumours that lack EGFR or K-ras mutations. The present study reports the case of a patient possessing the EML4-ALK rearrangement that was initially treated with erlotinib and achieved a lasting clinical response. To the best of our knowledge, the current study is the first report of a clinical response to EGFR-TKI in a patient with lung adenocarcinoma harbouring the EML4-ALK fusion gene, but no EGFR mutations. However, as the disease progressed, the ALK gene status of the tumour was investigated, and based upon a positive result, the patient was treated with crizotinib and achieved a complete response. In conclusion, the present study suggests that the EML4-ALK rearrangement is not always associated with resistance to EGFR-TKIs. Further studies are required to clarify the biological features of these tumours and to investigate the mechanisms underlying the primary resistance to EGFR-TKIs when the EML4-ALK rearrangement is present.

Amphiregulin triggered epidermal growth factor receptor activation confers in vivo crizotinib-resistance of EML4-ALK lung cancer and circumvention by epidermal growth factor receptor inhibitors.

PubMed

Taniguchi, Hirokazu; Takeuchi, Shinji; Fukuda, Koji; Nakagawa, Takayuki; Arai, Sachiko; Nanjo, Shigeki; Yamada, Tadaaki; Yamaguchi, Hiroyuki; Mukae, Hiroshi; Yano, Seiji

2017-01-01

Crizotinib, a first-generation anaplastic lymphoma kinase (ALK) tyrosine-kinase inhibitor, is known to be effective against echinoderm microtubule-associated protein-like 4 (EML4)-ALK-positive non-small cell lung cancers. Nonetheless, the tumors subsequently become resistant to crizotinib and recur in almost every case. The mechanism of the acquired resistance needs to be deciphered. In this study, we established crizotinib-resistant cells (A925LPE3-CR) via long-term administration of crizotinib to a mouse model of pleural carcinomatous effusions; this model involved implantation of the A925LPE3 cell line, which harbors the EML4-ALK gene rearrangement. The resistant cells did not have the secondary ALK mutations frequently occurring in crizotinib-resistant cells, and these cells were cross-resistant to alectinib and ceritinib as well. In cell clone #2, which is one of the clones of A925LPE3-CR, crizotinib sensitivity was restored via the inhibition of epidermal growth factor receptor (EGFR) by means of an EGFR tyrosine-kinase inhibitor (erlotinib) or an anti-EGFR antibody (cetuximab) in vitro and in the murine xenograft model. Cell clone #2 did not have an EGFR mutation, but the expression of amphiregulin (AREG), one of EGFR ligands, was significantly increased. A knockdown of AREG with small interfering RNAs restored the sensitivity to crizotinib. These data suggest that overexpression of EGFR ligands such as AREG can cause resistance to crizotinib, and that inhibition of EGFR signaling may be a promising strategy to overcome crizotinib resistance in EML4-ALK lung cancer. © 2016 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

Analysis of EGFR, EML4-ALK, KRAS, and c-MET mutations in Chinese lung adenocarcinoma patients.

PubMed

Xia, Ning; An, Jian; Jiang, Qing-qing; Li, Min; Tan, Jun; Hu, Cheng-ping

2013-10-01

Mutation analysis of cancer driver genes is helpful for determining an optimal treatment strategy. We evaluated mutations in four driver genes, namely epidermal growth factor receptor (EGFR), Kirsten ras oncogene (KRAS), c-MET, and echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK), in Chinese lung adenocarcinoma patients from Hunan Province. We enrolled 110 lung adenocarcinoma patients in a single institution. EGFR and KRAS mutations were examined by direct sequencing, the EML4-ALK fusion gene was analyzed by fluorescence in situ hybridization, and c-MET amplification and c-Met protein expression were detected by quantitative PCR and immunohistochemistry, respectively. EGFR and KRAS mutations were observed in 52.7% (58/110) and 3.6% (4/106) of patients, respectively. c-MET amplification was detected in 5.5% (6/110) of patients. In addition, 30% (33/110) of the cases expressed c-Met protein, including all of the patients harboring c-MET amplification. Ten percent (11/110) of patients harbored the EML4-ALK fusion gene, and the frequency of ALK rearrangement was higher than that of other cohort analyses involving patients from other regions in China. Almost all of these gene mutations were exclusive except that in two female non-smoking patients, who harbored an EGFR mutation and EML4-ALK rearrangement simultaneously. In total, 70% of patients in the study harbored one of the four gene mutations. Most Chinese lung adenocarcinoma patients harbor driver gene mutations, among which ALK rearrangements were more common in Hunan patients than in previously reported populations. Future clinical trials should be conducted to determine the safety and efficacy of drug combination targeting different driver mutations.

A causal link from ALK to hexokinase II overexpression and hyperactive glycolysis in EML4-ALK-positive lung cancer.

PubMed

Ma, Y; Yu, C; Mohamed, E M; Shao, H; Wang, L; Sundaresan, G; Zweit, J; Idowu, M; Fang, X

2016-11-24

A high rate of aerobic glycolysis is a hallmark of malignant transformation. Accumulating evidence suggests that diverse regulatory mechanisms mediate this cancer-associated metabolic change seen in a wide spectrum of cancer. The echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) fusion protein is found in approximately 3-7% of non-small cell lung carcinomas (NSCLC). Molecular evidence and therapeutic effectiveness of FDA-approved ALK inhibitors indicated that EML4-ALK is a driving factor of lung tumorigenesis. A recent clinical study showed that NSCLC harboring EML4-ALK rearrangements displayed higher glucose metabolism compared with EML4-ALK-negative NSCLC. In the current work, we presented evidence that EML4-ALK is coupled to overexpression of hexokinase II (HK2), one of the rate-limiting enzymes of the glycolytic pathway. The link from EML4-ALK to HK2 upregulation is essential for a high rate of glycolysis and proliferation of EML4-ALK-rearranged NSCLC cells. We identified hypoxia-inducible factor 1α (HIF1α) as a key transcription factor to drive HK2 gene expression in normoxia in these cells. EML4-ALK induced hypoxia-independent but glucose-dependent accumulation of HIF1α protein via both transcriptional activation of HIF1α mRNA and the phosphatidylinositol 3 kinase-AKT pathway to enhance HIF1α protein synthesis. The EML4-ALK-mediated upregulation of HIF1α, HK2 and glycolytic metabolism was also highly active in vivo as demonstrated by fluorodeoxyglucose-positron emission tomography imaging of xenografts grown from EML4-ALK-positive NSCLC cells. Our data reveal a novel EML4-ALK-HIF1α-HK2 cascade to enhance glucose metabolism in EML4-ALK-positive NSCLC.

Effective enrichment strategy for EML4-ALK fusion gene screening in patients with non-small cell lung cancer.

PubMed

Kobayashi, Makoto; Sakakibara, Tomohiro; Inoue, Akira; Fukuhara, Tatsuro; Sasano, Hironobu; Ichinose, Masakazu; Nukiwa, Toshihiro

2014-01-01

A novel fusion gene that comprises the echinoderm microtubule-associated protein-like 4 (EML4) and anaplastic lymphoma kinase (ALK) genes was recently identified in non-small cell lung cancer (NSCLC), particularly in adenocarcinoma. A specific ALK inhibitor has been shown to exert anti-tumor effects in NSCLC with the EML4-ALK fusion gene. Previous reports suggested an EML4-ALK incidence of approximately 5% in a pan-NSCLC population, with an increased frequency in younger patients, but an appropriate strategy for further selecting patients with the EML4-ALK fusion gene remains unknown. Patients, 55 years of age or younger, who were diagnosed with NSCLC without typical squamous cell carcinoma features at our institute were retrospectively evaluated. The tumor specimens were examined by immunohistochemistry for the EML4-ALK fusion gene and by polymerase chain reaction for epidermal growth factor receptor (EGFR) mutations. Between January 2004 and September 2011, the EML4-ALK fusion gene was detected in 19.6% (9/46) of patients. The fusion gene incidence increased to 31% (9/29) when patients with EGFR mutations were excluded. The EML4-ALK fusion gene was further detected in 2 cases of undifferentiated cell carcinoma. EML4-ALK fusion gene examinations could be more effectively performed by selecting young NSCLC patients without EGFR mutations, whereas selection on the basis of a non-smoking or adenocarcinoma history, as reported in previous studies, may not correctly identify the patient groups with potential EML4-ALK fusion gene. Copyright © 2013 The Japanese Respiratory Society. Published by Elsevier B.V. All rights reserved.

The expression of SALL4 is significantly associated with EGFR, but not KRAS or EML4-ALK mutations in lung cancer.

PubMed

Jia, Xiangbo; Qian, Rulin; Zhang, Binbin; Zhao, Song

2016-10-01

Lung cancer is the leading cause of cancer-related deaths worldwide; unfortunately, its prognosis is still very poor. Therefore, developing the target molecular is very important for lung cancer diagnosis and treatment, especially in the early stage. With this in view, spalt-like transcription factor 4 ( SALL4 ) is considered a potential biomarker for diagnosis and prognosis in cancers, including lung cancer. In order to better investigate the association between the expression of SALL4 and driver genes mutation, 450 histopathologically diagnosed patients with lung cancer and 11 non-cancer patients were enrolled to test the expression of SALL4 and the status of driver genes mutation. This investigation included epidermal growth factor receptor ( EGFR ), kirsten rat sarcoma viral oncogene homolog ( KRAS ), and a fusion gene of the echinoderm microtubule-associated protein-like 4 ( EML4 ) and the anaplastic lymphoma kinase ( ALK ). The results of the study showed that females harbored more EGFR mutation in adenocarcinoma (ADC). The mutation rate of KRAS and EML4-ALK was about 5%, and the double mutations of EGFR/EML4-ALK were higher than EGFR/KRAS . In the expression analysis, the expression of SALL4 was much higher in cancer tissues than normally expected, especially in tissues that carried EGFR mutation (P<0.05), however, there were no significant differences between different mutation types. Likewise, there were no significant differences between expression of SALL4 and KRAS and EML4-ALK mutations. SALL4 is up regulated in lung cancer specimens and harbors EGFR mutation; this finding indicates that SALL4 expression may be relevant with EGFR , which could provide a new insight to lung cancer therapy. The mechanism needs further investigation and analysis.

Novel Antimicrobial Peptides EeCentrocins 1, 2 and EeStrongylocin 2 from the Edible Sea Urchin Echinus esculentus Have 6-Br-Trp Post-Translational Modifications

PubMed Central

Solstad, Runar Gjerp; Li, Chun; Isaksson, Johan; Johansen, Jostein; Svenson, Johan; Stensvåg, Klara; Haug, Tor

2016-01-01

The global problem of microbial resistance to antibiotics has resulted in an urgent need to develop new antimicrobial agents. Natural antimicrobial peptides are considered promising candidates for drug development. Echinoderms, which rely on innate immunity factors in the defence against harmful microorganisms, are sources of novel antimicrobial peptides. This study aimed to isolate and characterise antimicrobial peptides from the Edible sea urchin Echinus esculentus. Using bioassay-guided purification and cDNA cloning, three antimicrobial peptides were characterised from the haemocytes of the sea urchin; two heterodimeric peptides and a cysteine-rich peptide. The peptides were named EeCentrocin 1 and 2 and EeStrongylocin 2, respectively, due to their apparent homology to the published centrocins and strongylocins isolated from the green sea urchin Strongylocentrotus droebachiensis. The two centrocin-like peptides EeCentrocin 1 and 2 are intramolecularly connected via a disulphide bond to form a heterodimeric structure, containing a cationic heavy chain of 30 and 32 amino acids and a light chain of 13 amino acids. Additionally, the light chain of EeCentrocin 2 seems to be N-terminally blocked by a pyroglutamic acid residue. The heavy chains of EeCentrocins 1 and 2 were synthesised and shown to be responsible for the antimicrobial activity of the natural peptides. EeStrongylocin 2 contains 6 cysteines engaged in 3 disulphide bonds. A fourth peptide (Ee4635) was also discovered but not fully characterised. Using mass spectrometric and NMR analyses, EeCentrocins 1 and 2, EeStrongylocin 2 and Ee4635 were all shown to contain post-translationally brominated Trp residues in the 6 position of the indole ring. PMID:27007817

Trilobite-based biostratigraphy (arthropoda-trilobita) and related faunas of the Cambrian from Sonora, Mexico

NASA Astrophysics Data System (ADS)

Cuen-Romero, F. J.; Valdez-Holguín, J. E.; Buitrón-Sánchez, B. E.; Monreal, R.; Enríquez-Ocaña, L. F.; Aguirre-Hinojosa, E.; Ochoa-Granillo, J. A.; Palafox-Reyes, J. J.

2018-04-01

A biostratigraphic analysis based on trilobites of the main Cambrian outcrops from Sonora, Mexico is performed. The data are based on a combination of field work and published sources, including four previously studied locations from northern and eastern Sonora (Caborca, Cananea, Mazatán, and Arivechi) as well as a new location in the central part of the state of Sonora (San José de Gracia). Chronostratigraphic positions are assigned to the Cambrian outcrops according to Peng et al., 2012 and Cohen et al., 2017. In the Caborca area, the Puerto Blanco, Proveedora, Buelna, Cerro Prieto, Arrojos and El Tren formations comprise a wide range of biozones, which starts from the Fritzaspis Zone until the Glossopleura walcotti Zone (Begadean-Lincolnian Series, global Stage 3-Stage 5, Series 2-Series 3). The Bolsa Quartzite and the Abrigo Limestone exposed in Cananea area are assigned to the Cedaria/Cedarina dakotaensis Zone until the Crepicephalus Zone (Lincolnian Series-Marjuman Stage, global Series 3-Guzhangian). In the San José de Gracia area, The Proveedora, Buelna, Cerro Prieto and El Gavilán formations range from the ?Bristolia mohavensis or ?Bristolia insolens zones until the upper part of Mexicella mexicana Zone, Albertella highlandensis Subzone (Series 2-Series 3, Stage 4-Stage 5). In the Arivechi area, the La Sata, El Mogallón, La Huerta and the Milpillas formations range from Poliella denticulata Zone to the Elvinia Zone (Lincolnian-Millardan, Delamaran-Steptoean, global Series 3-Furongian, Stage 5-Paibian). Paleozoic marine fauna distribution in northwest Mexico and the southwest United States of America, suggest that during this time an extensive faunal province existed, containing a great variety of marine invertebrates with notorious intraspecific affinity. The biotic association includes poriferans, archaeocyathids, brachiopods, mollusks, arthropods and echinoderms as predominant elements.

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms

PubMed Central

Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Rashid, Iliyas; Sharma, Jyoti; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra; Murali, S.

2016-01-01

A voluminous information is available on karyological studies of fishes; however, limited efforts were made for compilation and curation of the available karyological data in a digital form. ‘Fish Karyome’ database was the preliminary attempt to compile and digitize the available karyological information on finfishes belonging to the Indian subcontinent. But the database had limitations since it covered data only on Indian finfishes with limited search options. Perceiving the feedbacks from the users and its utility in fish cytogenetic studies, the Fish Karyome database was upgraded by applying Linux, Apache, MySQL and PHP (pre hypertext processor) (LAMP) technologies. In the present version, the scope of the system was increased by compiling and curating the available chromosomal information over the globe on fishes and other aquatic organisms, such as echinoderms, molluscs and arthropods, especially of aquaculture importance. Thus, Fish Karyome version 2.1 presently covers 866 chromosomal records for 726 species supported with 253 published articles and the information is being updated regularly. The database provides information on chromosome number and morphology, sex chromosomes, chromosome banding, molecular cytogenetic markers, etc. supported by fish and karyotype images through interactive tools. It also enables the users to browse and view chromosomal information based on habitat, family, conservation status and chromosome number. The system also displays chromosome number in model organisms, protocol for chromosome preparation and allied techniques and glossary of cytogenetic terms. A data submission facility has also been provided through data submission panel. The database can serve as a unique and useful resource for cytogenetic characterization, sex determination, chromosomal mapping, cytotaxonomy, karyo-evolution and systematics of fishes. Database URL: http://mail.nbfgr.res.in/Fish_Karyome PMID:26980518

Acute water quality criteria for polycyclic aromatic hydrocarbons, pesticides, plastic additives, and 4-Nonylphenol in seawater.

PubMed

Durán, I; Beiras, R

2017-05-01

Probabilistic environmental quality criteria for Naphthalene (Nap), Phenanthrene (Phe), Fluoranthene (Flu), Pyrene (Pyr), Triclosan (TCS), Tributyltin (TBT), Chlorpyrifos (CPY), Diuron (DUR), γ-Hexaclorocyclohexane (γ-HCH), Bisphenol A (BPA) and 4-Nonylphenol (4-NP) were derived from acute toxicity data using saltwater species representative of marine ecosystems, including algae, mollusks, crustaceans, echinoderms and chordates. Preferably, data concerns sublethal endpoints and early life stages from bioassays conducted in our laboratory, but the data set was completed with a broad literature survey. The Water Quality Criteria (WQC) obtained for TBT (7.1·10 -3  μg L -1 ) and CPY (6.6· 10 -3  μg L -1 ) were orders of magnitude lower than those obtained for PAHs (ranging from 3.75 to 45.2 μg L -1 ), BPA (27.7 μg L -1 ), TCS (8.66 μg L -1 ) and 4-NP (1.52 μg L -1 ). Critical values for DUR and HCH were 0.1 and 0.057 μg L -1 respectively. Within this context, non-selective toxicants could be quantitatively defined as those showing a maximum variability in toxicity thresholds (TT) of 3 orders of magnitude across the whole range of marine diversity, and a cumulative distribution of the TT fitting to a single log-logistic curve, while for selective toxicants variability was consistently found to span 5 orders of magnitude and the TT distribution showed a bimodal pattern. For the latter, protective WQC must be derived taking into account the SSD of the sensitive taxa only. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Estuary health assessment using a benthic-index of biotic integrity in Yangtze Estuary and its adjacent waters].

PubMed

Zhou, Xiao-wei; Wang, Li-ping; Zheng, Bing-hui; Liu, Lu-san; Fu, Qing

2009-01-01

A benthic index of biotic integrity (B-IBI) was developed for application in estuaries health assessment of the Yangtze Estuary and its adjacent waters. Benthic macro-invertebrate samples were collected from 41 stream sites (13 non-degraded stations and 28 degraded stations) in the Yangtze Estuary and its adjacent waters in July, 2005. The analyses of the range of index value distribution, Pearson correlation and judgment ability were performed on fourteen candidate metrics. Six biological metrics were selected for the establishment of B-IBI, which were Shannon-Wiener index, the species number, total density, total biomass, Carapace Animals density percentage and Echinoderms density percentage. B-IBI was obtained by sum up all these indices after which were transformed into a uniform score by using the ratio scoring method. Base on 50 percentile of B-IBI value in reference sites, the criteria of health ranking was determined. The proposed criteria of benthic-index of biotic integrity were as follows: B-IBI > 2.48 was regarded as health, 1.86-2.48 sub-health, 1.24-1.86 fair, 0.62-1.24 poor, and B-IBI < 0.62 very poor. Assessing with these criteria, the results showed that among the 41 sites in Yangtze Estuary and its adjacent waters, 7 sites were health, 2 sites were sub-health, 8 sites were fair, 8 sites were poor and 16 sites were very poor. An independent data set sampled in June of 2006 was used to validate the index, the results indicated that final combined index correctly classified 89% of stations in the validation data set.

Pairing Quaternary paleoecology and modern ROV exploration to produce novel reconstructions of marine ecosystem responses to millennial-scale climate change

NASA Astrophysics Data System (ADS)

Myhre, S. E.; Pak, D. K.; Borreggine, M. J.; Hill, T. M.; Kennett, J.; Nicholson, C.; Deutsch, C. A.

2017-12-01

One of the most interesting problems for 21st Century marine ecology is understanding the potential physical, chemical, and biological scale of future climate-forced oceanographic changes. These fundamental questions can be informed through the examination of micro- and macrofauna from Quaternary sedimentary sequences, combined with modern observations of continental margin ecosystems. Here we examine Remotely Operated Vehicle (ROV) exploratory videos and sedimentary push cores, to identify biological assemblages, including mollusc, echinoderm, ostracod, and foraminifera density, diversity, and community structure from Santa Barbara Basin in the California Borderland. ROV explorations, from 380-500 meters below sea level (mbsl), describe the zonation of benthic fauna and the distribution of chemosynthetic trophic webs, which are consequences of gradations in the oxygen minimum zone and the ventilating sill depth (475 mbsl). Such observations reveal the modern vertical distribution of chemosynthetic bacterial communities and shallower, diverse communities associated with detrital food webs. Biological assemblages from 16.1-3.4 ka (from core MV0811-15JC, collected at 418 mbsl) produce a suite of paleoceanographic indicators, such as dissolved oxygen concentrations (foraminifera), chemosynthetic trophic webs (molluscs), and water masses (ostracods). These assemblages demonstrate how continental margin ecosystems reorganize vertically (through the water column) and geographically through climate events, for example through the loss of cryophilic species, the ephemeral occurrence of chemosynthetic communities, and the trace fossil evidence (through predation scarring on mollusc shells) of higher trophic web interactions. Together with ROV seafloor observations, these communities can reconstruct step-by-step vertical changes in the zonation of the continental margin, and can identify intervals of zonation change in relation to both Santa Barbara Basin ventilation and the regional California Borderland oxygen minimum zone.

No barrier to emergence of bathyal king crabs on the Antarctic shelf.

PubMed

Aronson, Richard B; Smith, Kathryn E; Vos, Stephanie C; McClintock, James B; Amsler, Margaret O; Moksnes, Per-Olav; Ellis, Daniel S; Kaeli, Jeffrey; Singh, Hanumant; Bailey, John W; Schiferl, Jessica C; van Woesik, Robert; Martin, Michael A; Steffel, Brittan V; Deal, Michelle E; Lazarus, Steven M; Havenhand, Jonathan N; Swalethorp, Rasmus; Kjellerup, Sanne; Thatje, Sven

2015-10-20

Cold-water conditions have excluded durophagous (skeleton-breaking) predators from the Antarctic seafloor for millions of years. Rapidly warming seas off the western Antarctic Peninsula could now facilitate their return to the continental shelf, with profound consequences for the endemic fauna. Among the likely first arrivals are king crabs (Lithodidae), which were discovered recently on the adjacent continental slope. During the austral summer of 2010 ‒ 2011, we used underwater imagery to survey a slope-dwelling population of the lithodid Paralomis birsteini off Marguerite Bay, western Antarctic Peninsula for environmental or trophic impediments to shoreward expansion. The population density averaged ∼ 4.5 individuals × 1,000 m(-2) within a depth range of 1,100 ‒ 1,500 m (overall observed depth range 841-2,266 m). Images of juveniles, discarded molts, and precopulatory behavior, as well as gravid females in a trapping study, suggested a reproductively viable population on the slope. At the time of the survey, there was no thermal barrier to prevent the lithodids from expanding upward and emerging on the outer shelf (400- to 550-m depth); however, near-surface temperatures remained too cold for them to survive in inner-shelf and coastal environments (<200 m). Ambient salinity, composition of the substrate, and the depth distribution of potential predators likewise indicated no barriers to expansion of lithodids onto the outer shelf. Primary food resources for lithodids--echinoderms and mollusks--were abundant on the upper slope (550-800 m) and outer shelf. As sea temperatures continue to rise, lithodids will likely play an increasingly important role in the trophic structure of subtidal communities closer to shore.

Assessing the impact of diclofenac, ibuprofen and sildenafil citrate (Viagra®) on the fertilisation biology of broadcast spawning marine invertebrates.

PubMed

Mohd Zanuri, Norlaila Binti; Bentley, Matthew G; Caldwell, Gary S

2017-06-01

Exposure to synthetic chemicals is a key environmental challenge faced by aquatic organisms. The time and dose effects of the pharmaceuticals diclofenac, ibuprofen, and sildenafil citrate on sperm motility and successful fertilisation are studied using the echinoderms, Asterias rubens and Psammechinus miliaris, and the polychaete worm Arenicola marina, all important components of the marine benthos. Motility was reduced for all species when exposed to diclofenac concentrations ≥0.1 μg/L. Exposure to ≥1.0 μg/L of ibuprofen affected only P. miliaris gametes and fertilisation success of A. marina. A. rubens and P. miliaris sperm increased in both percentage motility and swimming velocity when exposed to sildenafil citrate at concentrations ≥18 and ≥ 50 ng/L, respectively. Pre-incubation of sperm with sildenafil citrate significantly increased fertilisation success in A. rubens and P. miliaris but not in A. marina. Pre-incubated A. rubens oocytes fertilised successfully in ibuprofen. According to EU Directive 93/67/EEC, diclofenac is classified as a very toxic substance to gametes of A. rubens, P. miliaris, and A. marina (EC 50  = 100-1000 μg/L) while ibuprofen is classified as very toxic to gametes of P. miliaris but non-toxic to gametes of A. marina (EC 50  > 10,000 μg/L). The present study indicates that diclofenac exposure may have negative impacts on invertebrate reproductive success, whereas ibuprofen potentially may compromise P. miliaris reproduction. This study provides a valuable insight into the mechanisms that allow marine invertebrates to survive and reproduce in contaminated and changing habitats. Copyright © 2017 Elsevier Ltd. All rights reserved.

Specific cross-reactivity of antibodies raised against two major stress proteins, stress 70 and chaperonin 60, in diverse species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanders, B.M.; Martin, L.S.; Nakagawa, P.A.

1994-08-01

Immunoblot analysis using several antibodies raised against two major families of stress proteins, stress 70 and chaperonin 60 (cpn60), which are highly conserved in mammals, was carried out in diverse species often used in environmental research, including molluscs, annelids, crustaceans, echinoderms, and fish. The study revealed surprisingly different patterns of antibody cross-reactivity among species. The monoclonal anti-stress 70 antibody (mAb) C92 was the least cross-reactive for all species tested. The mAbs anti-stress 70 N27, BRM-22, and 3a3 were more broadly cross-reactive, but their binding specifities to stress 70 isoforms in the diverse species tested did not correlate with one anothermore » or follow taxonomic lines. The polyclonal anti-stress 70 antibody reacted to proteins in the 70 to 74 kDa range in all fish examined and in most invertebrates. When a polyclonal antibody (pAb) raised against cpn60 from a moth was used as a probe, specific binding was observed with proteins in the 60 to 64 kDa range in all fish examined and in most invertebrates. However, the size and number of isoforms that reacted with the pAb were species specific. These data suggest that these two major stress protein families are less highly conserved in invertebrates and fish than in mammals. Therefore, to minimize misinterpretation when using antibodies in heterologous assays with species in which the stress response has not been well characterized, it is important to determine which isoforms of stress 70 react with a particular antibody and to take into account the differential regulation of each member of this multigene family.« less

Visual orientation by the crown-of-thorns starfish ( Acanthaster planci)

NASA Astrophysics Data System (ADS)

Petie, Ronald; Hall, Michael R.; Hyldahl, Mia; Garm, Anders

2016-12-01

Photoreception in echinoderms has been known for over 200 years, but their visual capabilities remain poorly understood. As has been reported for some asteroids, the crown-of-thorns starfish ( Acanthaster planci) possess a seemingly advanced eye at the tip of each of its 7-23 arms. With such an array of eyes, the starfish can integrate a wide field of view of its surroundings. We hypothesise that, at close range, orientation and directional movements of the crown-of-thorns starfish are visually guided. In this study, the eyes and vision of A. planci were examined by means of light microscopy, electron microscopy, underwater goniometry, electroretinograms and behavioural experiments in the animals' natural habitat. We found that only animals with intact vision could orient to a nearby coral reef, whereas blinded animals, with olfaction intact, walked in random directions. The eye had peak sensitivity in the blue part (470 nm) of the visual spectrum and a narrow, horizontal visual field of approximately 100° wide and 30° high. With approximately 250 ommatidia in each adult compound eye and average interommatidial angles of 8°, crown-of-thorns starfish have the highest spatial resolution of any starfish studied to date. In addition, they have the slowest vision of all animals examined thus far, with a flicker fusion frequency of only 0.6-0.7 Hz. This may be adaptive as fast vision is not required for the detection of stationary objects such as reefs. In short, the eyes seem optimised for detecting large, dark, stationary objects contrasted against an ocean blue background. Our results show that the visual sense of the crown-of-thorns starfish is much more elaborate than has been thus far appreciated and is essential for orientation and localisation of suitable habitats.

Therapeutic strategies to overcome crizotinib resistance in non-small cell lung cancers harboring the fusion oncogene EML4-ALK

PubMed Central

Katayama, Ryohei; Khan, Tahsin M.; Benes, Cyril; Lifshits, Eugene; Ebi, Hiromichi; Rivera, Victor M.; Shakespeare, William C.; Iafrate, A. John; Engelman, Jeffrey A.; Shaw, Alice T.

2011-01-01

The echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) fusion oncogene represents a molecular target in a small subset of non-small cell lung cancers (NSCLCs). This fusion leads to constitutive ALK activation with potent transforming activity. In a pivotal phase 1 clinical trial, the ALK tyrosine kinase inhibitor (TKI) crizotinib (PF-02341066) demonstrated impressive antitumor activity in the majority of patients with NSCLC harboring ALK fusions. However, despite these remarkable initial responses, cancers eventually develop resistance to crizotinib, usually within 1 y, thereby limiting the potential clinical benefit. To determine how cancers acquire resistance to ALK inhibitors, we established a model of acquired resistance to crizotinib by exposing a highly sensitive EML4-ALK–positive NSCLC cell line to increasing doses of crizotinib until resistance emerged. We found that cells resistant to intermediate doses of crizotinib developed amplification of the EML4-ALK gene. Cells resistant to higher doses (1 μM) also developed a gatekeeper mutation, L1196M, within the kinase domain, rendering EML4-ALK insensitive to crizotinib. This gatekeeper mutation was readily detected using a unique and highly sensitive allele-specific PCR assay. Although crizotinib was ineffectual against EML4-ALK harboring the gatekeeper mutation, we observed that two structurally different ALK inhibitors, NVP-TAE684 and AP26113, were highly active against the resistant cancer cells in vitro and in vivo. Furthermore, these resistant cells remained highly sensitive to the Hsp90 inhibitor 17-AAG. Thus, we have developed a model of acquired resistance to ALK inhibitors and have shown that second-generation ALK TKIs or Hsp90 inhibitors are effective in treating crizotinib-resistant tumors harboring secondary gatekeeper mutations. PMID:21502504

Insights into the evolution of mammalian telomerase: Platypus TERT shares similarities with genes of birds and other reptiles and localizes on sex chromosomes

PubMed Central

2012-01-01

Background The TERT gene encodes the catalytic subunit of the telomerase complex and is responsible for maintaining telomere length. Vertebrate telomerase has been studied in eutherian mammals, fish, and the chicken, but less attention has been paid to other vertebrates. The platypus occupies an important evolutionary position, providing unique insight into the evolution of mammalian genes. We report the cloning of a platypus TERT (OanTERT) ortholog, and provide a comparison with genes of other vertebrates. Results The OanTERT encodes a protein with a high sequence similarity to marsupial TERT and avian TERT. Like the TERT of sauropsids and marsupials, as well as that of sharks and echinoderms, OanTERT contains extended variable linkers in the N-terminal region suggesting that they were present already in basal vertebrates and lost independently in ray-finned fish and eutherian mammals. Several alternatively spliced OanTERT variants structurally similar to avian TERT variants were identified. Telomerase activity is expressed in all platypus tissues like that of cold-blooded animals and murine rodents. OanTERT was localized on pseudoautosomal regions of sex chromosomes X3/Y2, expanding the homology between human chromosome 5 and platypus sex chromosomes. Synteny analysis suggests that TERT co-localized with sex-linked genes in the last common mammalian ancestor. Interestingly, female platypuses express higher levels of telomerase in heart and liver tissues than do males. Conclusions OanTERT shares many features with TERT of the reptilian outgroup, suggesting that OanTERT represents the ancestral mammalian TERT. Features specific to TERT of eutherian mammals have, therefore, evolved more recently after the divergence of monotremes. PMID:22655747

Insights into the evolution of mammalian telomerase: platypus TERT shares similarities with genes of birds and other reptiles and localizes on sex chromosomes.

PubMed

Hrdličková, Radmila; Nehyba, Jiří; Lim, Shu Ly; Grützner, Frank; Bose, Henry R

2012-06-01

The TERT gene encodes the catalytic subunit of the telomerase complex and is responsible for maintaining telomere length. Vertebrate telomerase has been studied in eutherian mammals, fish, and the chicken, but less attention has been paid to other vertebrates. The platypus occupies an important evolutionary position, providing unique insight into the evolution of mammalian genes. We report the cloning of a platypus TERT (OanTERT) ortholog, and provide a comparison with genes of other vertebrates. The OanTERT encodes a protein with a high sequence similarity to marsupial TERT and avian TERT. Like the TERT of sauropsids and marsupials, as well as that of sharks and echinoderms, OanTERT contains extended variable linkers in the N-terminal region suggesting that they were present already in basal vertebrates and lost independently in ray-finned fish and eutherian mammals. Several alternatively spliced OanTERT variants structurally similar to avian TERT variants were identified. Telomerase activity is expressed in all platypus tissues like that of cold-blooded animals and murine rodents. OanTERT was localized on pseudoautosomal regions of sex chromosomes X3/Y2, expanding the homology between human chromosome 5 and platypus sex chromosomes. Synteny analysis suggests that TERT co-localized with sex-linked genes in the last common mammalian ancestor. Interestingly, female platypuses express higher levels of telomerase in heart and liver tissues than do males. OanTERT shares many features with TERT of the reptilian outgroup, suggesting that OanTERT represents the ancestral mammalian TERT. Features specific to TERT of eutherian mammals have, therefore, evolved more recently after the divergence of monotremes.

No barrier to emergence of bathyal king crabs on the Antarctic shelf

PubMed Central

Aronson, Richard B.; Smith, Kathryn E.; Vos, Stephanie C.; McClintock, James B.; Amsler, Margaret O.; Moksnes, Per-Olav; Ellis, Daniel S.; Kaeli, Jeffrey; Singh, Hanumant; Bailey, John W.; Schiferl, Jessica C.; van Woesik, Robert; Martin, Michael A.; Steffel, Brittan V.; Deal, Michelle E.; Lazarus, Steven M.; Havenhand, Jonathan N.; Swalethorp, Rasmus; Kjellerup, Sanne; Thatje, Sven

2015-01-01

Cold-water conditions have excluded durophagous (skeleton-breaking) predators from the Antarctic seafloor for millions of years. Rapidly warming seas off the western Antarctic Peninsula could now facilitate their return to the continental shelf, with profound consequences for the endemic fauna. Among the likely first arrivals are king crabs (Lithodidae), which were discovered recently on the adjacent continental slope. During the austral summer of 2010‒2011, we used underwater imagery to survey a slope-dwelling population of the lithodid Paralomis birsteini off Marguerite Bay, western Antarctic Peninsula for environmental or trophic impediments to shoreward expansion. The population density averaged ∼4.5 individuals × 1,000 m−2 within a depth range of 1,100‒1,500 m (overall observed depth range 841–2,266 m). Images of juveniles, discarded molts, and precopulatory behavior, as well as gravid females in a trapping study, suggested a reproductively viable population on the slope. At the time of the survey, there was no thermal barrier to prevent the lithodids from expanding upward and emerging on the outer shelf (400- to 550-m depth); however, near-surface temperatures remained too cold for them to survive in inner-shelf and coastal environments (<200 m). Ambient salinity, composition of the substrate, and the depth distribution of potential predators likewise indicated no barriers to expansion of lithodids onto the outer shelf. Primary food resources for lithodids—echinoderms and mollusks—were abundant on the upper slope (550–800 m) and outer shelf. As sea temperatures continue to rise, lithodids will likely play an increasingly important role in the trophic structure of subtidal communities closer to shore. PMID:26417090

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms.

PubMed

Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Rashid, Iliyas; Sharma, Jyoti; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra; Murali, S

2016-01-01

A voluminous information is available on karyological studies of fishes; however, limited efforts were made for compilation and curation of the available karyological data in a digital form. 'Fish Karyome' database was the preliminary attempt to compile and digitize the available karyological information on finfishes belonging to the Indian subcontinent. But the database had limitations since it covered data only on Indian finfishes with limited search options. Perceiving the feedbacks from the users and its utility in fish cytogenetic studies, the Fish Karyome database was upgraded by applying Linux, Apache, MySQL and PHP (pre hypertext processor) (LAMP) technologies. In the present version, the scope of the system was increased by compiling and curating the available chromosomal information over the globe on fishes and other aquatic organisms, such as echinoderms, molluscs and arthropods, especially of aquaculture importance. Thus, Fish Karyome version 2.1 presently covers 866 chromosomal records for 726 species supported with 253 published articles and the information is being updated regularly. The database provides information on chromosome number and morphology, sex chromosomes, chromosome banding, molecular cytogenetic markers, etc. supported by fish and karyotype images through interactive tools. It also enables the users to browse and view chromosomal information based on habitat, family, conservation status and chromosome number. The system also displays chromosome number in model organisms, protocol for chromosome preparation and allied techniques and glossary of cytogenetic terms. A data submission facility has also been provided through data submission panel. The database can serve as a unique and useful resource for cytogenetic characterization, sex determination, chromosomal mapping, cytotaxonomy, karyo-evolution and systematics of fishes. Database URL: http://mail.nbfgr.res.in/Fish_Karyome. © The Author(s) 2016. Published by Oxford University Press.

Is the idea of a fast block to polyspermy based on artifact?

PubMed

Dale, Brian

2014-08-01

This purpose of this review is to look at the experimental evidence, both kinetic and electrophysiological, that led to the hypothesis of a fast electrical block to polyspermy in sea urchin eggs. The idea of a fast partial block, forwarded in the 1950's, that would reduce the receptivity of the egg surface by 1/20th following its interaction with the fertilizing spermatozoon, was based on experiments that treated fertilization as a first order chemical reaction. Here, I outline the criticisms of the Rothschild theory and demonstrate that the hypothesis of a fast partial block to polyspermy is unfounded. Notwithstanding, it was suggested in the 1970's that the membrane depolarization, induced by the fertilizing spermatozoon, prevented the interaction of supernumerary spermatozoa, the fast electrical block to polyspermy. While trans-membrane voltage recording has permitted a better understanding of the sequence of events occurring at fertilization, there is no evidence that depolarization prevents the interaction of supernumerary spermatozoa. Sperm entry is prevented at positive and negative potentials, in the voltage clamp configuration, however this is an artifact caused by the currents injected into the egg employed to hold the voltage constant in a non-physiological range. At permissive voltages, around -20 mV, where the current required to hold the voltage is minimal, only one spermatozoon normally enters the egg. Thus, irrespective of the egg voltage, the fertilizing spermatozoon is, in any case, attached to a privileged interaction site that permits entry and distinguishes it from supernumerary spermatozoa. Competence for monospermy is acquired during oocyte maturation and data on cortical organization in echinoderm eggs points to the actin filament system for regulating sperm entry. Copyright © 2014 Elsevier Inc. All rights reserved.

Effect of multiple cycles of freeze-thawing on the RNA quality of lung cancer tissues.

PubMed

Yu, Keke; Xing, Jie; Zhang, Jie; Zhao, Ruiying; Zhang, Ye; Zhao, Lanxiang

2017-09-01

RNA degradation is a major problem in tissue banking. We explored the effect of thawing flash-frozen biospecimens on the quality and integrity of RNA for genetic testing as well as for other cancer research studies. The histological quality of the frozen tumor sections was evaluated by using hematoxylin and eosin staining. RNA extraction from 60 lung cancer tissue samples subjected to various freeze/thaw cycles was performed using the RNeasy Plus isolation kit. RNA integrity was assessed by using an Agilent bioanalyzer to obtain RNA integrity numbers (RIN). Furthermore, RNA from different groups was used for fluorescence Reverse transcription-polymerase chain reaction (RT-PCR) analysis of the echinoderm microtubule-associated protein-like 4 and anaplastic lymphoma kinase (EML4-ALK) fusion gene mutation to verify whether it can be used for research or clinical testing. Highly variable RIN values were observed among the samples, which showed no correlation with the number of freeze/thaw cycles conducted. However, after 3 freeze/thaw cycles (each thaw event lasted for 10 min), an increasing number of changes in peak intensity in RINs were observed. After 5 freeze/thaw cycles, RNA integrity decreased to approximately 35%. After 3 freeze/thaw cycles, the RNA could still be used for RT-PCR analysis of EML4-ALK fusion gene mutations; whereas those subjected to 5 freeze/thaw cycles could not. Limited (<3) freeze/thaw cycles did not adversely affect the quality of RNA extracted from tumor tissues and subsequent RT-PCR analysis. Our data could be utilized in the establishment of a standardized procedure for tissue biospecimen collection and storage.

The rise of the starlet sea anemone Nematostella vectensis as a model system to investigate development and regeneration

PubMed Central

Rentzsch, Fabian; Röttinger, Eric

2016-01-01

Reverse genetics and next‐generation sequencing unlocked a new era in biology. It is now possible to identify an animal(s) with the unique biology most relevant to a particular question and rapidly generate tools to functionally dissect that biology. This review highlights the rise of one such novel model system, the starlet sea anemone Nematostella vectensis. Nematostella is a cnidarian (corals, jellyfish, hydras, sea anemones, etc.) animal that was originally targeted by EvoDevo researchers looking to identify a cnidarian animal to which the development of bilaterians (insects, worms, echinoderms, vertebrates, mollusks, etc.) could be compared. Studies in Nematostella have accomplished this goal and informed our understanding of the evolution of key bilaterian features. However, Nematostella is now going beyond its intended utility with potential as a model to better understand other areas such as regenerative biology, EcoDevo, or stress response. This review intends to highlight key EvoDevo insights from Nematostella that guide our understanding about the evolution of axial patterning mechanisms, mesoderm, and nervous systems in bilaterians, as well as to discuss briefly the potential of Nematostella as a model to better understand the relationship between development and regeneration. Lastly, the sum of research to date in Nematostella has generated a variety of tools that aided the rise of Nematostella to a viable model system. We provide a catalogue of current resources and techniques available to facilitate investigators interested in incorporating Nematostella into their research. WIREs Dev Biol 2016, 5:408–428. doi: 10.1002/wdev.222 For further resources related to this article, please visit the WIREs website. PMID:26894563

Pedal peptide/orcokinin‐type neuropeptide signaling in a deuterostome: The anatomy and pharmacology of starfish myorelaxant peptide in Asterias rubens

PubMed Central

Lin, Ming; Egertová, Michaela; Zampronio, Cleidiane G.; Jones, Alexandra M.

2017-01-01

Abstract Pedal peptide (PP) and orcokinin (OK) are related neuropeptides that were discovered in protostomian invertebrates (mollusks, arthropods). However, analysis of genome/transcriptome sequence data has revealed that PP/OK‐type neuropeptides also occur in a deuterostomian phylum—the echinoderms. Furthermore, a PP/OK‐type neuropeptide (starfish myorelaxant peptide, SMP) was recently identified as a muscle relaxant in the starfish Patiria pectinifera. Here mass spectrometry was used to identify five neuropeptides (ArPPLN1a‐e) derived from the SMP precursor (PP‐like neuropeptide precursor 1; ArPPLNP1) in the starfish Asterias rubens. Analysis of the expression of ArPPLNP1 and neuropeptides derived from this precursor in A. rubens using mRNA in situ hybridization and immunohistochemistry revealed a widespread pattern of expression, with labeled cells and/or processes present in the radial nerve cords, circumoral nerve ring, digestive system (e.g., cardiac stomach) and body wall‐associated muscles (e.g., apical muscle) and appendages (e.g., tube feet and papulae). Furthermore, our data provide the first evidence that neuropeptides are present in the lateral motor nerves and in nerve processes innervating interossicular muscles. In vitro pharmacological tests with SMP (ArPPLN1b) revealed that it causes dose‐dependent relaxation of apical muscle, tube foot and cardiac stomach preparations from A. rubens. Collectively, these anatomical and pharmacological data indicate that neuropeptides derived from ArPPLNP1 act as inhibitory neuromuscular transmitters in starfish, which contrasts with the myoexcitatory actions of PP/OK‐type neuropeptides in protostomian invertebrates. Thus, the divergence of deuterostomes and protostomes may have been accompanied by an inhibitory–excitatory transition in the roles of PP/OK‐type neuropeptides as regulators of muscle activity. PMID:28880392

The substantial first impact of bottom fishing on rare biodiversity hotspots: a dilemma for evidence-based conservation.

PubMed

Cook, Robert; Fariñas-Franco, Jose M; Gell, Fiona R; Holt, Rohan H F; Holt, Terry; Lindenbaum, Charles; Porter, Joanne S; Seed, Ray; Skates, Lucie R; Stringell, Thomas B; Sanderson, William G

2013-01-01

This study describes the impact of the first passage of two types of bottom-towed fishing gear on rare protected shellfish-reefs formed by the horse mussel Modiolus modiolus (L.). One of the study sites was trawled and the other was scallop-dredged. Divers collected HD video imagery of epifauna from quadrats at the two study sites and directed infaunal samples from one site. The total number of epifaunal organisms was significantly reduced following a single pass of a trawl (90%) or scallop dredge (59%), as was the diversity of the associated community and the total number of M. modiolus at the trawled site. At both sites declines in anthozoans, hydrozoans, bivalves, echinoderms and ascidians accounted for most of the change. A year later, no recovery was evident at the trawled site and significantly fewer infaunal taxa (polychaetes, malacostracans, bivalves and ophuroids) were recorded in the trawl track. The severity of the two types of impact reflected the undisturbed status of the habitats compared to previous studies. As a 'priority habitat' the nature of the impacts described on M. modiolus communities are important to the development of conservation management policy and indicators of condition in Marine Protected Areas (EU Habitats Directive) as well as indicators of 'Good Environmental Status' under the European Union Marine Strategy Framework Directive. Conservation managers are under pressure to support decisions with good quality evidence. Elsewhere, indirect studies have shown declines of M. modiolus biogenic communities in fishing grounds. However, given the protected status of the rare habitat, premeditated demonstration of direct impact is unethical or illegal in Marine Protected Areas. This study therefore provides a unique opportunity to investigate the impact from fishing gear whilst at the same time reflecting on the dilemma of evidence-based conservation management.

Bioenergetic trade-offs in the sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea) in response to CO2-driven ocean acidification.

PubMed

Yuan, Xiutang; Shao, Senlin; Yang, Xiaolong; Yang, Dazuo; Xu, Qinzeng; Zong, Humin; Liu, Shilin

2016-05-01

Ocean acidification (OA) caused by excessive CO2 is a potential ecological threat to marine organisms. The impacts of OA on echinoderms are well-documented, but there has been a strong bias towards sea urchins, and limited information is available on sea cucumbers. This work examined the effect of medium-term (60 days) exposure to three pH levels (pH 8.06, 7.72, and 7.41, covering present and future pH variability) on the bioenergetic responses of the sea cucumber, Apostichopus japonicus, an ecologically and economically important holothurian in Asian coasts. Results showed that the measured specific growth rate linearly decreased with decreased pH, leading to a 0.42 %·day(-1) decrease at pH 7.41 compared with that at pH 8.06. The impacts of pH on physiological energetics were variable: measured energy consumption and defecation rates linearly decreased with decreased pH, whereas maintenance energy in calculated respiration and excretion were not significantly affected. No shift in energy allocation pattern was observed in A. japonicus upon exposure to pH 7.72 compared with pH 8.06. However, a significant shift in energy budget occurred upon exposure to pH 7.41, leading to decreased energy intake and increased percentage of energy that was lost in feces, thereby resulting in a significantly lowered allocation into somatic growth. These findings indicate that adult A. japonicus is resilient to the OA scenario at the end of the twenty-first century, but further acidification may negatively influence the grazing capability and growth, thereby influencing its ecological functioning as an "ecosystem engineer" and potentially harming its culture output.

Fauna and predator-prey relationships of Ettling, an actinopterygian fish-dominated Konservat-Lagerstätte from the Late Jurassic of southern Germany.

PubMed

Ebert, Martin; Kölbl-Ebert, Martina; Lane, Jennifer A

2015-01-01

The newly recognized Konservat-Lagerstätte of Ettling (Bavaria), field site of the Jura-Museum Eichstätt (JME), is unique among Late Jurassic plattenkalk basins (Solnhofen region) in its abundant, extremely well preserved fossil vertebrates, almost exclusively fishes. We report actinopterygians (ginglymodins, pycnodontiforms, halecomorphs, aspidorynchiforms, "pholidophoriforms," teleosts); turtles; and non-vertebrates (echinoderms, arthropods, brachiopods, mollusks, jellyfish, sponges, biomats, plants) in a current faunal list. Ettling has yielded several new fish species (Bavarichthys incognitus; Orthogonikleithrus hoelli; Aspidorhynchus sanzenbacheri; Macrosemimimus fegerti). Upper and lower Ettling strata differ in faunal content, with the lower dominated by the small teleost Orthogonikleithrus hoelli (absent from the upper layers, where other prey fishes, Leptolepides sp. and Tharsis sp., occur instead). Pharyngeal and stomach contents of Ettling fishes provide direct evidence that Orthogonikleithrus hoelli was a primary food source during early Ettling times. Scarcity of ammonites and absence of vampyromorph coleoids at Ettling differ markedly from the situation at other nearby localities in the region (e.g., Eichstätt, Painten, Schamhaupten, the Mörnsheim beds), where they are more common. Although the exact biochronological age of Ettling remains uncertain (lack of suitable index fossils), many Ettling fishes occur in other plattenkalk basins of Germany (e.g., Kelheim) and France (Cerin) dated as Late Kimmeridgian to Early Tithonian (eigeltingense horizon), suggesting a comparable geologic age. The Ettling deposits represent an independent basin within the larger Upper Jurassic "Solnhofen Archipelago", a shallow subtropical sea containing scattered islands, sponge-microbial and coral reefs, sandbars, and deeper basins on a vast carbonate platform along the northern margin of the Tethys Ocean.

CRISPR/Cas9 Technology-Based Xenograft Tumors as Candidate Reference Materials for Multiple EML4-ALK Rearrangements Testing.

PubMed

Peng, Rongxue; Zhang, Rui; Lin, Guigao; Yang, Xin; Li, Ziyang; Zhang, Kuo; Zhang, Jiawei; Li, Jinming

2017-09-01

The echinoderm microtubule-associated protein-like 4 and anaplastic lymphoma kinase (ALK) receptor tyrosine kinase (EML4-ALK) rearrangement is an important biomarker that plays a pivotal role in therapeutic decision making for non-small-cell lung cancer (NSCLC) patients. Ensuring accuracy and reproducibility of EML4-ALK testing by fluorescence in situ hybridization, immunohistochemistry, RT-PCR, and next-generation sequencing requires reliable reference materials for monitoring assay sensitivity and specificity. Herein, we developed novel reference materials for various kinds of EML4-ALK testing. CRISPR/Cas9 was used to edit various NSCLC cell lines containing EML4-ALK rearrangement variants 1, 2, and 3a/b. After s.c. inoculation, the formalin-fixed, paraffin-embedded (FFPE) samples from xenografts were prepared and tested for suitability as candidate reference materials by fluorescence in situ hybridization, immunohistochemistry, RT-PCR, and next-generation sequencing. Sample validation and commutability assessments showed that all types of FFPE samples derived from xenograft tumors have typical histological structures, and EML4-ALK testing results were similar to the clinical ALK-positive NSCLC specimens. Among the four methods for EML4-ALK detection, the validation test showed 100% concordance. Furthermore, these novel FFPE reference materials showed good stability and homogeneity. Without limitations on variant types and production, our novel FFPE samples based on CRISPR/Cas9 editing and xenografts are suitable as candidate reference materials for the validation, verification, internal quality control, and proficiency testing of EML4-ALK detection. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Molecular cloning of hsf1 and hsbp1 cDNAs, and the expression of hsf1, hsbp1 and hsp70 under heat stress in the sea cucumber Apostichopus japonicus.

PubMed

Xu, Dongxue; Sun, Lina; Liu, Shilin; Zhang, Libin; Yang, Hongsheng

2016-08-01

The heat shock response (HSR) is known for the elevated synthesis of heat shock proteins (HSPs) under heat stress, which is mediated primarily by heat shock factor 1 (HSF1). Heat shock factor binding protein 1 (HSBP1) and feedback control of heat shock protein 70 (HSP70) are major regulators of the activity of HSF1. We obtained full-length cDNA of genes hsf1 and hsbp1 in the sea cucumber Apostichopus japonicus, which are the second available for echinoderm (after Strongylocentrotus purpuratus), and the first available for holothurian. The full-length cDNA of hsf1 was 2208bp, containing a 1326bp open reading frame encoding 441 amino acids. The full-length cDNA of hsbp1 was 2850bp, containing a 225bp open reading frame encoding 74 amino acids. The similarities of A. japonicus HSF1 with other species are low, and much higher similarity identities of A. japonicus HSBP1 were shared. Phylogenetic trees showed that A. japonicus HSF1 and HSBP1 were clustered with sequences from S. purpuratus, and fell into distinct clades with sequences from mollusca, arthropoda and vertebrata. Analysis by real-time PCR showed hsf1 and hsbp1 mRNA was expressed constitutively in all tissues examined. The expression of hsf1, hsbp1 and hsp70 in the intestine at 26°C was time-dependent. The results of this study might provide new insights into the regulation of heat shock response in this species. Copyright © 2016. Published by Elsevier Inc.

The Unique Morgue Ubiquitination Protein Is Conserved in a Diverse but Restricted Set of Invertebrates

PubMed Central

Zhou, Ying; Carpenter, Zachary W.; Brennan, Gregory

2009-01-01

Drosophila Morgue is a unique ubiquitination protein that facilitates programmed cell death and associates with DIAP1, a critical cell death inhibitor with E3 ubiquitin ligase activity. Morgue possesses a unique combination of functional domains typically associated with distinct types of ubiquitination enzymes. This includes an F box characteristic of the substrate-binding subunit in Skp, Cullin, and F box (SCF)-type ubiquitin E3 ligase complexes and a variant ubiquitin E2 conjugase domain where the active site cysteine is replaced by a glycine. Morgue also contains a single C4-type zinc finger motif. This architecture suggests potentially novel ubiquitination activities for Morgue. In this study, we address the evolutionary origins of this distinctive protein utilizing a combination of bioinformatics and molecular biology approaches. We find that Morgue exhibits widespread but restricted phylogenetic distribution among metazoans. Morgue proteins were identified in a wide range of Protostome phyla, including Arthropoda, Annelida, Mollusca, Nematoda, and Platyhelminthes. However, with one potential exception, Morgue was not detected in Deuterostomes, including Chordates, Hemichordates, or Echinoderms. Morgue was also not found in Ctenophora, Cnidaria, Placozoa, or Porifera. Characterization of Morgue sequences within specific animal lineages suggests that gene deletion or acquisition has occurred during divergence of nematodes and that at least one arachnid expresses an atypical form of Morgue consisting only of the variant E2 conjugase domain. Analysis of the organization of several morgue genes suggests that exon-shuffling events have contributed to the evolution of the Morgue protein. These results suggest that Morgue mediates conserved and distinctive ubiquitination functions in specific cell death pathways. PMID:19602541

Protocol Design for the Bench to Bed Trial in Alectinib-Refractory Non-Small-Cell Lung Cancer Patients Harboring the EML4-ALK Fusion Gene (ALRIGHT/OLCSG1405).

PubMed

Isozaki, Hideko; Hotta, Katsuyuki; Ichihara, Eiki; Takigawa, Nagio; Ohashi, Kadoaki; Kubo, Toshio; Ninomiya, Takashi; Ninomiya, Kiichiro; Oda, Naohiro; Yoshioka, Hiroshige; Ichikawa, Hirohisa; Inoue, Masaaki; Takata, Ichiro; Shibayama, Takuo; Kuyama, Shoichi; Sugimoto, Keisuke; Harada, Daijiro; Harita, Shingo; Sendo, Toshiaki; Tanimoto, Mitsune; Kiura, Katsuyuki

2016-11-01

Based on our preclinical study results, which showed that the activation of the hepatocyte growth factor/MET pathway is a potential mechanism of acquired resistance to alectinib, we launched the ALRIGHT (OLCSG1405 [alectinib-refractory non-small-cell lung cancer patients harboring the EML4-ALK fusion gene]), a phase II trial of the anaplastic lymphoma kinase (ALK)/MET inhibitor crizotinib in patients with non-small-cell lung cancer refractory to alectinib and harboring the echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusion gene. Patients with ALK-rearranged tumors who have developed disease progression during alectinib treatment will receive crizotinib monotherapy until disease progression or the occurrence of unacceptable toxicity. The primary endpoint is set as the objective response rate, assuming that a response in 50% of eligible patients will indicate potential usefulness and that 15% would be the lower limit of interest (1-sided α of 0.05, β of 0.20). The estimated accrual number of patients is 9. The secondary endpoints include progression-free survival, overall survival, adverse events, and patient-reported outcomes. We will also take tissue samples before crizotinib monotherapy to conduct an exploratory analysis of ALK and hepatocyte growth factor/MET expression levels and gene alterations (eg, mutations, amplifications, and translocations). We will obtain information regarding whether crizotinib, which targets not only ALK, but also MET, can truly produce efficacy with acceptable safety profiles in ALK + non-small-cell lung cancer even in the alectinib-refractory setting. Copyright © 2016 Elsevier Inc. All rights reserved.

Tolerance of Sponge Assemblages to Temperature Anomalies: Resilience and Proliferation of Sponges following the 1997–8 El-Niño Southern Oscillation

PubMed Central

Kelmo, Francisco; Bell, James J.; Attrill, Martin J.

2013-01-01

Coral reefs across the world are under threat from a range of stressors, and while there has been considerable focus on the impacts of these stressors on corals, far less is known about their effect on other reef organisms. The 1997–8 El-Niño Southern Oscillation (ENSO) had notable and severe impacts on coral reefs worldwide, but not all reef organisms were negatively impacted by this large-scale event. Here we describe how the sponge fauna at Bahia, Brazil was influenced by the 1997–8 ENSO event. Sponge assemblages from three contrasting reef habitats (reef tops, walls and shallow banks) at four sites were assessed annually from 1995 to 2011. The within-habitat sponge diversity did not vary significantly across the study period; however, there was a significant increase in density in all habitats. Multivariate analyses revealed no significant difference in sponge assemblage composition (ANOSIM) between pre- and post-ENSO years for any of the habitats, suggesting that neither the 1997–8 nor any subsequent smaller ENSO events have had any measurable impact on the reef sponge assemblage. Importantly, this is in marked contrast to the results previously reported for a suite of other taxa (including corals, echinoderms, bryozoans, and ascidians), which all suffered mass mortalities as a result of the ENSO event. Our results suggest that of all reef taxa, sponges have the potential to be resilient to large-scale thermal stress events and we hypothesize that sponges might be less affected by projected increases in sea surface temperature compared to other major groups of reef organisms. PMID:24116109

Acid-base physiology response to ocean acidification of two ecologically and economically important holothuroids from contrasting habitats, Holothuria scabra and Holothuria parva.

PubMed

Collard, Marie; Eeckhaut, Igor; Dehairs, Frank; Dubois, Philippe

2014-12-01

Sea cucumbers are dominant invertebrates in several ecosystems such as coral reefs, seagrass meadows and mangroves. As bioturbators, they have an important ecological role in making available calcium carbonate and nutrients to the rest of the community. However, due to their commercial value, they face overexploitation in the natural environment. On top of that, occurring ocean acidification could impact these organisms, considered sensitive as echinoderms are osmoconformers, high-magnesium calcite producers and have a low metabolism. As a first investigation of the impact of ocean acidification on sea cucumbers, we tested the impact of short-term (6 to 12 days) exposure to ocean acidification (seawater pH 7.7 and 7.4) on two sea cucumbers collected in SW Madagascar, Holothuria scabra, a high commercial value species living in the seagrass meadows, and H. parva, inhabiting the mangroves. The former lives in a habitat with moderate fluctuations of seawater chemistry (driven by day-night differences) while the second lives in a highly variable intertidal environment. In both species, pH of the coelomic fluid was significantly negatively affected by reduced seawater pH, with a pronounced extracellular acidosis in individuals maintained at pH 7.7 and 7.4. This acidosis was due to an increased dissolved inorganic carbon content and pCO2 of the coelomic fluid, indicating a limited diffusion of the CO2 towards the external medium. However, respiration and ammonium excretion rates were not affected. No evidence of accumulation of bicarbonate was observed to buffer the coelomic fluid pH. If this acidosis stays uncompensated for when facing long-term exposure, other processes could be affected in both species, eventually leading to impacts on their ecological role.

Middle Devonian depositional environments for Rapid Member (Cedar Valley Group) interpreted from exposures at the Coralville spillway and elsewhere in eastern Iowa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Witzke, B.J.; Bunker, B.J.

1994-04-01

Ongoing studies of the Cedar Valley Group were fortuitously aided by the exhumation of Rapid Mbr (Little Cedar Fm) carbonate strata below the coralville spillway, Johnson Co., Iowa, during the summer floods of 1993. Extensive bedding-plane exposures provided an exceptional opportunity to document fine-scale lateral biotic and lithologic variations within the member, and to compare these with data from elsewhere in eastern Iowa. The base of the Rapid Mbr is drawn at an abrupt lithic change above packstones of the Solon Mbr, marking a regional transgressive event. The basal 2.6 m of the Rapid is dominated by argillaceous skeletal wackestonesmore » with common brachiopods and echinoderm debris, interspersed with thin mudstones. The overlying 4 m comprises a series of 50--100 cm thick couplets which display alternations of thin mudstones and thicker brachiopod-rich wackepackstones. The next unit (2.9 m) is dominated by sparse-skeletal argillaceous mudstones. The paucity of burrowing and skeletal benthos through much of the unit is interpreted to reflect bottom oxygen stress in a relatively deep, possibly stratified cratonic seaway. Nevertheless, skeletal horizons within the unit indicate episodically favorable benthic conditions. The mudstone unit shallows upward into a brachiopod-rich wackestone interval which is, in turn, capped by a condensed horizon of phosphatic and glauconitic enrichment (near base of subterminus Fauna). Above this, two regionally extensive coral-rich biostromes occur. Upper Rapid strata show a complex of wackestone and packstone facies, with glauconitic enrichment and hardgrounds noted. The member is capped by shoal-water grainstones in the Coralville area, and by peritidal facies in northern Iowa.« less

Molecular phylogeny of extant Holothuroidea (Echinodermata).

PubMed

Miller, Allison K; Kerr, Alexander M; Paulay, Gustav; Reich, Mike; Wilson, Nerida G; Carvajal, Jose I; Rouse, Greg W

2017-06-01

Sea cucumbers (Holothuroidea) are a morphologically diverse, ecologically important, and economically valued clade of echinoderms; however, the understanding of the overall systematics of the group remains controversial. Here, we present a phylogeny of extant Holothuroidea assessed with maximum parsimony, maximum likelihood, and Bayesian approaches using approximately 4.3kb of mt- (COI, 16S, 12S) and nDNA (H3, 18S, 28S) sequences from 82 holothuroid terminals representing 23 of the 27 widely-accepted family-ranked taxa. Currently five holothuroid taxa of ordinal rank are accepted. We find that three of the five orders are non-monophyletic, and we revise the taxonomy of the groups accordingly. Apodida is sister to the rest of Holothuroidea, here considered Actinopoda. Within Actinopoda, Elasipodida in part is sister to the remaining Actinopoda. This latter clade, comprising holothuroids with respiratory trees, is now called Pneumonophora. The traditional Aspidochirotida is paraphyletic, with representatives from three orders (Molpadida, Dendrochirotida, and Elasipodida in part) nested within. Therefore, we discontinue the use of Aspidochirotida and instead erect Holothuriida as the sister group to the remaining Pneumonophora, here termed Neoholothuriida. We found four well-supported major clades in Neoholothuriida: Dendrochirotida, Molpadida and two new clades, Synallactida and Persiculida. The mapping of traditionally-used morphological characters in holothuroid systematics onto the phylogeny revealed marked homoplasy in most characters demonstrating that further taxonomic revision of Holothuroidea is required. Two time-tree analyses, one based on calibrations for uncontroversial crown group dates for Eleutherozoa, Echinozoa and Holothuroidea and another using these calibrations plus four more from within Holothuroidea, showed major discrepancies, suggesting that fossils of Holothuroidea may need reassessment in terms of placing these forms with existing crown clades. Copyright © 2017 Elsevier Inc. All rights reserved.

Modular Evolution of DNA-Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks

PubMed Central

Cheatle Jarvela, Alys M.; Brubaker, Lisa; Vedenko, Anastasia; Gupta, Anisha; Armitage, Bruce A.; Bulyk, Martha L.; Hinman, Veronica F.

2014-01-01

Gene regulatory networks (GRNs) describe the progression of transcriptional states that take a single-celled zygote to a multicellular organism. It is well documented that GRNs can evolve extensively through mutations to cis-regulatory modules (CRMs). Transcription factor proteins that bind these CRMs may also evolve to produce novelty. Coding changes are considered to be rarer, however, because transcription factors are multifunctional and hence are more constrained to evolve in ways that will not produce widespread detrimental effects. Recent technological advances have unearthed a surprising variation in DNA-binding abilities, such that individual transcription factors may recognize both a preferred primary motif and an additional secondary motif. This provides a source of modularity in function. Here, we demonstrate that orthologous transcription factors can also evolve a changed preference for a secondary binding motif, thereby offering an unexplored mechanism for GRN evolution. Using protein-binding microarray, surface plasmon resonance, and in vivo reporter assays, we demonstrate an important difference in DNA-binding preference between Tbrain protein orthologs in two species of echinoderms, the sea star, Patiria miniata, and the sea urchin, Strongylocentrotus purpuratus. Although both orthologs recognize the same primary motif, only the sea star Tbr also has a secondary binding motif. Our in vivo assays demonstrate that this difference may allow for greater evolutionary change in timing of regulatory control. This uncovers a layer of transcription factor binding divergence that could exist for many pairs of orthologs. We hypothesize that this divergence provides modularity that allows orthologous transcription factors to evolve novel roles in GRNs through modification of binding to secondary sites. PMID:25016582

Cement Distribution and Diagenetic Pathway of the Miocene Sediments on Kardiva Platform, Maldives.

NASA Astrophysics Data System (ADS)

Laya, J. C.; Prince, K.; Betzler, C.; Eberli, G. P.; Blättler, C. L.; Swart, P. K.; Reolid, J.; Alvarez Zarikian, C. A.; Reijmer, J.

2017-12-01

The Maldives archipelago is an ideal example for understanding the dynamics of isolated carbonate platforms. While previous sedimentological studies have focused on oceanographic and climatic controls on deposition, there have been limited studies on the diagenetic evolution of the Maldives archipelago. This project seeks to establish a relationship between the facies, cement distribution, and diagenetic evolution of the Kardiva Platform and associated diagenetic fluids. Samples from cores of IODP Expedition 359 at Sites U1645, U1469, and U1470 were analyzed for stable isotope geochemistry and detailed petrography including SEM, confocal and CL microscopy to investigate variations in facies, cements, porosity and diagenetic products. The facies analyzed consist mainly of planktonic and benthic foraminifers, red coralline algae, echinoderm, coral and skeletal fragments. The main facies include foraminifera grain/packstone, red algae rich grain/packstone, algal floatstone and coral floatstone. Those facies present a cyclic and general shallowing upwards trend. These facies are interpreted as shallow platform deposits on proximal areas to the margin associated with the oligophotic zone. Cement volume varies between 5% and 48%, and they have been classified as isopachous, bladed to fibrous (dog tooth), drusy and equant. Equant and drusy show recognizable growth bands with CL and confocal. Evidence of intense dissolution is shown by extensive moldic porosity within phreatic and limited vadose zones. In addition, dolomite appears as a replacement phase associated with red-algae-rich horizons and as cement on pore walls and voids. These deposits experienced a variety of diagenetic processes driven by the evolution of diagenetic fluid chemistry and by the nature of the skeletal components. Those processes can be tied to external controls such as climate (monsoonal effects), sea-level and currents.

CALCIFICATION IN ECHINODERMS: EFFECTS OF TEMPERATURE AND DIAMOX ON INCORPORATION OF CALCIUM-45 IN VITRO BY REGENERATING SPINES OF STRONGYLOCENTROTUS PURPURATUS.

PubMed

Heatfield, Barry M

1970-08-01

1. Calcification during regeneration of experimentally fractured spines of the sea urchin, Strongylocentrotus purpuratus (Stimpson), was studied quantitatively under different conditions with calcium-45 as a tracer. 2. Fractured spines rapidly incorporated 45 Ca in vivo or in vitro after a lag period of about two days. The lag period is attributed to wound healing and reorganization of tissue at the site of fracture. 3. Additional experiments were conducted while calcification was in progress by allowing fractured spines to regenerate for four days in vivo followed by incubation in 45 Ca in vivo or in vitro up to 24 hours. In these experiments incorporation of the label was nearly linear with time and no significant difference was observed in the rate of uptake of 45 Ca between regenerating spines incubated in vivo and those from the same urchin incubated simultaneously in vitro. 4. Incorporation of 45 Ca in vitro was directly proportional to temperature between 4.7° and 20° C, at which a maximum occurred. A temperature of 26° C appeared to be lethal and little incorporation of 45 Ca took place. Values of Q 10 and the energy of activation varied inversely with temperature, with overall means of 2.72 and 15,504 calories per mole, respectively, between 4.7° and 20° C. 5. Diamox (acetazolamide) at concentrations from 10 -3 to 10 -6 M, inhibited incorporation of 45 Ca in vitro by 50% to 61%. It is inferred from these results that carbonic anhydrase is involved in calcification of regenerating spines of S. purpuratus.

Echinoderm phosphorylated matrix proteins UTMP16 and UTMP19 have different functions in sea urchin tooth mineralization.

PubMed

Alvares, Keith; Dixit, Saryu N; Lux, Elizabeth; Veis, Arthur

2009-09-18

Studies of mineralization of embryonic spicules and of the sea urchin genome have identified several putative mineralization-related proteins. These predicted proteins have not been isolated or confirmed in mature mineralized tissues. Mature Lytechinus variegatus teeth were demineralized with 0.6 N HCl after prior removal of non-mineralized constituents with 4.0 M guanidinium HCl. The HCl-extracted proteins were fractionated on ceramic hydroxyapatite and separated into bound and unbound pools. Gel electrophoresis compared the protein distributions. The differentially present bands were purified and digested with trypsin, and the tryptic peptides were separated by high pressure liquid chromatography. NH2-terminal sequences were determined by Edman degradation and compared with the genomic sequence bank data. Two of the putative mineralization-related proteins were found. Their complete amino acid sequences were cloned from our L. variegatus cDNA library. Apatite-binding UTMP16 was found to be present in two isoforms; both isoforms had a signal sequence, a Ser-Asp-rich extracellular matrix domain, and a transmembrane and cytosolic insertion sequence. UTMP19, although rich in Glu and Thr did not bind to apatite. It had neither signal peptide nor transmembrane domain but did have typical nuclear localization and nuclear exit signal sequences. Both proteins were phosphorylated and good substrates for phosphatase. Immunolocalization studies with anti-UTMP16 show it to concentrate at the syncytial membranes in contact with the mineral. On the basis of our TOF-SIMS analyses of magnesium ion and Asp mapping of the mineral phase composition, we speculate that UTMP16 may be important in establishing the high magnesium columns that fuse the calcite plates together to enhance the mechanical strength of the mineralized tooth.

On the formation and functions of high and very high magnesium calcites in the continuously growing teeth of the echinoderm Lytechinus variegatus: development of crystallinity and protein involvement.

PubMed

Veis, Arthur; Stock, Stuart R; Alvares, Keith; Lux, Elizabeth

2011-01-01

Sea urchin teeth grow continuously and develop a complex mineralized structure consisting of spatially separate but crystallographically aligned first stage calcitic elements of high Mg content (5-15 mol% mineral). These become cemented together by epitaxially oriented second stage very high Mg calcite (30-40 mol% mineral). In the tooth plumula, ingressing preodontoblasts create layered cellular syncytia. Mineral deposits develop within membrane-bound compartments between cellular syncytial layers. We seek to understand how this complex tooth architecture is developed, how individual crystalline calcitic elements become crystallographically aligned, and how their Mg composition is regulated. Synchrotron microbeam X-ray scattering was performed on live, freshly dissected teeth. We observed that the initial diffracting crystals lie within independent syncytial spaces in the plumula. These diffraction patterns match those of mature tooth calcite. Thus, the spatially separate crystallites grow with the same crystallographic orientation seen in the mature tooth. Mineral-related proteins from regions with differing Mg contents were isolated, sequenced, and characterized. A tooth cDNA library was constructed, and selected matrix-related proteins were cloned. Antibodies were prepared and used for immunolocaliztion. Matrix-related proteins are acidic, phosphorylated, and associated with the syncytial membranes. Time-of-flight secondary ion mass spectroscopy of various crystal elements shows unique amino acid, Mg, and Ca ion distributions. High and very high Mg calcites differ in Asp content. Matrix-related proteins are phosphorylated. Very high Mg calcite is associated with Asp-rich protein, and it is restricted to the second stage mineral. Thus, the composition at each part of the tooth is related to architecture and function. Copyright © 2011 S. Karger AG, Basel.

Characterization of calcium phosphate powders originating from Phyllacanthus imperialis and Trochidae Infundibulum concavus marine shells.

PubMed

Tămăşan, M; Ozyegin, L S; Oktar, F N; Simon, V

2013-07-01

The study reports the preparation and characterization of powders consisting of the different phases of calcium phosphates that were obtained from the naturally derived raw materials of sea-shell origins reacted with H3PO4. Species of sea origin, such as corals and nacres, attracted a special interest in bone tissue engineering area. Nacre shells are built up of calcium carbonate in aragonite form crystallized in an organic matrix. In this work two natural marine origin materials (shells of echinoderm Sputnik sea urchin - Phyllacanthus imperialis and Trochidae Infundibulum concavus mollusk) were involved in the developing powders of calcium phosphate based biomaterials (as raw materials for bone-scaffolds) by hotplate and ultrasound methods. Thermal analyses of the as-prepared materials were made for an assessment of the thermal behavior and heat treatment temperatures. Samples from both sea shells each of them prepared by the above mentioned methods were subjected to thermal treatments at 450 °C and 850 °C in order to evaluate the crystalline transformations of the calcium phosphate structures in the heating process. By X-ray diffraction analyses various calcium phosphate phases were identified. In Sputnik sea urchins originated samples were found predominantly brushite and calcite as a small secondary phase, while in Trochidae I. concavus samples mainly monetite and HA phases were identified. Thermal treatment at 850 °C resulted flat-plate whitlockite crystals - β-MgTCP [(Ca, Mg)3 (PO4)2] for both samples regardless the preparation method (ultrasound or hotplate) or the targeted Ca/P molar ratio according with XRD patterns. Scanning electron microscopy and Fourier transformed infrared spectroscopy were involved more in the characterization of these materials and the good correlations of the results of these methods were made. Copyright © 2013 Elsevier B.V. All rights reserved.

Community structure and trophic ecology of megabenthic fauna from the deep basins in the Interior Sea of Chiloé, Chile (41-43° S)

NASA Astrophysics Data System (ADS)

Zapata-Hernández, Germán; Sellanes, Javier; Thiel, Martin; Henríquez, Camila; Hernández, Sebastián; Fernández, Julio C. C.; Hajdu, Eduardo

2016-11-01

Estuarine environments are complex ecological systems, which depend on multiple inputs of organic sources that could support their benthic communities. The deep-water megabenthic communities of the Interior Sea of Chiloé (ISCh, northern part of the fjord region of Chile) were studied to characterize their taxonomic composition and to trace the energy pathways supporting them by using stable isotope analysis (SIA). Megabenthic and demersal organisms as well as sunken macroalgal debris and terrestrial organic matter (TOM: wood, leaves, branches) were obtained by bottom trawling along an estuarine gradient covering 100-460 m water depth. Additionally, particulate organic matter (POM) and the sedimentary organic matter (SOM) were sampled and carbon (δ13C) and nitrogen (δ15N) isotope ratios were determined for all these organisms and potential food sources. A total of 140 taxa were obtained, including invertebrates (e.g. polychaetes, mollusks, crustaceans and echinoderms) bony fishes, rays and sharks. Based on the stable isotope values it was possible to infer a strong dependence on primary production derived from phytoplankton which is exported to the benthos. A potentially important contribution from sunken macroalgae to megabenthic consumers was established only for some invertebrates, such as the irregular echinoid Tripylaster philippii and the decapod Eurypodius latreillii. The trophic structure metrics suggest a similar isotopic niche width, trophic diversity and species packaging in the food webs among the major basins in the ISCh. It is thus concluded that the benthic food webs are supported principally by surface primary production, but macroalgal subsidies could be exploited by selected invertebrate taxa (e.g. detritivores) and terrestrial carbon pathways are important for certain specialized taxa (e.g. Xylophaga dorsalis).

HIP1-ALK, a novel fusion protein identified in lung adenocarcinoma.

PubMed

Hong, Mineui; Kim, Ryong Nam; Song, Ji-Young; Choi, So-Jung; Oh, Ensel; Lira, Maruja E; Mao, Mao; Takeuchi, Kengo; Han, Joungho; Kim, Jhingook; Choi, Yoon-La

2014-03-01

The most common mechanism underlying overexpression and activation of anaplastic lymphoma kinase (ALK) in non-small-cell lung carcinoma could be attributed to the formation of a fusion protein. To date, five fusion partners of ALK have been reported, namely, echinoderm microtubule associated protein like 4, tropomyosin-related kinase-fused gene, kinesin family member 5B, kinesin light chain 1, and protein tyrosine phosphatase, nonreceptor type 3. In this article, we report a novel fusion gene huntingtin interacting protein 1 (HIP1)-ALK, which is conjoined between the huntingtin-interacting protein 1 gene HIP1 and ALK. Reverse-transcriptase polymerase chain reaction and immunohistochemical analysis were used to detect this fusion gene's transcript and protein expression, respectively. We had amplified the full-length cDNA sequence of this novel fusion gene by using 5'-rapid amplification of cDNA ends. The causative genomic translocation t(2;7)(p23;q11.23) for generating this novel fusion gene was verified by using genomic sequencing. The examined adenocarcinoma showed predominant acinar pattern, and ALK immunostaining was localized to the cytoplasm, with intense staining in the submembrane region. In break-apart, fluorescence in situ hybridization analysis for ALK, split of the 5' and 3' probe signals, and isolated 3' signals were observed. Reverse-transcriptase polymerase chain reaction revealed that the tumor harbored a novel fusion transcript in which exon 21 of HIP1 was fused to exon 20 of ALK in-frame. The novel fusion gene and its protein HIP1-ALK harboring epsin N-terminal homology, coiled-coil, juxtamembrane, and kinase domains, which could play a role in carcinogenesis, could become diagnostic and therapeutic target of the lung adenocarcinoma and deserve a further study in the future.

Morphometric and ultrastructural comparison of the olfactory system in elasmobranchs: the significance of structure-function relationships based on phylogeny and ecology.

PubMed

Schluessel, Vera; Bennett, Michael B; Bleckmann, Horst; Blomberg, Simon; Collin, Shaun P

2008-11-01

This study investigated the relationship between olfactory morphology, habitat occupancy, and lifestyle in 21 elasmobranch species in a phylogenetic context. Four measures of olfactory capability, that is, the number of olfactory lamellae, the surface area of the olfactory epithelium, the mass of the olfactory bulb, and the mass of the olfactory rosette were compared between individual species and groups, comprised of species with similar habitat and/or lifestyle. Statistical analyses using generalized least squares phylogenetic regression revealed that bentho-pelagic sharks and rays possess significantly more olfactory lamellae and larger sensory epithelial surface areas than benthic species. There was no significant correlation between either olfactory bulb or rosette mass and habitat type. There was also no significant difference between the number of lamellae or the size of the sensory surface area in groups comprised of species with similar diets, that is, groups preying predominantly on crustaceans, cephalopods, echinoderms, polychaetes, molluscs, or teleosts. However, some groups had significantly larger olfactory bulb or rosette masses than others. There was little evidence to support a correlation between phylogeny and morphology, indicating that differences in olfactory capabilities are the result of functional rather than phylogenetic adaptations. All olfactory epithelia exhibited microvilli and cilia, with microvilli in both nonsensory and sensory areas, and cilia only in sensory areas. Cilia over the sensory epithelia originated from supporting cells. In contrast to teleosts, which possess ciliated and microvillous olfactory receptor types, no ciliated olfactory receptor cells were observed. This is the first comprehensive study comparing olfactory morphology to several aspects of elasmobranch ecology in a phylogenetic context.

Durable brain response with pulse-dose crizotinib and ceritinib in ALK-positive non-small cell lung cancer compared with brain radiotherapy.

PubMed

Dudnik, Elizabeth; Siegal, Tali; Zach, Leor; Allen, Aaron M; Flex, Dov; Yust-Katz, Shlomit; Limon, Dror; Hirsch, Fred R; Peled, Nir

2016-04-01

Crizotinib achieves excellent systemic control in anaplastic lymphoma kinase-rearranged (ALK+) non-small cell lung cancer (NSCLC); however, central nervous system (CNS) metastases frequently occur as an early event. Whole brain irradiation, the standard treatment, results in neurocognitive impairment. We present a case series of three ALK+ NSCLC patients with progressing CNS metastases who were treated with pulse-dose crizotinib followed by ceritinib. Three ALK+ NSCLC patients treated between 2011 and 2014 (two males, two never smokers, age range 20-54years, all echinoderm microtubule-associated protein-like 4/ALK rearrangement), were diagnosed with progressing cerebral disease while receiving crizotinib. Clinico-pathological characteristics, treatments, and outcomes were analyzed. In two patients the progression was limited to the CNS, and radiological evidence of leptomeningeal spread was present in one patient. Sequential use of crizotinib 500mg administered once daily (pulse-dose) followed by ceritinib on progression achieved control of the disease in the CNS for over 18 months and over 7 months in Patient 1 and Patient 2, respectively. This strategy provided durable CNS control after whole-brain radiotherapy failure in Patient 1, and allowed the whole-brain radiotherapy to be deferred in Patient 2. Limited CNS progression was documented in Patient 3 while he was on standard-dose/pulse-dose crizotinib for 15months; durable (over 7 months) complete remission was achieved with stereotactic radiotherapy and ceritinib. Manipulating the crizotinib schedule in ALK+ NSCLC patients with CNS metastases and using a novel ALK-inhibitor at the time of further progression may provide durable CNS control and allow brain radiotherapy to be deferred. Copyright © 2015 Elsevier Ltd. All rights reserved.

Stiparin: a glycoprotein from sea cucumber dermis that aggregates collagen fibrils.

PubMed

Trotter, J A; Lyons-Levy, G; Luna, D; Koob, T J; Keene, D R; Atkinson, M A

1996-07-01

The interactions between collagen fibrils in many echinoderm connective tissues are rapidly altered by the secretions of resident neurosecretory cells. Recent evidence has suggested that a secreted protein is responsible for the interactions that lead to an increase in tissue stiffness (Trotter and Koob, 1995). Structurally intact collagen fibrils have been isolated from such a connective tissue- the dermis of the sea cucumber Cucumaria frondosa- and used in an assay in vitro to identify a protein that binds to them and causes them to aggregate. This protein has been purified by anion-exchange and molecular sieve chromatography. It is eluted from a MonoQ column at approximately 0.55 M NaCl. Its isoelectric point is 5.2. It elutes from a Superose-6 column in a position corresponding to a molecule with a Stokes radius of 11.5 nm. Its native molecular weight estimated from sedimentation equilibrium analysis under non-denaturing conditions is 375,000, and its monomer molecular weight, estimated by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate, is approximately 350,000. Sedimentation velocity measurements indicated for the native molecule a sedimentation coefficient of 11 x 10(-13)s, a diffusion coefficient of 3.274 x 10(-7) cm2s-1, and a frictional ratio of 1.95, which corresponds to a prolate ellipsoid of revolution with an axial ratio of 19. The highly asymmetric structure suggested by the above correlated well with the images obtained by transmission electron microscopy following rotary shadowing, which revealed a flexible structure approximately 125 nm long. Based on its ability to aggregate collagen fibrils, this protein has been named "stiparin," from the Latin stipare, "to pack together."

A geographical information system for the management of the aquaculture data in the Adriatic Sea - the Strengthening of Centres for Aquaculture Production and Safety surveillance in the Adriatic countries experience: Present capabilities, tools and functions.

PubMed

Tora, Susanna; Sacchini, Silvio; Listeš, Eddy; Bogdanović, Tanja; Di Lorenzo, Alessio; Smajlović, Muhamed; Smajlović, Ahmed; Filipović, Jelena V; Tahirović, Vildana; Šuković, Danijela; Beljkas, Bojan; Xinxo, Ardian; Maçi, Renis; Colangeli, Patrizia; Di Giacinto, Federica; Conte, Annamaria

2017-11-08

The European Commission (EC) regulation no. 854/2004 requires a systematic monitoring of chemical and microbiological contaminants in live bivalve molluscs, live echinoderms, live tunicates and live marine gastropods for human consumption through surveillance plans to be implemented in all European Union (EU) countries.A consortium of five Adriatic countries was set up in the framework of the Instrument of Pre-accession Assistance Adriatic Cross-border Cooperation Programme (IPA Adriatic CBC) 2007- 2013 with the aim of collecting data and distribute information on harvesting and production in mollusc areas. A web-based geographical information system (GIS) application was developed to support the partners to manage data and to make these data available to final users, policy makers and to risk assessors. The GIS for the Strengthening of Centres for Aquaculture Production and Safety surveillance in the Adriatic countries (CAPS2) is divided into two levels, the national and the supranational one, and it distributes spatial and epidemiological information coming from various data acquisition and management sites. The great innovation is the possibility for each country to use online drawing, modifying and change of the geographic areas according to national surveillance needs. Currently it hosts data coming from about 230 production and relay areas with more than 29,478 laboratory tests performed on collected samples since August 2014. Data collected are used by each national competent authority to classify production or relay areas according to the EC regulation mentioned and to conduct risk assessment studies to evaluate the level of consumers' exposure to contaminants in the consumption of bivalve mollusc products.

Anthropogenic disturbance and biodiversity of marine benthic communities in Antarctica: a regional comparison.

PubMed

Stark, Jonathan S; Kim, Stacy L; Oliver, John S

2014-01-01

The impacts of two Antarctic stations in different regions, on marine sediment macrofaunal communities were compared: McMurdo, a very large station in the Ross Sea; and Casey, a more typical small station in East Antarctica. Community structure and diversity were compared along a gradient of anthropogenic disturbance from heavily contaminated to uncontaminated locations. We examined some of the inherent problems in comparing data from unrelated studies, such as different sampling methods, spatial and temporal scales of sampling and taxonomic uncertainty. These issues generated specific biases which were taken into account when interpreting patterns. Control sites in the two regions had very different communities but both were dominated by crustaceans. Community responses to anthropogenic disturbance (sediment contamination by metals, oils and sewage) were also different. At McMurdo the proportion of crustaceans decreased in disturbed areas and polychaetes became dominant, whereas at Casey, crustaceans increased in response to disturbance, largely through an increase in amphipods. Despite differing overall community responses there were some common elements. Ostracods, cumaceans and echinoderms were sensitive to disturbance in both regions. Capitellid, dorvelleid and orbiniid polychaetes were indicative of disturbed sites. Amphipods, isopods and tanaids had different responses at each station. Biodiversity and taxonomic distinctness were significantly lower at disturbed locations in both regions. The size of the impact, however, was not related to the level of contamination, with a larger reduction in biodiversity at Casey, the smaller, less polluted station. The impacts of small stations, with low to moderate levels of contamination, can thus be as great as those of large or heavily contaminated stations. Regional broad scale environmental influences may be important in determining the composition of communities and thus their response to disturbance, but there are some generalizations regarding responses which will aid future management of stations.

(Tele)presenting Secrets from the Deep Southern California Margin

NASA Astrophysics Data System (ADS)

Levin, L. A.; Girguis, P. R.; Brennan, M.; German, C. R.; Raineault, N.; Le, J. T.; Grupe, B.; Gallo, N.; Inderbitzen, K. E.; Tuzun, S.; Wagner, J.

2016-02-01

This past summer scientists, students and the public participated through telepresence in 2 weeks of deep-sea exploration via the EV Nautilus, visiting a tremendous diversity of sites found along the southern California continental margin (200-900m). We observed previously unknown cold seeps; new and unexpected assemblages and species distributions; and novel animal behaviors; all under the overarching influence of strong oxygen gradients from the East Pacific oxygen minimum zone (OMZ). The expedition discovered four new methane seep sites, each with distinct biota reflecting varying depth and oxygen levels. OMZ specialists such as lucinid clams, hagfish, and thornyhead fishes coexisted with seep biota (vesicoymid clams) at a 1.4-km long seep off Point Dume (Malibu, CA), forming a blended ecosystem with distinct zonation. A range of habitats (canyons, knolls, mounds) within the OMZ hosted fish, crustacean, echinoderm and cnidarian species with unusual hypoxia tolerance to < 3 µM O2 or lower. Organic falls (a sunken whale and naturally occurring kelp holdfasts) hosted many invertebrates and served as clear magnets for scavengers and predators. In situ observations revealed unusual behaviors including "parasailing" snails and drifting benthic siphonophores in the Santa Monica Basin, fish aggregating at seep carbonates, and cruising catsharks and their egg cases at methane seeps. Many of these observations advance understanding of the ecosystem services provided by deep-sea, margin habitats, while stimulating public interest in ocean exploration. Telepresence permitted broad engagement of students and scientists from as near as Los Angeles and as far as South Africa, as well as meaningful interactions with the public. In situ exploration and observation can and will play increasingly important roles in environmental management of the deep ocean as disturbance from resource extraction and climate change intensify.

Megafaunal Community Structure of Andaman Seamounts Including the Back-Arc Basin – A Quantitative Exploration from the Indian Ocean

PubMed Central

Sautya, Sabyasachi; Ingole, Baban; Ray, Durbar; Stöhr, Sabine; Samudrala, Kiranmai; Raju, K. A. Kamesh; Mudholkar, Abhay

2011-01-01

Species rich benthic communities have been reported from some seamounts, predominantly from the Atlantic and Pacific Oceans, but the fauna and habitats on Indian Ocean seamounts are still poorly known. This study focuses on two seamounts, a submarine volcano (cratered seamount – CSM) and a non-volcano (SM2) in the Andaman Back–arc Basin (ABB), and the basin itself. The main purpose was to explore and generate regional biodiversity data from summit and flank (upper slope) of the Andaman seamounts for comparison with other seamounts worldwide. We also investigated how substratum types affect the megafaunal community structure along the ABB. Underwater video recordings from TeleVision guided Gripper (TVG) lowerings were used to describe the benthic community structure along the ABB and both seamounts. We found 13 varieties of substratum in the study area. The CSM has hard substratum, such as boulders and cobbles, whereas the SM2 was dominated by cobbles and fine sediment. The highest abundance of megabenthic communities was recorded on the flank of the CSM. Species richness and diversity were higher at the flank of the CSM than other are of ABB. Non-metric multi-dimensional scaling (nMDS) analysis of substratum types showed 50% similarity between the flanks of both seamounts, because both sites have a component of cobbles mixed with fine sediments in their substratum. Further, nMDS of faunal abundance revealed two groups, each restricted to one of the seamounts, suggesting faunal distinctness between them. The sessile fauna corals and poriferans showed a significant positive relation with cobbles and fine sediments substratum, while the mobile categories echinoderms and arthropods showed a significant positive relation with fine sediments only. PMID:21297959

An evaluation of intertidal feeding habitats from a shorebird perspective: Towards relevant comparisons between temperate and tropical mudflats

NASA Astrophysics Data System (ADS)

Piersma, Theunis; de Goeij, Petra; Tulp, Ingrid

Macrozoobenthic communities of intertidal soft sediments are reviewed worldwide from the perspective of a mollusc-eating shorebird species. Based on 19 sites, total biomass figures varied between 5 and 80 g AFDM per m 2 (average 24 g AFDM per m 2); no latitudinal trends are apparent. The contribution made by bivalves and gastropods varies between 1% and 99%, north-temperate intertidal flats having relatively more molluscs than tropical flats. Intertidal flats in the tropics contain a greater variety of taxa, with brachiopods in Indonesia and echinoderms in northwest Australia contributing significantly to biomass only there. Limits to the occurrence of avian predators of intertidal benthos are set by the harvestable fraction of the biomass on offer and the costs of living at a particular site. No systematic differences in the harvestable fraction of the total mollusc-biomass for a worldwide occurring shorebird species specializing on molluscs (knots Calidris canutus) were apparent between temperate and tropical intertidal areas, in spite of large differences in maintenance metabolism incurred by these birds. The harvestable fractions of bivalves in the two West African areas (Banc d'Arguin, Mauritania and Guinea-Bissau) tended to be high (23-84% of total biomass in six species), they were relatively low (2-52% in five species) in the temperate Wadden Sea and the tropical northwest Australian site. Harvestable biomass determines the intake rate of shorebirds, as illustrated by functional-response curves of knots feeding on two bivalves species. We argue that the collection of information on size-depth relationships along with faunal and biomass surveys at a range of sites is bound to greatly increase our understanding of both the biology of tidal-flat invertebrates and the resource base underpinning the spectacular seasonal migrations of shorebirds.

Rapid changes and long-term cycles in the benthic megafaunal community observed over 24 years in the abyssal northeast Pacific

NASA Astrophysics Data System (ADS)

Kuhnz, Linda A.; Ruhl, Henry A.; Huffard, Christine L.; Smith, Kenneth L.

2014-05-01

The abyssal seafloor community in the NE Pacific (Station M, ∼4000 m depth) was studied between 2006 and 2012 using remotely operated vehicles (ROVs) as part of a continuing 24-year time-series study. New patterns continue to emerge showing that the deep-sea can be dynamic on short time scales, rather than static over long periods. In just over 2 years the community shifted from a sessile, suspension-feeding, sponge-dominated community to a mobile, detritus-feeding, sea cucumber-dominated assemblage. In 2006 megafaunal diversity (Simpson’s Diversity Index, SDI) was high, yet the community was depauperate in terms of density compared to later periods. Over an 18-month period beginning in spring 2011, the densities of mobile organisms increased by nearly an order of magnitude while diversity decreased below 2006 levels. In late 2012 four sea cucumbers (two Peniagone spp., Elpidia sp. A, and Scotoplanes globosa) were at the highest densities recorded since investigations began at Station M in 1989. For a group of 10 echinoderms investigated over the entire study period, we saw evidence of a long-term cycle spanning 2 decades. These changes can be tied to a variable food supply originating in shallow water. Large variations over decadal-scales indicate that remote abyssal communities are dynamic and likely subject to impacts from anthropogenic changes like ocean warming, acidification, and pollution manifested in the upper ocean. The degree of dynamism indicates that one-time or short-term investigations are not sufficient for assessing biological community structure in conservation or exploitation studies in the deep sea.

Selective toxicity of persian gulf sea cucumber holothuria parva on human chronic lymphocytic leukemia b lymphocytes by direct mitochondrial targeting.

PubMed

Salimi, Ahmad; Motallebi, Abbasali; Ayatollahi, Maryam; Seydi, Enayatollah; Mohseni, Ali Reza; Nazemi, Melika; Pourahmad, Jalal

2017-04-01

Natural products isolated from marine environment are well known for their pharmacodynamic potential in diversity of disease treatments such as cancer or inflammatory conditions. Sea cucumbers are one of the marine animals of the phylum Echinoderm. Many studies have shown that the sea cucumber contains antioxidants and anti-cancer compounds. Chronic lymphocytic leukemia (CLL) is a disease characterized by the relentless accumulation of CD5 + B lymphocytes. CLL is the most common leukemia in adults, about 25-30% of all leukemias. In this study B lymphocytes and their mitochondria (cancerous and non-cancerous) were obtained from peripheral blood of human subjects and B lymphocyte cytotoxicity assay, and caspase 3 activation along with mitochondrial upstream events of apoptosis signaling including reactive oxygen species (ROS) production, collapse of mitochondrial membrane potential (MMP) and mitochondrial swelling were determined following the addition of Holothuria parva extract to both cancerous and non-cancerous B lymphocytes and their mitochondria. Our in vitro finding showed that mitochondrial ROS formation, MMP collapse, and mitochondrial swelling and cytochrome c release were significantly (P < 0.05) increased after addition of different concentrations of H. parva only in cancerous BUT NOT normal non-cancerous mitochondria. Consistently, different concentrations of H. parva significantly (P < 0.05) increased cytotoxicity and caspase 3 activation only in cancerous BUT NOT normal non-cancerous B lymphocytes. These results showed that H. parva methanolic extract has a selective mitochondria mediated apoptotic effect on chronic lymphocytic leukemia B lymphocytes hence may be promising in the future anticancer drug development for treatment of CLL. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 1158-1169, 2017. © 2016 Wiley Periodicals, Inc.

Aspects of reproductive ecology and benthic-pelagic coupling in the sub-antarctic sea cucumber Pseudostichopus mollis (Theel)

NASA Astrophysics Data System (ADS)

Morgan, Andrew; Neal, Lance

2012-07-01

For deeper regions of the continental shelf environmental cues entraining reproduction in echinoderms are often absent, which contributes to adoption of continuous reproduction, having larger eggs, and a lecithotrophic mode of larval development. In the present study the sub-Antarctic sea cucumber Pseudostichopus mollis from the family Synallactidae was obtained during June (winter) and September (spring) from a depth of approximately 300 m north of the Auckland Islands in an area abundant in biogenic sediments. Samples were processed for body indices and gonad development. Features characteristic of non-continuous reproduction were exhibited. Although a larger egg size was found (212±14 μm), two distinct winter cohorts of oocytes occurred (41-81 and 161-201 μm) and body wall weight fluctuations (7.6% increase in males and 27.5% reduction in females) coincided with changes in gonad indices between sample dates. For males gonad as a proportion of body wall weight decreased from 3.31±0.9 to 2.11±0.37% and for females it increased from 1.59±0.28 to 2.5±0.30%. For both sample dates the gonad of males maintained mature spermatozoa whereas female gonad shifted from mainly recovery and growth of oocytes to growth and advanced growth of mature oocytes. In habitats with low or variable food availability intermittent reproduction is predicted as resources are too low for a high reproductive effort and too erratic for synchrony. A pattern of reproduction where fluctuations in seasonal organic input into an accumulated benthic food source initiates and synchronises gametogenesis for future spawning is proposed.

Genetic and structural analyses of cytochrome P450 hydroxylases in sex hormone biosynthesis: Sequential origin and subsequent coevolution.

PubMed

Goldstone, Jared V; Sundaramoorthy, Munirathinam; Zhao, Bin; Waterman, Michael R; Stegeman, John J; Lamb, David C

2016-01-01

Biosynthesis of steroid hormones in vertebrates involves three cytochrome P450 hydroxylases, CYP11A1, CYP17A1 and CYP19A1, which catalyze sequential steps in steroidogenesis. These enzymes are conserved in the vertebrates, but their origin and existence in other chordate subphyla (Tunicata and Cephalochordata) have not been clearly established. In this study, selected protein sequences of CYP11A1, CYP17A1 and CYP19A1 were compiled and analyzed using multiple sequence alignment and phylogenetic analysis. Our analyses show that cephalochordates have sequences orthologous to vertebrate CYP11A1, CYP17A1 or CYP19A1, and that echinoderms and hemichordates possess CYP11-like but not CYP19 genes. While the cephalochordate sequences have low identity with the vertebrate sequences, reflecting evolutionary distance, the data show apparent origin of CYP11 prior to the evolution of CYP19 and possibly CYP17, thus indicating a sequential origin of these functionally related steroidogenic CYPs. Co-occurrence of the three CYPs in early chordates suggests that the three genes may have coevolved thereafter, and that functional conservation should be reflected in functionally important residues in the proteins. CYP19A1 has the largest number of conserved residues while CYP11A1 sequences are less conserved. Structural analyses of human CYP11A1, CYP17A1 and CYP19A1 show that critical substrate binding site residues are highly conserved in each enzyme family. The results emphasize that the steroidogenic pathways producing glucocorticoids and reproductive steroids are several hundred million years old and that the catalytic structural elements of the enzymes have been conserved over the same period of time. Analysis of these elements may help to identify when precursor functions linked to these enzymes first arose. Copyright © 2015 Elsevier Inc. All rights reserved.

Metal dealing at the origin of the Chordata phylum: the metallothionein system and metal overload response in amphioxus.

PubMed

Guirola, Maria; Pérez-Rafael, Sílvia; Capdevila, Mercè; Palacios, Oscar; Atrian, Sílvia

2012-01-01

Non-vertebrate chordates, specifically amphioxus, are considered of the utmost interest for gaining insight into the evolutionary trends, i.e. differentiation and specialization, of gene/protein systems. In this work, MTs (metallothioneins), the most important metal binding proteins, are characterized for the first time in the cephalochordate subphylum at both gene and protein level, together with the main features defining the amphioxus response to cadmium and copper overload. Two MT genes (BfMT1 and BfMT2) have been identified in a contiguous region of the genome, as well as several ARE (antioxidant response element) and MRE (metal response element) located upstream the transcribed region. Their corresponding cDNAs exhibit identical sequence in the two lancelet species (B. floridae and B. lanceolatum), BfMT2 cDNA resulting from an alternative splicing event. BfMT1 is a polyvalent metal binding peptide that coordinates any of the studied metal ions (Zn, Cd or Cu) rendering complexes stable enough to last in physiological environments, which is fully concordant with the constitutive expression of its gene, and therefore, with a metal homeostasis housekeeping role. On the contrary, BfMT2 exhibits a clear ability to coordinate Cd(II) ions, while it is absolutely unable to fold into stable Cu (I) complexes, even as mixed species. This identifies it as an essential detoxification agent, which is consequently only induced in emergency situations. The cephalochordate MTs are not directly related to vertebrate MTs, neither by gene structure, protein similarity nor metal-binding behavior of the encoded peptides. The closest relative is the echinoderm MT, which confirm proposed phylogenetic relationships between these two groups. The current findings support the existence in most organisms of two types of MTs as for their metal binding preferences, devoted to different biological functions: multivalent MTs for housekeeping roles, and specialized MTs that evolve either as Cd-thioneins or Cu-thioneins, according to the ecophysiological needs of each kind of organisms.

Metal Dealing at the Origin of the Chordata Phylum: The Metallothionein System and Metal Overload Response in Amphioxus

PubMed Central

Capdevila, Mercè; Palacios, Òscar; Atrian, Sílvia

2012-01-01

Non-vertebrate chordates, specifically amphioxus, are considered of the utmost interest for gaining insight into the evolutionary trends, i.e. differentiation and specialization, of gene/protein systems. In this work, MTs (metallothioneins), the most important metal binding proteins, are characterized for the first time in the cephalochordate subphylum at both gene and protein level, together with the main features defining the amphioxus response to cadmium and copper overload. Two MT genes (BfMT1 and BfMT2) have been identified in a contiguous region of the genome, as well as several ARE (antioxidant response element) and MRE (metal response element) located upstream the transcribed region. Their corresponding cDNAs exhibit identical sequence in the two lancelet species (B. floridae and B. lanceolatum), BfMT2 cDNA resulting from an alternative splicing event. BfMT1 is a polyvalent metal binding peptide that coordinates any of the studied metal ions (Zn, Cd or Cu) rendering complexes stable enough to last in physiological environments, which is fully concordant with the constitutive expression of its gene, and therefore, with a metal homeostasis housekeeping role. On the contrary, BfMT2 exhibits a clear ability to coordinate Cd(II) ions, while it is absolutely unable to fold into stable Cu (I) complexes, even as mixed species. This identifies it as an essential detoxification agent, which is consequently only induced in emergency situations. The cephalochordate MTs are not directly related to vertebrate MTs, neither by gene structure, protein similarity nor metal-binding behavior of the encoded peptides. The closest relative is the echinoderm MT, which confirm proposed phylogenetic relationships between these two groups. The current findings support the existence in most organisms of two types of MTs as for their metal binding preferences, devoted to different biological functions: multivalent MTs for housekeeping roles, and specialized MTs that evolve either as Cd-thioneins or Cu-thioneins, according to the ecophysiological needs of each kind of organisms. PMID:22905252

Template-assisted mineral formation via an amorphous liquid phase precursor route

NASA Astrophysics Data System (ADS)

Amos, Fairland F.

The search for alternative routes to synthesize inorganic materials has led to the biomimetic route of producing ceramics. In this method, materials are manufactured at ambient temperatures and in aqueous solutions with soluble additives and insoluble matrix, similar to the biological strategy for the formation of minerals by living organisms. Using this approach, an anionic polypeptide additive was used to induce an amorphous liquid-phase precursor to either calcium carbonate or calcium phosphate. This precursor was then templated on either organic or inorganic substrates. Non-equilibrium morphologies, such as two-dimensional calcium carbonate films, one-dimensional calcium carbonate mesostructures and "molten" calcium phosphate spherulites were produced, which are not typical of the traditional (additive-free) solution grown crystals in the laboratory. In the study of calcium carbonate, the amorphous calcium carbonate mineral formed via the liquid-phase precursor, either underwent a dissolution-recrystallization event or a pseudo-solid-state transformation to produce different morphologies and polymorphs of the mineral. Discrete or aggregate calcite crystals were formed via the dissolution of the amorphous phase to allow the reprecipitation of the stable crystal. Non-equilibrium morphologies, e.g., films, mesotubules and mesowires were templated using organic and inorganic substrates and compartments. These structures were generated via an amorphous solid to crystalline solid transformation. Single crystalline tablets and mesowires of aragonite, which are reported to be found only in nature as skeletal structures of marine organisms, such as mollusk nacre and echinoderm teeth, were successfully synthesized. These biomimetic structures were grown via the polymer-induced liquid-phase precursor route in the presence of magnesium. Only low magnesium-bearing calcite was formed in the absence of the polymer. A similar approach of using a polymeric additive was implemented in calcium phosphate. Spherulitic crystals and films, seemingly formed from a molten state, were produced. These structures served as nucleating surfaces for the radial formation of calcium oxalate minerals. The composite calcium phosphate-calcium oxalate assemblies are similar to the core-shell structures found in certain kidney stones.

Feeding ecology of two demersal opportunistic predators coexisting in the northwestern Mediterranean Sea

NASA Astrophysics Data System (ADS)

López, Nieves; Navarro, Joan; Barría, Claudio; Albo-Puigserver, Marta; Coll, Marta; Palomera, Isabel

2016-06-01

The study of the feeding ecology of marine organisms is crucial to understanding their ecological roles and advancing our knowledge of marine ecosystem functioning. The aim of this study was to analyse the trophic ecology of two demersal predator species, black anglerfish (Lophius budegassa) and white anglerfish (L. piscatorius), in the northwestern Mediterranean Sea. Both species are important in the study area due to their high abundance and economic value, but information about their feeding behaviour is scarce. Here, we described the diet composition and ecological role of these two species, investigating whether trophic segregation exists between them and amongst fish of different sizes. In addition, by using experimental survey data we described the spatial distribution of both species to help us interpret trophic behaviour patterns. We gathered samples of two different sizes (small individuals of a total length <30 cm and large individuals ≥30 cm) of both species and combined stomach content analyses (SCA) and stable isotope analyses (SIA) of nitrogen and carbon with isotopic mixing models. Our results revealed that both anglerfish species are opportunistic predators, showing a diet composed mainly of fishes and, to a lesser extent, of crustaceans, with a small proportion of cephalopods, gastropods, bivalves and echinoderms. We found trophic segregation between the two species and the two sizes, indicating that they feed on different prey, in line with differences in their spatial distribution within the study area. This partial partition of food resources could also be explained by the differences in rhythms of activity that were reported in previous studies. In addition, although both species occupied a high position within the food web, our results showed that white anglerfish individuals and the large-sized fish of both species held higher trophic positions. This study demonstrates the usefulness of complementary approaches for trophic studies and confirms that both anglerfish species play an important role as predators in the northwestern Mediterranean Sea food web.

Discovery, structural characterization and functional analysis of alpha-2-macroglobulin, a novel immune-related molecule from Holothuria atra.

PubMed

Qian, Jing; Ren, Chunhua; Xia, Jianjun; Chen, Ting; Yu, Zonghe; Hu, Chaoqun

2016-07-10

The non-specific protease inhibitor alpha-2-macroglobulin (A2M) is a key macromolecular glycoprotein that involved in host immune defense against pathogens in vertebrates and invertebrates. However, no research regarding A2M has been developed in echinoderms to date. In this study, the full-length cDNA of A2M was cloned from the sea cucumber (Holothuria atra), which is a tropical species widely distributed along the coasts of the South China Sea and designated HaA2M. HaA2M possesses all three conserved functional domains of known A2M proteins, including the bait region domain, thioester domain and receptor-binding domain. Compared to fish and shrimp A2Ms, the histidine residue from the catalytical regions is well conserved in HaA2M. HaA2M mRNA was predominantly expressed in coelomocytes and, to a lesser extent, in the body wall, intestine and respiratory tree. A2M activity was detected in the coelomic fluids of H. atra. The mRNA expression and activity levels were investigated in the major immune tissues and coelomic fluids of H. atra after challenge with inactivated Vibrio alginolyticus or polyriboinosinic polyribocytidylic acid [Poly (I: C)]. RNA interference (RNAi)-mediated knockdown of HaA2M resulted in a significant reduction of HaA2M gene transcript level (86%). RNAi-mediated silencing of HaA2M gene significantly decreased the A2M activity (38%) and increased the number of viable bacteria (2.8-fold) in the coelomic fluids of H. atra infected by V. alginolyticus. Our study, as a whole, supplied the evidences for HaA2M as an immune-relevant molecule and it might have multiple functions in the innate immune system of H. atra. Copyright © 2016 Elsevier B.V. All rights reserved.

Pedal peptide/orcokinin-type neuropeptide signaling in a deuterostome: The anatomy and pharmacology of starfish myorelaxant peptide in Asterias rubens.

PubMed

Lin, Ming; Egertová, Michaela; Zampronio, Cleidiane G; Jones, Alexandra M; Elphick, Maurice R

2017-12-15

Pedal peptide (PP) and orcokinin (OK) are related neuropeptides that were discovered in protostomian invertebrates (mollusks, arthropods). However, analysis of genome/transcriptome sequence data has revealed that PP/OK-type neuropeptides also occur in a deuterostomian phylum-the echinoderms. Furthermore, a PP/OK-type neuropeptide (starfish myorelaxant peptide, SMP) was recently identified as a muscle relaxant in the starfish Patiria pectinifera. Here mass spectrometry was used to identify five neuropeptides (ArPPLN1a-e) derived from the SMP precursor (PP-like neuropeptide precursor 1; ArPPLNP1) in the starfish Asterias rubens. Analysis of the expression of ArPPLNP1 and neuropeptides derived from this precursor in A. rubens using mRNA in situ hybridization and immunohistochemistry revealed a widespread pattern of expression, with labeled cells and/or processes present in the radial nerve cords, circumoral nerve ring, digestive system (e.g., cardiac stomach) and body wall-associated muscles (e.g., apical muscle) and appendages (e.g., tube feet and papulae). Furthermore, our data provide the first evidence that neuropeptides are present in the lateral motor nerves and in nerve processes innervating interossicular muscles. In vitro pharmacological tests with SMP (ArPPLN1b) revealed that it causes dose-dependent relaxation of apical muscle, tube foot and cardiac stomach preparations from A. rubens. Collectively, these anatomical and pharmacological data indicate that neuropeptides derived from ArPPLNP1 act as inhibitory neuromuscular transmitters in starfish, which contrasts with the myoexcitatory actions of PP/OK-type neuropeptides in protostomian invertebrates. Thus, the divergence of deuterostomes and protostomes may have been accompanied by an inhibitory-excitatory transition in the roles of PP/OK-type neuropeptides as regulators of muscle activity. © 2017 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

Molecular and functional identification of a novel photopigment in Pecten ciliary photoreceptors.

PubMed

Arenas, Oscar; Osorno, Tomás; Malagón, Gerardo; Pulido, Camila; Gomez, María Del Pilar; Nasi, Enrico

2018-01-26

The two basic animal photoreceptor types, ciliary and microvillar, use different light-transduction schemes: their photopigments couple to G t versus G q proteins, respectively, to either mobilize cyclic nucleotides or trigger a lipid signaling cascade. A third class of photoreceptors has been described in the dual retina of some marine invertebrates; these present a ciliary morphology but operate via radically divergent mechanisms, prompting the suggestion that they comprise a novel lineage of light sensors. In one of these organisms, an uncommon putative opsin was uncovered that was proposed to signal through G o Orthologues subsequently emerged in diverse phyla, including mollusks, echinoderms, and chordates, but the cells in which they express have not been identified, and no studies corroborated their function as visual pigments or their suggested signaling mode. Conversely, in only one invertebrate species, Pecten irradians , have the ciliary photoreceptors been physiologically characterized, but their photopigment has not been identified molecularly. We used the transcriptome of Pecten retina to guide the cloning by polymerase chain reaction (PCR) and rapid amplification of cDNA ends (RACE) extensions of a new member of this group of putative opsins. In situ hybridization shows selective transcription in the distal retina, and specific antibodies identify a single band of the expected molecular mass in Western blots and distinctly label ciliary photoreceptors in retina sections. RNA interference knockdown resulted in a reduction in the early receptor current-the first manifestation of light transduction-and prevented the prolonged aftercurrent, which requires a large buildup of activated rhodopsin. We also obtained a full-length clone of the α-subunit of a G o from Pecten retina complementary DNA and localized it by in situ hybridization to the distal photoreceptors. Small interfering RNA targeting this G o caused a specific depression of the photocurrent. These results establish this novel putative opsin as a bona fide visual pigment that couples to G o to convey the light signal. © 2018 Arenas et al.

Giant Clams and Rising CO2: Light May Ameliorate Effects of Ocean Acidification on a Solar-Powered Animal

PubMed Central

Watson, Sue-Ann

2015-01-01

Global climate change and ocean acidification pose a serious threat to marine life. Marine invertebrates are particularly susceptible to ocean acidification, especially highly calcareous taxa such as molluscs, echinoderms and corals. The largest of all bivalve molluscs, giant clams, are already threatened by a variety of local pressures, including overharvesting, and are in decline worldwide. Several giant clam species are listed as ‘Vulnerable’ on the IUCN Red List of Threatened Species and now climate change and ocean acidification pose an additional threat to their conservation. Unlike most other molluscs, giant clams are ‘solar-powered’ animals containing photosynthetic algal symbionts suggesting that light could influence the effects of ocean acidification on these vulnerable animals. In this study, juvenile fluted giant clams Tridacna squamosa were exposed to three levels of carbon dioxide (CO2) (control ~400, mid ~650 and high ~950 μatm) and light (photosynthetically active radiation 35, 65 and 304 μmol photons m-2 s-1). Elevated CO2 projected for the end of this century (~650 and ~950 μatm) reduced giant clam survival and growth at mid-light levels. However, effects of CO2 on survival were absent at high-light, with 100% survival across all CO2 levels. Effects of CO2 on growth of surviving clams were lessened, but not removed, at high-light levels. Shell growth and total animal mass gain were still reduced at high-CO2. This study demonstrates the potential for light to alleviate effects of ocean acidification on survival and growth in a threatened calcareous marine invertebrate. Managing water quality (e.g. turbidity and sedimentation) in coastal areas to maintain water clarity may help ameliorate some negative effects of ocean acidification on giant clams and potentially other solar-powered calcifiers, such as hard corals. PMID:26083404

Nitric oxide acts as a positive regulator to induce metamorphosis of the ascidian Herdmania momus.

PubMed

Ueda, Nobuo; Degnan, Sandie M

2013-01-01

Marine invertebrates commonly have a biphasic life cycle in which the metamorphic transition from a pelagic larva to a benthic post-larva is mediated by the nitric oxide signalling pathway. Nitric oxide (NO) is synthesised by nitric oxide synthase (NOS), which is a client protein of the molecular chaperon heat shock protein 90 (HSP90). It is notable, then, that both NO and HSP90 have been implicated in regulating metamorphosis in marine invertebrates as diverse as urochordates, echinoderms, molluscs, annelids, and crustaceans. Specifically, the suppression of NOS activity by the application of either NOS- or HSP90-inhibiting pharmacological agents has been shown consistently to induce the initiation of metamorphosis, leading to the hypothesis that a negative regulatory role of NO is widely conserved in biphasic life cycles. Further, the induction of metamorphosis by heat-shock has been demonstrated for multiple species. Here, we investigate the regulatory role of NO in induction of metamorphosis of the solitary tropical ascidian, Herdmania momus. By coupling pharmacological treatments with analysis of HmNOS and HmHSP90 gene expression, we present compelling evidence of a positive regulatory role for NO in metamorphosis of this species, in contrast to all existing ascidian data that supports the hypothesis of NO as a conserved negative regulator of metamorphosis. The exposure of competent H. momus larvae to a NOS inhibitor or an NO donor results in an up-regulation of NOS and HSP90 genes. Heat shock of competent larvae induces metamorphosis in a temperature dependent manner, up to a thermal tolerance that approaches 35°C. Both larval/post-larval survival and the appearance of abnormal morphologies in H. momus post-larvae reflect the magnitude of up-regulation of the HSP90 gene in response to heat-shock. The demonstrated role of NO as a positive metamorphic regulator in H. momus suggests the existence of inter-specific adaptations of NO regulation in ascidian metamorphosis.

Structural and functional changes of soft-bottom ecosystems in northern fjords invaded by the red king crab (Paralithodes camtschaticus)

NASA Astrophysics Data System (ADS)

Oug, Eivind; Sundet, Jan H.; Cochrane, Sabine K. J.

2018-04-01

The red king crab invaded Norwegian coastal waters in the early 1990s after having been introduced from the northern Pacific to the Russian Barents Sea coast. The crab stock increased rapidly in NE northern Norway in the latter half of the 1990s, and since 2002 there has been a commercial fishery in the eastern invaded areas. The crab is an active predator on benthic fauna especially feeding in deep soft-bottom environments. The present study is a follow-up of previous studies (2007-09) to assess the effects of the king crab predation on soft bottom species composition, ecological functioning and sediment quality. Macroinfauna (> 1 mm) was investigated in three fjord areas in the Varanger region with low, moderate and very high crab abundances, respectively. Compared with data from 1994, most benthic species were markedly reduced in abundance, in particular non-moving burrowing and tube-dwelling polychaetes, bivalves and echinoderms. However, a few species appeared to recover from 2007-09 to 2012. Changes in ecological functioning were assessed using 'biological traits analysis (BTA)'. Following the crab invasion there was a relative reduction of suspension and surface deposit feeding species, an increase in mobile and predatory organisms and an increase in those with planktotrophic larval development. From low to high crab abundances functioning changed from tube-building, deep deposit feeding and fairly large size to free-living, shallow burrowing and rather small size. With regard to sediment reworking, downward and upward conveyors were reduced whereas surficial modifiers increased. The changes imply that sediment biomixing and bioirrigation were reduced leading to a degraded sedimentary environment. It is suggested that establishing relationships between ecosystem functioning and crab abundances may form the basis for estimating ecological costs of the crab invasion. Such knowledge is important for managing the crab in the Barents Sea area being both a non-indigenous species affecting native ecosystems as well as a valuable resource for commercial fishery.

Assessing the Extent of Sediment Contamination Around Creosote-treated Pilings Through Chemical and Biological Analyses

NASA Astrophysics Data System (ADS)

Stefansson, E. S.

2008-12-01

Creosote is a common wood preservative used to treat marine structures, such as docks and bulkheads. Treated dock pilings continually leach polycyclic aromatic hydrocarbons (PAHs) and other creosote compounds into the surrounding water and sediment. Over time, these compounds can accumulate in marine sediments, reaching much greater concentrations than those in seawater. The purpose of this study was to assess the extent of creosote contamination in sediments, at a series of distances from treated pilings. Three pilings were randomly selected from a railroad trestle in Fidalgo Bay, WA and sediment samples were collected at four distances from each: 0 meters, 0.5 meters, 1 meter, and 2 meters. Samples were used to conduct two bioassays: an amphipod bioassay (Rhepoxynius abronius) and a sand dollar embryo bioassay. Grain size and PAH content (using a fluorometric method) were also measured. Five samples in the amphipod bioassay showed significantly lower effective survival than the reference sediment. These consisted of samples closest to the piling at 0 and 0.5 meters. One 0 m sample in the sand dollar embryo bioassay also showed a significantly lower percentage of normal embryos than the reference sediment. Overall, results strongly suggest that creosote-contaminated sediments, particularly those closest to treated pilings, can negatively affect both amphipods and echinoderm embryos. Although chemical data were somewhat ambiguous, 0 m samples had the highest levels of PAHs, which corresponded to the lowest average survival in both bioassays. Relatively high levels of PAHs were found as far as 2 meters away from pilings. Therefore, we cannot say how far chemical contamination can spread from creosote-treated pilings, and at what distance this contamination can still affect marine organisms. These results, as well as future research, are essential to the success of proposed piling removal projects. In addition to creosote-treated pilings, contaminated sediments must be removed and disposed of properly, in order to make future piling removals as effective and beneficial to ecosystem health as possible.

Thyroid hormones determine developmental mode in sand dollars (Echinodermata: Echinoidea).

PubMed

Heyland, Andreas; Reitzel, Adam M; Hodin, Jason

2004-01-01

Evolutionary transitions in larval nutritional mode have occurred on numerous occasions independently in many marine invertebrate phyla. Although the evolutionary transition from feeding to nonfeeding development has received considerable attention through both experimental and theoretical studies, mechanisms underlying the change in life history remain poorly understood. Facultative feeding larvae (larvae that can feed but will complete metamorphosis without food) presumably represent an intermediate developmental mode between obligate feeding and nonfeeding. Here we show that an obligatorily feeding larva can be transformed into a facultative feeding larva when exposed to the thyroid hormone thyroxine. We report that larvae of the subtropical sand dollar Leodia sexiesperforata (Echinodermata: Echinoidea) completed metamorphosis without exogenous food when treated with thyroxine, whereas the starved controls (no thyroxine added) did not. Leodia sexiesperforata juveniles from the thyroxine treatment were viable after metamorphosis but were significantly smaller and contained less energy than sibling juveniles reared with exogenous food. In a second starvation experiment, using an L. sexiesperforata female whose eggs were substantially larger than in the first experiment (202+/-5 vs. 187+/-5 microm), a small percentage of starved L. sexiesperforata larvae completed metamorphosis in the absence of food. Still, thyroxine-treated larvae in this experiment completed metamorphosis faster and in much higher numbers than in the starved controls. Furthermore, starved larvae of the sand dollar Mellita tenuis, which developed from much smaller eggs (100+/-2 microm), did not complete metamorphosis either with or without excess thyroxine. Based on these data, and from recent experiments with other echinoids, we hypothesize that thyroxine plays a major role in echinoderm metamorphosis and the evolution of life history transitions in this group. We discuss our results in the context of current life history models for marine invertebrates, emphasizing the role of egg size, juvenile size, and endogenous hormone production for the evolution of nonfeeding larval development.

HIP1-ALK, a novel ALK fusion variant that responds to crizotinib.

PubMed

Fang, Douglas D; Zhang, Bin; Gu, Qingyang; Lira, Maruja; Xu, Qiang; Sun, Hongye; Qian, Maoxiang; Sheng, Weiqi; Ozeck, Mark; Wang, Zhenxiong; Zhang, Cathy; Chen, Xinsheng; Chen, Kevin X; Li, Jian; Chen, Shu-Hui; Christensen, James; Mao, Mao; Chan, Chi-Chung

2014-03-01

The aim of this study was to identify anaplastic lymphoma kinase (ALK) rearrangements in lung cancer patient-derived xenograft (PDX) models and to explore their responses to crizotinib. Screening of 99 lung cancer PDX models by the NanoString ALK fusion assay identified two ALK-rearranged non-small-cell lung cancer (NSCLC) tumors, including one harboring a previously known echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusion and another containing an unknown ALK fusion variant. Expression array, RNA-Seq, reverse transcription polymerase chain reaction, and direct sequencing were then conducted to confirm the rearrangements and to identify the novel fusion partner in the xenograft and/or the primary patient tumor. Finally, pharmacological studies were performed in PDX models to evaluate their responses to ALK inhibitor crizotinib. Two ALK-rearranged NSCLC PDX models were identified: one carried a well-known EML4-ALK variant 3a/b and the other harbored a novel huntingtin interacting protein 1 (HIP1)-ALK fusion gene. Exon 28 of the HIP1 gene located on chromosome 7 was fused to exon 20 of the ALK gene located on chromosome 2. Both cases were clinically diagnosed as squamous cell carcinoma. Compared with the other lung cancer PDX models, both ALK-rearranged models displayed elevated ALK mRNA expression. Furthermore, in vivo efficacy studies demonstrated that, similar to the EML4-ALK-positive model, the HIP1-ALK-containing PDX model was sensitive to treatment with crizotinib. Discovery of HIP1 as a fusion partner of ALK in NSCLC is a novel finding. In addition, the HIP1-ALK-rearranged tumor is sensitive to treatment with crizotinib in vivo, implicating HIP1-ALKas an oncogenic driver of lung tumorigenesis. Collectively, our results indicate that HIP1-ALK-positive NSCLC may benefit from clinical applications of crizotinib.

Spotlight on ceritinib in the treatment of ALK+ NSCLC: design, development and place in therapy

PubMed Central

Santarpia, Mariacarmela; Daffinà, Maria Grazia; D’Aveni, Alessandro; Marabello, Grazia; Liguori, Alessia; Giovannetti, Elisa; Karachaliou, Niki; Gonzalez Cao, Maria; Rosell, Rafael; Altavilla, Giuseppe

2017-01-01

The identification of echinoderm microtubule-associated protein-like 4 (EML4) and anaplastic lymphoma kinase (ALK) fusion gene in non-small cell lung cancer (NSCLC) has radically changed the treatment of a subset of patients harboring this oncogenic driver. Crizotinib was the first ALK tyrosine kinase inhibitor to receive fast approval and is currently indicated as the first-line therapy for advanced, ALK-positive NSCLC patients. However, despite crizotinib’s efficacy, patients almost invariably progress, with the central nervous system being one of the most common sites of relapse. Different mechanisms of acquired resistance have been identified, including secondary ALK mutations, ALK copy number alterations and activation of bypass tracks. Different highly potent and brain-penetrant next-generation ALK inhibitors have been developed and tested in NSCLC patients with ALK rearrangements. Ceritinib, a structurally distinct and selective ALK inhibitor, showed 20 times higher potency than crizotinib in inhibiting ALK and had activity against the most common crizotinib-resistant mutations, including L1196M and G1269A, in preclinical models. In Phase I and II studies, ceritinib demonstrated pronounced activity in both crizotinib-naïve and crizotinib-refractory patients, with responses observed regardless of the presence of ALK resistance mutations. Ceritinib was the first ALK inhibitor to be approved for the treatment of crizotinib-refractory, ALK-rearranged NSCLC, and recent results from a Phase III study have demonstrated superior efficacy compared to standard chemotherapy in the first- and second-line setting. We provide an extensive overview of ceritinib from the design of the compound through preclinical data until efficacy and toxicity results from Phase I–III clinical studies. We review the molecular alterations associated with resistance to ceritinib and highlight the importance of obtaining tumor biopsy at progression to tailor therapy based upon the underlying resistance mechanism. We finally provide an outlook on novel rational therapeutic combinations. PMID:28740365

Ancestry and evolution of a secretory pathway serpin

PubMed Central

2008-01-01

Background The serpin (serine protease inhibitor) superfamily constitutes a class of functionally highly diverse proteins usually encompassing several dozens of paralogs in mammals. Though phylogenetic classification of vertebrate serpins into six groups based on gene organisation is well established, the evolutionary roots beyond the fish/tetrapod split are unresolved. The aim of this study was to elucidate the phylogenetic relationships of serpins involved in surveying the secretory pathway routes against uncontrolled proteolytic activity. Results Here, rare genomic characters are used to show that orthologs of neuroserpin, a prominent representative of vertebrate group 3 serpin genes, exist in early diverging deuterostomes and probably also in cnidarians, indicating that the origin of a mammalian serpin can be traced back far in the history of eumetazoans. A C-terminal address code assigning association with secretory pathway organelles is present in all neuroserpin orthologs, suggesting that supervision of cellular export/import routes by antiproteolytic serpins is an ancient trait, though subtle functional and compartmental specialisations have developed during their evolution. The results also suggest that massive changes in the exon-intron organisation of serpin genes have occurred along the lineage leading to vertebrate neuroserpin, in contrast with the immediately adjacent PDCD10 gene that is linked to its neighbour at least since divergence of echinoderms. The intron distribution pattern of closely adjacent and co-regulated genes thus may experience quite different fates during evolution of metazoans. Conclusion This study demonstrates that the analysis of microsynteny and other rare characters can provide insight into the intricate family history of metazoan serpins. Serpins with the capacity to defend the main cellular export/import routes against uncontrolled endogenous and/or foreign proteolytic activity represent an ancient trait in eukaryotes that has been maintained continuously in metazoans though subtle changes affecting function and subcellular location have evolved. It is shown that the intron distribution pattern of neuroserpin gene orthologs has undergone substantial rearrangements during metazoan evolution. PMID:18793432

Ancestry and evolution of a secretory pathway serpin.

PubMed

Kumar, Abhishek; Ragg, Hermann

2008-09-15

The serpin (serine protease inhibitor) superfamily constitutes a class of functionally highly diverse proteins usually encompassing several dozens of paralogs in mammals. Though phylogenetic classification of vertebrate serpins into six groups based on gene organisation is well established, the evolutionary roots beyond the fish/tetrapod split are unresolved. The aim of this study was to elucidate the phylogenetic relationships of serpins involved in surveying the secretory pathway routes against uncontrolled proteolytic activity. Here, rare genomic characters are used to show that orthologs of neuroserpin, a prominent representative of vertebrate group 3 serpin genes, exist in early diverging deuterostomes and probably also in cnidarians, indicating that the origin of a mammalian serpin can be traced back far in the history of eumetazoans. A C-terminal address code assigning association with secretory pathway organelles is present in all neuroserpin orthologs, suggesting that supervision of cellular export/import routes by antiproteolytic serpins is an ancient trait, though subtle functional and compartmental specialisations have developed during their evolution. The results also suggest that massive changes in the exon-intron organisation of serpin genes have occurred along the lineage leading to vertebrate neuroserpin, in contrast with the immediately adjacent PDCD10 gene that is linked to its neighbour at least since divergence of echinoderms. The intron distribution pattern of closely adjacent and co-regulated genes thus may experience quite different fates during evolution of metazoans. This study demonstrates that the analysis of microsynteny and other rare characters can provide insight into the intricate family history of metazoan serpins. Serpins with the capacity to defend the main cellular export/import routes against uncontrolled endogenous and/or foreign proteolytic activity represent an ancient trait in eukaryotes that has been maintained continuously in metazoans though subtle changes affecting function and subcellular location have evolved. It is shown that the intron distribution pattern of neuroserpin gene orthologs has undergone substantial rearrangements during metazoan evolution.

Antarctic Marine Biodiversity – What Do We Know About the Distribution of Life in the Southern Ocean?

PubMed Central

Griffiths, Huw J.

2010-01-01

The remote and hostile Southern Ocean is home to a diverse and rich community of life that thrives in an environment dominated by glaciations and strong currents. Marine biological studies in the region date back to the nineteenth century, but despite this long history of research, relatively little is known about the complex interactions between the highly seasonal physical environment and the species that inhabit the Southern Ocean. Oceanographically, the Southern Ocean is a major driver of global ocean circulation and plays a vital role in interacting with the deep water circulation in each of the Pacific, Atlantic, and Indian oceans. The Census of Antarctic Marine Life and the Scientific Committee on Antarctic Research Marine Biodiversity Information Network (SCAR-MarBIN) have strived to coordinate and unify the available scientific expertise and biodiversity data to improve our understanding of Southern Ocean biodiversity. Taxonomic lists for all marine species have been compiled to form the Register of Antarctic Marine Species, which currently includes over 8,200 species. SCAR-MarBIN has brought together over 1 million distribution records for Southern Ocean species, forming a baseline against which future change can be judged. The sample locations and numbers of known species from different regions were mapped and the depth distributions of benthic samples plotted. Our knowledge of the biodiversity of the Southern Ocean is largely determined by the relative inaccessibility of the region. Benthic sampling is largely restricted to the shelf; little is known about the fauna of the deep sea. The location of scientific bases heavily influences the distribution pattern of sample and observation data, and the logistical supply routes are the focus of much of the at-sea and pelagic work. Taxa such as mollusks and echinoderms are well represented within existing datasets with high numbers of georeferenced records. Other taxa, including the species-rich nematodes, are represented by just a handful of digital records. PMID:20689841

Microtubule association of EML proteins and the EML4-ALK variant 3 oncoprotein require an N-terminal trimerization domain.

PubMed

Richards, Mark W; O'Regan, Laura; Roth, Daniel; Montgomery, Jessica M; Straube, Anne; Fry, Andrew M; Bayliss, Richard

2015-05-01

Proteins of the echinoderm microtubule (MT)-associated protein (EMAP)-like (EML) family contribute to formation of the mitotic spindle and interphase MT network. EML1-4 consist of Trp-Asp 40 (WD40) repeats and an N-terminal region containing a putative coiled-coil. Recurrent gene rearrangements in non-small cell lung cancer (NSCLC) fuse EML4 to anaplastic lymphoma kinase (ALK) causing expression of several oncogenic fusion variants. The fusions have constitutive ALK activity due to self-association through the EML4 coiled-coil. We have determined crystal structures of the coiled-coils from EML2 and EML4, which describe the structural basis of both EML self-association and oncogenic EML4-ALK activation. The structures reveal a trimeric oligomerization state directed by a conserved pattern of hydrophobic residues and salt bridges. We show that the trimerization domain (TD) of EML1 is necessary and sufficient for self-association. The TD is also essential for MT binding; however, this property requires an adjacent basic region. These observations prompted us to investigate MT association of EML4-ALK and EML1-ABL1 (Abelson 1) fusions in which variable portions of the EML component are present. Uniquely, EML4-ALK variant 3, which includes the TD and basic region of EML4 but none of the WD40 repeats, was localized to MTs, both when expressed recombinantly and when expressed in a patient-derived NSCLC cell line (H2228). This raises the question of whether the mislocalization of ALK activity to MTs might influence downstream signalling and malignant properties of cells. Furthermore, the structure of EML4 TD may enable the development of protein-protein interaction inhibitors targeting the trimerization interface, providing a possible avenue towards therapeutic intervention in EML4-ALK NSCLC.

Variation in the macrofaunal community over large temporal and spatial scales in the southern Yellow Sea

NASA Astrophysics Data System (ADS)

Xu, Yong; Sui, Jixing; Yang, Mei; Sun, Yue; Li, Xinzheng; Wang, Hongfa; Zhang, Baolin

2017-09-01

To detect large, temporal- and spatial-scale variations in the macrofaunal community in the southern Yellow Sea, data collected along the western, middle and eastern regions of the southern Yellow Sea from 1958 to 2014 were organized and analyzed. Statistical methods such as cluster analysis, non-metric multidimensional scaling ordination (nMDS), permutational multivariate analysis of variance (PERMANOVA), redundancy analysis (RDA) and canonical correspondence analysis (CCA) were applied. The abundance of polychaetes increased in the western region but decreased in the eastern region from 1958 to 2014, whereas the abundance of echinoderms showed an opposite trend. For the entire macrofaunal community, Margalef's richness (d), the Shannon-Wiener index (H‧) and Pielou's evenness (J‧) were significantly lower in the eastern region when compared with the other two regions. No significant temporal differences were found for d and H‧, but there were significantly lower values of J‧ in 2014. Considerable variation in the macrofaunal community structure over the past several decades and among the geographical regions at the species, genus and family levels were observed. The species, genera and families that contributed to the temporal variation in each region were also identified. The most conspicuous pattern was the increase in the species Ophiura sarsii vadicola in the eastern region. In the western region, five polychaetes (Ninoe palmata, Notomastus latericeus, Paralacydonia paradoxa, Paraprionospio pinnata and Sternaspis scutata) increased consistently from 1958 to 2014. The dominance curves showed that both the species diversity and the dominance patterns were relatively stable in the western and middle regions. Environmental parameters such as depth, temperature and salinity could only partially explain the observed biological variation in the southern Yellow Sea. Anthropogenic activities such as demersal fishing and other unmeasured environmental variables may be more responsible for the long-term changes in the macrofaunal community.

Could the acid-base status of Antarctic sea urchins indicate a better-than-expected resilience to near-future ocean acidification?

PubMed

Collard, Marie; De Ridder, Chantal; David, Bruno; Dehairs, Frank; Dubois, Philippe

2015-02-01

Increasing atmospheric carbon dioxide concentration alters the chemistry of the oceans towards more acidic conditions. Polar oceans are particularly affected due to their low temperature, low carbonate content and mixing patterns, for instance upwellings. Calcifying organisms are expected to be highly impacted by the decrease in the oceans' pH and carbonate ions concentration. In particular, sea urchins, members of the phylum Echinodermata, are hypothesized to be at risk due to their high-magnesium calcite skeleton. However, tolerance to ocean acidification in metazoans is first linked to acid-base regulation capacities of the extracellular fluids. No information on this is available to date for Antarctic echinoderms and inference from temperate and tropical studies needs support. In this study, we investigated the acid-base status of 9 species of sea urchins (3 cidaroids, 2 regular euechinoids and 4 irregular echinoids). It appears that Antarctic regular euechinoids seem equipped with similar acid-base regulation systems as tropical and temperate regular euechinoids but could rely on more passive ion transfer systems, minimizing energy requirements. Cidaroids have an acid-base status similar to that of tropical cidaroids. Therefore Antarctic cidaroids will most probably not be affected by decreasing seawater pH, the pH drop linked to ocean acidification being negligible in comparison of the naturally low pH of the coelomic fluid. Irregular echinoids might not suffer from reduced seawater pH if acidosis of the coelomic fluid pH does not occur but more data on their acid-base regulation are needed. Combining these results with the resilience of Antarctic sea urchin larvae strongly suggests that these organisms might not be the expected victims of ocean acidification. However, data on the impact of other global stressors such as temperature and of the combination of the different stressors needs to be acquired to assess the sensitivity of these organisms to global change. © 2014 John Wiley & Sons Ltd.

Sea Hare Aplysia punctata (Mollusca: Gastropoda) Can Maintain Shell Calcification under Extreme Ocean Acidification.

PubMed

Carey, Nicholas; Dupont, Sam; Sigwart, Julia D

2016-10-01

Ocean acidification is expected to cause energetic constraints upon marine calcifying organisms such as molluscs and echinoderms, because of the increased costs of building or maintaining shell material in lower pH. We examined metabolic rate, shell morphometry, and calcification in the sea hare Aplysia punctata under short-term exposure (19 days) to an extreme ocean acidification scenario (pH 7.3, ∼2800 μatm pCO 2 ), along with a group held in control conditions (pH 8.1, ∼344 μatm pCO 2 ). This gastropod and its congeners are broadly distributed and locally abundant grazers, and have an internal shell that protects the internal organs. Specimens were examined for metabolic rate via closed-chamber respirometry, followed by removal and examination of the shell under confocal microscopy. Staining using calcein determined the amount of new calcification that occurred over 6 days at the end of the acclimation period. The width of new, pre-calcified shell on the distal shell margin was also quantified as a proxy for overall shell growth. Aplysia punctata showed a 30% reduction in metabolic rate under low pH, but calcification was not affected. This species is apparently able to maintain calcification rate even under extreme low pH, and even when under the energetic constraints of lower metabolism. This finding adds to the evidence that calcification is a largely autonomous process of crystallization that occurs as long as suitable haeomocoel conditions are preserved. There was, however, evidence that the accretion of new, noncalcified shell material may have been reduced, which would lead to overall reduced shell growth under longer-term exposures to low pH independent of calcification. Our findings highlight that the chief impact of ocean acidification upon the ability of marine invertebrates to maintain their shell under low pH may be energetic constraints that hinder growth of supporting structure, rather than maintenance of calcification.

Giant Clams and Rising CO2: Light May Ameliorate Effects of Ocean Acidification on a Solar-Powered Animal.

PubMed

Watson, Sue-Ann

2015-01-01

Global climate change and ocean acidification pose a serious threat to marine life. Marine invertebrates are particularly susceptible to ocean acidification, especially highly calcareous taxa such as molluscs, echinoderms and corals. The largest of all bivalve molluscs, giant clams, are already threatened by a variety of local pressures, including overharvesting, and are in decline worldwide. Several giant clam species are listed as 'Vulnerable' on the IUCN Red List of Threatened Species and now climate change and ocean acidification pose an additional threat to their conservation. Unlike most other molluscs, giant clams are 'solar-powered' animals containing photosynthetic algal symbionts suggesting that light could influence the effects of ocean acidification on these vulnerable animals. In this study, juvenile fluted giant clams Tridacna squamosa were exposed to three levels of carbon dioxide (CO2) (control ~400, mid ~650 and high ~950 μatm) and light (photosynthetically active radiation 35, 65 and 304 μmol photons m-2 s-1). Elevated CO2 projected for the end of this century (~650 and ~950 μatm) reduced giant clam survival and growth at mid-light levels. However, effects of CO2 on survival were absent at high-light, with 100% survival across all CO2 levels. Effects of CO2 on growth of surviving clams were lessened, but not removed, at high-light levels. Shell growth and total animal mass gain were still reduced at high-CO2. This study demonstrates the potential for light to alleviate effects of ocean acidification on survival and growth in a threatened calcareous marine invertebrate. Managing water quality (e.g. turbidity and sedimentation) in coastal areas to maintain water clarity may help ameliorate some negative effects of ocean acidification on giant clams and potentially other solar-powered calcifiers, such as hard corals.

Identification of a transformer homolog in the acorn worm, Saccoglossus kowalevskii, and analysis of its activity in insect cells.

PubMed

Suzuki, Masataka G; Tochigi, Mayuko; Sakaguchi, Honami; Aoki, Fugaku; Miyamoto, Norio

2015-06-01

The transformer (tra) gene is an intermediate component of the sex determination hierarchy in many insect species. The homolog of tra is also found in two branchiopod crustacean species but is not known outside arthropods. We have isolated a tra homolog in the acorn worm, Saccoglossus kowalevskii, which is a hemichordate belonging to the deuterostome superphylum. The full-length complementary DNA (cDNA) of the S. kowalevskii tra homolog (Sktra) has a 3786-bp open reading frame that encodes a 1261-amino acid sequence including a TRA-CAM domain and an arginine/serine (RS)-rich domain, both of which are characteristic of TRA orthologs. Reverse transcription PCR (RT-PCR) analyses demonstrated that Sktra showed no differences in expression patterns between testes and ovaries, but its expression level was approximately 7.5-fold higher in the testes than in the ovaries. TRA, together with the protein product of the transformer-2 (tra-2) gene, assembles on doublesex (dsx) pre-messenger RNA (mRNA) via the cis-regulatory element, enhancing female-specific splicing of dsx in Drosophila. To understand functional conservation of the SkTRA protein as a dsx-splicing activator, we investigated whether SkTRA is capable of inducing female-specific splicing of the Drosophila dsx. Ectopic expression of Sktra cDNA in insect cultured cells did not induce the female-specific splicing of dsx. On the other hand, forced expression of Sktra-2 (a tra-2 homolog of S. kowalevskii) was able to induce the female-specific dsx splicing. These results demonstrate that the function as a dsx-splicing activator is not conserved in SkTRA even though SkTRA-2 is capable of functionally replacing the Drosophila TRA-2. We have also found a tra homolog in an echinoderm genome. This study provides the first evidence that that tra is conserved not only in arthropods but also in basal species of deuterostoms.