Chromatin organization and global regulation of Hox gene clusters

PubMed Central

Montavon, Thomas; Duboule, Denis

2013-01-01

During development, a properly coordinated expression of Hox genes, within their different genomic clusters is critical for patterning the body plans of many animals with a bilateral symmetry. The fascinating correspondence between the topological organization of Hox clusters and their transcriptional activation in space and time has served as a paradigm for understanding the relationships between genome structure and function. Here, we review some recent observations, which revealed highly dynamic changes in the structure of chromatin at Hox clusters, in parallel with their activation during embryonic development. We discuss the relevance of these findings for our understanding of large-scale gene regulation. PMID:23650639

Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes.

PubMed

Fortunato, Sofia A V; Adamski, Marcin; Ramos, Olivia Mendivil; Leininger, Sven; Liu, Jing; Ferrier, David E K; Adamska, Maja

2014-10-30

Sponges are simple animals with few cell types, but their genomes paradoxically contain a wide variety of developmental transcription factors, including homeobox genes belonging to the Antennapedia (ANTP) class, which in bilaterians encompass Hox, ParaHox and NK genes. In the genome of the demosponge Amphimedon queenslandica, no Hox or ParaHox genes are present, but NK genes are linked in a tight cluster similar to the NK clusters of bilaterians. It has been proposed that Hox and ParaHox genes originated from NK cluster genes after divergence of sponges from the lineage leading to cnidarians and bilaterians. On the other hand, synteny analysis lends support to the notion that the absence of Hox and ParaHox genes in Amphimedon is a result of secondary loss (the ghost locus hypothesis). Here we analysed complete suites of ANTP-class homeoboxes in two calcareous sponges, Sycon ciliatum and Leucosolenia complicata. Our phylogenetic analyses demonstrate that these calcisponges possess orthologues of bilaterian NK genes (Hex, Hmx and Msx), a varying number of additional NK genes and one ParaHox gene, Cdx. Despite the generation of scaffolds spanning multiple genes, we find no evidence of clustering of Sycon NK genes. All Sycon ANTP-class genes are developmentally expressed, with patterns suggesting their involvement in cell type specification in embryos and adults, metamorphosis and body plan patterning. These results demonstrate that ParaHox genes predate the origin of sponges, thus confirming the ghost locus hypothesis, and highlight the need to analyse the genomes of multiple sponge lineages to obtain a complete picture of the ancestral composition of the first animal genome.

Hox cluster polarity in early transcriptional availability: a high order regulatory level of clustered Hox genes in the mouse.

PubMed

Roelen, Bernard A J; de Graaff, Wim; Forlani, Sylvie; Deschamps, Jacqueline

2002-11-01

The molecular mechanism underlying the 3' to 5' polarity of induction of mouse Hox genes is still elusive. While relief from a cluster-encompassing repression was shown to lead to all Hoxd genes being expressed like the 3'most of them, Hoxd1 (Kondo and Duboule, 1999), the molecular basis of initial activation of this 3'most gene, is not understood yet. We show that, already before primitive streak formation, prior to initial expression of the first Hox gene, a dramatic transcriptional stimulation of the 3'most genes, Hoxb1 and Hoxb2, is observed upon a short pulse of exogenous retinoic acid (RA), whereas it is not in the case for more 5', cluster-internal, RA-responsive Hoxb genes. In contrast, the RA-responding Hoxb1lacZ transgene that faithfully mimics the endogenous gene (Marshall et al., 1994) did not exhibit the sensitivity of Hoxb1 to precocious activation. We conclude that polarity in initial activation of Hoxb genes reflects a greater availability of 3'Hox genes for transcription, suggesting a pre-existing (susceptibility to) opening of the chromatin structure at the 3' extremity of the cluster. We discuss the data in the context of prevailing models involving differential chromatin opening in the directionality of clustered Hox gene transcription, and regarding the importance of the cluster context for correct timing of initial Hox gene expression.Interestingly, Cdx1 manifested the same early transcriptional availability as Hoxb1. Copyright 2002 Elsevier Science Ireland Ltd.

Evolution of homeobox genes.

PubMed

Holland, Peter W H

2013-01-01

Many homeobox genes encode transcription factors with regulatory roles in animal and plant development. Homeobox genes are found in almost all eukaryotes, and have diversified into 11 gene classes and over 100 gene families in animal evolution, and 10 to 14 gene classes in plants. The largest group in animals is the ANTP class which includes the well-known Hox genes, plus other genes implicated in development including ParaHox (Cdx, Xlox, Gsx), Evx, Dlx, En, NK4, NK3, Msx, and Nanog. Genomic data suggest that the ANTP class diversified by extensive tandem duplication to generate a large array of genes, including an NK gene cluster and a hypothetical ProtoHox gene cluster that duplicated to generate Hox and ParaHox genes. Expression and functional data suggest that NK, Hox, and ParaHox gene clusters acquired distinct roles in patterning the mesoderm, nervous system, and gut. The PRD class is also diverse and includes Pax2/5/8, Pax3/7, Pax4/6, Gsc, Hesx, Otx, Otp, and Pitx genes. PRD genes are not generally arranged in ancient genomic clusters, although the Dux, Obox, and Rhox gene clusters arose in mammalian evolution as did several non-clustered PRD genes. Tandem duplication and genome duplication expanded the number of homeobox genes, possibly contributing to the evolution of developmental complexity, but homeobox gene loss must not be ignored. Evolutionary changes to homeobox gene expression have also been documented, including Hox gene expression patterns shifting in concert with segmental diversification in vertebrates and crustaceans, and deletion of a Pitx1 gene enhancer in pelvic-reduced sticklebacks. WIREs Dev Biol 2013, 2:31-45. doi: 10.1002/wdev.78 For further resources related to this article, please visit the WIREs website. The author declares that he has no conflicts of interest. Copyright © 2012 Wiley Periodicals, Inc.

Evolution of coding and non-coding genes in HOX clusters of a marsupial.

PubMed

Yu, Hongshi; Lindsay, James; Feng, Zhi-Ping; Frankenberg, Stephen; Hu, Yanqiu; Carone, Dawn; Shaw, Geoff; Pask, Andrew J; O'Neill, Rachel; Papenfuss, Anthony T; Renfree, Marilyn B

2012-06-18

The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals. Here we report a comparative analysis of HOX gene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation of HOX gene sequence and structure and non-protein coding genes including the microRNAs miR-196a, miR-196b, miR-10a and miR-10b and the long non-coding RNAs HOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such as miR-10, miR-414 and miR-464, were found in the tammar HOX clusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammar HOXB and HOXD clusters. This study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation of HOX genes to influence the body plan of this marsupial.

Evolution of coding and non-coding genes in HOX clusters of a marsupial

PubMed Central

2012-01-01

Background The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals. Results Here we report a comparative analysis of HOX gene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation of HOX gene sequence and structure and non-protein coding genes including the microRNAs miR-196a, miR-196b, miR-10a and miR-10b and the long non-coding RNAs HOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such as miR-10, miR-414 and miR-464, were found in the tammar HOX clusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammar HOXB and HOXD clusters. Conclusions This study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation of HOX genes to influence the body plan of this marsupial. PMID:22708672

Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica.

PubMed

Seo, Hee-Chan; Edvardsen, Rolf Brudvik; Maeland, Anne Dorthea; Bjordal, Marianne; Jensen, Marit Flo; Hansen, Anette; Flaat, Mette; Weissenbach, Jean; Lehrach, Hans; Wincker, Patrick; Reinhardt, Richard; Chourrout, Daniel

2004-09-02

Tunicate embryos and larvae have small cell numbers and simple anatomical features in comparison with other chordates, including vertebrates. Although they branch near the base of chordate phylogenetic trees, their degree of divergence from the common chordate ancestor remains difficult to evaluate. Here we show that the tunicate Oikopleura dioica has a complement of nine Hox genes in which all central genes are lacking but a full vertebrate-like set of posterior genes is present. In contrast to all bilaterians studied so far, Hox genes are not clustered in the Oikopleura genome. Their expression occurs mostly in the tail, with some tissue preference, and a strong partition of expression domains in the nerve cord, in the notochord and in the muscle. In each tissue of the tail, the anteroposterior order of Hox gene expression evokes spatial collinearity, with several alterations. We propose a relationship between the Hox cluster breakdown, the separation of Hox expression domains, and a transition to a determinative mode of development.

Transcription and Regulation of the Bidirectional Hydrogenase in the Cyanobacterium Nostoc sp. Strain PCC 7120▿

PubMed Central

Sjöholm, Johannes; Oliveira, Paulo; Lindblad, Peter

2007-01-01

The filamentous, heterocystous cyanobacterium Nostoc sp. strain PCC 7120 (Anabaena sp. strain PCC 7120) possesses an uptake hydrogenase and a bidirectional enzyme, the latter being capable of catalyzing both H2 production and evolution. The completely sequenced genome of Nostoc sp. strain PCC 7120 reveals that the five structural genes encoding the bidirectional hydrogenase (hoxEFUYH) are separated in two clusters at a distance of approximately 8.8 kb. The transcription of the hox genes was examined under nitrogen-fixing conditions, and the results demonstrate that the cluster containing hoxE and hoxF can be transcribed as one polycistronic unit together with the open reading frame alr0750. The second cluster, containing hoxU, hoxY, and hoxH, is transcribed together with alr0763 and alr0765, located between the hox genes. Moreover, alr0760 and alr0761 form an additional larger operon. Nevertheless, Northern blot hybridizations revealed a rather complex transcription pattern in which the different hox genes are expressed differently. Transcriptional start points (TSPs) were identified 66 and 57 bp upstream from the start codon of alr0750 and hoxU, respectively. The transcriptions of the two clusters containing the hox genes are both induced under anaerobic conditions concomitantly with the induction of a higher level of hydrogenase activity. An additional TSP, within the annotated alr0760, 244 bp downstream from the suggested translation start codon, was identified. Electrophoretic mobility shift assays with purified LexA from Nostoc sp. strain PCC 7120 demonstrated specific interactions between the transcriptional regulator and both hox promoter regions. However, when LexA from Synechocystis sp. strain PCC 6803 was used, the purified protein interacted only with the promoter region of the alr0750-hoxE-hoxF operon. A search of the whole Nostoc sp. strain PCC 7120 genome demonstrated the presence of 216 putative LexA binding sites in total, including recA and recF. This indicates that, in addition to the bidirectional hydrogenase gene, a number of other genes, including open reading frames connected to DNA replication, recombination, and repair, may be part of the LexA regulatory network in Nostoc sp. strain PCC 7120. PMID:17630298

Deregulated HOX genes in ameloblastomas are located in physical contiguity to keratin genes.

PubMed

Schiavo, Giulia; D'Antò, Vincenzo; Cantile, Monica; Procino, Alfredo; Di Giovanni, Stefano; Valletta, Rossella; Terracciano, Luigi; Baumhoer, Daniel; Jundt, Gernot; Cillo, Clemente

2011-11-01

The expression of the HOX gene network in mid-stage human tooth development mostly concerns the epithelial tooth germ compartment and involves the C and D HOX loci. To further dissect the HOX gene implication with tooth epithelium differentiation we compared the expression of the whole HOX network in human ameloblastomas, as paradigm of epithelial odontogenic tumors, with tooth germs. We identified two ameloblastoma molecular types with respectively low and high number of active HOX C genes. The highly expressing HOX C gene ameloblastomas were characterized by a strong keratinized phenotype. Locus C HOX genes are located on chromosome 12q13-15 in physical contiguity with one of the two keratin gene clusters included in the human genome. The most posterior HOX C gene, HOX C13, is capable to interact with hair keratin genes located on the other keratin gene cluster in physical contiguity with the HOX B locus on chromosome 17q21-22. Inside the HOX C locus, a 2.2 kb ncRNA (HOTAIR) able to repress transcription, in cis, along the entire HOX C locus and, in trans, at the posterior region of the HOX D locus has recently been identified. Interestingly both loci are deregulated in ameloblastomas. Our finding support an important role of the HOX network in characterizing the epithelial tooth compartment. Furthermore, the physical contiguity between locus C HOX and keratin genes in normal tooth epithelium and their deregulation in the neoplastic counterparts suggest they may act on the same mechanism potentially involved with epithelial tumorigenesis. Copyright © 2011 Wiley Periodicals, Inc.

Are Hox genes ancestrally involved in axial patterning? Evidence from the hydrozoan Clytia hemisphaerica (Cnidaria).

PubMed

Chiori, Roxane; Jager, Muriel; Denker, Elsa; Wincker, Patrick; Da Silva, Corinne; Le Guyader, Hervé; Manuel, Michaël; Quéinnec, Eric

2009-01-01

The early evolution and diversification of Hox-related genes in eumetazoans has been the subject of conflicting hypotheses concerning the evolutionary conservation of their role in axial patterning and the pre-bilaterian origin of the Hox and ParaHox clusters. The diversification of Hox/ParaHox genes clearly predates the origin of bilaterians. However, the existence of a "Hox code" predating the cnidarian-bilaterian ancestor and supporting the deep homology of axes is more controversial. This assumption was mainly based on the interpretation of Hox expression data from the sea anemone, but growing evidence from other cnidarian taxa puts into question this hypothesis. Hox, ParaHox and Hox-related genes have been investigated here by phylogenetic analysis and in situ hybridisation in Clytia hemisphaerica, an hydrozoan species with medusa and polyp stages alternating in the life cycle. Our phylogenetic analyses do not support an origin of ParaHox and Hox genes by duplication of an ancestral ProtoHox cluster, and reveal a diversification of the cnidarian HOX9-14 genes into three groups called A, B, C. Among the 7 examined genes, only those belonging to the HOX9-14 and the CDX groups exhibit a restricted expression along the oral-aboral axis during development and in the planula larva, while the others are expressed in very specialised areas at the medusa stage. Cross species comparison reveals a strong variability of gene expression along the oral-aboral axis and during the life cycle among cnidarian lineages. The most parsimonious interpretation is that the Hox code, collinearity and conservative role along the antero-posterior axis are bilaterian innovations.

Are Hox Genes Ancestrally Involved in Axial Patterning? Evidence from the Hydrozoan Clytia hemisphaerica (Cnidaria)

PubMed Central

Chiori, Roxane; Jager, Muriel; Denker, Elsa; Wincker, Patrick; Da Silva, Corinne; Le Guyader, Hervé; Manuel, Michaël; Quéinnec, Eric

2009-01-01

Background The early evolution and diversification of Hox-related genes in eumetazoans has been the subject of conflicting hypotheses concerning the evolutionary conservation of their role in axial patterning and the pre-bilaterian origin of the Hox and ParaHox clusters. The diversification of Hox/ParaHox genes clearly predates the origin of bilaterians. However, the existence of a “Hox code” predating the cnidarian-bilaterian ancestor and supporting the deep homology of axes is more controversial. This assumption was mainly based on the interpretation of Hox expression data from the sea anemone, but growing evidence from other cnidarian taxa puts into question this hypothesis. Methodology/Principal Findings Hox, ParaHox and Hox-related genes have been investigated here by phylogenetic analysis and in situ hybridisation in Clytia hemisphaerica, an hydrozoan species with medusa and polyp stages alternating in the life cycle. Our phylogenetic analyses do not support an origin of ParaHox and Hox genes by duplication of an ancestral ProtoHox cluster, and reveal a diversification of the cnidarian HOX9-14 genes into three groups called A, B, C. Among the 7 examined genes, only those belonging to the HOX9-14 and the CDX groups exhibit a restricted expression along the oral-aboral axis during development and in the planula larva, while the others are expressed in very specialised areas at the medusa stage. Conclusions/Significance Cross species comparison reveals a strong variability of gene expression along the oral-aboral axis and during the life cycle among cnidarian lineages. The most parsimonious interpretation is that the Hox code, collinearity and conservative role along the antero-posterior axis are bilaterian innovations. PMID:19156208

Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications

PubMed Central

Siegel, Nicol; Hoegg, Simone; Salzburger, Walter; Braasch, Ingo; Meyer, Axel

2007-01-01

Background The evolutionary lineage leading to the teleost fish underwent a whole genome duplication termed FSGD or 3R in addition to two prior genome duplications that took place earlier during vertebrate evolution (termed 1R and 2R). Resulting from the FSGD, additional copies of genes are present in fish, compared to tetrapods whose lineage did not experience the 3R genome duplication. Interestingly, we find that ParaHox genes do not differ in number in extant teleost fishes despite their additional genome duplication from the genomic situation in mammals, but they are distributed over twice as many paralogous regions in fish genomes. Results We determined the DNA sequence of the entire ParaHox C1 paralogon in the East African cichlid fish Astatotilapia burtoni, and compared it to orthologous regions in other vertebrate genomes as well as to the paralogous vertebrate ParaHox D paralogons. Evolutionary relationships among genes from these four chromosomal regions were studied with several phylogenetic algorithms. We provide evidence that the genes of the ParaHox C paralogous cluster are duplicated in teleosts, just as it had been shown previously for the D paralogon genes. Overall, however, synteny and cluster integrity seems to be less conserved in ParaHox gene clusters than in Hox gene clusters. Comparative analyses of non-coding sequences uncovered conserved, possibly co-regulatory elements, which are likely to contain promoter motives of the genes belonging to the ParaHox paralogons. Conclusion There seems to be strong stabilizing selection for gene order as well as gene orientation in the ParaHox C paralogon, since with a few exceptions, only the lengths of the introns and intergenic regions differ between the distantly related species examined. The high degree of evolutionary conservation of this gene cluster's architecture in particular – but possibly clusters of genes more generally – might be linked to the presence of promoter, enhancer or inhibitor motifs that serve to regulate more than just one gene. Therefore, deletions, inversions or relocations of individual genes could destroy the regulation of the clustered genes in this region. The existence of such a regulation network might explain the evolutionary conservation of gene order and orientation over the course of hundreds of millions of years of vertebrate evolution. Another possible explanation for the highly conserved gene order might be the existence of a regulator not located immediately next to its corresponding gene but further away since a relocation or inversion would possibly interrupt this interaction. Different ParaHox clusters were found to have experienced differential gene loss in teleosts. Yet the complete set of these homeobox genes was maintained, albeit distributed over almost twice the number of chromosomes. Selection due to dosage effects and/or stoichiometric disturbance might act more strongly to maintain a modal number of homeobox genes (and possibly transcription factors more generally) per genome, yet permit the accumulation of other (non regulatory) genes associated with these homeobox gene clusters. PMID:17822543

Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex

PubMed Central

Negre, Bárbara; Casillas, Sònia; Suzanne, Magali; Sánchez-Herrero, Ernesto; Akam, Michael; Nefedov, Michael; Barbadilla, Antonio; de Jong, Pieter; Ruiz, Alfredo

2005-01-01

Homeotic (Hox) genes are usually clustered and arranged in the same order as they are expressed along the anteroposterior body axis of metazoans. The mechanistic explanation for this colinearity has been elusive, and it may well be that a single and universal cause does not exist. The Hox-gene complex (HOM-C) has been rearranged differently in several Drosophila species, producing a striking diversity of Hox gene organizations. We investigated the genomic and functional consequences of the two HOM-C splits present in Drosophila buzzatii. Firstly, we sequenced two regions of the D. buzzatii genome, one containing the genes labial and abdominal A, and another one including proboscipedia, and compared their organization with that of D. melanogaster and D. pseudoobscura in order to map precisely the two splits. Then, a plethora of conserved noncoding sequences, which are putative enhancers, were identified around the three Hox genes closer to the splits. The position and order of these enhancers are conserved, with minor exceptions, between the three Drosophila species. Finally, we analyzed the expression patterns of the same three genes in embryos and imaginal discs of four Drosophila species with different Hox-gene organizations. The results show that their expression patterns are conserved despite the HOM-C splits. We conclude that, in Drosophila, Hox-gene clustering is not an absolute requirement for proper function. Rather, the organization of Hox genes is modular, and their clustering seems the result of phylogenetic inertia more than functional necessity. PMID:15867430

Murine mesenchymal and embryonic stem cells express a similar Hox gene profile.

PubMed

Phinney, Donald G; Gray, Andrew J; Hill, Katy; Pandey, Amitabh

2005-12-30

Using degenerate oligonucleotide primers targeting the homeobox domain, we amplified by PCR and sequenced 723 clones from five murine cell populations and lines derived from embryonic mesoderm and adult bone marrow. Transcripts from all four vertebrate Hox clusters were expressed by the different populations. Hierarchical clustering of the data revealed that mesenchymal stem cells (MSCs) and the embryonic stem (ES) cell line D3 shared a similar Hox expression profile. These populations exclusively expressed Hoxb2, Hoxb5, Hoxb7, and Hoxc4, transcripts regulating self-renewal and differentiation of other stem cells. Additionally, Hoxa7 transcript quantified by real-time PCR strongly correlated (r2=0.89) with the number of Hoxa7 clones identified by sequencing, validating that data from the PCR screen reflects differences in Hox mRNA abundance between populations. This is the first study to catalogue Hox transcripts in murine MSCs and by comparative analyses identify specific Hox genes that may contribute to their stem cell character.

Hox gene expression during postlarval development of the polychaete Alitta virens.

PubMed

Bakalenko, Nadezhda I; Novikova, Elena L; Nesterenko, Alexander Y; Kulakova, Milana A

2013-05-01

Hox genes are the family of transcription factors that play a key role in the patterning of the anterior-posterior axis of all bilaterian animals. These genes display clustered organization and colinear expression. Expression boundaries of individual Hox genes usually correspond with morphological boundaries of the body. Previously, we studied Hox gene expression during larval development of the polychaete Alitta virens (formerly Nereis virens) and discovered that Hox genes are expressed in nereid larva according to the spatial colinearity principle. Adult Alitta virens consist of multiple morphologically similar segments, which are formed sequentially in the growth zone. Since the worm grows for most of its life, postlarval segments constantly change their position along the anterior-posterior axis. We studied the expression dynamics of the Hox cluster during postlarval development of the nereid Alitta virens and found that 8 out of 11 Hox genes are transcribed as wide gene-specific gradients in the ventral nerve cord, ectoderm, and mesoderm. The expression domains constantly shift in accordance with the changing proportions of the growing worm, so expression domains of most Hox genes do not have stable anterior or/and posterior boundaries.In the course of our study, we revealed long antisense RNA (asRNA) for some Hox genes. Expression patterns of two of these genes were analyzed using whole-mount in-situ hybridization. This is the first discovery of antisense RNA for Hox genes in Lophotrochozoa. Hox gene expression in juvenile A. virens differs significantly from Hox gene expression patterns both in A. virens larva and in other Bilateria.We suppose that the postlarval function of the Hox genes in this polychaete is to establish and maintain positional coordinates in a constantly growing body, as opposed to creating morphological difference between segments.

Characterization of a HoxEFUYH type of [NiFe] hydrogenase from Allochromatium vinosum and some EPR and IR properties of the hydrogenase module.

PubMed

Long, Minnan; Liu, Jingjing; Chen, Zhifeng; Bleijlevens, Boris; Roseboom, Winfried; Albracht, Simon P J

2007-01-01

A soluble hydrogenase from Allochromatium vinosum was purified. It consisted of a large (M (r) = 52 kDa) and a small (M (r) = 23 kDa) subunit. The genes encoding for both subunits were identified. They belong to an open reading frame where they are preceded by three more genes. A DNA fragment containing all five genes was cloned and sequenced. The deduced amino acid sequences of the products characterized the complex as a member of the HoxEFUYH type of [NiFe] hydrogenases. Detailed sequence analyses revealed binding sites for eight Fe-S clusters, three [2Fe-2S] clusters and five [4Fe-4S] clusters, six of which are also present in homologous subunits of [FeFe] hydrogenases and NADH:ubiquione oxidoreductases (complex I). This makes the HoxEFUYH type of hydrogenases the one that is evolutionary closest to complex I. The relative positions of six of the potential Fe-S clusters are predicted on the basis of the X-ray structures of the Clostridium pasteurianum [FeFe] hydrogenase I and the hydrophilic domain of complex I from Thermus thermophilus. Although the HoxF subunit contains binding sites for flavin mononucleotide and NAD(H), cell-free extracts of A. vinosum did not catalyse a H(2)-dependent reduction of NAD(+). Only the hydrogenase module (HoxYH) could be purified. Its electron paramagnetic resonance (EPR) and IR spectral properties showed the presence of a Ni-Fe active site and a [4Fe-4S] cluster. Its activity was sensitive to carbon monoxide. No EPR signals from a light-sensitive Ni(a)-C* state could be observed. This study presents the first IR spectroscopic data on the HoxYH module of a HoxEFUYH type of [NiFe] hydrogenase.

HOX genes in human lung: altered expression in primary pulmonary hypertension and emphysema.

PubMed

Golpon, H A; Geraci, M W; Moore, M D; Miller, H L; Miller, G J; Tuder, R M; Voelkel, N F

2001-03-01

HOX genes belong to the large family of homeodomain genes that function as transcription factors. Animal studies indicate that they play an essential role in lung development. We investigated the expression pattern of HOX genes in human lung tissue by using microarray and degenerate reverse transcriptase-polymerase chain reaction survey techniques. HOX genes predominantly from the 3' end of clusters A and B were expressed in normal human adult lung and among them HOXA5 was the most abundant, followed by HOXB2 and HOXB6. In fetal (12 weeks old) and diseased lung specimens (emphysema, primary pulmonary hypertension) additional HOX genes from clusters C and D were expressed. Using in situ hybridization, transcripts for HOXA5 were predominantly found in alveolar septal and epithelial cells, both in normal and diseased lungs. A 2.5-fold increase in HOXA5 mRNA expression was demonstrated by quantitative reverse transcriptase-polymerase chain reaction in primary pulmonary hypertension lung specimens when compared to normal lung tissue. In conclusion, we demonstrate that HOX genes are selectively expressed in the human lung. Differences in the pattern of HOX gene expression exist among fetal, adult, and diseased lung specimens. The altered pattern of HOX gene expression may contribute to the development of pulmonary diseases.

HOX Genes in Human Lung

PubMed Central

Golpon, Heiko A.; Geraci, Mark W.; Moore, Mark D.; Miller, Heidi L.; Miller, Gary J.; Tuder, Rubin M.; Voelkel, Norbert F.

2001-01-01

HOX genes belong to the large family of homeodomain genes that function as transcription factors. Animal studies indicate that they play an essential role in lung development. We investigated the expression pattern of HOX genes in human lung tissue by using microarray and degenerate reverse transcriptase-polymerase chain reaction survey techniques. HOX genes predominantly from the 3′ end of clusters A and B were expressed in normal human adult lung and among them HOXA5 was the most abundant, followed by HOXB2 and HOXB6. In fetal (12 weeks old) and diseased lung specimens (emphysema, primary pulmonary hypertension) additional HOX genes from clusters C and D were expressed. Using in situ hybridization, transcripts for HOXA5 were predominantly found in alveolar septal and epithelial cells, both in normal and diseased lungs. A 2.5-fold increase in HOXA5 mRNA expression was demonstrated by quantitative reverse transcriptase-polymerase chain reaction in primary pulmonary hypertension lung specimens when compared to normal lung tissue. In conclusion, we demonstrate that HOX genes are selectively expressed in the human lung. Differences in the pattern of HOX gene expression exist among fetal, adult, and diseased lung specimens. The altered pattern of HOX gene expression may contribute to the development of pulmonary diseases. PMID:11238043

An Overview of Hox Genes in Lophotrochozoa: Evolution and Functionality

PubMed Central

Barucca, Marco; Canapa, Adriana; Biscotti, Maria Assunta

2016-01-01

Hox genes are regulators of animal embryonic development. Changes in the number and sequence of Hox genes as well as in their expression patterns have been related to the evolution of the body plan. Lophotrochozoa is a clade of Protostomia characterized by several phyla which show a wide morphological diversity. Despite that the works summarized in this review emphasize the fragmentary nature of the data available regarding the presence and expression of Hox genes, they also offer interesting insight into the evolution of the Hox cluster and the role played by Hox genes in several phyla. However, the number of genes involved in the cluster of the lophotrochozoan ancestor is still a question of debate. The data presented here suggest that at least nine genes were present while two other genes, Lox4 and Post-2, may either have been present in the ancestor or may have arisen as a result of duplication in the Brachiopoda-Mollusca-Annelida lineage. Spatial and temporal collinearity is a feature of Hox gene expression which was probably present in the ancestor of deuterostomes and protostomes. However, in Lophotrochozoa, it has been detected in only a few species belonging to Annelida and Mollusca. PMID:29615580

Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

PubMed Central

Noordermeer, Daan; Leleu, Marion; Schorderet, Patrick; Joye, Elisabeth; Chabaud, Fabienne; Duboule, Denis

2014-01-01

Hox genes are essential regulators of embryonic development. Their step-wise transcriptional activation follows their genomic topology and the various states of activation are subsequently memorized into domains of progressively overlapping gene products. We have analyzed the 3D chromatin organization of Hox clusters during their early activation in vivo, using high-resolution circular chromosome conformation capture. Initially, Hox clusters are organized as single chromatin compartments containing all genes and bivalent chromatin marks. Transcriptional activation is associated with a dynamic bi-modal 3D organization, whereby the genes switch autonomously from an inactive to an active compartment. These local 3D dynamics occur within a framework of constitutive interactions within the surrounding Topological Associated Domains, indicating that this regulation process is mostly cluster intrinsic. The step-wise progression in time is fixed at various body levels and thus can account for the chromatin architectures previously described at a later stage for different anterior to posterior levels. DOI: http://dx.doi.org/10.7554/eLife.02557.001 PMID:24843030

Rubredoxin-related Maturation Factor Guarantees Metal Cofactor Integrity during Aerobic Biosynthesis of Membrane-bound [NiFe] Hydrogenase*

PubMed Central

Fritsch, Johannes; Siebert, Elisabeth; Priebe, Jacqueline; Zebger, Ingo; Lendzian, Friedhelm; Teutloff, Christian; Friedrich, Bärbel; Lenz, Oliver

2014-01-01

The membrane-bound [NiFe] hydrogenase (MBH) supports growth of Ralstonia eutropha H16 with H2 as the sole energy source. The enzyme undergoes a complex biosynthesis process that proceeds during cell growth even at ambient O2 levels and involves 14 specific maturation proteins. One of these is a rubredoxin-like protein, which is essential for biosynthesis of active MBH at high oxygen concentrations but dispensable under microaerobic growth conditions. To obtain insights into the function of HoxR, we investigated the MBH protein purified from the cytoplasmic membrane of hoxR mutant cells. Compared with wild-type MBH, the mutant enzyme displayed severely decreased hydrogenase activity. Electron paramagnetic resonance and infrared spectroscopic analyses revealed features resembling those of O2-sensitive [NiFe] hydrogenases and/or oxidatively damaged protein. The catalytic center resided partially in an inactive Niu-A-like state, and the electron transfer chain consisting of three different Fe-S clusters showed marked alterations compared with wild-type enzyme. Purification of HoxR protein from its original host, R. eutropha, revealed only low protein amounts. Therefore, recombinant HoxR protein was isolated from Escherichia coli. Unlike common rubredoxins, the HoxR protein was colorless, rather unstable, and essentially metal-free. Conversion of the atypical iron-binding motif into a canonical one through genetic engineering led to a stable reddish rubredoxin. Remarkably, the modified HoxR protein did not support MBH-dependent growth at high O2. Analysis of MBH-associated protein complexes points toward a specific interaction of HoxR with the Fe-S cluster-bearing small subunit. This supports the previously made notion that HoxR avoids oxidative damage of the metal centers of the MBH, in particular the unprecedented Cys6[4Fe-3S] cluster. PMID:24448806

Hox genes and chordate evolution.

PubMed

Holland, P W; Garcia-Fernàndez, J

1996-02-01

Hox genes are implicated in the control of axial patterning during embryonic development of many, perhaps all, animals. Here we review recent data on Hox gene diversity, genomic organization, and embryonic expression in chordates (including tunicates, amphioxus, hagfish, lampreys, teleosts) plus their putative sister group, the hemichordates. We consider the potential of comparative Hox gene data to resolve some outstanding controversies in chordate phylogeny. The use of Hox gene expression patterns to identify homologies between body plans both within the vertebrates and between the chordate subphyla is also discussed. Homology between the vertebrate hindbrain and an extensive region of amphioxus neural tube is suggested by comparison of Hox-3 homologues and strengthened by new data on amphioxus Hox-1 gene expression reported here. Finally, we give two examples of how Hox genes are giving glimpses into chordate developmental evolution. The first relates changes in Hox gene expression to transposition of vertebral of vertebral identities; the second describes a correlation between vertebrate origins and Hox gene cluster duplication. We suggest that the simultaneous duplication of many classes of genes, often interacting in gene networks, allowed the elaboration of new developmental control mechanisms at vertebrate origins.

Evolutionary conservation of regulatory elements in vertebrate HOX gene clusters

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

Santini, Simona; Boore, Jeffrey L.; Meyer, Axel

2003-12-31

Due to their high degree of conservation, comparisons of DNA sequences among evolutionarily distantly-related genomes permit to identify functional regions in noncoding DNA. Hox genes are optimal candidate sequences for comparative genome analyses, because they are extremely conserved in vertebrates and occur in clusters. We aligned (Pipmaker) the nucleotide sequences of HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human and mouse (over 500 million years of evolutionary distance). We identified several highly conserved intergenic sequences, likely to be important in gene regulation. Only a few of these putative regulatory elements have been previously described as being involvedmore » in the regulation of Hox genes, while several others are new elements that might have regulatory functions. The majority of these newly identified putative regulatory elements contain short fragments that are almost completely conserved and are identical to known binding sites for regulatory proteins (Transfac). The conserved intergenic regions located between the most rostrally expressed genes in the developing embryo are longer and better retained through evolution. We document that presumed regulatory sequences are retained differentially in either A or A clusters resulting from a genome duplication in the fish lineage. This observation supports both the hypothesis that the conserved elements are involved in gene regulation and the Duplication-Deletion-Complementation model.« less

Protonation/reduction dynamics at the [4Fe-4S] cluster of the hydrogen-forming cofactor in [FeFe]-hydrogenases.

PubMed

Senger, Moritz; Mebs, Stefan; Duan, Jifu; Shulenina, Olga; Laun, Konstantin; Kertess, Leonie; Wittkamp, Florian; Apfel, Ulf-Peter; Happe, Thomas; Winkler, Martin; Haumann, Michael; Stripp, Sven T

2018-01-31

The [FeFe]-hydrogenases of bacteria and algae are the most efficient hydrogen conversion catalysts in nature. Their active-site cofactor (H-cluster) comprises a [4Fe-4S] cluster linked to a unique diiron site that binds three carbon monoxide (CO) and two cyanide (CN - ) ligands. Understanding microbial hydrogen conversion requires elucidation of the interplay of proton and electron transfer events at the H-cluster. We performed real-time spectroscopy on [FeFe]-hydrogenase protein films under controlled variation of atmospheric gas composition, sample pH, and reductant concentration. Attenuated total reflection Fourier-transform infrared spectroscopy was used to monitor shifts of the CO/CN - vibrational bands in response to redox and protonation changes. Three different [FeFe]-hydrogenases and several protein and cofactor variants were compared, including element and isotopic exchange studies. A protonated equivalent (HoxH) of the oxidized state (Hox) was found, which preferentially accumulated at acidic pH and under reducing conditions. We show that the one-electron reduced state Hred' represents an intrinsically protonated species. Interestingly, the formation of HoxH and Hred' was independent of the established proton pathway to the diiron site. Quantum chemical calculations of the respective CO/CN - infrared band patterns favored a cysteine ligand of the [4Fe-4S] cluster as the protonation site in HoxH and Hred'. We propose that proton-coupled electron transfer facilitates reduction of the [4Fe-4S] cluster and prevents premature formation of a hydride at the catalytic diiron site. Our findings imply that protonation events both at the [4Fe-4S] cluster and at the diiron site of the H-cluster are important in the hydrogen conversion reaction of [FeFe]-hydrogenases.

Hox gene duplications correlate with posterior heteronomy in scorpions

PubMed Central

Sharma, Prashant P.; Schwager, Evelyn E.; Extavour, Cassandra G.; Wheeler, Ward C.

2014-01-01

The evolutionary success of the largest animal phylum, Arthropoda, has been attributed to tagmatization, the coordinated evolution of adjacent metameres to form morphologically and functionally distinct segmental regions called tagmata. Specification of regional identity is regulated by the Hox genes, of which 10 are inferred to be present in the ancestor of arthropods. With six different posterior segmental identities divided into two tagmata, the bauplan of scorpions is the most heteronomous within Chelicerata. Expression domains of the anterior eight Hox genes are conserved in previously surveyed chelicerates, but it is unknown how Hox genes regionalize the three tagmata of scorpions. Here, we show that the scorpion Centruroides sculpturatus has two paralogues of all Hox genes except Hox3, suggesting cluster and/or whole genome duplication in this arachnid order. Embryonic anterior expression domain boundaries of each of the last four pairs of Hox genes (two paralogues each of Antp, Ubx, abd-A and Abd-B) are unique and distinguish segmental groups, such as pectines, book lungs and the characteristic tail, while maintaining spatial collinearity. These distinct expression domains suggest neofunctionalization of Hox gene paralogues subsequent to duplication. Our data reconcile previous understanding of Hox gene function across arthropods with the extreme heteronomy of scorpions. PMID:25122224

DNA methylation and differentiation: HOX genes in muscle cells

PubMed Central

2013-01-01

Background Tight regulation of homeobox genes is essential for vertebrate development. In a study of genome-wide differential methylation, we recently found that homeobox genes, including those in the HOX gene clusters, were highly overrepresented among the genes with hypermethylation in the skeletal muscle lineage. Methylation was analyzed by reduced representation bisulfite sequencing (RRBS) of postnatal myoblasts, myotubes and adult skeletal muscle tissue and 30 types of non-muscle-cell cultures or tissues. Results In this study, we found that myogenic hypermethylation was present in specific subregions of all four HOX gene clusters and was associated with various chromatin epigenetic features. Although the 3′ half of the HOXD cluster was silenced and enriched in polycomb repression-associated H3 lysine 27 trimethylation in most examined cell types, including myoblasts and myotubes, myogenic samples were unusual in also displaying much DNA methylation in this region. In contrast, both HOXA and HOXC clusters displayed myogenic hypermethylation bordering a central region containing many genes preferentially expressed in myogenic progenitor cells and consisting largely of chromatin with modifications typical of promoters and enhancers in these cells. A particularly interesting example of myogenic hypermethylation was HOTAIR, a HOXC noncoding RNA gene, which can silence HOXD genes in trans via recruitment of polycomb proteins. In myogenic progenitor cells, the preferential expression of HOTAIR was associated with hypermethylation immediately downstream of the gene. Other HOX gene regions also displayed myogenic DNA hypermethylation despite being moderately expressed in myogenic cells. Analysis of representative myogenic hypermethylated sites for 5-hydroxymethylcytosine revealed little or none of this base, except for an intragenic site in HOXB5 which was specifically enriched in this base in skeletal muscle tissue, whereas myoblasts had predominantly 5-methylcytosine at the same CpG site. Conclusions Our results suggest that myogenic hypermethylation of HOX genes helps fine-tune HOX sense and antisense gene expression through effects on 5′ promoters, intragenic and intergenic enhancers and internal promoters. Myogenic hypermethylation might also affect the relative abundance of different RNA isoforms, facilitate transcription termination, help stop the spread of activation-associated chromatin domains and stabilize repressive chromatin structures. PMID:23916067

Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards.

PubMed

Feiner, Nathalie

2016-10-12

Transposable elements (TEs) are DNA sequences that can insert elsewhere in the genome and modify genome structure and gene regulation. The role of TEs in evolution is contentious. One hypothesis posits that TE activity generates genomic incompatibilities that can cause reproductive isolation between incipient species. This predicts that TEs will accumulate during speciation events. Here, I tested the prediction that extant lineages with a relatively high rate of speciation have a high number of TEs in their genomes. I sequenced and analysed the TE content of a marker genomic region (Hox clusters) in Anolis lizards, a classic case of an adaptive radiation. Unlike other vertebrates, including closely related lizards, Anolis lizards have high numbers of TEs in their Hox clusters, genomic regions that regulate development of the morphological adaptations that characterize habitat specialists in these lizards. Following a burst of TE activity in the lineage leading to extant Anolis, TEs have continued to accumulate during or after speciation events, resulting in a positive relationship between TE density and lineage speciation rate. These results are consistent with the prediction that TE activity contributes to adaptive radiation by promoting speciation. Although there was no evidence that TE density per se is associated with ecological morphology, the activity of TEs in Hox clusters could have been a rich source for phenotypic variation that may have facilitated the rapid parallel morphological adaptation to microhabitats seen in extant Anolis lizards. © 2016 The Author(s).

Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards

PubMed Central

2016-01-01

Transposable elements (TEs) are DNA sequences that can insert elsewhere in the genome and modify genome structure and gene regulation. The role of TEs in evolution is contentious. One hypothesis posits that TE activity generates genomic incompatibilities that can cause reproductive isolation between incipient species. This predicts that TEs will accumulate during speciation events. Here, I tested the prediction that extant lineages with a relatively high rate of speciation have a high number of TEs in their genomes. I sequenced and analysed the TE content of a marker genomic region (Hox clusters) in Anolis lizards, a classic case of an adaptive radiation. Unlike other vertebrates, including closely related lizards, Anolis lizards have high numbers of TEs in their Hox clusters, genomic regions that regulate development of the morphological adaptations that characterize habitat specialists in these lizards. Following a burst of TE activity in the lineage leading to extant Anolis, TEs have continued to accumulate during or after speciation events, resulting in a positive relationship between TE density and lineage speciation rate. These results are consistent with the prediction that TE activity contributes to adaptive radiation by promoting speciation. Although there was no evidence that TE density per se is associated with ecological morphology, the activity of TEs in Hox clusters could have been a rich source for phenotypic variation that may have facilitated the rapid parallel morphological adaptation to microhabitats seen in extant Anolis lizards. PMID:27733546

SET1A/COMPASS and shadow enhancers in the regulation of homeotic gene expression

PubMed Central

Cao, Kaixiang; Collings, Clayton K.; Marshall, Stacy A.; Morgan, Marc A.; Rendleman, Emily J.; Wang, Lu; Sze, Christie C.; Sun, Tianjiao; Bartom, Elizabeth T.; Shilatifard, Ali

2017-01-01

The homeotic (Hox) genes are highly conserved in metazoans, where they are required for various processes in development, and misregulation of their expression is associated with human cancer. In the developing embryo, Hox genes are activated sequentially in time and space according to their genomic position within Hox gene clusters. Accumulating evidence implicates both enhancer elements and noncoding RNAs in controlling this spatiotemporal expression of Hox genes, but disentangling their relative contributions is challenging. Here, we identify two cis-regulatory elements (E1 and E2) functioning as shadow enhancers to regulate the early expression of the HoxA genes. Simultaneous deletion of these shadow enhancers in embryonic stem cells leads to impaired activation of HoxA genes upon differentiation, while knockdown of a long noncoding RNA overlapping E1 has no detectable effect on their expression. Although MLL/COMPASS (complex of proteins associated with Set1) family of histone methyltransferases is known to activate transcription of Hox genes in other contexts, we found that individual inactivation of the MLL1-4/COMPASS family members has little effect on early Hox gene activation. Instead, we demonstrate that SET1A/COMPASS is required for full transcriptional activation of multiple Hox genes but functions independently of the E1 and E2 cis-regulatory elements. Our results reveal multiple regulatory layers for Hox genes to fine-tune transcriptional programs essential for development. PMID:28487406

Recent advances in functional perturbation and genome editing techniques in studying sea urchin development.

PubMed

Cui, Miao; Lin, Che-Yi; Su, Yi-Hsien

2017-09-01

Studies on the gene regulatory networks (GRNs) of sea urchin embryos have provided a basic understanding of the molecular mechanisms controlling animal development. The causal links in GRNs have been verified experimentally through perturbation of gene functions. Microinjection of antisense morpholino oligonucleotides (MOs) into the egg is the most widely used approach for gene knockdown in sea urchin embryos. The modification of MOs into a membrane-permeable form (vivo-MOs) has allowed gene knockdown at later developmental stages. Recent advances in genome editing tools, such as zinc-finger nucleases, transcription activator-like effector-based nucleases and the clustered regularly interspaced short palindromic repeat/clustered regularly interspaced short palindromic repeat-associated protein 9 (CRISPR/Cas9) system, have provided methods for gene knockout in sea urchins. Here, we review the use of vivo-MOs and genome editing tools in sea urchin studies since the publication of its genome in 2006. Various applications of the CRISPR/Cas9 system and their potential in studying sea urchin development are also discussed. These new tools will provide more sophisticated experimental methods for studying sea urchin development. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Ancient Expansion of the Hox Cluster in Lepidoptera Generated Four Homeobox Genes Implicated in Extra-Embryonic Tissue Formation

PubMed Central

Taylor, William R.; Gibbs, Melanie; Breuker, Casper J.; Holland, Peter W. H.

2014-01-01

Gene duplications within the conserved Hox cluster are rare in animal evolution, but in Lepidoptera an array of divergent Hox-related genes (Shx genes) has been reported between pb and zen. Here, we use genome sequencing of five lepidopteran species (Polygonia c-album, Pararge aegeria, Callimorpha dominula, Cameraria ohridella, Hepialus sylvina) plus a caddisfly outgroup (Glyphotaelius pellucidus) to trace the evolution of the lepidopteran Shx genes. We demonstrate that Shx genes originated by tandem duplication of zen early in the evolution of large clade Ditrysia; Shx are not found in a caddisfly and a member of the basally diverging Hepialidae (swift moths). Four distinct Shx genes were generated early in ditrysian evolution, and were stably retained in all descendent Lepidoptera except the silkmoth which has additional duplications. Despite extensive sequence divergence, molecular modelling indicates that all four Shx genes have the potential to encode stable homeodomains. The four Shx genes have distinct spatiotemporal expression patterns in early development of the Speckled Wood butterfly (Pararge aegeria), with ShxC demarcating the future sites of extraembryonic tissue formation via strikingly localised maternal RNA in the oocyte. All four genes are also expressed in presumptive serosal cells, prior to the onset of zen expression. Lepidopteran Shx genes represent an unusual example of Hox cluster expansion and integration of novel genes into ancient developmental regulatory networks. PMID:25340822

Reduced Abd-B Hox function during kidney development results in lineage infidelity.

PubMed

Magella, Bliss; Mahoney, Robert; Adam, Mike; Potter, S Steven

2018-06-15

Hox genes can function as key drivers of segment identity, with Hox mutations in Drosophila often resulting in dramatic homeotic transformations. In addition, however, they can serve other essential functions. In mammals, the study of Hox gene roles in development is complicated by the presence of four Hox clusters with a total of 39 genes showing extensive functional overlap. In this study, in order to better understand shared core Hox functions, we examined kidney development in mice with frameshift mutations of multiple Abd-B type Hox genes. The resulting phenotypes included dramatically reduced branching morphogenesis of the ureteric bud, premature depletion of nephron progenitors and abnormal development of the stromal compartment. Most unexpected, however, we also observed a cellular level lineage infidelity in nephron segments. Scattered cells within the proximal tubules, for example, expressed genes normally expressed only in collecting ducts. Multiple combinations of inappropriate nephron segment specific marker expression were found. In some cases, cells within a tubule showed incorrect identity, while in other cases cells showed ambiguous character, with simultaneous expression of genes associated with more than one nephron segment. These results give evidence that Hox genes have an overlapping core function at the cellular level in driving and/or maintaining correct differentiation decisions. Copyright © 2018 Elsevier Inc. All rights reserved.

Catalytic properties of the isolated diaphorase fragment of the NAD-reducing [NiFe]-hydrogenase from Ralstonia eutropha.

PubMed

Lauterbach, Lars; Idris, Zulkifli; Vincent, Kylie A; Lenz, Oliver

2011-01-01

The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha H16 catalyzes the H₂-driven reduction of NAD+, as well as reverse electron transfer from NADH to H+, in the presence of O₂. It comprises six subunits, HoxHYFUI₂, and incorporates a [NiFe] H+/H₂ cycling catalytic centre, two non-covalently bound flavin mononucleotide (FMN) groups and an iron-sulfur cluster relay for electron transfer. This study provides the first characterization of the diaphorase sub-complex made up of HoxF and HoxU. Sequence comparisons with the closely related peripheral subunits of Complex I in combination with UV/Vis spectroscopy and the quantification of the metal and FMN content revealed that HoxFU accommodates a [2Fe2S] cluster, FMN and a series of [4Fe4S] clusters. Protein film electrochemistry (PFE) experiments show clear electrocatalytic activity for both NAD+ reduction and NADH oxidation with minimal overpotential relative to the potential of the NAD+/NADH couple. Michaelis-Menten constants of 56 µM and 197 µM were determined for NADH and NAD+, respectively. Catalysis in both directions is product inhibited with K(I) values of around 0.2 mM. In PFE experiments, the electrocatalytic current was unaffected by O₂, however in aerobic solution assays, a moderate superoxide production rate of 54 nmol per mg of protein was observed, meaning that the formation of reactive oxygen species (ROS) observed for the native SH can be attributed mainly to HoxFU. The results are discussed in terms of their implications for aerobic functioning of the SH and possible control mechanism for the direction of catalysis.

Biotechnology Symposium

DTIC Science & Technology

1990-10-01

entire phylum of animals, the Echinodermata (seastars, sea urchins , sea cucumbers, sea lillies, and brittle stars), the voluntary control of mechanical...these materials can vary from stretchy to rigid, they are called catch connective tissues [10]. At the base of each rigid calcitic spine of a sea urchin ...ligament of sea urchins there is a ganglion (cluster of nerve cells) attached to each ligament. Axons extend from nerve cell bodies in the ganglion 898

The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes

PubMed Central

Rodríguez-Carballo, Eddie; Lopez-Delisle, Lucille; Zhan, Ye; Fabre, Pierre J.; Beccari, Leonardo; El-Idrissi, Imane; Huynh, Thi Hanh Nguyen; Ozadam, Hakan; Dekker, Job; Duboule, Denis

2017-01-01

The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos, we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region were removed. The resulting progressive release in boundary effect triggered inter-TAD contacts, favored by the activity of the newly accessed enhancers. However, the boundary was highly resilient, and only a 400-kb deletion, including the whole-gene cluster, was eventually able to merge the neighboring TADs into a single structure. In this unified TAD, both proximal and distal limb enhancers nevertheless continued to work independently over a targeted transgenic reporter construct. We propose that the whole HoxD cluster is a dynamic TAD border and that the exact boundary position varies depending on both the transcriptional status and the developmental context. PMID:29273679

Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan.

PubMed

Guerreiro, Isabel; Gitto, Sandra; Novoa, Ana; Codourey, Julien; Nguyen Huynh, Thi Hanh; Gonzalez, Federico; Milinkovitch, Michel C; Mallo, Moises; Duboule, Denis

2016-08-01

Within land vertebrate species, snakes display extreme variations in their body plan, characterized by the absence of limbs and an elongated morphology. Such a particular interpretation of the basic vertebrate body architecture has often been associated with changes in the function or regulation of Hox genes. Here, we use an interspecies comparative approach to investigate different regulatory aspects at the snake HoxD locus. We report that, unlike in other vertebrates, snake mesoderm-specific enhancers are mostly located within the HoxD cluster itself rather than outside. In addition, despite both the absence of limbs and an altered Hoxd gene regulation in external genitalia, the limb-associated bimodal HoxD chromatin structure is maintained at the snake locus. Finally, we show that snake and mouse orthologous enhancer sequences can display distinct expression specificities. These results show that vertebrate morphological evolution likely involved extensive reorganisation at Hox loci, yet within a generally conserved regulatory framework.

A functionally conserved Polycomb response element from mouse HoxD complex responds to heterochromatin factors

NASA Astrophysics Data System (ADS)

Vasanthi, Dasari; Nagabhushan, A.; Matharu, Navneet Kaur; Mishra, Rakesh K.

2013-10-01

Anterior-posterior body axis in all bilaterians is determined by the Hox gene clusters that are activated in a spatio-temporal order. This expression pattern of Hox genes is established and maintained by regulatory mechanisms that involve higher order chromatin structure and Polycomb group (PcG) and trithorax group (trxG) proteins. We identified earlier a Polycomb response element (PRE) in the mouse HoxD complex that is functionally conserved in flies. We analyzed the molecular and genetic interactions of mouse PRE using Drosophila melanogaster and vertebrate cell culture as the model systems. We demonstrate that the repressive activity of this PRE depends on PcG/trxG genes as well as the heterochromatin components. Our findings indicate that a wide range of factors interact with the HoxD PRE that can contribute to establishing the expression pattern of homeotic genes in the complex early during development and maintain that pattern at subsequent stages.

Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan

PubMed Central

Guerreiro, Isabel; Gitto, Sandra; Novoa, Ana; Codourey, Julien; Nguyen Huynh, Thi Hanh; Gonzalez, Federico; Milinkovitch, Michel C; Mallo, Moises; Duboule, Denis

2016-01-01

Within land vertebrate species, snakes display extreme variations in their body plan, characterized by the absence of limbs and an elongated morphology. Such a particular interpretation of the basic vertebrate body architecture has often been associated with changes in the function or regulation of Hox genes. Here, we use an interspecies comparative approach to investigate different regulatory aspects at the snake HoxD locus. We report that, unlike in other vertebrates, snake mesoderm-specific enhancers are mostly located within the HoxD cluster itself rather than outside. In addition, despite both the absence of limbs and an altered Hoxd gene regulation in external genitalia, the limb-associated bimodal HoxD chromatin structure is maintained at the snake locus. Finally, we show that snake and mouse orthologous enhancer sequences can display distinct expression specificities. These results show that vertebrate morphological evolution likely involved extensive reorganisation at Hox loci, yet within a generally conserved regulatory framework. DOI: http://dx.doi.org/10.7554/eLife.16087.001 PMID:27476854

Epigenetic repression of HOXB cluster in oral cancer cell lines.

PubMed

Xavier, Flávia Caló Aquino; Destro, Maria Fernanda de Souza Setubal; Duarte, Carina Magalhães Esteves; Nunes, Fabio Daumas

2014-08-01

Aberrant DNA methylation is a fundamental transcriptional control mechanism in carcinogenesis. The expression of homeobox genes is usually controlled by an epigenetic mechanism, such as the methylation of CpG islands in the promoter region. The aim of this study was to describe the differential methylation pattern of HOX genes in oral squamous cell carcinoma (OSCC) cell lines and transcript status in a group of hypermethylated and hypomethylated genes. Quantitative analysis of DNA methylation was performed on two OSCC cell lines (SCC4 and SCC9) using a method denominated Human Homeobox Genes EpiTect Methyl qPCR Arrays, which allowed fast, precise methylation detection of 24 HOX specific genes without bisulfite conversion. Methylation greater than 50% was detected in HOXA11, HOXA6, HOXA7, HOXA9, HOXB1, HOXB2, HOXB3, HOXB4, HOXB5, HOXB6, HOXC8 and HOXD10. Both cell lines demonstrated similar hypermethylation status for eight HOX genes. A similar pattern of promoter hypermethylation and hypomethylation was demonstrated for the HOXB cluster and HOXA cluster, respectively. Moreover, the hypermethylation profile of the HOXB cluster, especially HOXB4, was correlated with decreased transcript expression, which was restored following treatment with 5-aza-2'-deoxycytidine. The homeobox methylation profile in OSCC cell lines is consistent with an epigenetic biomarker. Copyright © 2014 Elsevier Ltd. All rights reserved.

The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes.

PubMed

Rodríguez-Carballo, Eddie; Lopez-Delisle, Lucille; Zhan, Ye; Fabre, Pierre J; Beccari, Leonardo; El-Idrissi, Imane; Huynh, Thi Hanh Nguyen; Ozadam, Hakan; Dekker, Job; Duboule, Denis

2017-11-15

The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos , we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region were removed. The resulting progressive release in boundary effect triggered inter-TAD contacts, favored by the activity of the newly accessed enhancers. However, the boundary was highly resilient, and only a 400-kb deletion, including the whole-gene cluster, was eventually able to merge the neighboring TADs into a single structure. In this unified TAD, both proximal and distal limb enhancers nevertheless continued to work independently over a targeted transgenic reporter construct. We propose that the whole HoxD cluster is a dynamic TAD border and that the exact boundary position varies depending on both the transcriptional status and the developmental context. © 2017 Rodríguez-Carballo et al.; Published by Cold Spring Harbor Laboratory Press.

Genetic Interactions Between Shox2 and Hox Genes During the Regional Growth and Development of the Mouse Limb

PubMed Central

Neufeld, Stanley J.; Wang, Fan; Cobb, John

2014-01-01

The growth and development of the vertebrate limb relies on homeobox genes of the Hox and Shox families, with their independent mutation often giving dose-dependent effects. Here we investigate whether Shox2 and Hox genes function together during mouse limb development by modulating their relative dosage and examining the limb for nonadditive effects on growth. Using double mRNA fluorescence in situ hybridization (FISH) in single embryos, we first show that Shox2 and Hox genes have associated spatial expression dynamics, with Shox2 expression restricted to the proximal limb along with Hoxd9 and Hoxa11 expression, juxtaposing the distal expression of Hoxa13 and Hoxd13. By generating mice with all possible dosage combinations of mutant Shox2 alleles and HoxA/D cluster deletions, we then show that their coordinated proximal limb expression is critical to generate normally proportioned limb segments. These epistatic interactions tune limb length, where Shox2 underexpression enhances, and Shox2 overexpression suppresses, Hox-mutant phenotypes. Disruption of either Shox2 or Hox genes leads to a similar reduction in Runx2 expression in the developing humerus, suggesting their concerted action drives cartilage maturation during normal development. While we furthermore provide evidence that Hox gene function influences Shox2 expression, this regulation is limited in extent and is unlikely on its own to be a major explanation for their genetic interaction. Given the similar effect of human SHOX mutations on regional limb growth, Shox and Hox genes may generally function as genetic interaction partners during the growth and development of the proximal vertebrate limb. PMID:25217052

Genetic interactions between Shox2 and Hox genes during the regional growth and development of the mouse limb.

PubMed

Neufeld, Stanley J; Wang, Fan; Cobb, John

2014-11-01

The growth and development of the vertebrate limb relies on homeobox genes of the Hox and Shox families, with their independent mutation often giving dose-dependent effects. Here we investigate whether Shox2 and Hox genes function together during mouse limb development by modulating their relative dosage and examining the limb for nonadditive effects on growth. Using double mRNA fluorescence in situ hybridization (FISH) in single embryos, we first show that Shox2 and Hox genes have associated spatial expression dynamics, with Shox2 expression restricted to the proximal limb along with Hoxd9 and Hoxa11 expression, juxtaposing the distal expression of Hoxa13 and Hoxd13. By generating mice with all possible dosage combinations of mutant Shox2 alleles and HoxA/D cluster deletions, we then show that their coordinated proximal limb expression is critical to generate normally proportioned limb segments. These epistatic interactions tune limb length, where Shox2 underexpression enhances, and Shox2 overexpression suppresses, Hox-mutant phenotypes. Disruption of either Shox2 or Hox genes leads to a similar reduction in Runx2 expression in the developing humerus, suggesting their concerted action drives cartilage maturation during normal development. While we furthermore provide evidence that Hox gene function influences Shox2 expression, this regulation is limited in extent and is unlikely on its own to be a major explanation for their genetic interaction. Given the similar effect of human SHOX mutations on regional limb growth, Shox and Hox genes may generally function as genetic interaction partners during the growth and development of the proximal vertebrate limb. Copyright © 2014 by the Genetics Society of America.

Evolutionary changes of Hox genes and relevant regulatory factors provide novel insights into mammalian morphological modifications.

PubMed

Li, Kui; Sun, Xiaohui; Chen, Meixiu; Sun, Yingying; Tian, Ran; Wang, Zhengfei; Xu, Shixia; Yang, Guang

2018-01-01

The diversity of body plans of mammals accelerates the innovation of lifestyles and the extensive adaptation to different habitats, including terrestrial, aerial and aquatic habitats. However, the genetic basis of those phenotypic modifications, which have occurred during mammalian evolution, remains poorly explored. In the present study, we synthetically surveyed the evolutionary pattern of Hox clusters that played a powerful role in the morphogenesis along the head-tail axis of animal embryos and the main regulatory factors (Mll, Bmi1 and E2f6) that control the expression of Hox genes. A deflected density of repetitive elements and lineage-specific radical mutations of Mll have been determined in marine mammals with morphological changes, suggesting that evolutionary changes may alter Hox gene expression in these lineages, leading to the morphological modification of these lineages. Although no positive selection was detected at certain ancestor nodes of lineages, the increased ω values of Hox genes implied the relaxation of functional constraints of these genes during the mammalian evolutionary process. More importantly, 49 positively-selected sites were identified in mammalian lineages with phenotypic modifications, indicating adaptive evolution acting on Hox genes and regulatory factors. In addition, 3 parallel amino acid substitutions in some Hox genes were examined in marine mammals, which might be responsible for their streamlined body. © 2017 The Authors. Integrative Zoology published by International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

The zipper effect: Why different positions along the chromosome suffer different selection pressures

NASA Astrophysics Data System (ADS)

de Oliveira, P. M. C.; Moss de Oliveira, S.

2011-02-01

Variability within diploid sexual populations comes from two ingredients: mutations and recombination (or crossing-over). On average, the first introduces genetic defects in offspring genomes, while the second is a mechanism which tends to eliminate them, continuously “cleaning” the population genetic pool from harmful mutations along the generations. Here, we propose that loci near the chromosome tips are more effectively cleaned by the recombination mechanism than loci near the chromosome centre. This result implies that clusters of neighbouring, orchestrated-functioning genes, supposed to be more robust against the effects of genetic mutations, are more likely found near the chromosome centres, while isolated genes are more likely found near the tips. We confirm the tip-centre asymmetry through a simple computer agent-based model. In order to test this effect in reality, we also analyse as an example the particular case of HOX genes distributed along the 24 human chromosomes and verify that indeed, most HOX genes belong to such clustered networks located near the chromosome centres. Accordingly, isolated HOX genes are located closer to the tips.

HOX gene expression in phenotypic and genotypic subgroups and low HOXA gene expression as an adverse prognostic factor in pediatric ALL.

PubMed

Starkova, Julia; Zamostna, Blanka; Mejstrikova, Ester; Krejci, Roman; Drabkin, Harry A; Trka, Jan

2010-12-01

HOX genes play an important role in both normal lymphopoiesis and leukemogenesis. However, HOX expression patterns in leukemia cells compared to normal lymphoid progenitors have not been systematically studied in acute lymphoblastic leukemia (ALL) subtypes. The RNA expression levels of HOXA, HOXB, and CDX1/2 genes were analyzed by qRT-PCR in a cohort of 61 diagnostic pediatric ALL samples and FACS-sorted subpopulations of normal lymphoid progenitors. The RNA expression of HOXA7-10, HOXA13, and HOXB2-4 genes was exclusively detected in leukemic cells and immature progenitors. The RNA expression of HOXB6 and CDX2 genes was exclusively detected in leukemic cells but not in B-lineage cells at any of the studied developmental stages. HOXA3-4, HOXA7, and HOXB3-4 genes were differentially expressed between BCP-ALL and T-ALL subgroups, and among genotypically defined MLL/AF4, TEL/AML1, BCR/ABL, hyperdiploid and normal karyotype subgroups. However, this differential expression did not define specific clusters in hierarchical cluster analysis. HOXA7 gene was low expressed at the RNA level in patients with hyperdiploid leukemia, whereas HOXB7 and CDX2 genes were low expressed in TEL/AML1-positive and BCR/ABL-positive cases, respectively. In contrast to previous findings in acute myeloid leukemia, high HOXA RNA expression was associated with an excellent prognosis in Cox's regression model (P = 0.03). In MLL/AF4-positive ALL, lower HOXA RNA expression correlated with the methylation status of their promoters. HOX gene RNA expression cannot discriminate leukemia subgroups or relative maturity of leukemic cells. However, HOXA RNA expression correlates with prognosis, and particular HOX genes are expressed in specific genotypically characterized subgroups.

Short germ insects utilize both the ancestral and derived mode of Polycomb group-mediated epigenetic silencing of Hox genes

PubMed Central

Matsuoka, Yuji; Bando, Tetsuya; Watanabe, Takahito; Ishimaru, Yoshiyasu; Noji, Sumihare; Popadić, Aleksandar; Mito, Taro

2015-01-01

In insect species that undergo long germ segmentation, such as Drosophila, all segments are specified simultaneously at the early blastoderm stage. As embryogenesis progresses, the expression boundaries of Hox genes are established by repression of gap genes, which is subsequently replaced by Polycomb group (PcG) silencing. At present, however, it is not known whether patterning occurs this way in a more ancestral (short germ) mode of embryogenesis, where segments are added gradually during posterior elongation. In this study, two members of the PcG family, Enhancer of zeste (E(z)) and Suppressor of zeste 12 (Su(z)12), were analyzed in the short germ cricket, Gryllus bimaculatus. Results suggest that although stepwise negative regulation by gap and PcG genes is present in anterior members of the Hox cluster, it does not account for regulation of two posterior Hox genes, abdominal-A (abd-A) and Abdominal-B (Abd-B). Instead, abd-A and Abd-B are predominantly regulated by PcG genes, which is the mode present in vertebrates. These findings suggest that an intriguing transition of the PcG-mediated silencing of Hox genes may have occurred during animal evolution. The ancestral bilaterian state may have resembled the current vertebrate mode of regulation, where PcG-mediated silencing of Hox genes occurs before their expression is initiated and is responsible for the establishment of individual expression domains. Then, during insect evolution, the repression by transcription factors may have been acquired in anterior Hox genes of short germ insects, while PcG silencing was maintained in posterior Hox genes. PMID:25948756

Hox genes and the parasitic flatworms: new opportunities, challenges and lessons from the free-living.

PubMed

Olson, P D

2008-03-01

Research into the roles played by Hox and related homeotic gene families in the diverse and complex developmental programmes exhibited by parasitic flatworms (Platyhelminthes) can hardly be said to have begun, and thus presents considerable opportunity for new research. Although featured in some of the earliest screens for homeotic genes outside Drosophila and mice, surveys in parasitic flatworms are few in number and almost nothing is yet known of where or when the genes are expressed during ontogeny. This contrasts sharply with a significant body of literature concerning Hox genes in free-living flatworms which have long served as models for the study of regeneration and the maintenance of omnipotent cell lines. Nevertheless, available information suggests that the complement of Hox genes and other classes of homeobox-containing genes in parasitic flatworms is typical of their free-living cousins and of other members of the Lophotrochozoa. Recent work on Schistosoma combined with information on Hox gene expression in planarians indicates that at least some disruption of the clustered genomic arrangement of the genes, as well as of the strict spatial and temporal colinear patterns of expression typical in other groups, may be characteristic of flatworms. However, available data on the genomic arrangement and expression of flatworm Hox genes is so limited at present that such generalities are highly tenuous. Moreover, a basic underlying pattern of colinearity is still observed in their spatial expression patterns making them suitable as cell or region-specific markers. I discuss a number of fundamental developmental questions and some of the challenges to addressing them in relation to each of the major parasitic lineages. In addition, I present newly characterized Hox genes from the model tapeworm Hymenolepis and analyze these by Bayesian inference together with >100 Hox and ParaHox homeodomains of flatworms and select lophotrochozoan taxa, providing a phylogenetic scaffold for their identification.

Stratospheric hydrogen peroxide (H2O2): Comparison between MIPAS observations and KASIMA model results with focus on the SPE 2003

NASA Astrophysics Data System (ADS)

Versick, S.

2009-04-01

H, OH and HO2 (collectively called HOx) are fast-reacting radicals in the middle atmosphere. These radicals are efficient catalysts for destroying ozone and play an important role in atmospheric chemistry. An important reservoir gas for HOx is Hydrogen Peroxide (H2O2). For all these important species at the moment only few measurements exist, e.g. in-situ measurements in the troposphere, balloon and rocket measurements, few HOx measurements by aircraft, and global satellite measurements of OH and HO2 by Aura/MLS since 2005. We present results for H2O2 for global day and night measurements with the MIPAS instrument on the ESA satellite ENVISAT. We find is a strong annual cycle with high values for H2O2 in polar summer consitent with the strong coupling to HOx chemistry. We investigated in more detail the Solar Proton Event (SPE) that occurred in October/November 2003. During SPEs, precipitation of energetic protons into the polar atmosphere produces ions in the middle atmosphere which form, partly via ion-cluster-reactions, odd hydrogen (HOx ) and odd nitrogen (NOx ). Increased levels of HOx and NOx, in turn, depletes the ozone in the polar stratosphere and mesosphere. We present the results of our retrievals of H2O2 for this event and compare the observations with results of the KASIMA model which has been upgraded to handle the ionization of the atmosphere due to the SPE and subsequent chemical reactions due to the NOx/HOx enhancements.

Divergent role of the Hox gene Antennapedia in spiders is responsible for the convergent evolution of abdominal limb repression.

PubMed

Khadjeh, Sara; Turetzek, Natascha; Pechmann, Matthias; Schwager, Evelyn E; Wimmer, Ernst A; Damen, Wim G M; Prpic, Nikola-Michael

2012-03-27

Evolution often results in morphologically similar solutions in different organisms, a phenomenon known as convergence. However, there is little knowledge of the processes that lead to convergence at the genetic level. The genes of the Hox cluster control morphology in animals. They may also be central to the convergence of morphological traits, but whether morphological similarities also require similar changes in Hox gene function is disputed. In arthropods, body subdivision into a region with locomotory appendages ("thorax") and a region with reduced appendages ("abdomen") has evolved convergently in several groups, e.g., spiders and insects. In insects, legs develop in the expression domain of the Hox gene Antennapedia (Antp), whereas the Hox genes Ultrabithorax (Ubx) and abdominal-A mediate leg repression in the abdomen. Here, we show that, unlike Antp in insects, the Antp gene in the spider Achaearanea tepidariorum represses legs in the first segment of the abdomen (opisthosoma), and that Antp and Ubx are redundant in the following segment. The down-regulation of Antp in A. tepidariorum leads to a striking 10-legged phenotype. We present evidence from ectopic expression of the spider Antp gene in Drosophila embryos and imaginal tissue that this unique function of Antp is not due to changes in the Antp protein, but likely due to divergent evolution of cofactors, Hox collaborators or target genes in spiders and flies. Our results illustrate an interesting example of convergent evolution of abdominal leg repression in arthropods by altering the role of distinct Hox genes at different levels of their action.

Large scale genomic reorganization of topological domains at the HoxD locus.

PubMed

Fabre, Pierre J; Leleu, Marion; Mormann, Benjamin H; Lopez-Delisle, Lucille; Noordermeer, Daan; Beccari, Leonardo; Duboule, Denis

2017-08-07

The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD genes in developing digits is controlled by regulatory elements located in the centromeric TAD (C-DOM) through long-range contacts. To assess the structure-function relationships underlying such interactions, we measured compaction levels and TAD discreteness using a combination of chromosome conformation capture (4C-seq) and DNA FISH. We assessed the robustness of the TAD architecture by using a series of genomic deletions and inversions that impact the integrity of this chromatin domain and that remodel long-range contacts. We report multi-partite associations between HoxD genes and up to three enhancers. We find that the loss of native chromatin topology leads to the remodeling of TAD structure following distinct parameters. Our results reveal that the recomposition of TAD architectures after large genomic re-arrangements is dependent on a boundary-selection mechanism in which CTCF mediates the gating of long-range contacts in combination with genomic distance and sequence specificity. Accordingly, the building of a recomposed TAD at this locus depends on distinct functional and constitutive parameters.

Characterization of three different clusters of 18S-26S ribosomal DNA genes in the sea urchin P. lividus: Genetic and epigenetic regulation synchronous to 5S rDNA.

PubMed

Bellavia, Daniele; Dimarco, Eufrosina; Caradonna, Fabio

2016-04-15

We previously reported the characterization 5S ribosomal DNA (rDNA) clusters in the common sea urchin Paracentrotus lividus and demonstrated the presence of DNA methylation-dependent silencing of embryo specific 5S rDNA cluster in adult tissue. In this work, we show genetic and epigenetic characterization of 18S-26S rDNA clusters in this specie. The results indicate the presence of three different 18S-26S rDNA clusters with different Non-Transcribed Spacer (NTS) regions that have different chromosomal localizations. Moreover, we show that the two largest clusters are hyper-methylated in the promoter-containing NTS regions in adult tissues, as in the 5S rDNA. These findings demonstrate an analogous epigenetic regulation in small and large rDNA clusters and support the logical synchronism in building ribosomes. In fact, all the ribosomal RNA genes must be synchronously and equally transcribed to perform their unique final product. Copyright © 2016 Elsevier B.V. All rights reserved.

Juxtaposed Polycomb complexes co-regulate vertebral identity.

PubMed

Kim, Se Young; Paylor, Suzanne W; Magnuson, Terry; Schumacher, Armin

2006-12-01

Best known as epigenetic repressors of developmental Hox gene transcription, Polycomb complexes alter chromatin structure by means of post-translational modification of histone tails. Depending on the cellular context, Polycomb complexes of diverse composition and function exhibit cooperative interaction or hierarchical interdependency at target loci. The present study interrogated the genetic, biochemical and molecular interaction of BMI1 and EED, pivotal constituents of heterologous Polycomb complexes, in the regulation of vertebral identity during mouse development. Despite a significant overlap in dosage-sensitive homeotic phenotypes and co-repression of a similar set of Hox genes, genetic analysis implicated eed and Bmi1 in parallel pathways, which converge at the level of Hox gene regulation. Whereas EED and BMI1 formed separate biochemical entities with EzH2 and Ring1B, respectively, in mid-gestation embryos, YY1 engaged in both Polycomb complexes. Strikingly, methylated lysine 27 of histone H3 (H3-K27), a mediator of Polycomb complex recruitment to target genes, stably associated with the EED complex during the maintenance phase of Hox gene repression. Juxtaposed EED and BMI1 complexes, along with YY1 and methylated H3-K27, were detected in upstream regulatory regions of Hoxc8 and Hoxa5. The combined data suggest a model wherein epigenetic and genetic elements cooperatively recruit and retain juxtaposed Polycomb complexes in mammalian Hox gene clusters toward co-regulation of vertebral identity.

Delayed transition to new cell fates during cellular reprogramming

PubMed Central

Cheng, Xianrui; Lyons, Deirdre C.; Socolar, Joshua E. S.; McClay, David R.

2014-01-01

In many embryos specification toward one cell fate can be diverted to a different cell fate through a reprogramming process. Understanding how that process works will reveal insights into the developmental regulatory logic that emerged from evolution. In the sea urchin embryo, cells at gastrulation were found to reprogram and replace missing cell types after surgical dissections of the embryo. Non-skeletogenic mesoderm (NSM) cells reprogrammed to replace missing skeletogenic mesoderm cells and animal caps reprogrammed to replace all endomesoderm. In both cases evidence of reprogramming onset was first observed at the early gastrula stage, even if the cells to be replaced were removed earlier in development. Once started however, the reprogramming occurred with compressed gene expression dynamics. The NSM did not require early contact with the skeletogenic cells to reprogram, but the animal cap cells gained the ability to reprogram early in gastrulation only after extended contact with the vegetal halves prior to that time. If the entire vegetal half was removed at early gastrula, the animal caps reprogrammed and replaced the vegetal half endomesoderm. If the animal caps carried morpholinos to either hox11/13b or foxA (endomesoderm specification genes), the isolated animal caps failed to reprogram. Together these data reveal that the emergence of a reprogramming capability occurs at early gastrulation in the sea urchin embryo and requires activation of early specification components of the target tissues. PMID:24780626

Systems-level analysis of cell-specific AQP2 gene expression in renal collecting duct.

PubMed

Yu, Ming-Jiun; Miller, R Lance; Uawithya, Panapat; Rinschen, Markus M; Khositseth, Sookkasem; Braucht, Drew W W; Chou, Chung-Lin; Pisitkun, Trairak; Nelson, Raoul D; Knepper, Mark A

2009-02-17

We used a systems biology-based approach to investigate the basis of cell-specific expression of the water channel aquaporin-2 (AQP2) in the renal collecting duct. Computational analysis of the 5'-flanking region of the AQP2 gene (Genomatix) revealed 2 conserved clusters of putative transcriptional regulator (TR) binding elements (BEs) centered at -513 bp (corresponding to the SF1, NFAT, and FKHD TR families) and -224 bp (corresponding to the AP2, SRF, CREB, GATA, and HOX TR families). Three other conserved motifs corresponded to the ETS, EBOX, and RXR TR families. To identify TRs that potentially bind to these BEs, we carried out mRNA profiling (Affymetrix) in mouse mpkCCDc14 collecting duct cells, revealing expression of 25 TRs that are also expressed in native inner medullary collecting duct. One showed a significant positive correlation with AQP2 mRNA abundance among mpkCCD subclones (Ets1), and 2 showed a significant negative correlation (Elf1 and an orphan nuclear receptor Nr1h2). Transcriptomic profiling in native proximal tubules (PT), medullary thick ascending limbs (MTAL), and IMCDs from kidney identified 14 TRs (including Ets1 and HoxD3) expressed in the IMCD but not PT or MTAL (candidate AQP2 enhancer roles), and 5 TRs (including HoxA5, HoxA9 and HoxA10) expressed in PT and MTAL but not in IMCD (candidate AQP2 repressor roles). In luciferase reporter assays, overexpression of 3 ETS family TRs transactivated the mouse proximal AQP2 promoter. The results implicate ETS family TRs in cell-specific expression of AQP2 and point to HOX, RXR, CREB and GATA family TRs as playing likely additional roles.

Geographic extent and variation of a coral reef trophic cascade.

PubMed

McClanahan, T R; Muthiga, N A

2016-07-01

Trophic cascades caused by a reduction in predators of sea urchins have been reported in Indian Ocean and Caribbean coral reefs. Previous studies have been constrained by their site-specific nature and limited spatial replication, which has produced site and species-specific understanding that can potentially preclude larger community-organization nuances and generalizations. In this study, we aimed to evaluate the extent and variability of the cascade community in response to fishing across ~23° of latitude and longitude in coral reefs in the southwestern Indian Ocean. The taxonomic composition of predators of sea urchins, the sea urchin community itself, and potential effects of changing grazer abundance on the calcifying benthic organisms were studied in 171 unique coral reef sites. We found that geography and habitat were less important than the predator-prey relationships. There were seven sea urchin community clusters that aligned with a gradient of declining fishable biomass and the abundance of a key predator, the orange-lined triggerfish (Balistapus undulatus). The orange-lined triggerfish dominated where sea urchin numbers and diversity were low but the relative abundance of wrasses and emperors increased where sea urchin numbers were high. Two-thirds of the study sites had high sea urchin biomass (>2,300 kg/ha) and could be dominated by four different sea urchin species, Echinothrix diadema, Diadema savignyi, D. setosum, and Echinometra mathaei, depending on the community of sea urchin predators, geographic location, and water depth. One-third of the sites had low sea urchin biomass and diversity and were typified by high fish biomass, predators of sea urchins, and herbivore abundance, representing lightly fished communities with generally higher cover of calcifying algae. Calcifying algal cover was associated with low urchin abundance where as noncalcifying fleshy algal cover was not clearly associated with herbivore abundance. Fishing of the orange-lined triggerfish, an uncommon, slow-growing by-catch species with little monetary value drives the cascade and other predators appear unable to replace its ecological role in the presence of fishing. This suggests that restrictions on the catch of this species could increase the calcification service of coral reefs on a broad scale. © 2016 by the Ecological Society of America.

HOXB homeobox gene expression in cervical carcinoma.

PubMed

López, R; Garrido, E; Piña, P; Hidalgo, A; Lazos, M; Ochoa, R; Salcedo, M

2006-01-01

The homeobox (HOX) genes are a family of transcription factors that bind to specific DNA sequences in target genes regulating gene expression. Thirty-nine HOX genes have been mapped in four conserved clusters: A, B, C, and D; they act as master genes regulating the identity of body segments along the anteroposterior axis of the embryo. The role played by HOX genes in adult cell differentiation is unclear to date, but growing evidence suggests that they may play an important role in the development of cancer. To study the role played by HOX genes in cervical cancer, in the present work, we analyzed the expression of HOXB genes and the localization of their transcripts in human cervical tissues. Reverse transcription-polymerase chain reaction analysis and nonradioactive RNA in situ hybridization were used to detect HOXB expression in 11 normal cervical tissues and 17 cervical carcinomas. It was determined that HOXB1, B3, B5, B6, B7, B8, and B9 genes are expressed in normal adult cervical epithelium and squamous cervical carcinomas. Interestingly, HOXB2, HOXB4, and HOXB13 gene expression was found only in tumor tissues. Our findings suggest that the new expression of HOXB2, HOXB4, and B13 genes is involved in cervical cancer.

DNA-methylation dependent regulation of embryo-specific 5S ribosomal DNA cluster transcription in adult tissues of sea urchin Paracentrotus lividus.

PubMed

Bellavia, Daniele; Dimarco, Eufrosina; Naselli, Flores; Caradonna, Fabio

2013-10-01

We have previously reported a molecular and cytogenetic characterization of three different 5S rDNA clusters in the sea urchin Paracentrotus lividus and recently, demonstrated the presence of high heterogeneity in functional 5S rRNA. In this paper, we show some important distinctive data on 5S rRNA transcription for this organism. Using single strand conformation polymorphism (SSCP) analysis, we demonstrate the existence of two classes of 5S rRNA, one which is embryo-specific and encoded by the smallest (700 bp) cluster and the other which is expressed at every stage and encoded by longer clusters (900 and 950 bp). We also demonstrate that the embryo-specific class of 5S rRNA is expressed in oocytes and embryonic stages and is silenced in adult tissue and that this phenomenon appears to be due exclusively to DNA methylation, as indicated by sensitivity to 5-azacytidine, unlike Xenopus where this mechanism is necessary but not sufficient to maintain the silenced status. © 2013 Elsevier Inc. All rights reserved.

Genome sequence of a diabetes-prone rodent reveals a mutation hotspot around the ParaHox gene cluster.

PubMed

Hargreaves, Adam D; Zhou, Long; Christensen, Josef; Marlétaz, Ferdinand; Liu, Shiping; Li, Fang; Jansen, Peter Gildsig; Spiga, Enrico; Hansen, Matilde Thye; Pedersen, Signe Vendelbo Horn; Biswas, Shameek; Serikawa, Kyle; Fox, Brian A; Taylor, William R; Mulley, John Frederick; Zhang, Guojie; Heller, R Scott; Holland, Peter W H

2017-07-18

The sand rat Psammomys obesus is a gerbil species native to deserts of North Africa and the Middle East, and is constrained in its ecology because high carbohydrate diets induce obesity and type II diabetes that, in extreme cases, can lead to pancreatic failure and death. We report the sequencing of the sand rat genome and discovery of an unusual, extensive, and mutationally biased GC-rich genomic domain. This highly divergent genomic region encompasses several functionally essential genes, and spans the ParaHox cluster which includes the insulin-regulating homeobox gene Pdx1. The sequence of sand rat Pdx1 has been grossly affected by GC-biased mutation, leading to the highest divergence observed for this gene across the Bilateria. In addition to genomic insights into restricted caloric intake in a desert species, the discovery of a localized chromosomal region subject to elevated mutation suggests that mutational heterogeneity within genomes could influence the course of evolution.

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

Primary structure and nuclear localization of a murine homeodomain protein.

PubMed Central

Kessel, M; Schulze, F; Fibi, M; Gruss, P

1987-01-01

The murine homeobox Hox 1.1 (m6) is the first of a cluster of six boxes on chromosome 6. Using probes and synthetic peptides derived from the Hox 1.1 sequence, we were able to isolate cDNAs and antibodies that allowed us to characterize the product of this homeobox-containing gene. From the open reading frame on the cDNA clone B21, a protein could be predicted, made up of 229 amino acids and having a calculated molecular weight of 25,740. A unique feature of this protein is that it has 15 glutamic acid residues as its carboxyl terminus, which gives it a very hydrophilic and acidic carboxyl terminal structure, most probably folding onto an alpha-helix. A second domain of six amino acids is present on the Hox 1.1 protein, which is conserved in other homeodomain proteins. Antibodies generated against synthetic peptides from the homeobox region were used in the immunoblotting procedure and revealed a major protein band of Mr 31,000 in extracts from 3T3 cells and F9 teratocarcinoma cells induced by retinoic acid and cAMP. The nuclear location of the protein was established by immunofluorescence. The presence of this protein in F9 cell nuclei is in faithful accordance with the kinetics established for the 2.4-kilobase Hox 1.1 transcript during differentiation into parietal endoderm cells. Images PMID:2885847

Substituting mouse transcription factor Pou4f2 with a sea urchin orthologue restores retinal ganglion cell development.

PubMed

Mao, Chai-An; Agca, Cavit; Mocko-Strand, Julie A; Wang, Jing; Ullrich-Lüter, Esther; Pan, Ping; Wang, Steven W; Arnone, Maria Ina; Frishman, Laura J; Klein, William H

2016-03-16

Pou domain transcription factor Pou4f2 is essential for the development of retinal ganglion cells (RGCs) in the vertebrate retina. A distant orthologue of Pou4f2 exists in the genome of the sea urchin (class Echinoidea) Strongylocentrotus purpuratus (SpPou4f1/2), yet the photosensory structure of sea urchins is strikingly different from that of the mammalian retina. Sea urchins have no obvious eyes, but have photoreceptors clustered around their tube feet disc. The mechanisms that are associated with the development and function of photoreception in sea urchins are largely unexplored. As an initial approach to better understand the sea urchin photosensory structure and relate it to the mammalian retina, we asked whether SpPou4f1/2 could support RGC development in the absence of Pou4f2. To answer this question, we replaced genomic Pou4f2 with an SpPou4f1/2 cDNA. In Pou4f2-null mice, retinas expressing SpPou4f1/2 were outwardly identical to those of wild-type mice. SpPou4f1/2 retinas exhibited dark-adapted electroretinogram scotopic threshold responses, indicating functionally active RGCs. During retinal development, SpPou4f1/2 activated RGC-specific genes and in S. purpuratus, SpPou4f2 was expressed in photoreceptor cells of tube feet in a pattern distinct from Opsin4 and Pax6. Our results suggest that SpPou4f1/2 and Pou4f2 share conserved components of a gene network for photosensory development and they maintain their conserved intrinsic functions despite vast morphological differences in mouse and sea urchin photosensory structures. © 2016 The Authors.

Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution.

PubMed

Marlétaz, Ferdinand; Maeso, Ignacio; Faas, Laura; Isaacs, Harry V; Holland, Peter W H

2015-08-01

The functional consequences of whole genome duplications in vertebrate evolution are not fully understood. It remains unclear, for instance, why paralogues were retained in some gene families but extensively lost in others. Cdx homeobox genes encode conserved transcription factors controlling posterior development across diverse bilaterians. These genes are part of the ParaHox gene cluster. Multiple Cdx copies were retained after genome duplication, raising questions about how functional divergence, overlap, and redundancy respectively contributed to their retention and evolutionary fate. We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xenopus tropicalis followed by RNA-seq. We found that one paralogue, Cdx4, has a much stronger effect on gene expression than the others, including a strong regulatory effect on FGF and Wnt genes. Functional annotation revealed distinct and overlapping roles and subtly different temporal windows of action for each gene. The data also reveal a colinear-like effect of Cdx genes on Hox genes, with repression of Hox paralogy groups 1 and 2, and activation increasing from Hox group 5 to 11. We also highlight cases in which duplicated genes regulate distinct paralogous targets revealing pathway elaboration after whole genome duplication. Despite shared core pathways, Cdx paralogues have acquired distinct regulatory roles during development. This implies that the degree of functional overlap between paralogues is relatively low and that gene expression pattern alone should be used with caution when investigating the functional evolution of duplicated genes. We therefore suggest that developmental programmes were extensively rewired after whole genome duplication in the early evolution of vertebrates.

Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers

PubMed Central

Finnerty, John R; Mazza, Maureen E; Jezewski, Peter A

2009-01-01

Background Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs. Results Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between MSX1 and MSX2 reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (Hmx, NK1, Emx) in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal), were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion. Conclusion Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies. PMID:19154605

Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers.

PubMed

Finnerty, John R; Mazza, Maureen E; Jezewski, Peter A

2009-01-20

Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs. Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between MSX1 and MSX2 reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (Hmx, NK1, Emx) in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal), were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion. Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies.

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.

Homeosis and beyond. What is the function of the Hox genes?

PubMed

Deutsch, Jean S

2010-01-01

What is the function of the Hox genes? At first glance, it is a curious question. Indeed, the answer seems so obvious that several authors have spoken of 'the Hox function' about some of the Hox genes, namely Hox3/zen and Hox6/ftz that seem to have lost it during the evolution of Arthropods. What these authors meant is that these genes have lost their 'homeotic' function. Indeed, 'homeotic' refers to a functional property that is so often associated with the Hox genes. However, the word 'Hox' should not be used to refer to a function, but to a group of genes. The above examples of Hox3/zen (see Schmitt-Ott's chapter, this book) and Hox6/ftz show that the homeotic function may be not so tightly linked to the Hox genes. Reversely, many genes, not belonging to the Hox group, do present a homeotic function. In the present chapter, I will first give a definition of the Hox genes. I will then ask what is the 'function' of a gene, examining its various meanings at different levels of biological organization. I will review and revisit the relation between the Hox genes and homeosis. I will suggest that their morphological homeotic function has been secondarily derived during the evolution of the Bilateria.

A pancreatic exocrine-like cell regulatory circuit operating in the upper stomach of the sea urchin Strongylocentrotus purpuratus larva.

PubMed

Perillo, Margherita; Wang, Yue Julia; Leach, Steven D; Arnone, Maria Ina

2016-05-26

Digestive cells are present in all metazoans and provide the energy necessary for the whole organism. Pancreatic exocrine cells are a unique vertebrate cell type involved in extracellular digestion of a wide range of nutrients. Although the organization and regulation of this cell type is intensively studied in vertebrates, its evolutionary history is still unknown. In order to understand which are the elements that define the pancreatic exocrine phenotype, we have analyzed the expression of genes that contribute to specification and function of this cell-type in an early branching deuterostome, the sea urchin Strongylocentrotus purpuratus. We defined the spatial and temporal expression of sea urchin orthologs of pancreatic exocrine genes and described a unique population of cells clustered in the upper stomach of the sea urchin embryo where exocrine markers are co-expressed. We used a combination of perturbation analysis, drug and feeding experiments and found that in these cells of the sea urchin embryo gene expression and gene regulatory interactions resemble that of bona fide pancreatic exocrine cells. We show that the sea urchin Ptf1a, a key transcriptional activator of digestive enzymes in pancreatic exocrine cells, can substitute for its vertebrate ortholog in activating downstream genes. Collectively, our study is the first to show with molecular tools that defining features of a vertebrate cell-type, the pancreatic exocrine cell, are shared by a non-vertebrate deuterostome. Our results indicate that the functional cell-type unit of the vertebrate pancreas may evolutionarily predate the emergence of the pancreas as a discrete organ. From an evolutionary perspective, these results encourage to further explore the homologs of other vertebrate cell-types in traditional or newly emerging deuterostome systems.

Genome editing in sea urchin embryos by using a CRISPR/Cas9 system.

PubMed

Lin, Che-Yi; Su, Yi-Hsien

2016-01-15

Sea urchin embryos are a useful model system for investigating early developmental processes and the underlying gene regulatory networks. Most functional studies using sea urchin embryos rely on antisense morpholino oligonucleotides to knockdown gene functions. However, major concerns related to this technique include off-target effects, variations in morpholino efficiency, and potential morpholino toxicity; furthermore, such problems are difficult to discern. Recent advances in genome editing technologies have introduced the prospect of not only generating sequence-specific knockouts, but also providing genome-engineering applications. Two genome editing tools, zinc-finger nuclease (ZFN) and transcription activator-like effector nucleases (TALENs), have been utilized in sea urchin embryos, but the resulting efficiencies are far from satisfactory. The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system serves as an easy and efficient method with which to edit the genomes of several established and emerging model organisms in the field of developmental biology. Here, we apply the CRISPR/Cas9 system to the sea urchin embryo. We designed six guide RNAs (gRNAs) against the well-studied nodal gene and discovered that five of the gRNAs induced the expected phenotype in 60-80% of the injected embryos. In addition, we developed a simple method for isolating genomic DNA from individual embryos, enabling phenotype to be precisely linked to genotype, and revealed that the mutation rates were 67-100% among the sequenced clones. Of the two potential off-target sites we examined, no off-target effects were observed. The detailed procedures described herein promise to accelerate the usage of CRISPR/Cas9 system for genome editing in sea urchin embryos. Copyright © 2015 Elsevier Inc. All rights reserved.

Expression pattern of vascular endothelial growth factor 2 during sea urchin development.

PubMed

Kipryushina, Yulia O; Yakovlev, Konstantin V; Kulakova, Milana A; Odintsova, Nelly A

2013-12-01

The VEGF family in the sea urchin is comprised of three members designated Vegf1 through Vegf3. In this study, we found a high level of similarity between the PDGF/VEGF domain of the predicted gene Sp-Vegf2 in the sea urchin Strongylocentrotus purpuratus and the same domain of a gene that we found in a closely related sea urchin, Strongylocentrotus intermedius. The sequence of the Si-Vegf2 cDNA was determined, and the expression of the Si-Vegf2 mRNA throughout early sea urchin development was studied by RT-PCR and in situ hybridization. Also we analyzed phylogenetic relationships of Si-Vegf2 and other members of the PDGF and VEGF families. We have found that the Si-Vegf2 present during the time span from the egg to the 4-arm pluteus stage. This mRNA is uniformly distributed in eggs, cleaving embryos and early blastulae. At the gastrula stage, the Si-Vegf2 transcripts are localized in the ventrolateral clusters of primary mesenchyme cells, and later, at the prism stage, they are detected in the forming apex. At the early pluteus stage, Si-Vegf2 mRNAs are found in two groups of mesenchyme cells in the scheitel region on the apical pole. We have determined that Si-Vegf2 is a mesenchyme-expressed factor but its developmental function is unknown. Copyright © 2013 Elsevier B.V. All rights reserved.

Hox proteins activate the IGFBP-1 promoter and suppress the function of hPR in human endometrial cells.

PubMed

Gao, Jiaguo; Mazella, James; Tseng, Linda

2002-11-01

Previous studies have shown that progestin activates the transcription of IGFBP-1 (insulin-like growth factor binding protein-1). Four regions in the IGFBP-1 promotor have been identified to enhance the transcription. Two of the regions, located at -73 to -65 bp and -319 to -311 bp formed identical DNA-protein complexes with the nuclear extracts of endometrial stromal/decidual cells. To identify the binding protein(s) in endometrial cells that interact with these two regions, we have used the TGTCAATTA repeats (-319 to -11 bp of the IGFBP-1 promoter) to screen the human decidual cDNA library by yeast one-hybrid system. We found that Hox A10, HoxA11, HoxB2, HoxB4, and HoxD11 interacted with the TGTCAATTA repeats in yeast cells. Among these hox genes, the full-length coding region of HoxA10, HoxA11, and HoxB4 were used for functional analysis in three types of endometrial cells, undifferentiated endometrial stromal cells, decidual cells (differentiated stromal cells) and endometrial adenocarcinoma cell line (HEC1-B). All these endometrial cells produce IGFBP-1. Transient transfection assay showed that HoxA10 expression vector increased the promoter activity (the IGFBP-1 proximal promoter containing TGC/TCAATTA and two functional PRE sites) in endometrial stromal cells and in HEC-1B cells, but not in decidual cells. HoxB4 enhanced the promoter activity only in decidual cells, while HoxA11 had no apparent effect in all three types of cells. To evaluate whether Hox proteins would interact with progesterone receptor (hPR), cells were transfected with the promoter construct, Hox and hPR expression vectors. hPR alone activated the IGFBP-1 promoter activity, but expression of Hox gene suppressed the activation. Hox proteins also suppressed the hPR enhanced promoter activities of MMTV (containing consensus-PRE sites) and glycodelin (GdA, containing Sp1 site which mediates the hPR function). These data showed that Hox genes selectively activate the transcription of the IGFBP-1 and GdA genes in different types of endometrial cells. Hox genes, however, suppress the hPR enhanced activities. In addition, we found that HoxB4 expression was induced by estrogen and progestin. Other investigators have shown that HoxA10 and 11 were stimulated by progestin. These findings show that Hox proteins are molecular mediators of the steroid hormones during endometrial cell development.

Nipbl and mediator cooperatively regulate gene expression to control limb development.

PubMed

Muto, Akihiko; Ikeda, Shingo; Lopez-Burks, Martha E; Kikuchi, Yutaka; Calof, Anne L; Lander, Arthur D; Schilling, Thomas F

2014-09-01

Haploinsufficiency for Nipbl, a cohesin loading protein, causes Cornelia de Lange Syndrome (CdLS), the most common "cohesinopathy". It has been proposed that the effects of Nipbl-haploinsufficiency result from disruption of long-range communication between DNA elements. Here we use zebrafish and mouse models of CdLS to examine how transcriptional changes caused by Nipbl deficiency give rise to limb defects, a common condition in individuals with CdLS. In the zebrafish pectoral fin (forelimb), knockdown of Nipbl expression led to size reductions and patterning defects that were preceded by dysregulated expression of key early limb development genes, including fgfs, shha, hand2 and multiple hox genes. In limb buds of Nipbl-haploinsufficient mice, transcriptome analysis revealed many similar gene expression changes, as well as altered expression of additional classes of genes that play roles in limb development. In both species, the pattern of dysregulation of hox-gene expression depended on genomic location within the Hox clusters. In view of studies suggesting that Nipbl colocalizes with the mediator complex, which facilitates enhancer-promoter communication, we also examined zebrafish deficient for the Med12 Mediator subunit, and found they resembled Nipbl-deficient fish in both morphology and gene expression. Moreover, combined partial reduction of both Nipbl and Med12 had a strongly synergistic effect, consistent with both molecules acting in a common pathway. In addition, three-dimensional fluorescent in situ hybridization revealed that Nipbl and Med12 are required to bring regions containing long-range enhancers into close proximity with the zebrafish hoxda cluster. These data demonstrate a crucial role for Nipbl in limb development, and support the view that its actions on multiple gene pathways result from its influence, together with Mediator, on regulation of long-range chromosomal interactions.

Long noncoding RNA HOTTIP cooperates with CCCTC-binding factor to coordinate HOXA gene expression.

PubMed

Wang, Feng; Tang, Zhongqiong; Shao, Honglian; Guo, Jun; Tan, Tao; Dong, Yang; Lin, Lianbing

2018-06-12

The spatiotemporal control of HOX gene expression is dependent on positional identity and often correlated to their genomic location within each loci. Maintenance of HOX expression patterns is under complex transcriptional and epigenetic regulation, which is not well understood. Here we demonstrate that HOTTIP, a lincRNA transcribed from the 5' edge of the HOXA locus, physically associates with the CCCTC-binding factor (CTCF) that serves as an insulator by organizing HOXA cluster into disjoint domains, to cooperatively maintain the chromatin modifications of HOXA genes and thus coordinate the transcriptional activation of distal HOXA genes in human foreskin fibroblasts. Our results reveal the functional connection of HOTTIP and CTCF, and shed light on lincRNAs in gene activation and CTCF mediated chromatin organization. Copyright © 2018 Elsevier Inc. All rights reserved.

HoxB2, HoxB4 and Alx4 genes are downregulated in the cadmium-induced omphalocele in the chick model.

PubMed

Doi, Takashi; Puri, Prem; Bannigan, John; Thompson, Jennifer

2010-10-01

In the chick embryo, administration of cadmium (Cd) induces omphalocele phenotype. HoxB2 and HoxB4, expressed in cell types that contribute to ventral body wall (VBW) formation, act together to mediate proper closure of the VBW, involving a key downstream transcription factor, Alx4. HoxB2 and HoxB4 knockout mice display VBW defects with specific downregulation of Alx4 gene expression, while homozygous Alx4 knockouts show omphalocele phenotype. Although the earliest histological changes in the Cd chick model occur commencing at 4H post treatment, the exact timing and molecular mechanism by which Cd acts is still unclear. We hypothesized that HoxB2, HoxB4 and Alx4 genes are downregulated during the critical timing of very early embryogenesis in the Cd-induced omphalocele chick model. After 60H incubation, chick embryos were harvested at 1H, 4H and 8H after treatment with saline or Cd and divided into controls and Cd group (n = 24 for each group). RT-PCR was performed to investigate the gene expression of HoxB2, HoxB4 and Alx4 and statistically analyzed (significance was accepted at p < 0.05). Immunohistochemical staining was also performed to evaluate the protein expression/distribution of HoxB2, HoxB4 and Alx4 in the chick embryo. The expression levels of HoxB2, HoxB4 and Alx4 gene at 4H were significantly downregulated in the Cd group as compared to controls, whereas there were no significant differences at the other time points. Immunoreactivity of HoxB2, HoxB4 and Alx4 at 4H is also markedly decreased in the ectoderm and the dermomyotome in the Cd chick model as compared to controls. Downregulation of HoxB2, HoxB4 and Alx4 expression during the narrow window of early embryogenesis may cause omphalocele in the Cd chick model by interfering with molecular signaling required for proper VBW formation. Furthermore, these results support the concept that HoxB2, HoxB4 and Alx4 genes work together to mediate proper VBW formation.

Evolution of Hox-like genes in Cnidaria: Study of Hydra Hox repertoire reveals tailor-made Hox-code for Cnidarians.

PubMed

Reddy, Puli Chandramouli; Unni, Manu K; Gungi, Akhila; Agarwal, Pallavi; Galande, Sanjeev

2015-11-01

Hox and ParaHox genes play decisive roles in patterning the anterior-posterior body axis in Bilateria. Evolutionary origin of Hox genes and primary body axis predate the divergence of Bilateria and Cnidaria. However, function of Cnidarian Hox-like genes and their regulation in axis determination is obscure due to studies limited to a few representative model systems. Present investigation is conducted using Hydra, a Hydrozoan member of phylum Cnidaria, to gain insights into the roles of Cnidarian Hox-like genes in primary axis formation. Here, we report identification of six Hox-like genes from our in-house transcriptome data. Phylogenetic analysis of these genes shows bilaterian counterparts of Hox1, Gsx and Mox. Additionally, we report CnoxB_HVUL, CnoxC2_HVUL and CnoxC3_HVUL belonging to two Cnidarian specific groups. In situ hybridization analysis of Hydra homologues provided important clues about their possible roles in pattern formation of polyps and bud development. Specifically, Hox1_HVUL is regulated by Wnt signaling and plays critical role in head formation. Collating information about expression patterns of different Hox-like genes from previous reports and this study reveals no conformity within Cnidaria. Indicating that unlike in Bilateria, there is no consolidated Hox-code determining primary body axis in Cnidaria. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Evolution of Antp-class genes and differential expression of Hydra Hox/paraHox genes in anterior patterning

PubMed Central

Gauchat, Dominique; Mazet, Françoise; Berney, Cédric; Schummer, Michèl; Kreger, Sylvia; Pawlowski, Jan; Galliot, Brigitte

2000-01-01

The conservation of developmental functions exerted by Antp-class homeoproteins in protostomes and deuterostomes suggested that homologs with related functions are present in diploblastic animals. Our phylogenetic analyses showed that Antp-class homeodomains belong either to non-Hox or to Hox/paraHox families. Among the 13 non-Hox families, 9 have diploblastic homologs, Msx, Emx, Barx, Evx, Tlx, NK-2, and Prh/Hex, Not, and Dlx, reported here. Among the Hox/paraHox, poriferan sequences were not found, and the cnidarian sequences formed at least five distinct cnox families. Two are significantly related to the paraHox Gsx (cnox-2) and the mox (cnox-5) sequences, whereas three display some relatedness to the Hox paralog groups 1 (cnox-1), 9/10 (cnox-3) and the paraHox cdx (cnox-4). Intermediate Hox/paraHox genes (PG 3 to 8 and lox) did not have clear cnidarian counterparts. In Hydra, cnox-1, cnox-2, and cnox-3 were not found chromosomally linked within a 150-kb range and displayed specific expression patterns in the adult head. During regeneration, cnox-1 was expressed as an early gene whatever the polarity, whereas cnox-2 was up-regulated later during head but not foot regeneration. Finally, cnox-3 expression was reestablished in the adult head once it was fully formed. These results suggest that the Hydra genes related to anterior Hox/paraHox genes are involved at different stages of apical differentiation. However, the positional information defining the oral/aboral axis in Hydra cannot be correlated strictly to that characterizing the anterior–posterior axis in vertebrates or arthropods. PMID:10781050

Hox gene control of segment-specific bristle patterns in Drosophila

PubMed Central

Rozowski, Marion; Akam, Michael

2002-01-01

Hox genes specify the different morphologies of segments along the anteroposterior axis of animals. How they control complex segment morphologies is not well understood. We have studied how the Hox gene Ultrabithorax (Ubx) controls specific differences between the bristle patterns of the second and third thoracic segments (T2 and T3) of Drosophila melanogaster. We find that Ubx blocks the development of two particular bristles on T3 at different points in sensory organ development. For the apical bristle, a precursor is singled out and undergoes a first division in both the second and third legs, but in the third leg further differentiation of the second-order precursors is blocked. For the posterior sternopleural bristle, development on T3 ceases after proneural cluster initiation. Analysis of the temporal requirement for Ubx shows that in both cases Ubx function is required shortly before bristle development is blocked. We suggest that interactions between Ubx and the bristle patterning hierarchy have evolved independently on many occasions, affecting different molecular steps. The effects of Ubx on bristle development are highly dependent on the context of other patterning information. Suppression of bristle development or changes in bristle morphology in response to endogenous and ectopic Ubx expression are limited to bristles at specific locations. PMID:12000797

Hox Proteins Display a Common and Ancestral Ability to Diversify Their Interaction Mode with the PBC Class Cofactors

PubMed Central

Hudry, Bruno; Remacle, Sophie; Delfini, Marie-Claire; Rezsohazy, René; Graba, Yacine; Merabet, Samir

2012-01-01

Hox transcription factors control a number of developmental processes with the help of the PBC class proteins. In vitro analyses have established that the formation of Hox/PBC complexes relies on a short conserved Hox protein motif called the hexapeptide (HX). This paradigm is at the basis of the vast majority of experimental approaches dedicated to the study of Hox protein function. Here we questioned the unique and general use of the HX for PBC recruitment by using the Bimolecular Fluorescence Complementation (BiFC) assay. This method allows analyzing Hox-PBC interactions in vivo and at a genome-wide scale. We found that the HX is dispensable for PBC recruitment in the majority of investigated Drosophila and mouse Hox proteins. We showed that HX-independent interaction modes are uncovered by the presence of Meis class cofactors, a property which was also observed with Hox proteins of the cnidarian sea anemone Nematostella vectensis. Finally, we revealed that paralog-specific motifs convey major PBC-recruiting functions in Drosophila Hox proteins. Altogether, our results highlight that flexibility in Hox-PBC interactions is an ancestral and evolutionary conserved character, which has strong implications for the understanding of Hox protein functions during normal development and pathologic processes. PMID:22745600

Induction of HoxB Transcription by Retinoic Acid Requires Actin Polymerization

PubMed Central

Ferrai, Carmelo; Naum-Onganía, Gabriela; Longobardi, Elena; Palazzolo, Martina; Disanza, Andrea; Diaz, Victor M.; Crippa, Massimo P.; Scita, Giorgio

2009-01-01

We have analyzed the role of actin polymerization in retinoic acid (RA)-induced HoxB transcription, which is mediated by the HoxB regulator Prep1. RA induction of the HoxB genes can be prevented by the inhibition of actin polymerization. Importantly, inhibition of actin polymerization specifically affects the transcription of inducible Hox genes, but not that of their transcriptional regulators, the RARs, nor of constitutively expressed, nor of actively transcribed Hox genes. RA treatment induces the recruitment to the HoxB2 gene enhancer of a complex composed of “elongating” RNAPII, Prep1, β-actin, and N-WASP as well as the accessory splicing components p54Nrb and PSF. We show that inhibition of actin polymerization prevents such recruitment. We conclude that inducible Hox genes are selectively sensitive to the inhibition of actin polymerization and that actin polymerization is required for the assembly of a transcription complex on the regulatory region of the Hox genes. PMID:19477923

Induction of HoxB transcription by retinoic acid requires actin polymerization.

PubMed

Ferrai, Carmelo; Naum-Onganía, Gabriela; Longobardi, Elena; Palazzolo, Martina; Disanza, Andrea; Diaz, Victor M; Crippa, Massimo P; Scita, Giorgio; Blasi, Francesco

2009-08-01

We have analyzed the role of actin polymerization in retinoic acid (RA)-induced HoxB transcription, which is mediated by the HoxB regulator Prep1. RA induction of the HoxB genes can be prevented by the inhibition of actin polymerization. Importantly, inhibition of actin polymerization specifically affects the transcription of inducible Hox genes, but not that of their transcriptional regulators, the RARs, nor of constitutively expressed, nor of actively transcribed Hox genes. RA treatment induces the recruitment to the HoxB2 gene enhancer of a complex composed of "elongating" RNAPII, Prep1, beta-actin, and N-WASP as well as the accessory splicing components p54Nrb and PSF. We show that inhibition of actin polymerization prevents such recruitment. We conclude that inducible Hox genes are selectively sensitive to the inhibition of actin polymerization and that actin polymerization is required for the assembly of a transcription complex on the regulatory region of the Hox genes.

Comparing anterior and posterior Hox complex formation reveals guidelines for predicting cis-regulatory elements

PubMed Central

Uhl, Juli D.; Cook, Tiffany A.; Gebelein, Brian

2010-01-01

Hox transcription factors specify numerous cell fates along the anterior-posterior axis by regulating the expression of downstream target genes. While expression analysis has uncovered large numbers of de-regulated genes in cells with altered Hox activity, determining which are direct versus indirect targets has remained a significant challenge. Here, we characterize the DNA binding activity of Hox transcription factor complexes on eight experimentally verified cis-regulatory elements. Hox factors regulate the activity of each element by forming protein complexes with two cofactor proteins, Extradenticle (Exd) and Homothorax (Hth). Using comparative DNA binding assays, we found that a number of flexible arrangements of Hox, Exd, and Hth binding sites mediate cooperative transcription factor complexes. Moreover, analysis of a Distal-less regulatory element (DMXR) that is repressed by abdominal Hox factors revealed that suboptimal binding sites can be combined to form high affinity transcription complexes. Lastly, we determined that the anterior Hox factors are more dependent upon Exd and Hth for complex formation than posterior Hox factors. Based upon these findings, we suggest a general set of guidelines to serve as a basis for designing bioinformatics algorithms aimed at identifying Hox regulatory elements using the wealth of recently sequenced genomes. PMID:20398649

Secreted HoxA3 Promotes Epidermal Proliferation and Angiogenesis in Genetically Modified Three-Dimensional Composite Skin Constructs

PubMed Central

Kuo, Jennifer H.; Cuevas, Ileana; Chen, Amy; Dunn, Ashley; Kuri, Mauricio; Boudreau, Nancy

2014-01-01

Objective: Homeobox (HOX) transcription factors coordinate gene expression in wound repair and angiogenesis. Previous studies have shown that gene transfer of HoxA3 to wounds of diabetic mice accelerates wound healing, increasing angiogenesis and keratinocyte migration. In this study, we examined whether HoxA3 can also improve angiogenesis, epidermal integrity, and viability of composite skin grafts. Approach: To determine the effects of HoxA3 on composite skin grafts, we constructed bilayered composite grafts incorporating fibroblasts engineered to constitutively secrete HoxA3. We then transplanted these composite grafts in vivo. Results: The composite grafts produced a stratified epidermal layer after seventeen days in culture and following transplantation in vivo, these grafts exhibit normal epidermal differentiation and reduced contraction compared to controls. In addition, HoxA3 grafts showed increased angiogenesis. Quantitative polymerase chain reaction (PCR) analyses of HoxA3 graft tissue reveal an increase in the downstream HoxA3 target genes MMP-14 and uPAR expression, as well as a reduction in CCL-2 and CxCl-12. Innovation: Expression of secreted HoxA3 in composite grafts represents a comprehensive approach that targets both keratinocytes and endothelial cells to promote epidermal proliferation and angiogenesis. Conclusion: Secreted HoxA3 improves angiogenesis, reduces expression of inflammatory mediators, and prolongs composite skin graft integrity. PMID:25302136

Hox genes and study of Hox genes in crustacean

NASA Astrophysics Data System (ADS)

Hou, Lin; Chen, Zhijuan; Xu, Mingyu; Lin, Shengguo; Wang, Lu

2004-12-01

Homeobox genes have been discovered in many species. These genes are known to play a major role in specifying regional identity along the anterior-posterior axis of animals from a wide range of phyla. The products of the homeotic genes are a set of evolutionarily conserved transcription factors that control elaborate developmental processes and specify cell fates in metazoans. Crustacean, presenting a variety of body plans not encountered in any other class or phylum of the Metazoa, has been shown to possess a single set of homologous Hox genes like insect. The ancestral crustacean Hox gene complex comprised ten genes: eight homologous to the hometic Hox genes and two related to nonhomeotic genes presented within the insect Hox complexes. The crustacean in particular exhibits an abundant diversity segment specialization and tagmosis. This morphological diversity relates to the Hox genes. In crustacean body plan, different Hox genes control different segments and tagmosis.

Multiple structure-intrinsic disorder interactions regulate and coordinate Hox protein function

NASA Astrophysics Data System (ADS)

Bondos, Sarah

During animal development, Hox transcription factors determine fate of developing tissues to generate diverse organs and appendages. Hox proteins are famous for their bizarre mutant phenotypes, such as replacing antennae with legs. Clearly, the functions of individual Hox proteins must be distinct and reliable in vivo, or the organism risks malformation or death. However, within the Hox protein family, the DNA-binding homeodomains are highly conserved and the amino acids that contact DNA are nearly invariant. These observations raise the question: How do different Hox proteins correctly identify their distinct target genes using a common DNA binding domain? One possible means to modulate DNA binding is through the influence of the non-homeodomain protein regions, which differ significantly among Hox proteins. However genetic approaches never detected intra-protein interactions, and early biochemical attempts were hindered because the special features of ``intrinsically disordered'' sequences were not appreciated. We propose the first-ever structural model of a Hox protein to explain how specific contacts between distant, intrinsically disordered regions of the protein and the homeodomain regulate DNA binding and coordinate this activity with other Hox molecular functions.

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

Morra, Simone; Maurelli, Sara; Chiesa, Mario

A conserved cysteine located in the signature motif of the catalytic center (H-cluster) of [FeFe]-hydrogenases functions in proton transfer. This residue corresponds to C298 in Clostridium acetobutylicum CaHydA. Despite the chemical and structural difference, the mutant C298D retains fast catalytic activity, while replacement with any other amino acid caused significant activity loss. Given the proximity of C298 to the H-cluster, the effect of the C298D mutation on the catalytic center was studied by continuous wave (CW) and pulse electron paramagnetic resonance (EPR) and by Fourier transform infrared (FTIR) spectroscopies. Comparison of the C298D mutant with the wild type CaHydA bymore » CW and pulse EPR showed that the electronic structure of the center is not altered. FTIR spectroscopy confirmed that absorption peak values observed in the mutant are virtually identical to those observed in the wild type, indicating that the H-cluster is not generally affected by the mutation. Significant differences were observed only in the inhibited state Hox-CO: the vibrational modes assigned to the COexo and Fed-CO in this state are shifted to lower values in C298D, suggesting different interaction of these ligands with the protein moiety when C298 is changed to D298. More relevant to the catalytic cycle, the redox equilibrium between the Hox and Hred states is modified by the mutation, causing a prevalence of the oxidized state. This work highlights how the interactions between the protein environment and the H-cluster, a dynamic closely interconnected system, can be engineered and studied in the perspective of designing bio-inspired catalysts and mimics.« less

Up-regulation of HOXB cluster genes are epigenetically regulated in tamoxifen-resistant MCF7 breast cancer cells.

PubMed

Yang, Seoyeon; Lee, Ji-Yeon; Hur, Ho; Oh, Ji Hoon; Kim, Myoung Hee

2018-05-28

Tamoxifen (TAM) is commonly used to treat estrogen receptor (ER)-positive breast cancer. Despite the remarkable benefits, resistance to TAM presents a serious therapeutic challenge. Since several HOX transcription factors have been proposed as strong candidates in the development of resistance to TAM therapy in breast cancer, we generated an in vitro model of acquired TAM resistance using ER-positive MCF7 breast cancer cells (MCF7-TAMR), and analyzed the expression pattern and epigenetic states of HOX genes. HOXB cluster genes were uniquely up-regulated in MCF7-TAMR cells. Survival analysis of in slico data showed the correlation of high expression of HOXB genes with poor response to TAM in ER-positive breast cancer patients treated with TAM. Gain- and loss-of-function experiments showed that the overexpression of multi HOXB genes in MCF7 renders cancer cells more resistant to TAM, whereas the knockdown restores TAM sensitivity. Furthermore, activation of HOXB genes in MCF7-TAMR was associated with histone modifications, particularly the gain of H3K9ac. These findings imply that the activation of HOXB genes mediate the development of TAM resistance, and represent a target for development of new strategies to prevent or reverse TAM resistance.

The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts

PubMed Central

Bian, Chao; Hu, Yinchang; Ravi, Vydianathan; Kuznetsova, Inna S.; Shen, Xueyan; Mu, Xidong; Sun, Ying; You, Xinxin; Li, Jia; Li, Xiaofeng; Qiu, Ying; Tay, Boon-Hui; Thevasagayam, Natascha May; Komissarov, Aleksey S.; Trifonov, Vladimir; Kabilov, Marsel; Tupikin, Alexey; Luo, Jianren; Liu, Yi; Song, Hongmei; Liu, Chao; Wang, Xuejie; Gu, Dangen; Yang, Yexin; Li, Wujiao; Polgar, Gianluca; Fan, Guangyi; Zeng, Peng; Zhang, He; Xiong, Zijun; Tang, Zhujing; Peng, Chao; Ruan, Zhiqiang; Yu, Hui; Chen, Jieming; Fan, Mingjun; Huang, Yu; Wang, Min; Zhao, Xiaomeng; Hu, Guojun; Yang, Huanming; Wang, Jian; Wang, Jun; Xu, Xun; Song, Linsheng; Xu, Gangchun; Xu, Pao; Xu, Junmin; O’Brien, Stephen J.; Orbán, László; Venkatesh, Byrappa; Shi, Qiong

2016-01-01

The Asian arowana (Scleropages formosus), one of the world’s most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining teleosts. The arowana genome retains the full complement of eight Hox clusters unlike the African butterfly fish (Pantodon buchholzi), another bonytongue fish, which possess only five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high-quality reference genome of the golden arowana and the draft assemblies of the red and green varieties are valuable resources for understanding the biology, adaptation and behaviour of Asian arowanas. PMID:27089831

HoxD3 accelerates wound healing in diabetic mice

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

Hansen, Scott L.; Myers, Connie A.; Charboneau, Aubri

Poorly healing diabetic wounds are characterized by diminished collagen production and impaired angiogenesis. HoxD3, a homeobox transcription factor that promotes angiogenesis and collagen synthesis, is up-regulated during normal wound repair whereas its expression is diminished in poorly healing wounds of the genetically diabetic (db/db) mouse. To determine whether restoring expression of HoxD3 would accelerate diabetic wound healing, we devised a novel method of gene transfer, which incorporates HoxD3 plasmid DNA into a methylcellulose film that is placed on wounds created on db/db mice. The HoxD3 transgene was expressed in endothelial cells, fibroblasts, and keratinocytes of the wounds for up tomore » 10 days. More importantly, a single application of HoxD3 to db/db mice resulted in a statistically significant acceleration of wound closure compared to control-treated wounds. Furthermore, we also observed that the HoxD3-mediated improvement in diabetic wound repair was accompanied by increases in mRNA expression of the HoxD3 target genes, Col1A1 and beta 3-integrin leading to enhanced angiogenesis and collagen deposition in the wounds. Although HoxD3-treated wounds also show improved re-epithelialization as compared to control db/db wounds, this effect was not due to direct stimulation of keratinocyte migration by HoxD3. Finally, we show that despite the dramatic increase in collagen synthesis and deposition in HoxD3-treated wounds, these wounds showed normal remodeling and we found no evidence of abnormal wound healing. These results indicate that HoxD3 may provide a means to directly improve collagen deposition, angiogenesis and closure in poorly healing diabetic wounds.« less

Molecular insights into the origin of the Hox-TALE patterning system.

PubMed

Hudry, Bruno; Thomas-Chollier, Morgane; Volovik, Yael; Duffraisse, Marilyne; Dard, Amélie; Frank, Dale; Technau, Ulrich; Merabet, Samir

2014-03-18

Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior-posterior axis. Hox proteins exert their function by interaction with TALE transcription factors. Hox and TALE members are also present in some but not all non-bilaterian phyla, raising the question of how Hox-TALE interactions evolved to provide positional information. By using proteins from unicellular and multicellular lineages, we showed that these networks emerged from an ancestral generic motif present in Hox and other related protein families. Interestingly, Hox-TALE networks experienced additional and extensive molecular innovations that were likely crucial for differentiating Hox functions along body plans. Together our results highlight how homeobox gene families evolved during eukaryote evolution to eventually constitute a major patterning system in Eumetazoans. DOI: http://dx.doi.org/10.7554/eLife.01939.001.

Human HOX Proteins Use Diverse and Context-Dependent Motifs to Interact with TALE Class Cofactors.

PubMed

Dard, Amélie; Reboulet, Jonathan; Jia, Yunlong; Bleicher, Françoise; Duffraisse, Marilyne; Vanaker, Jean-Marc; Forcet, Christelle; Merabet, Samir

2018-03-13

HOX proteins achieve numerous functions by interacting with the TALE class PBX and MEIS cofactors. In contrast to this established partnership in development and disease, how HOX proteins could interact with PBX and MEIS remains unclear. Here, we present a systematic analysis of HOX/PBX/MEIS interaction properties, scanning all paralog groups with human and mouse HOX proteins in vitro and in live cells. We demonstrate that a previously characterized HOX protein motif known to be critical for HOX-PBX interactions becomes dispensable in the presence of MEIS in all except the two most anterior paralog groups. We further identify paralog-specific TALE-binding sites that are used in a highly context-dependent manner. One of these binding sites is involved in the proliferative activity of HOXA7 in breast cancer cells. Together these findings reveal an extraordinary level of interaction flexibility between HOX proteins and their major class of developmental cofactors. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine

USGS Publications Warehouse

Guerreiro, Isabel; Nunes, Andreia; Woltering, Joost M.; Casaca, Ana; Nóvoa, Ana; Vinagre, Tânia; Hunter, Margaret E.; Duboule, Denis; Mallo, Moisés

2013-01-01

Patterning of the vertebrate skeleton requires the coordinated activity of Hox genes. In particular, Hox10 proteins are essential to set the transition from thoracic to lumbar vertebrae because of their rib-repressing activity. In snakes, however, the thoracic region extends well into Hox10-expressing areas of the embryo, suggesting that these proteins are unable to block rib formation. Here, we show that this is not a result of the loss of rib-repressing properties by the snake proteins, but rather to a single base pair change in a Hox/Paired box (Pax)-responsive enhancer, which prevents the binding of Hox proteins. This polymorphism is also found in Paenungulata, such as elephants and manatees, which have extended rib cages. In vivo, this modified enhancer failed to respond to Hox10 activity, supporting its role in the extension of rib cages. In contrast, the enhancer could still interact with Hoxb6 and Pax3 to promote rib formation. These results suggest that a polymorphism in the Hox/Pax-responsive enhancer may have played a role in the evolution of the vertebrate spine by differently modulating its response to rib-suppressing and rib-promoting Hox proteins.

Correct Hox gene expression established independently of position in Caenorhabditis elegans.

PubMed

Cowing, D; Kenyon, C

1996-07-25

The Hox genes are expressed in a conserved sequence of spatial domains along the anteroposterior (A/P) body axes of many organisms. In Drosophila, position-specific signals located along the A/P axis establish the pattern of Hox gene expression. In the nematode Caenorhabditis elegans, it is not known how the pattern of Hox gene expression is established. C. elegans uses lineal control mechanisms and local cell interactions to specify early blastomere identities. However, many cells expressing the same Hox gene are unrelated by lineage, suggesting that, as in Drosophila, domains of Hox gene expression may be defined by cell-extrinsic A/P positional signals. To test this, we have investigated whether posterior mesodermal and ectodermal cells will express their normal posterior Hox gene when they are mispositioned in the anterior. Surprisingly, we find that correct Hox gene expression does not depend on cell position, but is highly correlated with cell lineage. Thus, although the most striking feature of Hox gene expression is its positional specificity, in C. elegans the pattern is achieved, at least in part, by a lineage-specific control system that operates without regard to A/P position.

The TALE face of Hox proteins in animal evolution.

PubMed

Merabet, Samir; Galliot, Brigitte

2015-01-01

Hox genes are major regulators of embryonic development. One of their most conserved functions is to coordinate the formation of specific body structures along the anterior-posterior (AP) axis in Bilateria. This architectural role was at the basis of several morphological innovations across bilaterian evolution. In this review, we traced the origin of the Hox patterning system by considering the partnership with PBC and Meis proteins. PBC and Meis belong to the TALE-class of homeodomain-containing transcription factors and act as generic cofactors of Hox proteins for AP axis patterning in Bilateria. Recent data indicate that Hox proteins acquired the ability to interact with their TALE partners in the last common ancestor of Bilateria and Cnidaria. These interactions relied initially on a short peptide motif called hexapeptide (HX), which is present in Hox and non-Hox protein families. Remarkably, Hox proteins can also recruit the TALE cofactors by using specific PBC Interaction Motifs (SPIMs). We describe how a functional Hox/TALE patterning system emerged in eumetazoans through the acquisition of SPIMs. We anticipate that interaction flexibility could be found in other patterning systems, being at the heart of the astonishing morphological diversity observed in the animal kingdom.

The TALE face of Hox proteins in animal evolution

PubMed Central

Merabet, Samir; Galliot, Brigitte

2015-01-01

Hox genes are major regulators of embryonic development. One of their most conserved functions is to coordinate the formation of specific body structures along the anterior-posterior (AP) axis in Bilateria. This architectural role was at the basis of several morphological innovations across bilaterian evolution. In this review, we traced the origin of the Hox patterning system by considering the partnership with PBC and Meis proteins. PBC and Meis belong to the TALE-class of homeodomain-containing transcription factors and act as generic cofactors of Hox proteins for AP axis patterning in Bilateria. Recent data indicate that Hox proteins acquired the ability to interact with their TALE partners in the last common ancestor of Bilateria and Cnidaria. These interactions relied initially on a short peptide motif called hexapeptide (HX), which is present in Hox and non-Hox protein families. Remarkably, Hox proteins can also recruit the TALE cofactors by using specific PBC Interaction Motifs (SPIMs). We describe how a functional Hox/TALE patterning system emerged in eumetazoans through the acquisition of SPIMs. We anticipate that interaction flexibility could be found in other patterning systems, being at the heart of the astonishing morphological diversity observed in the animal kingdom. PMID:26347770

The prognostic significance of specific HOX gene expression patterns in ovarian cancer.

PubMed

Kelly, Zoe; Moller-Levet, Carla; McGrath, Sophie; Butler-Manuel, Simon; Kavitha Madhuri, Thumuluru; Kierzek, Andrzej M; Pandha, Hardev; Morgan, Richard; Michael, Agnieszka

2016-10-01

HOX genes are vital for all aspects of mammalian growth and differentiation, and their dysregulated expression is related to ovarian carcinogenesis. The aim of the current study was to establish the prognostic value of HOX dysregulation as well as its role in platinum resistance. The potential to target HOX proteins through the HOX/PBX interaction was also explored in the context of platinum resistance. HOX gene expression was determined in ovarian cancer cell lines and primary EOCs by QPCR, and compared to expression in normal ovarian epithelium and fallopian tube tissue samples. Statistical analysis included one-way ANOVA and t-tests, using statistical software R and GraphPad. The analysis identified 36 of the 39 HOX genes as being overexpressed in high grade serous EOC compared to normal tissue. We detected a molecular HOX gene-signature that predicted poor outcome. Overexpression of HOXB4 and HOXB9 was identified in high grade serous cell lines after platinum resistance developed. Targeting the HOX/PBX dimer with the HXR9 peptide enhanced the cytotoxicity of cisplatin in platinum-resistant ovarian cancer. In conclusion, this study has shown the HOX genes are highly dysregulated in ovarian cancer with high expression of HOXA13, B6, C13, D1 and D13 being predictive of poor clinical outcome. Targeting the HOX/PBX dimer in platinum-resistant cancer represents a potentially new therapeutic option that should be further developed and tested in clinical trials. © 2016 The Authors International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UICC.

DNA methylation analysis of Homeobox genes implicates HOXB7 hypomethylation as risk factor for neural tube defects

PubMed Central

Rochtus, Anne; Izzi, Benedetta; Vangeel, Elise; Louwette, Sophie; Wittevrongel, Christine; Lambrechts, Diether; Moreau, Yves; Winand, Raf; Verpoorten, Carla; Jansen, Katrien; Van Geet, Chris; Freson, Kathleen

2015-01-01

Neural tube defects (NTDs) are common birth defects of complex etiology. Though family- and population-based studies have confirmed a genetic component, the responsible genes for NTDs are still largely unknown. Based on the hypothesis that folic acid prevents NTDs by stimulating methylation reactions, epigenetic factors, such as DNA methylation, are predicted to be involved in NTDs. Homeobox (HOX) genes play a role in spinal cord development and are tightly regulated in a spatiotemporal and collinear manner, partly by epigenetic modifications. We have quantified DNA methylation for the different HOX genes by subtracting values from a genome-wide methylation analysis using leukocyte DNA from 10 myelomeningocele (MMC) patients and 6 healthy controls. From the 1575 CpGs profiled for the 4 HOX clusters, 26 CpGs were differentially methylated (P-value < 0.05; β-difference > 0.05) between MMC patients and controls. Seventy-seven percent of these CpGs were located in the HOXA and HOXB clusters, with the most profound difference for 3 CpGs within the HOXB7 gene body. A validation case-control study including 83 MMC patients and 30 unrelated healthy controls confirmed a significant association between MMC and HOXB7 hypomethylation (-14.4%; 95% CI: 11.9–16.9%; P-value < 0.0001) independent of the MTHFR 667C>T genotype. Significant HOXB7 hypomethylation was also present in 12 unaffected siblings, each related to a MMC patient, suggestive of an epigenetic change induced by the mother. The inclusion of a neural tube formation model using zebrafish showed that Hoxb7a overexpression but not depletion resulted in deformed body axes with dysmorphic neural tube formation. Our results implicate HOXB7 hypomethylation as risk factor for NTDs and highlight the importance for future genome-wide DNA methylation analyses without preselecting candidate pathways. PMID:25565354

Conservation of gene linkage in dispersed vertebrate NK homeobox clusters.

PubMed

Wotton, Karl R; Weierud, Frida K; Juárez-Morales, José L; Alvares, Lúcia E; Dietrich, Susanne; Lewis, Katharine E

2009-10-01

Nk homeobox genes are important regulators of many different developmental processes including muscle, heart, central nervous system and sensory organ development. They are thought to have arisen as part of the ANTP megacluster, which also gave rise to Hox and ParaHox genes, and at least some NK genes remain tightly linked in all animals examined so far. The protostome-deuterostome ancestor probably contained a cluster of nine Nk genes: (Msx)-(Nk4/tinman)-(Nk3/bagpipe)-(Lbx/ladybird)-(Tlx/c15)-(Nk7)-(Nk6/hgtx)-(Nk1/slouch)-(Nk5/Hmx). Of these genes, only NKX2.6-NKX3.1, LBX1-TLX1 and LBX2-TLX2 remain tightly linked in humans. However, it is currently unclear whether this is unique to the human genome as we do not know which of these Nk genes are clustered in other vertebrates. This makes it difficult to assess whether the remaining linkages are due to selective pressures or because chance rearrangements have "missed" certain genes. In this paper, we identify all of the paralogs of these ancestrally clustered NK genes in several distinct vertebrates. We demonstrate that tight linkages of Lbx1-Tlx1, Lbx2-Tlx2 and Nkx3.1-Nkx2.6 have been widely maintained in both the ray-finned and lobe-finned fish lineages. Moreover, the recently duplicated Hmx2-Hmx3 genes are also tightly linked. Finally, we show that Lbx1-Tlx1 and Hmx2-Hmx3 are flanked by highly conserved noncoding elements, suggesting that shared regulatory regions may have resulted in evolutionary pressure to maintain these linkages. Consistent with this, these pairs of genes have overlapping expression domains. In contrast, Lbx2-Tlx2 and Nkx3.1-Nkx2.6, which do not seem to be coexpressed, are also not associated with conserved noncoding sequences, suggesting that an alternative mechanism may be responsible for the continued clustering of these genes.

The Role of Hox Genes in Female Reproductive Tract Development, Adult Function, and Fertility.

PubMed

Du, Hongling; Taylor, Hugh S

2015-11-09

HOX genes convey positional identity that leads to the proper partitioning and adult identity of the female reproductive track. Abnormalities in reproductive tract development can be caused by HOX gene mutations or altered HOX gene expression. Diethylstilbestrol (DES) and other endocrine disruptors cause Müllerian defects by changing HOX gene expression. HOX genes are also essential regulators of adult endometrial development. Regulated HOXA10 and HOXA11 expression is necessary for endometrial receptivity; decreased HOXA10 or HOXA11 expression leads to decreased implantation rates. Alternation of HOXA10 and HOXA11 expression has been identified as a mechanism of the decreased implantation associated with endometriosis, polycystic ovarian syndrome, leiomyoma, polyps, adenomyosis, and hydrosalpinx. Alteration of HOX gene expression causes both uterine developmental abnormalities and impaired adult endometrial development that prevent implantation and lead to female infertility. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

To Be Specific or Not: The Critical Relationship Between Hox And TALE Proteins.

PubMed

Merabet, Samir; Mann, Richard S

2016-06-01

Hox proteins are key regulatory transcription factors that act in different tissues of the embryo to provide specific spatial and temporal coordinates to each cell. These patterning functions often depend on the presence of the TALE-homeodomain class cofactors, which form cooperative DNA-binding complexes with all Hox proteins. How this family of cofactors contributes to the highly diverse and specific functions of Hox proteins in vivo remains an important unsolved question. We review here the most recent advances in understanding the molecular mechanisms underlying Hox-TALE function. In particular, we discuss the role of DNA shape, DNA-binding affinity, and protein-protein interaction flexibility in dictating Hox-TALE specificity. We propose several models to explain how these mechanisms are integrated with each other in the context of the many distinct functions that Hox and TALE factors carry out in vivo. Copyright © 2016 Elsevier Ltd. All rights reserved.

Specification of anteroposterior cell fates in Caenorhabditis elegans by Drosophila Hox proteins.

PubMed

Hunter, C P; Kenyon, C

1995-09-21

Antennapedia class homeobox (Hox) genes specify cell fates in successive anteroposterior body domains in vertebrates, insects and nematodes. The DNA-binding homeodomain sequences are very similar between vertebrate and Drosophila Hox proteins, and this similarity allows vertebrate Hox proteins to function in Drosophila. In contrast, the Caenorhabditis elegans homeodomains are substantially divergent. Further, C. elegans differs from both insects and vertebrates in having a non-segmented body as well as a distinctive mode of development that involves asymmetric early cleavages and invariant cell lineages. Here we report that, despite these differences, Drosophila Hox proteins expressed in C. elegans can substitute for C. elegans Hox proteins in the control of three different cell-fate decisions: the regulation of cell migration, the specification of serotonergic neurons, and the specification of a sensory structure. We also show that the specificity of one C. elegans Hox protein is partly determined by two amino acids that have been implicated in sequence-specific DNA binding. Together these findings suggest that factors important for target recognition by specific Hox proteins have been conserved throughout much of the animal kingdom.

HoxD10 gene delivery using adenovirus/adeno-associate hybrid virus inhibits the proliferation and tumorigenicity of GH4 pituitary lactotrope tumor cells

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

Cho, Mi Ae; Endocrinology, Dong Rae Bong Seng Hospital, Busan; Yashar, Parham

2008-07-04

Prolactinoma is one of the most common types of pituitary adenoma. It has been reported that a variety of growth factors and cytokines regulating cell growth and angiogenesis play an important role in the growth of prolactinoma. HoxD10 has been shown to impair endothelial cell migration, block angiogenesis, and maintain a differentiated phenotype of cells. We investigated whether HoxD10 gene delivery could inhibit the growth of prolactinoma. Rat GH4 lactotrope tumor cells were infected with adenovirus/adeno-associated virus (Ad/AAV) hybrid vectors carrying the mouse HoxD10 gene (Hyb-HoxD10) or the {beta}-galactosidase gene (Hyb-Gal). Hyb-HoxD10 expression inhibited GH4 cell proliferation in vitro. Themore » expression of FGF-2 and cyclin D2 was inhibited in GH4 cells infected with Hyb-HoxD10. GH4 cells transduced with Hyb-HoxD10 did not form tumors in nude mice. These results indicate that the delivery of HoxD10 could potentially inhibit the growth of PRL-secreting tumors. This approach may be a useful tool for targeted therapy of prolactinoma and other neoplasms.« less

[Up regulation of phenylacetate to glioma homeobox gene expression].

PubMed

Tian, Yu; Yang, Chaohua; Zhao, Conghai

2002-03-01

Even though phenylacetate (PA) bas been shown to inhibit the growth and induce differentiation in rat C6 glioma cell line, its mechanisms are still poorly understood. This study is aimed to identify which Hox gene is related to glioma and to observe the change in expression on mRNA level as treated by phenylasetate. Twenty-two kinds of Hox gene were divided into 3 groups according to their primer sequence. Semiquantitative reverse transcription- polymerase chain reaction (RT-PCR) was used to investigate the mRNA expression of Hox gene groups and some Hox gene in rat C6 glioma cell line following differentiation induced by PA. The level of Hox gene expression was expressed as ratio expression rate (RER) of Hox gene/beta-actin according to computer image analysis and the difference between C6 cells and PA treated C6 cells was analyzed by student t-test. It was found that Hox genes matching to primers P2 were mildly expressed in C6 cells and the expression of HoxB2 mRNA was significantly up-regulated in PA treated C6 cells (P < 0.001). The weak expression of HoxB2 may be involved in glioma origin and the mechanisms of PA action are correlated with transcription process in the glioma cells.

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

Zhong, Yiming; Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, OH; Sullenbarger, Brent

Research highlights: {yields} HoxB4 overexpression in human TF1 cells increased the expression of CD61 and CD41a. {yields} HoxB4 fusion protein enhanced megakaryocytic development of CD34{sup +} cord blood cells. {yields} Ectopic HoxB4 increased Tpo receptor expression and decreased c-Myb expression. {yields} HoxB4 RNA silencing increased c-Myb expression and decreased Fli-1 expression. -- Abstract: In order to produce clinically useful quantities of platelets ex vivo we may need to firstly enhance early self-renewal of hematopoietic stem cells (HSCs) and/or megakaryocyte (Mk) progenitors. The homeodomain transcription factor HoxB4 has been shown to be an important regulator of stem cell renewal and hematopoiesis;more » however, its effect on megakaryopoiesis is unclear. In this study, we investigated the effect of HoxB4 overexpression or RNA silencing on megakaryocytic development in the human TF1 progenitor cell line; we then used recombinant tPTD-HoxB4 fusion protein to study the effect of exogenous HoxB4 on megakaryocytic development of human CD34 positively-selected cord blood cells. We found that ectopic HoxB4 in TF1 cells increased the antigen expression of CD61and CD41a, increased the gene expression of thrombopoietin receptor (TpoR), Scl-1, Cyclin D1, Fog-1 and Fli-1 while it decreased c-Myb expression. HoxB4 RNA silencing in TF1 cells decreased the expression of CD61 and CD41a and decreased Fli-1 expression while it increased the expression of c-Myb. Recombinant tPTD-HoxB4 fusion protein increased the percentages and absolute numbers of CD41a and CD61 positive cells during megakaryocytic differentiation of CD34 positively-selected cord blood cells and increased the numbers of colony-forming unit-megakaryocyte (CFU-Mk). Adding tPTD-HoxB4 fusion protein increased the gene expression of TpoR, Cyclin D1, Fog-1 and Fli-1 while it inhibited c-Myb expression. Our data suggest that increased HoxB4 enhanced early megakaryocytic development in human TF1 cells and CD34 positively-selected cord blood cells primarily by upregulating TpoR and Fli-1 expression and downregulating c-Myb expression. Increasing HoxB4 expression or adding recombinant HoxB4 protein might be a way to expand Mks for the production of platelets for use in transfusion medicine.« less

Chance and necessity in eye evolution.

PubMed

Gehring, Walter J

2011-01-01

Charles Darwin has proposed the theory that evolution of live organisms is based on random variation and natural selection. Jacques Monod in his classic book Chance and Necessity, published 40 years ago, presented his thesis "that the biosphere does not contain a predictable class of objects or events, but constitutes a particular occurrence, compatible indeed with the first principles, but not deducible from those principals and therefore, essentially unpredictable." Recent discoveries in eye evolution are in agreement with both of these theses. They confirm Darwin's assumption of a simple eye prototype and lend strong support for the notion of a monophyletic origin of the various eye types. Considering the complexity of the underlying gene regulatory networks the unpredictability is obvious. The evolution of the Hox gene cluster and the specification of the body plan starting from an evolutionary prototype segment is discussed. In the course of evolution, a series of similar prototypic segments gradually undergoes cephalization anteriorly and caudalization posteriorly through diversification of the Hox genes.

Chance and Necessity in Eye Evolution

PubMed Central

Gehring, Walter J.

2011-01-01

Charles Darwin has proposed the theory that evolution of live organisms is based on random variation and natural selection. Jacques Monod in his classic book Chance and Necessity, published 40 years ago, presented his thesis “that the biosphere does not contain a predictable class of objects or events, but constitutes a particular occurrence, compatible indeed with the first principles, but not deducible from those principals and therefore, essentially unpredictable.” Recent discoveries in eye evolution are in agreement with both of these theses. They confirm Darwin's assumption of a simple eye prototype and lend strong support for the notion of a monophyletic origin of the various eye types. Considering the complexity of the underlying gene regulatory networks the unpredictability is obvious. The evolution of the Hox gene cluster and the specification of the body plan starting from an evolutionary prototype segment is discussed. In the course of evolution, a series of similar prototypic segments gradually undergoes cephalization anteriorly and caudalization posteriorly through diversification of the Hox genes. PMID:21979158

Control of DNA replication: a new facet of Hox proteins?

PubMed

Miotto, Benoit; Graba, Yacine

2010-09-01

Hox proteins are well-known as developmental transcription factors controlling cell and tissue identity, but recent findings suggest that they are also part of the cell replication machinery. Hox-mediated control of transcription and replication may ensure coordinated control of cell growth and differentiation, two processes that need to be tightly and precisely coordinated to allow proper organ formation and patterning. In this review we summarize the available data linking Hox proteins to the replication machinery and discuss the developmental and pathological implications of this new facet of Hox protein function.

Differential pleiotropy and HOX functional organization.

PubMed

Sivanantharajah, Lovesha; Percival-Smith, Anthony

2015-02-01

Key studies led to the idea that transcription factors are composed of defined modular protein motifs or domains, each with separable, unique function. During evolution, the recombination of these modular domains could give rise to transcription factors with new properties, as has been shown using recombinant molecules. This archetypic, modular view of transcription factor organization is based on the analyses of a few transcription factors such as GAL4, which may represent extreme exemplars rather than an archetype or the norm. Recent work with a set of Homeotic selector (HOX) proteins has revealed differential pleiotropy: the observation that highly-conserved HOX protein motifs and domains make small, additive, tissue specific contributions to HOX activity. Many of these differentially pleiotropic HOX motifs may represent plastic sequence elements called short linear motifs (SLiMs). The coupling of differential pleiotropy with SLiMs, suggests that protein sequence changes in HOX transcription factors may have had a greater impact on morphological diversity during evolution than previously believed. Furthermore, differential pleiotropy may be the genetic consequence of an ensemble nature of HOX transcription factor allostery, where HOX proteins exist as an ensemble of states with the capacity to integrate an extensive array of developmental information. Given a new structural model for HOX functional domain organization, the properties of the archetypic TF may require reassessment. Copyright © 2014 Elsevier Inc. All rights reserved.

Rice HOX12 Regulates Panicle Exsertion by Directly Modulating the Expression of ELONGATED UPPERMOST INTERNODE1[OPEN

PubMed Central

Gao, Shaopei; Fang, Jun; Xu, Fan; Wang, Wei

2016-01-01

Bioactive gibberellins (GAs) are key endogenous regulators of plant growth. Previous work identified ELONGATED UPPERMOST INTERNODE1 (EUI1) as a GA-deactivating enzyme that plays an important role in panicle exsertion from the flag leaf sheath in rice (Oryza sativa). However, the mechanism that regulates EUI1 activity during development is still largely unexplored. In this study, we identified the dominant panicle enclosure mutant regulator of eui1 (ree1-D), whose phenotype is caused by the activation of the homeodomain-leucine zipper transcription factor HOX12. Diminished HOX12 expression by RNA interference enhanced panicle exsertion, mimicking the eui1 phenotype. HOX12 knockdown plants contain higher levels of the major biologically active GAs (such as GA1 and GA4) than the wild type. The expression of EUI1 is elevated in the ree1-D mutant but reduced in HOX12 knockdown plants. Interestingly, both HOX12 and EUI1 are predominantly expressed in panicles, where GA4 is highly accumulated. Yeast one-hybrid, electrophoretic mobility shift assay, and chromatin immunoprecipitation analyses showed that HOX12 physically interacts with the EUI1 promoter both in vitro and in vivo. Furthermore, plants overexpressing HOX12 in the eui1 mutant background retained the elongated uppermost internode phenotype. These results indicate that HOX12 acts directly through EUI1 to regulate panicle exsertion in rice. PMID:26977084

Solar powered biohydrogen production requires specific localization of the hydrogenase

DOE PAGES

Burroughs, Nigel J.; Boehm, Marko; Eckert, Carrie; ...

2014-09-04

Cyanobacteria contain a bidirectional [NiFe] hydrogenase which transiently produces hydrogen upon exposure of anoxic cells to light, potentially acting as a “valve” releasing excess electrons from the electron transport chain. However, its interaction with the photosynthetic electron transport chain remains unclear. By GFP-tagging the HoxF diaphorase subunit we show that the hydrogenase is thylakoid associated, comprising a population dispersed uniformly through the thylakoids and a subpopulation localized to discrete puncta in the distal thylakoid. Thylakoid localisation of both the HoxH and HoxY hydrogenase subunits is confirmed by immunogold electron microscopy. The diaphorase HoxE subunit is essential for recruitment to themore » dispersed thylakoid population, potentially anchoring the hydrogenase to the membrane, but aggregation to puncta occurs through a distinct HoxE-independent mechanism. Membrane association does not require NDH-1. Localization is dynamic on a scale of minutes, with anoxia and high light inducing a significant redistribution between these populations in favour of puncta. Lastly, since HoxE is essential for access to its electron donor, electron supply to the hydrogenase depends on a physiologically controlled localization, potentially offering a new avenue to enhance photosynthetic hydrogen production by exploiting localization/aggregation signals.« less

The zinc finger gene Krox20 regulates HoxB2 (Hox2.8) during hindbrain segmentation.

PubMed

Sham, M H; Vesque, C; Nonchev, S; Marshall, H; Frain, M; Gupta, R D; Whiting, J; Wilkinson, D; Charnay, P; Krumlauf, R

1993-01-29

The zinc finger gene Krox20 and many Hox homeobox genes are expressed in segment-restricted domains in the hindbrain. The restricted expression patterns appear before morphological segmentation, suggesting that these transcription factors may play an early role in the establishment and identity of rhombomeric segments. In this paper, we show that the HoxB2 (Hox2.8) gene is normally upregulated in rhombomeres (r) 3, 4, and 5, and we identify an enhancer region upstream of the gene that imposes r3/r5 expression in transgenic mice. This enhancer contains three Krox20-binding sites required in vitro for complex formation with Krox20 protein and in vivo for rhombomere-restricted expression. In transgenic mice, Krox20 expressed in ectopic domains can transactivate a reporter construct containing the HoxB2 r3/r5 enhancer. These data demonstrate that Krox20 is a part of the upstream transcriptional cascade that directly regulates HoxB2 expression during hindbrain segmentation.

Disruption of Hox9,10,11 function results in cellular level lineage infidelity in the kidney.

PubMed

Drake, Keri A; Adam, Mike; Mahoney, Robert; Potter, S Steven

2018-04-20

Hox genes are important regulators of development. The 39 mammalian Hox genes have considerable functional overlap, greatly confounding their study. In this report, we generated mice with multiple combinations of paralogous and flanking Abd-B Hox gene mutations to investigate functional redundancies in kidney development. The resulting mice developed a number of kidney abnormalities, including hypoplasia, agenesis, and severe cysts, with distinct Hox functions observed in early metanephric kidney formation and nephron progenitor maintenance. Most surprising, however, was that extensive removal of Hox shared function in these kidneys resulted in cellular level lineage infidelity. Strikingly, mutant nephron tubules consisted of intermixed cells with proximal tubule, loop of Henle, and collecting duct identities, with some single cells expressing markers associated with more than one nephron segment. These results indicate that Hox genes are required for proper lineage selection/maintenance and full repression of genes involved in cell fate restriction in the developing kidney.

MicroRNA filters Hox temporal transcription noise to confer boundary formation in the spinal cord

NASA Astrophysics Data System (ADS)

Li, Chung-Jung; Hong, Tian; Tung, Ying-Tsen; Yen, Ya-Ping; Hsu, Ho-Chiang; Lu, Ya-Lin; Chang, Mien; Nie, Qing; Chen, Jun-An

2017-03-01

The initial rostrocaudal patterning of the neural tube leads to differential expression of Hox genes that contribute to the specification of motor neuron (MN) subtype identity. Although several 3' Hox mRNAs are expressed in progenitors in a noisy manner, these Hox proteins are not expressed in the progenitors and only become detectable in postmitotic MNs. MicroRNA biogenesis impairment leads to precocious expression and propagates the noise of Hoxa5 at the protein level, resulting in an imprecise Hoxa5-Hoxc8 boundary. Here we uncover, using in silico simulation, two feed-forward Hox-miRNA loops accounting for the precocious and noisy Hoxa5 expression, as well as an ill-defined boundary phenotype in Dicer mutants. Finally, we identify mir-27 as a major regulator coordinating the temporal delay and spatial boundary of Hox protein expression. Our results provide a novel trans Hox-miRNA circuit filtering transcription noise and controlling the timing of protein expression to confer robust individual MN identity.

Molecular insights into the origin of the Hox-TALE patterning system

PubMed Central

Hudry, Bruno; Thomas-Chollier, Morgane; Volovik, Yael; Duffraisse, Marilyne; Dard, Amélie; Frank, Dale; Technau, Ulrich; Merabet, Samir

2014-01-01

Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior–posterior axis. Hox proteins exert their function by interaction with TALE transcription factors. Hox and TALE members are also present in some but not all non-bilaterian phyla, raising the question of how Hox–TALE interactions evolved to provide positional information. By using proteins from unicellular and multicellular lineages, we showed that these networks emerged from an ancestral generic motif present in Hox and other related protein families. Interestingly, Hox-TALE networks experienced additional and extensive molecular innovations that were likely crucial for differentiating Hox functions along body plans. Together our results highlight how homeobox gene families evolved during eukaryote evolution to eventually constitute a major patterning system in Eumetazoans. DOI: http://dx.doi.org/10.7554/eLife.01939.001 PMID:24642410

Rice homeobox transcription factor HOX1a positively regulates gibberellin responses by directly suppressing EL1.

PubMed

Wen, Bi-Qing; Xing, Mei-Qing; Zhang, Hua; Dai, Cheng; Xue, Hong-Wei

2011-11-01

Homeobox transcription factors are involved in various aspects of plant development, including maintenance of the biosynthesis and signaling pathways of different hormones. However, few direct targets of homeobox proteins have been identified. We here show that overexpression of rice homeobox gene HOX1a resulted in enhanced gibberellin (GA) response, indicating a positive effect of HOX1a in GA signaling. HOX1a is induced by GA and encodes a homeobox transcription factor with transcription repression activity. In addition, HOX1a suppresses the transcription of early flowering1 (EL1), a negative regulator of GA signaling, and further electrophoretic mobility shift assay and chromatin immunoprecipitation analysis revealed that HOX1a directly bound to the promoter region of EL1 to suppress its expression and stimulate GA signaling. These results demonstrate that HOX1a functions as a positive regulator of GA signaling by suppressing EL1, providing informative hints on the study of GA signaling. © 2011 Institute of Botany, Chinese Academy of Sciences.

Effect of increased HoxB4 on human megakaryocytic development

PubMed Central

Zhong, Yiming; Sullenbarger, Brent; Lasky, Larry C.

2010-01-01

In order to ex vivo produce clinically useful quantity of platelets, we may need to firstly enhance early self-renewal of hematopoietic stem cells (HSCs) and/or megakaryocyte (Mk) progenitors. The homeodomain transcription factor HoxB4 has been shown to be an important regulator of stem cell renewal and hematopoiesis; however, its effect on megakaryopoiesis is unclear. In this study, we investigated the effect of HoxB4 overexpression or RNA silencing on megakaryocytic development in the human TF1 progenitor cell line; we then used recombinant tPTD-HoxB4 fusion protein to study the effect of exogenous HoxB4 on megakaryocytic development of human CD34 positively-selected cord blood cells. We found that ectopic HoxB4 in TF1 cells increased the antigen expression of CD61and CD41a, increased the gene expression of thrombopoietin receptor (TpoR), Scl-1, Cyclin D1, Fog-1 and Fli-1 while it decreased c-Myb expression. HoxB4 RNA silencing in TF1 cells decreased the expression of CD61 and CD41a and decreased Fli-1 expression while it increased the expression of c-Myb. Recombinant tPTD-HoxB4 fusion protein increased the percentages and absolute numbers of CD41a and CD61 positive cells during megakaryocytic differentiation of CD34 positively-selected cord blood cells and increased the numbers of colony forming unit-megakaryocyte (CFU-Mk). Adding tPTD-HoxB4 fusion protein increased the gene expression of TpoR, Cyclin D1, Fog-1 and Fli-1 while it inhibited c-Myb expression. Our data indicate that increased HoxB4 enhanced early megakaryocytic development in human TF1 cells and CD34 positively-selected cord blood cells primarily by upregulating Tpo R and Fli-1 expression and downregulating c-Myb expression. Increasing HoxB4 expression or adding recombinant HoxB4 protein might be a way to expand Mks for the production of platelets for use in transfusion medicine. PMID:20599537

The HOX genes are expressed, in vivo, in human tooth germs: in vitro cAMP exposure of dental pulp cells results in parallel HOX network activation and neuronal differentiation.

PubMed

D'Antò, Vincenzo; Cantile, Monica; D'Armiento, Maria; Schiavo, Giulia; Spagnuolo, Gianrico; Terracciano, Luigi; Vecchione, Raffaela; Cillo, Clemente

2006-03-01

Homeobox-containing genes play a crucial role in odontogenesis. After the detection of Dlx and Msx genes in overlapping domains along maxillary and mandibular processes, a homeobox odontogenic code has been proposed to explain the interaction between different homeobox genes during dental lamina patterning. No role has so far been assigned to the Hox gene network in the homeobox odontogenic code due to studies on specific Hox genes and evolutionary considerations. Despite its involvement in early patterning during embryonal development, the HOX gene network, the most repeat-poor regions of the human genome, controls the phenotype identity of adult eukaryotic cells. Here, according to our results, the HOX gene network appears to be active in human tooth germs between 18 and 24 weeks of development. The immunohistochemical localization of specific HOX proteins mostly concerns the epithelial tooth germ compartment. Furthermore, only a few genes of the network are active in embryonal retromolar tissues, as well as in ectomesenchymal dental pulp cells (DPC) grown in vitro from adult human molar. Exposure of DPCs to cAMP induces the expression of from three to nine total HOX genes of the network in parallel with phenotype modifications with traits of neuronal differentiation. Our observations suggest that: (i) by combining its component genes, the HOX gene network determines the phenotype identity of epithelial and ectomesenchymal cells interacting in the generation of human tooth germ; (ii) cAMP treatment activates the HOX network and induces, in parallel, a neuronal-like phenotype in human primary ectomesenchymal dental pulp cells. 2005 Wiley-Liss, Inc.

HOXA9 is critical in the proliferation, differentiation, and malignancy of leukaemia cells both in vitro and in vivo.

PubMed

Chen, Shibing; Yu, Juan; Lv, Xin; Zhang, Lijuan

2017-10-01

Progress in the understanding of the molecular mechanism for acute myeloid leukaemia is of great significance to generate new potential targets for treatment. Recent studies showed that HOXA9, a homeodomain-containing transcription factor, is commonly deregulated in acute leukaemia. In this study, we elucidated the direct correlation between HoxA9 expression and progression of leukaemia using 2 different types of leukaemia cells HL-60 and MOLT-3. The HoxA9 expression level was decreased in leukaemia cells with the treatment of all-trans retinoic acid or arsenic trioxide (As 2 O 3 ). Downregulation of HoxA9 could impair the proliferation and promote the leukaemia cell death. HoxA9 silencing also potentiated the differentiation of leukaemia cells, and in vivo studies demonstrated that HoxA9 downregulation could interfere the tumour growth. Interestingly, HoxA9 silencing also led to the alteration in miRNA expression, mediating the promoting effect on the leukaemia cell differentiation. Therefore, this work provided a promising and potentially efficient target to leukaemia treatment, indicating that HoxA9 is likely to be an ideal candidate in the gene therapy against acute myeloid leukaemia. In this study, we elucidated the critical role of HoxA9 in the proliferation and differentiation of leukaemia cells both in vitro and in vivo. The effect of HoxA9 modulation was correlated with the clinical effect of all-trans retinoic acid and As 2 O 3 . Furthermore, HoxA9 also regulated the miRNA expression, controlling the leukaemia cell differentiation. Therefore, this work provided new insights into molecular mechanism underlying the leukaemia treatment, potentially putting forward a brand new target to the gene therapy against leukaemia. Copyright © 2017 John Wiley & Sons, Ltd.

Zebrafish hox paralogue group 2 genes function redundantly as selector genes to pattern the second pharyngeal arch.

PubMed

Hunter, Michael P; Prince, Victoria E

2002-07-15

The pharyngeal arches are one of the defining features of the vertebrates, with the first arch forming the mandibles of the jaw and the second forming jaw support structures. The cartilaginous elements of each arch are formed from separate migratory neural crest cell streams, which derive from the dorsal aspect of the neural tube. The second and more posterior crest streams are characterized by specific Hox gene expression. The zebrafish has a larger overall number of Hox genes than the tetrapod vertebrates, as the result of a duplication event in its lineage. However, in both zebrafish and mouse, there are just two members of Hox paralogue group 2 (PG2): Hoxa2 and Hoxb2. Here, we show that morpholino-mediated "knock-down" of both zebrafish Hox PG2 genes results in major defects in second pharyngeal arch cartilages, involving replacement of ventral elements with a mirror-image duplication of first arch structures, and accompanying changes to pharyngeal musculature. In the mouse, null mutants of Hoxa2 have revealed that this single Hox gene is required for normal second arch patterning. By contrast, loss-of-function of either zebrafish Hox PG2 gene individually has no phenotypic consequence, showing that these two genes function redundantly to confer proper pattern to the second pharyngeal arch. We have also used hoxb1a mis-expression to induce localized ectopic expression of zebrafish Hox PG2 genes in the first arch; using this strategy, we find that ectopic expression of either Hox PG2 gene can confer second arch identity onto first arch structures, suggesting that the zebrafish Hox PG2 genes act as "selector genes." 2002 Elsevier Science (USA).

Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus

PubMed Central

Mason, Mandy K.; VanderMeer, Julia E.; Zhao, Jingjing; Eckalbar, Walter L.; Logan, Malcolm; Illing, Nicola; Pollard, Katherine S.; Ahituv, Nadav

2016-01-01

The molecular events leading to the development of the bat wing remain largely unknown, and are thought to be caused, in part, by changes in gene expression during limb development. These expression changes could be instigated by variations in gene regulatory enhancers. Here, we used a comparative genomics approach to identify regions that evolved rapidly in the bat ancestor, but are highly conserved in other vertebrates. We discovered 166 bat accelerated regions (BARs) that overlap H3K27ac and p300 ChIP-seq peaks in developing mouse limbs. Using a mouse enhancer assay, we show that five Myotis lucifugus BARs drive gene expression in the developing mouse limb, with the majority showing differential enhancer activity compared to the mouse orthologous BAR sequences. These include BAR116, which is located telomeric to the HoxD cluster and had robust forelimb expression for the M. lucifugus sequence and no activity for the mouse sequence at embryonic day 12.5. Developing limb expression analysis of Hoxd10-Hoxd13 in Miniopterus natalensis bats showed a high-forelimb weak-hindlimb expression for Hoxd10-Hoxd11, similar to the expression trend observed for M. lucifugus BAR116 in mice, suggesting that it could be involved in the regulation of the bat HoxD complex. Combined, our results highlight novel regulatory regions that could be instrumental for the morphological differences leading to the development of the bat wing. PMID:27019019

Glimpse into Hox and tale regulation of cell differentiation and reprogramming.

PubMed

Cerdá-Esteban, Nuria; Spagnoli, Francesca M

2014-01-01

During embryonic development, cells become gradually restricted in their developmental potential and start elaborating lineage-specific transcriptional networks to ultimately acquire a unique differentiated state. Hox genes play a central role in specifying regional identities, thereby providing the cell with critical information on positional value along its differentiation path. The exquisite DNA-binding specificity of the Hox proteins is frequently dependent upon their interaction with members of the TALE family of homeodomain proteins. In addition to their function as Hox-cofactors, TALE homeoproteins control multiple crucial developmental processes through Hox-independent mechanisms. Here, we will review recent findings on the function of both Hox and TALE proteins in cell differentiation, referring mostly to vertebrate species. In addition, we will discuss the direct implications of this knowledge on cell plasticity and cell reprogramming. Copyright © 2013 Wiley Periodicals, Inc.

Role of the HoxZ subunit in the electron transfer pathway of the membrane-bound [NiFe]-hydrogenase from Ralstonia eutropha immobilized on electrodes.

PubMed

Sezer, Murat; Frielingsdorf, Stefan; Millo, Diego; Heidary, Nina; Utesch, Tillman; Mroginski, Maria-Andrea; Friedrich, Bärbel; Hildebrandt, Peter; Zebger, Ingo; Weidinger, Inez M

2011-09-01

The role of the diheme cytochrome b (HoxZ) subunit in the electron transfer pathway of the membrane-bound [NiFe]-hydrogenase (MBH) heterotrimer from Ralstonia eutropha H16 has been investigated. The MBH in its native heterotrimeric state was immobilized on electrodes and subjected to spectroscopic and electrochemical analysis. Surface enhanced resonance Raman spectroscopy was used to monitor the redox and coordination state of the HoxZ heme cofactors while concomitant protein film voltammetric measurements gave insights into the catalytic response of the enzyme on the electrode. The entire MBH heterotrimer as well as its isolated HoxZ subunit were immobilized on silver electrodes coated with self-assembled monolayers of ω-functionalized alkylthiols, displaying the preservation of the native heme pocket structure and an electrical communication between HoxZ and the electrode. For the immobilized MBH heterotrimer, catalytic reduction of the HoxZ heme cofactors was observed upon H(2) addition. The catalytic currents of MBH with and without the HoxZ subunit were measured and compared with the heterogeneous electron transfer rates of the isolated HoxZ. On the basis of the spectroscopic and electrochemical results, we conclude that the HoxZ subunit under these artificial conditions is not primarily involved in the electron transfer to the electrode but plays a crucial role in stabilizing the enzyme on the electrode. © 2011 American Chemical Society

HO(x) Measurements in PEM Tropics B with the Airborne Tropospheric Hydrogen Oxides Sensor (ATHOS)

NASA Technical Reports Server (NTRS)

Brune, William H.

2001-01-01

The primary objective of PEM Tropics B was to study the processes responsible for the production and loss of tropospheric ozone over the tropical Pacific. This region of the globe contains very clean air as well as aged, polluted air that was advected from both the Asian and American continents. Understanding ozone requires understanding of HO(x) (HO(x) = OH + HO2) chemistry, since the reaction between H02 and NO leads to ozone production and the production of OH often requires ozone loss. In addition, OH is the atmosphere's primary oxidant. Since most atmospheric oxidation is thought to occur in the tropical lower troposphere, measurements during PEM Tropics B should provide an important test of the OH abundances and distributions. Thus, understanding and thoroughly testing HO(x) processes was an important objective of PEM Tropics B. Several issues need to be tested, One is HO, production rates and sources, since HO,, production directly affects ozone production and loss. Another is HO(x) behavior in and around clouds, since HO(x) is lost to cloud particles, but convection may bring HO(x) precursors from near the surface to the upper troposphere. A third is the rise and fall of HO(x) at sunrise and sunset, since these variations give strong indications of the important sources and sinks of HO(x). Making and interpreting high-quality OH and H02 measurements from the NASA DC-8 during PEM Tropics B is the objective of this research effort.

Aggregation of Sea Urchin Phagocytes Is Augmented In Vitro by Lipopolysaccharide

PubMed Central

Majeske, Audrey J.; Bayne, Christopher J.; Smith, L. Courtney

2013-01-01

Development of protocols and media for culturing immune cells from marine invertebrates has not kept pace with advancements in mammalian immune cell culture, the latter having been driven by the need to understand the causes of and develop therapies for human and animal diseases. However, expansion of the aquaculture industry and the diseases that threaten these systems creates the need to develop cell and tissue culture methods for marine invertebrates. Such methods will enable us to better understand the causes of disease outbreaks and to develop means to avoid and remedy epidemics. We report a method for the short-term culture of phagocytes from the purple sea urchin, Strongylocentrotus purpuratus, by modifying an approach previously used to culture cells from another sea urchin species. The viability of cultured phagocytes from the purple sea urchin decreases from 91.6% to 57% over six days and phagocyte morphology changes from single cells to aggregates leading to the formation of syncytia-like structures. This process is accelerated in the presence of lipopolysaccharide suggesting that phagocytes are capable of detecting this molecular pattern in culture conditions. Sea urchin immune response proteins, called Sp185/333, are expressed on the surface of a subset of phagocytes and have been associated with syncytia-like structures. We evaluated their expression in cultured phagocytes to determine their possible role in cell aggregation and in the formation of syncytia-like structures. Between 0 and 3 hr, syncytia-like structures were observed in cultures when only ∼10% of the cells were positive for Sp185/333 proteins. At 24 hr, ∼90% of the nuclei were Sp185/333-positive when all of the phagocytes had aggregated into syncytia-like structures. Consequently, we conclude that the Sp185/333 proteins do not have a major role in initiating the aggregation of cultured phagocytes, however the Sp185/333 proteins are associated with the clustered nuclei within the syncytia-like structures. PMID:23613847

Aggregation of sea urchin phagocytes is augmented in vitro by lipopolysaccharide.

PubMed

Majeske, Audrey J; Bayne, Christopher J; Smith, L Courtney

2013-01-01

Development of protocols and media for culturing immune cells from marine invertebrates has not kept pace with advancements in mammalian immune cell culture, the latter having been driven by the need to understand the causes of and develop therapies for human and animal diseases. However, expansion of the aquaculture industry and the diseases that threaten these systems creates the need to develop cell and tissue culture methods for marine invertebrates. Such methods will enable us to better understand the causes of disease outbreaks and to develop means to avoid and remedy epidemics. We report a method for the short-term culture of phagocytes from the purple sea urchin, Strongylocentrotus purpuratus, by modifying an approach previously used to culture cells from another sea urchin species. The viability of cultured phagocytes from the purple sea urchin decreases from 91.6% to 57% over six days and phagocyte morphology changes from single cells to aggregates leading to the formation of syncytia-like structures. This process is accelerated in the presence of lipopolysaccharide suggesting that phagocytes are capable of detecting this molecular pattern in culture conditions. Sea urchin immune response proteins, called Sp185/333, are expressed on the surface of a subset of phagocytes and have been associated with syncytia-like structures. We evaluated their expression in cultured phagocytes to determine their possible role in cell aggregation and in the formation of syncytia-like structures. Between 0 and 3 hr, syncytia-like structures were observed in cultures when only ~10% of the cells were positive for Sp185/333 proteins. At 24 hr, ~90% of the nuclei were Sp185/333-positive when all of the phagocytes had aggregated into syncytia-like structures. Consequently, we conclude that the Sp185/333 proteins do not have a major role in initiating the aggregation of cultured phagocytes, however the Sp185/333 proteins are associated with the clustered nuclei within the syncytia-like structures.

Co-expression of HoxA9 and bcr-abl genes in chronic myeloid leukemia.

PubMed

Tedeschi, Fabián A; Cardozo, Maria A; Valentini, Rosanna; Zalazar, Fabián E

2010-05-01

We have analyzed the co-expression of the bcr-abl and HoxA9 genes in the follow-up of patients with chronic myeloid leukemia (CML). In the present work we measured the HoxA9 and bcr-abl gene expression in sequential samples. In all patients, bcr-abl and HoxA9 were expressed at detectable levels in every sample. When the results were expressed in relation to abl, two different situations were found: (a) patients clinically stable at second sampling, with low relative risk at diagnosis (low Sokal's score), did not show significant differences in both bcr-abl and HoxA9 levels in the sequential samples analyzed, and (b) patients with poor prognosis (showing intermediate or high Sokal's score at diagnosis) had increased expression of bcr-abl as well as HoxA9 genes (p < 0.05). Since HoxA9 gene expression remains at relatively constant levels throughout adult life, our results could reflect actual changes in the expression rate of this gene associated with bcr-abl during the progression of CML.

The vertebrate Hox gene regulatory network for hindbrain segmentation: Evolution and diversification: Coupling of a Hox gene regulatory network to hindbrain segmentation is an ancient trait originating at the base of vertebrates.

PubMed

Parker, Hugo J; Bronner, Marianne E; Krumlauf, Robb

2016-06-01

Hindbrain development is orchestrated by a vertebrate gene regulatory network that generates segmental patterning along the anterior-posterior axis via Hox genes. Here, we review analyses of vertebrate and invertebrate chordate models that inform upon the evolutionary origin and diversification of this network. Evidence from the sea lamprey reveals that the hindbrain regulatory network generates rhombomeric compartments with segmental Hox expression and an underlying Hox code. We infer that this basal feature was present in ancestral vertebrates and, as an evolutionarily constrained developmental state, is fundamentally important for patterning of the vertebrate hindbrain across diverse lineages. Despite the common ground plan, vertebrates exhibit neuroanatomical diversity in lineage-specific patterns, with different vertebrates revealing variations of Hox expression in the hindbrain that could underlie this diversification. Invertebrate chordates lack hindbrain segmentation but exhibit some conserved aspects of this network, with retinoic acid signaling playing a role in establishing nested domains of Hox expression. © 2016 WILEY Periodicals, Inc.

Hydroxyl and Hydroperoxy Radical Chemistry during the MCMA-2006 Field Campaign: Measurement and Model Comparison

NASA Astrophysics Data System (ADS)

Dusanter, S.; Vimal, D.; Stevens, P. S.; Volkamer, R.; Molina, L. T.

2007-12-01

The Mexico City Metropolitan Area (MCMA) field campaign, held in March 2006, was a unique opportunity to collect data in one of the most polluted megacities in the world. Such environments exhibit a complex oxidation chemistry involving a strong coupling between odd hydrogen radicals (HOX=OH+HO2) and nitrogen oxides species (NOX=NO+NO2). High levels of volatile organic compounds (VOCs) and NOX control the HOX budget and lead to elevated tropospheric ozone formation. The HOX-NOX coupling can be investigated by comparing measured and model-predicted HOx concentrations. Atmospheric HOX concentrations were measured by the Indiana University laser-induced fluorescence instrument and data were collected at the Instituto Mexicano del Petroleo between 14 and 31 March. Measured hydroxyl radical (OH) concentrations are comparable to that measured in less polluted urban environments and suggest that the OH concentrations are highly buffered under high NOX conditions. In contrast, hydroperoxy radical (HO2) concentrations are more sensitive to the NOX levels and are highly variable between different urban sites. Enhanced levels of OH and HO2 radicals were observed on several days between 9h30-11h00 AM and suggest an additional HOX source for the morning hours and/or a fast HOX cycling under the high NOX conditions of the MCMA. A preliminary investigation of the HOX chemistry occurring in the MCMA urban atmosphere was performed using a photochemical box model based on the Regional Atmospheric Chemistry Mechanism (RACM). Model comparisons will be presented and the agreement between measured and predicted HOX concentrations will be discussed.

A Hox regulatory network of hindbrain segmentation is conserved to the base of vertebrates.

PubMed

Parker, Hugo J; Bronner, Marianne E; Krumlauf, Robb

2014-10-23

A defining feature governing head patterning of jawed vertebrates is a highly conserved gene regulatory network that integrates hindbrain segmentation with segmentally restricted domains of Hox gene expression. Although non-vertebrate chordates display nested domains of axial Hox expression, they lack hindbrain segmentation. The sea lamprey, a jawless fish, can provide unique insights into vertebrate origins owing to its phylogenetic position at the base of the vertebrate tree. It has been suggested that lamprey may represent an intermediate state where nested Hox expression has not been coupled to the process of hindbrain segmentation. However, little is known about the regulatory network underlying Hox expression in lamprey or its relationship to hindbrain segmentation. Here, using a novel tool that allows cross-species comparisons of regulatory elements between jawed and jawless vertebrates, we report deep conservation of both upstream regulators and segmental activity of enhancer elements across these distant species. Regulatory regions from diverse gnathostomes drive segmental reporter expression in the lamprey hindbrain and require the same transcriptional inputs (for example, Kreisler (also known as Mafba), Krox20 (also known as Egr2a)) in both lamprey and zebrafish. We find that lamprey hox genes display dynamic segmentally restricted domains of expression; we also isolated a conserved exonic hox2 enhancer from lamprey that drives segmental expression in rhombomeres 2 and 4. Our results show that coupling of Hox gene expression to segmentation of the hindbrain is an ancient trait with origin at the base of vertebrates that probably led to the formation of rhombomeric compartments with an underlying Hox code.

Non-homeodomain regions of Hox proteins mediate activation versus repression of Six2 via a single enhancer site in vivo

PubMed Central

Yallowitz, Alisha R.; Gong, Ke-Qin; Swinehart, Ilea T.; Nelson, Lisa T.; Wellik, Deneen M.

2009-01-01

Summary Hox genes control many developmental events along the AP axis, but few target genes have been identified. Whether target genes are activated or repressed, what enhancer elements are required for regulation, and how different domains of the Hox proteins contribute to regulatory specificity is poorly understood. Six2 is genetically downstream of both the Hox11 paralogous genes in the developing mammalian kidney and Hoxa2 in branchial arch and facial mesenchyme. Loss-of-function of Hox11 leads to loss of Six2 expression and loss-of-function of Hoxa2 leads to expanded Six2 expression. Herein we demonstrate that a single enhancer site upstream of the Six2 coding sequence is responsible for both activation by Hox11 proteins in the kidney and repression by Hoxa2 in the branchial arch and facial mesenchyme in vivo. DNA binding activity is required for both activation and repression, but differential activity is not controlled by differences in the homeodomains. Rather, protein domains N- and C-terminal to the homeodomain confer activation versus repression activity. These data support a model in which the DNA binding specificity of Hox proteins in vivo may be similar, consistent with accumulated in vitro data, and that unique functions result mainly from differential interactions mediated by non-homeodomain regions of Hox proteins. PMID:19716816

Molecular integration of HoxB4 and STAT3 for self-renewal of hematopoietic stem cells: a model of molecular convergence for stemness.

PubMed

Hong, Sung-Hyun; Yang, Seung-Jip; Kim, Tae-Min; Shim, Jae-Seung; Lee, Ho-Sun; Lee, Ga-Young; Park, Bo-Bae; Nam, Suk Woo; Ryoo, Zae Young; Oh, Il-Hoan

2014-05-01

The upregulation of HoxB4 promotes self-renewal of hematopoietic stem cells (HSCs) without overriding the normal stem cell pool size. A similar enhancement of HSC self-renewal occurs when signal transducer and activator of transcription 3 (STAT3) is activated in HSCs. In this study, to gain insight into the functional organization of individual transcription factors (TFs) that have similar effects on HSCs, we investigated the molecular interplay between HoxB4 and STAT3 in the regulation of HSC self-renewal. We found that while STAT3-C or HoxB4 similarly enhanced the in vitro self-renewal and in vivo repopulating activities of HSCs, simultaneous transduction of both TFs did not have additive effects, indicating their functional redundancy in HSCs. In addition, activation of STAT3 did not cause changes in the expression levels of HoxB4. In contrast, the inhibition of STAT3 activity in HoxB4-overexpressing hematopoietic cells significantly abrogated the enhancing effects of HoxB4, and the upregulation of HoxB4 caused a ligand-independent Tyr-phosphorylation of STAT3. Microarray analysis revealed a significant overlap of the transcriptomes regulated by STAT3 and HoxB4 in undifferentiated hematopoietic cells. Moreover, a gene set enrichment analysis showed significant overlap in the candidate TFs that can recapitulate the transcriptional changes induced by HoxB4 or STAT3. Interestingly, among these common TFs were the pluripotency-related genes Oct-4 and Nanog. These results indicate that tissue-specific TFs regulating HSC self-renewal are functionally organized to play an equivalent role in transcription and provide insights into the functional convergence of multiple entries of TFs toward a conserved transcription program for the stem cell state. © 2014 AlphaMed Press.

Correlation between Hox code and vertebral morphology in archosaurs.

PubMed

Böhmer, Christine; Rauhut, Oliver W M; Wörheide, Gert

2015-07-07

The relationship between developmental genes and phenotypic variation is of central interest in evolutionary biology. An excellent example is the role of Hox genes in the anteroposterior regionalization of the vertebral column in vertebrates. Archosaurs (crocodiles, dinosaurs including birds) are highly variable both in vertebral morphology and number. Nevertheless, functionally equivalent Hox genes are active in the axial skeleton during embryonic development, indicating that the morphological variation across taxa is likely owing to modifications in the pattern of Hox gene expression. By using geometric morphometrics, we demonstrate a correlation between vertebral Hox code and quantifiable vertebral morphology in modern archosaurs, in which the boundaries between morphological subgroups of vertebrae can be linked to anterior Hox gene expression boundaries. Our findings reveal homologous units of cervical vertebrae in modern archosaurs, each with their specific Hox gene pattern, enabling us to trace these homologies in the extinct sauropodomorph dinosaurs, a group with highly variable vertebral counts. Based on the quantifiable vertebral morphology, this allows us to infer the underlying genetic mechanisms in vertebral evolution in fossils, which represents not only an important case study, but will lead to a better understanding of the origin of morphological disparity in recent archosaur vertebral columns.

Correlation between Hox code and vertebral morphology in archosaurs

PubMed Central

Böhmer, Christine; Rauhut, Oliver W. M.; Wörheide, Gert

2015-01-01

The relationship between developmental genes and phenotypic variation is of central interest in evolutionary biology. An excellent example is the role of Hox genes in the anteroposterior regionalization of the vertebral column in vertebrates. Archosaurs (crocodiles, dinosaurs including birds) are highly variable both in vertebral morphology and number. Nevertheless, functionally equivalent Hox genes are active in the axial skeleton during embryonic development, indicating that the morphological variation across taxa is likely owing to modifications in the pattern of Hox gene expression. By using geometric morphometrics, we demonstrate a correlation between vertebral Hox code and quantifiable vertebral morphology in modern archosaurs, in which the boundaries between morphological subgroups of vertebrae can be linked to anterior Hox gene expression boundaries. Our findings reveal homologous units of cervical vertebrae in modern archosaurs, each with their specific Hox gene pattern, enabling us to trace these homologies in the extinct sauropodomorph dinosaurs, a group with highly variable vertebral counts. Based on the quantifiable vertebral morphology, this allows us to infer the underlying genetic mechanisms in vertebral evolution in fossils, which represents not only an important case study, but will lead to a better understanding of the origin of morphological disparity in recent archosaur vertebral columns. PMID:26085583

HoxBlinc RNA Recruits Set1/MLL Complexes to Activate Hox Gene Expression Patterns and Mesoderm Lineage Development.

PubMed

Deng, Changwang; Li, Ying; Zhou, Lei; Cho, Joonseok; Patel, Bhavita; Terada, Naohiro; Li, Yangqiu; Bungert, Jörg; Qiu, Yi; Huang, Suming

2016-01-05

Trithorax proteins and long-intergenic noncoding RNAs are critical regulators of embryonic stem cell pluripotency; however, how they cooperatively regulate germ layer mesoderm specification remains elusive. We report here that HoxBlinc RNA first specifies Flk1(+) mesoderm and then promotes hematopoietic differentiation through regulation of hoxb pathways. HoxBlinc binds to the hoxb genes, recruits Setd1a/MLL1 complexes, and mediates long-range chromatin interactions to activate transcription of the hoxb genes. Depletion of HoxBlinc by shRNA-mediated knockdown or CRISPR-Cas9-mediated genetic deletion inhibits expression of hoxb genes and other factors regulating cardiac/hematopoietic differentiation. Reduced hoxb expression is accompanied by decreased recruitment of Set1/MLL1 and H3K4me3 modification, as well as by reduced chromatin loop formation. Re-expression of hoxb2-b4 genes in HoxBlinc-depleted embryoid bodies rescues Flk1(+) precursors that undergo hematopoietic differentiation. Thus, HoxBlinc plays an important role in controlling hoxb transcription networks that mediate specification of mesoderm-derived Flk1(+) precursors and differentiation of Flk1(+) cells into hematopoietic lineages. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

HoxBlinc RNA recruits Set1/MLL complexes to activate Hox gene expression patterns and mesoderm lineage development

PubMed Central

Deng, Changwang; Li, Ying; Zhou, Lei; Cho, Joonseok; Patel, Bhavita; Terada, Nao; Li, Yangqiu; Bungert, Jörg; Qiu, Yi; Huang, Suming

2015-01-01

Summary Trithorax proteins and long-intergenic noncoding RNAs are critical regulators of embryonic stem cell pluripotency; however, how they cooperatively regulate germ layer mesoderm specification remains elusive. We report here that HoxBlinc RNA first specifies Flk1+ mesoderm and then promotes hematopoietic differentiation through regulating hoxb gene pathways. HoxBlinc binds to the hoxb genes, recruits Setd1a/MLL1 complexes, and mediates long-range chromatin interactions to activate transcription of the hoxb genes. Depletion of HoxBlinc by shRNA-mediated KD or CRISPR-Cas9-mediated genetic deletion inhibits expression of hoxb genes and other factors regulating cardiac/hematopoietic differentiation. Reduced hoxb gene expression is accompanied by decreased recruitment of Set1/MLL1 and H3K4me3 modification, as well as by reduced chromatin loop formation. Re-expression of hoxb2-b4 genes in HoxBlinc-depleted embryoid bodies rescues Flk1+ precursors that undergo hematopoietic differentiation. Thus, HoxBlinc plays an important role in controlling hoxb transcription networks that mediate specification of mesoderm-derived Flk1+ precursors and differentiation of Flk1+ cells into hematopoietic lineages. PMID:26725110

Wavelength-Resolved Photon Fluxes of Indoor Light Sources: Implications for HOx Production

NASA Astrophysics Data System (ADS)

Kowal, S.; Kahan, T.

2017-12-01

Only a handful of studies have considered photolytic reactions indoors because photon fluxes at short wavelengths are generally considered to be negligible. We have measured wavelength resolved photon fluxes from indoor light sources including incandescent, halogen, compact fluorescent (CFL), and light emitting diodes (LED). In addition, fluorescent tubes, used in many offices and industrial buildings, and sunlight through windows were measured. The measured photon fluxes were used to calculate photolysis rate constants for potential indoor hydroxyl and peroxy radical (OH and HO2, "HOx") precursors: acetaldehyde (CH3CHO), formaldehyde (HCHO), hydrogen peroxide (H2O2), nitrous acid (HONO) and ozone (O3). Rate constants in conjunction with typical indoor concentrations were used to predict HOx production rates under various lighting conditions. Our results illustrate that all light sources except LEDs emit light at high enough energy to photolyze HOx precursors. Under typical lighting conditions only fluorescent tubes and sunlight will initiate significant photochemical HOx formation, and HONO and HCHO will be the only molecules that will have a strong influence on HOx levels indoors. Data from our experiments can be used in indoor air models to better predict HOx levels indoors.

Clinical significance of HOX11L2 expression linked to t(5;14)(q35;q32), of HOX11 expression, and of SIL-TAL fusion in childhood T-cell malignancies: results of EORTC studies 58881 and 58951.

PubMed

Cavé, Hélène; Suciu, Stefan; Preudhomme, Claude; Poppe, Bruce; Robert, Alain; Uyttebroeck, Anne; Malet, Michèle; Boutard, Patrick; Benoit, Yves; Mauvieux, Laurent; Lutz, Patrick; Méchinaud, Françoise; Grardel, Nathalie; Mazingue, Francoise; Dupont, Madeleine; Margueritte, Geneviève; Pages, Marie-Pierre; Bertrand, Yves; Plouvier, Emmanuel; Brunie, Ghislaine; Bastard, Christian; Plantaz, Dominique; Vande Velde, Isabel; Hagemeijer, Anne; Speleman, Frank; Lessard, Michel; Otten, Jacques; Vilmer, Etienne; Dastugue, Nicole

2004-01-15

In a series of 153 children with T-cell malignancies enrolled in 2 consecutive European Organization for Research and Treatment of Cancer (EORTC) trials, we assessed the HOX11L2 expression and/or the presence of a t(5;14)(q35;q32). Additionally, in 138 of these patients, HOX11 expression and SIL-TAL rearrangement were also assessed. These alterations were mutually exclusive, and their frequency was 23% (n = 35), 7% (n = 10), and 12% (n = 17), respectively. HOX11L2/t(5;14) positivity was more frequent in acute lymphoblastic leukemia (ALL) with cortical T immunophenotype and in children aged between 6 and 9 years. In contrast with previously reported data, patients positive and negative for HOX11L2/t(5;14) were comparable with regard to clinical outcome as well as to the response to a 7-day prephase treatment or to residual disease at completion of induction therapy. The 3-year event-free survival (EFS) rate (+/- SE percentage) for patients positive and negative for HOX11L2/t(5;14) was 75.5% (+/- 8.1%) and 68.3% (+/- 5.0%), respectively; the hazard ratio was 0.84 (95% confidence interval, 0.40-1.80). Patients with HOX11-high expression and those with SIL-TAL fusion had low levels of residual disease at the end of induction and a favorable prognosis: the 3-year EFS rate was 83.3% (+/- 8.5%) and 75.3% (+/- 12.6%), respectively. The results obtained in HOX11L2/t(5;14) patients in this study do not confirm the unfavorable prognosis reported in previous studies.

HoxB2 binds mutant SOD1 and is altered in transgenic model of ALS.

PubMed

Zhai, Jinbin; Lin, Hong; Canete-Soler, Rafaela; Schlaepfer, William W

2005-09-15

Mutations in Cu/Zn superoxide dismutase (SOD1) cause approximately 20% of familial amyotrophic lateral sclerosis by a toxic gain of function; however, the precise mechanisms remain unclear. Here, we report the identification of HoxB2, a homeodomain-containing transcription factor, as a G93A mutant SOD1 interactive protein in a yeast two-hybrid screen. We show that HoxB2 co-precipitates and co-localizes with mutant SOD1 in neuronal cell lines, as well as in brain and spinal cord of G93A mutant SOD1 transgenic mice. Mutagenesis further shows that this interaction is mediated by the central homeodomain of HoxB2. In motor neuron-like NSC-34 cells, overexpression of HoxB2 or its homeodomain decreases the insolubility of mutant SOD1 and inhibits G93A or G86R mutant SOD1-induced neuronal cell death. In human and mouse tissues, we show that expression of HoxB2 persists in adult spinal cord and is primarily localized in nuclei of motor neurons. In G93A transgenic mice, HoxB2 co-localizes with mutant SOD1 and is redistributed to perikarya and proximal neurites of motor neurons. In addition, there is progressive accumulation of HoxB2 and mutant SOD1 as punctate inclusions in the neuropil surrounding motor neurons. Taken together, our findings demonstrate that interaction of HoxB2 with mutant SOD1 occurs in motor neurons of G93A mutant SOD1 transgenic mice and suggest that this interaction may modulate the neurotoxicity of mutant SOD1.

Evolution of the snake body form reveals homoplasy in amniote Hox gene function.

PubMed

Head, Jason J; Polly, P David

2015-04-02

Hox genes regulate regionalization of the axial skeleton in vertebrates, and changes in their expression have been proposed to be a fundamental mechanism driving the evolution of new body forms. The origin of the snake-like body form, with its deregionalized pre-cloacal axial skeleton, has been explained as either homogenization of Hox gene expression domains, or retention of standard vertebrate Hox domains with alteration of downstream expression that suppresses development of distinct regions. Both models assume a highly regionalized ancestor, but the extent of deregionalization of the primaxial domain (vertebrae, dorsal ribs) of the skeleton in snake-like body forms has never been analysed. Here we combine geometric morphometrics and maximum-likelihood analysis to show that the pre-cloacal primaxial domain of elongate, limb-reduced lizards and snakes is not deregionalized compared with limbed taxa, and that the phylogenetic structure of primaxial morphology in reptiles does not support a loss of regionalization in the evolution of snakes. We demonstrate that morphometric regional boundaries correspond to mapped gene expression domains in snakes, suggesting that their primaxial domain is patterned by a normally functional Hox code. Comparison of primaxial osteology in fossil and modern amniotes with Hox gene distributions within Amniota indicates that a functional, sequentially expressed Hox code patterned a subtle morphological gradient along the anterior-posterior axis in stem members of amniote clades and extant lizards, including snakes. The highly regionalized skeletons of extant archosaurs and mammals result from independent evolution in the Hox code and do not represent ancestral conditions for clades with snake-like body forms. The developmental origin of snakes is best explained by decoupling of the primaxial and abaxial domains and by increases in somite number, not by changes in the function of primaxial Hox genes.

Three genes in the human MHC class III region near the junction with the class II: Gene for receptor of advanced glycosylation end products, PBX2 homeobox gene and a notch homolog, human counterpart of mouse mammary tumor gene int-3

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

Sugaya, K.; Fukagawa, T.; Matsumoto, K.

Cosmid walking of about 250 kb from MHC class III gene CYP21 to class II was conducted. The gene for receptor of advanced glycosylation end products of proteins (RAGE, a member of immunoglobulin super-family molecules), the PBX2 homeobox gene designated HOX12, and the human counterpart of the mouse mammary tumor gene int-3 were found. The contiguous RAGE and HOX12 genes were completely sequenced, and the human int-3 counterpart was partially sequenced and assigned to a Notch homolog. This human Notch homolog, designated NOTCH3, showed both the intracellular portion present in the mouse int-3 sequence and the extracellular portion absent inmore » the int-3. It thus corresponds to the intact form of a Notch-type transmembrane protein. About 20 kb of dense Alu clustering was found just centromeric to the NOTCH3. 48 refs., 9 figs., 2 tabs.« less

Hox repertoires for motor neuron diversity and connectivity gated by a single accessory factor, FoxP1.

PubMed

Dasen, Jeremy S; De Camilli, Alessandro; Wang, Bin; Tucker, Philip W; Jessell, Thomas M

2008-07-25

The precision with which motor neurons innervate target muscles depends on a regulatory network of Hox transcription factors that translates neuronal identity into patterns of connectivity. We show that a single transcription factor, FoxP1, coordinates motor neuron subtype identity and connectivity through its activity as a Hox accessory factor. FoxP1 is expressed in Hox-sensitive motor columns and acts as a dose-dependent determinant of columnar fate. Inactivation of Foxp1 abolishes the output of the motor neuron Hox network, reverting the spinal motor system to an ancestral state. The loss of FoxP1 also changes the pattern of motor neuron connectivity, and in the limb motor axons appear to select their trajectories and muscle targets at random. Our findings show that FoxP1 is a crucial determinant of motor neuron diversification and connectivity, and clarify how this Hox regulatory network controls the formation of a topographic neural map.

Grappling with the HOX network in hematopoiesis and leukemia.

PubMed

McGonigle, Glenda J; Lappin, Terence R J; Thompson, Alexander

2008-05-01

The mammalian HOX gene network encodes a family of proteins which act as master regulators of developmental processes such as embryogenesis and hematopoiesis. The complex arrangement, regulation and co-factor association of HOX has been an area of intense research, particularly in cancer biology, for over a decade. The concept of redeployment of embryonic regulators in the neoplastic arena has received support from many quarters. Observations of altered HOX gene expression in various solid tumours and leukemia appear to support the thesis that 'oncology recapitulates ontogeny' but the identification of critical HOX subsets and their functional role in cancer onset and maintenance requires further investigation. The application of novel techniques and model systems will continue to enhance our understanding of the HOX network in the years to come. Better understanding of the intricacy of the complex as well as identification of functional pathways and direct targets of the encoded proteins will permit harnessing of this family of genes for clinical application.

HOX and TALE signatures specify human stromal stem cell populations from different sources.

PubMed

Picchi, Jacopo; Trombi, Luisa; Spugnesi, Laura; Barachini, Serena; Maroni, Giorgia; Brodano, Giovanni Barbanti; Boriani, Stefano; Valtieri, Mauro; Petrini, Mario; Magli, Maria Cristina

2013-04-01

Human stromal stem cell populations reside in different tissues and anatomical sites, however a critical question related to their efficient use in regenerative medicine is whether they exhibit equivalent biological properties. Here, we compared cellular and molecular characteristics of stromal stem cells derived from the bone marrow, at different body sites (iliac crest, sternum, and vertebrae) and other tissues (dental pulp and colon). In particular, we investigated whether homeobox genes of the HOX and TALE subfamilies might provide suitable markers to identify distinct stromal cell populations, as HOX proteins control cell positional identity and, together with their co-factors TALE, are involved in orchestrating differentiation of adult tissues. Our results show that stromal populations from different sources, although immunophenotypically similar, display distinct HOX and TALE signatures, as well as different growth and differentiation abilities. Stromal stem cells from different tissues are characterized by specific HOX profiles, differing in the number and type of active genes, as well as in their level of expression. Conversely, bone marrow-derived cell populations can be essentially distinguished for the expression levels of specific HOX members, strongly suggesting that quantitative differences in HOX activity may be crucial. Taken together, our data indicate that the HOX and TALE profiles provide positional, embryological and hierarchical identity of human stromal stem cells. Furthermore, our data suggest that cell populations derived from different body sites may not represent equivalent cell sources for cell-based therapeutical strategies for regeneration and repair of specific tissues. Copyright © 2012 Wiley Periodicals, Inc.

HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets

PubMed Central

De Kumar, Bony; Parker, Hugo J.; Paulson, Ariel; Parrish, Mark E.; Pushel, Irina; Singh, Narendra Pratap; Zhang, Ying; Slaughter, Brian D.; Unruh, Jay R.; Florens, Laurence; Zeitlinger, Julia; Krumlauf, Robb

2017-01-01

Hoxa1 has diverse functional roles in differentiation and development. We identify and characterize properties of regions bound by HOXA1 on a genome-wide basis in differentiating mouse ES cells. HOXA1-bound regions are enriched for clusters of consensus binding motifs for HOX, PBX, and MEIS, and many display co-occupancy of PBX and MEIS. PBX and MEIS are members of the TALE family and genome-wide analysis of multiple TALE members (PBX, MEIS, TGIF, PREP1, and PREP2) shows that nearly all HOXA1 targets display occupancy of one or more TALE members. The combinatorial binding patterns of TALE proteins define distinct classes of HOXA1 targets, which may create functional diversity. Transgenic reporter assays in zebrafish confirm enhancer activities for many HOXA1-bound regions and the importance of HOX-PBX and TGIF motifs for their regulation. Proteomic analyses show that HOXA1 physically interacts on chromatin with PBX, MEIS, and PREP family members, but not with TGIF, suggesting that TGIF may have an independent input into HOXA1-bound regions. Therefore, TALE proteins appear to represent a wide repertoire of HOX cofactors, which may coregulate enhancers through distinct mechanisms. We also discover extensive auto- and cross-regulatory interactions among the Hoxa1 and TALE genes, indicating that the specificity of HOXA1 during development may be regulated though a complex cross-regulatory network of HOXA1 and TALE proteins. This study provides new insight into a regulatory network involving combinatorial interactions between HOXA1 and TALE proteins. PMID:28784834

An abundance of Epsilonproteobacteria revealed in the gut microbiome of the laboratory cultured sea urchin, Lytechinus variegatus

PubMed Central

Hakim, Joseph A.; Koo, Hyunmin; Dennis, Lacey N.; Kumar, Ranjit; Ptacek, Travis; Morrow, Casey D.; Lefkowitz, Elliot J.; Powell, Mickie L.; Bej, Asim K.; Watts, Stephen A.

2015-01-01

In this study, we have examined the bacterial community composition of the laboratory cultured sea urchin Lytechinus variegatus gut microbiome and its culture environment using NextGen amplicon sequencing of the V4 segment of the 16S rRNA gene, and downstream bioinformatics tools. Overall, the gut and tank water was dominated by Proteobacteria, whereas the feed consisted of a co-occurrence of Proteobacteria and Firmicutes at a high abundance. The gut tissue represented Epsilonproteobacteria as dominant, with order Campylobacterales at the highest relative abundance (>95%). However, the pharynx tissue was dominated by class Alphaproteobacteria. The gut digesta and egested fecal pellets had a high abundance of class Gammaproteobacteria, from which Vibrio was found to be the primary genus, and Epsilonproteobacteria, with genus Arcobacter occurring at a moderate level. At the class level, the tank water was dominated by Gammaproteobacteria, and the feed by Alphaproteobacteria. Multi-Dimensional Scaling analysis showed that the microbial community of the gut tissue clustered together, as did the pharynx tissue to the feed. The gut digesta and egested fecal pellets showed a similarity relationship to the tank water. Further analysis of Campylobacterales at a lower taxonomic level using the oligotyping method revealed 37 unique types across the 10 samples, where Oligotype 1 was primarily represented in the gut tissue. BLAST analysis identified Oligotype 1 to be Arcobacter sp., Sulfuricurvum sp., and Arcobacter bivalviorum at an identity level >90%. This study showed that although distinct microbial communities are evident across multiple components of the sea urchin gut ecosystem, there is a noticeable correlation between the overall microbial communities of the gut with the sea urchin L. variegatus culture environment. PMID:26528245

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.

Non-transcriptional interactions of Hox proteins: inventory, facts, and future directions.

PubMed

Rezsohazy, René

2014-01-01

Hox proteins are conserved homeodomain transcription factors involved in the control of embryo patterning, organ development, and cell differentiation during animal development and adult life. Although recognizably active in gene regulation, accumulating reports support that Hox proteins are also active in controlling other molecular processes like mRNA translation, DNA repair, initiation of DNA replication, and possibly modulation of signal transduction. Here we review experimental evidence as well as databases entries indicative of non-transcriptional activities of Hox proteins. Copyright © 2013 Wiley Periodicals, Inc.

Hox11 paralogous genes are essential for metanephric kidney induction

PubMed Central

Wellik, Deneen M.; Hawkes, Patrick J.; Capecchi, Mario R.

2002-01-01

The mammalian Hox complex is divided into four linkage groups containing 13 sets of paralogous genes. These paralogous genes have retained functional redundancy during evolution. For this reason, loss of only one or two Hox genes within a paralogous group often results in incompletely penetrant phenotypes which are difficult to interpret by molecular analysis. For example, mice individually mutant for Hoxa11 or Hoxd11 show no discernible kidney abnormalities. Hoxa11/Hoxd11 double mutants, however, demonstrate hypoplasia of the kidneys. As described in this study, removal of the last Hox11 paralogous member, Hoxc11, results in the complete loss of metanephric kidney induction. In these triple mutants, the metanephric blastema condenses, and expression of early patterning genes, Pax2 and Wt1, is unperturbed. Eya1 expression is also intact. Six2 expression, however, is absent, as is expression of the inducing growth factor, Gdnf. In the absence of Gdnf, ureteric bud formation is not initiated. Molecular analysis of this phenotype demonstrates that Hox11 control of early metanephric induction is accomplished by the interaction of Hox11 genes with the pax-eya-six regulatory cascade, a pathway that may be used by Hox genes more generally for the induction of multiple structures along the anteroposterior axis. PMID:12050119

Inhibition of HOX/PBX dimer formation leads to necroptosis in acute myeloid leukemia cells.

PubMed

Alharbi, Raed A; Pandha, Hardev S; Simpson, Guy R; Pettengell, Ruth; Poterlowicz, Krzysztof; Thompson, Alexander; Harrington, Kevin; El-Tanani, Mohamed; Morgan, Richard

2017-10-27

The HOX genes encode a family of transcription factors that have key roles in both development and malignancy. Disrupting the interaction between HOX proteins and their binding partner, PBX, has been shown to cause apoptotic cell death in a range of solid tumors. However, despite HOX proteins playing a particularly significant role in acute myeloid leukemia (AML), the relationship between HOX gene expression and patient survival has not been evaluated (with the exception of HOXA9 ), and the mechanism by which HOX/PBX inhibition induces cell death in this malignancy is not well understood. In this study, we show that the expression of HOXA5 , HOXB2 , HOXB4 , HOXB9 , and HOXC9 , but not HOXA9, in primary AML samples is significantly related to survival. Furthermore, the previously described inhibitor of HOX/PBX dimerization, HXR9, is cytotoxic to both AML-derived cell lines and primary AML cells from patients. The mechanism of cell death is not dependent on apoptosis but instead involves a regulated form of necrosis referred to as necroptosis. HXR9-induced necroptosis is enhanced by inhibitors of protein kinase C (PKC) signaling, and HXR9 combined with the PKC inhibitor Ro31 causes a significantly greater reduction in tumor growth compared to either reagent alone.

Inhibition of HOX/PBX dimer formation leads to necroptosis in acute myeloid leukemia cells

PubMed Central

Alharbi, Raed A.; Pandha, Hardev S.; Simpson, Guy R.; Pettengell, Ruth; Poterlowicz, Krzysztof; Thompson, Alexander; Harrington, Kevin; El-Tanani, Mohamed; Morgan, Richard

2017-01-01

The HOX genes encode a family of transcription factors that have key roles in both development and malignancy. Disrupting the interaction between HOX proteins and their binding partner, PBX, has been shown to cause apoptotic cell death in a range of solid tumors. However, despite HOX proteins playing a particularly significant role in acute myeloid leukemia (AML), the relationship between HOX gene expression and patient survival has not been evaluated (with the exception of HOXA9), and the mechanism by which HOX/PBX inhibition induces cell death in this malignancy is not well understood. In this study, we show that the expression of HOXA5, HOXB2, HOXB4, HOXB9, and HOXC9, but not HOXA9, in primary AML samples is significantly related to survival. Furthermore, the previously described inhibitor of HOX/PBX dimerization, HXR9, is cytotoxic to both AML-derived cell lines and primary AML cells from patients. The mechanism of cell death is not dependent on apoptosis but instead involves a regulated form of necrosis referred to as necroptosis. HXR9-induced necroptosis is enhanced by inhibitors of protein kinase C (PKC) signaling, and HXR9 combined with the PKC inhibitor Ro31 causes a significantly greater reduction in tumor growth compared to either reagent alone. PMID:29163771

Hox11 paralogous genes are essential for metanephric kidney induction.

PubMed

Wellik, Deneen M; Hawkes, Patrick J; Capecchi, Mario R

2002-06-01

The mammalian Hox complex is divided into four linkage groups containing 13 sets of paralogous genes. These paralogous genes have retained functional redundancy during evolution. For this reason, loss of only one or two Hox genes within a paralogous group often results in incompletely penetrant phenotypes which are difficult to interpret by molecular analysis. For example, mice individually mutant for Hoxa11 or Hoxd11 show no discernible kidney abnormalities. Hoxa11/Hoxd11 double mutants, however, demonstrate hypoplasia of the kidneys. As described in this study, removal of the last Hox11 paralogous member, Hoxc11, results in the complete loss of metanephric kidney induction. In these triple mutants, the metanephric blastema condenses, and expression of early patterning genes, Pax2 and Wt1, is unperturbed. Eya1 expression is also intact. Six2 expression, however, is absent, as is expression of the inducing growth factor, Gdnf. In the absence of Gdnf, ureteric bud formation is not initiated. Molecular analysis of this phenotype demonstrates that Hox11 control of early metanephric induction is accomplished by the interaction of Hox11 genes with the pax-eya-six regulatory cascade, a pathway that may be used by Hox genes more generally for the induction of multiple structures along the anteroposterior axis.

Retinoic acid signaling targets Hox genes during the amphioxus gastrula stage: insights into early anterior-posterior patterning of the chordate body plan.

PubMed

Koop, Demian; Holland, Nicholas D; Sémon, Marie; Alvarez, Susana; de Lera, Angel Rodriguez; Laudet, Vincent; Holland, Linda Z; Schubert, Michael

2010-02-01

Previous studies of vertebrate development have shown that retinoic acid (RA) signaling at the gastrula stage strongly influences anterior-posterior (A-P) patterning of the neurula and later stages. However, much less is known about the more immediate effects of RA signaling on gene transcription and developmental patterning at the gastrula stage. To investigate the targets of RA signaling during the gastrula stage, we used the basal chordate amphioxus, in which gastrulation involves very minimal tissue movements. First, we determined the effect of altered RA signaling on expression of 42 genes (encoding transcription factors and components of major signaling cascades) known to be expressed in restricted domains along the A-P axis during the gastrula and early neurula stage. Of these 42 genes, the expression domains during gastrulation of only four (Hox1, Hox3, HNF3-1 and Wnt3) were spatially altered by exposure of the embryos to excess RA or to the RA antagonist BMS009. Moreover, blocking protein synthesis with puromycin before adding RA or BMS009 showed that only three of these genes (Hox1, Hox3 and HNF3-1) are direct RA targets at the gastrula stage. From these results we conclude that in the amphioxus gastrula RA signaling primarily acts via regulation of Hox transcription to establish positional identities along the A-P axis and that Hox1, Hox3, HNF3-1 and Wnt3 constitute a basal module of RA action during chordate gastrulation.

Effects of the antirheumatic remedy hox alpha--a new stinging nettle leaf extract--on matrix metalloproteinases in human chondrocytes in vitro.

PubMed

Schulze-Tanzil, G; de, Souza P; Behnke, B; Klingelhoefer, S; Scheid, A; Shakibaei, M

2002-04-01

Inflammatory joint diseases are characterized by enhanced extracellular matrix degradation which is predominantly mediated by cytokine-stimulated upregulation of matrix metalloproteinase (MMP) expression. Besides tumour necrosis factor-alpha (TNF-alpha), Interleukin-1beta (IL-1beta) produced by articular chondrocytes and synovial macrophages, is the most important cytokine stimulating MMP expression under inflammatory conditions. Blockade of these two cytokines and their downstream effectors are suitable molecular targets of antirheumatic therapy. Hox alpha is a novel stinging nettle (Urtica dioica/Urtica urens) leaf extract used for treatment of rheumatic diseases. The aim of the present study was to clarify the effects of Hox alpha and the monosubstance 13-HOTrE (13-Hydroxyoctadecatrienic acid) on the expression of matrix metalloproteinase-1, -3 and -9 proteins (MMP-1, -3, -9). Human chondrocytes were cultured on collagen type-II-coated petri dishes, exposed to IL-1beta and treated with or without Hox alpha and 13-HOTrE. A close analysis by immunofluorescence microscopy and western blot analysis showed that Hox alpha and 13-HOTrE significantly suppressed IL-1beta-induced expression of matrix metalloproteinase-1, -3 and -9 proteins on the chondrocytes in vitro. The potential of Hox alpha and 13-HOTrE to suppress the expression of matrix metalloproteinases may explain the clinical efficacy of stinging nettle leaf extracts in treatment of rheumatoid arthritis. These results suggest that the monosubstance 13-HOTrE is one of the more active antiinflammatory substances in Hox alpha and that Hox alpha may be a promising remedy for therapy of inflammatory joint diseases.

LIN-39/Hox triggers cell division and represses EFF-1/fusogen-dependent vulval cell fusion

PubMed Central

Shemer, Gidi; Podbilewicz, Benjamin

2002-01-01

General mechanisms by which Hox genes establish cell fates are known. However, a few Hox effectors mediating cell behaviors have been identified. Here we found the first effector of LIN-39/HoxD4/Dfd in Caenorhabditis elegans. In specific vulval precursor cells (VPCs), LIN-39 represses early and late expression of EFF-1, a membrane protein essential for cell fusion. Repression of eff-1 is also achieved by the activity of CEH-20/Exd/Pbx, a known cofactor of Hox proteins. Unfused VPCs in lin-39(−);eff-1(−) double mutants fail to divide but migrate, executing vulval fates. Thus, lin-39 is essential for inhibition of EFF-1-dependent cell fusion and stimulation of cell proliferation during vulva formation. Supplemental material is available at http://www.genesdev.org. PMID:12502736

Response of sediment microbial community structure in a freshwater reservoir to manipulations in oxygen availability.

PubMed

Bryant, Lee D; Little, John C; Bürgmann, Helmut

2012-04-01

Hypolimnetic oxygenation systems (HOx) are being increasingly used in freshwater reservoirs to elevate dissolved oxygen levels in the hypolimnion and suppress sediment-water fluxes of soluble metals (e.g. Fe and Mn) which are often microbially mediated. We assessed changes in sediment microbial community structure and corresponding biogeochemical cycling on a reservoir-wide scale as a function of HOx operations. Sediment microbial biomass as quantified by DNA concentration was increased in regions most influenced by the HOx. Following an initial decrease in biomass in the upper sediment while oxygen concentrations were low, biomass typically increased at all depths as the 4-month-long oxygenation season progressed. A distinct shift in microbial community structure was only observed at the end of the season in the upper sediment near the HOx. While this shift was correlated to HOx-enhanced oxygen availability, increased TOC levels and precipitation of Fe- and Mn-oxides, abiotic controls on Fe and Mn cycling, and/or the adaptability of many bacteria to variations in prevailing electron acceptors may explain the delayed response and the comparatively limited changes at other locations. While the sediment microbial community proved remarkably resistant to relatively short-term changes in HOx operations, HOx-induced variation in microbial structure, biomass, and activity was observed after a full season of oxygenation. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Protection of large predators in a marine reserve alters size-dependent prey mortality

PubMed Central

Gaines, Steven D.; Hamilton, Scott L.; Warner, Robert R.

2017-01-01

Where predator–prey interactions are size-dependent, reductions in predator size owing to fishing has the potential to disrupt the ecological role of top predators in marine ecosystems. In southern California kelp forests, we investigated the size-dependence of the interaction between herbivorous sea urchins and one of their predators, California sheephead (Semicossyphus pulcher). Empirical tests examined how differences in predator size structure between reserve and fished areas affected size-specific urchin mortality. Sites inside marine reserves had greater sheephead size and biomass, while empirical feeding trials indicated that larger sheephead were required to successfully consume urchins of increasing test diameter. Evaluations of the selectivity of sheephead for two urchin species indicated that shorter-spined purple urchins were attacked more frequently and successfully than longer-spined red urchins of the same size class, particularly at the largest test diameters. As a result of these size-specific interactions and the higher biomass of large sheephead inside reserves, urchin mortality rates were three times higher inside the reserve for both species. In addition, urchin mortality rates decreased with urchin size, and very few large urchins were successfully consumed in fished areas. The truncation of sheephead size structure that commonly occurs owing to fishing will probably result in reductions in urchin mortality, which may reduce the resilience of kelp beds to urchin barren formation. By contrast, the recovery of predator size structure in marine reserves may restore this resilience, but may be delayed until fish grow to sizes capable of consuming larger urchins. PMID:28123086

Measurements of OH and HO2 Radicals and OH Reactivity at Tropical Locations Using Laser-Induced Fluorescence Spectroscopy

NASA Astrophysics Data System (ADS)

Furneaux, K. L.; Whalley, L. K.; Edwards, P.; Goddard, A.; Ingham, T.; Evans, M. J.; Heard, D. E.

2009-04-01

The OH radical is the dominant daytime oxidant in the atmosphere. Together with the closely coupled HO2 radical, these two species (termed HOx) play an important role in determining the composition of the atmosphere. Tropical latitudes are active regions of atmospheric chemistry due to high solar radiation, humidity and temperature. For these reasons, field measurements of HOx in the tropics are crucial to improve understanding of atmospheric chemistry through model - measurement comparisons. Due to the low number of HOx measurements in the tropics, these comparisons are sparse. An aircraft campaign over the pristine Amazon rainforest found HOx concentrations to be high1,2. It has been proposed that this is due to a previously overlooked OH recycling mechanism via the oxidation of isoprene1,2. The need to determine if this is ubiquitous across tropical rainforest regions is necessary. The Leeds FAGE instrument was deployed at the Bukit Atur Global Atmospheric Watch Station, Borneo (5.0N, 117.8E) from April - July 2008 as part of the OP3 project (Oxidant and Particle Photochemical Processes above a South-East Asian tropical rainforest) to measure OH and HO2 concentrations and the OH chemical lifetime by Fluorescence Assay by Gas Expansion (FAGE). These measurements represent the first ground based [HOx] measurements in a tropical rainforest. Chemical activity differed significantly throughout the measurement period. HOx concentrations were elevated in July (average peak [OH] = 5.3 ×106 molecule cm-3) compared to April (average peak [OH] = 2.5 ×106 molecule cm-3), attributed to higher OH sinks in April. Measurements of the OH chemical lifetime can be used to quantify unknown OH sinks. The OH chemical lifetime displayed a diurnal cycle that correlated with isoprene concentrations. At this site isoprene represents the major OH loss route but there are significant unknown fractions. Model calculations result in an under prediction of HOx when measured sinks are included, indicating a missing HOx source. Both OH and HO2 were observed at night. Measurements of HOx at the Cape Verde Atmospheric Observatory (16.9N, 24.9W) were made from May - June 2007 as part of the RHaMBLe (Reactive Halogens in the Marine Boundary Layer) programme. The site is located adjacent to the ocean with an absence of macro algae, providing conditions analogous to open ocean, clean marine air. However, background tropical conditions were not dictated by simple chemistry. Peak OH and HO2 concentrations were 9 × 106 molecule cm-3 and 6 ×108 molecule cm-3, respectively. HO2 was observed at night between 5 - 20 × 106 molecule cm-3. Modelling studies determined oxygenated-VOCs and halogen chemistry to play an important role in HOx chemistry. A comparison of HOx measurements at tropical open ocean and tropical rainforest locations shows that HOx chemistry varies greatly throughout the tropics. Higher HOx sinks in tropical rainforest environments result in a decrease of HOx compared to the tropical open ocean. 1. Lelieveld, J., T. M. Butler, et al. (2008). Atmospheric oxidation capacity sustained by a tropical forest, Nature, 452(7188): 737-740. 2. Martinez, M., Harder, H., et al. (2008). Hydroxyl radicals in the tropical troposphere over the Suriname rainforest: airborne measurements, ACPD, 8, 15491-15536.

Overexpression of HOXA4 and HOXA9 genes promotes self-renewal and contributes to colon cancer stem cell overpopulation.

PubMed

Bhatlekar, Seema; Viswanathan, Vignesh; Fields, Jeremy Z; Boman, Bruce M

2018-02-01

Because HOX genes encode master regulatory transcription factors that regulate stem cells (SCs) during development and aberrant expression of HOX genes occurs in various cancers, our goal was to determine if dysregulation of HOX genes is involved in the SC origin of colorectal cancer (CRC). We previously reported that HOXA4 and HOXD10 are expressed in the colonic SC niche and are overexpressed in CRC. HOX gene expression was studied in SCs from human colon tissue and CRC cells (CSCs) using qPCR and immunostaining. siRNA-mediated knockdown of HOX expression was used to evaluate the role of HOX genes in modulating cancer SC (CSC) phenotype at the level of proliferation, SC marker expression, and sphere formation. All-trans-retinoic-acid (ATRA), a differentiation-inducing agent was evaluated for its effects on HOX expression and CSC growth. We found that HOXA4 and HOXA9 are up-regulated in CRC SCs. siRNA knockdown of HOXA4 and HOXA9 reduced: (i) proliferation and sphere-formation and (ii) gene expression of known SC markers (ALDH1, CD166, LGR5). These results indicate that proliferation and self-renewal ability of CRC SCs are reduced in HOXA4 and HOXA9 knockdown cells. ATRA decreased HOXA4, HOXA9, and HOXD10 expression in parallel with reduction in ALDH1 expression, self-renewal, and proliferation. Overall, our findings indicate that overexpression of HOXA4 and HOXA9 contributes to self-renewal and overpopulation of SCs in CRC. Strategies designed to modulate HOX expression may provide ways to target malignant SCs and to develop more effective therapies for CRC. © 2017 Wiley Periodicals, Inc.

Establishment of Hox vertebral identities in the embryonic spine precursors

PubMed Central

Iimura, Tadahiro; Denans, Nicolas; Pourquié, Olivier

2012-01-01

Summary The vertebrate spine exhibits two striking characteristics. The first one is the periodic arrangement of its elements – the vertebrae – along the antero-posterior axis. This segmented organization is the result of somitogenesis, which takes place during organogenesis. The segmentation machinery involves a molecular oscillator – the segmentation clock – which delivers a periodic signal controlling somite production. During embryonic axis elongation, this signal is displaced posteriorly by a system of traveling signaling gradients – the wavefront – which depends on the Wnt, FGF and retinoic acid pathways. The other characteristic feature of the spine is the subdivision of groups of vertebrae into anatomical domains, such as the cervical, thoracic, lumbar, sacral and caudal regions. This axial regionalization is controlled by a set of transcription factors called Hox genes. Hox genes exhibit nested expression domains in the somites which reflect their linear arrangement along the chromosomes– a property termed colinearity. The colinear disposition of Hox genes expression domains provides a blueprint for the regionalization of the future vertebral territories of the spine. In amniotes, Hox genes are activated in the somite precursors of the epiblast in a temporal colinear sequence and they were proposed to control their progressive ingression into the nascent paraxial mesoderm. Consequently, the positioning of the expression domains of Hox genes along the antero-posterior axis is largely controlled by the timing of Hox activation during gastrulation. Positioning of the somitic Hox domains is subsequently refined through a cross talk with the segmentation machinery in the presomitic mesoderm. In this review, we focus on our current understanding of the embryonic mechanisms that establish vertebral identities during vertebrate development. PMID:19651306

Trimeric association of Hox and TALE homeodomain proteins mediates Hoxb2 hindbrain enhancer activity.

PubMed

Jacobs, Y; Schnabel, C A; Cleary, M L

1999-07-01

Pbx/exd proteins modulate the DNA binding affinities and specificities of Hox proteins and contribute to the execution of Hox-dependent developmental programs in arthropods and vertebrates. Pbx proteins also stably heterodimerize and bind DNA with Meis and Pknox1-Prep1, additional members of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins that function on common genetic pathways with a subset of Hox proteins. In this study, we demonstrated that Pbx and Meis bind DNA as heterotrimeric complexes with Hoxb1 on a genetically defined Hoxb2 enhancer, r4, that mediates the cross-regulatory transcriptional effects of Hoxb1 in vivo. The DNA binding specificity of the heterotrimeric complex for r4 is mediated by a Pbx-Hox site in conjunction with a distal Meis site, which we showed to be required for ternary complex formation and Meis-enhanced transcription. Formation of heterotrimeric complexes in which all three homeodomains bind their cognate DNA sites is topologically facilitated by the ability of Pbx and Meis to interact through their amino termini and bind DNA without stringent half-site orientation and spacing requirements. Furthermore, Meis site mutation in the Hoxb2 enhancer phenocopies Pbx-Hox site mutation to abrogate enhancer-directed expression of a reporter transgene in the murine embryonic hindbrain, demonstrating that DNA binding by all three proteins is required for trimer function in vivo. Our data provide in vitro and in vivo evidence for the combinatorial regulation of Hox and TALE protein functions that are mediated, in part, by their interdependent DNA binding activities as ternary complexes. As a consequence, Hoxb1 employs Pbx and Meis-related proteins, as a pair of essential cofactors in a higher-order molecular complex, to mediate its transcriptional effects on an endogenous Hox response element.

A Reevaluation of Airborne HO(x) Observations from NASA Field Campaigns

NASA Technical Reports Server (NTRS)

Olson, Jennifer; Crawford, James H.; Chen, Gao; Brune, William H.; Faloona, Ian C.; Tan, David; Harder, Hartwig; Martinez, Monica

2006-01-01

In-situ observations of tropospheric HO(x) (OH and HO2) obtained during four NASA airborne campaigns (SUCCESS, SONEX, PEM-Tropics B and TRACE-P) are reevaluated using the NASA Langley time-dependent photochemical box model. Special attention is given to previously diagnosed discrepancies between observed and predicted HO2 which increase with higher NO(x) levels and at high solar zenith angles. This analysis shows that much of the model discrepancy at high NO(x) during SUCCESS can be attributed to modeling observations at time-scales too long to capture the nonlinearity of HO(x) chemistry under highly variable conditions for NO(x). Discrepancies at high NO(x) during SONEX can be moderated to a large extent by complete use of all available precursor observations. Differences in kinetic rate coefficients and photolysis frequencies available for previous studies versus current recommendations also explain some of the disparity. Each of these causes is shown to exert greater influence with increasing NO(x) due to both the chemical nonlinearity between HO(x) and NO(x) and the increased sensitivity of HO(x) to changes in sources at high NO(x). In contrast, discrepancies at high solar zenith angles will persist until an adequate nighttime source of HO(x) can be identified. It is important to note that this analysis falls short of fully eliminating the issue of discrepancies between observed and predicted HO(x) for high NO(x) environments. These discrepancies are not resolved with the above causes in other data sets from ground-based field studies. Nevertheless, these results highlight important considerations in the application of box models to observationally based predictions of HO(x) radicals.

Phase-Shift Dynamics of Sea Urchin Overgrazing on Nutrified Reefs.

PubMed

Kriegisch, Nina; Reeves, Simon; Johnson, Craig R; Ling, Scott D

2016-01-01

Shifts from productive kelp beds to impoverished sea urchin barrens occur globally and represent a wholesale change to the ecology of sub-tidal temperate reefs. Although the theory of shifts between alternative stable states is well advanced, there are few field studies detailing the dynamics of these kinds of transitions. In this study, sea urchin herbivory (a 'top-down' driver of ecosystems) was manipulated over 12 months to estimate (1) the sea urchin density at which kelp beds collapse to sea urchin barrens, and (2) the minimum sea urchin density required to maintain urchin barrens on experimental reefs in the urbanised Port Phillip Bay, Australia. In parallel, the role of one of the 'bottom-up' drivers of ecosystem structure was examined by (3) manipulating local nutrient levels and thus attempting to alter primary production on the experimental reefs. It was found that densities of 8 or more urchins m-2 (≥ 427 g m-2 biomass) lead to complete overgrazing of kelp beds while kelp bed recovery occurred when densities were reduced to ≤ 4 urchins m-2 (≤ 213 g m-2 biomass). This experiment provided further insight into the dynamics of transition between urchin barrens and kelp beds by exploring possible tipping-points which in this system can be found between 4 and 8 urchins m-2 (213 and 427 g m-2 respectively). Local enhancement of nutrient loading did not change the urchin density required for overgrazing or kelp bed recovery, as algal growth was not affected by nutrient enhancement.

Food webs and fishing affect parasitism of the sea urchin Eucidaris galapagensis in the Galápagos

USGS Publications Warehouse

Sonnenholzner, Jorge I.; Lafferty, Kevin D.; Ladah, Lydia B.

2011-01-01

In the Galápagos Islands, two eulimid snails parasitize the common pencil sea urchin, Eucidaris galapagensis. Past work in the Galápagos suggests that fishing reduces lobster and fish densities and, due to this relaxation of predation pressure, indirectly increases urchin densities, creating the potential for complex indirect interactions between fishing and parasitic snails. To measure indirect effects of fishing on these parasitic snails, we investigated the spatial relationships among urchins, parasitic snails, commensal crabs, and large urchin predators (hogfish and lobsters). Parasitic snails had higher densities at sites where urchins were abundant, probably due to increased resource availability. Commensal crabs that shelter under urchin spines, particularly the endemic Mithrax nodosus, preyed on the parasitic snails in aquaria, and snails were less abundant at field sites where these crabs were common. In aquaria, hogfish and lobsters readily ate crabs, but crabs were protected from predation under urchin spines, leading to a facultative mutualism between commensal crabs and urchins. In the field, fishing appeared to indirectly increase the abundance of urchins and their commensal crabs by reducing predation pressure from fish and lobsters. Fished sites had fewer snails per urchin, probably due to increased predation from commensal crabs. However, because fished sites also tended to have more urchins, there was no significant net effect of fishing on the number of snails per square meter. These results suggest that fishing can have complex indirect effects on parasites by altering food webs.

Functional specificity of a Hox protein mediated by the recognition of minor groove structure.

PubMed

Joshi, Rohit; Passner, Jonathan M; Rohs, Remo; Jain, Rinku; Sosinsky, Alona; Crickmore, Michael A; Jacob, Vinitha; Aggarwal, Aneel K; Honig, Barry; Mann, Richard S

2007-11-02

The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via residues located in these extended regions that insert into the minor groove but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.

The management of hand injuries caused by sea urchin spines.

PubMed

Nassab, R; Rayatt, S; Peart, F

2005-08-01

Injuries to the hand by sea urchin spines are not commonly seen in the United Kingdom. There are many varieties of sea urchins (Echinoidea) throughout the world. They have a spherical calcium carbonate exoskeleton covered with spines. Certain varieties may be venomous, in particular the flower urchin (Toxopneustes pileolus) found in the Indo-Pacific oceans. Injury may also be caused by the urchin spines or pedicellaria (delicate seizing organs equipped with jaws). A small number of hand injuries associated with sea urchin spines have been reported in the literature.

A Hox regulatory network establishes motor neuron pool identity and target-muscle connectivity.

PubMed

Dasen, Jeremy S; Tice, Bonnie C; Brenner-Morton, Susan; Jessell, Thomas M

2005-11-04

Spinal motor neurons acquire specialized "pool" identities that determine their ability to form selective connections with target muscles in the limb, but the molecular basis of this striking example of neuronal specificity has remained unclear. We show here that a Hox transcriptional regulatory network specifies motor neuron pool identity and connectivity. Two interdependent sets of Hox regulatory interactions operate within motor neurons, one assigning rostrocaudal motor pool position and a second directing motor pool diversity at a single segmental level. This Hox regulatory network directs the downstream transcriptional identity of motor neuron pools and defines the pattern of target-muscle connectivity.

Regulation of Silk Genes by Hox and Homeodomain Proteins in the Terminal Differentiated Silk Gland of the Silkworm Bombyx mori

PubMed Central

Takiya, Shigeharu; Tsubota, Takuya; Kimoto, Mai

2016-01-01

The silk gland of the silkworm Bombyx mori is a long tubular organ that is divided into several subparts along its anteroposterior (AP) axis. As a trait of terminal differentiation of the silk gland, several silk protein genes are expressed with unique regional specificities. Most of the Hox and some of the homeobox genes are also expressed in the differentiated silk gland with regional specificities. The expression patterns of Hox genes in the silk gland roughly correspond to those in embryogenesis showing “colinearity”. The central Hox class protein Antennapedia (Antp) directly regulates the expression of several middle silk gland–specific silk genes, whereas the Lin-1/Isl-1/Mec3 (LIM)-homeodomain transcriptional factor Arrowhead (Awh) regulates the expression of posterior silk gland–specific genes for silk fiber proteins. We summarize our results and discuss the usefulness of the silk gland of Bombyx mori for analyzing the function of Hox genes. Further analyses of the regulatory mechanisms underlying the region-specific expression of silk genes will provide novel insights into the molecular bases for target-gene selection and regulation by Hox and homeodomain proteins. PMID:29615585

Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model

PubMed Central

Woltering, Joost M.; Duboule, Denis

2015-01-01

The tetrapod vertebral column has become increasingly complex during evolution as an adaptation to a terrestrial life. At the same time, the evolution of the vertebral formula became subject to developmental constraints acting on the size of the cervical and thoraco-lumbar regions. In the course of our studies concerning the evolution of Hox gene regulation, we produced a transgenic mouse model expressing fish Hox genes, which displayed a reduced number of thoraco-lumbar vertebrae and concurrent sacral homeotic transformations. Here, we analyze this mutant stock and conclude that the ancestral, pre-tetrapodial Hox code already possessed the capacity to induce vertebrae with sacral characteristics. This suggests that alterations in the interpretation of the Hox code may have participated to the evolution of this region in tetrapods, along with potential modifications of the HOX proteins themselves. With its reduced vertebral number, this mouse stock violates a previously described developmental constraint, which applies to the thoraco-lumbar region. The resulting offset between motor neuron morphology, vertebral patterning and the relative positioning of hind limbs illustrates that the precise orchestration of the Hox-clock in parallel with other ontogenetic pathways places constraints on the evolvability of the body plan. PMID:26238020

Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies

PubMed Central

Otto, Wolfgang; Stadler, Peter F.; López-Giraldéz, Francesc; Townsend, Jeffrey P.; Lynch, Vincent J.

2009-01-01

A major mode of gene expression evolution is based on changes in cis-regulatory elements (CREs) whose function critically depends on the presence of transcription factor–binding sites (TFBS). Because CREs experience extensive TFBS turnover even with conserved function, alignment-based studies of CRE sequence evolution are limited to very closely related species. Here, we propose an alternative approach based on a stochastic model of TFBS turnover. We implemented a maximum likelihood model that permits variable turnover rates in different parts of the species tree. This model can be used to detect changes in turnover rate as a proxy for differences in the selective pressures acting on TFBS in different clades. We applied this method to five TFBS in the fungi methionine biosynthesis pathway and three TFBS in the HoxA clusters of vertebrates. We find that the estimated turnover rate is generally high, with half-life ranging between ∼5 and 150 My and a mode around tens of millions of years. This rate is consistent with the finding that even functionally conserved enhancers can show very low sequence similarity. We also detect statistically significant differences in the equilibrium densities of estrogen- and progesterone-response elements in the HoxA clusters between mammal and nonmammal vertebrates. Even more extreme clade-specific differences were found in the fungal data. We conclude that stochastic models of TFBS turnover enable the detection of shifts in the selective pressures acting on CREs in different organisms. The analysis tool, called CRETO (Cis-Regulatory Element Turn-Over) can be downloaded from http://www.bioinf.uni-leipzig.de/Software/creto/. PMID:20333180

HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets.

PubMed

De Kumar, Bony; Parker, Hugo J; Paulson, Ariel; Parrish, Mark E; Pushel, Irina; Singh, Narendra Pratap; Zhang, Ying; Slaughter, Brian D; Unruh, Jay R; Florens, Laurence; Zeitlinger, Julia; Krumlauf, Robb

2017-09-01

Hoxa1 has diverse functional roles in differentiation and development. We identify and characterize properties of regions bound by HOXA1 on a genome-wide basis in differentiating mouse ES cells. HOXA1-bound regions are enriched for clusters of consensus binding motifs for HOX, PBX, and MEIS, and many display co-occupancy of PBX and MEIS. PBX and MEIS are members of the TALE family and genome-wide analysis of multiple TALE members (PBX, MEIS, TGIF, PREP1, and PREP2) shows that nearly all HOXA1 targets display occupancy of one or more TALE members. The combinatorial binding patterns of TALE proteins define distinct classes of HOXA1 targets, which may create functional diversity. Transgenic reporter assays in zebrafish confirm enhancer activities for many HOXA1-bound regions and the importance of HOX-PBX and TGIF motifs for their regulation. Proteomic analyses show that HOXA1 physically interacts on chromatin with PBX, MEIS, and PREP family members, but not with TGIF, suggesting that TGIF may have an independent input into HOXA1-bound regions. Therefore, TALE proteins appear to represent a wide repertoire of HOX cofactors, which may coregulate enhancers through distinct mechanisms. We also discover extensive auto- and cross-regulatory interactions among the Hoxa1 and TALE genes, indicating that the specificity of HOXA1 during development may be regulated though a complex cross-regulatory network of HOXA1 and TALE proteins. This study provides new insight into a regulatory network involving combinatorial interactions between HOXA1 and TALE proteins. © 2017 De Kumar et al.; Published by Cold Spring Harbor Laboratory Press.

Phase-Shift Dynamics of Sea Urchin Overgrazing on Nutrified Reefs

PubMed Central

Kriegisch, Nina; Reeves, Simon; Johnson, Craig R.; Ling, Scott D.

2016-01-01

Shifts from productive kelp beds to impoverished sea urchin barrens occur globally and represent a wholesale change to the ecology of sub-tidal temperate reefs. Although the theory of shifts between alternative stable states is well advanced, there are few field studies detailing the dynamics of these kinds of transitions. In this study, sea urchin herbivory (a ‘top-down’ driver of ecosystems) was manipulated over 12 months to estimate (1) the sea urchin density at which kelp beds collapse to sea urchin barrens, and (2) the minimum sea urchin density required to maintain urchin barrens on experimental reefs in the urbanised Port Phillip Bay, Australia. In parallel, the role of one of the ‘bottom-up’ drivers of ecosystem structure was examined by (3) manipulating local nutrient levels and thus attempting to alter primary production on the experimental reefs. It was found that densities of 8 or more urchins m-2 (≥ 427 g m-2 biomass) lead to complete overgrazing of kelp beds while kelp bed recovery occurred when densities were reduced to ≤ 4 urchins m-2 (≤ 213 g m-2 biomass). This experiment provided further insight into the dynamics of transition between urchin barrens and kelp beds by exploring possible tipping-points which in this system can be found between 4 and 8 urchins m-2 (213 and 427 g m-2 respectively). Local enhancement of nutrient loading did not change the urchin density required for overgrazing or kelp bed recovery, as algal growth was not affected by nutrient enhancement. PMID:28030596

Identification and characterization of Hoxa9 binding sites in hematopoietic cells

PubMed Central

Huang, Yongsheng; Sitwala, Kajal; Bronstein, Joel; Sanders, Daniel; Dandekar, Monisha; Collins, Cailin; Robertson, Gordon; MacDonald, James; Cezard, Timothee; Bilenky, Misha; Thiessen, Nina; Zhao, Yongjun; Zeng, Thomas; Hirst, Martin; Hero, Alfred; Jones, Steven

2012-01-01

The clustered homeobox proteins play crucial roles in development, hematopoiesis, and leukemia, yet the targets they regulate and their mechanisms of action are poorly understood. Here, we identified the binding sites for Hoxa9 and the Hox cofactor Meis1 on a genome-wide level and profiled their associated epigenetic modifications and transcriptional targets. Hoxa9 and the Hox cofactor Meis1 cobind at hundreds of highly evolutionarily conserved sites, most of which are distant from transcription start sites. These sites show high levels of histone H3K4 monomethylation and CBP/P300 binding characteristic of enhancers. Furthermore, a subset of these sites shows enhancer activity in transient transfection assays. Many Hoxa9 and Meis1 binding sites are also bound by PU.1 and other lineage-restricted transcription factors previously implicated in establishment of myeloid enhancers. Conditional Hoxa9 activation is associated with CBP/P300 recruitment, histone acetylation, and transcriptional activation of a network of proto-oncogenes, including Erg, Flt3, Lmo2, Myb, and Sox4. Collectively, this work suggests that Hoxa9 regulates transcription by interacting with enhancers of genes important for hematopoiesis and leukemia. PMID:22072553

Sutural loosening and skeletal flexibility during growth: determination of drop-like shapes in sea urchins.

PubMed

Johnson, Amy S; Ellers, Olaf; Lemire, Jim; Minor, Melissa; Leddy, Holly A

2002-02-07

The shape of sea urchins may be determined mechanically by patterns of force analogous to those that determine the shape of a water droplet. This mechanical analogy implies skeletal flexibility at the time of growth. Although comprised of many rigid calcite plates, sutural collagenous ligaments could confer such flexibility if the sutures between plates loosened and acted as joints at the time of growth. We present experimental evidence of such flexibility associated with weight gain and growth. Over 13-, 4-, and 2-week periods, fed urchins (Strongylocentrotus droebachiensis) gained weight and developed looser sutures than unfed urchins that maintained or lost weight. Further, skeletons of fed urchins force-relaxed more than did those of unfed urchins and urchins with loose sutures force-relaxed more than those with tight sutures. Urchins (Strongylocentrotus franciscanus) fed for two and a half weeks, gained weight, also had looser skeletons and deposited calcite at sutural margins, whereas unfed ones did not. In field populations of S. droebachiensis the percentage having loose sutures varied with urchin diameter and reflected their size-specific growth rate. The association between feeding, weight gain, calcite deposition, force relaxation and sutural looseness supports the hypothesis that urchins deform flexibly while growing, thus determining their drop-like shapes.

Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803

PubMed Central

Maeda, Toshinari; Vardar, Gönül; Self, William T; Wood, Thomas K

2007-01-01

Background Molecular hydrogen is an environmentally-clean fuel and the reversible (bi-directional) hydrogenase of the cyanobacterium Synechocystis sp. PCC 6803 as well as the native Escherichia coli hydrogenase 3 hold great promise for hydrogen generation. These enzymes perform the simple reaction 2H+ + 2e- ↔ H2 (g). Results Hydrogen yields were enhanced up to 41-fold by cloning the bidirectional hydrogenase (encoded by hoxEFUYH) from the cyanobacterium into E. coli. Using an optimized medium, E. coli cells expressing hoxEFUYH also produced twice as much hydrogen as the well-studied Enterobacter aerogenes HU-101, and hydrogen gas bubbles are clearly visible from the cultures. Overexpression of HoxU alone (small diaphorase subunit) accounts for 43% of the additional hydrogen produced by HoxEFUYH. In addition, hydrogen production in E. coli mutants with defects in the native formate hydrogenlyase system show that the cyanobacterial hydrogenase depends on both the native E. coli hydrogenase 3 as well as on its maturation proteins. Hydrogen absorption by cells expressing hoxEFUYH was up to 10 times lower than cells which lack the cloned cyanobacterial hydrogenase; hence, the enhanced hydrogen production in the presence of hoxEFUYH is due to inhibition of hydrogen uptake activity in E. coli. Hydrogen uptake by cells expressing hoxEFUYH was suppressed in three wild-type strains and in two hycE mutants but not in a double mutant defective in hydrogenase 1 and hydrogenase 2; hence, the active cyanobacterial locus suppresses hydrogen uptake by hydrogenase 1 and hydrogenase 2 but not by hydrogenase 3. Differential gene expression indicated that overexpression of HoxEFUYH does not alter expression of the native E. coli hydrogenase system; instead, biofilm-related genes are differentially regulated by expression of the cyanobacterial enzymes which resulted in 2-fold elevated biofilm formation. This appears to be the first enhanced hydrogen production by cloning a cyanobacterial enzyme into a heterologous host. Conclusion Enhanced hydrogen production in E. coli cells expressing the cyanobacterial HoxEFUYH is by inhibiting hydrogen uptake of both hydrogenase 1 and hydrogenase 2. PMID:17521447

Trophic Cascades Induced by Lobster Fishing Are Not Ubiquitous in Southern California Kelp Forests

PubMed Central

Guenther, Carla M.; Lenihan, Hunter S.; Grant, Laura E.; Lopez-Carr, David; Reed, Daniel C.

2012-01-01

Fishing can trigger trophic cascades that alter community structure and dynamics and thus modify ecosystem attributes. We combined ecological data of sea urchin and macroalgal abundance with fishery data of spiny lobster (Panulirus interruptus) landings to evaluate whether: (1) patterns in the abundance and biomass among lobster (predator), sea urchins (grazer), and macroalgae (primary producer) in giant kelp forest communities indicated the presence of top-down control on urchins and macroalgae, and (2) lobster fishing triggers a trophic cascade leading to increased sea urchin densities and decreased macroalgal biomass. Eight years of data from eight rocky subtidal reefs known to support giant kelp forests near Santa Barbara, CA, USA, were analyzed in three-tiered least-squares regression models to evaluate the relationships between: (1) lobster abundance and sea urchin density, and (2) sea urchin density and macroalgal biomass. The models included reef physical structure and water depth. Results revealed a trend towards decreasing urchin density with increasing lobster abundance but little evidence that urchins control the biomass of macroalgae. Urchin density was highly correlated with habitat structure, although not water depth. To evaluate whether fishing triggered a trophic cascade we pooled data across all treatments to examine the extent to which sea urchin density and macroalgal biomass were related to the intensity of lobster fishing (as indicated by the density of traps pulled). We found that, with one exception, sea urchins remained more abundant at heavily fished sites, supporting the idea that fishing for lobsters releases top-down control on urchin grazers. Macroalgal biomass, however, was positively correlated with lobster fishing intensity, which contradicts the trophic cascade model. Collectively, our results suggest that factors other than urchin grazing play a major role in controlling macroalgal biomass in southern California kelp forests, and that lobster fishing does not always catalyze a top-down trophic cascade. PMID:23209573

Reduced density of the herbivorous urchin Diadema antillarum inside a Caribbean marine reserve linked to increased predation pressure by fishes

NASA Astrophysics Data System (ADS)

Harborne, A. R.; Renaud, P. G.; Tyler, E. H. M.; Mumby, P. J.

2009-09-01

Disease has dramatically reduced populations of the herbivorous urchin Diadema antillarum Philippi on Caribbean reefs, contributing to an increased abundance of macroalgae and reduction of coral cover. Therefore, recovery of D. antillarum populations is critically important, but densities are still low on many reefs. Among the many potential factors limiting these densities, the focus of this study is on predation pressure by fishes. Marine reserves provide opportunities to examine large-scale manipulations of predator-prey interactions and, therefore, D. antillarum densities were compared inside and outside a reserve in The Bahamas (Exuma Cays Land and Sea Park; ECLSP). Urchins and their fish predators were surveyed at nine sites inside and outside the ECLSP. Because of lower fishing effort, the total biomass of urchin predators, weighted by their dietary preferences for urchins, was significantly higher inside the ECLSP. Furthermore, fish community structure was significantly different inside the Park because of the increased biomass of the majority of species. No urchins were seen inside the ECLSP and this was significantly lower than the density of 0.04 urchin m-2 outside the Park. Regression analysis indicated that the relationship between the biomass of urchin predators and the proportion of transects containing urchins was non-linear, suggesting that small increases in fish biomass dramatically reduce urchin abundances. The link between lower density of urchins and higher density of their predators inside the ECLSP is strengthened by discounting five alternative primary mechanisms (variations in macroalgal cover, larval supply, environmental setting, density of other urchin species and abundance of predators not surveyed). Caribbean marine reserves have an important conservation role, but increased fish predation appears to reduce densities of D. antillarum. Urchins currently have limited functional significance on Bahamian reefs, but any future recovery of D. antillarum is likely to be limited in reserves, with potentially important ecological consequences.

The SpTransformer Gene Family (Formerly Sp185/333) in the Purple Sea Urchin and the Functional Diversity of the Anti-Pathogen rSpTransformer-E1 Protein

PubMed Central

Smith, L. Courtney; Lun, Cheng Man

2017-01-01

The complex innate immune system of sea urchins is underpinned by several multigene families including the SpTransformer family (SpTrf; formerly Sp185/333) with estimates of ~50 members, although the family size is likely variable among individuals of Strongylocentrotus purpuratus. The genes are small with similar structure, are tightly clustered, and have several types of repeats in the second of two exons and that surround each gene. The density of repeats suggests that the genes are positioned within regions of genomic instability, which may be required to drive sequence diversification. The second exon encodes the mature protein and is composed of blocks of sequence called elements that are present in mosaics of defined element patterns and are the major source of sequence diversity. The SpTrf genes respond swiftly to immune challenge, but only a single gene is expressed per phagocyte. Many of the mRNAs appear to be edited and encode proteins with altered and/or missense sequence that are often truncated, of which some may be functional. The standard SpTrf protein structure is an N-terminal glycine-rich region, a central RGD motif, a histidine-rich region, and a C-terminal region. Function is predicted from a recombinant protein, rSpTransformer-E1 (rSpTrf-E1), which binds to Vibrio and Saccharomyces, but not to Bacillus, and binds tightly to lipopolysaccharide, β-1,3-glucan, and flagellin, but not to peptidoglycan. rSpTrf-E1 is intrinsically disordered but transforms to α helical structure in the presence of binding targets including lipopolysaccharide, which may underpin the characteristics of binding to multiple targets. SpTrf proteins associate with coelomocyte membranes, and rSpTrf-E1 binds specifically to phosphatidic acid (PA). When rSpTrf-E1 is bound to PA in liposome membranes, it induces morphological changes in liposomes that correlate with PA clustering and leakage of luminal contents, and it extracts or removes PA from the bilayer. The multitasking activities of rSpTrf-E1 infer multiple and perhaps overlapping activities for the hundreds of native SpTrf proteins that are produced by individual sea urchins. This likely generates a flexible and highly protective immune system for the sea urchin in its marine habitat that it shares with broad arrays of microbes that may be pathogens and opportunists. PMID:28713368

Identification of Lmo1 as part of a Hox-dependent regulatory network for hindbrain patterning.

PubMed

Matis, Christelle; Oury, Franck; Remacle, Sophie; Lampe, Xavier; Gofflot, Françoise; Picard, Jacques J; Rijli, Filippo M; Rezsohazy, René

2007-09-01

The embryonic functions of Hox proteins have been extensively investigated in several animal phyla. These transcription factors act as selectors of developmental programmes, to govern the morphogenesis of multiple structures and organs. However, despite the variety of morphogenetic processes Hox proteins are involved in, only a limited set of their target genes has been identified so far. To find additional targets, we used a strategy based upon the simultaneous overexpression of Hoxa2 and its cofactors Pbx1 and Prep in a cellular model. Among genes whose expression was upregulated, we identified LMO1, which codes for an intertwining LIM-only factor involved in protein-DNA oligomeric complexes. By analysing its expression in Hox knockout mice, we show that Lmo1 is differentially regulated by Hoxa2 and Hoxb2, in specific columns of hindbrain neuronal progenitors. These results suggest that Lmo1 takes part in a Hox paralogue 2-dependent network regulating anteroposterior and dorsoventral hindbrain patterning. (c) 2007 Wiley-Liss, Inc.

Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13

DOE PAGES

Sheth, Rushikesh; Barozzi, Iros; Langlais, David; ...

2016-12-13

The combinatorial expression of Hox genes along the body axes is a major determinant of cell fate and plays a pivotal role in generating the animal body plan. Loss of HOXA13 and HOXD13 transcription factors (HOX13) leads to digit agenesis in mice, but how HOX13 proteins regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. Here, we report on the genome-wide profiling of HOXA13 and HOXD13 in vivo binding and changes of the transcriptome and chromatin state in the transition from the early to the late-distal limb developmental program, as well as in Hoxa13–/–; Hoxd13–/– limbs. Ourmore » results show that proper termination of the early limb transcriptional program and activation of the late-distal limb program are coordinated by the dual action of HOX13 on cis-regulatory modules.« less

Activation Thermodynamics and H/D Kinetic Isotope Effect of the Hox to HredH+ Transition in [FeFe] Hydrogenase.

PubMed

Ratzloff, Michael W; Wilker, Molly B; Mulder, David W; Lubner, Carolyn E; Hamby, Hayden; Brown, Katherine A; Dukovic, Gordana; King, Paul W

2017-09-20

Molecular complexes between CdSe nanocrystals and Clostridium acetobutylicum [FeFe] hydrogenase I (CaI) enabled light-driven control of electron transfer for spectroscopic detection of redox intermediates during catalytic proton reduction. Here we address the route of electron transfer from CdSe→CaI and activation thermodynamics of the initial step of proton reduction in CaI. The electron paramagnetic spectroscopy of illuminated CdSe:CaI showed how the CaI accessory FeS cluster chain (F-clusters) functions in electron transfer with CdSe. The H ox →H red H + reduction step measured by Fourier-transform infrared spectroscopy showed an enthalpy of activation of 19 kJ mol -1 and a ∼2.5-fold kinetic isotope effect. Overall, these results support electron injection from CdSe into CaI involving F-clusters, and that the H ox →H red H + step of catalytic proton reduction in CaI proceeds by a proton-dependent process.

Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model.

PubMed

Woltering, Joost M; Duboule, Denis

2015-11-01

The tetrapod vertebral column has become increasingly complex during evolution as an adaptation to a terrestrial life. At the same time, the evolution of the vertebral formula became subject to developmental constraints acting on the size of the cervical and thoraco-lumbar regions. In the course of our studies concerning the evolution of Hox gene regulation, we produced a transgenic mouse model expressing fish Hox genes, which displayed a reduced number of thoraco-lumbar vertebrae and concurrent sacral homeotic transformations. Here, we analyze this mutant stock and conclude that the ancestral, pre-tetrapodial Hox code already possessed the capacity to induce vertebrae with sacral characteristics. This suggests that alterations in the interpretation of the Hox code may have participated to the evolution of this region in tetrapods, along with potential modifications of the HOX proteins themselves. With its reduced vertebral number, this mouse stock violates a previously described developmental constraint, which applies to the thoraco-lumbar region. The resulting offset between motor neuron morphology, vertebral patterning and the relative positioning of hind limbs illustrates that the precise orchestration of the Hox-clock in parallel with other ontogenetic pathways places constraints on the evolvability of the body plan. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Embryonic origin and Hox status determine progenitor cell fate during adult bone regeneration.

PubMed

Leucht, Philipp; Kim, Jae-Beom; Amasha, Raimy; James, Aaron W; Girod, Sabine; Helms, Jill A

2008-09-01

The fetal skeleton arises from neural crest and from mesoderm. Here, we provide evidence that each lineage contributes a unique stem cell population to the regeneration of injured adult bones. Using Wnt1Cre::Z/EG mice we found that the neural crest-derived mandible heals with neural crest-derived skeletal stem cells, whereas the mesoderm-derived tibia heals with mesoderm-derived stem cells. We tested whether skeletal stem cells from each lineage were functionally interchangeable by grafting mesoderm-derived cells into mandibular defects, and vice versa. All of the grafting scenarios, except one, healed through the direct differentiation of skeletal stem cells into osteoblasts; when mesoderm-derived cells were transplanted into tibial defects they differentiated into osteoblasts but when transplanted into mandibular defects they differentiated into chondrocytes. A mismatch between the Hox gene expression status of the host and donor cells might be responsible for this aberration in bone repair. We found that initially, mandibular skeletal progenitor cells are Hox-negative but that they adopt a Hoxa11-positive profile when transplanted into a tibial defect. Conversely, tibial skeletal progenitor cells are Hox-positive and maintain this Hox status even when transplanted into a Hox-negative mandibular defect. Skeletal progenitor cells from the two lineages also show differences in osteogenic potential and proliferation, which translate into more robust in vivo bone regeneration by neural crest-derived cells. Thus, embryonic origin and Hox gene expression status distinguish neural crest-derived from mesoderm-derived skeletal progenitor cells, and both characteristics influence the process of adult bone regeneration.

IGFBP3, a transcriptional target of homeobox D10, is correlated with the prognosis of gastric cancer.

PubMed

Xue, Meng; Fang, Yanfei; Sun, Guoming; Zhuo, Wei; Zhong, Jing; Qian, Cuijuan; Wang, Lan; Wang, Liangjing; Si, Jianmin; Chen, Shujie

2013-01-01

Homeobox D10 (HoxD10) plays important roles in the differentiation of embryonic cells and progression of breast cancer. Our previous report revealed that insulin-like growth factor binding protein-3 (IGFBP3) was regulated by HoxD10 in gastric cancer cells; however, the functional roles and underlying mechanisms of IGFBP3 in gastric cancer remain unclear. Here, we found that the expression of IGFBP3 were upregulated after ectopic expression of HoxD10 in gastric cancer cells. Chromatin immunoprecipitation assay showed that HoxD10 bound to three potential regions of IGFBP3 promoter. Exogenous HoxD10 significantly enhanced the activity of luciferase reporter containing these binding regions in gastric cancer cells. Further data showed that all of these binding sites had Hox binding element "TTAT". Immunohistochemical staining results revealed that IGFBP3 expression was significantly downregulated in 86 gastric adenocarcinomas tissues relative to their adjacent non-cancerous tissues (p<0.001). Moreover, IGFBP3 expression was significantly lower in gastric tumor with lymph node metastasis compared with that without lymph node metastasis (p=0.045). Patients with high expression level of IGFBP3 showed favorable 5 year overall survival (p=0.011). Knockdown of IGFBP3 accelerated gastric cancer cell migration and invasion and induced the expression of invasive factors including MMP14, uPA and uPAR. Thus, our data suggest that HoxD10-targeted gene IGFBP3 may suppress gastric cancer cell invasion and favors the survival of gastric cancer patients.

Comparison of Model and Observations of Middle Atmospheric HOx Response to Solar 27-day Cycles: Quantifying Model Uncertainties due to Photochemistry

NASA Astrophysics Data System (ADS)

Wang, S.; Li, K. F.; Shia, R. L.; Yung, Y. L.; Sander, S. P.

2016-12-01

HO2 and OH (known as odd oxygen HOx), play an important role in middle atmospheric chemistry, in particular, O3 destruction through catalytic HOx reaction cycles. Due to their photochemical production and short chemical lifetimes, HOx species response rapidly to solar UV irradiance changes during solar cycles, resulting in variability in the corresponding O3 chemistry. Observational evidences for both OH and HO2 variability due to solar cycles have been reported. However, puzzling discrepancies remain. In particular, the large discrepancy between model and observations of solar 11-year cycle signal in OH and the significantly different model results when adopting different solar spectral irradiance (SSI) [Wang et al., 2013] suggest that both uncertainties in SSI variability and uncertainties in our current understanding of HOx-O3 chemistry could contribute to the discrepancy. Since the short-term SSI variability (e.g. changes during solar 27-day cycles) has little uncertainty, investigating 27-day solar cycle signals in HOx allows us to simplify the complex problem and to focus on the uncertainties in chemistry alone. We use the Caltech-JPL photochemical model to simulate observed HOx variability during 27-day cycles. The comparison between Aura Microwave Limb Sounder (MLS) observations and our model results (using standard chemistry and "adjusted chemistry", respectively) will be discussed. A better understanding of uncertainties in chemistry will eventually help us separate the contribution of chemistry from contributions of SSI uncertainties to the complex discrepancy between model and observations of OH responses to solar 11-year cycles.

Effects of a range-expanding sea urchin on behaviour of commercially fished abalone.

PubMed

Strain, Elisabeth M A; Johnson, Craig R; Thomson, Russell J

2013-01-01

Global climate change has resulted in a southerly range expansion of the habitat modifying sea urchin Centrostephanus rodgersii to the east coast of Tasmania, Australia. Various studies have suggested that this urchin outcompetes black-lipped abalone (Haliotis rubra) for resources, but experiments elucidating the mechanisms are lacking. We outline a new framework involving experimental manipulations and Markov chain and Pareto modelling to examine the effects of interspecific competition between urchins and abalone and the effect of intraspecific competition in abalone, assessed as effects on behaviour. Manipulations of abalone densities had no detectable effect on urchin behavioural transitions, movement patterns or resightability through time. In contrast, additions of urchins resulted in abalone shifting microhabitats from exposed to sheltered positions, an increase in the proportion of mobile abalone, and declines in abalone resightability through time relative to controls without the urchins. Our results support the hypothesis of asymmetrical competitive interactions between urchins and abalone. The introduction of urchins to intact algal beds causes abalone to flee and seek shelter in cryptic microhabitat which will negatively impact both their accessibility to such microhabitats, and productivity of the abalone fishery, and will potentially affect their growth and survival, while the presence of the abalone has no detectable effect on the urchin. Our approach involving field-based experiments and modelling could be used to test the effects of other invasive species on native species behaviour.

Trimeric Association of Hox and TALE Homeodomain Proteins Mediates Hoxb2 Hindbrain Enhancer Activity

PubMed Central

Jacobs, Yakop; Schnabel, Catherine A.; Cleary, Michael L.

1999-01-01

Pbx/exd proteins modulate the DNA binding affinities and specificities of Hox proteins and contribute to the execution of Hox-dependent developmental programs in arthropods and vertebrates. Pbx proteins also stably heterodimerize and bind DNA with Meis and Pknox1-Prep1, additional members of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins that function on common genetic pathways with a subset of Hox proteins. In this study, we demonstrated that Pbx and Meis bind DNA as heterotrimeric complexes with Hoxb1 on a genetically defined Hoxb2 enhancer, r4, that mediates the cross-regulatory transcriptional effects of Hoxb1 in vivo. The DNA binding specificity of the heterotrimeric complex for r4 is mediated by a Pbx-Hox site in conjunction with a distal Meis site, which we showed to be required for ternary complex formation and Meis-enhanced transcription. Formation of heterotrimeric complexes in which all three homeodomains bind their cognate DNA sites is topologically facilitated by the ability of Pbx and Meis to interact through their amino termini and bind DNA without stringent half-site orientation and spacing requirements. Furthermore, Meis site mutation in the Hoxb2 enhancer phenocopies Pbx-Hox site mutation to abrogate enhancer-directed expression of a reporter transgene in the murine embryonic hindbrain, demonstrating that DNA binding by all three proteins is required for trimer function in vivo. Our data provide in vitro and in vivo evidence for the combinatorial regulation of Hox and TALE protein functions that are mediated, in part, by their interdependent DNA binding activities as ternary complexes. As a consequence, Hoxb1 employs Pbx and Meis-related proteins, as a pair of essential cofactors in a higher-order molecular complex, to mediate its transcriptional effects on an endogenous Hox response element. PMID:10373562

Traditional Chinese medicine--sea urchin.

PubMed

Shang, Xiao-Hui; Liu, Xiao-Yu; Zhang, Jian-Peng; Gao, Yun; Jiao, Bing-Hua; Zheng, Heng; Lu, Xiao-Ling

2014-01-01

The sea urchin is an ancient, common, seafloor-dwelling marine invertebrate that belongs to the phylum Echinodermata. There are multiple species of sea urchin with resources that are widely distributed in China, where they were used in ancient times as Traditional Chinese Medicine for treating a variety of diseases. At present, it is known that the shell, spine and gonad of the sea urchin have many medicinal values determined through modern research. In this paper, we summarized the major chemical constituents and medicinal value of the sea urchin.

Fishing for lobsters indirectly increases epidemics in sea urchins

USGS Publications Warehouse

Lafferty, Kevin D.

2004-01-01

Two ecological paradigms, the trophic cascade and the host-density threshold in disease, interact in the kelp-forest ecosystem to structure the community. To investigate what happens when a trophic cascade pushes a host population over a host-threshold density, I analyzed a 20-year data set of kelp forest communities at 16 sites in the region of the Channel Islands National Park, California, USA. Historically, lobsters, and perhaps other predators, kept urchin populations at low levels and kelp forests developed a community-level trophic cascade. In geographic areas where the main predators on urchins were fished, urchin populations increased to the extent that they overgrazed algae and starvation eventually limited urchin-population growth. Despite the limitation of urchin population size by food availability, urchin densities, at times, well exceeded the host-density threshold for epidemics. An urchin-specific bacterial disease entered the region after 1992 and acted as a density-dependent mortality source. Dense populations were more likely to experience epidemics and suffer higher mortality. Disease did not reduce the urchin population at a site to the density that predators previously did. Therefore, disease did not fully replace predators in the trophic cascade. These results indicate how fishing top predators can indirectly favor disease transmission in prey populations.

Effects of a Range-Expanding Sea Urchin on Behaviour of Commercially Fished Abalone

PubMed Central

Strain, Elisabeth M. A.; Johnson, Craig R.; Thomson, Russell J.

2013-01-01

Background Global climate change has resulted in a southerly range expansion of the habitat modifying sea urchin Centrostephanus rodgersii to the east coast of Tasmania, Australia. Various studies have suggested that this urchin outcompetes black-lipped abalone (Haliotis rubra) for resources, but experiments elucidating the mechanisms are lacking. Methodology/Principal Findings We outline a new framework involving experimental manipulations and Markov chain and Pareto modelling to examine the effects of interspecific competition between urchins and abalone and the effect of intraspecific competition in abalone, assessed as effects on behaviour. Manipulations of abalone densities had no detectable effect on urchin behavioural transitions, movement patterns or resightability through time. In contrast, additions of urchins resulted in abalone shifting microhabitats from exposed to sheltered positions, an increase in the proportion of mobile abalone, and declines in abalone resightability through time relative to controls without the urchins. Our results support the hypothesis of asymmetrical competitive interactions between urchins and abalone. Conclusions/Significance The introduction of urchins to intact algal beds causes abalone to flee and seek shelter in cryptic microhabitat which will negatively impact both their accessibility to such microhabitats, and productivity of the abalone fishery, and will potentially affect their growth and survival, while the presence of the abalone has no detectable effect on the urchin. Our approach involving field-based experiments and modelling could be used to test the effects of other invasive species on native species behaviour. PMID:24073195

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.

Bioerosion by pit-forming, temperate-reef sea urchins: History, rates and broader implications.

PubMed

Russell, Michael P; Gibbs, Victoria K; Duwan, Emily

2018-01-01

Sea urchins are dominant members of rocky temperate reefs around the world. They often occur in cavities within the rock, and fit so tightly, it is natural to assume they sculpted these "pits." However, there are no experimental data demonstrating they bore pits. If they do, what are the rates and consequences of bioerosion to nearshore systems? We sampled purple sea urchins, Strongylocentrotus purpuratus, from sites with four rock types, three sedimentary (two sandstones and one mudstone) and one metamorphic (granite). A year-long experiment showed urchins excavated depressions on sedimentary rocks in just months. The rate of pit formation varied with rock type and ranged from <5 yr for medium-grain sandstone to >100 yr for granite. In the field, there were differences in pit size and shapes of the urchins (height:diameter ratio). The pits were shallow and urchins flatter at the granite site, and the pits were deeper and urchins taller at the sedimentary sites. Although overall pit sizes were larger on mudstone than on sandstone, urchin size accounted for this difference. A second, short-term experiment, showed the primary mechanism for bioerosion was ingestion of the substratum. This experiment eliminated potential confounding factors of the year-long experiment and yielded higher bioerosion rates. Given the high densities of urchins, large amounts of rock can be converted to sediment over short time periods. Urchins on sandstone can excavate as much as 11.4 kg m-2 yr-1. On a broader geographic scale, sediment production can exceed 100 t ha-1 yr-1, and across their range, their combined bioerosion is comparable to the sediment load of many rivers. The phase shift between urchin barrens and kelp bed habitats in the North Pacific is controlled by the trophic cascade of sea otters. By limiting urchin populations, these apex predators also may indirectly control a substantial component of coastal rates of bioerosion.

Bioerosion by pit-forming, temperate-reef sea urchins: History, rates and broader implications

PubMed Central

Gibbs, Victoria K.; Duwan, Emily

2018-01-01

Sea urchins are dominant members of rocky temperate reefs around the world. They often occur in cavities within the rock, and fit so tightly, it is natural to assume they sculpted these “pits.” However, there are no experimental data demonstrating they bore pits. If they do, what are the rates and consequences of bioerosion to nearshore systems? We sampled purple sea urchins, Strongylocentrotus purpuratus, from sites with four rock types, three sedimentary (two sandstones and one mudstone) and one metamorphic (granite). A year-long experiment showed urchins excavated depressions on sedimentary rocks in just months. The rate of pit formation varied with rock type and ranged from <5 yr for medium-grain sandstone to >100 yr for granite. In the field, there were differences in pit size and shapes of the urchins (height:diameter ratio). The pits were shallow and urchins flatter at the granite site, and the pits were deeper and urchins taller at the sedimentary sites. Although overall pit sizes were larger on mudstone than on sandstone, urchin size accounted for this difference. A second, short-term experiment, showed the primary mechanism for bioerosion was ingestion of the substratum. This experiment eliminated potential confounding factors of the year-long experiment and yielded higher bioerosion rates. Given the high densities of urchins, large amounts of rock can be converted to sediment over short time periods. Urchins on sandstone can excavate as much as 11.4 kg m-2 yr-1. On a broader geographic scale, sediment production can exceed 100 t ha-1 yr-1, and across their range, their combined bioerosion is comparable to the sediment load of many rivers. The phase shift between urchin barrens and kelp bed habitats in the North Pacific is controlled by the trophic cascade of sea otters. By limiting urchin populations, these apex predators also may indirectly control a substantial component of coastal rates of bioerosion. PMID:29466357

Speciation of polyploid Cyprinidae fish of common carp, crucian carp, and silver crucian carp derived from duplicated Hox genes.

PubMed

Yuan, Jian; He, Zhuzi; Yuan, Xiangnan; Jiang, Xiayun; Sun, Xiaowen; Zou, Shuming

2010-09-15

Recent studies on comparative genomics have suggested that a round of fish-specific whole genome duplication (3R) in ray-finned fishes might have occurred around 226-316 Mya. Additional genome duplication, specifically in cyprinids, may have occurred more recently after the divergence of the teleosts. The timing of this event, however, is unknown. To address this question, we sequenced four Hox genes from taxa representing the polyploid Cyprinidae fish, common carp (Cyprinus carpio, 2n=100), crucian carp (Carassius auratus auratus, 2n=100), and silver crucian carp (C. auratus gibelio, 2n=156), and then compared them with known sequences from the diploid Cyprinidae fish, blunt snout bream (Megalobrama amblycephala, 2n=48). Our results showed the presence of two distinct Hox duplicates in the genomes of common and crucian carp. Three distinct Hox sequences, one of them orthologous to a Hox gene in common carp and the other two orthologous to a Hox gene in crucian carp, were isolated in silver crucian carp, indicating a possible hybrid origin of silver crucian carp from crucian and common carp. The gene duplication resulting in the origin of the common ancestor of common and crucian carp likely occurred around 10.9-13.2 Mya. The speciations of common vs. crucian carp and silver crucian vs. crucian carp likely occurred around 8.1-11.4 and 2.3-3.0 Mya, respectively. Finally, nonfunctionalization resulting from point mutations in the coding region is a probable fate for some Hox duplicates. Taken together, these results suggested an evolutionary model for polyploidization in speciation and diversification of polyploid fish. (c) 2010 Wiley-Liss, Inc.

Hox gene expression in the specialized limbs of the Iberian mole (Talpa occidentalis).

PubMed

Bickelmann, Constanze; van der Vos, Wessel; de Bakker, Merijn A G; Jiménez, Rafael; Maas, Saskia; Sánchez-Villagra, Marcelo R

2017-01-01

Fossorial talpid moles use their limbs predominantly for digging, which explains their highly specialized anatomy. The humerus is particularly short and dorsoventrally rotated, with broadened distal and proximal parts where muscles attach and which facilitate powerful abductive movements. The radius and ulna are exceptionally robust and short. The ulna has an expanded olecranon process. The femur is generalized, but the fused tibia-fibula complex is short and robust. To understand the developmental bases of these specializations, we studied expression patterns of four 5' Hox genes in the fossorial Iberian mole (Talpa occidentalis). These genes are known to play major roles in patterning the developing limb skeleton in the mouse, with which comparisons were made (Mus musculus, C57BL/6Jico strain). We find that HoxA9 expression is spatially expanded in the developing stylopodial area in the mole forelimb, compared to the less specialized mouse forelimb and mole hind limb. HoxD9 expression does not extend into the thoracic body wall in the mole forelimb in contrast to the mouse, and is also reduced in the presumptive zeugopodium in mole forelimb, compared to mouse. Expression of HoxD11 is upregulated in the mole in the postaxial area of the hind limb zeugopod, compared to the mouse. On the other hand, HoxD13 is downregulated in the postaxial zeugopodial area in the forelimb of the mole, compared to the mouse. The differences in the expression patterns of these 5' Hox genes between Talpa and Mus are an indication of the developmental changes going hand in hand with anatomical digging adaptations in the mole adult. © 2016 Wiley Periodicals, Inc.

Adaptive evolution of the Hox gene family for development in bats and dolphins.

PubMed

Liang, Lu; Shen, Yong-Yi; Pan, Xiao-Wei; Zhou, Tai-Cheng; Yang, Chao; Irwin, David M; Zhang, Ya-Ping

2013-01-01

Bats and cetaceans (i.e., whales, dolphins, porpoises) are two kinds of mammals with unique locomotive styles and occupy novel niches. Bats are the only mammals capable of sustained flight in the sky, while cetaceans have returned to the aquatic environment and are specialized for swimming. Associated with these novel adaptations to their environment, various development changes have occurred to their body plans and associated structures. Given the importance of Hox genes in many aspects of embryonic development, we conducted an analysis of the coding regions of all Hox gene family members from bats (represented by Pteropus vampyrus, Pteropus alecto, Myotis lucifugus and Myotis davidii) and cetaceans (represented by Tursiops truncatus) for adaptive evolution using the available draft genome sequences. Differences in the selective pressures acting on many Hox genes in bats and cetaceans were found compared to other mammals. Positive selection, however, was not found to act on any of the Hox genes in the common ancestor of bats and only upon Hoxb9 in cetaceans. PCR amplification data from additional bat and cetacean species, and application of the branch-site test 2, showed that the Hoxb2 gene within bats had significant evidence of positive selection. Thus, our study, with genomic and newly sequenced Hox genes, identifies two candidate Hox genes that may be closely linked with developmental changes in bats and cetaceans, such as those associated with the pancreatic, neuronal, thymus shape and forelimb. In addition, the difference in our results from the genome-wide scan and newly sequenced data reveals that great care must be taken in interpreting results from draft genome data from a limited number of species, and deep genetic sampling of a particular clade is a powerful tool for generating complementary data to address this limitation.

Adaptive Evolution of the Hox Gene Family for Development in Bats and Dolphins

PubMed Central

Pan, Xiao-Wei; Zhou, Tai-Cheng; Yang, Chao; Irwin, David M.; Zhang, Ya-Ping

2013-01-01

Bats and cetaceans (i.e., whales, dolphins, porpoises) are two kinds of mammals with unique locomotive styles and occupy novel niches. Bats are the only mammals capable of sustained flight in the sky, while cetaceans have returned to the aquatic environment and are specialized for swimming. Associated with these novel adaptations to their environment, various development changes have occurred to their body plans and associated structures. Given the importance of Hox genes in many aspects of embryonic development, we conducted an analysis of the coding regions of all Hox gene family members from bats (represented by Pteropus vampyrus, Pteropus alecto, Myotis lucifugus and Myotis davidii) and cetaceans (represented by Tursiops truncatus) for adaptive evolution using the available draft genome sequences. Differences in the selective pressures acting on many Hox genes in bats and cetaceans were found compared to other mammals. Positive selection, however, was not found to act on any of the Hox genes in the common ancestor of bats and only upon Hoxb9 in cetaceans. PCR amplification data from additional bat and cetacean species, and application of the branch-site test 2, showed that the Hoxb2 gene within bats had significant evidence of positive selection. Thus, our study, with genomic and newly sequenced Hox genes, identifies two candidate Hox genes that may be closely linked with developmental changes in bats and cetaceans, such as those associated with the pancreatic, neuronal, thymus shape and forelimb. In addition, the difference in our results from the genome-wide scan and newly sequenced data reveals that great care must be taken in interpreting results from draft genome data from a limited number of species, and deep genetic sampling of a particular clade is a powerful tool for generating complementary data to address this limitation. PMID:23825528

Additional sex combs-like 1 belongs to the enhancer of trithorax and Polycomb Group and genetically interacts with Cbx2 in mice

PubMed Central

Fisher, C.L.; Lee, I.; Bloyer, S.; Bozza, S.; Chevalier, J.; Dahl, A; Bodner, C.; Helgason, C. D.; Hess, J.L.; Humphries, R.K.; Brock, H.W.

2009-01-01

The Additional sex combs (Asx) gene of Drosophila behaves genetically as an enhancer of trithorax and Polycomb (ETP) in displaying bidirectional homeotic phenotypes, suggesting that is required for maintenance of both activation and silencing of Hox genes. There are 3 murine homologs of Asx called Additional sex combs-like1, 2, and-3. Asxl1 is required for normal adult hematopoiesis; however its embryonic function is unknown. We used a targeted mouse mutant line Asxl1tm1Bc to determine if Asxl1 is required to silence and activate Hox genes in mice during axial patterning. The mutant embryos exhibit simultaneous anterior and posterior transformations of the axial skeleton, consistent with a role for Asxl1 in activation and silencing of Hox genes. Transformations of the axial skeleton are enhanced in compound mutant embryos for the Polycomb group gene M33/Cbx2. Hox a4, a7, and c8 are derepressed in Asxl1tm1Bc mutants in the antero-posterior axis, but Hox c8 expression is reduced in the brain of mutants, consistent with Asxl1 being required both for activation and repression of Hox genes. We discuss the genetic and molecular definition of ETPs, and suggest that the function of Asxl1 depends on its cellular context. PMID:19833123

Pantropic retroviruses as a transduction tool for sea urchin embryos

PubMed Central

Core, Amanda B.; Reyna, Arlene E.; Conaway, Evan A.; Bradham, Cynthia A.

2012-01-01

Sea urchins are an important model for experiments at the intersection of development and systems biology, and technical innovations that enhance the utility of this model are of great value. This study explores pantropic retroviruses as a transduction tool for sea urchin embryos, and demonstrates that pantropic retroviruses infect sea urchin embryos with high efficiency and genomically integrate at a copy number of one per cell. We successfully used a self-inactivation strategy to both insert a sea urchin-specific enhancer and disrupt the endogenous viral enhancer. The resulting self-inactivating viruses drive global and persistent gene expression, consistent with genomic integration during the first cell cycle. Together, these data provide substantial proof of principle for transduction technology in sea urchin embryos. PMID:22431628

Head patterning and Hox gene expression in an onychophoran and its implications for the arthropod head problem.

PubMed

Eriksson, Bo Joakim; Tait, Noel N; Budd, Graham E; Janssen, Ralf; Akam, Michael

2010-09-01

The arthropod head problem has puzzled zoologists for more than a century. The head of adult arthropods is a complex structure resulting from the modification, fusion and migration of an uncertain number of segments. In contrast, onychophorans, which are the probable sister group to the arthropods, have a rather simple head comprising three segments that are well defined during development, and give rise to the adult head with three pairs of appendages specialised for sensory and food capture/manipulative purposes. Based on the expression pattern of the anterior Hox genes labial, proboscipedia, Hox3 and Deformed, we show that the third of these onychophoran segments, bearing the slime papillae, can be correlated to the tritocerebrum, the most anterior Hox-expressing arthropod segment. This implies that both the onychophoran antennae and jaws are derived from a more anterior, Hox-free region corresponding to the proto and deutocerebrum of arthropods. Our data provide molecular support for the proposal that the onychophoran head possesses a well-developed appendage that corresponds to the anterior, apparently appendage-less region of the arthropod head.

Combinatorial action of Grainyhead, Extradenticle and Notch in regulating Hox mediated apoptosis in Drosophila larval CNS

PubMed Central

Khandelwal, Risha; Govinda Rajan, Sriivatsan; Kumar, Raviranjan

2017-01-01

Hox mediated neuroblast apoptosis is a prevalent way to pattern larval central nervous system (CNS) by different Hox genes, but the mechanism of this apoptosis is not understood. Our studies with Abdominal-A (Abd-A) mediated larval neuroblast (pNB) apoptosis suggests that AbdA, its cofactor Extradenticle (Exd), a helix-loop-helix transcription factor Grainyhead (Grh), and Notch signaling transcriptionally contribute to expression of RHG family of apoptotic genes. We find that Grh, AbdA, and Exd function together at multiple motifs on the apoptotic enhancer. In vivo mutagenesis of these motifs suggest that they are important for the maintenance of the activity of the enhancer rather than its initiation. We also find that Exd function is independent of its known partner homothorax in this apoptosis. We extend some of our findings to Deformed expressing region of sub-esophageal ganglia where pNBs undergo a similar Hox dependent apoptosis. We propose a mechanism where common players like Exd-Grh-Notch work with different Hox genes through region specific enhancers to pattern respective segments of larval central nervous system. PMID:29023471

Combinatorial action of Grainyhead, Extradenticle and Notch in regulating Hox mediated apoptosis in Drosophila larval CNS.

PubMed

Khandelwal, Risha; Sipani, Rashmi; Govinda Rajan, Sriivatsan; Kumar, Raviranjan; Joshi, Rohit

2017-10-01

Hox mediated neuroblast apoptosis is a prevalent way to pattern larval central nervous system (CNS) by different Hox genes, but the mechanism of this apoptosis is not understood. Our studies with Abdominal-A (Abd-A) mediated larval neuroblast (pNB) apoptosis suggests that AbdA, its cofactor Extradenticle (Exd), a helix-loop-helix transcription factor Grainyhead (Grh), and Notch signaling transcriptionally contribute to expression of RHG family of apoptotic genes. We find that Grh, AbdA, and Exd function together at multiple motifs on the apoptotic enhancer. In vivo mutagenesis of these motifs suggest that they are important for the maintenance of the activity of the enhancer rather than its initiation. We also find that Exd function is independent of its known partner homothorax in this apoptosis. We extend some of our findings to Deformed expressing region of sub-esophageal ganglia where pNBs undergo a similar Hox dependent apoptosis. We propose a mechanism where common players like Exd-Grh-Notch work with different Hox genes through region specific enhancers to pattern respective segments of larval central nervous system.

Deregulation of ZPR1 causes respiratory failure in spinal muscular atrophy.

PubMed

Genabai, Naresh K; Kannan, Annapoorna; Ahmad, Saif; Jiang, Xiaoting; Bhatia, Kanchan; Gangwani, Laxman

2017-08-15

Spinal muscular atrophy (SMA) is caused by the low levels of survival motor neuron (SMN) protein and is characterized by motor neuron degeneration and muscle atrophy. Respiratory failure causes death in SMA but the underlying molecular mechanism is unknown. The zinc finger protein ZPR1 interacts with SMN. ZPR1 is down regulated in SMA patients. We report that ZPR1 functions downstream of SMN to regulate HoxA5 levels in phrenic motor neurons that control respiration. Spatiotemporal inactivation of Zpr1 gene in motor neurons down-regulates HoxA5 and causes defects in the function of phrenic motor neurons that results in respiratory failure and perinatal lethality in mice. Modulation in ZPR1 levels directly correlates and influences levels of HoxA5 transcription. In SMA mice, SMN-deficiency causes down-regulation of ZPR1 and HoxA5 that result in degeneration of phrenic motor neurons. Identification of ZPR1 and HoxA5 as potential targets provides a paradigm for developing strategies to treat respiratory distress in SMA.

Overexpression of HOXB7 homeobox gene in oral cancer induces cellular proliferation and is associated with poor prognosis.

PubMed

De Souza Setubal Destro, Maria Fernanda; Bitu, Carolina Cavalcanti; Zecchin, Karina G; Graner, Edgard; Lopes, Marcio A; Kowalski, Luis Paulo; Coletta, Ricardo D

2010-01-01

A growing body of evidence has confirmed the involvement of dysregulated expression of HOX genes in cancer. HOX genes are a family of 39 transcription factors, divided in 4 clusters (HOXA to HOXD), that during normal development regulate cell proliferation and specific cell fate. In the present study it was investigated whether genes of the HOXB cluster play a role in oral cancer. We showed that most of the genes in the HOXB network are inactive in oral tissues, with exception of HOXB2, HOXB7 and HOXB13. Expression of HOXB7 was significantly higher in oral squamous cell carcinomas (OSCC) compared to normal oral mucosas. We further demonstrated that HOXB7 overexpression in HaCAT human epithelial cell line promoted proliferation, whereas downregulation of HOXB7 endogenous levels in human oral carcinoma cells (SCC9 cells) decreased proliferation. In OSCCs, expression of HOXB7 and Ki67, a marker of proliferation, correlate strongly with each other (rs=0.79, p<0.006). High immunohistochemical expression of HOXB7 was correlated with T stage (p=0.06), N stage (p=0.07), disease stage (p=0.09) and Ki67 expression (p=0.01), and patients with tumors showing high number of HOXB7-positive cells had shorter overall survival (p=0.08) and shorter disease-free survival after treatment (p=0.10) compared with patients with tumors exhibiting low amount of HOXB7-positive cells. Our data suggest that HOXB7 may contribute to oral carcinogenesis by increasing tumor cell proliferation, and imply that HOXB7 may be an important determinant of OSCC patient prognosis.

Identification of a major yolk protein as an allergen in sea urchin roe.

PubMed

Yamasaki, Ayako; Higaki, Hiromi; Nakashima, Keiko; Yamamoto, Osamu; Hein, Kyaw Zaw; Takahashi, Hitoshi; Chinuki, Yuko; Morita, Eishin

2010-05-01

Anaphylaxis after eating sea urchin roe has been reported. However, its major allergens have not yet been identified. The aim of this study was to identify the major allergens of sea urchin roe. Proteins of sea urchin roe were separated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and two-dimensional electrophoresis (2-DE). An immunoglobulin (Ig)E-binding protein was detected by immunoblotting using the patient's serum. An allergen isolated from 2DE-gel was identified by peptide mass fingerprinting using matrix-assisted laser desorption/ionization-time of flight-mass spectrometry. Immunoblot analysis of sea urchin extracts showed that a 160-kDa protein at pI 6-7 was recognized by the patient's IgE. Peptide mass fingerprint analysis revealed that the protein was the major yolk protein (152 kDa, pI 6.9) of sea urchins. The results show that a major allergen of sea urchin roe is the major yolk protein.

Posterior Hox gene reduction in an arthropod: Ultrabithorax and Abdominal-B are expressed in a single segment in the mite Archegozetes longisetosus

PubMed Central

2013-01-01

Background Hox genes encode transcription factors that have an ancestral role in all bilaterian animals in specifying regions along the antero-posterior axis. In arthropods (insects, crustaceans, myriapods and chelicerates), Hox genes function to specify segmental identity, and changes in Hox gene expression domains in different segments have been causal to the evolution of novel arthropod morphologies. Despite this, the roles of Hox genes in arthropods that have secondarily lost or reduced their segmental composition have been relatively unexplored. Recent data suggest that acariform mites have a reduced segmental component of their posterior body tagma, the opisthosoma, in that only two segments are patterned during embryogenesis. This is in contrast to the observation that in many extinct and extant chelicerates (that is, horseshoe crabs, scorpions, spiders and harvestmen) the opisthosoma is comprised of ten or more segments. To explore the role of Hox genes in this reduced body region, we followed the expression of the posterior-patterning Hox genes Ultrabithorax (Ubx) and Abdominal-B (Abd-B), as well as the segment polarity genes patched (ptc) and engrailed (en), in the oribatid mite Archegozetes longisetosus. Results We find that the expression patterns of ptc are in agreement with previous reports of a reduced mite opisthosoma. In comparison to the ptc and en expression patterns, we find that Ubx and Abd-B are expressed in a single segment in A. longisetosus, the second opisthosomal segment. Abd-B is initially expressed more posteriorly than Ubx, that is, into the unsegmented telson; however, this domain clears in subsequent stages where it remains in the second opisthosomal segment. Conclusions Our findings suggest that Ubx and Abd-B are expressed in a single segment in the opisthosoma. This is a novel observation, in that these genes are expressed in several segments in all studied arthropods. These data imply that a reduction in opisthosomal segmentation may be tied to a dramatically reduced Hox gene input in the opisthosoma. PMID:23991696

New developmental evidence supports a homeotic frameshift of digit identity in the evolution of the bird wing

PubMed Central

2014-01-01

Background The homology of the digits in the bird wing is a high-profile controversy in developmental and evolutionary biology. The embryonic position of the digits cartilages with respect to the primary axis (ulnare and ulna) corresponds to 2, 3, 4, but comparative-evolutionary morphology supports 1, 2, 3. A homeotic frameshift of digit identity in evolution could explain how cells in embryonic positions 2, 3, 4 began developing morphologies 1, 2, 3. Another alternative is that no re-patterning of cell fates occurred, and the primary axis shifted its position by some other mechanism. In the wing, only the anterior digit lacks expression of HoxD10 and HoxD12, resembling digit 1 of other limbs, as predicted by 1, 2, 3. However, upon loss of digit 1 in evolution, the most anterior digit 2 could have lost their expression, deceitfully resembling a digit 1. To test this notion, we observed HoxD10 and HoxD12 in a limb where digit 2 is the most anterior digit: The rabbit foot. We also explored whether early inhibition of Shh signalling in the embryonic wing bud induces an experimental homeotic frameshift, or an experimental axis shift. We tested these hypotheses using DiI injections to study the fate of cells in these experimental wings. Results We found strong transcription of HoxD10 and HoxD12 was present in the most anterior digit 2 of the rabbit foot. Thus, we found no evidence to question the use of HoxD expression as support for 1, 2, 3. When Shh signalling in early wing buds is inhibited, our fate maps demonstrate that an experimental homeotic frameshift is induced. Conclusion Along with comparative morphology, HoxD expression provides strong support for 1, 2, 3 identity of wing digits. As an explanation for the offset 2, 3, 4 embryological position, the homeotic frameshift hypothesis is consistent with known mechanisms of limb development, and further proven to be experimentally possible. In contrast, the underlying mechanisms and experimental plausibility of an axis shift remain unclear. PMID:24725625

New developmental evidence supports a homeotic frameshift of digit identity in the evolution of the bird wing.

PubMed

Salinas-Saavedra, Miguel; Gonzalez-Cabrera, Cristian; Ossa-Fuentes, Luis; Botelho, Joao F; Ruiz-Flores, Macarena; Vargas, Alexander O

2014-04-12

The homology of the digits in the bird wing is a high-profile controversy in developmental and evolutionary biology. The embryonic position of the digits cartilages with respect to the primary axis (ulnare and ulna) corresponds to 2, 3, 4, but comparative-evolutionary morphology supports 1, 2, 3. A homeotic frameshift of digit identity in evolution could explain how cells in embryonic positions 2, 3, 4 began developing morphologies 1, 2, 3. Another alternative is that no re-patterning of cell fates occurred, and the primary axis shifted its position by some other mechanism. In the wing, only the anterior digit lacks expression of HoxD10 and HoxD12, resembling digit 1 of other limbs, as predicted by 1, 2, 3. However, upon loss of digit 1 in evolution, the most anterior digit 2 could have lost their expression, deceitfully resembling a digit 1. To test this notion, we observed HoxD10 and HoxD12 in a limb where digit 2 is the most anterior digit: The rabbit foot. We also explored whether early inhibition of Shh signalling in the embryonic wing bud induces an experimental homeotic frameshift, or an experimental axis shift. We tested these hypotheses using DiI injections to study the fate of cells in these experimental wings. We found strong transcription of HoxD10 and HoxD12 was present in the most anterior digit 2 of the rabbit foot. Thus, we found no evidence to question the use of HoxD expression as support for 1, 2, 3. When Shh signalling in early wing buds is inhibited, our fate maps demonstrate that an experimental homeotic frameshift is induced. Along with comparative morphology, HoxD expression provides strong support for 1, 2, 3 identity of wing digits. As an explanation for the offset 2, 3, 4 embryological position, the homeotic frameshift hypothesis is consistent with known mechanisms of limb development, and further proven to be experimentally possible. In contrast, the underlying mechanisms and experimental plausibility of an axis shift remain unclear.

Hox11 genes regulate postnatal longitudinal bone growth and growth plate proliferation.

PubMed

Pineault, Kyriel M; Swinehart, Ilea T; Garthus, Kayla N; Ho, Edward; Yao, Qing; Schipani, Ernestina; Kozloff, Kenneth M; Wellik, Deneen M

2015-10-23

Hox genes are critical regulators of skeletal development and Hox9-13 paralogs, specifically, are necessary for appendicular development along the proximal to distal axis. Loss of function of both Hoxa11 and Hoxd11 results in severe malformation of the forelimb zeugopod. In the radius and ulna of these mutants, chondrocyte development is perturbed, growth plates are not established, and skeletal growth and maturation fails. In compound mutants in which one of the four Hox11 alleles remains wild-type, establishment of a growth plate is preserved and embryos develop normally through newborn stages, however, skeletal phenotypes become evident postnatally. During postnatal development, the radial and ulnar growth rate slows compared to wild-type controls and terminal bone length is reduced. Growth plate height is decreased in mutants and premature growth plate senescence occurs along with abnormally high levels of chondrocyte proliferation in the reserve and proliferative zones. Compound mutants additionally develop an abnormal curvature of the radius, which causes significant distortion of the carpal elements. The progressive bowing of the radius appears to result from physical constraint caused by the disproportionately slower growth of the ulna than the radius. Collectively, these data are consistent with premature depletion of forelimb zeugopod progenitor cells in the growth plate of Hox11 compound mutants, and demonstrate a continued function for Hox genes in postnatal bone growth and patterning. © 2015. Published by The Company of Biologists Ltd.

Functional dissection of the Hox protein Abdominal-B in Drosophila cell culture

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

Zhai, Zongzhao; CellNetworks - Cluster of Excellence, Centre for Organismal Studies; Graduate School of Chinese Academy of Sciences, Beijing 100039

2011-11-04

Highlights: Black-Right-Pointing-Pointer ct340 CRM was identified to be the posterior spiracle enhancer of gene cut. Black-Right-Pointing-Pointer ct340 is under the direct transcriptional control of Hox protein Abd-B. Black-Right-Pointing-Pointer An efficient cloning system was developed to assay protein-DNA interaction. Black-Right-Pointing-Pointer New features of Abd-B dependent target gene regulation were detected. -- Abstract: Hox transcription factors regulate the morphogenesis along the anterior-posterior (A/P) body axis through the interaction with small cis-regulatory modules (CRMs) of their target gene, however so far very few Hox CRMs are known and have been analyzed in detail. In this study we have identified a new Hox CRM,more » ct340, which guides the expression of the cell type specification gene cut (ct) in the posterior spiracle under the direct control of the Hox protein Abdominal-B (Abd-B). Using the ct340 enhancer activity as readout, an efficient cloning system to generate VP16 activation domain fusion protein was developed to unambiguously test protein-DNA interaction in Drosophila cell culture. By functionally dissecting the Abd-B protein, new features of Abd-B dependent target gene regulation were detected. Due to its easy adaptability, this system can be generally used to map functional domains within sequence-specific transcriptional factors in Drosophila cell culture, and thus provide preliminary knowledge of the protein functional domain structure for further in vivo analysis.« less

Experimental demonstration of a trophic cascade in the Galápagos rocky subtidal: Effects of consumer identity and behavior.

PubMed

Witman, Jon D; Smith, Franz; Novak, Mark

2017-01-01

In diverse tropical webs, trophic cascades are presumed to be rare, as species interactions may dampen top-down control and reduce their prevalence. To test this hypothesis, we used an open experimental design in the Galápagos rocky subtidal that enabled a diverse guild of fish species, in the presence of each other and top predators (sea lions and sharks), to attack two species of sea urchins grazing on benthic algae. Time-lapse photography of experiments on natural and experimental substrates revealed strong species identity effects: only two predator species-blunthead triggerfish (Pseudobalistes naufragium) and finescale triggerfish (Balistes polylepis)-drove a diurnal trophic cascade extending to algae, and they preferred large pencil urchins (Eucidaris galapagensis) over green urchins (Lytechinus semituberculatus). Triggerfish predation effects were strong, causing a 24-fold reduction of pencil urchin densities during the initial 21 hours of a trophic cascade experiment. A trophic cascade was demonstrated for pencil urchins, but not for green urchins, by significantly higher percent cover of urchin-grazed algae in cages that excluded predatory fish than in predator access (fence) treatments. Pencil urchins were more abundant at night when triggerfish were absent, suggesting that this species persists by exploiting a nocturnal predation refuge. Time-series of pencil urchin survivorship further demonstrated per capita interference effects of hogfish and top predators. These interference effects respectively weakened and extended the trophic cascade to a fourth trophic level through behavioral modifications of the triggerfish-urchin interaction. We conclude that interference behaviors capable of modifying interaction strength warrant greater attention as mechanisms for altering top-down control, particularly in speciose food webs.

Experimental demonstration of a trophic cascade in the Galápagos rocky subtidal: Effects of consumer identity and behavior

PubMed Central

Witman, Jon D.; Smith, Franz; Novak, Mark

2017-01-01

In diverse tropical webs, trophic cascades are presumed to be rare, as species interactions may dampen top-down control and reduce their prevalence. To test this hypothesis, we used an open experimental design in the Galápagos rocky subtidal that enabled a diverse guild of fish species, in the presence of each other and top predators (sea lions and sharks), to attack two species of sea urchins grazing on benthic algae. Time-lapse photography of experiments on natural and experimental substrates revealed strong species identity effects: only two predator species–blunthead triggerfish (Pseudobalistes naufragium) and finescale triggerfish (Balistes polylepis)–drove a diurnal trophic cascade extending to algae, and they preferred large pencil urchins (Eucidaris galapagensis) over green urchins (Lytechinus semituberculatus). Triggerfish predation effects were strong, causing a 24-fold reduction of pencil urchin densities during the initial 21 hours of a trophic cascade experiment. A trophic cascade was demonstrated for pencil urchins, but not for green urchins, by significantly higher percent cover of urchin-grazed algae in cages that excluded predatory fish than in predator access (fence) treatments. Pencil urchins were more abundant at night when triggerfish were absent, suggesting that this species persists by exploiting a nocturnal predation refuge. Time-series of pencil urchin survivorship further demonstrated per capita interference effects of hogfish and top predators. These interference effects respectively weakened and extended the trophic cascade to a fourth trophic level through behavioral modifications of the triggerfish-urchin interaction. We conclude that interference behaviors capable of modifying interaction strength warrant greater attention as mechanisms for altering top-down control, particularly in speciose food webs. PMID:28430794

Aquatic antagonists: cutaneous sea urchin spine injury.

PubMed

Hsieh, Clifford; Aronson, Erica R; Ruiz de Luzuriaga, Arlene M

2016-11-01

Injuries from sea urchin spines are commonly seen in coastal regions with high levels of participation in water activities. Although these injuries may seem minor, the consequences vary based on the location of the injury. Sea urchin spine injuries may cause arthritis and synovitis from spines in the joints. Nonjoint injuries have been reported, and dermatologic aspects of sea urchin spine injuries rarely have been discussed. We present a case of a patient with sea urchin spines embedded in the thigh who subsequently developed painful skin nodules. Tissue from the site of the injury demonstrated foreign-body type granulomas. Following the removal of the spines and granulomatous tissue, the patient experienced resolution of the nodules and associated pain. Extraction of sea urchin spines can attenuate the pain and decrease the likelihood of granuloma formation, infection, and long-term sequelae.

CuO urchin-nanostructures synthesized from a domestic hydrothermal microwave method

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

Keyson, D.; Laboratorio de Ensino de Ciencias, DME Universidade Federal da Paraiba, PB; Volanti, D.P.

This letter reports the synthesis of CuO urchin-nanostructures by a simple and novel hydrothermal microwave method. The formation and growth of urchin-nanostructures is mainly affected by the addition of polyethylene glycol (PEG). The hierarchical malachite particles are uniform spheres with a diameter of 0.7-1.9 {mu}m. CuO urchin-nanostructures were characterized by X-ray diffraction (XRD), field-emission scanning electron microscopy (FEG-SEM) and nitrogen adsorption (BET). The specific surface area of the CuO nanostructured microspheres was about 170.5 m{sup 2}/g. A possible mechanism for the formation of such CuO urchin-nanostructures is proposed.

Diversity of Polyhydroxynaphthoquinone Pigments in North Pacific Sea Urchins.

PubMed

Vasileva, Elena A; Mishchenko, Natalia P; Fedoreyev, Sergey A

2017-09-01

Using high-performance liquid chromatography with diode-array detection and mass spectrometry (HPLC-DAD/MS) we investigated the composition of polyhydroxynaphthoquinone (PHNQ) pigments from sea urchins Strongylocentrotus pallidus, St. polyacanthus, St. droebachiensis, Brisaster latifrons and Echinarachnius parma, collected in the Sea of Okhotsk and the Bering Sea. Identification of PHNQ pigments from sea urchins St. polyacanthus, B. latifrons, and E. parma was performed for the first time. Among the usual PHNQ pigments, mono- and dimethoxy derivatives of spinochrome E, not previously found in other sea urchins, were discovered in St. polyacanthus and St. droebachiensis. In St. droebachiensis, two monomethoxy derivatives of echinochrome A were detected, isolated previously from only tropical sea urchins. It was found that the composition and total content of pigments of St. droebachiensis depends on the collection area of the sea urchins and its depth and varies from 88 to 331 μg/g of dry shells. Sea urchins St. pallidus, B. latifrons and E. parma had average values for PHNQ pigment content, approximately 30 μg/g, and St. polyacanthus had a low PHNQ content, 13 μg/g. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Survivorship and feeding preferences among size classes of outplanted sea urchins, Tripneustes gratilla, and possible use as biocontrol for invasive alien algae

PubMed Central

Ringang, Rory R.; Cantero, Sean Michael A.; Toonen, Robert J.

2015-01-01

We investigate the survivorship, growth and diet preferences of hatchery-raised juvenile urchins, Tripneustes gratilla, to evaluate the efficacy of their use as biocontrol agents in the efforts to reduce alien invasive algae. In flow-through tanks, we measured urchin growth rates, feeding rates and feeding preferences among diets of the most common invasive algae found in Kāneʻohe Bay, Hawaiʻi: Acanthophora spicifera, Gracilaria salicornia, Eucheuma denticulatum and Kappaphycus clade B. Post-transport survivorship of outplanted urchins was measured in paired open and closed cages in three different reef environments (lagoon, reef flat and reef slope) for a month. Survivorship in closed cages was highest on the reef flat (∼75%), and intermediate in the lagoon and reef slope (∼50%). In contrast, open cages showed similar survivorship on the reef flat and in the lagoon, but only 20% of juvenile urchins survived in open cages placed on the reef slope. Urchins grew significantly faster on diets of G. salicornia (1.58 mm/week ± 0.14 SE) and Kappaphycus clade B (1.69 ± 0.14 mm/wk) than on E. denticulatum (0.97 ± 0.14 mm/wk), with intermediate growth when fed on A. spicifera (1.23 ± 0.11 mm/wk). Interestingly, urchins display size-specific feeding preferences. In non-choice feeding trials, small urchins (17.5–22.5 mm test diameter) consumed G. salicornia fastest (6.08 g/day ± 0.19 SE), with A. spicifera (4.25 ± 0.02 g/day) and Kappaphycus clade B (3.83 ± 0.02 g/day) intermediate, and E. denticulatum was clearly the least consumed (2.32 ± 0.37 g/day). Medium-sized (29.8–43.8 mm) urchins likewise preferentially consumed G. salicornia (12.60 ± 0.08 g/day), with less clear differences among the other species in which E. denticulatum was still consumed least (9.35 ± 0.90 g/day). In contrast, large urchins (45.0–65.0 mm) showed no significant preferences among the different algae species at all (12.43–15.24 g/day). Overall consumption rates in non-choice trials were roughly equal to those in the choice trials, but differences among feeding rates on each species were not predictive of feeding preferences when urchins were presented all four species simultaneously. In the choice feeding trials, both small and medium urchins clearly preferred A. spicifera over all other algae (roughly twice as much consumed as any other species). Again, however, differences were less pronounced among adult urchins, with adults showing a significant preference for A. spicifera and Kappaphycus clade B compared to the other two algal species. These findings indicate that outplanted urchins are surviving on the reef flats and eating a variety of alien invasive algae as intended. Although juvenile urchins show stronger feeding preferences, these animals grow quickly, and adult urchins are more generalist herbivores that consume all four alien invasive algae. PMID:26401450

Butterfly eyespot serial homology: enter the Hox genes

PubMed Central

2011-01-01

Hox genes modify serial homology patterns in many organisms, exemplified in vertebrates by modification of the axial skeleton and in arthropods by diversification of the body segments. Butterfly wing eyespots also appear in a serial homologous pattern that, in certain species, is subject to local modification. A paper in EvoDevo reports the Hox gene Antp is the earliest known gene to have eyespot-specific expression; however, not all Lepidoptera express Antp in eyespots, suggesting some developmental flexibility. See research article: http://www.evodevojournal.com/content/2/1/9 PMID:21527048

Hydrothermal Synthesis of Nanostructured Vanadium Oxides

PubMed Central

Livage, Jacques

2010-01-01

A wide range of vanadium oxides have been obtained via the hydrothermal treatment of aqueous V(V) solutions. They exhibit a large variety of nanostructures ranging from molecular clusters to 1D and 2D layered compounds. Nanotubes are obtained via a self-rolling process while amazing morphologies such as nano-spheres, nano-flowers and even nano-urchins are formed via the self-assembling of nano-particles. This paper provides some correlation between the molecular structure of precursors in the solution and the nanostructure of the solid phases obtained by hydrothermal treatment. PMID:28883325

EG-05COMBINATION OF GENE COPY GAIN AND EPIGENETIC DEREGULATION ARE ASSOCIATED WITH THE ABERRANT EXPRESSION OF A STEM CELL RELATED HOX-SIGNATURE IN GLIOBLASTOMA

PubMed Central

Kurscheid, Sebastian; Bady, Pierre; Sciuscio, Davide; Samarzija, Ivana; Shay, Tal; Vassallo, Irene; Van Criekinge, Wim; Domany, Eytan; Stupp, Roger; Delorenzi, Mauro; Hegi, Monika

2014-01-01

We previously reported a stem cell related HOX gene signature associated with resistance to chemo-radiotherapy (TMZ/RT- > TMZ) in glioblastoma. However, underlying mechanisms triggering overexpression remain mostly elusive. Interestingly, HOX genes are neither involved in the developing brain, nor expressed in normal brain, suggestive of an acquired gene expression signature during gliomagenesis. HOXA genes are located on CHR 7 that displays trisomy in most glioblastoma which strongly impacts gene expression on this chromosome, modulated by local regulatory elements. Furthermore we observed more pronounced DNA methylation across the HOXA locus as compared to non-tumoral brain (Human methylation 450K BeadChip Illumina; 59 glioblastoma, 5 non-tumoral brain sampes). CpG probes annotated for HOX-signature genes, contributing most to the variability, served as input into the analysis of DNA methylation and expression to identify key regulatory regions. The structural similarity of the observed correlation matrices between DNA methylation and gene expression in our cohort and an independent data-set from TCGA (106 glioblastoma) was remarkable (RV-coefficient, 0.84; p-value < 0.0001). We identified a CpG located in the promoter region of the HOXA10 locus exerting the strongest mean negative correlation between methylation and expression of the whole HOX-signature. Applying this analysis the same CpG emerged in the external set. We then determined the contribution of both, gene copy aberration (CNA) and methylation at the selected probe to explain expression of the HOX-signature using a linear model. Statistically significant results suggested an additive effect between gene dosage and methylation at the key CpG identified. Similarly, such an additive effect was also observed in the external data-set. Taken together, we hypothesize that overexpression of the stem-cell related HOX signature is triggered by gain of trisomy 7 and escape from compensatory DNA methylation at positions controlling the effect of enhanced gene dose on expression.

EGL-20/Wnt and MAB-5/Hox Act Sequentially to Inhibit Anterior Migration of Neuroblasts in C. elegans

PubMed Central

Josephson, Matthew P.; Chai, Yongping; Ou, Guangshuo; Lundquist, Erik A.

2016-01-01

Directed neuroblast and neuronal migration is important in the proper development of nervous systems. In C. elegans the bilateral Q neuroblasts QR (on the right) and QL (on the left) undergo an identical pattern of cell division and differentiation but migrate in opposite directions (QR and descendants anteriorly and QL and descendants posteriorly). EGL-20/Wnt, via canonical Wnt signaling, drives the expression of MAB-5/Hox in QL but not QR. MAB-5 acts as a determinant of posterior migration, and mab-5 and egl-20 mutants display anterior QL descendant migrations. Here we analyze the behaviors of QR and QL descendants as they begin their anterior and posterior migrations, and the effects of EGL-20 and MAB-5 on these behaviors. The anterior and posterior daughters of QR (QR.a/p) after the first division immediately polarize and begin anterior migration, whereas QL.a/p remain rounded and non-migratory. After ~1 hour, QL.a migrates posteriorly over QL.p. We find that in egl-20/Wnt, bar-1/β-catenin, and mab-5/Hox mutants, QL.a/p polarize and migrate anteriorly, indicating that these molecules normally inhibit anterior migration of QL.a/p. In egl-20/Wnt mutants, QL.a/p immediately polarize and begin migration, whereas in bar-1/β-catenin and mab-5/Hox, the cells transiently retain a rounded, non-migratory morphology before anterior migration. Thus, EGL-20/Wnt mediates an acute inhibition of anterior migration independently of BAR-1/β-catenin and MAB-5/Hox, and a later, possible transcriptional response mediated by BAR-1/β-catenin and MAB-5/Hox. In addition to inhibiting anterior migration, MAB-5/Hox also cell-autonomously promotes posterior migration of QL.a (and QR.a in a mab-5 gain-of-function). PMID:26863303

Hox genes require homothorax and extradenticle for body wall identity specification but not for appendage identity specification during metamorphosis of Tribolium castaneum.

PubMed

Smith, Frank W; Jockusch, Elizabeth L

2014-11-01

The establishment of segment identity is a key developmental process that allows for divergence along the anteroposterior body axis in arthropods. In Drosophila, the identity of a segment is determined by the complement of Hox genes it expresses. In many contexts, Hox transcription factors require the protein products of extradenticle (exd) and homothorax (hth) as cofactors to perform their identity specification functions. In holometabolous insects, segment identity may be specified twice, during embryogenesis and metamorphosis. To glean insight into the relationship between embryonic and metamorphic segmental identity specification, we have compared these processes in the flour beetle Tribolium castaneum, which develops ventral appendages during embryogenesis that later metamorphose into adult appendages with distinct morphologies. At metamorphosis, comparisons of RNAi phenotypes indicate that Hox genes function jointly with Tc-hth and Tc-exd to specify several region-specific aspects of the adult body wall. On the other hand, Hox genes specify appendage identities along the anteroposterior axis independently of Tc-hth/Tc-exd and Tc-hth/Tc-exd specify proximal vs. distal identity within appendages independently of Hox genes during this stage. During embryogenesis, Tc-hth and Tc-exd play a broad role in the segmentation process and are required for specification of body wall identities in the thorax; however, contrasting with results from other species, we did not obtain homeotic transformations of embryonic appendages in response to Tc-hth or Tc-exd RNAi. In general, the homeotic effects of interference with the function of Hox genes and Tc-hth/Tc-exd during metamorphosis did not match predictions based on embryonic roles of these genes. Comparing metamorphic patterning in T. castaneum to embryonic and post-embryonic development in hemimetabolous insects suggests that holometabolous metamorphosis combines patterning processes of both late embryogenesis and metamorphosis of the hemimetabolous life cycle. Copyright © 2014 Elsevier Inc. All rights reserved.

Directed Neural Differentiation of Mouse Embryonic Stem Cells Is a Sensitive System for the Identification of Novel Hox Gene Effectors

PubMed Central

Bami, Myrto; Episkopou, Vasso; Gavalas, Anthony; Gouti, Mina

2011-01-01

The evolutionarily conserved Hox family of homeodomain transcription factors plays fundamental roles in regulating cell specification along the anterior posterior axis during development of all bilaterian animals by controlling cell fate choices in a highly localized, extracellular signal and cell context dependent manner. Some studies have established downstream target genes in specific systems but their identification is insufficient to explain either the ability of Hox genes to direct homeotic transformations or the breadth of their patterning potential. To begin delineating Hox gene function in neural development we used a mouse ES cell based system that combines efficient neural differentiation with inducible Hoxb1 expression. Gene expression profiling suggested that Hoxb1 acted as both activator and repressor in the short term but predominantly as a repressor in the long run. Activated and repressed genes segregated in distinct processes suggesting that, in the context examined, Hoxb1 blocked differentiation while activating genes related to early developmental processes, wnt and cell surface receptor linked signal transduction and cell-to-cell communication. To further elucidate aspects of Hoxb1 function we used loss and gain of function approaches in the mouse and chick embryos. We show that Hoxb1 acts as an activator to establish the full expression domain of CRABPI and II in rhombomere 4 and as a repressor to restrict expression of Lhx5 and Lhx9. Thus the Hoxb1 patterning activity includes the regulation of the cellular response to retinoic acid and the delay of the expression of genes that commit cells to neural differentiation. The results of this study show that ES neural differentiation and inducible Hox gene expression can be used as a sensitive model system to systematically identify Hox novel target genes, delineate their interactions with signaling pathways in dictating cell fate and define the extent of functional overlap among different Hox genes. PMID:21637844

A Stable Thoracic Hox Code and Epimorphosis Characterize Posterior Regeneration in Capitella teleta

PubMed Central

de Jong, Danielle M.; Seaver, Elaine C.

2016-01-01

Regeneration, the ability to replace lost tissues and body parts following traumatic injury, occurs widely throughout the animal tree of life. Regeneration occurs either by remodeling of pre-existing tissues, through addition of new cells by cell division, or a combination of both. We describe a staging system for posterior regeneration in the annelid, Capitella teleta, and use the C. teleta Hox gene code as markers of regional identity for regenerating tissue along the anterior-posterior axis. Following amputation of different posterior regions of the animal, a blastema forms and by two days, proliferating cells are detected by EdU incorporation, demonstrating that epimorphosis occurs during posterior regeneration of C. teleta. Neurites rapidly extend into the blastema, and gradually become organized into discrete nerves before new ganglia appear approximately seven days after amputation. In situ hybridization shows that seven of the ten Hox genes examined are expressed in the blastema, suggesting roles in patterning the newly forming tissue, although neither spatial nor temporal co-linearity was detected. We hypothesized that following amputation, Hox gene expression in pre-existing segments would be re-organized to scale, and the remaining fragment would express the complete suite of Hox genes. Surprisingly, most Hox genes display stable expression patterns in the ganglia of pre-existing tissue following amputation at multiple axial positions, indicating general stability of segmental identity. However, the three Hox genes, CapI-lox4, CapI-lox2 and CapI-Post2, each shift its anterior expression boundary by one segment, and each shift includes a subset of cells in the ganglia. This expression shift depends upon the axial position of the amputation. In C. teleta, thoracic segments exhibit stable positional identity with limited morphallaxis, in contrast with the extensive body remodeling that occurs during regeneration of some other annelids, planarians and acoel flatworms. PMID:26894631

Hox Genes: Choreographers in Neural Development, Architects of Circuit Organization

PubMed Central

Philippidou, Polyxeni; Dasen, Jeremy S.

2013-01-01

Summary The neural circuits governing vital behaviors, such as respiration and locomotion, are comprised of discrete neuronal populations residing within the brainstem and spinal cord. Work over the past decade has provided a fairly comprehensive understanding of the developmental pathways that determine the identity of major neuronal classes within the neural tube. However, the steps through which neurons acquire the subtype diversities necessary for their incorporation into a particular circuit are still poorly defined. Studies on the specification of motor neurons indicate that the large family of Hox transcription factors has a key role in generating the subtypes required for selective muscle innervation. There is also emerging evidence that Hox genes function in multiple neuronal classes to shape synaptic specificity during development, suggesting a broader role in circuit assembly. This review highlights the functions and mechanisms of Hox gene networks, and their multifaceted roles during neuronal specification and connectivity. PMID:24094100

Retinoic acid influences anteroposterior positioning of epidermal sensory neurons and their gene expression in a developing chordate (amphioxus)

PubMed Central

Schubert, Michael; Holland, Nicholas D.; Escriva, Hector; Holland, Linda Z.; Laudet, Vincent

2004-01-01

In developing chordates, retinoic acid (RA) signaling patterns the rostrocaudal body axis globally and affects gene expression locally in some differentiating cell populations. Here we focus on development of epidermal sensory neurons in an invertebrate chordate (amphioxus) to determine how RA signaling influences their rostrocaudal distribution and gene expression (for AmphiCoe, a neural precursor gene; for amphioxus islet and AmphiERR, two neural differentiation genes; and for AmphiHox1, -3, -4, and -6). Treatments with RA or an RA antagonist (BMS009) shift the distribution of developing epidermal neurons anteriorly or posteriorly, respectively. These treatments also affect gene expression patterns in the epidermal neurons, suggesting that RA levels may influence specification of neuronal subtypes. Although colinear expression of Hox genes is well known for the amphioxus central nervous system, we find an unexpected comparable colinearity for AmphiHox1, -3, -4, and -6 in the developing epidermis; moreover, RA levels affect the anteroposterior extent of these Hox expression domains, suggesting that RA signaling controls a colinear Hox code for anteroposterior patterning of the amphioxus epidermis. Thus, in amphioxus, the developing peripheral nervous system appears to be structured by mechanisms parallel to those that structure the central nervous system. One can speculate that, during evolution, an ancestral deuterostome that structured its panepidermal nervous system with an RA-influenced Hox code gave rise to chordates in which this patterning mechanism persisted within the epidermal elements of the peripheral nervous system and was transferred to the neuroectoderm as the central nervous system condensed dorsally. PMID:15226493

Demonstration of an Integrated Compliance Model for Predicting Copper Fate and Effects in DoD Harbors

DTIC Science & Technology

2008-12-01

shaped larvae (120 µm), (c) purple sea urchin (Strongylocentrotus purpuratus; adults, 5- to 7-cm diameter), (d) sea urchin pluteus larva (200 µm...development tests with mussels (M. galloprovin- cialis) and purple sea urchins (S. purpuratus) expressed as water concentration or whole-body residues...galloprovincialis (bay mussel), D. excentricus (sand dollar) and S. purpuratus (purple sea urchin ) by the integrated CH3D/seawater-BLM model for the

Hierarchical Structures in Biology as a Guide for New Materials Technology

DTIC Science & Technology

1994-01-01

properties--to changes in performance requirements. For example, while the spines of the sea urchin are moving, the attached ligaments are soft and...by studying how sea urchins control the material properties of their bodies as a function of the local environment. Sea stars, sea urchins , and sea ...Materials Research Society Bulletin 16(7):23-28. Trotter, J. A., and T. J. Koob. 1989. Collagen and proteoglycan in a sea urchin ligament with mutable

Effects of marine reserves and urchin disease on southern Californian rocky reef communities

USGS Publications Warehouse

Behrens, Michael D.; Lafferty, Kevin D.

2004-01-01

While the species level effects of marine reserves are widely recognized, community level shifts due to marine reserves have only recently been documented. Protection from fishing of top predators may lead to trophic cascades, which have community-wide implications. Disease may act in a similar manner, regulating population levels of dominant species within a community. Two decades of data from the Channel Islands National Park Service's Kelp Forest Monitoring database allowed us to compare the effects of fishing and urchin disease on rocky reef community patterns and dynamics. Different size-frequency distributions of urchins inside and outside of reserves indicated reduced predation on urchins at sites where fishing removes urchin predators. Rocky reefs inside reserves were more likely to support kelp forests than were fished areas. We suggest that this results from cascading effects of the fishery on urchin predators outside the reserves, which releases herbivores (urchins) from predation. After periods of prevalent urchin disease, the reef community shifted more towards kelp forest assemblages. Specific groups of algae and invertebrates were associated with kelp forest and barrens communities. The community dynamics leading to transitions between kelp forests and barrens are driven by both fishing and disease; however the fishery effect was of greater magnitude. This study further confirms the importance of marine reserves not only for fisheries conservation, but also for the conservation of historically dominant community types.

Predation cues rather than resource availability promote cryptic behaviour in a habitat-forming sea urchin.

PubMed

Spyksma, Arie J P; Taylor, Richard B; Shears, Nick T

2017-03-01

It is well known that predators often influence the foraging behaviour of prey through the so-called "fear effect". However, it is also possible that predators could change prey behaviour indirectly by altering the prey's food supply through a trophic cascade. The predator-sea urchin-kelp trophic cascade is widely assumed to be driven by the removal of sea urchins by predators, but changes in sea urchin behaviour in response to predators or increased food availability could also play an important role. We tested whether increased crevice occupancy by herbivorous sea urchins in the presence of abundant predatory fishes and lobsters is a response to the increased risk of predation, or an indirect response to higher kelp abundances. Inside two New Zealand marine reserves with abundant predators and kelp, individuals of the sea urchin Evechinus chloroticus were rarer and remained cryptic (i.e. found in crevices) to larger sizes than on adjacent fished coasts where predators and kelp are rare. In a mesocosm experiment, cryptic behaviour was induced by simulated predation (the addition of crushed conspecifics), but the addition of food in the form of drift kelp did not induce cryptic behaviour. These findings demonstrate that the 'fear' of predators is more important than food availability in promoting sea urchin cryptic behaviour and suggest that both density- and behaviourally mediated interactions are important in the predator-sea urchin-kelp trophic cascade.

Genetics Home Reference: hand-foot-genital syndrome

MedlinePlus

... article on PubMed Central Goodman FR, Scambler PJ. Human HOX gene mutations. Clin Genet. 2001 Jan;59(1):1- ... on PubMed Goodman FR. Limb malformations and the human HOX genes. Am J Med Genet. 2002 Oct 15;112( ...

Relationships among predatory fish, sea urchins and barrens in Mediterranean rocky reefs across a latitudinal gradient.

PubMed

Guidetti, P; Dulcić, J

2007-03-01

Previous studies conducted on a local scale emphasised the potential of trophic cascades in Mediterranean rocky reefs (involving predatory fish, sea urchins and macroalgae) in affecting the transition between benthic communities dominated by erected macroalgae and barrens (i.e., bare rock with partial cover of encrusting algae). Distribution patterns of fish predators of sea urchins (Diplodus sargus sargus, Diplodus vulgaris, Coris julis and Thalassoma pavo), sea urchins (Paracentrotus lividus and Arbacia lixula) and barrens, and fish predation rates upon sea urchins, were assessed in shallow (3-6m depth) sublittoral rocky reefs in the northern, central and southern sectors of the eastern Adriatic Sea, i.e., on a large spatial scale of hundreds of kilometres. No dramatic differences were observed in predatory fish density across latitude, except for a lower density of small D. sargus sargus in the northern Adriatic and an increasing density of T. pavo from north to south. P. lividus did not show any significant difference across latitude, whereas A. lixula was more abundant in the southern than in the central Adriatic. Barrens were more extended in the southern than in the central and northern sectors, and were related with sea urchin density. Fish predation upon adult sea urchins did not change on a large scale, whereas it was slightly higher in the southern sector for juveniles when predation rates of both urchins were pooled. Results show that: (1) assemblages of predatory fish and sea urchins, and barren extent change across latitude in the eastern Adriatic Sea, (2) the weak relations between predatory fish density and predation rates on urchins reveal that factors other than top-down control can be important over large scale (with the caveat that the study was conducted in fished areas) and (3) patterns of interaction among strongly interacting taxa could change on large spatial scales and the number of species involved.

Overgrazing of a large seagrass bed by the sea urchin Lytechinus variegatus in Outer Florida Bay

USGS Publications Warehouse

Rose, C.D.; Sharp, W.C.; Kenworthy, W.J.; Hunt, J.H.; Lyons, W.G.; Prager, E.J.; Valentine, J.F.; Hall, M.O.; Whitfield, P.E.; Fourqurean, J.W.

1999-01-01

Unusually dense aggregations of the sea urchin Lytechinus variegatus overgrazed at least 0.81 km2 of seagrass habitat in Outer Florida Bay (USA) between August 1997 and May 1998. Initially, sea-urchin densities were as high as 364 sea urchins m-2, but they steadily declined to within a range of 20 to 50 sea urchins m-2 by December 1998. Prior to this event, sea-urchin densities were 95% of the short-shoot apical meristems were removed by sea-urchin grazing in our study area. Such extensive loss may severely limit recovery of this seagrass community by vegetative reproduction. Effects of the removal of seagrass biomass have already resulted in the depletion of epifaunal-infaunal mollusk assemblages and resuspension of fine-grained (<64 ??m) surface sediments - which have caused significant changes in community structure and in the physical properties of the sediments. These changes, coupled with the loss of essential fishery habitat, reductions in primary and secondary production, and degradation of water quality, may lead to additional, longer-term, indirect effects that may extend beyond the boundaries of the grazed areas and into adjacent coastal ecosystems.

Observation of different core water cluster ions Y-(H2O)n (Y = O2, HCN, HOx, NOx, COx) and magic number in atmospheric pressure negative corona discharge mass spectrometry

NASA Astrophysics Data System (ADS)

Sekimoto, K.; Takayama, M.

2010-12-01

Atmospheric ion water clusters have been of long-standing interest in the field of atmospheric sciences, because of them playing a central role in the formation of tropospheric aerosols which affect the photochemistry, radiation budget of the atmosphere and climate. On the basis of a mechanism of aerosol formation in the troposphere proposed by Yu and Turco, termed “ion-mediated nucleation” (Geophys. Res. Lett. 2000, 27, 883), atmospheric ion water clusters are most likely to be produced via two processes; 1) direct attachment of polar solvent molecules H2O to atmospheric ions due to them having strong binding energy via ion-dipole interactions, and 2) growth of ion-induced hydrates into larger water clusters bound via hydrogen-bonding networks by condensation with H2O molecules. The stability and growth rates of water clusters are strongly dependent on the thermochemical properties of individual atmospheric core ions. A large number of thermochemical information of the positive atmospheric ion H3O+ and its hydrates H3O+(H2O)n have been reported so far, while there has been little information of the water clusters with the negative atmospheric core ions. Therefore, fundamental studies of the thermochemistry of various negative atmospheric ion water clusters will contribute towards furthering an understanding of their unique role in atmospheric sciences and climate change. We have recently established an atmospheric pressure DC corona discharge device containing a specific corona needle electrode that made it possible to reproducibly generate negative core ions Y- originating from ambient air (Int. J. Mass Spectrom. 2007, 261, 38; Eur. Phys. J. D 2008, 50, 297). The change in electric field strength on the needle tip resulted in the formation of negative atmospheric core ions Y- with various different lifetimes in air. The low field strength brought about the dominant formation of core ions with short lifetimes in air such as O2- and HOx-, while the longer-lived core ions HCN-, NOx- and COx- were mainly produced at higher field strength. Furthermore, the use of the discharge system coupled to mass spectrometers led to the stable formation of large water clusters Y-(H2O)n due to adiabatic expansion caused by the pressure difference between the ambient discharge area (760 torr) and vacuum region in the mass spectrometers (≈ 1 torr). Here we show the resulting mass spectra of large water clusters Y-(H2O)n (0 ≤ n ≥ 80) with the dominant negative core ion Y- such as O2-, HO-, HO2-, HCN-, NO2-, NO3-, NO3-(HNO3)2, CO3- and HCO4- which play a central role in tropospheric ion chemistry, as well as the detailed mechanism of formation of those negative ion water clusters by atmospheric pressure DC corona discharge mass spectrometry. Here we also provide new thermochemical information about magic numbers and first hydrated shells for individual negative core ions Y-, which have particular stability in the Y-(H2O)n cluster series, by using the reliable mass spectrometry data obtained and the relationship between the temperature condition in a reaction chamber and the resulting cluster distribution.

Submaximal exercise with self-contained breathing apparatus: the effects of hyperoxia and inspired gas density.

PubMed

Eves, Neil D; Petersen, Stewart R; Jones, Richard L

2003-10-01

The self-contained breathing apparatus (SCBA) used by firefighters, and other working in dangerous environments, adds an external resistance to expiration, which increases expiratory work during heavy exercise. Compressed air is typically used with the SCBA and we hypothesized that changing the inspired oxygen concentration and/or gas density with helium would reduce the external expiratory resistance. On separate days, 15 men completed four 30-min bouts of treadmill exercise dressed in protective clothing and breathing the test gases through the SCBA. Four different gas mixtures were assigned in random order: [compressed air (NOX: 21% O2, 79% N2), hyperoxia (HOX: 40% O2, 60% N2), normoxic-helium (HE-OX: 21% O2, 79% He), and helium-hyperoxia (HE-HOX: 40% O2, 60% He)]. Compared with NOX, the two helium mixtures (but not HOX), decreased the external breathing resistance and all three gas mixtures decreased the peak expired mask pressure and the ventilatory mass moved. Both hyperoxic mixtures decreased blood lactate and the rating of perceived exertion was decreased at 30 min with HE-HOX. These results demonstrate that the helium-based gas mixtures, and to a lesser extent HOX, reduce the expiratory work associated with the SCBA during strenuous exercise.

Proliferating cell nuclear antigen (Pcna) as a direct downstream target gene of Hoxc8

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

Min, Hyehyun; Lee, Ji-Yeon; Bok, Jinwoong

2010-02-19

Hoxc8 is a member of Hox family transcription factors that play crucial roles in spatiotemporal body patterning during embryogenesis. Hox proteins contain a conserved 61 amino acid homeodomain, which is responsible for recognition and binding of the proteins onto Hox-specific DNA binding motifs and regulates expression of their target genes. Previously, using proteome analysis, we identified Proliferating cell nuclear antigen (Pcna) as one of the putative target genes of Hoxc8. Here, we asked whether Hoxc8 regulates Pcna expression by directly binding to the regulatory sequence of Pcna. In mouse embryos at embryonic day 11.5, the expression pattern of Pcna wasmore » similar to that of Hoxc8 along the anteroposterior body axis. Moreover, Pcna transcript levels as well as cell proliferation rate were increased by overexpression of Hoxc8 in C3H10T1/2 mouse embryonic fibroblast cells. Characterization of 2.3 kb genomic sequence upstream of Pcna coding region revealed that the upstream sequence contains several Hox core binding sequences and one Hox-Pbx binding sequence. Direct binding of Hoxc8 proteins to the Pcna regulatory sequence was verified by chromatin immunoprecipitation assay. Taken together, our data suggest that Pcna is a direct downstream target of Hoxc8.« less

Bmi1 represses Ink4a/Arf and Hox genes to regulate stem cells in the rodent incisor

PubMed Central

Biehs, Brian; Hu, Jimmy Kuang-Hsien; Strauli, Nicolas B.; Sangiorgi, Eugenio; Jung, Heekyung; Heber, Ralf-Peter; Ho, Sunita; Goodwin, Alice F.; Dasen, Jeremy S.; Capecchi, Mario R.; Klein, Ophir D.

2013-01-01

The polycomb group gene Bmi1 is required for maintenance of adult stem cells in many organs1, 2. Inactivation of Bmi1 leads to impaired stem cell self-renewal due to deregulated gene expression. One critical target of BMI1 is Ink4a/Arf, which encodes the cell cycle inhibitors p16ink4a and p19Arf3. However, deletion of Ink4a/Arf only partially rescues Bmi1 null phenotypes4, indicating that other important targets of BMI1 exist. Here, using the continuously-growing mouse incisor as a model system, we report that Bmi1 is expressed by incisor stem cells and that deletion of Bmi1 resulted in fewer stem cells, perturbed gene expression, and defective enamel production. Transcriptional profiling revealed that Hox expression is normally repressed by BMI1 in the adult, and functional assays demonstrated that BMI1-mediated repression of Hox genes preserves the undifferentiated state of stem cells. As Hox gene upregulation has also been reported in other systems when Bmi1 is inactivated1, 2, 5–7, our findings point to a general mechanism whereby BMI1-mediated repression of Hox genes is required for the maintenance of adult stem cells and for prevention of inappropriate differentiation. PMID:23728424

HOXB9 Expression Correlates with Histological Grade and Prognosis in LSCC

PubMed Central

2017-01-01

The purpose of this study was to investigate the HOX gene expression profile in laryngeal squamous cell carcinoma (LSCC) and assess whether some genes are associated with the clinicopathological features and prognosis in LSCC patients. The HOX gene levels were tested by microarray and validated by qRT-PCR in paired cancerous and adjacent noncancerous LSCC tissue samples. The microarray testing data of 39 HOX genes revealed 15 HOX genes that were at least 2-fold upregulated and 2 that were downregulated. After qRT-PCR evaluation, the three most upregulated genes (HOXB9, HOXB13, and HOXD13) were selected for tissue microarray (TMA) analysis. The correlations between the HOXB9, HOXB13, and HOXD13 expression levels and both clinicopathological features and prognosis were analyzed. Three HOX gene expression levels were markedly increased in LSCC tissues compared with adjacent noncancerous tissues (P < 0.001). HOXB9 was found to correlate with histological grade (P < 0.01) and prognosis (P < 0.01) in LSCC. In conclusion, this study revealed that HOXB9, HOXB13, and HOXD13 were upregulated and may play important roles in LSCC. Moreover, HOXB9 may serve as a novel marker of poor prognosis and a potential therapeutic target in LSCC patients. PMID:28808656

Changes in sea urchins and kelp following a reduction in sea otter density as a result of the Exxon Valdez oil spill

USGS Publications Warehouse

Dean, Thomas A.; Bodkin, James L.; Jewett, Stephen C.; Monson, Daniel H.; Jung, D.

2000-01-01

Interactions between sea otters Enhydra lutris, sea urchins Strongylocentrotus droebachiensis, and kelp were investigated following the reduction in sea otter density in Prince William Sound, Alaska, after the Exxon Valdez oil spill in 1989. At northern Knight Island, a heavily oiled portion of the sound, sea otter abundance was reduced by a minimum of 50% by the oil spill, and from 1995 through 1998 remained at an estimated 66% lower than in 1973. Where sea otter densities were reduced, there were proportionally more large sea urchins. However, except in some widely scattered aggregations, both density and biomass of sea urchins were similar in an area of reduced sea otter density compared with an area where sea otters remained about 10 times more abundant. Furthermore, there was no change in kelp abundance in the area of reduced sea otter density. This is in contrast to greatly increased biomass of sea urchins and greatly reduced kelp density observed following an approximate 90% decline in sea otter abundance in the western Aleutian Islands. The variation in community response to a reduction in sea otters may be related to the magnitude of the reduction and the non-linear response by sea urchins to changes in predator abundance. The number of surviving sea otters may have been high enough to suppress sea urchin populations in Prince William Sound, but not in the Aleutians. Alternatively, differences in response may have been due to differences in the frequency or magnitude of sea urchin recruitment. Densities of small sea urchins were much higher in the Aleutian system even prior to the reduction in sea otters, suggesting a higher rate of recruitment.

Observations of different core water cluster ions Y-(H2O)n (Y = O2, HOx, NOx, COx) and magic number in atmospheric pressure negative corona discharge mass spectrometry.

PubMed

Sekimoto, Kanako; Takayama, Mitsuo

2011-01-01

Reliable mass spectrometry data from large water clusters Y(-)(H(2)O)(n) with various negative core ions Y(-) such as O(2)(-), HO(-), HO(2)(-), NO(2)(-), NO(3)(-), NO(3)(-)(HNO(3))(2), CO(3)(-) and HCO(4)(-) have been obtained using atmospheric pressure negative corona discharge mass spectrometry. All the core Y(-) ions observed were ionic species that play a central role in tropospheric ion chemistry. These mass spectra exhibited discontinuities in ion peak intensity at certain size clusters Y(-)(H(2)O)(m) indicating specific thermochemical stability. Thus, Y(-)(H(2)O)(m) may correspond to the magic number or first hydrated shell in the cluster series Y(-)(H(2)O)(n). The high intensity discontinuity at HO(-)(H(2)O)(3) observed was the first mass spectrometric evidence for the specific stability of HO(-)(H(2)O)(3) as the first hydrated shell which Eigen postulated in 1964. The negative ion water clusters Y(-)(H(2)O)(n) observed in the mass spectra are most likely to be formed via core ion formation in the ambient discharge area (760 torr) and the growth of water clusters by adiabatic expansion in the vacuum region of the mass spectrometers (≈1 torr). The detailed mechanism of the formation of the different core water cluster ions Y(-)(H(2)O)(n) is described. Copyright © 2010 John Wiley & Sons, Ltd.

Juvenile growth of the tropical sea urchin Lytechinus variegatus exposed to near-future ocean acidification scenarios

PubMed Central

Albright, Rebecca; Bland, Charnelle; Gillette, Phillip; Serafy, Joseph E.; Langdon, Chris; Capo, Thomas R.

2012-01-01

To evaluate the effect of elevated pCO2 exposure on the juvenile growth of the sea urchin Lytechinus variegatus, we reared individuals for three months in one of three target pCO2 levels: ambient seawater (380 µatm) and two scenarios that are projected to occur by the middle (560 µatm) and end (800 µatm) of this century. At the end of 89 days, urchins reared at ambient pCO2 weighed 12% more than those reared at 560 µatm and 28% more than those reared at 800 µatm. Skeletons were analyzed using scanning electron miscroscopy, revealing degradation of spines in urchins reared at elevated pCO2 (800 µatm). Our results indicate that elevated pCO2 levels projected to occur this century may adversely affect the development of juvenile sea urchins. Acidification-induced changes to juvenile urchin development would likely impair performance and functioning of juvenile stages with implications for adult populations. PMID:22833691

Juvenile growth of the tropical sea urchin Lytechinus variegatus exposed to near-future ocean acidification scenarios.

PubMed

Albright, Rebecca; Bland, Charnelle; Gillette, Phillip; Serafy, Joseph E; Langdon, Chris; Capo, Thomas R

2012-09-01

To evaluate the effect of elevated pCO(2) exposure on the juvenile growth of the sea urchin Lytechinus variegatus, we reared individuals for three months in one of three target pCO(2) levels: ambient seawater (380 µatm) and two scenarios that are projected to occur by the middle (560 µatm) and end (800 µatm) of this century. At the end of 89 days, urchins reared at ambient pCO(2) weighed 12% more than those reared at 560 µatm and 28% more than those reared at 800 µatm. Skeletons were analyzed using scanning electron miscroscopy, revealing degradation of spines in urchins reared at elevated pCO(2) (800 µatm). Our results indicate that elevated pCO(2) levels projected to occur this century may adversely affect the development of juvenile sea urchins. Acidification-induced changes to juvenile urchin development would likely impair performance and functioning of juvenile stages with implications for adult populations.

Characterization of lipids in three species of sea urchin.

PubMed

Zhou, Xin; Zhou, Da-Yong; Lu, Ting; Liu, Zhong-Yuan; Zhao, Qi; Liu, Yu-Xin; Hu, Xiao-Pei; Zhang, Jiang-Hua; Shahidi, Fereidoon

2018-02-15

Sea urchin gonad has been regarded as a "healthy" food. Although previous studies have suggested that sea urchin gonad might serve as a potential rich source of long chain omega-3 polyunsaturated fatty acids (n-3 LC-PUFA) enriched phospholipid (PL), the molecular species profile of its PL has rarely been reported. In this study, about 200 molecular species of glycerophospholipid (GP), including glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoserine, glycerophosphoinositol, lysoglycerophosphocholine and lysoglycerophosphoethanolamine, in gonads from three species of sea urchin (Glyptocidaris crenularis, Strongylocentrotus intermedius and Strongylocentrotus nudus) were characterized using tandem mass spectrometry. Most of the predominant GP molecular species contained PUFA, especially eicosapentaenoic acid (EPA). Meanwhile, the sea urchin lipids contained a high proportion of PL (39.45-50.30% of total lipids) and PUFA (34.47-46.56% of total FA). Among PL, phosphatidylcholine (67.88-72.58mol%) was dominant. Considering the high level of PUFA enriched GP, sea urchin gonads provide great potential as health-promoting food for human consumption. Copyright © 2017 Elsevier Ltd. All rights reserved.

Habitat-dependent growth in a Caribbean sea urchin Tripneustes ventricosus: the importance of food type

NASA Astrophysics Data System (ADS)

Maciá, Silvia; Robinson, Michael P.

2008-12-01

The sea urchin Tripneustes ventricosus is a common, yet relatively poorly known, grazer of seagrass beds and coral reefs throughout the Caribbean. We compared the size and abundance of urchins between adjacent seagrass and coral reef habitats (where macroalgae are the dominant primary producers). We also conducted a laboratory experiment comparing the growth rate of juvenile urchins fed a diet of either macroalgae or seagrass. Reef urchins had significantly larger test diameter than those in the seagrass on some sampling dates. This size difference may be at least partially explained by diet, because laboratory-reared urchins fed macroalgae grew significantly faster than those fed seagrass. The seagrass population, however, was stable over time, whereas the reef population exhibited strong fluctuations in abundance. Overall, our study indicates that both the seagrass and coral reef habitats are capable of supporting healthy, reproductive populations of T. ventricosus. Each, however, appears to offer a distinct advantage: faster growth on the reef and greater population stability in the seagrass.

Solvothermal synthesis and high optical performance of three-dimensional sea-urchin-like TiO{sub 2}

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

Zhou, Yi, E-mail: zhouyihn@163.com; Wang, Yutang; Li, Mengyao

Graphical abstract: I–V characteristics of different TiO{sub 2} microspheres based DSSCs (a) 3D sphere-like, (b) 3D flower-like, (c) 3D sea-urchin-like. - Highlights: • 3D sea-urchin-like TiO{sub 2} was synthesized by solvothermal method. • The effects of preparation parameters on the microstructure of the microspheres were investigated. • The photoelectric properties of 3D sea-urchin-like TiO{sub 2} were studied upon DSSCs. • The PCE of the 3D sea-urchin-like TiO{sub 2} was higher than that of other morphologies. - Abstract: Three-dimensional (3D) sea-urchin-like TiO{sub 2} microspheres were successfully synthesised by solvothermal method. The effects of preparation parameters including reaction temperature, concentration and massmore » fraction of precursor, and solvent volume on the microstructure of the microspheres were investigated. Results of scanning electron microscopy showed that the preparation parameters played a critical role in the morphology of 3D sea-urchin-like TiO{sub 2}. In addition, when the sea-urchin-like TiO{sub 2} nanostructures were used as the dye-sensitized solar cells (DSSCs) anode, the power-conversion efficiency was higher than that of other morphologies, which was due to the special 3D hierarchical nanostructure, large specific surface area, and enhanced absorption of UV–vis of the TiO{sub 2} nanostructures.« less

Toxicity and DNA methylation changes induced by perfluorooctane sulfonate (PFOS) in sea urchin Glyptocidaris crenularis.

PubMed

Ding, Guanghui; Wang, Luyan; Zhang, Jing; Wei, Yuanyuan; Wei, Lie; Li, Yang; Shao, Mihua; Xiong, Deqi

2015-06-01

Perfluorooctane sulfonate (PFOS) is an ubiquitous persistent organic pollutant, which can be bioaccumulated and cause adverse effects on organisms. However, there is very limited information about the toxic effects of PFOS to marine organisms and its mechanisms. Therefore, in the present study, adult sea urchins Glyptocidaris crenularis were exposed to PFOS for 21 d, followed by a 7-d depuration period, in order to investigate the toxicity of PFOS to sea urchin and its potential epigenetic mechanisms. Sea urchins dropped spines, and lowered down the motor ability and feeding ability after the PFOS exposure. Superoxide dismutase activities in supernatant of coelomic fluid of sea urchin increased firstly and then dropped down, while the change of the catalase activity took an opposite trend during the exposure period. They both approached to the corresponding activity of the control after the depuration period. The DNA methylation polymorphism, methylation rate and demethylation rate in sea urchin gonad all increased following the prolonged exposure time, and then decreased after the depuration period. The demethylation rates were lower than the corresponding methylation rates, therefore methylation events were dominant during the whole experimental period. This might suggest that sea urchin have strong self-protection mechanisms and can survive from the PFOS exposure presented in this study. Further efforts are needed to more precisely investigate the DNA methylation effects of PFOS and the self-protection mechanism of sea urchin. Copyright © 2015 Elsevier Ltd. All rights reserved.

Unique spatial and cellular expression patterns of Hoxa5, Hoxb4 and Hoxb6 proteins in normal developing murine lung are modified in pulmonary hypoplasia

PubMed Central

Volpe, MaryAnn Vitoria; Wang, Karen Ting Wai; Nielsen, Heber Carl; Chinoy, Mala Romeshchandra

2009-01-01

Background Hox transcription factors modulate signaling pathways controlling organ morphogenesis and maintain cell fate and differentiation in adults. Retinoid signaling, key in regulating Hox expression, is altered in pulmonary hypoplasia. Information on pattern-specific expression of Hox proteins in normal lung development and in pulmonary hypoplasia is minimal. Our objective was to determine how pulmonary hypoplasia alters temporal, spatial and cellular expression of Hoxa5, Hoxb4 and Hoxb6 proteins compared to normal lung development. Methods Temporal, spatial and cellular Hoxa5, Hoxb4 and Hoxb6 expression was studied in normal (untreated) and nitrofen-induced hypoplastic (NT-PH) lungs from gestational day 13.5, 16, 19 fetuses and neonates using western blot and immunohistochemistry. Results Modification of protein levels and spatial and cellular Hox expression patterns in NT-PH lungs was consistent with delayed lung development. Distinct protein isoforms were detected for each Hox protein. Expression levels of the Hoxa5 and Hoxb6 isoforms changed with development and further in NT-PH lungs. Compared to normal lungs, Gd19 and neonatal NT-PH lungs had decreased Hoxb6 and increased Hoxa5 and Hoxb4. Hoxa5 cellular localization changed from mesenchyme to epithelia earlier in normal lungs. Hoxb4 was expressed in mesenchyme and epithelial cells throughout development. Hoxb6 remained mainly in mesenchymal cells around distal airways. Conclusions Unique spatial and cellular expression of Hoxa5, Hoxb4 and Hoxb6 participates in branching morphogenesis and terminal sac formation. Altered Hox protein temporal and cellular balance of expression either contributes to pulmonary hypoplasia or functions as a compensatory mechanism attempting to correct abnormal lung development and maturation in this condition. PMID:18553509

A-Mating-Type Gene Expression Can Drive Clamp Formation in the Bipolar Mushroom Pholiota microspora (Pholiota nameko) ▿

PubMed Central

Yi, Ruirong; Mukaiyama, Hiroyuki; Tachikawa, Takashi; Shimomura, Norihiro; Aimi, Tadanori

2010-01-01

In the bipolar basidiomycete Pholiota microspora, a pair of homeodomain protein genes located at the A-mating-type locus regulates mating compatibility. In the present study, we used a DNA-mediated transformation system in P. microspora to investigate the homeodomain proteins that control the clamp formation. When a single homeodomain protein gene (A3-hox1 or A3-hox2) from the A3 monokaryon strain was transformed into the A4 monokaryon strain, the transformants produced many pseudoclamps but very few clamps. When two homeodomain protein genes (A3-hox1 and A3-hox2) were transformed either separately or together into the A4 monokaryon, the ratio of clamps to the clamplike cells in the transformants was significantly increased to ca. 50%. We therefore concluded that the gene dosage of homeodomain protein genes is important for clamp formation. When the sip promoter was connected to the coding region of A3-hox1 and A3-hox2 and the fused fragments were introduced into NGW19-6 (A4), the transformants achieved more than 85% clamp formation and exhibited two nuclei per cell, similar to the dikaryon (NGW12-163 × NGW19-6). The results of real-time reverse transcription-PCR confirmed that sip promoter activity is greater than that of the native promoter of homeodomain protein genes in P. microspora. Thus, we concluded that nearly 100% clamp formation requires high expression levels of homeodomain protein genes and that altered expression of the A-mating-type genes alone is sufficient to drive true clamp formation. PMID:20453073

Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma.

PubMed

Kocak, H; Ackermann, S; Hero, B; Kahlert, Y; Oberthuer, A; Juraeva, D; Roels, F; Theissen, J; Westermann, F; Deubzer, H; Ehemann, V; Brors, B; Odenthal, M; Berthold, F; Fischer, M

2013-04-11

Neuroblastoma is an embryonal malignancy of the sympathetic nervous system. Spontaneous regression and differentiation of neuroblastoma is observed in a subset of patients, and has been suggested to represent delayed activation of physiologic molecular programs of fetal neuroblasts. Homeobox genes constitute an important family of transcription factors, which play a fundamental role in morphogenesis and cell differentiation during embryogenesis. In this study, we demonstrate that expression of the majority of the human HOX class I homeobox genes is significantly associated with clinical covariates in neuroblastoma using microarray expression data of 649 primary tumors. Moreover, a HOX gene expression-based classifier predicted neuroblastoma patient outcome independently of age, stage and MYCN amplification status. Among all HOX genes, HOXC9 expression was most prominently associated with favorable prognostic markers. Most notably, elevated HOXC9 expression was significantly associated with spontaneous regression in infant neuroblastoma. Re-expression of HOXC9 in three neuroblastoma cell lines led to a significant reduction in cell viability, and abrogated tumor growth almost completely in neuroblastoma xenografts. Neuroblastoma growth arrest was related to the induction of programmed cell death, as indicated by an increase in the sub-G1 fraction and translocation of phosphatidylserine to the outer membrane. Programmed cell death was associated with the release of cytochrome c from the mitochondria into the cytosol and activation of the intrinsic cascade of caspases, indicating that HOXC9 re-expression triggers the intrinsic apoptotic pathway. Collectively, our results show a strong prognostic impact of HOX gene expression in neuroblastoma, and may point towards a role of Hox-C9 in neuroblastoma spontaneous regression.

The mouse homeobox gene, S8, is expressed during embryogenesis predominantly in mesenchyme.

PubMed

Opstelten, D J; Vogels, R; Robert, B; Kalkhoven, E; Zwartkruis, F; de Laaf, L; Destrée, O H; Deschamps, J; Lawson, K A; Meijlink, F

1991-03-01

The murine S8 gene, originally identified by Kongsuwan et al. [EMBO J. 7(1988)2131-2138] encodes a homeodomain which resembles those of the paired family. We studied the expression pattern during mid-gestation embryogenesis of S8 by in situ hybridization. Expression was detected locally in craniofacial mesenchyme, in the limb, the heart and the somites and sclerotomes all along the axis, and was absent from the central and peripheral nervous system, splanchnopleure, and endodermal derivatives. This pattern differs considerably from that of most previously described homeobox containing genes. By genetic analysis, the gene was located on chromosome 2, about 20 cM from the HOX-4 cluster.

Hoxa2 Selectively Enhances Meis Binding to Change a Branchial Arch Ground State

PubMed Central

Amin, Shilu; Donaldson, Ian J.; Zannino, Denise A.; Hensman, James; Rattray, Magnus; Losa, Marta; Spitz, François; Ladam, Franck; Sagerström, Charles; Bobola, Nicoletta

2015-01-01

Summary Hox transcription factors (TFs) are essential for vertebrate development, but how these evolutionary conserved proteins function in vivo remains unclear. Because Hox proteins have notoriously low binding specificity, they are believed to bind with cofactors, mainly homeodomain TFs Pbx and Meis, to select their specific targets. We mapped binding of Meis, Pbx, and Hoxa2 in the branchial arches, a series of segments in the developing vertebrate head. Meis occupancy is largely similar in Hox-positive and -negative arches. Hoxa2, which specifies second arch (IIBA) identity, recognizes a subset of Meis prebound sites that contain Hox motifs. Importantly, at these sites Meis binding is strongly increased. This enhanced Meis binding coincides with active enhancers, which are linked to genes highly expressed in the IIBA and regulated by Hoxa2. These findings show that Hoxa2 operates as a tissue-specific cofactor, enhancing Meis binding to specific sites that provide the IIBA with its anatomical identity. PMID:25640223

Impact of homeobox genes in gastrointestinal cancer.

PubMed

Joo, Moon Kyung; Park, Jong-Jae; Chun, Hoon Jai

2016-10-07

Homeobox genes, including HOX and non- HOX genes, have been identified to be expressed aberrantly in solid tumors. In gastrointestinal (GI) cancers, most studies have focused on the function of non- HOX genes including caudal-related homeobox transcription factor 1 (CDX1) and CDX2. CDX2 is a crucial factor in the development of pre-cancerous lesions such as Barrett's esophagus or intestinal metaplasia in the stomach, and its tumor suppressive role has been investigated in colorectal cancers. Recently, several HOX genes were reported to have specific roles in GI cancers; for example, HOXA13 in esophageal squamous cell cancer and HOXB7 in stomach and colorectal cancers. HOXD10 is upregulated in colorectal cancer while it is silenced epigenetically in gastric cancer. Thus, it is essential to examine the differential expression pattern of various homeobox genes in specific tumor types or cell lineages, and understand their underlying mechanisms. In this review, we summarize the available research on homeobox genes and present their potential value for the prediction of prognosis in GI cancers.

Tbx16 regulates hox gene activation in mesodermal progenitor cells

PubMed Central

Payumo, Alexander Y.; McQuade, Lindsey E.; Walker, Whitney J.; Yamazoe, Sayumi; Chen, James K.

2016-01-01

The transcription factor T-box 16 (Tbx16/Spadetail) is an essential regulator of paraxial mesoderm development in zebrafish (Danio rerio). Mesodermal progenitor cells (MPCs) fail to differentiate into trunk somites in tbx16 mutants and instead accumulate within the tailbud in an immature state. The mechanisms by which Tbx16 controls mesoderm patterning have remained enigmatic, and we describe here the application of photoactivatable morpholino oligonucleotides to determine the Tbx16 transcriptome in MPCs. We identify 124 Tbx16-regulated genes that are expressed in zebrafish gastrulae, including several developmental signaling proteins and regulators of gastrulation, myogenesis, and somitogenesis. Unexpectedly, we observe that loss of Tbx16 function precociously activates posterior hox genes in MPCs, and overexpression of a single posterior hox gene is sufficient to disrupt MPC migration. Our studies support a model in which Tbx16 regulates the timing of collinear hox gene activation to coordinate the anterior-posterior fates and positions of paraxial MPCs. PMID:27376691

Micropredation on sea urchins as a potential stabilizing process for rocky reefs

NASA Astrophysics Data System (ADS)

Bonaviri, Chiara; Gianguzza, Paola; Pipitone, Carlo; Hereu, Bernat

2012-10-01

Rocky reefs can shift from forest, a state dominated by erect algae with high biodiversity, to barren, an impoverished state dominated by encrusting algae. Sea urchins, abundant in barrens, are usually held responsible for the maintenance of this state. Predation by large fish can revert the barren state to forest by controlling sea urchin populations. However, the persistence of a community state sometimes seems to be independent from the presence of such large predators, suggesting the existence of other unknown mechanisms ensuring their stability. Theoretical studies suggest that the settler stage of sea urchins is determinant for maintaining a given rocky reef state. In this study, we have identified several potential invertebrate micropredators of settlers of the sea urchin Paracentrotus lividus and measured their predation activity. Predation rates showed marked differences among species, possibly due to morphological and/or behavioral traits. Micropredators were more abundant in the forest than in barren, and their potential impact on the sea urchin community differed between the two states by two orders of magnitude. These findings suggest a novel self-perpetuating mechanism stabilizing rocky reef systems, where the abundance of micropredators may contribute to shape the sea urchin population, which in turn is responsible for the persistence of the state.

Allergen analysis of sea urchin roe using sera from five patients.

PubMed

Tanaka, Kenichi; Kondo, Yasuto; Inuo, Chisato; Nakajima, Yoichi; Tsuge, Ikuya; Doi, Satoru; Yanagihara, Shigeto; Yoshikawa, Tetsushi; Urisu, Atsuo

2014-01-01

Sea urchin roe can cause anaphylactic reactions the first time they are consumed; therefore, careful clinical attention should be paid to their effects. However, no previous study has examined the allergens in sea urchin roe using sera from more than one patient. We attempted to identify sea urchin allergens using sera from 5 patients with sea urchin allergies. We enrolled 5 patients with relevant medical histories, positive results on a skin prick test and/or a food challenge test, and high levels of sea urchin-specific IgE in an enzyme-linked immunosorbent assay. We performed SDS-PAGE, immunoblotting, immunoblot inhibition, and N-terminal amino acid sequence detection. Ten protein bands ranging from 18 to 170 kDa were detected in more than 2 patients' sera. In immunoblotting, the protein band for the 170-kDa major yolk protein was recognized by 4 of the 5 sera. Furthermore, the reaction between IgE and the protein band for egg cortical vesicle protein (18 kDa) was inhibited by the addition of salmon roe extract. Major yolk protein was confirmed to be one of the main allergens in sea urchin roe. In addition, egg cortical vesicle protein (18 kDa) was demonstrated to be an important protein for cross-reactivity with salmon roe. © 2014 S. Karger AG, Basel.

Identification of nickel response genes in abnormal early developments of sea urchin by differential display polymerase chain reaction.

PubMed

Ryu, Tae Kwon; Lee, Gunsup; Rhee, Yong; Park, Heung-Sik; Chang, Man; Lee, Sukchan; Lee, Jaean; Lee, Taek-Kyun

2012-10-01

Bioassays and biomarkers have been previously developed to assess the effects of heavy metal contaminants on the early life stages of the sea urchin. In this study, malformation in the early developmental processes was observed in sea urchin (Strongylocentrotus intermedius) larvae exposed to 10 ppm Ni for over 30 h. The most critical stage at which the triggering of nickel effects takes place is thought to be the blastula stage, which occurs after fertilization in larval development. To investigate the molecular-level responses of sea urchin exposed to heavy metal stress and to explore the differentially expressed genes that are induced or repressed by nickel, differential display polymerase chain reaction (DD-PCR) was used with sea urchin mRNAs. The malformation-related genes expressed in the early life stages of the sea urchin were cloned from larvae exposed to 10 ppm of nickel for 15 h, and accessed via DD-PCR. Sequence analysis results revealed that each of the genes evidenced high homology with EGF2, PCSK9, serine/threonine protein kinase, apolipophorin precursor protein, and MGC80921 protein/transcript variant 2. This result may prove useful in the development of novel biomarkers for the assessment of heavy metal stresses on sea urchin embryos. Copyright © 2012 Elsevier Inc. All rights reserved.

Will altered climate affect a discrete population of the sea urchin Strongylocentrotus droebachiensis?

NASA Astrophysics Data System (ADS)

Nyhagen, Fredrik Oulie; Christie, Hartvig; Norderhaug, Kjell Magnus

2018-02-01

The Green sea urchin Strongylocentrotus droebachiensis is a cold-water species that in the 70s and 80s was the main culprit in the major grazing of macrophytes in the Norwegian fjords and coastal areas. Recent reports have questioned a decline in the S. droebachiensis in the Oslofjord, similar to what was observed to occur in the Norwegian coastal population of S. droebachiensis after the 1990s. In surveys from 2013 we collected data on urchin density, test diameter, early urchin settlement and Gonad Index and created a framework in order to investigate if the current Inner Oslofjord populations of S. droebachiensis are different from surveys conducted in 1979 and 1992. This study found significant differences in density, diameter and settlement over time. Highest density in 1992 was at 10 and 15 m, while being at 20 m in 2013. Urchin diameter at the station with most urchins was on average 5 cm in 1992 compared to 3 cm in 2013. Settlement differed both between the number of settlers between 1992 and 2013, and season for highest settlement (summer in 1992, and autumn in 2013). The inner Oslofjord sea urchin data indicate a still healthy population, although environmental data (as temperature and salinity) have changed to less favorable conditions for this species.

Trophic cascades result in large-scale coralline algae loss through differential grazer effects.

PubMed

O'Leary, Jennifer K; McClanahan, Timothy R

2010-12-01

Removal of predators can have strong indirect effects on primary producers through trophic cascades. Crustose coralline algae (CCA) are major primary producers worldwide that may be influenced by predator removal through changes in grazer composition and biomass. CCA have been most widely studied in Caribbean and temperate reefs, where cover increases with increasing grazer biomass due to removal of competitive fleshy algae. However, each of these systems has one dominant grazer type, herbivorous fishes or sea urchins, which may not be functionally equivalent. Where fishes and sea urchins co-occur, fishing can result in a phase shift in the grazing community with subsequent effects on CCA and other substrata. Kenyan reefs have herbivorous fishes and sea urchins, providing an opportunity to determine the relative impacts of each grazer type and evaluate potential human-induced trophic cascades. We hypothesized that fish benefit CCA, abundant sea urchins erode CCA, and that fishing indirectly reduces CCA cover by removing sea urchin predators. We used closures and fished reefs as a large-scale, long-term natural experiment to assess how fishing and resultant changes in communities affect CCA abundance. We used a short-term caging experiment to directly test the effects of grazing on CCA. CCA cover declined with increasing fish and sea urchin abundance, but the negative impact of sea urchin grazing was much stronger than that of fishes. Abundant sea urchins reduced the CCA growth rate to almost zero and prevented CCA accumulation. A warming event (El Niño Southern Oscillation, ENSO) occurred during the 18-year study and had a strong but short-term positive effect on CCA cover. However, the effect of the ENSO on CCA was lower in magnitude than the effect of sea urchin grazing. We compare our results with worldwide literature on bioerosion by fishes and sea urchins. Grazer influence depends on whether benefits of fleshy algae removal outweigh costs of grazer-induced bioerosion. However, the cost-benefit ratio for CCA appears to change with grazer type, grazer abundance, and environment. In Kenya, predator removal leads to a trophic cascade that is expected to reduce net calcification of reefs and therefore reduce reef stability, growth, and resilience.

Modeling the oxidative capacity of the atmosphere of the south coast air basin of California. 2. HOx radical production.

PubMed

Griffin, Robert J

2004-02-01

The production of HOx radicals in the South Coast Air Basin of California is investigated during the smog episode of September 9, 1993 using the California Institute of Technology (CIT) air-quality model. Sources of HOx(hydroxyl, hydroperoxy, and organic peroxy radicals) incorporated into the associated gas-phase chemical mechanism include the combination of excited-state singlet oxygen (formed from ozone (O3) photolysis (hv)) with water, the photolysis of nitrous acid, hydrogen peroxide (H2O2), and carbonyl compounds (formaldehyde (HCHO) or higher aldehydes and ketones), the consumption of aldehydes and alkenes (ALK) by the nitrate radical, and the consumption of alkenes by O3 and the oxygen atom (O). At a given time or location for surface cells and vertical averages, each route of HOx formation may be the greatest contributor to overall formation except HCHO-hv, H2O2-hv, and ALK-O, the latter two of which are insignificant pathways in general. The contribution of the ALK-O3 pathway is dependent on the stoichiometric yield of OH, but this pathway, at least for the studied smog episode, may not be as generally significant as previous research suggests. Future emissions scenarios yield lower total HOx production rates and a shift in the relative importance of individual pathways.

The Recombinant Sea Urchin Immune Effector Protein, rSpTransformer-E1, Binds to Phosphatidic Acid and Deforms Membranes

PubMed Central

Lun, Cheng Man; Samuel, Robin L.; Gillmor, Susan D.; Boyd, Anthony; Smith, L. Courtney

2017-01-01

The purple sea urchin, Strongylocentrotus purpuratus, possesses a sophisticated innate immune system that functions without adaptive capabilities and responds to pathogens effectively by expressing the highly diverse SpTransformer gene family (formerly the Sp185/333 gene family). The swift gene expression response and the sequence diversity of SpTransformer cDNAs suggest that the encoded proteins have immune functions. Individual sea urchins can express up to 260 distinct SpTransformer proteins, and their diversity suggests that different versions may have different functions. Although the deduced proteins are diverse, they share an overall structure of a hydrophobic leader, a glycine-rich N-terminal region, a histidine-rich region, and a C-terminal region. Circular dichroism analysis of a recombinant SpTransformer protein, rSpTransformer-E1 (rSpTrf-E1) demonstrates that it is intrinsically disordered and transforms to α helical in the presence of buffer additives and binding targets. Although native SpTrf proteins are associated with the membranes of perinuclear vesicles in the phagocyte class of coelomocytes and are present on the surface of small phagocytes, they have no predicted transmembrane region or conserved site for glycophosphatidylinositol linkage. To determine whether native SpTrf proteins associate with phagocyte membranes through interactions with lipids, when rSpTrf-E1 is incubated with lipid-embedded nylon strips, it binds to phosphatidic acid (PA) through both the glycine-rich region and the histidine-rich region. Synthetic liposomes composed of PA and phosphatidylcholine show binding between rSpTrf-E1 and PA by fluorescence resonance energy transfer, which is associated with leakage of luminal contents suggesting changes in lipid organization and perhaps liposome lysis. Interactions with liposomes also change membrane curvature leading to liposome budding, fusion, and invagination, which is associated with PA clustering induced by rSpTrf-E1 binding. Longer incubations result in the extraction of PA from the liposomes, which form disorganized clusters. CD shows that when rSpTrf-E1 binds to PA, it changes its secondary structure from disordered to α helical. These results provide evidence for how SpTransformer proteins may associate with molecules that have exposed phosphates including PA on cell membranes and how the characteristic of protein multimerization may drive changes in the organization of membrane lipids. PMID:28553283

Motility and centrosomal organization during sea urchin and mouse fertilization

NASA Technical Reports Server (NTRS)

Schatten, Heide; Schatten, Gerald

1986-01-01

It is noted that microfilaments are essential for incorporation of sperm in sea urchins and for pronuclear apposition in mice. The ability of sea urchin sperm to fertilize eggs is lowered by latrunculin, giving evidence that acrosomal microfilaments are of importance to the process of fertilization. Due to the uncertainty regarding the presence of microfilaments in various mammalian sperm, it is interesting that latrunculin does not noticeably affect the ability of mouse sperm to fertilize oocytes. The movements of the sperm and egg nuclei at the time of sea urchin fertilization are dependent on microtubules arranged into a radial monastral array (the sperm aster). In the mouse egg, microtubule activity is also required during pronuclear apposition, but they are arranged by a number of egg cytoplasmic sites. Results of the investigations show that both microtubules and microfilaments are necessary for the successful completion of fertilization in both mice and sea urchins, but at different stages. Also, it is demonstrated that centrosomes are contributed by the sperm in the process of sea urchin fertilization, but in mammals they may be inherited maternally.

Trawling disturbance on the isotopic signature of a structure-building species, the sea urchin Gracilechinus acutus (Lamarck, 1816)

NASA Astrophysics Data System (ADS)

González-Irusta, José M.; Preciado, Izaskun; López-López, Lucia; Punzón, Antonio; Cartes, Joan E.; Serrano, Alberto

2014-08-01

Bottom trawling is one of the main sources of anthropogenic disturbance in benthic habitats with important direct and indirect effects on the ecosystem functional diversity. In this study, the effect of this impact on a structure-building species, the sea urchin Gracilechinus acutus, was studied in the Central Cantabrian Sea (southern Bay of Biscay) comparing its isotopic signature and additional population descriptors across different trawling pressures. Trawling disturbance had a significant effect on the studied descriptors. In trawling areas, this urchin showed significantly lower values of biomass and mean size and significantly higher values of fullness index. Moreover, the trawling disturbance effect was also significant in the isotopic signature of G. acutus. Urchins inhabiting untrawled areas showed significant lower values of δ15N than urchins dwelling areas under trawling pressure. The urchins' isotopic enrichment increased along the species ontogeny regardless of the trawling effort level. Stable isotope analyses are a suitable tool to detect trawling disturbance on the trophic pathways but do not suffice to explain these changes, especially if there is a lack of baseline information.

A Simple Model of Hox Genes: Bone Morphology Demonstration

ERIC Educational Resources Information Center

Shmaefsky, Brian

2008-01-01

Visual demonstrations of abstract scientific concepts are effective strategies for enhancing content retention (Shmaefsky 2004). The concepts associated with gene regulation of growth and development are particularly complex and are well suited for teaching with visual models. This demonstration provides a simple and accurate model of Hox gene…

Deciphering the molecular mechanisms underlying sea urchin reversible adhesion: A quantitative proteomics approach.

PubMed

Lebesgue, Nicolas; da Costa, Gonçalo; Ribeiro, Raquel Mesquita; Ribeiro-Silva, Cristina; Martins, Gabriel G; Matranga, Valeria; Scholten, Arjen; Cordeiro, Carlos; Heck, Albert J R; Santos, Romana

2016-04-14

Marine bioadhesives have unmatched performances in wet environments, being an inspiration for biomedical applications. In sea urchins specialized adhesive organs, tube feet, mediate reversible adhesion, being composed by a disc, producing adhesive and de-adhesive secretions, and a motile stem. After tube foot detachment, the secreted adhesive remains bound to the substratum as a footprint. Sea urchin adhesive is composed by proteins and sugars, but so far only one protein, Nectin, was shown to be over-expressed as a transcript in tube feet discs, suggesting its involvement in sea urchin adhesion. Here we use high-resolution quantitative mass-spectrometry to perform the first study combining the analysis of the differential proteome of an adhesive organ, with the proteome of its secreted adhesive. This strategy allowed us to identify 163 highly over-expressed disc proteins, specifically involved in sea urchin reversible adhesion; to find that 70% of the secreted adhesive components fall within five protein groups, involved in exocytosis and microbial protection; and to provide evidences that Nectin is not only highly expressed in tube feet discs but is an actual component of the adhesive. These results give an unprecedented insight into the molecular mechanisms underlying sea urchin adhesion, and opening new doors to develop wet-reliable, reversible, and ecological biomimetic adhesives. Sea urchins attach strongly but in a reversible manner to substratum, being a valuable source of inspiration for industrial and biomedical applications. Yet, the molecular mechanisms governing reversible adhesion are still poorly studied delaying the engineering of biomimetic adhesives. We used the latest mass spectrometry techniques to analyze the differential proteome of an adhesive organ and the proteome of its secreted adhesive, allowing us to uncover the key players in sea urchin reversible adhesion. We demonstrate, that Nectin, a protein previously pointed out as potentially involved in sea urchin adhesion, is not only highly expressed in tube feet discs, but is a genuine component of the secreted adhesive. Copyright © 2016 Elsevier B.V. All rights reserved.

Polysaccharide Constituents of Three Types of Sea Urchin Shells and Their Anti-Inflammatory Activities

PubMed Central

Jiao, Heng; Shang, Xiaohui; Dong, Qi; Wang, Shuang; Liu, Xiaoyu; Zheng, Heng; Lu, Xiaoling

2015-01-01

As a source of potent anti-inflammatory traditional medicines, the quantitative chromatographic fingerprints of sea urchin shell polysaccharides were well established via pre-column derivatization high performance liquid chromatography (HPLC) analysis. Based on the quantitative results, the content of fucose and glucose could be used as preliminary distinguishing indicators among three sea urchin shell species. Besides, the anti-inflammatory activities of the polysaccharides from sea urchin shells and their gonads were also determined. The gonad polysaccharide of Anthocidaris crassispina showed the most potent anti-inflammatory activity among all samples tested. PMID:26389925

Polysaccharide Constituents of Three Types of Sea Urchin Shells and Their Anti-Inflammatory Activities.

PubMed

Jiao, Heng; Shang, Xiaohui; Dong, Qi; Wang, Shuang; Liu, Xiaoyu; Zheng, Heng; Lu, Xiaoling

2015-09-16

As a source of potent anti-inflammatory traditional medicines, the quantitative chromatographic fingerprints of sea urchin shell polysaccharides were well established via pre-column derivatization high performance liquid chromatography (HPLC) analysis. Based on the quantitative results, the content of fucose and glucose could be used as preliminary distinguishing indicators among three sea urchin shell species. Besides, the anti-inflammatory activities of the polysaccharides from sea urchin shells and their gonads were also determined. The gonad polysaccharide of Anthocidaris crassispina showed the most potent anti-inflammatory activity among all samples tested.

Global regime shift dynamics of catastrophic sea urchin overgrazing

PubMed Central

Ling, S. D.; Scheibling, R. E.; Rassweiler, A.; Johnson, C. R.; Shears, N.; Connell, S. D.; Salomon, A. K.; Norderhaug, K. M.; Pérez-Matus, A.; Hernández, J. C.; Clemente, S.; Blamey, L. K.; Hereu, B.; Ballesteros, E.; Sala, E.; Garrabou, J.; Cebrian, E.; Zabala, M.; Fujita, D.; Johnson, L. E.

2015-01-01

A pronounced, widespread and persistent regime shift among marine ecosystems is observable on temperate rocky reefs as a result of sea urchin overgrazing. Here, we empirically define regime-shift dynamics for this grazing system which transitions between productive macroalgal beds and impoverished urchin barrens. Catastrophic in nature, urchin overgrazing in a well-studied Australian system demonstrates a discontinuous regime shift, which is of particular management concern as recovery of desirable macroalgal beds requires reducing grazers to well below the initial threshold of overgrazing. Generality of this regime-shift dynamic is explored across 13 rocky reef systems (spanning 11 different regions from both hemispheres) by compiling available survey data (totalling 10 901 quadrats surveyed in situ) plus experimental regime-shift responses (observed during a total of 57 in situ manipulations). The emergent and globally coherent pattern shows urchin grazing to cause a discontinuous ‘catastrophic’ regime shift, with hysteresis effect of approximately one order of magnitude in urchin biomass between critical thresholds of overgrazing and recovery. Different life-history traits appear to create asymmetry in the pace of overgrazing versus recovery. Once shifted, strong feedback mechanisms provide resilience for each alternative state thus defining the catastrophic nature of this regime shift. Importantly, human-derived stressors can act to erode resilience of desirable macroalgal beds while strengthening resilience of urchin barrens, thus exacerbating the risk, spatial extent and irreversibility of an unwanted regime shift for marine ecosystems.

A dermal HOX transcriptional program regulates site-specific epidermal fate

PubMed Central

Rinn, John L.; Wang, Jordon K.; Allen, Nancy; Brugmann, Samantha A.; Mikels, Amanda J.; Liu, Helen; Ridky, Todd W.; Stadler, H. Scott; Nusse, Roel; Helms, Jill A.; Chang, Howard Y.

2008-01-01

Reciprocal epithelial–mesenchymal interactions shape site-specific development of skin. Here we show that site-specific HOX expression in fibroblasts is cell-autonomous and epigenetically maintained. The distal-specific gene HOXA13 is continually required to maintain the distal-specific transcriptional program in adult fibroblasts, including expression of WNT5A, a morphogen required for distal development. The ability of distal fibroblasts to induce epidermal keratin 9, a distal-specific gene, is abrogated by depletion of HOXA13, but rescued by addition of WNT5A. Thus, maintenance of appropriate HOX transcriptional program in adult fibroblasts may serve as a source of positional memory to differentially pattern the epithelia during homeostasis and regeneration. PMID:18245445

A dermal HOX transcriptional program regulates site-specific epidermal fate.

PubMed

Rinn, John L; Wang, Jordon K; Allen, Nancy; Brugmann, Samantha A; Mikels, Amanda J; Liu, Helen; Ridky, Todd W; Stadler, H Scott; Nusse, Roel; Helms, Jill A; Chang, Howard Y

2008-02-01

Reciprocal epithelial-mesenchymal interactions shape site-specific development of skin. Here we show that site-specific HOX expression in fibroblasts is cell-autonomous and epigenetically maintained. The distal-specific gene HOXA13 is continually required to maintain the distal-specific transcriptional program in adult fibroblasts, including expression of WNT5A, a morphogen required for distal development. The ability of distal fibroblasts to induce epidermal keratin 9, a distal-specific gene, is abrogated by depletion of HOXA13, but rescued by addition of WNT5A. Thus, maintenance of appropriate HOX transcriptional program in adult fibroblasts may serve as a source of positional memory to differentially pattern the epithelia during homeostasis and regeneration.

Effect of Diets Supplemented with Different Sources of Astaxanthin on the Gonad of the Sea Urchin Anthocidaris crassispina

PubMed Central

Peng, Juan; Yuan, Jian-Ping; Wang, Jiang-Hai

2012-01-01

The effect of the microalgae Haematococcus pluvialis and Chorella zofingiensis, and synthetic astaxanthin on the gonad of the sea urchin Anthocidaris crassispina was studied. The basal diet was supplemented with H. pluvialis, C. zofingiensis, or synthetic astaxanthin, at two levels of astaxanthin (approximately 400 mg/kg and 100 mg/kg), to obtain the experimental diets HP1, HP2, CZ1, CZ2, AST1, and AST2, respectively, for two months of feeding experiment. The results showed that the concentrations of astaxanthin in the gonads of the sea urchins fed these experimental diets ranged from 0.15 to 3.01 mg/kg dry gonad weight. The higher astaxanthin levels (>2.90 mg/kg) were found in the gonads of the sea urchins fed the diets HP1 (containing 380 mg/kg of astaxanthins, mostly mono- and diesters) and AST1 (containing 385 mg/kg of synthetic astaxanthin). The lowest astaxanthin level (0.15 mg/kg) was detected in the gonads of the sea urchins fed the diet CZ2 (containing 98 mg/kg of astaxanthins, mostly diesters). Furthermore, the highest canthaxanthin level (7.48 mg/kg) was found in the gonads of the sea urchins fed the diet CZ1 (containing 387 mg/kg of astaxanthins and 142 mg/kg of canthaxanthin), suggesting that astaxanthins, especially astaxanthin esters, might not be assimilated as easily as canthaxanthin by the sea urchins. Our results show that sea urchins fed diets containing astaxanthin pigments show higher incorporation of these known antioxidant constituents, with the resultant seafood products therefore being of potential higher nutritive value. PMID:23016124

Habitat traits and patterns of abundance of the purple sea urchin, Paracentrotus lividus (Lamarck, 1816), at multiple scales along the north Portuguese coast

NASA Astrophysics Data System (ADS)

Domínguez, Rula; Domínguez Godino, Jorge; Freitas, Cristiano; Machado, Inês; Bertocci, Iacopo

2015-03-01

Spatial and temporal patterns of abundance and distribution of sea urchins (Paracentrotus lividus) from intertidal rockpools of the north Portuguese coast were examined in relation to physical (surface, altitude, depth, topographic complexity and exposure) and biological (substrate cover by dominant organisms) habitat traits. The methodology was based on a multi-factorial design where the total number and the abundance of urchins in each of six size classes were sampled over a range of spatial scales, from 10s of cm to kms, and a temporal scale of five months. The results highlighted three main features of the studied system: (1) the largest proportion of variability of sea urchins occurred at the smallest scale examined; (2) urchins from different size classes showed different patterns of abundance in relation to habitat traits; (3) variables normally invoked as potential drivers of distribution of urchins at a range of scales, such as hydrodynamics and shore height, were relatively less important than other abiotic (i.e. pool area, pool mean depth calculated over five replicate measures and sand cover) and biological (i.e. space occupancy by the reef-forming polychaete Sabellaria alveolata and mussels vs. availability of bare rock) variables to provide a considerable contribution to the variability of sea urchins. Intertidal populations of sea urchins are abundant on many rocky shores, where they are socially and economically important as food resource and ecologically key as habitat modelers. This study provides new clues on relatively unstudied populations, with relevant implications for possible management decisions, including the implementation of protection schemes able to preserve the main recruitment, settlement and development areas of P. lividus.

Retinoic acid signaling acts via Hox1 to establish the posterior limit of the pharynx in the chordate amphioxus.

PubMed

Schubert, Michael; Yu, Jr-Kai; Holland, Nicholas D; Escriva, Hector; Laudet, Vincent; Holland, Linda Z

2005-01-01

In the invertebrate chordate amphioxus, as in vertebrates, retinoic acid (RA) specifies position along the anterior/posterior axis with elevated RA signaling in the middle third of the endoderm setting the posterior limit of the pharynx. Here we show that AmphiHox1 is also expressed in the middle third of the developing amphioxus endoderm and is activated by RA signaling. Knockdown of AmphiHox1 function with an antisense morpholino oligonucleotide shows that AmphiHox1 mediates the role of RA signaling in setting the posterior limit of the pharynx by repressing expression of pharyngeal markers in the posterior foregut/midgut endoderm. The spatiotemporal expression of these endodermal genes in embryos treated with RA or the RA antagonist BMS009 indicates that Pax1/9, Pitx and Notch are probably more upstream than Otx and Nodal in the hierarchy of genes repressed by RA signaling. This work highlights the potential of amphioxus, a genomically simple, vertebrate-like invertebrate chordate, as a paradigm for understanding gene hierarchies similar to the more complex ones of vertebrates.

Assembly of the Auditory Circuitry by a Hox Genetic Network in the Mouse Brainstem

PubMed Central

Di Bonito, Maria; Narita, Yuichi; Avallone, Bice; Sequino, Luigi; Mancuso, Marta; Andolfi, Gennaro; Franzè, Anna Maria; Puelles, Luis; Rijli, Filippo M.; Studer, Michèle

2013-01-01

Rhombomeres (r) contribute to brainstem auditory nuclei during development. Hox genes are determinants of rhombomere-derived fate and neuronal connectivity. Little is known about the contribution of individual rhombomeres and their associated Hox codes to auditory sensorimotor circuitry. Here, we show that r4 contributes to functionally linked sensory and motor components, including the ventral nucleus of lateral lemniscus, posterior ventral cochlear nuclei (VCN), and motor olivocochlear neurons. Assembly of the r4-derived auditory components is involved in sound perception and depends on regulatory interactions between Hoxb1 and Hoxb2. Indeed, in Hoxb1 and Hoxb2 mutant mice the transmission of low-level auditory stimuli is lost, resulting in hearing impairments. On the other hand, Hoxa2 regulates the Rig1 axon guidance receptor and controls contralateral projections from the anterior VCN to the medial nucleus of the trapezoid body, a circuit involved in sound localization. Thus, individual rhombomeres and their associated Hox codes control the assembly of distinct functionally segregated sub-circuits in the developing auditory brainstem. PMID:23408898

Assembly of the auditory circuitry by a Hox genetic network in the mouse brainstem.

PubMed

Di Bonito, Maria; Narita, Yuichi; Avallone, Bice; Sequino, Luigi; Mancuso, Marta; Andolfi, Gennaro; Franzè, Anna Maria; Puelles, Luis; Rijli, Filippo M; Studer, Michèle

2013-01-01

Rhombomeres (r) contribute to brainstem auditory nuclei during development. Hox genes are determinants of rhombomere-derived fate and neuronal connectivity. Little is known about the contribution of individual rhombomeres and their associated Hox codes to auditory sensorimotor circuitry. Here, we show that r4 contributes to functionally linked sensory and motor components, including the ventral nucleus of lateral lemniscus, posterior ventral cochlear nuclei (VCN), and motor olivocochlear neurons. Assembly of the r4-derived auditory components is involved in sound perception and depends on regulatory interactions between Hoxb1 and Hoxb2. Indeed, in Hoxb1 and Hoxb2 mutant mice the transmission of low-level auditory stimuli is lost, resulting in hearing impairments. On the other hand, Hoxa2 regulates the Rig1 axon guidance receptor and controls contralateral projections from the anterior VCN to the medial nucleus of the trapezoid body, a circuit involved in sound localization. Thus, individual rhombomeres and their associated Hox codes control the assembly of distinct functionally segregated sub-circuits in the developing auditory brainstem.

Hox control of Drosophila larval anatomy; The Alary and Thoracic Alary-Related Muscles.

PubMed

Bataillé, Laetitia; Frendo, Jean-Louis; Vincent, Alain

2015-11-01

The body plan of arthropods and vertebrates involves the formation of repetitive segments, which subsequently diversify to give rise to different body parts along the antero-posterior/rostro-caudal body axis. Anatomical variations between body segments are crucial for organ function and organismal fitness. Pioneering work in Drosophila has established that Hox transcription factors play key roles both in endowing initially identical segments with distinct identities and organogenesis. The focus of this review is on Alary Muscles (AMs) and the newly discovered Thoracic Alary-Related Muscles (TARMs). AMs and TARMs are thin muscles which together connect the circulatory system and different midgut regions to the exoskeleton, while intertwining with the respiratory tubular network. They were hypothesized to represent a new type of muscles with spring-like properties, maintaining internal organs in proper anatomical positions during larval locomotion. Both the morphology of TARMs relative to AMs, and morphogenesis of connected tissues is under Hox control, emphasizing the key role of Hox proteins in coordinating the anatomical development of the larva. Copyright © 2015 Elsevier B.V. All rights reserved.

TALE factors poise promoters for activation by Hox proteins.

PubMed

Choe, Seong-Kyu; Ladam, Franck; Sagerström, Charles G

2014-01-27

Hox proteins form complexes with TALE cofactors from the Pbx and Prep/Meis families to control transcription, but it remains unclear how Hox:TALE complexes function. Examining a Hoxb1b:TALE complex that regulates zebrafish hoxb1a transcription, we find maternally deposited TALE proteins at the hoxb1a promoter already during blastula stages. These TALE factors recruit histone-modifying enzymes to promote an active chromatin profile at the hoxb1a promoter and also recruit RNA polymerase II (RNAPII) and P-TEFb. However, in the presence of TALE factors, RNAPII remains phosphorylated on serine 5 and hoxb1a transcription is inefficient. By gastrula stages, Hoxb1b binds together with TALE factors to the hoxb1a promoter. This triggers P-TEFb-mediated transitioning of RNAPII to the serine 2-phosphorylated form and efficient hoxb1a transcription. We conclude that TALE factors access promoters during early embryogenesis to poise them for activation but that Hox proteins are required to trigger efficient transcription. Copyright © 2014 Elsevier Inc. All rights reserved.

Expression of β-nerve growth factor and homeobox A10 in experimental cryptorchidism treated with exogenous nerve growth factor.

PubMed

Xian, Hua; Xian, Yun; Liu, Lili; Wang, Yongjun; He, Jianghong; Huang, Jianfei

2015-04-01

With the exception of standard inguinal orchidopexy, treatment of cryptorchidism with human chorionic gonadotropin has been performed for several years; however, its side effects have limited its application. The β‑nerve growth factor (NGF) and homeobox A10 (HoxA10) genes are closely associated with the development of the testes. To the best of our knowledge, whether exogenous NGF alters the endogenous levels of NGF and HoxA10 in cryptorchidism in rats remains to be elucidated. The aim of the present study was to evaluate the gene and protein expression of NGF and HoxA10 in experimental cryptorchidism following treatment with exogenous NGF. A unilateral mechanical cryptorchidism model in Sprague-Dawley rats was established and different concentrations of exogenous NGF were administered to observe the effects of NGF on cryptorchidism. Changes in the gene and protein expression levels of NGF and HoxA10 in the cryptorchid tissues of each group were identified using one step reverse transcription-quantitative polymerase chain reaction, in situ hybridization with digoxigenin‑labeled‑β‑NGF RNA probes, immunofluorescence and immunohistochemistry, respectively. The expression levels of NGF and HoxA10 were markedly higher in the group treated with a high dose of exogenous NGF compared with the group treated with a low dose of exogenous NGF and the group treated with human chorionic gonadotropin. These results confirmed the potential therapeutic effect of exogenous NGF in human cryptorchidism.

Analysis of Cytoskeletal and Motility Proteins in the Sea Urchin Genome Assembly

PubMed Central

RL, Morris; MP, Hoffman; RA, Obar; SS, McCafferty; IR, Gibbons; AD, Leone; J, Cool; EL, Allgood; AM, Musante; KM, Judkins; BJ, Rossetti; AP, Rawson; DR, Burgess

2007-01-01

The sea urchin embryo is a classical model system for studying the role of the cytoskeleton in such events as fertilization, mitosis, cleavage, cell migration and gastrulation. We have conducted an analysis of gene models derived from the Strongylocentrotus purpuratus genome assembly and have gathered strong evidence for the existence of multiple gene families encoding cytoskeletal proteins and their regulators in sea urchin. While many cytoskeletal genes have been cloned from sea urchin with sequences already existing in public databases, genome analysis reveals a significantly higher degree of diversity within certain gene families. Furthermore, genes are described corresponding to homologs of cytoskeletal proteins not previously documented in sea urchins. To illustrate the varying degree of sequence diversity that exists within cytoskeletal gene families, we conducted an analysis of genes encoding actins, specific actin-binding proteins, myosins, tubulins, kinesins, dyneins, specific microtubule-associated proteins, and intermediate filaments. We conducted ontological analysis of select genes to better understand the relatedness of urchin cytoskeletal genes to those of other deuterostomes. We analyzed developmental expression (EST) data to confirm the existence of select gene models and to understand their differential expression during various stages of early development. PMID:17027957

Relationships between of Sea Urchins Abundance, Macroalgae and Coral Closure on the Cemara Kecil island

NASA Astrophysics Data System (ADS)

Suryanti, Suryanti; Ain, Churun; Latifah, Nurul

2018-05-01

Sea urchins are one of the key species for coral reef communities because have the capability for controlling populations of microalgae. The existence of sea urchins in an waters ecosystem influenced by abiotic and biotic environmental factors such as intraspecific or intraspecific interactions. This study aims to determine the relationship between the abundance of Sea Urchins, Macroalga on massive coral, and coral cover on Cemara Kecil Island by PCA analysis. The study was conducted in May 2017 in Cemara Kecil Island. Method of research with Haphazard sampling technique. The results indicate that numbers of sea urchins found ranges from 78-130 ind/m2, an abundance of macroalgae found are Sargassum sp 1.36%, Caulerpa sp.7.43% and Padina sp 91.21%. The results of substrate cover are living coral 47,21%, dead coral 23.33%, other fauna 2.85% and abiotic element 26,61%. Based on the results of PCA analysis that Sea Urchin abundance has a positive correlation with the closure of Coral Reef and Caulerpa sp. While the Padina sp and Sargassum sp have a positive correlation as well as abiotic factors, dead coral, and other fauna.

Food Modulation Controls Astaxanthin Accumulation in Eggs of the Sea Urchin Arbacia lixula.

PubMed

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

2018-05-28

The carotenoid astaxanthin has strong antioxidant properties with beneficial effects for various degenerative diseases. This carotenoid is produced by some microalgae species when cultivated in particular conditions, and, interestingly, it is a predominant carotenoid in aquatic animals throughout a broad range of taxa. Recently, astaxanthin was detected in the eggs of the sea urchin Arbacia lixula in relevant concentrations when this organism was maintained in culture. These results have paved the way for deeper research into astaxanthin production by this species, particularly in regards to how astaxanthin production can be modulated by diet. Results showed that the highest content of astaxanthin in eggs was observed in sea urchins fed on a diet enriched with Spirulina platensis . This result was confirmed by the high antioxidant activity recorded in the egg extracts of these animals. Our results suggest that (i) the sea urchin A. lixula is able to synthesize astaxanthin from precursors obtained from food, and (ii) it is possible to modulate the astaxanthin accumulation in sea urchin eggs by modifying the proportions of different food ingredients provided in their diet. This study demonstrates the large potential of sea urchin cultivation for the eco-sustainable production of healthy supplements for nutraceutical applications.

A new computational growth model for sea urchin skeletons.

PubMed

Zachos, Louis G

2009-08-07

A new computational model has been developed to simulate growth of regular sea urchin skeletons. The model incorporates the processes of plate addition and individual plate growth into a composite model of whole-body (somatic) growth. A simple developmental model based on hypothetical morphogens underlies the assumptions used to define the simulated growth processes. The data model is based on a Delaunay triangulation of plate growth center points, using the dual Voronoi polygons to define plate topologies. A spherical frame of reference is used for growth calculations, with affine deformation of the sphere (based on a Young-Laplace membrane model) to result in an urchin-like three-dimensional form. The model verifies that the patterns of coronal plates in general meet the criteria of Voronoi polygonalization, that a morphogen/threshold inhibition model for plate addition results in the alternating plate addition pattern characteristic of sea urchins, and that application of the Bertalanffy growth model to individual plates results in simulated somatic growth that approximates that seen in living urchins. The model suggests avenues of research that could explain some of the distinctions between modern sea urchins and the much more disparate groups of forms that characterized the Paleozoic Era.

Implications of Deoxygenation and Acidification for Deep Sea Urchins in Southern California

NASA Astrophysics Data System (ADS)

Sato, Kirk Nicholas Suda

Implications of multiple climate drivers for sea urchins were investigated across a spectrum of biological organization ranging from the urchin guild scale, to individual life history traits, to the geochemistry, material properties and porosity of sea urchin calcium carbonate skeletal tests. Using pink fragile sea urchins (Strongylocentrotus fragilis) on the southern California upwelling margin as a model species, links between biological traits and environmental parameters in nature across multiple spatial and temporal scales revealed correlations with dissolved oxygen (DO), pH, and temperature. Temporal trends in sea urchin populations assessed from trawl surveys conducted in southern California over the last 20 years (1994-2013) revealed changes in deep-sea urchin densities and depth distributions that coincide with trends in DO and pH on multidecadal and interdecadal (El Nino Southern Oscillation) time scales. The shallower urchin species ( Lytechinus pictus) decreased in density in the upper 200 m by 80%, and the deeper S. fragilis increased in density by ˜300%, providing the first evidence of habitat compression and expansion in sea urchin populations associated with secular and interdecadal variability in DO and pH. In this context, marketable food quality properties of the roe were compared between S. fragilis and the currently fished California red urchin, Mesocentrotus franciscanus, to assess the feasibility of developing a climate change-tolerant future S. fragilis trap fishery. Although roe color, texture, and resilience were similar between the two species, smaller and softer S. fragilis roe suggest it may only supplement, but not replace M. franciscanus in future fisheries. In comparisons across natural margin depth and climate gradients from 100-1100 m, S. fragilis exhibited reduced gonad production, smaller, weaker and more porous calcified tests in the Oxygen Minimum Zone (DO < 22 mumol kg-1) and pH Minimum Zone (in situ pHTotal <7.57) than those collected from less acidic and more oxygenated shelf and oxygen limiting zones above and the lower OMZ below. Thus S. fragilis may be more vulnerable to crushing predators if low oxygen, low pH OMZs continue to shoal and intensify in the future. This research highlights the utility of quantifying natural variability in species' traits along natural gradients on upwelling margins to improve understanding about potential impacts of changing climate drivers.

Insulin-like growth factor-I increases bone sialoprotein (BSP) expression through fibroblast growth factor-2 response element and homeodomain protein-binding site in the proximal promoter of the BSP gene.

PubMed

Nakayama, Youhei; Nakajima, Yu; Kato, Naoko; Takai, Hideki; Kim, Dong-Soon; Arai, Masato; Mezawa, Masaru; Araki, Shouta; Sodek, Jaro; Ogata, Yorimasa

2006-08-01

Insulin-like growth factor-I (IGF-I) promotes bone formation by stimulating proliferation and differentiation of osteoblasts. Bone sialoprotein (BSP), is thought to function in the initial mineralization of bone, is selectively expressed by differentiated osteoblast. To determine the molecular mechanism of IGF-I regulation of osteogenesis, we analyzed the effects of IGF-I on the expression of BSP in osteoblast-like Saos2 and in rat stromal bone marrow (RBMC-D8) cells. IGF-I (50 ng/ml) increased BSP mRNA levels at 12 h in Saos2 cells. In RBMC-D8 cells, IGF-I increased BSP mRNA levels at 3 h. From transient transfection assays, a twofold increase in transcription by IGF-I was observed at 12 h in pLUC3 construct that included the promoter sequence from -116 to +60. Effect of IGF-I was abrogated by 2-bp mutations in either the FGF2 response element (FRE) or homeodomain protein-binding site (HOX). Gel shift analyses showed that IGF-I increased binding of nuclear proteins to the FRE and HOX elements. Notably, the HOX-protein complex was supershifted by Smad1 antibody, while the FRE-protein complex was shifted by Smad1 and Cbfa1 antibodies. Dlx2 and Dlx5 antibodies disrupted the formation of the FRE- and HOX-protein complexes. The IGF-I effects on the formation of FRE-protein complexes were abolished by tyrosine kinase inhibitor herbimycin A (HA), PI3-kinase/Akt inhibitor LY249002, and MAP kinase kinase inhibitor U0126, while IGF-I effects on HOX-protein complexes were abolished by HA and LY249002. These studies demonstrate that IGF-I stimulates BSP transcription by targeting the FRE and HOX elements in the proximal promoter of BSP gene.

Cross-regulation in the mouse HoxB complex: the expression of Hoxb2 in rhombomere 4 is regulated by Hoxb1.

PubMed

Maconochie, M K; Nonchev, S; Studer, M; Chan, S K; Pöpperl, H; Sham, M H; Mann, R S; Krumlauf, R

1997-07-15

Correct regulation of the segment-restricted patterns of Hox gene expression is essential for proper patterning of the vertebrate hindbrain. We have examined the molecular basis of restricted expression of Hoxb2 in rhombomere 4 (r4), by using deletion analysis in transgenic mice to identify an r4 enhancer from the mouse gene. A bipartite Hox/Pbx binding motif is located within this enhancer, and in vitro DNA binding experiments showed that the vertebrate labial-related protein Hoxb1 will cooperatively bind to this site in a Pbx/Exd-dependent manner. The Hoxb2 r4 enhancer can be transactivated in vivo by the ectopic expression of Hoxb1, Hoxa1, and Drosophila labial in transgenic mice. In contrast, ectopic Hoxb2 and Hoxb4 are unable to induce expression, indicating that in vivo this enhancer preferentially responds to labial family members. Mutational analysis demonstrated that the bipartite Hox/Pbx motif is required for r4 enhancer activity and the responses to retinoids and ectopic Hox expression. Furthermore, three copies of the Hoxb2 motif are sufficient to mediate r4 expression in transgenic mouse embryos and a labial pattern in Drosophila embryos. This reporter expression in Drosophila embryos is dependent upon endogenous labial and exd, suggesting that the ability of this Hox/Pbx site to interact with labial-related proteins has been evolutionarily conserved. The endogenous Hoxb2 gene is no longer upregulated in r4 in Hoxb1 homozygous mutant embryos. On the basis of these experiments we conclude that the r4-restricted domain of Hoxb2 in the hindbrain is the result of a direct cross-regulatory interaction by Hoxb1 involving vertebrate Pbx proteins as cofactors. This suggests that part of the functional role of Hoxb1 in maintaining r4 identity may be mediated by the Hoxb2 gene.

Exogenous hyalin and sea urchin gastrulation. Part III: Biological activity of hyalin isolated from Lytechinus pictus embryos

PubMed Central

Contreras, Azalia; Vitale, John; Hutchins-Carroll, Virginia; Carroll, Edward J.; Oppenheimer, Steven B.

2008-01-01

Summary Hyalin is a large glycoprotein, consisting of the hyalin repeat domain and non-repeated regions, and is the major component of the hyaline layer in the early sea urchin embryo of Strongylocentrotus purpuratus. The hyalin repeat domain has been identified in proteins from organisms as diverse as bacteria, sea urchins, worms, flies, mice and humans. While the specific function of hyalin and the hyalin repeat domain is incompletely understood, many studies suggest that it has a functional role in adhesive interactions. In part I of this series, we showed that hyalin isolated from the sea urchin S. purpuratus blocked archenteron elongation and attachment to the blastocoel roof occurring during gastrulation in S. purpuratus embryos, (Razinia et al., 2007). The cellular interactions that occur in the sea urchin, recognized by the U.S. National Institutes of Health as a model system, may provide insights into adhesive interactions that occur in human health and disease. In part II of this series, we showed that S. purpuratus hyalin heterospecifically blocked archenteron-ectoderm interaction in Lytechinus pictus embryos (Alvarez et al, 2007). In the current study, we have isolated hyalin from the sea urchin L. pictus and demonstrated that L. pictus hyalin homospecifically blocks archenteron-ectoderm interaction, suggesting a general role for this glycoprotein in mediating a specific set of adhesive interactions. We also found one major difference in hyalin activity in the two sea urchin species involving hyalin influence on gastrulation invagination. PMID:18925979

Trophic ecology of sea urchins in coral-rocky reef systems, Ecuador

PubMed Central

Loor-Andrade, Peggy; Rodríguez-Barreras, Ruber; Cortés, Jorge

2016-01-01

Sea urchins are important grazers and influence reef development in the Eastern Tropical Pacific (ETP). Diadema mexicanum and Eucidaris thouarsii are the most important sea urchins on the Ecuadorian coastal reefs. This study provided a trophic scenario for these two species of echinoids in the coral-rocky reef bottoms of the Ecuadorian coast, using stable isotopes. We evaluated the relative proportion of algal resources assimilated, and trophic niche of the two sea urchins in the most southern coral-rocky reefs of the ETP in two sites with different disturbance level. Bayesian models were used to estimate the contribution of algal sources, niche breadth, and trophic overlap between the two species. The sea urchins behaved as opportunistic feeders, although they showed differential resource assimilation. Eucidaris thouarsii is the dominant species in disturbed environments; likewise, their niche amplitude was broader than that of D. mexicanum when conditions were not optimal. However, there was no niche overlap between the species. The Stable Isotope Analysis in R (SIAR) indicated that both sea urchins shared limiting resources in the disturbed area, mainly Dictyota spp. (contributions of up to 85% for D. mexicanum and up to 75% for E. thouarsii). The Stable Isotope Bayesian Ellipses in R (SIBER) analysis results indicated less interspecific competition in the undisturbed site. Our results suggested a trophic niche partitioning between sympatric sea urchin species in coastal areas of the ETP, but the limitation of resources could lead to trophic overlap and stronger habitat degradation. PMID:26839748

Ca2+ release triggered by nicotinate adenine dinucleotide phosphate in intact sea urchin eggs.

PubMed Central

Perez-Terzic, C M; Chini, E N; Shen, S S; Dousa, T P; Clapham, D E

1995-01-01

Nicotinate adenine dinucleotide phosphate (NAADP) was recently identified [Lee and Aarhus (1995) J. Biol. Chem. 270, 2152-2157; Chini, Beers and Dousa (1995) J. Biol. Chem. 270, 3116-3223] as a potent Ca(2+)-releasing agent in sea urchin egg homogenates. NAADP triggered Ca2+ release by a mechanism that was distinct from inositol 1,4,5-trisphosphate (InsP3)- and cyclic ADP-ribose (cADPR)-induced Ca2+ release. When NAADP was microinjected into intact sea urchin eggs it induced a dose-dependent increase in cytoplasmic free Ca2+ which was independent of the extracellular [Ca2+]. The Ca2+ waves elicited by microinjections of NAADP originated at the site of injection and swept across the cytosol. As previously found in sea urchin egg homogenates, NAADP-induced Ca2+ release in intact eggs was not blocked by heparin or by prior desensitization to InsP3 or cADPR. Thio-NADP, a specific inhibitor of the NAADP-induced Ca2+ release in sea urchin homogenates [Chini, Beers and Dousa (1995) J. Biol. Chem. 270, 3116-3223] blocked NAADP (but not InsP3 or cADPR) injection-induced Ca2+ release in intact sea urchin eggs. Finally, fertilization of sea urchin eggs abrogated subsequent NAADP-induced Ca2+ release, suggesting that the NAADP-sensitive Ca2+ pool may participate in the fertilization response. This study demonstrates that NAADP acts as a selective Ca(2+)-releasing agonist in intact cells. Images Figure 2 PMID:8554544

Use of a free ocean CO₂ enrichment (FOCE) system to evaluate the effects of ocean acidification on the foraging behavior of a deep-sea urchin.

PubMed

Barry, James P; Lovera, Chris; Buck, Kurt R; Peltzer, Edward T; Taylor, Josi R; Walz, Peter; Whaling, Patrick J; Brewer, Peter G

2014-08-19

The influence of ocean acidification in deep-sea ecosystems is poorly understood but is expected to be large because of the presumed low tolerance of deep-sea taxa to environmental change. We used a newly developed deep-sea free ocean CO2 enrichment (dp-FOCE) system to evaluate the potential consequences of future ocean acidification on the feeding behavior of a deep-sea echinoid, the sea urchin, Strongylocentrotus fragilis. The dp-FOCE system simulated future ocean acidification inside an experimental enclosure where observations of feeding behavior were performed. We measured the average movement (speed) of urchins as well as the time required (foraging time) for S. fragilis to approach its preferred food (giant kelp) in the dp-FOCE chamber (-0.46 pH units) and a control chamber (ambient pH). Measurements were performed during each of 4 trials (days -2, 2, 24, 27 after CO2 injection) during the month-long period when groups of urchins were continuously exposed to low pH or control conditions. Although urchin speed did not vary significantly in relation to pH or time exposed, foraging time was significantly longer for urchins in the low-pH treatment. This first deep-sea FOCE experiment demonstrated the utility of the FOCE system approach and suggests that the chemosensory behavior of a deep-sea urchin may be impaired by ocean acidification.

Characteristics of algal succession following rock scraping at Imwon area in the east coast of Korea

NASA Astrophysics Data System (ADS)

Kim, Young Dae; Ahn, Jung Kwan; Nam, Myung Mo; Lee, Chu; Yoo, Hyun Il; Yeon, Su Yeoung; Kim, Young Hwan; Kim, Jang Kyun; Choi, Jae Suk

2016-12-01

This study was conducted to clarify the characteristics of algal succession following rock scraping using hoe or high-pressure water sprayer in the period from June 2010 to April 2011. We divided the research area off the eastern coast of Korean near Imwon into 3 categories depending upon the severity of the barren ground, i.e., the urchin barren-affected, urchin barren-ongoing and urchin barren-free areas. In April 2011, in the urchin barren-affected area with 25 seaweed species, the cover percentage and importance value (IV) of crustose coralline algae were higher than those of other species. In the urchin barren-ongoing area with 33 seaweed species, crustose coralline algae (mean IV = 62%) as well as Sargassum sp. (mean IV = 28%), and Gelidium amansii (mean IV = 19%) were observed following rock scraping. In the urchin barren-free area where seaweed communities were relatively abundant with 42 species, a variety of algal species including G. amansii (mean IV = 32%) underwent algal succession. Overall, it was observed that, as an aspect of algal succession, the weaker the barren ground severity was, the more frequent and diverse the seaweeds were, and the more complex the succession pattern was in the study. As an aspect of recovering algal community, rock scraping using hoe was shown to be superior to the method using high-pressure water spraying. Therefore, we conclude that rock scraping using hoe is a very effective strategy for recovering the algal community in urchin barren-ongoing area.

Transcriptome sequencing of Atlantic salmon (Salmo salar L.) notochord prior to development of the vertebrae provides clues to regulation of positional fate, chordoblast lineage and mineralisation.

PubMed

Wang, Shou; Furmanek, Tomasz; Kryvi, Harald; Krossøy, Christel; Totland, Geir K; Grotmol, Sindre; Wargelius, Anna

2014-02-19

In teleosts such as Atlantic salmon (Salmo salar L.), segmentation and subsequent mineralisation of the notochord during embryonic stages are essential for normal vertebrae formation. However, the molecular mechanisms leading to segmentation and mineralisation of the notochord are poorly understood. The aim of this study was to identify genes/pathways acting in gradients over time and along the anterior-posterior axis during notochord segmentation and immediately prior to mineralisation of the vertebral bodies in Atlantic salmon. Notochord samples were collected from unsegmented, pre-segmented and segmented developmental stages. In each stage, the cellular core of the notochord was cut into three pieces along the longitudinal axis (anterior, mid, posterior). RNA was sequenced (22 million pair-end 100 bp/ library) and mapped to the salmon genome. 66569 transcripts were predicted and 55775 were annotated. In order to identify possible gradients leading to segmentation of the notochord, all 71 notochord-expressed hox genes were investigated, most of them displaying a typical anterior-posterior expression pattern along the notochord axis. The clustering of hox genes revealed a pattern that could be related to notochord segmentation. We further investigated how mineralisation is initiated in the notochord, and several factors related to chondrogenic lineage were identified (sox9, sox5, sox6, tgfb3, ihhb and col2a1), suggesting a cartilage-like character of the notochord. KEGG analysis of differentially expressed genes between stages revealed down-regulation of pathways associated with ECM, cell division, metabolism and development at onset of notochord segmentation. This implies that inhibitory signals produce segmentation of the notochord. One such potential inhibitory signal was identified, col11a2, which was detected in segments of non-mineralising notochord. An incomplete salmon genome was successfully used to analyse RNA-seq data from the cellular core of the Atlantic salmon notochord. In transcriptome we found; hox gene patterns possibly linked to segmentation; down-regulation of pathways in the notochord at onset of segmentation; segmented expression of col11a2 in non-mineralised segments of the notochord; and a chondroblast-like footprint in the notochord.

JPRS Report, Science & Technology, Japan, 1989 ERATO Symposia.

DTIC Science & Technology

1990-03-20

urchin eggs in fertilization. In fertilization of sea urchin eggs with seminal fluid, ovoperoxidase is secreted from the eggs causing a hardening of the...amphibians, chickens, sea urchins and other species. Simultaneously, molecular biologists have been trying to understand living organisms at the molecular...Cypridina luciferin analogues and luminol). Our group is also continuing the biochemical study of the mechanism of biophoton emission from Japanese sea

Instruction at the Hopkins Marine Station

DTIC Science & Technology

1989-09-07

SEM observation on refertilization of sea urchin eggs. 3:30-3:45 Navdeep Jaikaria Effect of aphidicolin on chromosomal replication and condensation. 3...9:15 Bll Pavan Electropermeabilization and introduction of inhibitors into sea urchin embryos. 9:15-9:30 Robert Padgett Population explosion in the...David Nagajski Hydrostatic pressure effects on sea urchin development 10:15-10:30 Emily Carrington Thermal and osmotic stress in the intertidal red

Hox3/zen and the evolution of extraembryonic epithelia in insects.

PubMed

Schmidt-Ott, Urs; Rafiqi, Ab Matteen; Lemke, Steffen

2010-01-01

Insects have undergone dramatic evolutionary changes in extraembryonic development, which correlate with changes in the expression of the class-3 Hox gene zen. Here, we review the evolution of this gene in insects and point out how changes in zen expression may have affected extraembryonic development at the morphological and the genetic level.

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution.

PubMed

Schwager, Evelyn E; Sharma, Prashant P; Clarke, Thomas; Leite, Daniel J; Wierschin, Torsten; Pechmann, Matthias; Akiyama-Oda, Yasuko; Esposito, Lauren; Bechsgaard, Jesper; Bilde, Trine; Buffry, Alexandra D; Chao, Hsu; Dinh, Huyen; Doddapaneni, HarshaVardhan; Dugan, Shannon; Eibner, Cornelius; Extavour, Cassandra G; Funch, Peter; Garb, Jessica; Gonzalez, Luis B; Gonzalez, Vanessa L; Griffiths-Jones, Sam; Han, Yi; Hayashi, Cheryl; Hilbrant, Maarten; Hughes, Daniel S T; Janssen, Ralf; Lee, Sandra L; Maeso, Ignacio; Murali, Shwetha C; Muzny, Donna M; Nunes da Fonseca, Rodrigo; Paese, Christian L B; Qu, Jiaxin; Ronshaugen, Matthew; Schomburg, Christoph; Schönauer, Anna; Stollewerk, Angelika; Torres-Oliva, Montserrat; Turetzek, Natascha; Vanthournout, Bram; Werren, John H; Wolff, Carsten; Worley, Kim C; Bucher, Gregor; Gibbs, Richard A; Coddington, Jonathan; Oda, Hiroki; Stanke, Mario; Ayoub, Nadia A; Prpic, Nikola-Michael; Flot, Jean-François; Posnien, Nico; Richards, Stephen; McGregor, Alistair P

2017-07-31

The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.

TWIST1-WDR5-Hottip regulates Hoxa9 chromatin to facilitate prostate cancer metastasis

PubMed Central

Malek, Reem; Gajula, Rajendra P.; Williams, Russell D.; Nghiem, Belinda; Simons, Brian W.; Nugent, Katriana; Wang, Hailun; Taparra, Kekoa; Lemtiri-Chlieh, Ghali; Yoon, Arum R.; True, Lawrence; An, Steven S.; DeWeese, Theodore L.; Ross, Ashley E.; Schaeffer, Edward M.; Pienta, Kenneth J.; Hurley, Paula J.; Morrissey, Colm; Tran, Phuoc T.

2017-01-01

TWIST1 is a transcription factor critical for development which can promote prostate cancer metastasis. During embryonic development, TWIST1 and HOXA9 are co-expressed in mouse prostate and then silenced post-natally. Here we report that TWIST1 and HOXA9 co-expression are re-activated in mouse and human primary prostate tumors and are further enriched in human metastases, correlating with survival. TWIST1 formed a complex with WDR5 and the lncRNA Hottip/HOTTIP, members of the MLL/COMPASS-like H3K4 methylases, which regulate chromatin in the Hox/HOX cluster during development. TWIST1 overexpression led to co-enrichment of TWIST1 and WDR5 as well increased H3K4me3 chromatin at the Hoxa9/HOXA9 promoter which was dependent on WDR5. Expression of WDR5 and Hottip/HOTTIP was also required for TWIST1-induced upregulation of HOXA9 and aggressive cellular phenotypes such as invasion and migration. Pharmacological inhibition of HOXA9 prevented TWIST1-induced aggressive prostate cancer cellular phenotypes in vitro and metastasis in vivo. This study demonstrates a novel mechanism by which TWIST1 regulates chromatin and gene expression by cooperating with the COMPASS-like complex to increase H3K4 trimethylation at target gene promoters. Our findings highlight a TWIST1-HOXA9 embryonic prostate developmental program that is reactivated during prostate cancer metastasis and is therapeutically targetable. PMID:28484075

Synthesis of Mn-doped ZnS architectures in ternary solution and their optical properties

NASA Astrophysics Data System (ADS)

Wang, Xinjuan; Zhang, Qinglin; Zou, Bingsuo; Lei, Aihua; Ren, Pinyun

2011-10-01

Mn-doped ZnS sea urchin-like architectures were fabricated by a one-pot solvothermal route in a ternary solution made of ethylenediamine, ethanolamine and distilled water. The as-prepared products were characterized by X-ray diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM) and photoluminescence spectra (PL). It was demonstrated that the as-prepared sea urchin-like architectures with diameter of 0.5-1.5 μm were composed of nanorods, possessing a wurtzite structures. The preferred growth orientation of nanorods was found to be the [0 0 2] direction. The PL spectra of the Mn-doped ZnS sea urchin-like architectures show a strong orange emission at 587 nm, indicating the successful doping of Mn 2+ ions into ZnS host. Ethanolamine played the role of oriented-assembly agent in the formation of sea urchin-like architectures. A possible growth mechanism was proposed to explain the formation of sea urchin-like architectures.

Impact of elevated levels of CO2 on animal mediated ecosystem function: the modification of sediment nutrient fluxes by burrowing urchins.

PubMed

Widdicombe, S; Beesley, A; Berge, J A; Dashfield, S L; McNeill, C L; Needham, H R; Øxnevad, S

2013-08-30

A mesocosm experiment was conducted to quantify the relationships between the presence and body size of two burrowing heart urchins (Brissopsis lyrifera and Echinocardium cordatum) and rates of sediment nutrient flux. Furthermore, the impact of seawater acidification on these relationships was determined during this 40-day exposure experiment. Using carbon dioxide (CO2) gas, seawater was acidified to pHNBS 7.6, 7.2 or 6.8. Control treatments were maintained in natural seawater (pH≈8.0). Under normocapnic conditions, burrowing urchins were seen to reduce the sediment uptake of nitrite or nitrate whilst enhancing the release of silicate and phosphate. In acidified (hypercapnic) treatments, the biological control of biogeochemical cycles by urchins was significantly affected, probably through the combined impacts of high CO2 on nitrifying bacteria, benthic algae and urchin behaviour. This study highlights the importance of considering biological interactions when predicting the consequences of seawater acidification on ecosystem function. Copyright © 2012 Elsevier Ltd. All rights reserved.

Structural, optical and field emission properties of urchin-shaped ZnO nanostructures.

PubMed

Al-Heniti, Saleh; Umar, Ahmad

2013-01-01

In this work, well-crystallized urchin-shaped ZnO structures were synthesized on silicon substrate by simple non-catalytic thermal evaporation process by using metallic zinc powder in the presence of oxygen as source materials for zinc and oxygen, respectively. The synthesized ZnO structures were characterized in detail in terms of their morphological, structural, optical and field emission properties. The detailed morphological investigations revealed that the synthesized structures possess urchin-shape and grown in high-density over the substrate surface. The detailed structural and optical characterizations revealed that the synthesized urchin-shaped ZnO structures are well-crystallized and exhibiting good optical properties. The field emission analysis for urchin-shaped ZnO structures exhibits a turn-on field of 4.6 V/microm. The emission current density reached to 0.056 mA/cm2 at an applied electrical field of 6.4 V/microm and shows no saturation. The calculated field enhancement factor 'beta', from the F-N plot, was found to be approximately 2.2 x 10(3).

Hydrodynamic patterns favouring sea urchin recruitment in coastal areas: A Mediterranean study case.

PubMed

Farina, S; Quattrocchi, G; Guala, I; Cucco, A

2018-05-11

In invertebrate fisheries, sea urchin harvesting continues to grow with dramatic consequences for benthic ecosystems. The identification of areas with a marked natural recruitment and the mechanisms regulating it is crucial for the conservation of benthic communities and for planning the sustainable harvesting. This study evaluates the spatial distribution and density of recruits of the edible sea urchin Paracentrotus lividus along the Sinis + Peninsula (Sardinia) and explores its significant relationships with the local oceanographic features. Our results reveal that recruitment is favoured in areas with slow currents and high levels of confinement and trapping of the water masses. Analysis of the residual circulation indicates that the presence of local standing circulation structures promotes the sea urchin recruitment process. Our findings emphasize the importance of managing local sea urchin harvesting as a system of populations with their demographic influence mainly dependent on the most important ecological driver that is the recruitment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Community-level destruction of hard corals by the sea urchin Diadema setosum.

PubMed

Qiu, Jian-Wen; Lau, Dickey C C; Cheang, Chi-chiu; Chow, Wing-kuen

2014-08-30

Sea urchins are common herbivores and bioeroders of coral ecosystems, but rarely have they been reported as corallivores. We determined the spatial pattern of hard coral damage due to corallivory and bioerosion by the sea urchin Diadema setosum Leske in Hong Kong waters. Coral damage was common at the northeastern sites, with 23.7 - 90.3% colonies being either collapsed or severely damaged with >25% tissue loss. Many genera of corals were impacted by the sea urchin but the damage was most obvious for the structure forming genus Platygyra. The percentage of severely damaged and collapsed coral had significant positive correlation with the abundance of D. setosum, which ranged from 0.01 to 5.2 individuals per coral head or 0.1 - 21.1 individuals m(-2) across the study sites. Remedial management actions such as sea urchin removal are urgently needed to save these fringing coral communities. Copyright © 2013 Elsevier Ltd. All rights reserved.

A Rapid Colorimetric Method Reveals Fraudulent Substitutions in Sea Urchin Roe Marketed in Sardinia (Italy).

PubMed

Meloni, Domenico; Spina, Antonio; Satta, Gianluca; Chessa, Vittorio

2016-06-25

In recent years, besides the consumption of fresh sea urchin specimens, the demand of minimally-processed roe has grown considerably. This product has made frequent consumption in restaurants possible and frauds are becoming widespread with the partial replacement of sea urchin roe with surrogates that are similar in colour. One of the main factors that determines the quality of the roe is its colour and small differences in colour scale cannot be easily discerned by the consumers. In this study we have applied a rapid colorimetric method for reveal the fraudulent partial substitution of semi-solid sea urchin roe with liquid egg yolk. Objective assessment of whiteness (L*), redness (a*), yellowness (b*), hue (h*), and chroma (C*) was carried out with a digital spectrophotometer using the CIE L*a*b* colour measurement system. The colorimetric method highlighted statistically significant differences among sea urchin roe and liquid egg yolk that could be easily discerned quantitatively.

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.

A sea urchin in vivo model to evaluate Epithelial-Mesenchymal Transition.

PubMed

Romancino, Daniele P; Anello, Letizia; Lavanco, Antonella; Buffa, Valentina; Di Bernardo, Maria; Bongiovanni, Antonella

2017-04-01

Epithelial-mesenchymal transition (EMT) is an evolutionarily conserved cellular program, which is a prerequisite for the metastatic cascade in carcinoma progression. Here, we evaluate the EMT process using the sea urchin Paracentrotus lividus embryo. In sea urchin embryos, the earliest EMT event is related to the acquisition of a mesenchymal phenotype by the spiculogenetic primary mesenchyme cells (PMCs) and their migration into the blastocoel. We investigated the effect of inhibiting the epidermal growth factor (EGF) signaling pathway on this process, and we observed that mesenchyme cell differentiation was blocked. In order to extend and validate our studies, we investigated the migratory capability and the level of potential epidermal growth factor receptor (EGFr) targets in a breast cancer cell line after EGF modulation. Altogether, our data highlight the sensitivity of the sea urchin embryo to anti-EMT drugs and pinpoint the sea urchin embryo as a valuable in vivo model system for studying EMT and the screening of anti-EMT candidates. © 2017 Japanese Society of Developmental Biologists.

Nuclear lamins and peripheral nuclear antigens during fertilization and embryogenesis in mice and sea urchins

NASA Technical Reports Server (NTRS)

Schatten, G.; Schatten, H.; Simerly, C.; Maul, G. G.; Chaly, N.

1985-01-01

Nuclear structural changes during fertilization and embryogenesis in mice and sea urchins are traced using four antibodies. The oocytes from virgin female mice, morulae and blastocytes from mated females, and gametes from the sea urchin Lytechnius variegatis are studied using mouse monoclonal antibodies to nuclear lamin A/C, monoclonal antibody to P1, human autoimmune antibodies to lamin A/C, and to lamin B. The mouse fertilization data reveal no lamins on the oocyte; however, lamins are present on the pronuclei, and chromosomes are found on the oocytes and pronuclei. It is detected that on the sea urchin sperm the lamins are reduced to acrosomal and centriolar fossae and peripheral antigens are around the sperm nucleus. The mouse sperm bind lamin antibodies regionally and do not contain antigens. Lamins and antigens are observed on both pronuclei and chromosomes during sea urchin fertilization. Mouse embryogenesis reveals that lamin A/C is not recognized at morula and blastocyst stages; however, lamin B stains are retained. In sea urchin embryogenesis lamin recognition is lost at the blastrula, gastrula, and plutei stages. It is noted that nuclear lamins lost during spermatogenesis are restored at fertilization and peripheral antigens are associated with the surface of chromosomes during meiosis and mitosis and with the periphery of the pronuclei and nuclei during interphase.

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.

Bioaccumulation of persistent and emerging pollutants in wild sea urchin Paracentrotus lividus.

PubMed

Rocha, A Cristina; Camacho, Carolina; Eljarrat, Ethel; Peris, Andrea; Aminot, Yann; Readman, James W; Boti, Vasiliki; Nannou, Christina; Marques, António; Nunes, Maria Leonor; Almeida, C Marisa

2018-02-01

Marine pollution has been increasing as a consequence of anthropogenic activities. The preservation of marine ecosystems, as well as the safety of harvested seafood, are nowadays a global concern. Here, we report for the first time the contamination levels of a large set of 99 emerging and persistent organic contaminants (butyltins (BTs), polycyclic aromatic hydrocarbons (PAHs), pesticides including pyrethroids, pharmaceuticals and personal care products (PCPs) and flame retardants) in roe/gonads of sea urchin Paracentrotus lividus. Sea urchins are a highly prized worldwide delicacy, and the harvesting of this seafood has increased over the last decades, particularly in South West Atlantic coast, where this organism is harvested mainly for exportation. Sampling was performed in three harvesting sites of the NW Portuguese coast subjected to distinct anthropogenic pressures: Carreço, Praia Norte and Vila Chã, with sea urchins being collected in the north and south areas of each site. Butyltins and pharmaceuticals were not found at measurable levels. Several PAHs, four pyrethroids insecticides, four PCPs and eleven flame retardants were found in roe/gonads of sea urchins, though in general at low levels. Differences among harvesting sites and between areas within each site were found, the lowest levels of contaminants being registered in Carreço. The accumulation of contaminants in sea urchins' roe/gonads seemed to reflect the low anthropogenic pressure felt in the sampling sites. Nevertheless, taking into account the low accumulated levels of chemicals, results indicate that sea urchins collected in South West Atlantic coast are safe for human consumption. Copyright © 2017 Elsevier Inc. All rights reserved.

Prep1.1 has essential genetic functions in hindbrain development and cranial neural crest cell differentiation.

PubMed

Deflorian, Gianluca; Tiso, Natascia; Ferretti, Elisabetta; Meyer, Dirk; Blasi, Francesco; Bortolussi, Marino; Argenton, Francesco

2004-02-01

In this study we analysed the function of the Meinox gene prep1.1 during zebrafish development. Meinox proteins form heterotrimeric complexes with Hox and Pbx members, increasing the DNA binding specificity of Hox proteins in vitro and in vivo. However, a role for a specific Meinox protein in the regulation of Hox activity in vivo has not been demonstrated. In situ hybridization showed that prep1.1 is expressed maternally and ubiquitously up to 24 hours post-fertilization (hpf), and restricted to the head from 48 hpf onwards. Morpholino-induced prep1.1 loss-of-function caused significant apoptosis in the CNS. Hindbrain segmentation and patterning was affected severely, as revealed by either loss or defective expression of several hindbrain markers (foxb1.2/mariposa, krox20, pax2.1 and pax6.1), including anteriorly expressed Hox genes (hoxb1a, hoxa2 and hoxb2), the impaired migration of facial nerve motor neurons, and the lack of reticulospinal neurons (RSNs) except Mauthner cells. Furthermore, the heads of prep1.1 morphants lacked all pharyngeal cartilages. This was not caused by the absence of neural crest cells or their impaired migration into the pharyngeal arches, as shown by expression of dlx2 and snail1, but by the inability of these cells to differentiate into chondroblasts. Our results indicate that prep1.1 has a unique genetic function in craniofacial chondrogenesis and, acting as a member of Meinox-Pbc-Hox trimers, it plays an essential role in hindbrain development.

Expression of Hoxa2 in rhombomere 4 is regulated by a conserved cross-regulatory mechanism dependent upon Hoxb1.

PubMed

Tümpel, Stefan; Cambronero, Francisco; Ferretti, Elisabetta; Blasi, Francesco; Wiedemann, Leanne M; Krumlauf, Robb

2007-02-15

The Hoxa2 gene is an important component of regulatory events during hindbrain segmentation and head development in vertebrates. In this study we have used sequenced comparisons of the Hoxa2 locus from 12 vertebrate species in combination with detailed regulatory analyses in mouse and chicken embryos to characterize the mechanistic basis for the regulation of Hoxa2 in rhombomere (r) 4. A highly conserved region in the Hoxa2 intron functions as an r4 enhancer. In vitro binding studies demonstrate that within the conserved region three bipartite Hox/Pbx binding sites (PH1-PH3) in combination with a single binding site for Pbx-Prep/Meis (PM) heterodimers co-operate to regulate enhancer activity in r4. Mutational analysis reveals that these sites are required for activity of the enhancer, suggesting that the r4 enhancer from Hoxa2 functions in vivo as a Hox-response module in combination with the Hox cofactors, Pbx and Prep/Meis. Furthermore, this r4 enhancer is capable of mediating a response to ectopic HOXB1 expression in the hindbrain. These findings reveal that Hoxa2 is a target gene of Hoxb1 and permit us to develop a gene regulatory network for r4, whereby Hoxa2, along with Hoxb1, Hoxb2 and Hoxa1, is integrated into a series of auto- and cross-regulatory loops between Hox genes. These data highlight the important role played by direct cross-talk between Hox genes in regulating hindbrain patterning.

Thermal and Hydrodynamic Environments Mediate Individual and Aggregative Feeding of a Functionally Important Omnivore in Reef Communities

PubMed Central

Frey, Desta L.; Gagnon, Patrick

2015-01-01

In eastern Canada, the destruction of kelp beds by dense aggregations (fronts) of the omnivorous green sea urchin, Strongylocentrotus droebachiensis, is a key determinant of the structure and dynamics of shallow reef communities. Recent studies suggest that hydrodynamic forces, but not sea temperature, determine the strength of urchin-kelp interactions, which deviates from the tenets of the metabolic theory of ecology (MTE). We tested the hypothesis that water temperature can predict short-term kelp bed destruction by S. droebachiensis in calm hydrodynamic environments. Specifically, we experimentally determined relationships among water temperature, body size, and individual feeding in the absence of waves, as well as among wave velocity, season, and aggregative feeding. We quantified variation in kelp-bed boundary dynamics, sea temperature, and wave height over three months at one subtidal site in Newfoundland to test the validity of thermal tipping ranges and regression equations derived from laboratory results. Consistent with the MTE, individual feeding during early summer (June-July) obeyed a non-linear, size- and temperature-dependent relationship: feeding in large urchins was consistently highest and positively correlated with temperature <12°C and dropped within and above the 12–15°C tipping range. This relationship was more apparent in large than small urchins. Observed and expected rates of kelp loss based on sea temperature and urchin density and size structure at the front were highly correlated and differed by one order of magnitude. The present study speaks to the importance of considering body size and natural variation in sea temperature in studies of urchin-kelp interactions. It provides the first compelling evidence that sea temperature, and not only hydrodynamic forces, can predict kelp bed destruction by urchin fronts in shallow reef communities. Studying urchin-seaweed-predator interactions within the conceptual foundations of the MTE holds high potential for improving capacity to predict and manage shifts in marine food web structure and productivity. PMID:25774674

The Influence of Physical Factors on Kelp and Sea Urchin Distribution in Previously and Still Grazed Areas in the NE Atlantic

PubMed Central

Rinde, Eli; Christie, Hartvig; Fagerli, Camilla W.; Bekkby, Trine; Gundersen, Hege; Norderhaug, Kjell Magnus; Hjermann, Dag Ø.

2014-01-01

The spatial distribution of kelp (Laminaria hyperborea) and sea urchins (Strongylocentrotus droebachiensis) in the NE Atlantic are highly related to physical factors and to temporal changes in temperature. On a large scale, we identified borders for kelp recovery and sea urchin persistence along the north-south gradient. Sea urchin persistence was also related to the coast-ocean gradient. The southern border corresponds to summer temperatures exceeding about 10°C, a threshold value known to be critical for sea urchin recruitment and development. The outer border along the coast-ocean gradient is related to temperature, wave exposure and salinity. On a finer scale, kelp recovery occurs mainly at ridges in outer, wave exposed, saline and warm areas whereas sea urchins still dominate in inner, shallow and cold areas, particularly in areas with optimal current speed for sea urchin foraging. In contrast to other studies in Europe, we here show a positive influence of climate change to presence of a long-lived climax canopy-forming kelp. The extent of the coast-ocean gradient varies within the study area, and is especially wide in the southern part where the presence of islands and skerries increases the area of the shallow coastal zone. This creates a large area with intermediate physical conditions for the two species and a mosaic of kelp and sea urchin dominated patches. The statistical models (GAM and BRT) show high performance and indicate recovery of kelp in 45–60% of the study area. The study shows the value of combining a traditional (GAM) and a more complex (BRT) modeling approach to gain insight into complex spatial patterns of species or habitats. The results, methods and approaches are of general ecological relevance regardless of ecosystems and species, although they are particularly relevant for understanding and exploring the corresponding changes between algae and grazers in different coastal areas. PMID:24949954

The influence of physical factors on kelp and sea urchin distribution in previously and still grazed areas in the NE Atlantic.

PubMed

Rinde, Eli; Christie, Hartvig; Fagerli, Camilla W; Bekkby, Trine; Gundersen, Hege; Norderhaug, Kjell Magnus; Hjermann, Dag Ø

2014-01-01

The spatial distribution of kelp (Laminaria hyperborea) and sea urchins (Strongylocentrotus droebachiensis) in the NE Atlantic are highly related to physical factors and to temporal changes in temperature. On a large scale, we identified borders for kelp recovery and sea urchin persistence along the north-south gradient. Sea urchin persistence was also related to the coast-ocean gradient. The southern border corresponds to summer temperatures exceeding about 10°C, a threshold value known to be critical for sea urchin recruitment and development. The outer border along the coast-ocean gradient is related to temperature, wave exposure and salinity. On a finer scale, kelp recovery occurs mainly at ridges in outer, wave exposed, saline and warm areas whereas sea urchins still dominate in inner, shallow and cold areas, particularly in areas with optimal current speed for sea urchin foraging. In contrast to other studies in Europe, we here show a positive influence of climate change to presence of a long-lived climax canopy-forming kelp. The extent of the coast-ocean gradient varies within the study area, and is especially wide in the southern part where the presence of islands and skerries increases the area of the shallow coastal zone. This creates a large area with intermediate physical conditions for the two species and a mosaic of kelp and sea urchin dominated patches. The statistical models (GAM and BRT) show high performance and indicate recovery of kelp in 45-60% of the study area. The study shows the value of combining a traditional (GAM) and a more complex (BRT) modeling approach to gain insight into complex spatial patterns of species or habitats. The results, methods and approaches are of general ecological relevance regardless of ecosystems and species, although they are particularly relevant for understanding and exploring the corresponding changes between algae and grazers in different coastal areas.

TRICAINE METHANESULFONATE (MS-222) SEDATION AND ANESTHESIA IN THE PURPLE-SPINED SEA URCHIN (ARBACIA PUNCTULATA).

PubMed

Applegate, Jeffrey R; Dombrowski, Daniel S; Christian, Larry Shane; Bayer, Meredith P; Harms, Craig A; Lewbart, Gregory A

2016-12-01

The purple-spined sea urchin ( Arbacia punctulata ) is commonly found in shallow waters of the western Atlantic Ocean from the New England area of the United States to the Caribbean. Sea urchins play a major role in ocean ecology, echinoculture, and biomedical research. Additionally, sea urchins are commonly displayed in public aquaria. Baseline parameters were developed in unanesthetized urchins for righting reflex (time to regain oral recumbency) and spine response time to tactile stimulus. Tricaine methanesulfonate (MS-222) was used to sedate and anesthetize purple-spined sea urchins and assess sedation and anesthetic parameters, including adhesion to and release from a vertical surface, times to loss of response to tactile stimulus and recovery of righting reflex, and qualitative observations of induction of spawning and position of spines and pseudopodia. Sedation and anesthetic parameters were evaluated in 11 individuals in three circumstances: unaltered aquarium water for baseline behaviors, 0.4 g/L MS-222, and 0.8 g/L MS-222. Induction was defined as the release from a vertical surface with the loss of righting reflex, sedation as loss of righting reflex with retained tactile spine response, anesthesia as loss of righting reflex and loss of tactile spine response, and recovery as voluntary return to oral recumbency. MS-222 proved to be an effective sedative and anesthetic for the purple-spined sea urchin at 0.4 and 0.8 g/L, respectively. Sodium bicarbonate used to buffer MS-222 had no measurable sedative effects when used alone. Anesthesia was quickly reversed with transfer of each individual to anesthesia-free seawater, and no anesthetic-related mortality occurred. The parameters assessed in this study provide a baseline for sea urchin anesthesia and may provide helpful comparisons to similar species and populations that are in need of anesthesia for surgical procedures or research.

Thermal and hydrodynamic environments mediate individual and aggregative feeding of a functionally important omnivore in reef communities.

PubMed

Frey, Desta L; Gagnon, Patrick

2015-01-01

In eastern Canada, the destruction of kelp beds by dense aggregations (fronts) of the omnivorous green sea urchin, Strongylocentrotus droebachiensis, is a key determinant of the structure and dynamics of shallow reef communities. Recent studies suggest that hydrodynamic forces, but not sea temperature, determine the strength of urchin-kelp interactions, which deviates from the tenets of the metabolic theory of ecology (MTE). We tested the hypothesis that water temperature can predict short-term kelp bed destruction by S. droebachiensis in calm hydrodynamic environments. Specifically, we experimentally determined relationships among water temperature, body size, and individual feeding in the absence of waves, as well as among wave velocity, season, and aggregative feeding. We quantified variation in kelp-bed boundary dynamics, sea temperature, and wave height over three months at one subtidal site in Newfoundland to test the validity of thermal tipping ranges and regression equations derived from laboratory results. Consistent with the MTE, individual feeding during early summer (June-July) obeyed a non-linear, size- and temperature-dependent relationship: feeding in large urchins was consistently highest and positively correlated with temperature <12°C and dropped within and above the 12-15°C tipping range. This relationship was more apparent in large than small urchins. Observed and expected rates of kelp loss based on sea temperature and urchin density and size structure at the front were highly correlated and differed by one order of magnitude. The present study speaks to the importance of considering body size and natural variation in sea temperature in studies of urchin-kelp interactions. It provides the first compelling evidence that sea temperature, and not only hydrodynamic forces, can predict kelp bed destruction by urchin fronts in shallow reef communities. Studying urchin-seaweed-predator interactions within the conceptual foundations of the MTE holds high potential for improving capacity to predict and manage shifts in marine food web structure and productivity.

Fine Structure and Molecular Phylogeny of Parametopidium circumlabens (Ciliophora: Armophorea), Endocommensal of Sea Urchins.

PubMed

da Silva-Neto, Inácio Domingos; da Silva Paiva, Thiago; do Nascimento Borges, Bárbara; Harada, Maria Lúcia

2016-01-01

Metopid armophoreans are ciliates commonly found in anaerobic environments worldwide; however, very little is known of their fine structure. In this study, the metopid Parametopidium circumlabens (Biggar and Wenrich 1932) Aescht, 1980, a common endocommensal of sea urchins, is investigated for the first time with emphasis on transmission electron microscopy, revealing several previously unknown elements of its morphology. Somatic dikinetids of P. circumlabens have a typical ribbon of transverse microtubules, an isolated microtubule near triplets 4 and 5 of the anterior kinetosome, plus two other microtubules between anterior and posterior kinetosomes, a short kinetodesmal striated fiber and long postciliary microtubules. In the dikinetids of the perizonal stripe, the kinetodesmal fiber is very pronounced, and there is a conspicuous microfibrillar network system associated with the kinetosomes. A new structure, shaped as a dense, roughly cylindrical mass surrounded by microtubules, is found associated with the posterior kinetosome of perizonal dikinetids. The paroral membrane is diplostichomonad and the adoral membranelles are of the "paramembranelle" type. Bayesian inference and maximum-likelihood analysis of the 18S-rDNA gene unambiguously placed P. circumlabens as sister group of the cluster formed by ((Atopospira galeata, Atopospira violacea) Metopus laminarius) + Clevelandellida, corroborating its classification within the Metopida. © 2015 The Author(s) Journal of Eukaryotic Microbiology © 2015 International Society of Protistologists.

DEFECTS IN CERVICAL VERTEBRAE IN BORIC ACID-EXPOSED RAT EMBRYOS ARE ASSOCIATED WITH ANTERIOR SHIFTS OF HOX GENE EXPRESSION DOMAINS

EPA Science Inventory

Defects in cervical vertebrae in boric acid-exposed rat embryos are associated with anterior shifts of hox gene expression domains

Nathalie Wery,1 Michael G. Narotsky,2 Nathalie Pacico,1 Robert J. Kavlock,2 Jacques J. Picard,1 AND Francoise Gofflot,1*
1Unit of Developme...

Function and specificity of synthetic Hox transcription factors in vivo

PubMed Central

Papadopoulos, Dimitrios K.; Vukojević, Vladana; Adachi, Yoshitsugu; Terenius, Lars; Rigler, Rudolf; Gehring, Walter J.

2010-01-01

Homeotic (Hox) genes encode transcription factors that confer segmental identity along the anteroposterior axis of the embryo. However the molecular mechanisms underlying Hox-mediated transcription and the differential requirements for specificity in the regulation of the vast number of Hox-target genes remain ill-defined. Here we show that synthetic Sex combs reduced (Scr) genes that encode the Scr C terminus containing the homedomain (HD) and YPWM motif (Scr-HD) are functional in vivo. Synthetic Scr-HD peptides can induce ectopic salivary glands in the embryo and homeotic transformations in the adult fly, act as transcriptional activators and repressors during development, and participate in protein-protein interactions. Their transformation capacity was found to be enhanced over their full-length counterpart and mutations known to transform the full-length protein into constitutively active or inactive variants behaved accordingly in the synthetic peptides. Our results show that synthetic Scr-HD genes are sufficient for homeotic function in Drosophila and suggest that the N terminus of Scr has a role in transcriptional potency, rather than specificity. We also demonstrate that synthetic peptides behave largely in a predictable way, by exhibiting Scr-specific phenotypes throughout development, which makes them an important tool for synthetic biology. PMID:20147626

Transmembrane protein MIG-13 links the Wnt signaling and Hox genes to the cell polarity in neuronal migration

PubMed Central

Wang, Xiangming; Zhou, Fanli; Lv, Sijing; Yi, Peishan; Zhu, Zhiwen; Yang, Yihong; Feng, Guoxin; Li, Wei; Ou, Guangshuo

2013-01-01

Directional cell migration is a fundamental process in neural development. In Caenorhabditis elegans, Q neuroblasts on the left (QL) and right (QR) sides of the animal generate cells that migrate in opposite directions along the anteroposterior body axis. The homeobox (Hox) gene lin-39 promotes the anterior migration of QR descendants (QR.x), whereas the canonical Wnt signaling pathway activates another Hox gene, mab-5, to ensure the QL descendants’ (QL.x) posterior migration. However, the regulatory targets of LIN-39 and MAB-5 remain elusive. Here, we showed that MIG-13, an evolutionarily conserved transmembrane protein, cell-autonomously regulates the asymmetric distribution of the actin cytoskeleton in the leading migratory edge. We identified mig-13 as a cellular target of LIN-39 and MAB-5. LIN-39 establishes QR.x anterior polarity by binding to the mig-13 promoter and promoting mig-13 expression, whereas MAB-5 inhibits QL.x anterior polarity by associating with the lin-39 promoter and downregulating lin-39 and mig-13 expression. Thus, MIG-13 links the Wnt signaling and Hox genes that guide migrations, to the actin cytoskeleton, which executes the motility response in neuronal migration. PMID:23784779

Chromatin-Bound IκBα Regulates a Subset of Polycomb Target Genes in Differentiation and Cancer

PubMed Central

Mulero, María Carmen; Ferres-Marco, Dolors; Islam, Abul; Margalef, Pol; Pecoraro, Matteo; Toll, Agustí; Drechsel, Nils; Charneco, Cristina; Davis, Shelly; Bellora, Nicolás; Gallardo, Fernando; López-Arribillaga, Erika; Asensio-Juan, Elena; Rodilla, Verónica; González, Jessica; Iglesias, Mar; Shih, Vincent; Albà, M. Mar; Di Croce, Luciano; Hoffmann, Alexander; Miyamoto, Shigeki; Villà-Freixa, Jordi; López-Bigas, Nuria; Keyes, William M.; Domínguez, María; Bigas, Anna; Espinosa, Lluís

2014-01-01

Summary IκB proteins are the primary inhibitors of NF-κB. Here, we demonstrate that sumoylated and phosphorylated IκBα accumulates in the nucleus of keratinocytes and interacts with histones H2A and H4 at the regulatory region of HOX and IRX genes. Chromatin-bound IκBα modulates Polycomb recruitment and imparts their competence to be activated by TNFα. Mutations in the Drosophila IκBα gene cactus enhance the homeotic phenotype of Polycomb mutants, which is not counteracted by mutations in dorsal/NF-κB. Oncogenic transformation of keratinocytes results in cytoplasmic IκBα translocation associated with a massive activation of Hox. Accumulation of cytoplasmic IκBα was found in squamous cell carcinoma (SCC) associated with IKK activation and HOX upregulation. PMID:23850221

Skeleton growth under uniformly distributed force conditions: producing spherical sea urchins

NASA Astrophysics Data System (ADS)

Cheng, Polly; Kambli, Ankita; Stone, Johnny

2017-10-01

Sea urchin skeletons, or tests, comprise rigid calcareous plates, interlocked and sutured together with collagen fibres. The tests are malleable due to mutability in the collagen fibres that loosen during active feeding, yielding interplate gaps. We designed an extraterrestrial simulation experiment wherein we subjected actively growing sea urchins to one factor associated with zero-gravity environments, by growing them under conditions in which reactionary gravitational forces were balanced, and observed how their tests responded. Preventing tests from adhering to surfaces during active growth produced more-spherical bodies, realized as increased height-to-diameter ratios. Sea urchin tests constitute ideal systems for obtaining data that could be useful in extraterrestrial biology research, particularly in how skeletons grow under altered-gravity conditions.

HOx Observation and Model Comparison During INTEX-A 2004

NASA Technical Reports Server (NTRS)

Ren, Xinrong; Olson, Jennifer R.; Crawford, James H.; Brune, William H.; Mao, Jingqiu; Long, Robert B.; Chen, Zhong; Chen, Gao; Avery, Melody A.; Sachse, Glen W.;

The contribution of apoptosis and necrosis in freezing injury of sea urchin embryonic cells.

PubMed

Boroda, Andrey V; Kipryushina, Yulia O; Yakovlev, Konstantin V; Odintsova, Nelly A

2016-08-01

Sea urchins have recently been reported to be a promising tool for investigations of oxidative stress, UV light perturbations and senescence. However, few available data describe the pathway of cell death that occurs in sea urchin embryonic cells after cryopreservation. Our study is focused on the morphological and functional alterations that occur in cells of these animals during the induction of different cell death pathways in response to cold injury. To estimate the effect of cryopreservation on sea urchin cell cultures and identify the involved cell death pathways, we analyzed cell viability (via trypan blue exclusion test, MTT assay and DAPI staining), caspase activity (via flow cytometry and spectrophotometry), the level of apoptosis (via annexin V-FITC staining), and cell ultrastructure alterations (via transmission electron microscopy). Using general caspase detection, we found that the level of caspase activity was low in unfrozen control cells, whereas the number of apoptotic cells with activated caspases rose after freezing-thawing depending on cryoprotectants used, also as the number of dead cells and cells in a late apoptosis. The data using annexin V-binding assay revealed a very high apoptosis level in all tested samples, even in unfrozen cells (about 66%). Thus, annexin V assay appears to be unsuitable for sea urchin embryonic cells. Typical necrotic cells with damaged mitochondria were not detected after freezing in sea urchin cell cultures. Our results assume that physical cell disruption but not freezing-induced apoptosis or necrosis is the predominant reason of cell death in sea urchin cultures after freezing-thawing with any cryoprotectant combination. Copyright © 2016 Elsevier Inc. All rights reserved.

Cloning, Characterization, and Expression Levels of the Nectin Gene from the Tube Feet of the Sea Urchin Paracentrotus Lividus.

PubMed

Toubarro, Duarte; Gouveia, Analuce; Ribeiro, Raquel Mesquita; Simões, Nélson; da Costa, Gonçalo; Cordeiro, Carlos; Santos, Romana

2016-06-01

Marine bioadhesives perform in ways that manmade products simply cannot match, especially in wet environments. Despite their technological potential, bioadhesive molecular mechanisms are still largely understudied, and sea urchin adhesion is no exception. These animals inhabit wave-swept shores, relying on specialized adhesive organs, tube feet, composed by an adhesive disc and a motile stem. The disc encloses a duo-gland adhesive system, producing adhesive and deadhesive secretions for strong reversible substratum attachment. The disclosure of sea urchin Paracentrotus lividus tube foot disc proteome led to the identification of a secreted adhesion protein, Nectin, never before reported in adult adhesive organs but, that given its adhesive function in eggs/embryos, was pointed out as a putative substratum adhesive protein in adults. To further understand Nectin involvement in sea urchin adhesion, Nectin cDNA was amplified for the first time from P. lividus adhesive organs, showing that not only the known Nectin mRNA, called Nectin-1 (GenBank AJ578435), is expressed in the adults tube feet but also a new mRNA sequence, called Nectin-2 (GenBank KT351732), differing in 15 missense nucleotide substitutions. Nectin genomic DNA was also obtained for the first time, indicating that both Nectin-1 and Nectin-2 derive from a single gene. In addition, expression analysis showed that both Nectins are overexpressed in tube feet discs, its expression being significantly higher in tube feet discs from sea urchins just after collection from the field relative to sea urchin from aquarium. These data further advocate for Nectin involvement in sea urchin reversible adhesion, suggesting that its expression might be regulated according to the hydrodynamic conditions.

Bioerosion caused by the sea urchin Diadema Mexicanum (Echinodermata: Echinoidea) at Bahías de Huatulco, Western Mexico.

PubMed

Herrera-Escalante, T; López-Pérez, R A; Leyte-Morales, G E

2005-12-01

Mexican Pacific sea urchin studies have been focused mainly on species distribution, ecology and fisheries. Reef degradation by sea urchin bioerosion has not been studied previously en these reefs. We investigate the importance of Diadema mexicanum as a bioerosive agent of coral carbonate at Bahias de Huatulco, and the relative magnitude of coral accretion and bioerosion. At each of five localities in Bahias de Huatulco, sea urchin density, feeding and mechanical (spine) erosion was determined for three size class intervals. In general, D. mexicanum do not exert any significant role on coral reef community structure (live coral, dead coral or algal coverage) at the Huatulco area, probably because they are generally small (2.9-4 cm test size) and few in number (1.0-6.8 ind.m-2). Mean bioerosion rates are consistent with those measured for other diadematoids, as well as other urchin species in various eastern Pacific localities. However, the degree of bioerosive impact depends on species, test size, and population density of urchins. Coral carbonate removal by D. mexicanum erosion varies from 0.17 to 3.28 kgCaCO3m(-2)yr(-1). This represents a carbonate loss of < 5% of the annual coral carbonate production at Jicaral Chachacual, San Agustín and Isla Cacaluta, but 16 and 27% at Isla Montosa and La Entrega. On balance, coral accretion exceeds sea urchin erosion at all sites examined at Huatulco. At Bahias de Huatulco coral reef communities are actively growing, though in the coming years, it might be necessary to investigate the local effects of the interaction among erosion, and environmental and human induced perturbations.

An advanced method of contributing emissions to short-lived chemical species (OH and HO2): the TAGGING 1.1 submodel based on the Modular Earth Submodel System (MESSy 2.53)

NASA Astrophysics Data System (ADS)

Rieger, Vanessa S.; Mertens, Mariano; Grewe, Volker

2018-06-01

To mitigate the human impact on climate change, it is essential to determine the contribution of emissions to the concentration of trace gases. In particular, the source attribution of short-lived species such as OH and HO2 is important as they play a crucial role for atmospheric chemistry. This study presents an advanced version of a tagging method for OH and HO2 (HOx) which attributes HOx concentrations to emissions. While the former version (V1.0) only considered 12 reactions in the troposphere, the new version (V1.1), presented here, takes 19 reactions in the troposphere into account. For the first time, the main chemical reactions for the HOx chemistry in the stratosphere are also regarded (in total 27 reactions). To fully take into account the main HO2 source by the reaction of H and O2, the tagging of the H radical is introduced. In order to ensure the steady-state assumption, we introduce rest terms which balance the deviation of HOx production and loss. This closes the budget between the sum of all contributions and the total concentration. The contributions to OH and HO2 obtained by the advanced tagging method V1.1 deviate from V1.0 in certain source categories. For OH, major changes are found in the categories biomass burning, biogenic emissions and methane decomposition. For HO2, the contributions differ strongly in the categories biogenic emissions and methane decomposition. As HOx reacts with ozone (O3), carbon monoxide (CO), reactive nitrogen compounds (NOy), non-methane hydrocarbons (NMHCs) and peroxyacyl nitrates (PAN), the contributions to these species are also modified by the advanced HOx tagging method V1.1. The contributions to NOy, NMHC and PAN show only little change, whereas O3 from biogenic emissions and methane decomposition increases in the tropical troposphere. Variations for CO from biogenic emissions and biomass burning are only found in the Southern Hemisphere.

Direct EPP Affects on the Middle Atmosphere

NASA Technical Reports Server (NTRS)

Jackman, Charles H.

2011-01-01

Energetic precipitating particles (EPPs) can cause significant direct constituent changes in the mesosphere and stratosphere (middle atmosphere) during certain periods. Both protons and electrons can influence the polar middle atmosphere through ionization and dissociation processes. EPPs can enhance HOx (H, OH, HO2) through the formation of positive ions followed by complex ion chemistry and NOx (N, NO, NO2) through the dissociation of molecular nitrogen. The HOx increases result in direct ozone destruction in the mesosphere and upper stratosphere via several catalytic loss cycles. Such middle atmospheric HOx-caused ozone loss is rather short-lived due to the relatively short lifetime (hours) of the HOx constituents. The NOx family has a considerably longer lifetime than the HOx family and can also lead to catalytic ozone destruction. EPP-caused enhancements of the NOx family can affect ozone directly, if produced in the stratosphere. Ozone decreases from the EPPs lead to a reduction in atmospheric heating and, subsequent atmospheric cooling. Conversely, EPPs can cause direct atmospheric heating through Joule heating. Measured HOx constituents OH and HO2 showed increases due to solar protons. Observed NOx constituents NO and NO2 were enhanced due to both solar protons and precipitating electrons. Other hydrogen- and nitrogen-ocntaining constituents were also measured to be directly influenced by EPPs, including N2O, HNO3, HO2NO2, N2OS, H2O2, ClONO2, HCl, and HOCl. Observed constituents ClO and CO were directly affected by EPPs as well. Many measurements indicated significant direct ozone decreases. A significant number of satellites housed instruments, which observed direct EPP-caused atmospheric effects, including Nimbus 4 (BUV), Nimbus 7 (SBUV), several NOAA platforms (SBUV/2), SME, UARS (HALOE, CLAES), SCISAT-1 (ACE-FTS), Odin (OSIRIS), Envisat-l (GOMOS, MIPAS, SCIAMACHY), and Aura (MLS). Measurements by rockets and ground-based radar also indicated EPP direct impacts. Atmospheric models have been used with some success in predicting the direct EPP impacts on the mesosphere and stratosphere. A review of the observed direct effects of EPP on the middle atmosphere will be given in this presentation.

Parental exposure to heavy fuel oil induces developmental toxicity in offspring of the sea urchin Strongylocentrotus intermedius.

PubMed

Duan, Meina; Xiong, Deqi; Yang, Mengye; Xiong, Yijun; Ding, Guanghui

2018-05-03

The present study investigated the toxic effects of parental (maternal/paternal) exposure to heavy fuel oil (HFO) on the adult reproductive state, gamete quality and development of the offspring of the sea urchin Strongylocentrotus intermedius. Adult sea urchins were exposed to effluents from HFO-oiled gravel columns for 7 days to simulate an oil-contaminated gravel shore, and then gametes of adult sea urchins were used to produce embryos to determine developmental toxicity. For adult sea urchins, no significant difference in the somatic size and weight was found between the various oil loadings tested, while the gonad weight and gonad index were significantly decreased at higher oil loadings. The spawning ability of adults and fecundity of females significantly decreased. For gametes, no effect was observed on the egg size and fertilization success in any of the groups. However, a significant increase in the percentage of anomalies in the offspring was observed and then quantified by an integrative toxicity index (ITI) at 24 and 48 h post fertilization. The offspring from exposed parents showed higher ITI values with more malformed embryos. The results confirmed that parental exposure to HFO can cause adverse effects on the offspring and consequently affect the recruitment and population maintenance of sea urchins. Copyright © 2018 Elsevier Inc. All rights reserved.

The impact of rising sea temperature on innate immune parameters in the tropical subtidal sea urchin Lytechinus variegatus and the intertidal sea urchin Echinometra lucunter.

PubMed

Branco, Paola Cristina; Borges, João Carlos Shimada; Santos, Marinilce Fagundes; Jensch Junior, Bernard Ernesto; da Silva, José Roberto Machado Cunha

2013-12-01

Ocean temperatures are rising throughout the world, making it necessary to evaluate the impact of these temperature changes on sea urchins, which are well-known bioindicators. This study evaluated the effect of an increase in temperature on the immune response of the subtidal Lytechinus variegatus and the intertidal Echinometra lucunter sea urchins. Both species were exposed to 20 (control), 25 and 30 °C temperatures for 24 h, 2, 7 and 14 days. Counting of coelomocytes and assays on the phagocytic response, adhesion and spreading of coelomocytes were performed. Red and colorless sphere cells were considered biomarkers for heat stress. Moreover, a significant decrease in the phagocytic indices and a decrease in both cell adhesion and cell spreading were observed at 25 and 30 °C for L. variegatus. For E. lucunter, the only alteration observed was for the cell proportions. This report shows how different species of sea urchins respond immunologically to rising temperatures. Copyright © 2013 Elsevier Ltd. All rights reserved.

Characterization of the lipid fraction of wild sea urchin from the Sardinian Sea (western Mediterranean).

PubMed

Angioni, Alberto; Addis, Pierantonio

2014-02-01

The fatty acid (FA) composition of Spatangus purpureus, Echinus melo, Sphaerechinus granularis, and Paracentrotus lividus, sea urchins, has been studied. Sea urchins were collected at different depth along Sardinia coast in the Mediterranean sea, and their gonad was measured, separated, and analyzed for FA composition by gas chromatography-mass spectrometry. A total of 53 FAs were detected, 16 saturated (SFA), 10 monounsaturated (MUFA), 9 polyunsaturated (PUFA), and 13 highly unsaturated (HUFA). Moreover, 5 furan FAs (FFAs) were revealed for the first time in sea urchin. The HUFA and PUFA classes were the most represented accounting for almost 80% of total FAs. Among these compounds, C20:4 n6 (19.64, 20.52, 23.37, and 8.48 mg/g, respectively) and C22:6 n3 (19.68, 20.05, 3.83, and 1.78 mg/g, respectively) were the most abundant. The results of principal component analysis indicated that the sea urchin samples could be clearly discriminated with respect to their FAs composition. © 2014 Institute of Food Technologists®

Probing safety of nanoparticles by outlining sea urchin sensing and signaling cascades.

PubMed

Alijagic, Andi; Pinsino, Annalisa

2017-10-01

Among currently identified issues presenting risks and benefits to human and ocean health, engineered nanoparticles (ENP) represent a priority. Predictions of their economic and social impact appear extraordinary, but their release in the environment at an uncontrollable rate is in striking contrast with the extremely limited number of studies on environmental impact, especially on the marine environment. The sea urchin has a remarkable sensing environmental system whose function and diversity came into focus during the recent years, after sea urchin genome sequencing. The complex immune system may be the basis wherefore sea urchins can adapt to a dynamic environment and survive even in hazardous conditions both in the adult and in the embryonic life. This review is aimed at discussing the literature in nanotoxicological/ecotoxicological studies with a focus on stress and innate immune signaling in sea urchins. In addition, here we introduce our current development of in vitro-driven probes that could be used to dissect ENP aftermaths, suggesting their future use in immune-nanotoxicology. Copyright © 2017 Elsevier Inc. All rights reserved.

Predator-induced macroevolutionary trends in Mesozoic crinoids

PubMed Central

Gorzelak, Przemysław; Salamon, Mariusz A.; Baumiller, Tomasz K.

2012-01-01

Sea urchins are a major component of recent marine communities where they exert a key role as grazers and benthic predators. However, their impact on past marine organisms, such as crinoids, is hard to infer in the fossil record. Analysis of bite mark frequencies on crinoid columnals and comprehensive genus-level diversity data provide unique insights into the importance of sea urchin predation through geologic time. These data show that over the Mesozoic, predation intensity on crinoids, as measured by bite mark frequencies on columnals, changed in step with diversity of sea urchins. Moreover, Mesozoic diversity changes in the predatory sea urchins show a positive correlation with diversity of motile crinoids and a negative correlation with diversity of sessile crinoids, consistent with a crinoid motility representing an effective escape strategy. We contend that the Mesozoic diversity history of crinoids likely represents a macroevolutionary response to changes in sea urchin predation pressure and that it may have set the stage for the recent pattern of crinoid diversity in which motile forms greatly predominate and sessile forms are restricted to deep-water refugia. PMID:22509040

Multiple Intrinsically Disordered Sequences Alter DNA Binding by the Homeodomain of the Drosophila Hox Protein Ultrabithorax*S⃞

PubMed Central

Liu, Ying; Matthews, Kathleen S.; Bondos, Sarah E.

2008-01-01

During animal development, distinct tissues, organs, and appendages are specified through differential gene transcription by Hox transcription factors. However, the conserved Hox homeodomains bind DNA with high affinity yet low specificity. We have therefore explored the structure of the Drosophila melanogaster Hox protein Ultrabithorax and the impact of its nonhomeodomain regions on DNA binding properties. Computational and experimental approaches identified several conserved, intrinsically disordered regions outside the homeodomain of Ultrabithorax that impact DNA binding by the homeodomain. Full-length Ultrabithorax bound to target DNA 2.5-fold weaker than its isolated homeodomain. Using N-terminal and C-terminal deletion mutants, we demonstrate that the YPWM region and the disordered microexons (termed the I1 region) inhibit DNA binding ∼2-fold, whereas the disordered I2 region inhibits homeodomain-DNA interaction a further ∼40-fold. Binding is restored almost to homeodomain affinity by the mostly disordered N-terminal 174 amino acids (R region) in a length-dependent manner. Both the I2 and R regions contain portions of the activation domain, functionally linking DNA binding and transcription regulation. Given that (i) the I1 region and a portion of the R region alter homeodomain-DNA binding as a function of pH and (ii) an internal deletion within I1 increases Ultrabithorax-DNA affinity, I1 must directly impact homeodomain-DNA interaction energetics. However, I2 appears to indirectly affect DNA binding in a manner countered by the N terminus. The amino acid sequences of I2 and much of the I1 and R regions vary significantly among Ultrabithorax orthologues, potentially diversifying Hox-DNA interactions. PMID:18508761

Regulatory interactions between the human HOXB1, HOXB2, and HOXB3 proteins and the upstream sequence of the Otx2 gene in embryonal carcinoma cells.

PubMed

Guazzi, S; Pintonello, M L; Viganò, A; Boncinelli, E

1998-05-01

Vertebrate Hox and Otx genes encode homeodomain-containing transcription factors thought to transduce positional information along the body axis in the segmental portion of the trunk and in the rostral brain, respectively. Moreover, Hox and Otx2 genes show a complementary spatial regulation during embryogenesis. In this report, we show that a 1821-base pair (bp) upstream DNA fragment of the Otx2 gene is positively regulated by co-transfection with expression vectors for the human HOXB1, HOXB2, and HOXB3 proteins in an embryonal carcinoma cell line (NT2/D1) and that a shorter fragment of only 534 bp is able to drive this regulation. We also identified the HOXB1, HOXB2, and HOXB3 DNA-binding region on the 534-bp Otx2 genomic fragment using nuclear extracts from Hox-transfected COS cells and 12.5 days postcoitum mouse embryos or HOXB3 homeodomain-containing bacterial extracts. HOXB1, HOXB3, and nuclear extracts from 12.5 days postcoitum mouse embryos bind to a sequence containing two palindromic TAATTA sites, which bear four copies of the ATTA core sequence, a common feature of most HOM-C/HOX binding sites. HOXB2 protected an adjacent site containing a direct repeat of an ACTT sequence, quite divergent from the ATTA consensus. The region bound by the three homeoproteins is strikingly conserved through evolution and necessary (at least for HOXB1 and HOXB3) to mediate the up-regulation of the Otx2 transcription. Taken together, our data support the hypothesis that anteriorly expressed Hox genes might play a role in the refinement of the Otx2 early expression boundaries in vivo.

The [NiFe]-hydrogenase of the cyanobacterium Synechocystis sp. PCC 6803 works bidirectionally with a bias to H2 production.

PubMed

McIntosh, Chelsea L; Germer, Frauke; Schulz, Rüdiger; Appel, Jens; Jones, Anne K

2011-07-27

Protein film electrochemistry (PFE) was utilized to characterize the catalytic activity and oxidative inactivation of a bidirectional [NiFe]-hydrogenase (HoxEFUYH) from the cyanobacterium Synechocystis sp. PCC 6803. PFE provides precise control of the redox potential of the adsorbed enzyme so that its activity can be monitored under changing experimental conditions as current. The properties of HoxEFUYH are different from those of both the standard uptake and the "oxygen-tolerant" [NiFe]-hydrogenases. First, HoxEFUYH is biased toward proton reduction as opposed to hydrogen oxidation. Second, despite being expressed under aerobic conditions in vivo, HoxEFUYH is clearly not oxygen-tolerant. Aerobic inactivation of catalytic hydrogen oxidation by HoxEFUYH is total and nearly instantaneous, producing two inactive states. However, unlike the Ni-A and Ni-B inactive states of standard [NiFe]-hydrogenases, both of these states are quickly (<90 s) reactivated by removal of oxygen and exposure to reducing conditions. Third, proton reduction continues at 25-50% of the maximal rate in the presence of 1% oxygen. Whereas most previously characterized [NiFe]-hydrogenases seem to be preferential hydrogen oxidizing catalysts, the cyanobacterial enzyme works effectively in both directions. This unusual catalytic bias as well as the ability to be quickly reactivated may be essential to fulfilling the physiological role in cyanobacteria, organisms expected to experience swings in cellular reduction potential as they switch between aerobic conditions in the light and dark anaerobic conditions. Our results suggest that the uptake [NiFe]-hydrogenases alone are not representative of the catalytic diversity of [NiFe]-hydrogenases, and the bidirectional heteromultimeric enzymes may serve as valuable models to understand the diverse mechanisms of tuning the reactivity of the hydrogen activating site.

Resuscitation of Preterm Neonates With Limited Versus High Oxygen Strategy

PubMed Central

Kapadia, Vishal S.; Chalak, Lina F.; Sparks, John E.; Allen, James R.; Savani, Rashmin C.

2013-01-01

OBJECTIVE: To determine whether a limited oxygen strategy (LOX) versus a high oxygen strategy (HOX) during delivery room resuscitation decreases oxidative stress in preterm neonates. METHODS: A randomized trial of neonates of 24 to 34 weeks’ gestational age (GA) who received resuscitation was performed. LOX neonates received room air as the initial resuscitation gas, and fraction of inspired oxygen (Fio2) was adjusted by 10% every 30 seconds to achieve target preductal oxygen saturations (Spo2) as described by the 2010 Neonatal Resuscitation Program guidelines. HOX neonates received 100% O2 as initial resuscitation gas, and Fio2 was adjusted by 10% to keep preductal Spo2 at 85% to 94%. Total hydroperoxide (TH), biological antioxidant potential (BAP), and the oxidative balance ratio (BAP/TH) were analyzed in cord blood and the first hour of life. Secondary outcomes included delivery room interventions, respiratory support on NICU admission, and short-term morbidities. RESULTS: Forty-four LOX (GA: 30 ± 3 weeks; birth weight: 1678 ± 634 g) and 44 HOX (GA: 30 ± 3 weeks; birth weight: 1463 ± 606 g) neonates were included. LOX decreased integrated excess oxygen (∑Fio2 × time [min]) in the delivery room compared with HOX (401 ± 151 vs 662 ± 249; P < .01). At 1 hour of life, BAP/TH was 60% higher for LOX versus HOX neonates (13 [9–16] vs 8 [6–9]) µM/U.CARR, P < .01). LOX decreased ventilator days (3 [0–64] vs 8 [0–96]; P < .05) and reduced the incidence of bronchopulmonary dysplasia (7% vs 25%; P < .05). CONCLUSIONS: LOX is feasible and results in less oxygen exposure, lower oxidative stress, and decreased respiratory morbidities and thus is a reasonable alternative for resuscitation of preterm neonates in the delivery room. PMID:24218465

Sea urchin skeleton: Structure, composition, and application as a template for biomimetic materials

NASA Astrophysics Data System (ADS)

Shapkin, Nikolay P.; Khalchenko, Irina G.; Panasenko, Alexander E.; Drozdov, Anatoly L.

2017-07-01

SEM and optical microscopy, chemical and EDX analysis, XRD, and FT-IR spectroscopy of three sea urchins skeletons (tests) show that the test is a spongy stereom, consisting of calcite with high content of magnesium. The tests are composed of mineral-organic composite of calcite-magnesite crystals, coated with organic film, containing silicon in form of polyphenylsiloxane. In the test of sea urchin pore spaces are linked into united system of regular structure with structure motive period about 20 um. This developed three-dimensional structure was used as a template for polymer material based on polyferrofenilsiloxane [OSiC6H5OH]x[OSiC6H5O]y[OFeO]z, which is chemically similar to the native film, coating sea urchins skeleton.

MicroRaman, PXRD, EDS and microscopic investigation of magnesium calcite biomineral phases. The case of sea urchin biominerals

NASA Astrophysics Data System (ADS)

Borzęcka-Prokop, B.; Wesełucha-Birczyńska, A.; Koszowska, E.

2007-02-01

This study concerns Mg-calcite characterization (and in particular molecular structure and microstructural studies of mineral phases) of a sea urchin mineralised test and spines. Sea urchins are spiny sea animals (kingdom Animalia, phylum Echinodermata, class Echinoidea). Microscopic observations, SEM, EDS, PXRD and spectroscopic microRaman methods have been applied to characterize the biomineral parts of the sea urchin. The latter technique is very useful in research of biological systems and especially suitable for monitoring differences within biomineral phases exhibiting varieties of morphological forms. Crystalline magnesium calcium carbonate, Mg xCa 1- xCO 3 (magnesian calcite; space group R-3 cH; a = 4.9594(8) Å, c = 16.886(6) Å), has been identified as the predominant biomineral component.

Two ultrastructurally distinct tubulin paracrystals induced in sea-urchin eggs by vinblastine sulphate.

PubMed

Starling, D

1976-01-01

Two types of ultrastructurally distinct tubulin paracrystals have been induced in sea-urchin eggs with vinblastine sulphate (VLB) under different sets of conditions. One type of paracrystal appears to consist of hexagonally-close packed microtubules and closely resembles paracrystals present in mammalian cells treated with vinblastine or vincristine sulphate, but not previously reported in sea-urchin eggs. The other type is also made up of tubulin subunits, but these do not seem to have polymerized into microtubules. Both types of paracrystal are induced in sea-urchin eggs in the presence of VLB at a time when tubulin subunits would not normally polymerize. Possible mechanisms for tubulin activation and the induction of paracrystal formation are discussed in respect to the available information on the binding sites of the tubulin subunits.

Targeted mutagenesis in sea urchin embryos using TALENs.

PubMed

Hosoi, Sayaka; Sakuma, Tetsushi; Sakamoto, Naoaki; Yamamoto, Takashi

2014-01-01

Genome editing with engineered nucleases such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) has been reported in various animals. We previously described ZFN-mediated targeted mutagenesis and insertion of reporter genes in sea urchin embryos. In this study, we demonstrate that TALENs can induce mutagenesis at specific genomic loci of sea urchin embryos. Injection of TALEN mRNAs targeting the HpEts transcription factor into fertilized eggs resulted in the impairment of skeletogenesis. Sequence analyses of the mutations showed that deletions and/or insertions occurred at the HpEts target site in the TALEN mRNAs-injected embryos. The results suggest that targeted gene disruption using TALENs is feasible in sea urchin embryos. © 2013 The Authors Development, Growth & Differentiation © 2013 Japanese Society of Developmental Biologists.

Chromatin-bound IκBα regulates a subset of polycomb target genes in differentiation and cancer.

PubMed

Mulero, María Carmen; Ferres-Marco, Dolors; Islam, Abul; Margalef, Pol; Pecoraro, Matteo; Toll, Agustí; Drechsel, Nils; Charneco, Cristina; Davis, Shelly; Bellora, Nicolás; Gallardo, Fernando; López-Arribillaga, Erika; Asensio-Juan, Elena; Rodilla, Verónica; González, Jessica; Iglesias, Mar; Shih, Vincent; Mar Albà, M; Di Croce, Luciano; Hoffmann, Alexander; Miyamoto, Shigeki; Villà-Freixa, Jordi; López-Bigas, Nuria; Keyes, William M; Domínguez, María; Bigas, Anna; Espinosa, Lluís

2013-08-12

IκB proteins are the primary inhibitors of NF-κB. Here, we demonstrate that sumoylated and phosphorylated IκBα accumulates in the nucleus of keratinocytes and interacts with histones H2A and H4 at the regulatory region of HOX and IRX genes. Chromatin-bound IκBα modulates Polycomb recruitment and imparts their competence to be activated by TNFα. Mutations in the Drosophila IκBα gene cactus enhance the homeotic phenotype of Polycomb mutants, which is not counteracted by mutations in dorsal/NF-κB. Oncogenic transformation of keratinocytes results in cytoplasmic IκBα translocation associated with a massive activation of Hox. Accumulation of cytoplasmic IκBα was found in squamous cell carcinoma (SCC) associated with IKK activation and HOX upregulation. Copyright © 2013 Elsevier Inc. All rights reserved.

The Early ANTP Gene Repertoire: Insights from the Placozoan Genome

PubMed Central

Schierwater, Bernd; Kamm, Kai; Srivastava, Mansi; Rokhsar, Daniel; Rosengarten, Rafael D.; Dellaporta, Stephen L.

2008-01-01

The evolution of ANTP genes in the Metazoa has been the subject of conflicting hypotheses derived from full or partial gene sequences and genomic organization in higher animals. Whole genome sequences have recently filled in some crucial gaps for the basal metazoan phyla Cnidaria and Porifera. Here we analyze the complete genome of Trichoplax adhaerens, representing the basal metazoan phylum Placozoa, for its set of ANTP class genes. The Trichoplax genome encodes representatives of Hox/ParaHox-like, NKL, and extended Hox genes. This repertoire possibly mirrors the condition of a hypothetical cnidarian-bilaterian ancestor. The evolution of the cnidarian and bilaterian ANTP gene repertoires can be deduced by a limited number of cis-duplications of NKL and “extended Hox” genes and the presence of a single ancestral “ProtoHox” gene. PMID:18716659

Weighing the Evidence of Ecological Risk From Chemical Contamination in the Estuarine Environment Adjacent to the Portsmouth Naval Shipyard, Kittery, Maine, USA

DTIC Science & Technology

2001-05-30

for mussel growth and sea urchin toxicity were medium, we seasonal variations of AVS- SEM in sediments and the degree concluded medium weight of...and phaeopigments), toxicity to fertilization of sea iment (Table 3). Conversely, the measures used for the pelagic urchin (Arbacia punctulata...account for temporal and spatial variability. fidence level (C) for each assessment endpoint were assigned For toxicity to sea urchins , data quality

The California Central Coast Research Partnership: Building Relationships, Partnerships, and Paradigms for University-Industry Research Collaboration

DTIC Science & Technology

2010-03-08

on the Cell Cycle and Development of Sea Urchins NATIONAL SCIENCE FOUNDATION (RUI) Lab Technician TBD Adams, Nikki 04-144 08/01/04-07/31/09...376,678 Mass spectroscopy analysis of effects of ultraviolet radiation on the proteome of sea urchin embryos CSUPERB: CSU FACULTY-STUDENT COLLABORATIVE...Development of Sea Urchins NATIONAL SCIENCE FOUNDATION (REU) 07-250 06/01/07-07/31/08 $6,000 CHRISTOPHER CLARK Clark, Christopher Moline, Mark Personnel

Amorphous calcium carbonate transforms into calcite during sea urchin larval spicule growth

PubMed Central

Beniash, E.; Aizenberg, J.; Addadi, L.; Weiner, S.

1997-01-01

Sea urchin larvae form an endoskeleton composed of a pair of spicules. For more than a century it has been stated that each spicule comprises a single crystal of the CaCO3 mineral, calcite. We show that an additional mineral phase, amorphous calcium carbonate, is present in the sea urchin larval spicule, and that this inherently unstable mineral transforms into calcite with time. This observation significantly changes our concepts of mineral formation in this well-studied organism.

The Homeobox BcHOX8 Gene in Botrytis Cinerea Regulates Vegetative Growth and Morphology

PubMed Central

Antal, Zsuzsanna; Rascle, Christine; Cimerman, Agnès; Viaud, Muriel; Billon-Grand, Geneviève; Choquer, Mathias; Bruel, Christophe

2012-01-01

Filamentous growth and the capacity at producing conidia are two critical aspects of most fungal life cycles, including that of many plant or animal pathogens. Here, we report on the identification of a homeobox transcription factor encoding gene that plays a role in these two particular aspects of the development of the phytopathogenic fungus Botrytis cinerea. Deletion of the BcHOX8 gene in both the B. cinerea B05-10 and T4 strains causes similar phenotypes, among which a curved, arabesque-like, hyphal growth on hydrophobic surfaces; the mutants were hence named Arabesque. Expression of the BcHOX8 gene is higher in conidia and infection cushions than in developing appressorium or mycelium. In the Arabesque mutants, colony growth rate is reduced and abnormal infection cushions are produced. Asexual reproduction is also affected with abnormal conidiophore being formed, strongly reduced conidia production and dramatic changes in conidial morphology. Finally, the mutation affects the fungus ability to efficiently colonize different host plants. Analysis of the B. cinerea genome shows that BcHOX8 is one member of a nine putative homeobox genes family. Available gene expression data suggest that these genes are functional and sequence comparisons indicate that two of them would be specific to B. cinerea and its close relative Sclerotinia sclerotiorum. PMID:23133556

A unique stylopod patterning mechanism by Shox2-controlled osteogenesis

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

Ye, Wenduo; Song, Yingnan; Huang, Zhen

Here, vertebrate appendage patterning is programmed by Hox-TALE factorbound regulatory elements. However, it remains unclear which cell lineages are commissioned by Hox-TALE factors to generate regional specific patterns and whether other Hox-TALE co-factors exist. In this study, we investigated the transcriptional mechanisms controlled by the Shox2 transcriptional regulator in limb patterning. Harnessing an osteogenic lineage-specific Shox2 inactivation approach we show that despite widespread Shox2 expression in multiple cell lineages, lack of the stylopod observed upon Shox2 deficiency is a specific result of Shox2 loss of function in the osteogenic lineage. ChIP-Seq revealed robust interaction of Shox2 with cis-regulatory enhancers clusteringmore » around skeletogenic genes that are also bound by Hox-TALE factors, supporting a lineage autonomous function of Shox2 in osteogenic lineage fate determination and skeleton patterning. Pbx ChIP-Seq further allowed the genome-wide identification of cis-regulatory modules exhibiting co-occupancy of Pbx, Meis and Shox2 transcriptional regulators. Integrative analysis of ChIP-Seq and RNA-Seq data and transgenic enhancer assays indicate that Shox2 patterns the stylopod as a repressor via interaction with enhancers active in the proximal limb mesenchyme and antagonizes the repressive function of TALE factors in osteogenesis.« less

Distinct subsets of Eve-positive pericardial cells stabilise cardiac outflow and contribute to Hox gene-triggered heart morphogenesis in Drosophila.

PubMed

Zmojdzian, Monika; de Joussineau, Svetlana; Da Ponte, Jean Philippe; Jagla, Krzysztof

2018-01-17

The Drosophila heart, composed of discrete subsets of cardioblasts and pericardial cells, undergoes Hox-triggered anterior-posterior morphogenesis, leading to a functional subdivision into heart proper and aorta, with its most anterior part forming a funnel-shaped cardiac outflow. Cardioblasts differentiate into Tin-positive 'working myocytes' and Svp-expressing ostial cells. However, developmental fates and functions of heart-associated pericardial cells remain elusive. Here, we show that the pericardial cells that express the transcription factor Even Skipped adopt distinct fates along the anterior-posterior axis. Among them, the most anterior Antp-Ubx-AbdA - negative cells form a novel cardiac outflow component we call the outflow hanging structure, whereas the Antp-expressing cells differentiate into wing heart precursors. Interestingly, Hox gene expression in the Even Skipped-positive cells not only underlies their antero-posterior diversification, but also influences heart morphogenesis in a non-cell-autonomous way. In brief, we identify a new cardiac outflow component derived from a subset of Even Skipped-expressing cells that stabilises the anterior heart tip, and demonstrate non-cell-autonomous effects of Hox gene expression in the Even Skipped-positive cells on heart morphogenesis. © 2018. Published by The Company of Biologists Ltd.

Zebrafish Meis functions to stabilize Pbx proteins and regulate hindbrain patterning.

PubMed

Waskiewicz, A J; Rikhof, H A; Hernandez, R E; Moens, C B

2001-11-01

Homeodomain-containing Hox proteins regulate segmental identity in Drosophila in concert with two partners known as Extradenticle (Exd) and Homothorax (Hth). These partners are themselves DNA-binding, homeodomain proteins, and probably function by revealing the intrinsic specificity of Hox proteins. Vertebrate orthologs of Exd and Hth, known as Pbx and Meis (named for a myeloid ecotropic leukemia virus integration site), respectively, are encoded by multigene families and are present in multimeric complexes together with vertebrate Hox proteins. Previous results have demonstrated that the zygotically encoded Pbx4/Lazarus (Lzr) protein is required for segmentation of the zebrafish hindbrain and proper expression and function of Hox genes. We demonstrate that Meis functions in the same pathway as Pbx in zebrafish hindbrain development, as expression of a dominant-negative mutant Meis results in phenotypes that are remarkably similar to that of lzr mutants. Surprisingly, expression of Meis protein partially rescues the lzr(-) phenotype. Lzr protein levels are increased in embryos overexpressing Meis and are reduced for lzr mutants that cannot bind to Meis. This implies a mechanism whereby Meis rescues lzr mutants by stabilizing maternally encoded Lzr. Our results define two functions of Meis during zebrafish hindbrain segmentation: that of a DNA-binding partner of Pbx proteins, and that of a post-transcriptional regulator of Pbx protein levels.

The Influence of the Several Very Large Solar Proton Events in Years 2000-2003 on the Neutral Middle Atmosphere

NASA Technical Reports Server (NTRS)

Jackman, Charles H.; Deland, Matthew T.; Labow, Gordon J.; Fleming, Eric L.; Weisenstein, Debra K.; Ko, Malcolm K. W.; Sinnhuber, Miriam; Anderson, John; Russell, James M.

2004-01-01

Solar proton events (SPEs) are known to have caused changes in constituents in the Earth's polar neutral middle atmosphere. The past four years, 2000-2003, have been replete with SPEs and huge fluxes of high energy protons occurred in July and November 2000, September and November 2001, and October 2003. The highly energetic protons produce ionizations, excitations, dissociations, and dissociative ionizations of the background constituents, which lead to the production of HOx (H, OH, HO2) and NOy (N, NO, NO2, NO3, N2O5, HNO3, HO2NO2, ClONO2, BrONO2). The HOx increases lead to short-lived ozone decreases in the polar mesosphere and upper stratosphere due to the short lifetimes of the HOx constituents. Large mesospheric ozone depletions (>70%) due to the HOx enhancements were observed and modeled as a result of the very large July 2000 SPE. The NOy increases lead to long-lived stratospheric ozone changes because of the long lifetime of the NOy family in this region. Polar total ozone depletions >1% were simulated in both hemispheres for extended periods of time (several months) as a result of the NOy enhancements due to the very large SPEs.

A unique stylopod patterning mechanism by Shox2-controlled osteogenesis

DOE PAGES

Ye, Wenduo; Song, Yingnan; Huang, Zhen; ...

2016-06-10

Here, vertebrate appendage patterning is programmed by Hox-TALE factorbound regulatory elements. However, it remains unclear which cell lineages are commissioned by Hox-TALE factors to generate regional specific patterns and whether other Hox-TALE co-factors exist. In this study, we investigated the transcriptional mechanisms controlled by the Shox2 transcriptional regulator in limb patterning. Harnessing an osteogenic lineage-specific Shox2 inactivation approach we show that despite widespread Shox2 expression in multiple cell lineages, lack of the stylopod observed upon Shox2 deficiency is a specific result of Shox2 loss of function in the osteogenic lineage. ChIP-Seq revealed robust interaction of Shox2 with cis-regulatory enhancers clusteringmore » around skeletogenic genes that are also bound by Hox-TALE factors, supporting a lineage autonomous function of Shox2 in osteogenic lineage fate determination and skeleton patterning. Pbx ChIP-Seq further allowed the genome-wide identification of cis-regulatory modules exhibiting co-occupancy of Pbx, Meis and Shox2 transcriptional regulators. Integrative analysis of ChIP-Seq and RNA-Seq data and transgenic enhancer assays indicate that Shox2 patterns the stylopod as a repressor via interaction with enhancers active in the proximal limb mesenchyme and antagonizes the repressive function of TALE factors in osteogenesis.« less

Changing Hydrozoan Bauplans by Silencing Hox-Like Genes

PubMed Central

Jakob, Wolfgang; Schierwater, Bernd

2007-01-01

Regulatory genes of the Antp class have been a major factor for the invention and radiation of animal bauplans. One of the most diverse animal phyla are the Cnidaria, which are close to the root of metazoan life and which often appear in two distinct generations and a remarkable variety of body forms. Hox-like genes have been known to be involved in axial patterning in the Cnidaria and have been suspected to play roles in the genetic control of many of the observed bauplan changes. Unfortunately RNAi mediated gene silencing studies have not been satisfactory for marine invertebrate organisms thus far. No direct evidence supporting Hox-like gene induced bauplan changes in cnidarians have been documented as of yet. Herein, we report a protocol for RNAi transfection of marine invertebrates and demonstrate that knock downs of Hox-like genes in Cnidaria create substantial bauplan alterations, including the formation of multiple oral poles (“heads”) by Cnox-2 and Cnox-3 inhibition, deformation of the main body axis by Cnox-5 inhibition and duplication of tentacles by Cnox-1 inhibition. All phenotypes observed in the course of the RNAi studies were identical to those obtained by morpholino antisense oligo experiments and are reminiscent of macroevolutionary bauplan changes. The reported protocol will allow routine RNAi studies in marine invertebrates to be established. PMID:17668071

The Sea Urchin Embryo: A Remarkable Classroom Tool.

ERIC Educational Resources Information Center

Oppenheimer, Steven B.

1989-01-01

Discussed are the uses of sea urchins in research and their usefulness and advantages in the classroom investigation of embryology. Ideas for classroom activities and student research are presented. Lists 25 references. (CW)

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

Liu, Shuling, E-mail: liusl8888@yahoo.com.cn; Li, Honglin; Yan, Lu

Graphical abstract: - Highlights: • 3D urchin-like ZnS/CdS composites were synthesized via a two-step method. • The CdS nanoparticles were assembled on the thorns of 3D ZnS urchins. • The ZnS/CdS composites show excellent photocatalytic degradation activities. • The modification of CdS on ZnS is responsible for the enhanced property. - Abstract: Urchin-like ZnS/CdS semiconductor composites were successfully synthesized by combining solvothermal route with homogeneous precipitation process. The as-obtained samples were characterized by means of XRD, EDX, TEM, HR-TEM, ED and FE-SEM techniques. The results show that the as-obtained composites were comprised of the hexagonal structure ZnS and CdS, andmore » CdS nanoparticles were assembled on the surfaces of the thorns of urchin-like ZnS. In addition, the optical properties and photocatalytic activities of the as-prepared ZnS/CdS composites toward some organic dyes (such as Methyl Orange, Pyronine B, Rhodamine B and Methylene Blue) were separately investigated. It is found that the ZnS/CdS composites exhibit excellent photocatalytic degradation activity for these dyes under UV irradiation, as compared to corresponding pure ZnS urchins and commercial anatase TiO{sub 2} (P-25). This enhanced activity may be related to the modification of CdS nanoparticles on the surfaces of thorns of ZnS urchins and a tentative mechanism for the enhanced photocatalytic degradation activities of the ZnS/CdS composite catalyst was proposed.« less

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.

Influence of potentially confounding factors on sea urchin porewater toxicity tests

USGS Publications Warehouse

Carr, R.S.; Biedenbach, J.M.; Nipper, M.

2006-01-01

The influence of potentially confounding factors has been identified as a concern for interpreting sea urchin porewater toxicity test data. The results from >40 sediment-quality assessment surveys using early-life stages of the sea urchin Arbacia punctulata were compiled and examined to determine acceptable ranges of natural variables such as pH, ammonia, and dissolved organic carbon on the fertilization and embryological development endpoints. In addition, laboratory experiments were also conducted with A. punctulata and compared with information from the literature. Pore water with pH as low as 6.9 is an unlikely contributor to toxicity for the fertilization and embryological development tests with A. punctulata. Other species of sea urchin have narrower pH tolerance ranges. Ammonia is rarely a contributing factor in pore water toxicity tests using the fertilization endpoint, but the embryological development endpoint may be influenced by ammonia concentrations commonly found in porewater samples. Therefore, ammonia needs to be considered when interpreting results for the embryological development test. Humic acid does not affect sea urchin fertilization at saturation concentrations, but it could have an effect on the embryological development endpoint at near-saturation concentrations. There was no correlation between sediment total organic carbon concentrations and porewater dissolved organic carbon concentrations. Because of the potential for many varying substances to activate parthenogenesis in sea urchin eggs, it is recommended that a no-sperm control be included with every fertilization test treatment. ?? 2006 Springer Science+Business Media, Inc.

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.

Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida.

PubMed

Faddeeva-Vakhrusheva, Anna; Kraaijeveld, Ken; Derks, Martijn F L; Anvar, Seyed Yahya; Agamennone, Valeria; Suring, Wouter; Kampfraath, Andries A; Ellers, Jacintha; Le Ngoc, Giang; van Gestel, Cornelis A M; Mariën, Janine; Smit, Sandra; van Straalen, Nico M; Roelofs, Dick

2017-06-28

Folsomia candida is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of Wolbachia, and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle. We applied Pacific Bioscience sequencing and assembly to generate a reference genome for F. candida of 221.7 Mbp, comprising only 162 scaffolds. The complete genome of its endosymbiont Wolbachia, was also assembled and turned out to be the largest strain identified so far. Substantial gene family expansions and lineage-specific gene clusters were linked to stress response. A large number of genes (809) were acquired by horizontal gene transfer. A substantial fraction of these genes are involved in lignocellulose degradation. Also, the presence of genes involved in antibiotic biosynthesis was confirmed. Intra-genomic rearrangements of collinear gene clusters were observed, of which 11 were organized as palindromes. The Hox gene cluster of F. candida showed major rearrangements compared to arthropod consensus cluster, resulting in a disorganized cluster. The expansion of stress response gene families suggests that stress defense was important to facilitate colonization of soils. The large number of HGT genes related to lignocellulose degradation could be beneficial to unlock carbohydrate sources in soil, especially those contained in decaying plant and fungal organic matter. Intra- as well as inter-scaffold duplications of gene clusters may be a consequence of its parthenogenetic lifestyle. This high quality genome will be instrumental for evolutionary biologists investigating deep phylogenetic lineages among arthropods and will provide the basis for a more mechanistic understanding in soil ecology and ecotoxicology.

Hierarchically assembled Au microspheres and sea urchin-like architectures: formation mechanism and SERS study

NASA Astrophysics Data System (ADS)

Wang, Xiansong; Yang, Da-Peng; Huang, Peng; Li, Min; Li, Chao; Chen, Di; Cui, Daxiang

2012-11-01

The hierarchically assembled Au microspheres/sea urchin-like structures have been synthesized in aqueous solution at room temperature with and without proteins (bovine serum albumin, BSA) as mediators. The average diameter of an individual Au microsphere is 300-600 nm, which is composed of some compact nanoparticles with an average diameter of about 15 nm. Meanwhile, the sea urchin-like Au architecture exhibits an average diameter of 600-800 nm, which is made up of some nanopricks with an average length of 100-200 nm. These products are characterized by means of scanning electron microscopy (SEM), X-ray diffraction (XRD) and transmission electronic microscopy (TEM). It is found that the BSA and ascorbic acid (AA) have great effects on the morphology of the resulting products. Two different growth mechanisms are proposed. The study on surface enhanced Raman scattering (SERS) activities is also carried out between Au microspheres and Au sea urchin-like architectures. It is found that Au urchin-like architectures possess much higher SERS activity than the Au microspheres. Our work may shed light on the design and synthesis of hierarchically self-assembled 3D micro/nano-architectures for SERS, catalysis and biosensors.The hierarchically assembled Au microspheres/sea urchin-like structures have been synthesized in aqueous solution at room temperature with and without proteins (bovine serum albumin, BSA) as mediators. The average diameter of an individual Au microsphere is 300-600 nm, which is composed of some compact nanoparticles with an average diameter of about 15 nm. Meanwhile, the sea urchin-like Au architecture exhibits an average diameter of 600-800 nm, which is made up of some nanopricks with an average length of 100-200 nm. These products are characterized by means of scanning electron microscopy (SEM), X-ray diffraction (XRD) and transmission electronic microscopy (TEM). It is found that the BSA and ascorbic acid (AA) have great effects on the morphology of the resulting products. Two different growth mechanisms are proposed. The study on surface enhanced Raman scattering (SERS) activities is also carried out between Au microspheres and Au sea urchin-like architectures. It is found that Au urchin-like architectures possess much higher SERS activity than the Au microspheres. Our work may shed light on the design and synthesis of hierarchically self-assembled 3D micro/nano-architectures for SERS, catalysis and biosensors. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr32405a

Seasonal assessment of biological indices, bioaccumulation, and bioavailability of heavy metals in sea urchins Paracentrotus lividus from Algerian west coast, applied to environmental monitoring.

PubMed

Rouane-Hacene, Omar; Boutiba, Zitouni; Benaissa, Meriem; Belhaouari, Benkhedda; Francour, Patrice; Guibbolini-Sabatier, Marielle E; Faverney, Christine Risso-De

2018-04-01

The aim of the present work was to extend our knowledge on the variability of trace metals in sea urchin tissues, focusing on seasonal fluctuations (2010 February for "winter," May for "spring," August for "summer," November for "autumn") in the three different sampling sites of Algerian west coast (Oran Harbor (S1), Ain Defla (S2), and Hadjaj (belonging to Mostaganem City S3)). For this purpose, the bioavailability (metal indices) and bioaccumulation (metal concentrations in soft tissues) of heavy metals (Zn, Cu, Pb, and Cd), the physiological characteristics (e.g., biological indices such as condition index (CI), repletion index (RI), gonad index (GI)), and the biometric parameters (diameter (D) and the height (H)) of sea urchins Paracentrotus lividus were assessed and related to seasons and sites. To investigate the metal bioavailability to sea urchins more precisely, the metal indices were used as a reliable tool in the present work, instead of the metal concentrations only. The interest to standardize metal concentrations with the weight of the urchin test is to overcome the metal burden variations in the soft tissues of urchin related to the seasonal weight changes of the soft body of animal. We evidence that the most contaminated sites were S1 and S2. Furthermore, it should be noted that the bioavailability of metals, corresponding to the values of metal indices, is also more pronounced in S1 and S2 compared to that measured in S3. Thus, a correlation is observed between seasonal metal content in urchin tissues from the three sites and the corresponding metal indices. The high metal concentrations were obtained during the period when RI and CI were highest. So, it appears that the bioaccumulation of metals in sea urchins of the three sites studied is significantly influenced by the reproductive cycle and diet, feeding activity, and physiological state of these organisms. We noticed that the sea urchins from the sites S1 and S2 were small in size. It is probable that these animals, whose internal tissues contained high concentrations of metals, have been exposed to metal pollution, which might have affected both their growth and altered their physiological capacity. This approach is very original and might be used in the monitoring of the quality of coastal waters, and the present work provided a useful data set for Mediterranean monitoring network.

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

PubMed Central

2011-01-01

Background We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. Results The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. Conclusions Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution. PMID:21854559

TWIST1-WDR5-Hottip Regulates Hoxa9 Chromatin to Facilitate Prostate Cancer Metastasis.

PubMed

Malek, Reem; Gajula, Rajendra P; Williams, Russell D; Nghiem, Belinda; Simons, Brian W; Nugent, Katriana; Wang, Hailun; Taparra, Kekoa; Lemtiri-Chlieh, Ghali; Yoon, Arum R; True, Lawrence; An, Steven S; DeWeese, Theodore L; Ross, Ashley E; Schaeffer, Edward M; Pienta, Kenneth J; Hurley, Paula J; Morrissey, Colm; Tran, Phuoc T

2017-06-15

TWIST1 is a transcription factor critical for development that can promote prostate cancer metastasis. During embryonic development, TWIST1 and HOXA9 are coexpressed in mouse prostate and then silenced postnatally. Here we report that TWIST1 and HOXA9 coexpression are reactivated in mouse and human primary prostate tumors and are further enriched in human metastases, correlating with survival. TWIST1 formed a complex with WDR5 and the lncRNA Hottip/HOTTIP, members of the MLL/COMPASS-like H3K4 methylases, which regulate chromatin in the Hox/HOX cluster during development. TWIST1 overexpression led to coenrichment of TWIST1 and WDR5 as well as increased H3K4me3 chromatin at the Hoxa9/HOXA9 promoter, which was dependent on WDR5. Expression of WDR5 and Hottip/HOTTIP was also required for TWIST1-induced upregulation of HOXA9 and aggressive cellular phenotypes such as invasion and migration. Pharmacologic inhibition of HOXA9 prevented TWIST1-induced aggressive prostate cancer cellular phenotypes in vitro and metastasis in vivo This study demonstrates a novel mechanism by which TWIST1 regulates chromatin and gene expression by cooperating with the COMPASS-like complex to increase H3K4 trimethylation at target gene promoters. Our findings highlight a TWIST1-HOXA9 embryonic prostate developmental program that is reactivated during prostate cancer metastasis and is therapeutically targetable. Cancer Res; 77(12); 3181-93. ©2017 AACR . ©2017 American Association for Cancer Research.

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

PubMed

Renfree, Marilyn B; Papenfuss, Anthony T; Deakin, Janine E; Lindsay, James; Heider, Thomas; Belov, Katherine; Rens, Willem; Waters, Paul D; Pharo, Elizabeth A; Shaw, Geoff; Wong, Emily S W; Lefèvre, Christophe M; Nicholas, Kevin R; Kuroki, Yoko; Wakefield, Matthew J; Zenger, Kyall R; Wang, Chenwei; Ferguson-Smith, Malcolm; Nicholas, Frank W; Hickford, Danielle; Yu, Hongshi; Short, Kirsty R; Siddle, Hannah V; Frankenberg, Stephen R; Chew, Keng Yih; Menzies, Brandon R; Stringer, Jessica M; Suzuki, Shunsuke; Hore, Timothy A; Delbridge, Margaret L; Patel, Hardip R; Mohammadi, Amir; Schneider, Nanette Y; Hu, Yanqiu; O'Hara, William; Al Nadaf, Shafagh; Wu, Chen; Feng, Zhi-Ping; Cocks, Benjamin G; Wang, Jianghui; Flicek, Paul; Searle, Stephen M J; Fairley, Susan; Beal, Kathryn; Herrero, Javier; Carone, Dawn M; Suzuki, Yutaka; Sugano, Sumio; Toyoda, Atsushi; Sakaki, Yoshiyuki; Kondo, Shinji; Nishida, Yuichiro; Tatsumoto, Shoji; Mandiou, Ion; Hsu, Arthur; McColl, Kaighin A; Lansdell, Benjamin; Weinstock, George; Kuczek, Elizabeth; McGrath, Annette; Wilson, Peter; Men, Artem; Hazar-Rethinam, Mehlika; Hall, Allison; Davis, John; Wood, David; Williams, Sarah; Sundaravadanam, Yogi; Muzny, Donna M; Jhangiani, Shalini N; Lewis, Lora R; Morgan, Margaret B; Okwuonu, Geoffrey O; Ruiz, San Juana; Santibanez, Jireh; Nazareth, Lynne; Cree, Andrew; Fowler, Gerald; Kovar, Christie L; Dinh, Huyen H; Joshi, Vandita; Jing, Chyn; Lara, Fremiet; Thornton, Rebecca; Chen, Lei; Deng, Jixin; Liu, Yue; Shen, Joshua Y; Song, Xing-Zhi; Edson, Janette; Troon, Carmen; Thomas, Daniel; Stephens, Amber; Yapa, Lankesha; Levchenko, Tanya; Gibbs, Richard A; Cooper, Desmond W; Speed, Terence P; Fujiyama, Asao; Graves, Jennifer A M; O'Neill, Rachel J; Pask, Andrew J; Forrest, Susan M; Worley, Kim C

2011-08-29

We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.

Hierarchically assembled Au microspheres and sea urchin-like architectures: formation mechanism and SERS study.

PubMed

Wang, Xiansong; Yang, Da-Peng; Huang, Peng; Li, Min; Li, Chao; Chen, Di; Cui, Daxiang

2012-12-21

The hierarchically assembled Au microspheres/sea urchin-like structures have been synthesized in aqueous solution at room temperature with and without proteins (bovine serum albumin, BSA) as mediators. The average diameter of an individual Au microsphere is 300-600 nm, which is composed of some compact nanoparticles with an average diameter of about 15 nm. Meanwhile, the sea urchin-like Au architecture exhibits an average diameter of 600-800 nm, which is made up of some nanopricks with an average length of 100-200 nm. These products are characterized by means of scanning electron microscopy (SEM), X-ray diffraction (XRD) and transmission electronic microscopy (TEM). It is found that the BSA and ascorbic acid (AA) have great effects on the morphology of the resulting products. Two different growth mechanisms are proposed. The study on surface enhanced Raman scattering (SERS) activities is also carried out between Au microspheres and Au sea urchin-like architectures. It is found that Au urchin-like architectures possess much higher SERS activity than the Au microspheres. Our work may shed light on the design and synthesis of hierarchically self-assembled 3D micro/nano-architectures for SERS, catalysis and biosensors.

bicaudal-C is required for the formation of anterior neurogenic ectoderm in the sea urchin embryo.

PubMed

Yaguchi, Shunsuke; Yaguchi, Junko; Inaba, Kazuo

2014-10-31

bicaudal-C (bicC) mRNA encodes a protein containing RNA-binding domains that is reported to be maternally present with deflection in the oocytes/eggs of some species. The translated protein plays a critical role in the regulation of cell fate specification along the body axis during early embryogenesis in flies and frogs. However, it is unclear how it functions in eggs in which bicC mRNA is uniformly distributed, for instance, sea urchin eggs. Here, we show the function of BicC in the formation of neurogenic ectoderm of the sea urchin embryo. Loss-of-function experiments reveal that BicC is required for serotonergic neurogenesis and for expression of ankAT-1 gene, which is essential for the formation of apical tuft cilia in the neurogenic ectoderm of the sea urchin embryo. In contrast, the expression of FoxQ2, the neurogenic ectoderm specification transcription factor, is invariant in BicC morphants. Because FoxQ2 is an upstream factor of serotonergic neurogenesis and ankAT-1 expression, these data indicate that BicC functions in regulating the events that are coordinated by FoxQ2 during sea urchin embryogenesis.

Dynamic changes in the interchromosomal interaction of early histone gene loci during development of sea urchin.

PubMed

Matsushita, Masaya; Ochiai, Hiroshi; Suzuki, Ken-Ichi T; Hayashi, Sayaka; Yamamoto, Takashi; Awazu, Akinori; Sakamoto, Naoaki

2017-12-15

The nuclear positioning and chromatin dynamics of eukaryotic genes are closely related to the regulation of gene expression, but they have not been well examined during early development, which is accompanied by rapid cell cycle progression and dynamic changes in nuclear organization, such as nuclear size and chromatin constitution. In this study, we focused on the early development of the sea urchin Hemicentrotus pulcherrimus and performed three-dimensional fluorescence in situ hybridization of gene loci encoding early histones (one of the types of histone in sea urchin). There are two non-allelic early histone gene loci per sea urchin genome. We found that during the morula stage, when the early histone gene expression levels are at their maximum, interchromosomal interactions were often formed between the early histone gene loci on separate chromosomes and that the gene loci were directed to locate to more interior positions. Furthermore, these interactions were associated with the active transcription of the early histone genes. Thus, such dynamic interchromosomal interactions may contribute to the efficient synthesis of early histone mRNA during the morula stage of sea urchin development. © 2017. Published by The Company of Biologists Ltd.

High-efficiency and conveniently recyclable photo-catalysts for dye degradation based on urchin-like CuO microparticle/polymer hybrid composites

NASA Astrophysics Data System (ADS)

Liu, Xiong; Cheng, Yuming; Li, Xuefeng; Dong, Jinfeng

2018-05-01

In this work, we developed a new type of photo-catalysts composed of the urchin-like cupric oxide (CuO) microparticle and polyvinylidene fluoride (PVDF) hybrid composites by the convenient organic-inorganic hybrid strategy, which show high-efficiency and conveniently recyclable for dye degradation including methylene blue (MB), Congo red (CR), and malachite green (MG) by visible light irradiation. The micro-structural characteristics of urchin-like CuO microparticles are crucial and dominant over the photo-degrading efficiency of hybrid catalyst because of their highly exposed {0 0 2} facet and larger specific surface area. Simultaneously, the intrinsic porous framework of PVDF membrane not only remains the excellent photo-catalytic activity of urchin-like CuO microparticles but also facilitates the enrichment of dyes on the membrane, and thereby synergistically contributing to the photo-catalytic efficiency. The microstructures of both urchin-like CuO microparticles and hybrid catalysts are systematically characterized by various techniques including scanning electron microscopy (SEM), transmission electron microscope (TEM), high-resolution transmission electron microscope (HRTEM), powder X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), and nitrogen adsorption/desorption isotherms, which evidently support the mentioned mechanism.

Hox2 Genes Are Required for Tonotopic Map Precision and Sound Discrimination in the Mouse Auditory Brainstem.

PubMed

Karmakar, Kajari; Narita, Yuichi; Fadok, Jonathan; Ducret, Sebastien; Loche, Alberto; Kitazawa, Taro; Genoud, Christel; Di Meglio, Thomas; Thierry, Raphael; Bacelo, Joao; Lüthi, Andreas; Rijli, Filippo M

2017-01-03

Tonotopy is a hallmark of auditory pathways and provides the basis for sound discrimination. Little is known about the involvement of transcription factors in brainstem cochlear neurons orchestrating the tonotopic precision of pre-synaptic input. We found that in the absence of Hoxa2 and Hoxb2 function in Atoh1-derived glutamatergic bushy cells of the anterior ventral cochlear nucleus, broad input topography and sound transmission were largely preserved. However, fine-scale synaptic refinement and sharpening of isofrequency bands of cochlear neuron activation upon pure tone stimulation were impaired in Hox2 mutants, resulting in defective sound-frequency discrimination in behavioral tests. These results establish a role for Hox factors in tonotopic refinement of connectivity and in ensuring the precision of sound transmission in the mammalian auditory circuit. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Differential Expression of Hox and Notch Genes in Larval and Adult Stages of Echinococcus granulosus.

PubMed

Dezaki, Ebrahim Saedi; Yaghoobi, Mohammad Mehdi; Taheri, Elham; Almani, Pooya Ghaseminejad; Tohidi, Farideh; Gottstein, Bruno; Harandi, Majid Fasihi

2016-10-01

This investigation aimed to evaluate the differential expression of HoxB7 and notch genes in different developmental stages of Echinococcus granulosus sensu stricto. The expression of HoxB7 gene was observed at all developmental stages. Nevertheless, significant fold differences in the expression level was documented in the juvenile worm with 3 or more proglottids, the germinal layer from infected sheep, and the adult worm from an experimentally infected dog. The notch gene was expressed at all developmental stages of E. granulosus ; however, the fold difference was significantly increased at the microcysts in monophasic culture medium and the germinal layer of infected sheep in comparison with other stages. The findings demonstrated that the 2 aforementioned genes evaluated in the present study were differentially expressed at different developmental stages of the parasite and may contribute to some important biological processes of E. granulosus .

A C. elegans Hox gene switches on, off, on and off again to regulate proliferation, differentiation and morphogenesis.

PubMed

Salser, S J; Kenyon, C

1996-05-01

Hox genes establish body pattern throughout the animal kingdom, but the role these genes play at the cellular level to modify and shape parts of the body remains a mystery. We find that the C. elegans Antennapedia homolog, mab-5, sequentially programs many independent events within individual cell lineages. In one body region, mab-5 first switches ON in a lineage to stimulate proliferation, then OFF to specify epidermal structures, then ON in just one branch of the lineage to promote neuroblast formation, and finally OFF to permit proper sense organ morphology. In a neighboring lineage, continuous mab-5 expression leads to a different pattern of development. Thus, this Hox gene achieves much of its power to diversify the anteroposterior axis through fine spatiotemporal differences in expression coupled with a changing pattern of cellular response.

Cascading Effects of Ocean Acidification in a Rocky Subtidal Community

PubMed Central

Asnaghi, Valentina; Chiantore, Mariachiara; Mangialajo, Luisa; Gazeau, Frédéric; Francour, Patrice; Alliouane, Samir; Gattuso, Jean-Pierre

2013-01-01

Temperate marine rocky habitats may be alternatively characterized by well vegetated macroalgal assemblages or barren grounds, as a consequence of direct and indirect human impacts (e.g. overfishing) and grazing pressure by herbivorous organisms. In future scenarios of ocean acidification, calcifying organisms are expected to be less competitive: among these two key elements of the rocky subtidal food web, coralline algae and sea urchins. In order to highlight how the effects of increased pCO2 on individual calcifying species will be exacerbated by interactions with other trophic levels, we performed an experiment simultaneously testing ocean acidification effects on primary producers (calcifying and non-calcifying algae) and their grazers (sea urchins). Artificial communities, composed by juveniles of the sea urchin Paracentrotus lividus and calcifying (Corallina elongata) and non-calcifying (Cystoseira amentacea var stricta, Dictyota dichotoma) macroalgae, were subjected to pCO2 levels of 390, 550, 750 and 1000 µatm in the laboratory. Our study highlighted a direct pCO2 effect on coralline algae and on sea urchin defense from predation (test robustness). There was no direct effect on the non-calcifying macroalgae. More interestingly, we highlighted diet-mediated effects on test robustness and on the Aristotle's lantern size. In a future scenario of ocean acidification a decrease of sea urchins' density is expected, due to lower defense from predation, as a direct consequence of pH decrease, and to a reduced availability of calcifying macroalgae, important component of urchins' diet. The effects of ocean acidification may therefore be contrasting on well vegetated macroalgal assemblages and barren grounds: in the absence of other human impacts, a decrease of biodiversity can be predicted in vegetated macroalgal assemblages, whereas a lower density of sea urchin could help the recovery of shallow subtidal rocky areas affected by overfishing from barren grounds to assemblages dominated by fleshy macroalgae. PMID:23613994

Cascading effects of ocean acidification in a rocky subtidal community.

PubMed

Asnaghi, Valentina; Chiantore, Mariachiara; Mangialajo, Luisa; Gazeau, Frédéric; Francour, Patrice; Alliouane, Samir; Gattuso, Jean-Pierre

2013-01-01

Temperate marine rocky habitats may be alternatively characterized by well vegetated macroalgal assemblages or barren grounds, as a consequence of direct and indirect human impacts (e.g. overfishing) and grazing pressure by herbivorous organisms. In future scenarios of ocean acidification, calcifying organisms are expected to be less competitive: among these two key elements of the rocky subtidal food web, coralline algae and sea urchins. In order to highlight how the effects of increased pCO2 on individual calcifying species will be exacerbated by interactions with other trophic levels, we performed an experiment simultaneously testing ocean acidification effects on primary producers (calcifying and non-calcifying algae) and their grazers (sea urchins). Artificial communities, composed by juveniles of the sea urchin Paracentrotus lividus and calcifying (Corallina elongata) and non-calcifying (Cystoseira amentacea var stricta, Dictyota dichotoma) macroalgae, were subjected to pCO2 levels of 390, 550, 750 and 1000 µatm in the laboratory. Our study highlighted a direct pCO2 effect on coralline algae and on sea urchin defense from predation (test robustness). There was no direct effect on the non-calcifying macroalgae. More interestingly, we highlighted diet-mediated effects on test robustness and on the Aristotle's lantern size. In a future scenario of ocean acidification a decrease of sea urchins' density is expected, due to lower defense from predation, as a direct consequence of pH decrease, and to a reduced availability of calcifying macroalgae, important component of urchins' diet. The effects of ocean acidification may therefore be contrasting on well vegetated macroalgal assemblages and barren grounds: in the absence of other human impacts, a decrease of biodiversity can be predicted in vegetated macroalgal assemblages, whereas a lower density of sea urchin could help the recovery of shallow subtidal rocky areas affected by overfishing from barren grounds to assemblages dominated by fleshy macroalgae.

Sea urchin puncture resulting in PIP joint synovial arthritis: case report and MRI study.

PubMed

Liram, N; Gomori, M; Perouansky, M

2000-01-01

Of the 600 species of sea urchins, approximately 80 may be venomous to humans. The long spined or black sea urchin, Diadema setosum may cause damage by the breaking off of its brittle spines after they penetrate the skin. Synovitis followed by arthritis may be an unusual but apparently not a rare sequel to such injury, when implantation occurs near a joint. In this case report, osseous changes were not seen by plain x-rays. Magnetic resonance imaging (MRI) was used to expose the more salient features of both soft tissue and bone changes of black sea urchin puncture injury 30 months after penetration. In all likelihood, this type of injury may be more common than the existing literature at present suggests. It is believed to be the first reported case in this part of the world as well as the first MRI study describing this type of joint pathology. Local and systemic reactions to puncture injuries from sea urchin spines have been described previously. These may range from mild, local irritation lasting a few days to granuloma formation, infection and on occasions systemic illness. The sea urchin spines are composed of calcium carbonate with proteinaceous covering. The covering tends to cause immune reactions of variable presentation. There are only a handful of reported cases with sea urchin stings on record, none of them from the Red Sea. However, this condition is probably more common than is thought and can present difficulty in diagnosis. In this case report, the inflammation responded well to heat treatment, mobilization and manipulation of the joint in its post acute and chronic stages. As some subtle changes in soft tissues and the changes in bone were not seen either on plain x-rays or ultrasound scan, gadolinium-enhanced MRI was used to unveil the marked changes in the joint.

[Sea urchin embryo, DNA-damaged cell cycle checkpoint and the mechanisms initiating cancer development].

PubMed

Bellé, Robert; Le Bouffant, Ronan; Morales, Julia; Cosson, Bertrand; Cormier, Patrick; Mulner-Lorillon, Odile

2007-01-01

Cell division is an essential process for heredity, maintenance and evolution of the whole living kingdom. Sea urchin early development represents an excellent experimental model for the analysis of cell cycle checkpoint mechanisms since embryonic cells contain a functional DNA-damage checkpoint and since the whole sea urchin genome is sequenced. The DNA-damaged checkpoint is responsible for an arrest in the cell cycle when DNA is damaged or incorrectly replicated, for activation of the DNA repair mechanism, and for commitment to cell death by apoptosis in the case of failure to repair. New insights in cancer biology lead to two fundamental concepts about the very first origin of cancerogenesis. Cancers result from dysfunction of DNA-damaged checkpoints and cancers appear as a result of normal stem cell (NCS) transformation into a cancer stem cell (CSC). The second aspect suggests a new definition of "cancer", since CSC can be detected well before any clinical evidence. Since early development starts from the zygote, which is a primary stem cell, sea urchin early development allows analysis of the early steps of the cancerization process. Although sea urchins do not develop cancers, the model is alternative and complementary to stem cells which are not easy to isolate, do not divide in a short time and do not divide synchronously. In the field of toxicology and incidence on human health, the sea urchin experimental model allows assessment of cancer risk from single or combined molecules long before any epidemiologic evidence is available. Sea urchin embryos were used to test the worldwide used pesticide Roundup that contains glyphosate as the active herbicide agent; it was shown to activate the DNA-damage checkpoint of the first cell cycle of development. The model therefore allows considerable increase in risk evaluation of new products in the field of cancer and offers a tool for the discovery of molecular markers for early diagnostic in cancer biology. Prevention and early diagnosis are two decisive elements of human cancer therapy.

For the Classroom: The Sea Urchin Fertilization and Embryology Lab.

ERIC Educational Resources Information Center

Brevoort, Douglas

1984-01-01

The sea urchin provides an ideal embryology laboratory because it is visually representative of the fertilization process in higher animals. Procedures for conducting such a laboratory (including methods for securing specimens) are provided. (JN)

Diversity of olfactomedin proteins in the sea urchin.

PubMed

Hillier, Brian J; Moy, Gary W; Vacquier, Victor D

2007-06-01

Olfactomedin (OLF) domain proteins maintain extracellular protein-protein interactions in diverse phyla. Only one OLF family member, amassin-1, has been described from the sea urchin Strongylocentrotus purpuratus, a basal invertebrate deuterostome. Amassin-1 mediates intercellular adhesion of coelomocytes (immunocytes). Here we describe the protein structural features of four additional OLF proteins, the total for the genome being five. Phylogenetically, four of these proteins (the amassins) form a subgroup among previously identified OLF proteins. The fifth OLF protein is within the colmedin subfamily and contains a type II transmembrane domain, collagen repeats, and an OLF domain. Sea urchin OLF proteins represent an intermediate diversification between protostomes and vertebrates. Transcripts of all five OLF family members are in coelomocytes and adult radial nerve tissue. Transcripts for some OLF proteins increase during late larval stages. Transcript levels for amassin-1 increase 1,000,000-fold, coinciding with formation of the adult urchin rudiment within the larval body.

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

EXTENDING THE VIABILITY OF SPERMATOZOA AND EGGS OF THE SEA URCHIN LYTECHINUS VARIEGATUS.

PubMed

Malgarin, Jéssica; Resgalla, Charrid

2015-01-01

The storage of spermatozoa and eggs of the sea urchin Lytecninus variegatus can meet the demand of different human activities. To develop a protocol easy to reproduce for spermatozoa cryopreservation and cooling of the eggs of the sea urchin. Different formulations of artificial sea water were tested for their effectiveness in the freezing of sea urchin spermatozoa and storage of the eggs. Protocol for freezing of spermatozoa in liquid nitrogen presented the positive results when the cryoprotectant solution was diluted in artificial seawater free of calcium and magnesium. For the conservation of the eggs by cooling, the calcium-free artificial sea water, the calcium- and magnesium-free sea water, and the low-sodium water proved more efficient in preserving the integrity of the eggs. The results showed success in the freezing protocol of spermatozoa and cooling of the eggs mainly in artificial calcium- and magnesium-free sea water.

Developmental effects of the protein kinase inhibitor kenpaullone on the sea urchin embryo.

PubMed

Anello, Letizia; Cavalieri, Vincenzo; Di Bernardo, Maria

2018-01-01

The selection and validation of bioactive compounds require multiple approaches, including in-depth analyses of their biological activity in a whole-animal context. We exploited the sea urchin embryo in a rapid, medium-scale range screening to test the effects of the small synthetic kinase inhibitor kenpaullone. We show that sea urchin embryos specifically respond to this molecule depending on both dose and timing of administration. Phenotypic effects of kenpaullone are not immediately visible, since this molecule affects neither the fertilization nor the spatial arrangement of blastomeres at early developmental stages. Nevertheless, kenpaullone exposure from the beginning of embryogenesis profoundly perturbs specification, detachment from the epithelium, and migration of the primary mesenchyme cells, thus affecting the whole embryonic epithelial mesenchymal transition process. Our results reaffirm the sea urchin embryo as an excellent and sensitive in vivo system, which provides straightforward and rapid response to external stimuli. Copyright © 2017 Elsevier Inc. All rights reserved.

Correlation analyses of covering and righting behaviors to fitness related traits of the sea urchin Glyptocidaris crenularis in different environmental conditions

NASA Astrophysics Data System (ADS)

Wei, Jing; Zhang, Lisheng; Zhao, Chong; Feng, Wenping; Sun, Ping; Chang, Yaqing

2016-11-01

Complex marine benthic environments shape a number of ecologically important behaviors in sea urchins, including covering and righting behaviors. The present study correlated covering and righting behaviors to a series of fitness-related traits in sea urchins. Righting response time of Glyptocidaris crenularis was significantly positively correlated with body size, but significantly negatively correlated with food consumption. Covering behavior was not significantly correlated with test diameter, test height or body weight, but covering response time was negatively correlated with body weight. A significantly negative correlation was found between righting response time and covering response time. Glyptocidaris crenularis showed a significantly positive correlation in covering response time with and without exposure to poured sand, but no significance in covering ability (number of shells used to cover). The present study provides new insight into internal mechanisms and evolutionary drives of covering and righting behaviors of sea urchins.

Microautophagy in nutritive phagocytes of sea urchins.

PubMed

Kalachev, Alexander V; Yurchenko, Olga V

2017-01-01

Two types of cells were observed in germinative epithelium of male and female sea urchins: germ cells and somatic accessory cells; the latter referred to as nutritive phagocytes. At the onset of gametogenesis, nutritive phagocytes accumulate nutrients and greatly increase in their size. As gametogenesis progresses, the accumulated nutrients are transferred from nutritive phagocytes into developing gametes, and size of the nutritive phagocytes decreases. An electron microscopic study of nutritive phagocytes in sea urchins, Strongylocentrotus intermedius, at different stages of annual reproductive cycle showed for the first time that both macro- and microautophagy take place in nutritive phagocytes. Both processes occur simultaneously and regulate size and composition of nutritive phagocytes in male and female sea urchins. Nutritive phagocytes consume redundant cytoplasm via macroautophagy. Microautophagy is probably involved in consumption of redundant membranes that appear within nutritive phagocytes due to destruction of nutrient-storing globules, macroautophagy, and phagocytosis of germ cells or their remnants.

Transcriptome sequencing of Atlantic salmon (Salmo salar L.) notochord prior to development of the vertebrae provides clues to regulation of positional fate, chordoblast lineage and mineralisation

PubMed Central

2014-01-01

Background In teleosts such as Atlantic salmon (Salmo salar L.), segmentation and subsequent mineralisation of the notochord during embryonic stages are essential for normal vertebrae formation. However, the molecular mechanisms leading to segmentation and mineralisation of the notochord are poorly understood. The aim of this study was to identify genes/pathways acting in gradients over time and along the anterior-posterior axis during notochord segmentation and immediately prior to mineralisation of the vertebral bodies in Atlantic salmon. Results Notochord samples were collected from unsegmented, pre-segmented and segmented developmental stages. In each stage, the cellular core of the notochord was cut into three pieces along the longitudinal axis (anterior, mid, posterior). RNA was sequenced (22 million pair-end 100 bp/ library) and mapped to the salmon genome. 66569 transcripts were predicted and 55775 were annotated. In order to identify possible gradients leading to segmentation of the notochord, all 71 notochord-expressed hox genes were investigated, most of them displaying a typical anterior-posterior expression pattern along the notochord axis. The clustering of hox genes revealed a pattern that could be related to notochord segmentation. We further investigated how mineralisation is initiated in the notochord, and several factors related to chondrogenic lineage were identified (sox9, sox5, sox6, tgfb3, ihhb and col2a1), suggesting a cartilage-like character of the notochord. KEGG analysis of differentially expressed genes between stages revealed down-regulation of pathways associated with ECM, cell division, metabolism and development at onset of notochord segmentation. This implies that inhibitory signals produce segmentation of the notochord. One such potential inhibitory signal was identified, col11a2, which was detected in segments of non-mineralising notochord. Conclusions An incomplete salmon genome was successfully used to analyse RNA-seq data from the cellular core of the Atlantic salmon notochord. In transcriptome we found; hox gene patterns possibly linked to segmentation; down-regulation of pathways in the notochord at onset of segmentation; segmented expression of col11a2 in non-mineralised segments of the notochord; and a chondroblast-like footprint in the notochord. PMID:24548379

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

Zuo, Shixiang, E-mail: mycollege6619@sina.com; School of Petrochemical Engineering, Changzhou University, Changzhou 213164; Jiang, Zhongsheng, E-mail: 290618069@qq.com

The urchin-like mischcrystal TiO{sub 2} using acid attapulgite as an introducer was synthesized after a subsequent low-temperature hydrolyzation and crystallization followed by removal of acid attapulgite. The samples were characterized by transmission electron microscope, X-ray diffraction, Fourier transform infrared spectra and X-ray photoelectron spectroscopy. Acid attapulgite plays a critical role in the morphology and crystal structure of TiO{sub 2}. The results suggest that the perfect urchin-like mischcrystal TiO{sub 2} is fabricated when the mass ratio of TiO{sub 2} and acid attapulgite is 0.7:1. The single urchin-like TiO{sub 2} is comprised of a nanosphere and plentiful nanoneedles. The nanoneedles grow radiallymore » on the surface of the nanosphere. The urchin-like TiO{sub 2} is around 100 nm, and the nanoneedles have a diameter ranging from 2 to 5 nm. It has been confirmed that the chemical groups of acid attapulgite have a significant influence on the growth of TiO{sub 2}. In addition, the urchin-like mischcrystal TiO{sub 2} exhibits excellent activity to assist photodegradation of Rhodamine B aqueous solution under ultraviolet light, and the degradation rate is about 94.15% for 80 min. The photocatalytic kinetics can be well described by the pseudo-first rate equation. - Highlights: • Acid attapulgite (HATP) is acted as a sacrificial introducer. • The urchin-like mischcrystal TiO{sub 2} is produced by a low-temperature method. • The morphology and crystal are controllable with the dosage of HATP. • The fabricated TiO{sub 2} exhibits excellent photocatalysis for Rhodamine B.« less

Effects of seawater acidification on gene expression: resolving broader-scale trends in sea urchins.

PubMed

Evans, Tyler G; Watson-Wynn, Priscilla

2014-06-01

Sea urchins are ecologically and economically important calcifying organisms threatened by acidification of the global ocean caused by anthropogenic CO2 emissions. Propelled by the sequencing of the purple sea urchin (Strongylocentrotus purpuratus) genome, profiling changes in gene expression during exposure to high pCO2 seawater has emerged as a powerful and increasingly common method to infer the response of urchins to ocean change. However, analyses of gene expression are sensitive to experimental methodology, and comparisons between studies of genes regulated by ocean acidification are most often made in the context of major caveats. Here we perform meta-analyses as a means of minimizing experimental discrepancies and resolving broader-scale trends regarding the effects of ocean acidification on gene expression in urchins. Analyses across eight studies and four urchin species largely support prevailing hypotheses about the impact of ocean acidification on marine calcifiers. The predominant expression pattern involved the down-regulation of genes within energy-producing pathways, a clear indication of metabolic depression. Genes with functions in ion transport were significantly over-represented and are most plausibly contributing to intracellular pH regulation. Expression profiles provided extensive evidence for an impact on biomineralization, epitomized by the down-regulation of seven spicule matrix proteins. In contrast, expression profiles provided limited evidence for CO2-mediated developmental delay or induction of a cellular stress response. Congruence between studies of gene expression and the ocean acidification literature in general validates the accuracy of gene expression in predicting the consequences of ocean change and justifies its continued use in future studies. © 2014 Marine Biological Laboratory.

Synthesis and enhanced acetone gas-sensing performance of ZnSnO3/SnO2 hollow urchin nanostructures

NASA Astrophysics Data System (ADS)

Lian, Dandan; Shi, Bing; Dai, Rongrong; Jia, Xiaohua; Wu, Xiangyang

2017-12-01

A kind of novel ZnSnO3/SnO2 hollow urchin nanostructure was synthesized by a facile, eco-friendly two-step liquid-phase process. The structure, morphology, and composition of samples were characterized using X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), and nitrogen adsorption-desorption techniques. The results revealed that many tiny needle-like SnO2 nanowires with the average diameter of 5 nm uniformly grew on the surface of the ZnSnO3 hollow microspheres and the ZnSnO3/SnO2 hollow urchin nanostructures with different SnO2 content also were successfully prepared. In order to comprehend the evolution process of the ZnSnO3/SnO2 hollow urchin nanostructures, the possible growth mechanism of samples was illustrated via several experiments in different reaction conditions. Moreover, the gas-sensing performance of as-prepared samples was investigated. The results showed that ZnSnO3/SnO2 hollow urchin nanostructures with high response to various concentration levels of acetone enhanced selectivity, satisfying repeatability, and good long-term stability for acetone detection. Specially, the 10 wt% ZnSnO3/SnO2 hollow urchin nanostructure exhibited the best gas sensitivity (17.03 for 50 ppm acetone) may be a reliable biomarker for the diabetes patients, which could be ascribed to its large specific surface area, complete pore permeability, and increase of chemisorbed oxygen due to the doping of SnO2.

The Effect of Solar Proton Events on Ozone and Other Constituents

NASA Technical Reports Server (NTRS)

Jackman, Charles H.; McPeters, Richard D.; Bhartia, P. K. (Technical Monitor)

2000-01-01

Solar proton events (SPEs) can cause changes in constituents in the Earth's middle atmosphere. The highly energetic protons cause ionizations, excitations, dissociations, and dissociative ionizations of the background constituents. Complicated ion chemistry leads to HO(x) production and dissociation of N2 leads to NO(y) production. Both the HO(x) and NO(y) increases can result in changes to ozone in the stratosphere and mesosphere. The HO(x) increases lead to short-lived ozone decreases in the mesosphere and upper stratosphere due to the short lifetimes of the HO(x) constituents. The NO(y) increases lead to long-lived stratospheric ozone changes because of the long lifetime of NO(y) constituents in this region. The NO(y) induced ozone changes are generally decreases, however, the NO(y) constituents can interfere with chlorine and bromine radicals in the lowest part of the stratosphere and cause ozone increases. Temperature changes have been predicted to occur as a result of the larger SPEs. Eleven SPEs have caused measurable atmospheric variations since 1969. Neutral wind variations were measured shortly after the July 1982 and April 1984 SPEs. The recent July 2000 SPE caused NO(x) increases that lasted for two months past the event. The two periods of largest SPEs (August 1972 and October 1989) caused ozone decreases that lasted for several weeks past the events.

The C. elegans Hox gene egl-5 is required for correct development of the hermaphrodite hindgut and for the response to rectal infection by Microbacterium nematophilum.

PubMed

Nicholas, Hannah R; Hodgkin, Jonathan

2009-05-01

Members of the Hox gene family encode transcription factors that specify positional identity along the anterior-posterior axis of nearly all metazoans. One among the Caenorhabditis elegans Hox genes is egl-5. A deletion allele of egl-5 was isolated in a screen for animals which fail to develop swollen tails when exposed to the bacterial pathogen Microbacterium nematophilum. We show that compromised rectal development, which occurs as a result of loss of egl-5 function, results in a failure of rectal epithelial cells to express the ERK MAP kinase mpk-1, which was previously shown to mediate tail-swelling in response to bacterial infection. Tissue-specific rescue experiments demonstrated that egl-5 and mpk-1 act autonomously in rectal cells in the morphological response. The weak egl-5 allele (n1439), which does not compromise rectal development, fails to affect tail-swelling. We find that this allele carries an inserted repeat element approximately 13.8 kb upstream of the egl-5 open reading frame, which specifically disrupts the cell-specific expression of this gene in HSN egg-laying neurons. Together these findings extend the complexity of regulation and function of Hox genes in C. elegans and demonstrate the importance of their tissue-specific expression for correct development and response to infection.

Pediatric acute myeloid leukemia with NPM1 mutations is characterized by a gene expression profile with dysregulated HOX gene expression distinct from MLL-rearranged leukemias.

PubMed

Mullighan, C G; Kennedy, A; Zhou, X; Radtke, I; Phillips, L A; Shurtleff, S A; Downing, J R

2007-09-01

Somatic mutations in nucleophosmin (NPM1) occur in approximately 35% of adult acute myeloid leukemia (AML). To assess the frequency of NPM1 mutations in pediatric AML, we sequenced NPM1 in the diagnostic blasts from 93 pediatric AML patients. Six cases harbored NPM1 mutations, with each case lacking common cytogenetic abnormalities. To explore the phenotype of the AMLs with NPM1 mutations, gene expression profiles were obtained using Affymetrix U133A microarrays. NPM1 mutations were associated with increased expression of multiple homeobox genes including HOXA9, A10, B2, B6 and MEIS1. As dysregulated homeobox gene expression is also a feature of MLL-rearranged leukemia, the gene expression signatures of NPM1-mutated and MLL-rearranged leukemias were compared. Significant differences were identified between these leukemia subtypes including the expression of different HOX genes, with NPM1-mutated AML showing higher levels of expression of HOXB2, B3, B6 and D4. These results confirm recent reports of perturbed HOX expression in NPM1-mutated adult AML, and provide the first evidence that the NPM1-mutated signature is distinct from MLL-rearranged AML. These findings suggest that mutated NPM1 leads to dysregulated HOX expression via a different mechanism than MLL rearrangement.

The origin of the Hox/ParaHox genes, the Ghost Locus hypothesis and the complexity of the first animal.

PubMed

Ferrier, David E K

2016-09-01

A key aim in evolutionary biology is to deduce ancestral states to better understand the evolutionary origins of clades of interest and the diversification process(es) that has/have elaborated them. These ancestral deductions can hit difficulties when undetected loss events are misinterpreted as ancestral absences. With the ever-increasing amounts of animal genomic sequence data, we are gaining a much clearer view of the preponderance of differential gene losses across animal lineages. This has become particularly clear with recent progress in our understanding of the origins of the Hox/ParaHox developmental control genes relative to the earliest branching lineages of the animal kingdom: the sponges (Porifera), comb jellies (Ctenophora) and placozoans (Placozoa). These reassessments of the diversity and complexity of developmental control genes in the earliest animal ancestors need to go hand-in-hand with complementary advances in comparative morphology, phylogenetics and palaeontology to clarify our understanding of the complexity of the last common ancestor of all animals. The field is currently undergoing a shift from the traditional consensus of a sponge-like animal ancestor from which morphological and molecular elaboration subsequently evolved, to a scenario of a more complex animal ancestor, with subsequent losses and simplifications in various lineages. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Segmental expression of Hoxb2 in r4 requires two separate sites that integrate cooperative interactions between Prep1, Pbx and Hox proteins.

PubMed

Ferretti, E; Marshall, H; Pöpperl, H; Maconochie, M; Krumlauf, R; Blasi, F

2000-01-01

Direct auto- and cross-regulatory interactions between Hox genes serve to establish and maintain segmentally restricted patterns in the developing hindbrain. Rhombomere r4-specific expression of both Hoxb1 and Hoxb2 depends upon bipartite cis Hox response elements for the group 1 paralogous proteins, Hoxal and Hoxbl. The DNA-binding ability and selectivity of these proteins depend upon the formation of specific heterodimeric complexes with members of the PBC homeodomain protein family (Pbx genes). The r4 enhancers from Hoxb1 and Hoxb2 have the same activity, but differ with respect to the number and organisation of bipartite Pbx/Hox (PH) sites required, suggesting the intervention of other components/sequences. We report here that another family of homeodomain proteins (TALE, Three-Amino acids-Loop-Extension: Prep1, Meis, HTH), capable of dimerizing with Pbx/EXD, is involved in the mechanisms of r4-restricted expression. We show that: (1) the r4-specific Hoxb1 and Hoxb2 enhancers are complex elements containing separate PH and Prep/Meis (PM) sites; (2) the PM site of the Hoxb2, but not Hoxb1, enhancer is essential in vivo for r4 expression and also influences other sites of expression; (3) both PM and PH sites are required for in vitro binding of Prepl-Pbx and formation and binding of a ternary Hoxbl-Pbxla (or 1b)-Prepl complex. (4) A similar ternary association forms in nuclear extracts from embryonal P19 cells, but only upon retinoic acid induction. This requires synthesis of Hoxbl and also contains Pbx with either Prepl or Meisl. Together these findings highlight the fact that PM sites are found in close proximity to bipartite PH motifs in several Hox responsive elements shown to be important in vivo and that such sites play an essential role in potentiating regulatory activity in combination with the PH motifs.

Isotopic evidence of multiple controls on atmospheric oxidants over climate transitions

NASA Astrophysics Data System (ADS)

Geng, Lei; Murray, Lee T.; Mickley, Loretta J.; Lin, Pu; Fu, Qiang; Schauer, Andrew J.; Alexander, Becky

2017-06-01

The abundance of tropospheric oxidants, such as ozone (O3) and hydroxyl (OH) and peroxy radicals (HO2 + RO2), determines the lifetimes of reduced trace gases such as methane and the production of particulate matter important for climate and human health. The response of tropospheric oxidants to climate change is poorly constrained owing to large uncertainties in the degree to which processes that influence oxidants may change with climate and owing to a lack of palaeo-records with which to constrain levels of atmospheric oxidants during past climate transitions. At present, it is thought that temperature-dependent emissions of tropospheric O3 precursors and water vapour abundance determine the climate response of oxidants, resulting in lower tropospheric O3 in cold climates while HOx (= OH + HO2 + RO2) remains relatively buffered. Here we report observations of oxygen-17 excess of nitrate (a proxy for the relative abundance of atmospheric O3 and HOx) from a Greenland ice core over the most recent glacial-interglacial cycle and for two Dansgaard-Oeschger events. We find that tropospheric oxidants are sensitive to climate change with an increase in the O3/HOx ratio in cold climates, the opposite of current expectations. We hypothesize that the observed increase in O3/HOx in cold climates is driven by enhanced stratosphere-to-troposphere transport of O3, and that reactive halogen chemistry is also enhanced in cold climates. Reactive halogens influence the oxidative capacity of the troposphere directly as oxidants themselves and indirectly via their influence on O3 and HOx. The strength of stratosphere-to-troposphere transport is largely controlled by the Brewer-Dobson circulation, which may be enhanced in colder climates owing to a stronger meridional gradient of sea surface temperatures, with implications for the response of tropospheric oxidants and stratospheric thermal and mass balance. These two processes may represent important, yet relatively unexplored, climate feedback mechanisms during major climate transitions.

Establishing the Dependence of [HO2]/[OH] on Temperature, Halogen Loading, O3, and NO(x) Based on in Situ Measurements from the NASA ER-2

NASA Technical Reports Server (NTRS)

Lanzendorf, E. J.; Hanisco, T. F.; Wennberg, P. O.; Cohen, R. C.; Stimpfle, R. M.; Anderson, J. G.; Gao, R. S.; Margitan, J. J.; Bui, T. P.

2001-01-01

In situ observations of OH and HO2 from the Airborne Southern Hemisphere Ozone Experiment/Measurements for Assessing the Effects of Stratospheric Aircraft (ASHOE/MAESA), Stratospheric TRacers of Atmospheric Transport (STRAT), and Polar Ozone Loss in the Arctic Region in Summer (POLARIS) NASA ER-2 field campaigns are used to examine the partitioning of HO(x) in the lower stratosphere (tropopause to approx.21 km) and upper troposphere (approx.10 km to tropopause). These measurements span a latitude range from 70degS to 90degN and a variety of atmospheric conditions as a result of seasonal changes and altitude. The response of the observed [HO2]/[OH] to changes in temperature, [03], [CO], [NO], [CIO], and [BrO] is investigated. The measured ratio is accurately described (approx.+/-10%) by a steady-state model constrained by the measured mixing ratios of O3, CO, NO, CIO, and BrO, where the model is valid for conditions of HO(x) cycling much faster than HO(x) production and loss. The concentration of HO2 depends on [OH], which, to first order, has been observed to be a simple function of the solar zenith angle in the lower stratosphere. The partitioning between OH and HO2 is controlled by the local chemistry between the HO, radicals and O3, CO, NO, CIO, and BrO. The response of [HO(x)] to changes in [NO(x)] and [O3] is demonstrated. Further observations are necessary to illustrate the response of HO(x) to changes in halogen concentrations. A quantitative understanding of [HO2]/[OH] is important, since many of the reactions that control this ratio are directly involved in catalytic removal of O3 in the lower stratosphere and production of O3 in the upper troposphere.

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

Song, Peng-Yuan; Zhang, Wei-De, E-mail: zhangwd@scut.edu.cn

Highlights: • Preparation of nanostructured In{sub 2}O{sub 3} microspheres. • Morphology and phase control of In{sub 2}O{sub 3}. • Gas sensors based on the In{sub 2}O{sub 3} microspheres exhibit excellent sensing properties for the detection of formaldehyde. - Abstract: Urchin-like InOOH microspheres were successfully prepared by a convenient and controllable method. Such experimental parameters as solvents and complexing reagents on the formation of the urchin-like InOOH microspheres were investigated. Scanning electron microscopy, X-ray diffraction and infrared spectroscopy were employed to investigate the evolution process of the urchin-like InOOH precursors. Furthermore, the formation mechanism of the urchin-like InOOH microspheres was proposed.more » By annealing the urchin-like InOOH precursor at different temperatures under ambient pressure, rhombohedral corundum-type indium oxide (rh-In{sub 2}O{sub 3}), cubic bixbyite-type indium oxide (c-In{sub 2}O{sub 3}) and mixed phases of rh-In{sub 2}O{sub 3} and c-In{sub 2}O{sub 3} were obtained. The gas sensing properties of the prepared In{sub 2}O{sub 3} samples were examined. It was found that the sensors based on the prepared In{sub 2}O{sub 3} samples exhibited excellent response and selectivity to formaldehyde.« less

Effects of ocean acidification and diet on thickness and carbonate elemental composition of the test of juvenile sea urchins.

PubMed

Asnaghi, Valentina; Mangialajo, Luisa; Gattuso, Jean-Pierre; Francour, Patrice; Privitera, Davide; Chiantore, Mariachiara

2014-02-01

Continuous anthropogenic CO2 emissions to the atmosphere and uptake by the oceans will cause a reduction of seawater pH and saturation state (Ω) of CaCO3 minerals from which marine calcifiers build their shells and skeletons. Sea urchins use the most soluble form of calcium carbonate, high-magnesium calcite, to build their skeleton, spines and grazing apparatus. In order to highlight the effects of increased pCO2 on the test thickness and carbonate elemental composition of juvenile sea urchins and potential differences in their responses linked to the diet, we performed a laboratory experiment on juvenile Paracentrotus lividus, grazing on calcifying (Corallina elongata) and non-calcifying (Cystoseira amentacea, Dictyota dichotoma) macroalgae, under different pH (corresponding to pCO2 values of 390, 550, 750 and 1000 μatm). Results highlighted the importance of the diet in determining sea urchin size irrespectively of the pCO2 level, and the relevance of macroalgal diet in modulating urchin Mg/Ca ratio. The present study provides relevant clues both in terms of the mechanism of mineral incorporation and in terms of bottom-up processes (algal diet) affecting top-down ones (fish predation) in rocky subtidal communities. Copyright © 2013 Elsevier Ltd. All rights reserved.

Biotic and environmental stress induces nitration and changes in structure and function of the sea urchin major yolk protein toposome.

PubMed

Castellano, Immacolata; Migliaccio, Oriana; Ferraro, Giarita; Maffioli, Elisa; Marasco, Daniela; Merlino, Antonello; Zingone, Adriana; Tedeschi, Gabriella; Palumbo, Anna

2018-03-15

The major yolk protein toposome plays crucial roles during gametogenesis and development of sea urchins. We previously found that nitration of toposome increases in the gonads of a Paracentrotus lividus population living in a marine protected area affected by toxic blooms of Ostreospsis cf. ovata, compared to control populations. This modification is associated with ovatoxin accumulation, high levels of nitric oxide in the gonads, and a remarkable impairment of progeny development. However, nothing is known about the environmental-mediated-regulation of the structure and biological function of toposome. Here, we characterize through wide-ranging biochemical and structural analyses the nitrated toposome of sea urchins exposed to the bloom, and subsequently detoxified. The increased number of nitrated tyrosines in toposome of sea urchins collected during algal bloom induced structural changes and improvement of the Ca 2+ -binding affinity of the protein. After 3 months' detoxification, ovatoxin was undetectable, and the number of nitric oxide-modified tyrosines was reduced. However, the nitration of specific residues was irreversible and occurred also in embryos treated with metals, used as a proxy of environmental pollutants. The structural and functional changes of toposome caused by nitration under adverse environmental conditions may be related to the defective development of sea urchins' progeny.

Quantitative developmental transcriptomes of the Mediterranean sea urchin Paracentrotus lividus.

PubMed

Gildor, Tsvia; Malik, Assaf; Sher, Noa; Avraham, Linor; Ben-Tabou de-Leon, Smadar

2016-02-01

Embryonic development progresses through the timely activation of thousands of differentially activated genes. Quantitative developmental transcriptomes provide the means to relate global patterns of differentially expressed genes to the emerging body plans they generate. The sea urchin is one of the classic model systems for embryogenesis and the models of its developmental gene regulatory networks are of the most comprehensive of their kind. Thus, the sea urchin embryo is an excellent system for studies of its global developmental transcriptional profiles. Here we produced quantitative developmental transcriptomes of the sea urchin Paracentrotus lividus (P. lividus) at seven developmental stages from the fertilized egg to prism stage. We generated de-novo reference transcriptome and identified 29,817 genes that are expressed at this time period. We annotated and quantified gene expression at the different developmental stages and confirmed the reliability of the expression profiles by QPCR measurement of a subset of genes. The progression of embryo development is reflected in the observed global expression patterns and in our principle component analysis. Our study illuminates the rich patterns of gene expression that participate in sea urchin embryogenesis and provide an essential resource for further studies of the dynamic expression of P. lividus genes. Copyright © 2015 Elsevier B.V. All rights reserved.

Overview of the molecular defense systems used by sea urchin embryos to cope with UV radiation.

PubMed

Bonaventura, Rosa; Matranga, Valeria

2017-07-01

The sea urchin embryo is a well-recognized developmental biology model and its use in toxicological studies has been widely appreciated. Many studies have focused on the evaluation of the effects of chemical stressors and their mixture in marine ecosystems using sea urchin embryos. These are well equipped with defense genes used to cope with chemical stressors. Recently, ultraviolet radiation (UVR), particularly UVB (280-315 nm), received more attention as a physical stressor. Mainly in the Polar Regions, but also at temperate latitudes, the penetration of UVB into the oceans increases as a consequence of the reduction of the Earth's ozone layer. In general, UVR induces oxidative stress in marine organisms affecting molecular targets such as DNA, proteins, and lipids. Depending on the UVR dose, developing sea urchin embryos show morphological perturbations affecting mainly the skeleton formation and patterning. Nevertheless, embryos are able to protect themselves against excessive UVR, using mechanisms acting at different levels: transcriptional, translational and post-translational. In this review, we recommend the sea urchin embryo as a suitable model for testing physical stressors such as UVR and summarize the mechanisms adopted to deal with UVR. Moreover, we review UV-induced apoptotic events and the combined effects of UVR and other stressors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification of neural transcription factors required for the differentiation of three neuronal subtypes in the sea urchin embryo.

PubMed

Slota, Leslie A; McClay, David R

2018-03-15

Correct patterning of the nervous system is essential for an organism's survival and complex behavior. Embryologists have used the sea urchin as a model for decades, but our understanding of sea urchin nervous system patterning is incomplete. Previous histochemical studies identified multiple neurotransmitters in the pluteus larvae of several sea urchin species. However, little is known about how, where and when neural subtypes are differentially specified during development. Here, we examine the molecular mechanisms of neuronal subtype specification in 3 distinct neural subtypes in the Lytechinus variegatus larva. We show that these subtypes are specified through Delta/Notch signaling and identify a different transcription factor required for the development of each neural subtype. Our results show achaete-scute and neurogenin are proneural for the serotonergic neurons of the apical organ and cholinergic neurons of the ciliary band, respectively. We also show that orthopedia is not proneural but is necessary for the differentiation of the cholinergic/catecholaminergic postoral neurons. Interestingly, these transcription factors are used similarly during vertebrate neurogenesis. We believe this study is a starting point for building a neural gene regulatory network in the sea urchin and for finding conserved deuterostome neurogenic mechanisms. Copyright © 2018 Elsevier Inc. All rights reserved.

Seasonal antioxidant responses in the sea urchin Paracentrotus lividus (Lamarck 1816) used as a bioindicator of the environmental contamination in the South-East Mediterranean.

PubMed

Amri, Sandra; Samar, Mohamed-Faouzi; Sellem, Fériel; Ouali, Kheireddine

2017-09-15

In this study, sea urchin Paracentrotus lividus were sampled seasonally at three stations during 2012 in the coastal areas of the Gulf of Annaba (southeast Mediterranean). For all sea urchins, the gonad index was calculated to determine sea urchin reproductive status. Moreover, a set of biochemical parameters, including biomarkers and oxidative stress parameters, was measured in gonads. The pesticides and physiochemical parameters were measured and dosed in sea water. The results obtained highlighted that the levels of pesticide were generally low and below those commonly applied by environmental quality standards (EQS), indicating that no alarm state is currently present in the Gulf of Annaba. In addition to pollution, seasonal change is an important factor influencing biomarker activity, and the significant increases in biomarker levels in spring are a major observed trend. This activity may also be related to reproductive status. Seasonal variability was confirmed by the significant results of the Kruskal-Wallis test and by the high degree of divergence between seasons in PCA, with a total of 83.83% of variance explained. These results indicate that environmental factors that vary seasonally may affect the antioxidant status of the sea urchin Paracentrotus lividus. Copyright © 2017 Elsevier Ltd. All rights reserved.

Assessment of sediment contamination by spermiotoxicity and embryotoxicity bioassays with sea urchins (Paracentrotus lividus) and oysters (Crassostrea gigas).

PubMed

Geffard, O; Budzinski, H; Augagneur, S; Seaman, M N; His, E

2001-07-01

Gametes (sperm) and fertilized eggs (embryos) of the Mediterranean sea urchin, Paracentrotus lividus, and the Japanese oyster, Crassostrea gigas, were used to investigate the toxicity of two marine sediments, one polluted by polycyclic aromatic hydrocarbons (PAH) and the other by heavy metals. The sediment samples were freeze-dried for storage, and three different treatments were used for analysis: whole sediment, unfiltered elutriate, and filtered elutriate. The two sediments were toxic to sea urchin spermatozoa but not to oyster spermatozoa, and embryotoxicity was almost always the more sensitive endpoint for toxicity assessment. As a rule, whole sediment was more toxic than the elutriates by nearly two orders of magnitude. With respect to embryotoxicity, the whole sediments and the elutriates of the PAH-contaminated sediment were more toxic to oyster embryos, whereas the elutriates of the sediment polluted by heavy metals had stronger effects on sea urchin embryos. The results confirm that bioassays with Japanese oyster embryos provide a more sensitive appraisal of toxicity in the marine environment than bioassays with other developmental stages. As a whole, Mediterranean sea urchins and Japanese oysters were similar in overall sensitivity and are therefore both equally suited as bioassay organisms, but tests with oysters are more reproducible because of the better performance of the controls.

Relationships between fish, sea urchins and macroalgae: The structure of shallow rocky sublittoral communities in the Cyclades, Eastern Mediterranean

NASA Astrophysics Data System (ADS)

Giakoumi, Sylvaine; Cebrian, Emma; Kokkoris, Giorgos D.; Ballesteros, Enric; Sala, Enric

2012-08-01

Historical overfishing is the most likely explanation for the depletion of the shallow sublittoral communities in many areas not least in the Cyclades Archipelago, Greece. The present study is the first quantitative study of the shallow rocky sublittoral of the Cyclades based on in situ underwater surveys of algal cover, and fish and sea urchin abundance at 181 sampling sites in 25 islands to provide a baseline and investigate the relationship between these communities. Algal turf was the most abundant algal functional group, and canopy algae of the genus Cystoseira were more abundant at the northern islands. A range in fish biomass of almost two orders of magnitude was found across islands, but overall the Cyclades displayed much lower values than fished areas of the Western Mediterranean. We observed apex predators only in 25% of our sampling sites, and their biomass was uncorrelated to total fish biomass, indicating a depleted ecosystem. Sea urchin biomass was also low but similar to values found in other Mediterranean islands and was positively correlated with barrens. We observed a gradient of benthic community complexity from sea urchin barrens to communities dominated by Cystoseira spp. There was no correlation between sea urchins and their predators Diplodus spp., which presented extremely low densities.

Effects of the toxic benthic dinoflagellate Ostreopsis cf. ovata on fertilization and early development of the sea urchin Lytechinus variegatus.

PubMed

Neves, Raquel A F; Contins, Mariana; Nascimento, Silvia M

2018-04-01

Blooms of the benthic dinoflagellate Ostreopsis cf. ovata have been recorded with increasing frequency, intensity and geographic distribution. This dinoflagellate produces potent toxins that may cause mortality of marine invertebrates. Adults of sea urchins are commonly affected by O. cf. ovata exposure with evidence of spines loss and high mortality during periods of high dinoflagellate abundances. Here, we report on the effects of the toxic dinoflagellate O. cf. ovata on fertilization and early development of the sea urchin Lytechinus variegatus, a key ecological herbivore. Lytechinus variegatus eggs and sperm were experimentally exposed to different concentrations of Ostreopsis cf. ovata (4, 40, 400, and 4000 cells ml -1 ) to test the hypothesis that fertilization success, embryonic and larval development of the sea urchin are negatively affected by the toxic dinoflagellate even at low abundances. Reduced fertilization, developmental failures, embryo and larval mortality, and occurrence of abnormal offspring were evident after exposure to O. cf. ovata. Fertilization decreased when gametes were exposed to high O. cf. ovata abundances (400 and 4000 cells ml -1 ), but just the exposure to the highest abundance significantly reduced fertilization success. Sea urchin early development was affected by O. cf. ovata in a dose-dependent way, high dinoflagellate abundances fully inhibited the early development of L. variegatus. Ostreopsis cf. ovata significantly increased the mortality of sea urchin eggs and embryos in the first hours of exposure (∼1-3 h), regardless of dinoflagellate abundance. Abundances of 400 and 4000 O. cf. ovata cells ml -1 induced significantly higher mortality on sea urchin initial stages in the first hours, and no egg or embryo was found in these treatments after 18 h of incubation. The early echinopluteus larva was only reached in the control and in treatments with low Ostreopsis cf. ovata abundances (4 and 40 cells ml -1 ). The exposure to O. cf. ovata led to significantly higher occurrence of skeletal anomalies in the early larva of L. variegatus. Interactions of sea urchin gametes and Ostreopsis cells may naturally occur in coastal areas due to the match between O. cf. ovata blooms and L. variegatus reproductive period. Reduced larval density and increased larval abnormalities were observed even at low abundances (4 and 40 cells ml -1 ) frequently found in tropical environments all year round. The chronic exposure to O. cf. ovata could significantly impact larval fitness, thus compromising recruitment success, and highlight the negative effects of benthic HABs on sea urchin populations and its possible broader ecological implications. Copyright © 2018 Elsevier Ltd. All rights reserved.

Aircraft HO sub x and NO sub x emission effects on stratospheric ozone and temperature

NASA Technical Reports Server (NTRS)

Glatt, L.; Widhopf, G. F.

1978-01-01

A simplified two-dimensional steady-state photochemical model of the atmosphere was developed. The model was used to study the effect on the thermal and chemical structure of the atmosphere of two types of pollution cases: (1) injection of NOx and HOx from a hypothetical fleet of supersonic and subsonic aircraft and (2) injection of HOx from a hypothetical fleet of liquid-fueled hydrogen aircraft. The results are discussed with regard to stratospheric perturbations in ozone, water vapor and temperature.

TROPICAL COLLECTOR URCHIN, TRIPNEUSTES GRATILLA, FERTILIZATION TEST METHOD

EPA Science Inventory

This document describes a fertilization method to estimate the chronic toxicity of effluents and receiving waters to the gametes of the tropical sea urchin (Tripneustes gratilla). This toxicity test measures the fertilizing capacity of sperm following a static, non-renewal 60-mi...

Proteomic dataset of the sea urchin Paracentrotus lividus adhesive organs and secreted adhesive.

PubMed

Lebesgue, Nicolas; da Costa, Gonçalo; Ribeiro, Raquel Mesquita; Ribeiro-Silva, Cristina; Martins, Gabriel G; Matranga, Valeria; Scholten, Arjen; Cordeiro, Carlos; Heck, Albert J R; Santos, Romana

2016-06-01

Sea urchins have specialized adhesive organs called tube feet, which mediate strong but reversible adhesion. Tube feet are composed by a disc, producing adhesive and de-adhesive secretions for substratum attachment, and a stem for movement. After detachment the secreted adhesive remains bound to the substratum as a footprint. Recently, a label-free quantitative proteomic approach coupled with the latest mass-spectrometry technology was used to analyze the differential proteome of Paracentrotus lividus adhesive organ, comparing protein expression levels in the tube feet adhesive part (the disc) versus the non-adhesive part (the stem), and also to profile the proteome of the secreted adhesive (glue). This data article contains complementary figures and results related to the research article "Deciphering the molecular mechanisms underlying sea urchin reversible adhesion: a quantitative proteomics approach" (Lebesgue et al., 2016) [1]. Here we provide a dataset of 1384 non-redundant proteins, their fragmented peptides and expression levels, resultant from the analysis of the tube feet differential proteome. Of these, 163 highly over-expressed tube feet disc proteins (>3-fold), likely representing the most relevant proteins for sea urchin reversible adhesion, were further annotated in order to determine the potential functions. In addition, we provide a dataset of 611 non-redundant proteins identified in the secreted adhesive proteome, as well as their functional annotation and grouping in 5 major protein groups related with adhesive exocytosis, and microbial protection. This list was further analyzed to identify the most abundant protein groups and pinpoint putative adhesive proteins, such as Nectin, the most abundant adhesive protein in sea urchin glue. The obtained data uncover the key proteins involved in sea urchins reversible adhesion, representing a step forward to the development of new wet-effective bio-inspired adhesives.

[Morphology of gametes in sea urchins from Peter the Great Bay, Sea of Japan].

PubMed

Drozdov, A L; Vinnikova, V V

2010-01-01

The fine structure of the gametes in six sea urchin species of the Sea of Japan was studied. The spermatozoons in Strongylocentrotus nudus, S. intermedius, Echinocardium cordatum, Scaphechinus mirabilis, Sc. grizeus and Echinarachnius parma are species-specific. The conical head and symmetrically disposed ring-shape mitochondrion are common to regular sea urchin sperm cells. S. nudus is characterized by the bulb-shaped head of the zoosperm; S. intermedius, by a bullet-shaped one. The zoosperm spearhead and small amount of postacrosome material are common to irregular sea urchins; the sperm width: length ratio varies for different species, with the highest for Sc. mirabilis. The zoosperm of Sc. griseus is characterized by two lipid drops in the cell center. Asymmetrical mitochondrion disposal is usual for E. parma. Actin filaments are found in the postacrosome material in the zoosperm of cordiform sea urchins. The differences in the fine structure of zoosperm in eurybiont species Ech. cordatum inhabiting the Sea of Japan and coastal areas of the Northeast Atlantic may bear record to the complex existence of species Ech. cordatum. The fine structure of zoosperm is unique for each of the studied families, Strongylocentrotidae, Scutellidae, and Loveniidae. The eggs of all the species are characterized by vitelline and tremelloid membranes. The vitelline membrane is formed by cytoplasm protrusions; the area between them is filled with fubrillary material. The tremelloid membrane is formed by fubrillary material associated with apical parts of microvilli of the vitelline membrane. The irregular sea urchins Sc. griseus, Sc. mirabilis and E. parma are characterized by chromatophores situated in the tremelloid membrane, with the highest abundance in Sc. mirabilis.

Alteration of neurotransmission and skeletogenesis in sea urchin Arbacia lixula embryos exposed to copper oxide nanoparticles.

PubMed

Cappello, Tiziana; Vitale, Valeria; Oliva, Sabrina; Villari, Valentina; Mauceri, Angela; Fasulo, Salvatore; Maisano, Maria

2017-09-01

The extensive use of copper oxide nanoparticles (CuO NPs) in many applications has raised concerns over their toxicity on environment and human health. Herein, the embryotoxicity of CuO NPs was assessed in the black sea urchin Arbacia lixula, an intertidal species commonly present in the Mediterranean. Fertilized eggs were exposed to 0.7, 10 and 20ppb of CuO NPs, until pluteus stage. Interferences with the normal neurotransmission pathways were observed in sea urchin embryos. In detail, evidence of cholinergic and serotoninergic systems affection was revealed by dose-dependent decreased levels of choline and N-acetyl serotonin, respectively, measured by nuclear magnetic resonance (NMR)-based metabolomics, applied for the first time to our knowledge on sea urchin embryos. The metabolic profile also highlighted a significant CuO NP dose-dependent increase of glycine, a component of matrix proteins involved in the biomineralization process, suggesting perturbed skeletogenesis accordingly to skeletal defects in spicule patterning observed previously in the same sea urchin embryos. However, the expression of skeletogenic genes, i.e. SM30 and msp130, did not differ among groups, and therefore altered primary mesenchyme cell (PMC) migration was hypothesized. Other unknown metabolites were detected from the NMR spectra, and their concentrations found to be reflective of the CuO NP exposure levels. Overall, these findings demonstrate the toxic potential of CuO NPs to interfere with neurotransmission and skeletogenesis of sea urchin embryos. The integrated use of embryotoxicity tests and metabolomics represents a highly sensitive and effective tool for assessing the impact of NPs on aquatic biota. Copyright © 2017 Elsevier Inc. All rights reserved.

SoxB2 in sea urchin development: implications in neurogenesis, ciliogenesis and skeletal patterning.

PubMed

Anishchenko, Evgeniya; Arnone, Maria Ina; D'Aniello, Salvatore

2018-01-01

Current studies in evolutionary developmental biology are focused on the reconstruction of gene regulatory networks in target animal species. From decades, the scientific interest on genetic mechanisms orchestrating embryos development has been increasing in consequence to the fact that common features shared by evolutionarily distant phyla are being clarified. In 2011, a study across eumetazoan species showed for the first time the existence of a highly conserved non-coding element controlling the SoxB2 gene, which is involved in the early specification of the nervous system. This discovery raised several questions about SoxB2 function and regulation in deuterostomes from an evolutionary point of view. Due to the relevant phylogenetic position within deuterostomes, the sea urchin Strongylocentrotus purpuratus represents an advantageous animal model in the field of evolutionary developmental biology. Herein, we show a comprehensive study of SoxB2 functions in sea urchins, in particular its expression pattern in a wide range of developmental stages, and its co-localization with other neurogenic markers, as SoxB1 , SoxC and Elav . Moreover, this work provides a detailed description of the phenotype of sea urchin SoxB2 knocked-down embryos, confirming its key function in neurogenesis and revealing, for the first time, its additional roles in oral and aboral ectoderm cilia and skeletal rod morphology. We concluded that SoxB2 in sea urchins has a neurogenic function; however, this gene could have multiple roles in sea urchin embryogenesis, expanding its expression in non-neurogenic cells. We showed that SoxB2 is functionally conserved among deuterostomes and suggested that in S. purpuratus this gene acquired additional functions, being involved in ciliogenesis and skeletal patterning.

Proteomic dataset of the sea urchin Paracentrotus lividus adhesive organs and secreted adhesive

PubMed Central

Lebesgue, Nicolas; da Costa, Gonçalo; Ribeiro, Raquel Mesquita; Ribeiro-Silva, Cristina; Martins, Gabriel G.; Matranga, Valeria; Scholten, Arjen; Cordeiro, Carlos; Heck, Albert J.R.; Santos, Romana

2016-01-01

Sea urchins have specialized adhesive organs called tube feet, which mediate strong but reversible adhesion. Tube feet are composed by a disc, producing adhesive and de-adhesive secretions for substratum attachment, and a stem for movement. After detachment the secreted adhesive remains bound to the substratum as a footprint. Recently, a label-free quantitative proteomic approach coupled with the latest mass-spectrometry technology was used to analyze the differential proteome of Paracentrotus lividus adhesive organ, comparing protein expression levels in the tube feet adhesive part (the disc) versus the non-adhesive part (the stem), and also to profile the proteome of the secreted adhesive (glue). This data article contains complementary figures and results related to the research article “Deciphering the molecular mechanisms underlying sea urchin reversible adhesion: a quantitative proteomics approach” (Lebesgue et al., 2016) [1]. Here we provide a dataset of 1384 non-redundant proteins, their fragmented peptides and expression levels, resultant from the analysis of the tube feet differential proteome. Of these, 163 highly over-expressed tube feet disc proteins (>3-fold), likely representing the most relevant proteins for sea urchin reversible adhesion, were further annotated in order to determine the potential functions. In addition, we provide a dataset of 611 non-redundant proteins identified in the secreted adhesive proteome, as well as their functional annotation and grouping in 5 major protein groups related with adhesive exocytosis, and microbial protection. This list was further analyzed to identify the most abundant protein groups and pinpoint putative adhesive proteins, such as Nectin, the most abundant adhesive protein in sea urchin glue. The obtained data uncover the key proteins involved in sea urchins reversible adhesion, representing a step forward to the development of new wet-effective bio-inspired adhesives. PMID:27182547

Genomic analysis of a new mammalian distal-less gene: Dlx7.

PubMed

Nakamura, S; Stock, D W; Wydner, K L; Bollekens, J A; Takeshita, K; Nagai, B M; Chiba, S; Kitamura, T; Freeland, T M; Zhao, Z; Minowada, J; Lawrence, J B; Weiss, K M; Ruddle, F H

1996-12-15

We have cloned a new Dlx gene (Dlx7) from human and mouse that may represent the mammalian orthologue of the newt gene NvHBox-5. The homeodomains of these genes are highly similar to all other vertebrate Dlx genes, and regions of similarity also exist between mammalian Dlx7 and a subset of vertebrate Dlx genes downstream of the homeodomain. The sequence divergence between human and mouse Dlx7 in these regions is greater than that predicted from comparisons of other vertebrate Dlx genes, however, and there is little sequence similarity upstream of the homeodomain both between these two genes and with other Dlx genes. We present evidence for alternative splicing of mouse Dlx7 upstream of the homeodomain that may account for some of this divergence. We have mapped human DLX7 distal to the 5' end of the HOXB cluster at an estimated distance of between 1 and 2 Mb by FISH. Both the human and the mouse Dlx7 are shown to be closely linked to Dlx3 in a convergently transcribed orientation. These mapping results support the possibility that vertebrate distal-less genes have been duplicated in concert with the Hox clusters.

The impact of temperature dependent CO2 cross section measurements: A role for heterogeneous chemistry in the atmosphere of Mars?

NASA Technical Reports Server (NTRS)

Anbar, A. D.; Allen, M.; Nair, H.; Leu, M-T.; Yung, Y. L.

1992-01-01

Carbon dioxide comprises over 95 percent of the Mars atmosphere, despite continuous photolysis of CO2 by solar ultraviolet (UV) radiation. Since the direct recombination of CO and O is spinforbidden, the chemical stability of CO2 in the Martian atmosphere is thought to be the result of a HO(x)-catalyzed recombination scheme. Thus the rate of CO oxidation is sensitive to the abundance and altitude distribution of OH, H, and HO2. Most Martian atmospheric models assume that HO(x) abundances are governed purely by gas phase chemistry. However, it is well established that reactive HO(x) radical are adsorbed by a wide variety of surfaces. The authors have combined laboratory studies of H, OH, and HO2 adsorption on inorganic surfaces, observational data of aerosol distributions, and an updated photochemical model to demonstrate that adsorption on either dust or ice aerosols is capable of reducing HO(x) abundances significantly, thereby retarding the rate of CO oxidation.

Advances in the Function and Regulation of Hydrogenase in the Cyanobacterium Synechocystis PCC6803

PubMed Central

Cassier-Chauvat, Corinne; Veaudor, Théo; Chauvat, Franck

2014-01-01

In order to use cyanobacteria for the biological production of hydrogen, it is important to thoroughly study the function and the regulation of the hydrogen-production machine in order to better understand its role in the global cell metabolism and identify bottlenecks limiting H2 production. Most of the recent advances in our understanding of the bidirectional [Ni-Fe] hydrogenase (Hox) came from investigations performed in the widely-used model cyanobacterium Synechocystis PCC6803 where Hox is the sole enzyme capable of combining electrons with protons to produce H2 under specific conditions. Recent findings suggested that the Hox enzyme can receive electrons from not only NAD(P)H as usually shown, but also, or even preferentially, from ferredoxin. Furthermore, plasmid-encoded functions and glutathionylation (the formation of a mixed-disulfide between the cysteines residues of a protein and the cysteine residue of glutathione) are proposed as possible new players in the function and regulation of hydrogen production. PMID:25365180

The C. elegans SoxC protein SEM-2 opposes differentiation factors to promote a proliferative blast cell fate in the postembryonic mesoderm

PubMed Central

Tian, Chenxi; Shi, Herong; Colledge, Clark; Stern, Michael; Waterston, Robert; Liu, Jun

2011-01-01

The proper development of multicellular organisms requires precise regulation and coordination of cell fate specification, cell proliferation and differentiation. Abnormal regulation and coordination of these processes could lead to disease, including cancer. We have examined the function of the sole C. elegans SoxC protein, SEM-2, in the M lineage, which produces the postembryonic mesoderm. We found that SEM-2/SoxC is both necessary and sufficient to promote a proliferating blast cell fate, the sex myoblast fate, over a differentiated striated bodywall muscle fate. A number of factors control the specific expression of sem-2 in the sex myoblast precursors and their descendants. This includes direct control of sem-2 expression by a Hox-PBC complex. The crucial nature of the HOX/PBC factors in directly enhancing expression of this proliferative factor in the C. elegans M lineage suggests a possible more general link between Hox-PBC factors and SoxC proteins in regulating cell proliferation. PMID:21307099

TALE transcription factors during early development of the vertebrate brain and eye.

PubMed

Schulte, Dorothea; Frank, Dale

2014-01-01

Our brain's cognitive performance arises from the coordinated activities of billions of nerve cells. Despite a high degree of morphological and functional differences, all neurons of the vertebrate central nervous system (CNS) arise from a common field of multipotent progenitors. Cell fate specification and differentiation are directed by multistep processes that include inductive/external cues, such as the extracellular matrix or growth factors, and cell-intrinsic determinants, such as transcription factors and epigenetic modulators of proteins and DNA. Here we review recent findings implicating TALE-homeodomain proteins in these processes. Although originally identified as HOX-cofactors, TALE proteins also contribute to many physiological processes that do not require HOX-activity. Particular focus is, therefore, given to HOX-dependent and -independent functions of TALE proteins during early vertebrate brain development. Additionally, we provide an overview about known upstream and downstream factors of TALE proteins in the developing vertebrate brain and discuss general concepts of how TALE proteins function to modulate neuronal cell fate specification. Copyright © 2013 Wiley Periodicals, Inc.

Apoptosis: Focus on sea urchin development.

PubMed

Agnello, Maria; Roccheri, Maria Carmela

2010-03-01

It has been proposed that the apoptosis is an essential requirement for the evolution of all animals, in fact the apoptotic program is highly conserved from nematodes to mammals. Throughout development, apoptosis is employed by multicellular organisms to eliminate damaged or unnecessary cells. Here, we will discuss both developmental programmed cell death (PCD) under normal conditions and stress induced apoptosis, in sea urchin embryos. Sea urchin represent an excellent model system for studying embryogenesis and cellular processes involved in metamorphosis. PCD plays an essential role in sculpting and remodelling the embryos and larvae undergoing metamorphosis. Moreover, this marine organism directly interacts with its environment, and is susceptible to effects of several aquatic contaminants. Apoptosis can be adopted as a defence mechanism against any environmental chemical, physical and mechanical stress, for removing irreversibly damaged cells. This review, while not comprehensive in its reporting, aims to provide an overview of current knowledge on mechanisms to regulate physiological and the induced apoptotic program in sea urchin embryos.

The Ars insulator facilitates I-SceI meganuclease-mediated transgenesis in the sea urchin embryo.

PubMed

Ochiai, Hiroshi; Sakamoto, Naoaki; Suzuki, Kenichi; Akasaka, Koji; Yamamoto, Takashi

2008-09-01

For the efficient generation of transgenic sea urchins, we have adopted an I-SceI meganuclease-mediated transgenesis method. Several types of promoter-GFP gene constructs flanked by two I-SceI recognition sequences were co-injected with I-SceI into sea urchin fertilized eggs. Using cell-lineage-specific promoter constructs, the frequency of transgene expression was elevated, and their level of mozaicism was reduced. The addition of the Ars insulator sequence, which is known to block the enhancer activity and protect transgenes from position effects, led to a reduction in ectopic transgene expression and an elevation of transgene expression frequency in this I-SceI-mediated system. However, the magnitude of the effects of the Ars insulator was dependent upon the promoter constructs. QPCR analysis also showed that the Ars insulator increases the transgene copy number. These results suggest that the I-SceI-mediated method using the Ars insulator is advantageous for transgenesis in the sea urchin embryo.

Thermal diffusivity measurement for urchin-like gold nanofluids with different solvents, sizes and concentrations/shapes.

PubMed

López-Muñoz, Gerardo A; Balderas-López, José Abraham; Ortega-Lopez, Jaime; Pescador-Rojas, José A; Salazar, Jaime Santoyo

2012-12-06

The thermal properties of nanofluids are an especially interesting research topic because of the variety of potential applications, which range from bio-utilities to next-generation heat-transfer fluids. In this study, photopyroelectric calorimetry for measuring the thermal diffusivity of urchin-like colloidal gold nanofluids as a function of particle size, concentration and shape in water, ethanol and ethylene glycol is reported. Urchin-like gold nanoparticles were synthesised in the presence of hydroquinone through seed-mediated growth with homogeneous shape and size ranging from 55 to 115 nm. The optical response, size and morphology of these nanoparticles were characterised using UV-visible spectroscopy and transmission electron microscopy. The thermal diffusivity of these nanofluids decreased as the size of the nanoparticles increased, and the enhancement depended on the thermal diffusivity of the solvent. The opposite effect (increase in thermal diffusivity) was observed when the nanoparticle concentration was increased. These effects were more evident for urchin-like gold nanofluids than for the corresponding spherical gold nanofluids.

MnO2 prepared by hydrothermal method and electrochemical performance as anode for lithium-ion battery.

PubMed

Feng, Lili; Xuan, Zhewen; Zhao, Hongbo; Bai, Yang; Guo, Junming; Su, Chang-Wei; Chen, Xiaokai

2014-01-01

Two α-MnO2 crystals with caddice-clew-like and urchin-like morphologies are prepared by the hydrothermal method, and their structure and electrochemical performance are characterized by scanning electron microscope (SEM), X-ray diffraction (XRD), galvanostatic cell cycling, cyclic voltammetry, and electrochemical impedance spectroscopy (EIS). The morphology of the MnO2 prepared under acidic condition is urchin-like, while the one prepared under neutral condition is caddice-clew-like. The identical crystalline phase of MnO2 crystals is essential to evaluate the relationship between electrochemical performances and morphologies for lithium-ion battery application. In this study, urchin-like α-MnO2 crystals with compact structure have better electrochemical performance due to the higher specific capacity and lower impedance. We find that the relationship between electrochemical performance and morphology is different when MnO2 material used as electrochemical supercapacitor or as anode of lithium-ion battery. For lithium-ion battery application, urchin-like MnO2 material has better electrochemical performance.

Wet-Chemical Preparation of TiO2-Based Composites with Different Morphologies and Photocatalytic Properties

PubMed Central

Xiang, Liqin; Zhao, Xiaopeng

2017-01-01

TiO2-based composites have been paid significant attention in the photocatalysis field. The size, crystallinity and nanomorphology of TiO2 materials have an important effect on the photocatalytic efficiency. The synthesis and photocatalytic activity of TiO2-based materials have been widely investigated in past decades. Based on our group’s research works on TiO2 materials, this review introduces several methods for the fabrication of TiO2, rare-earth-doped TiO2 and noble-metal-decorated TiO2 particles with different morphologies. We focused on the preparation and the formation mechanism of TiO2-based materials with unique structures including spheres, hollow spheres, porous spheres, hollow porous spheres and urchin-like spheres. The photocatalytical activity of urchin-like TiO2, noble metal nanoparticle-decorated 3D (three-dimensional) urchin-like TiO2 and bimetallic core/shell nanoparticle-decorated urchin-like hierarchical TiO2 are briefly discussed. PMID:28991208

Can sea urchins beat the heat? Sea urchins, thermal tolerance and climate change

PubMed Central

2015-01-01

The massive die-off of the long-spined sea urchin, Diadema antillarum, a significant reef grazer, in the mid 1980s was followed by phase shifts from coral dominated to macroalgae dominated reefs in the Caribbean. While Diadema populations have recovered in some reefs with concomitant increases in coral cover, the additional threat of increasing temperatures due to global climate change has not been investigated in adult sea urchins. In this study, I measured acute thermal tolerance of D. antillarum and that of a sympatric sea urchin not associated with coral cover, Echinometra lucunter, over winter, spring, and summer, thus exposing them to substantial natural thermal variation. Animals were taken from the wild and placed in laboratory tanks in room temperature water (∼22 °C) that was then heated at 0.16–0.3 °C min−1 and the righting behavior of individual sea urchins was recorded. I measured both the temperature at which the animal could no longer right itself (TLoR) and the righting time at temperatures below the TLoR. In all seasons, D. antillarum exhibited a higher mean TLoR than E. lucunter. The mean TLoR of each species increased with increasing environmental temperature revealing that both species acclimatize to seasonal changes in temperatures. The righting times of D. antillarum were much shorter than those of E. lucunter. The longer relative spine length of Diadema compared to that of Echinometra may contribute to their shorter righting times, but does not explain their higher TLoR. The thermal safety margin (the difference between the mean collection temperature and the mean TLoR) was between 3.07–3.66 °C for Echinometra and 3.79–5.67 °C for Diadema. While these thermal safety margins exceed present day temperatures, they are modest compared to those of temperate marine invertebrates. If sea temperatures increase more rapidly than can be accommodated by the sea urchins (either by genetic adaptation, phenotypic plasticity, or both), this will have important consequences for the structure of coral reefs. PMID:26082862

Macrofaunal involvement in the sublittoral decay of kelp debris: The sea urchin Psammechinus miliaris (Gmelin) (Echinodermata: Echinoidea)

NASA Astrophysics Data System (ADS)

Bedford, A. P.; Moore, P. G.

1985-01-01

Psammechinus miliaris occurs in the Clyde Sea area in large numbers (<18 individuals per 100 g -1 weed dry wt) on sublittoral beds of detached Laminaria saccharina. Its rôle in weed decomposition has been examined by comparing its responses (behavioural choice, growth rate, absorption efficiencies of both carbon and protein, gut retention times and rate of faecal output) to fresh and rotting weed. Younger urchins grew faster than older individuals on a diet of rotting weed but not on fresh weed. Large seasonal variation existed, however, with fast growth occurring in June-August and little, or no, growth in December-February, irrespective of diet. Starved controls did not grow. Correcting for seasonality, rotting kelp still promoted faster growth of young urchins than did fresh weed. Larger (older) individuals showed no difference. Urchins fed fresh weed had significantly longer gut retention times. Protein absorption efficiency was higher on fresh than rotting weed, varying with weed protein content and size of urchin. Very young individuals can only digest high protein weed efficiently, eg. material derived from near the frond meristem. Organic carbon content of rotting weed was significantly lower than fresh weed. Carbon absorption efficiencies were significantly higher on fresh weed which related to organic carbon content. Standard-sized urchins fed rotting weed produced larger dry weights of faeces per day, reflecting increased ingestion rate. In closed-system choice experiments urchins preferred rotting weed kinetically. Size-frequency analysis of field populations suggested that weed beds are principally colonized by larval settlement from the plankton. Mature Psammechinus have evolved different 'strategies' for exploiting fresh and rotting weed. Fresh weed is relatively difficult to digest and long gut retention times allow high protein absorption efficiencies to be attained. Rotting weed has microbial protein in quantities and a lower organic carbon fraction. Some bacterial protein is seemingly unavailable though and lower protein absorption efficiencies result. Thus gut retention time is shortened and more food passed through the gut. Growth remains equivalent. Substratum digestion is of paramount importance for Psammechinus feeding on either fresh or rotting weed, cf. the 'classical' microbe-stripping detritivore of Fenchel.

Adaptation of an In Situ Ground-Based Tropospheric OH/HO2 Instrument for Aircraft Use

NASA Technical Reports Server (NTRS)

Brune, William H.

1997-01-01

In-situ HO(x) (OH and HO2) measurements are an essential part of understanding the photochemistry of aircraft exhaust in the atmosphere. HO(x) affects the partitioning of nitrogen species in the NO(y) family. Its reactions are important sources and sinks for tropospheric ozone, thus providing a link between the NO(x) in aircraft exhaust and tropospheric ozone. OH mixing ratios are enhanced in aircraft wakes due to the photolysis of the HONO that is made close to the engine. Measurements of HO(x) in aircraft wakes, along with NO(x) measurements, thus provides a constraint on chemical models of the engine combustion and exhaust. The development of the Airborne Tropospheric Hydrogen Oxides Sensor (ATHOS) is reported. We designed, developed, and successfully flew this instrument. It was part of the instrument complement on board the NASA DC-8 during SUCCESS, which took place in Kansas in April and May, 1996. ATHOS has a limit-of-detection for OH (S/N = 2) of 10(exp 5) OH molecules cm(exp -3) in less than 150 seconds. While this sensitivity is about 2-3 times less than the initial projections in the proposal, it is more than adequate for good measurements of OH and HO2 from the planetary boundary layer to the stratosphere. Our participation in SUCCESS was to be engineering test flights for ATHOS; however, the high-quality measurements we obtained are being used to study HO(x) photochemistry in contrails, clouds, and the clear air.

Evidence for a functional role of epigenetically regulated midcluster HOXB genes in the development of Barrett esophagus

PubMed Central

di Pietro, Massimiliano; Lao-Sirieix, Pierre; Boyle, Shelagh; Cassidy, Andy; Castillo, Dani; Saadi, Amel; Eskeland, Ragnhild; Fitzgerald, Rebecca C.

2012-01-01

Barrett esophagus (BE) is a human metaplastic condition that is the only known precursor to esophageal adenocarcinoma. BE is characterized by a posterior intestinal-like phenotype in an anterior organ and therefore it is reminiscent of homeotic transformations, which can occur in transgenic animal models during embryonic development as a consequence of mutations in HOX genes. In humans, acquired deregulation of HOX genes during adulthood has been linked to carcinogenesis; however, little is known about their role in the pathogenesis of premalignant conditions. We hypothesized that HOX genes may be implicated in the development of BE. We demonstrated that three midcluster HOXB genes (HOXB5, HOXB6, and HOXB7) are overexpressed in BE, compared with the anatomically adjacent normal esophagus and gastric cardia. The midcluster HOXB gene signature in BE is identical to that seen in normal colonic epithelium. Ectopic expression of these three genes in normal squamous esophageal cells in vitro induces markers of intestinal differentiation, such as KRT20, MUC2, and VILLIN. In BE-associated adenocarcinoma, the activation midcluster HOXB gene is associated with loss of H3K27me3 and gain of AcH3, compared with normal esophagus. These changes in histone posttranslational modifications correlate with specific chromatin decompaction at the HOXB locus. We suggest that epigenetically regulated alterations of HOX gene expression can trigger changes in the transcriptional program of adult esophageal cells, with implications for the early stages of carcinogenesis. PMID:22603795

Integration of anteroposterior and dorsoventral regulation of Phox2b transcription in cranial motoneuron progenitors by homeodomain proteins.

PubMed

Samad, Omar Abdel; Geisen, Marc J; Caronia, Giuliana; Varlet, Isabelle; Zappavigna, Vincenzo; Ericson, Johan; Goridis, Christo; Rijli, Filippo M

2004-08-01

Little is known about the molecular mechanisms that integrate anteroposterior (AP) and dorsoventral (DV) positional information in neural progenitors that specify distinct neuronal types within the vertebrate neural tube. We have previously shown that in ventral rhombomere (r)4 of Hoxb1 and Hoxb2 mutant mouse embryos, Phox2b expression is not properly maintained in the visceral motoneuron progenitor domain (pMNv), resulting in a switch to serotonergic fate. Here, we show that Phox2b is a direct target of Hoxb1 and Hoxb2. We found a highly conserved Phox2b proximal enhancer that mediates rhombomere-restricted expression and contains separate Pbx-Hox (PH) and Prep/Meis (P/M) binding sites. We further show that both the PH and P/M sites are essential for Hox-Pbx-Prep ternary complex formation and regulation of the Phox2b enhancer activity in ventral r4. Moreover, the DV factor Nkx2.2 enhances Hox-mediated transactivation via a derepression mechanism. Finally, we show that induction of ectopic Phox2b-expressing visceral motoneurons in the chick hindbrain requires the combined activities of Hox and Nkx2 homeodomain proteins. This study takes an important first step to understand how activators and repressors, induced along the AP and DV axes in response to signaling pathways, interact to regulate specific target gene promoters, leading to neuronal fate specification in the appropriate developmental context.

Hoxd11 specifies a program of metanephric kidney development within the intermediate mesoderm of the mouse embryo.

PubMed

Mugford, Joshua W; Sipilä, Petra; Kobayashi, Akio; Behringer, Richard R; McMahon, Andrew P

2008-07-15

The mammalian kidney consists of an array of tubules connected to a ductal system that collectively function to control water/salt balance and to remove waste from the organisms' circulatory system. During mammalian embryogenesis, three kidney structures form within the intermediate mesoderm. The two most anterior structures, the pronephros and the mesonephros, are transitory and largely non-functional, while the most posterior, the metanephros, persists as the adult kidney. We have explored the mechanisms underlying regional specific differentiation of the kidney forming mesoderm. Previous studies have shown a requirement for Hox11 paralogs (Hoxa11, Hoxc11 and Hoxd11) in metanephric development. Mice lacking all Hox11 activity fail to form metanephric kidney structures. We demonstrate that the Hox11 paralog expression is restricted in the intermediate mesoderm to the posterior, metanephric level. When Hoxd11 is ectopically activated in the anterior mesonephros, we observe a partial transformation to a metanephric program of development. Anterior Hoxd11(+) cells activate Six2, a transcription factor required for the maintenance of metanephric tubule progenitors. Additionally, Hoxd11(+) mesonephric tubules exhibit an altered morphology and activate several metanephric specific markers normally confined to distal portions of the functional nephron. Collectively, our data support a model where Hox11 paralogs specify a metanephric developmental program in responsive intermediate mesoderm. This program maintains tubule forming progenitors and instructs a metanephric specific pattern of nephron differentiation.

Behavior of centrosomes during fertilization and cell division in mouse oocytes and in sea urchin eggs

NASA Technical Reports Server (NTRS)

Schatten, Heide; Schatten, Gerald; Balczon, Ron; Simerly, Calvin; Mazia, Daniel

1986-01-01

The behavior of centrosomes during the stages of fertilization and cell division in mouse oocytes and in sea urchin eggs was monitored in an immunofluorescence microscope, using autoimmune centrosomal antiserum derived from a patient with scleroderma to label the centrosomal material. These observations showed that centrosomes reproduce during the interphase and aggregate and separate during cell mitosis. Results supported the hypothesis of Mazia (1984), who proposed that centrosomes are 'flexible bodies'. It was also found that, while the sea urchin centrosomes are paternally inherited as was initially proposed by Bovery (1904), the mouse centrosomes are of maternal origin.

An evaluation of uranium-series dating of fossil echinoids from southern California Pleistocene marine terraces

USGS Publications Warehouse

Muhs, D.R.; Kennedy, G.L.

1985-01-01

Fossil sea urchins (Strongylocentrotus) from Pleistocene marine terraces on the southern California Channel Islands have been dated by the uranium-series method in order to test the suitability of echinoids for dating marine terraces. Results indicate that urchin plates and spines do not behave as closed systems with respect to both uranium and thorium. Calculated ages based on these data do not agree with uranium-series ages (120,000 and 127,000 yrs) obtained previously from corals from the same localities. Thus, fossil sea urchins (Strongylocentrotus) are not considered suitable for uraniumseries dating of Pleistocene marine terrace deposits. ?? 1985.

Urchin-like TiO₂@C core-shell microspheres: coupled synthesis and lithium-ion battery applications.

PubMed

Liu, Zhenyu; Liu, Jing; Liu, Junfeng; Wang, Li; Zhang, Guoxin; Sun, Xiaoming

2014-05-21

Carbon coated urchin-like TiO2 microspheres were prepared through coupled hydrolysis of titanium tetrachloride and catalyzed carbonization of glucose. Carbon coating endowed the composite with unusual structural stability at high temperature and reasonable Li-ion battery performance.

Effects of Dietary Carbohydrate on Weight Gain and Gonad Production in Small Sea Urchins, Lytechinus variegatus

PubMed Central

Taylor, Anna M.; Heflin, Laura E.; Powell, Mickie L.; Lawrence, Addison L.; Watts, Stephen A.

2015-01-01

In experiment 1, juvenile sea urchins (n = 80, 0.088 ± 0.001 g wet weight and 5.72 ± 0.04 mm diameter) were held individually and fed ad libitum one of three semi-purified formulated diets (n = 16 individuals treatment-1). In the diets, protein was held constant (310g kg-1 dry, as fed) and carbohydrate level varied (190, 260, or 380 g kg-1 dry, as fed). Wet weights were measured every 2 weeks. Total wet weight gain was inversely proportional to dietary carbohydrate level and energy content of the respective diet. In experiment 2, sea urchins (5.60 ± 0.48g wet weight, n= 40) fed 190 g kg-1 carbohydrate consumed significantly more dry feed than those fed 260 g kg-1, but not more than those fed 380 g kg-1 carbohydrate. Based on differential feed intake rates, sea urchins that consumed more feed also consumed higher levels of protein and had the highest weight gain. Consequently, protein content and/or protein: energy ratio may be important in determining feed utilization and growth among sea urchins in this study. The average digestible energy intake was approximately 70 kcal kg-1 body weight day-1, suggesting daily caloric intake of juvenile Lytechinus variegatus is lower than in shrimp and fish. PMID:28479861

The Roles of Spinochromes in Four Shallow Water Tropical Sea Urchins and Their Potential as Bioactive Pharmacological Agents

PubMed Central

Brasseur, Lola; Hennebert, Elise; Fievez, Laurence; Caulier, Guillaume; Bureau, Fabrice; Tafforeau, Lionel; Flammang, Patrick; Gerbaux, Pascal; Eeckhaut, Igor

2017-01-01

Spinochromes are principally known to be involved in sea urchin pigmentation as well as for their potentially interesting pharmacological properties. To assess their biological role in sea urchin physiology, experiments are undertaken on crude extracts from four species and on four isolated spinochromes in order to test their antibacterial, antioxidant, inflammatory and cytotoxic activities. First, the antibacterial assays show that the use of crude extracts as representatives of antibacterial effects of spinochromes are inaccurate. The assays on purified spinochromes showed a decrease in the growth of four strains with an intensity depending on the spinochromes/bacteria system, revealing the participation of spinochromes in the defense system against microorganisms. Secondly, in the 2,2-diphenyl-1-picrylhydrazyl antioxidant assays, spinochromes show an enhanced activity compared to the positive control. This latter observation suggests their involvement in ultraviolet radiation protection. Third, spinochromes present a pro-inflammatory effect on lipopolysaccharide-stimulated macrophages, highlighting their possible implication in the sea urchin immune system. Finally, cytotoxicity assays based on Trypan blue exclusion, performed in view of their possible future applications as drugs, show a weak cytotoxicity of these compounds against human cells. In conclusion, all results confirm the implication of spinochromes in sea urchin defense mechanisms against their external environment and reveal their potential for pharmacological and agronomical industries. PMID:28621734

Aryl sulfate formation in sea urchins (Strongylocentrotus droebachiensis) ingesting marine algae (Fucus distichus) containing 2,6-dimethylnapthalene

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

Malins, D.C.; Roubal, W.T.

1982-04-01

The metabolism of tritiated 2,6-dimethylnapthalene (2,6-DMN) was studied in sea urchins (Strongylocentrotus droebachiensis) feeding on marine algae (Fucus distichus). The Fucus accumulated this hydrocarbon from sea water without converting it to metabolites. Most of the tritium accumulated by the sea urchins (e.g., 70.8% after 3 days) from feeding on 2,6-DMN-exposed Fucus was present in the exoskeleton (shell and spines). Moreover, after 3 days feeding, about 90% of the tritium in the total metabolite fraction of the gonads and digestive tract of the sea urchin was present as sulfate derivatives. These metabolites were identified through hydrolysis with aryl sulfatase, followed bymore » thin-layer chromatography of the products. After 14 days of feeding, the tritium associated with the sulfate derivatives decreased in the gonads and digestive tract to 61 and 65%, respectively, of the total metabolite fraction. Hydroxy compounds from sulfatase hydrolysis were chromatographed using multiple elutions with toluene. The hydroxy isomers were separated and the R/sub f/ values were compared to those of pure reference compounds. The data indicated that 80% of the 2,6-dimethylnaphtyl sulfate contained the sulfate on the 1 and/or 3 position of the aromatic ring. Moreover, 6-methyl-2-naphthalenemethanol was not detected, which implies that sea urchins, unlike fish, metabolize alkyl-substituted aromatic hydrocarbons primarily through aromatic ring oxidations.« less

Selective expression of a sec1/munc18 member in sea urchin eggs and embryos.

PubMed

Leguia, Mariana; Wessel, Gary M

2004-10-01

Regulated secretion is mediated by SNAREs (soluble NSF attachment receptors) and their regulators and effectors, which include the SM (sec1/munc18) family of proteins. Homologs of the SNAREs have been identified in sea urchins, associated with cortical granule exocytosis at fertilization, with membranes of the cleavage furrow, and in secretory cells later in development. To contribute to the understanding of regulated secretion in sea urchins we have cloned the single SM protein homolog from two species of sea urchin, Lytechinus variegatus and Strongylocentrotus purpuratus. In oocytes and eggs, we find that it localizes to the plasma membrane and the cortical region of the egg, consistent with a role in one of the steps leading to cortical granule exocytosis. The protein is also expressed throughout development, enriched in membranes of the cleavage furrow in early embryos, and in cells of the gut in advanced embryos. Furthermore, we find that sec1/munc18 co-localizes with its cognate binding partner syntaxin. Finally, our biochemical analysis shows that the protein associates with rab3 in high molecular weight complexes, suggesting that the exocytotic machinery functions as a multi-protein subunit to mediate regulated secretion in sea urchins. These results will be instrumental in the future to functionally test the SNARE regulators associated with multiple membrane fusion events.

Ectoderm gene activation in sea urchin embryos mediated by the CCAAT-binding factor.

PubMed

Li, Xiaotao; Bhattacharya, Chitralekha; Dayal, Sandeep; Maity, Sankar; Klein, William H

2002-05-01

Transcriptional enhancers are short stretches of DNA that function to achieve highly specific patterns of gene expression. To identify the mechanisms by which enhancers achieve their specificity, we made use of an enhancer from the aboral ectoderm-specific spec2a gene of the sea urchin Strongylocentrotus purpuratus. The spec2a enhancer contains five cis-regulatory elements within 78 base pairs that interact with five distinct DNA-binding proteins to confer aboral ectoderm expression. Here, we present an analysis of the sea urchin CCAAT binding factor (CBF), which binds to a CCAAT motif within the spec2a enhancer. S. purpuratus CBF and SpOtx, a ubiquitously expressed factor, act together at closely placed cis-regulatory elements to mediate spec2a transcription in the ectoderm. SpCBF was the sole factor that bound to the spec2a CCAAT element, and two of the three subunits that make up the CBF holoprotein were cloned and shown to have high sequence conservation with their vertebrate orthologs. Based on its involvement in the regulation of several other sea urchin genes, SpCBF appears to be a major transcription factor in the sea urchin embryo for positive regulation of ectoderm gene expression. In addition to its role in vertebrate cell growth and proliferation, our results indicate that CBF also functions at the early stages of germ layer formation, namely ectoderm differentiation.

The Roles of Spinochromes in Four Shallow Water Tropical Sea Urchins and Their Potential as Bioactive Pharmacological Agents.

PubMed

Brasseur, Lola; Hennebert, Elise; Fievez, Laurence; Caulier, Guillaume; Bureau, Fabrice; Tafforeau, Lionel; Flammang, Patrick; Gerbaux, Pascal; Eeckhaut, Igor

2017-06-16

Spinochromes are principally known to be involved in sea urchin pigmentation as well as for their potentially interesting pharmacological properties. To assess their biological role in sea urchin physiology, experiments are undertaken on crude extracts from four species and on four isolated spinochromes in order to test their antibacterial, antioxidant, inflammatory and cytotoxic activities. First, the antibacterial assays show that the use of crude extracts as representatives of antibacterial effects of spinochromes are inaccurate. The assays on purified spinochromes showed a decrease in the growth of four strains with an intensity depending on the spinochromes/bacteria system, revealing the participation of spinochromes in the defense system against microorganisms. Secondly, in the 2,2-diphenyl-1-picrylhydrazyl antioxidant assays, spinochromes show an enhanced activity compared to the positive control. This latter observation suggests their involvement in ultraviolet radiation protection. Third, spinochromes present a pro-inflammatory effect on lipopolysaccharide-stimulated macrophages, highlighting their possible implication in the sea urchin immune system. Finally, cytotoxicity assays based on Trypan blue exclusion, performed in view of their possible future applications as drugs, show a weak cytotoxicity of these compounds against human cells. In conclusion, all results confirm the implication of spinochromes in sea urchin defense mechanisms against their external environment and reveal their potential for pharmacological and agronomical industries.

Determinants of Paracentrotus lividus sea urchin recruitment under oligotrophic conditions: Implications for conservation management.

PubMed

Oliva, Silvia; Farina, Simone; Pinna, Stefania; Guala, Ivan; Agnetta, Davide; Ariotti, Pierre Antoine; Mura, Francesco; Ceccherelli, Giulia

2016-06-01

Sea urchins may deeply shape the structure of macrophyte-dominated communities and require the implementation of sustainable management strategies. In the Mediterranean, the identification of the major recruitment determinants of the keystone sea urchin species Paracentrotus lividus is required, so that source areas of the populations can be identified and exploitation or programmed harvesting can be spatially managed. In this study a collection of eight possible determinants, these encompassing both the biotic (larvae, adult sea urchins, fish, encrusting coralline algae, habitat type and spatial arrangement of habitats) and abiotic (substrate complexity and nutritional status) realms was considered at different spatial scales (site, area, transect and quadrat). Data from a survey including sites subject to different levels of human influence (i.e. from urbanized to protected areas), but all corresponding to an oligotrophic and low-populated region were fitted by means of a generalized linear mixed model. Despite the extensive sampling effort of benthic quadrats, an overall paucity of recruits was found, recruits being aggregated in a very small number of quadrats and in few areas. The analysis of data detected substrate complexity, and adult sea urchin and predatory fish abundances as the momentous determinants of Paracentrotus lividus recruitment. Possible mechanisms of influence are discussed beyond the implications of conservation management. Copyright © 2016 Elsevier Ltd. All rights reserved.

Functional diversification of sea urchin ABCC1 (MRP1) by alternative splicing.

PubMed

Gökirmak, Tufan; Campanale, Joseph P; Reitzel, Adam M; Shipp, Lauren E; Moy, Gary W; Hamdoun, Amro

2016-06-01

The multidrug resistance protein (MRP) family encodes a diverse repertoire of ATP-binding cassette (ABC) transporters with multiple roles in development, disease, and homeostasis. Understanding MRP evolution is central to unraveling their roles in these diverse processes. Sea urchins occupy an important phylogenetic position for understanding the evolution of vertebrate proteins and have been an important invertebrate model system for study of ABC transporters. We used phylogenetic analyses to examine the evolution of MRP transporters and functional approaches to identify functional forms of sea urchin MRP1 (also known as SpABCC1). SpABCC1, the only MRP homolog in sea urchins, is co-orthologous to human MRP1, MRP3, and MRP6 (ABCC1, ABCC3, and ABCC6) transporters. However, efflux assays revealed that alternative splicing of exon 22, a region critical for substrate interactions, could diversify functions of sea urchin MRP1. Phylogenetic comparisons also indicate that while MRP1, MRP3, and MRP6 transporters potentially arose from a single transporter in basal deuterostomes, alternative splicing appears to have been the major mode of functional diversification in invertebrates, while duplication may have served a more important role in vertebrates. These results provide a deeper understanding of the evolutionary origins of MRP transporters and the potential mechanisms used to diversify their functions in different groups of animals. Copyright © 2016 the American Physiological Society.

Functional diversification of sea urchin ABCC1 (MRP1) by alternative splicing

PubMed Central

Gökirmak, Tufan; Campanale, Joseph P.; Reitzel, Adam M.; Shipp, Lauren E.; Moy, Gary W.

2016-01-01

The multidrug resistance protein (MRP) family encodes a diverse repertoire of ATP-binding cassette (ABC) transporters with multiple roles in development, disease, and homeostasis. Understanding MRP evolution is central to unraveling their roles in these diverse processes. Sea urchins occupy an important phylogenetic position for understanding the evolution of vertebrate proteins and have been an important invertebrate model system for study of ABC transporters. We used phylogenetic analyses to examine the evolution of MRP transporters and functional approaches to identify functional forms of sea urchin MRP1 (also known as SpABCC1). SpABCC1, the only MRP homolog in sea urchins, is co-orthologous to human MRP1, MRP3, and MRP6 (ABCC1, ABCC3, and ABCC6) transporters. However, efflux assays revealed that alternative splicing of exon 22, a region critical for substrate interactions, could diversify functions of sea urchin MRP1. Phylogenetic comparisons also indicate that while MRP1, MRP3, and MRP6 transporters potentially arose from a single transporter in basal deuterostomes, alternative splicing appears to have been the major mode of functional diversification in invertebrates, while duplication may have served a more important role in vertebrates. These results provide a deeper understanding of the evolutionary origins of MRP transporters and the potential mechanisms used to diversify their functions in different groups of animals. PMID:27053522

Involvement of l(-)-rhamnose in sea urchin gastrulation. Part II: α-l-Rhamnosidase.

PubMed

Liang, Jing; Aleksanyan, Heghush; Metzenberg, Stan; Oppenheimer, Steven B

2016-06-01

The sea urchin embryo is recognized as a model system to reveal developmental mechanisms involved in human health and disease. In Part I of this series, six carbohydrates were tested for their effects on gastrulation in embryos of the sea urchin Lytechinus pictus. Only l-rhamnose caused dramatic increases in the numbers of unattached archenterons and exogastrulated archenterons in living, swimming embryos. It was found that at 30 h post-fertilization the l-rhamnose had an unusual inverse dose-dependent effect, with low concentrations (1-3 mM) interfering with development and higher concentrations (30 mM) having little to no effect on normal development. In this study, embryos were examined for inhibition of archenteron development after treatment with α-l-rhamnosidase, an endoglycosidase that removes terminal l-rhamnose sugars from glycans. It was observed that the enzyme had profound effects on gastrulation, an effect that could be suppressed by addition of l-rhamnose as a competitive inhibitor. The involvement of l-rhamnose-containing glycans in sea urchin gastrulation was unexpected, since there are no characterized biosynthetic pathways for rhamnose utilization in animals. It is possible there exists a novel l-rhamnose-containing glycan in sea urchins, or that the enzyme and sugar interfere with the function of rhamnose-binding lectins, which are components of the innate immune system in many vertebrate and invertebrate species.

Extraordinary Diversity of Immune Response Proteins among Sea Urchins: Nickel-Isolated Sp185/333 Proteins Show Broad Variations in Size and Charge

PubMed Central

Sherman, Lauren S.; Schrankel, Catherine S.; Brown, Kristy J.; Smith, L. Courtney

2015-01-01

Effective protection against pathogens requires the host to produce a wide range of immune effector proteins. The Sp185/333 gene family, which is expressed by the California purple sea urchin Strongylocentrotus purpuratus in response to bacterial infection, encodes a highly diverse repertoire of anti-pathogen proteins. A subset of these proteins can be isolated by affinity to metal ions based on multiple histidines, resulting in one to four bands of unique molecular weight on standard Western blots, which vary depending on the individual sea urchin. Two dimensional gel electrophoresis (2DE) of nickel-isolated protein samples followed by Western blot was employed to detect nickel-isolated Sp185/333 (Ni-Sp185/333) proteins and to evaluate protein diversity in animals before and after immune challenge with marine bacteria. Ni-Sp185/333 proteins of the same molecular weight on standard Western blots appear as a broad complex of variants that differ in pI on 2DE Western blots. The Ni-Sp185/333 protein repertoire is variable among animals, and shows a variety of changes among individual sea urchins in response to immune challenges with both the same and different species of bacteria. The extraordinary diversity of the Ni-Sp185/333 proteins may provide significant anti-pathogen capabilities for sea urchins that survive solely on innate immunity. PMID:26406912

The sea urchin larva, a suitable model for biomineralisation studies in space (IML-2 ESA Biorack experiment '24-F urchin').

PubMed

Marthy, H J; Gasset, G; Tixador, R; Schatt, P; Eche, B; Dessommes, A; Giacomini, T; Tap, G; Gorand, D

1996-06-27

By the ESA Biorack 'F-24 urchin' experiment of the IML-2 mission, for the first time the biomineralisation process in developing sea urchin larvae could be studied under real microgravity conditions. The main objectives were to determine whether in microgravity the process of skeleton formation does occur correctly compared to normal gravity conditions and whether larvae with differentiated skeletons do 'de-mineralise'. These objectives have been essentially achieved. Postflight studies on the recovered 'sub-normal' skeletons focused on qualitative, statistical and quantitative aspects. Clear evidence is obtained that the basic biomineralisation process does actually occur normally in microgravity. No significant differences are observed between flight and ground samples. The sub-normal skeleton architectures indicate, however, that the process of positioning of the skeletogenic cells (determining primarily shape and size of the skeleton) is particularly sensitive to modifications of environmental factors, potentially including gravity. The anatomical heterogeneity of the recovered skeletons, interpreted as long term effect of an accidental thermal shock during artificial egg fertilisation (break of climatisation at LSSF), masks possible effects of microgravity. No pronounced demineralisation appears to occur in microgravity; the magnesium component of the skeleton seems yet less stable than the calcium. On the basis of these results, a continuation of biomineralisation studies in space, with the sea urchin larva as model system, appears well justified and desirable.

Innate Immune Complexity in the Purple Sea Urchin: Diversity of the Sp185/333 System

PubMed Central

Smith, L. Courtney

2012-01-01

The California purple sea urchin, Strongylocentrotus purpuratus, is a long-lived echinoderm with a complex and sophisticated innate immune system. There are several large gene families that function in immunity in this species including the Sp185/333 gene family that has ∼50 (±10) members. The family shows intriguing sequence diversity and encodes a broad array of diverse yet similar proteins. The genes have two exons of which the second encodes the mature protein and has repeats and blocks of sequence called elements. Mosaics of element patterns plus single nucleotide polymorphisms-based variants of the elements result in significant sequence diversity among the genes yet maintains similar structure among the members of the family. Sequence of a bacterial artificial chromosome insert shows a cluster of six, tightly linked Sp185/333 genes that are flanked by GA microsatellites. The sequences between the GA microsatellites in which the Sp185/333 genes and flanking regions are located, are much more similar to each other than are the sequences outside the microsatellites suggesting processes such as gene conversion, recombination, or duplication. However, close linkage does not correspond with greater sequence similarity compared to randomly cloned and sequenced genes that are unlikely to be linked. There are three segmental duplications that are bounded by GAT microsatellites and include three almost identical genes plus flanking regions. RNA editing is detectible throughout the mRNAs based on comparisons to the genes, which, in combination with putative post-translational modifications to the proteins, results in broad arrays of Sp185/333 proteins that differ among individuals. The mature proteins have an N-terminal glycine-rich region, a central RGD motif, and a C-terminal histidine-rich region. The Sp185/333 proteins are localized to the cell surface and are found within vesicles in subsets of polygonal and small phagocytes. The coelomocyte proteome shows full-length and truncated proteins, including some with missense sequence. Current results suggest that both native Sp185/333 proteins and a recombinant protein bind bacteria and are likely important in sea urchin innate immunity. PMID:22566951

Sea urchin egg fertilization and development

NASA Technical Reports Server (NTRS)

Young, R. S.

1971-01-01

The effects of subgravity (much less than unit gravity) on fertilization, cell division, differentiation, and growth of a relatively simple biological system (eggs of the sea urchin Arbacia punctulata) were considered. The experiment was flown on Gemini 3 and recovered as scheduled. However, the experiment objectives were not achieved, primarily for mechanical reasons.

Movements of echinochrome pigment granules in sea urchin embryos

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

Belanger, Ann Metcalf

1973-01-01

Characteristic movements of echinochrome pigment granules are known to accompany specific events in the embryonic development of the sea urchin Arbacia punctulata. This investigation has been concerned with processes involved in each of these movements, with particular emphasis on clear area formation and its relationship to mitosis and cleavage.

Design of hydrophobic polyoxometalate hybrid assemblies beyond surfactant encapsulation.

PubMed

Song, Yu-Fei; McMillan, Nicola; Long, De-Liang; Thiel, Johannes; Ding, Yulong; Chen, Haisheng; Gadegaard, Nikolaj; Cronin, Leroy

2008-01-01

Grafting of C-6, C-16 and C-18 alkyl chains onto the hydrophilic Mn-Anderson clusters (compounds 2-4) has been achieved. Exchange of the tetrabutyl ammonium (TBA) with dimethyldioctadecyl ammonium (DMDOA) results in the formation of new polyoxometalate (POM) assemblies (compounds 5-6), in which the POM cores are covalently functionalized by hydrophilic alkyl-chains and enclosed by surfactant of DMDOABr. As a result, we have been able to design and synthesize POM-containing hydrophobic materials beyond surfactant encapsulation. In solid state, scanning electron and transmission electron microscopy (SEM and TEM) studies of the TBA salts of compounds 3 and 4 show highly ordered, uniform, reproducible assemblies with unique segmented rodlike morphology. SEM and TEM studies of the DMDOA salts of compounds 5 and 6 show that they form spherical and sea urchin 3D objects in different solvent systems. In solution, the physical properties of compound 5 and 6 (combination of surfactant-encapsulated cluster (SEC) and surface-grafted cluster (SGC)) show a liquid-to-gel phase transition in pure chloroform below 0 degrees C, which are much lower than other reported SECs. By utilizing light scattering measurements, the nanoparticle size for compounds 5 and 6 were measured at 5 degrees C and 30 degrees C, respectively. Other physical properties including differential scanning calorimetry have been reported.

Antimitotic effect of an extract of the sea anemone Bunodosoma caissarum on sea urchin egg development.

PubMed

Malpezzi, E L; Freitas, J C

1990-01-01

A methanolic extract of the sea anemone Bunodosoma caissarum has an antimitotic effect on sea urchin egg development. The extract produces a dose-dependent inhibition of cell cleavage. When the extract is added together with sperm to unfertilized sea urchin eggs, the ED50 is 0.60 +/- 0.03 mg/ml (mean +/- SEM). When added shortly after fertilization, the extract produces the same kind of progressive inhibition but with an ED50 of 0.98 +/- 0.16 mg/ml. In the first case, detachment of the vitelline layer is inhibited whereas in the second case the extract inhibits cleavage even when the membrane is present.

Effects of low-intensity pulsed electromagnetic fields on the early development of sea urchins.

PubMed Central

Falugi, C; Grattarola, M; Prestipino, G

1987-01-01

The effects of weak electromagnetic signals on the early development of the sea urchin Paracentrotus lividus have been studied. The duration and repetition of the pulses were similar to those used for bone healing in clinical practice. A sequence of pulses, applied for a time ranging from 2 to 4 h, accelerates the cleavages of sea urchin embryo cells. This effect can be quantitatively assessed by determining the time shifts induced by the applied electromagnetic field on the completion of the first and second cleavages in a population of fertilized eggs. The exposed embryos were allowed to develop up to the pluteus stage, showing no abnormalities. Images FIGURE 3 FIGURE 4 PMID:3607217

Characterization and analysis of a transcriptome from the boreal spider crab Hyas araneus.

PubMed

Harms, Lars; Frickenhaus, Stephan; Schiffer, Melanie; Mark, Felix C; Storch, Daniela; Pörtner, Hans-Otto; Held, Christoph; Lucassen, Magnus

2013-12-01

Research investigating the genetic basis of physiological responses has significantly broadened our understanding of the mechanisms underlying organismic response to environmental change. However, genomic data are currently available for few taxa only, thus excluding physiological model species from this approach. In this study we report the transcriptome of the model organism Hyas araneus from Spitsbergen (Arctic). We generated 20,479 transcripts, using the 454 GS FLX sequencing technology in combination with an Illumina HiSeq sequencing approach. Annotation by Blastx revealed 7159 blast hits in the NCBI non-redundant protein database. The comparison between the spider crab H. araneus transcriptome and EST libraries of the European lobster Homarus americanus and the porcelain crab Petrolisthes cinctipes yielded 3229/2581 sequences with a significant hit, respectively. The clustering by the Markov Clustering Algorithm (MCL) revealed a common core of 1710 clusters present in all three species and 5903 unique clusters for H. araneus. The combined sequencing approaches generated transcripts that will greatly expand the limited genomic data available for crustaceans. We introduce the MCL clustering for transcriptome comparisons as a simple approach to estimate similarities between transcriptomic libraries of different size and quality and to analyze homologies within the selected group of species. In particular, we identified a large variety of reverse transcriptase (RT) sequences not only in the H. araneus transcriptome and other decapod crustaceans, but also sea urchin, supporting the hypothesis of a heritable, anti-viral immunity and the proposed viral fragment integration by host-derived RTs in marine invertebrates. © 2013.

Measurements of HOx radicals and the total OH reactivity (kOH) in the planetary boundary layer over southern Finland aboard the Zeppelin NT airship during the PEGASOS field campaign.

NASA Astrophysics Data System (ADS)

Broch, Sebastian; Gomm, Sebastian; Fuchs, Hendrik; Hofzumahaus, Andreas; Holland, Frank; Bachner, Mathias; Bohn, Birger; Häseler, Rolf; Jäger, Julia; Kaiser, Jennifer; Keutsch, Frank; Li, Xin; Lohse, Insa; Rohrer, Franz; Thayer, Mitchell; Tillmann, Ralf; Wegener, Robert; Mentel, Thomas F.; Kiendler-Scharr, Astrid; Wahner, Andreas

2014-05-01

The concentration of hydroxyl (OH) and hydroperoxy (HO2) radicals (also named HOx) and the total OH reactivity were measured over southern Finland and during transfer flights over Germany, Denmark and Sweden aboard the Zeppelin NT airship within the framework of the Pan-European Gas-AeroSOls-climate interaction Study (PEGASOS) field campaign in 2013. The measurements were performed with a remotely controlled Laser Induced Fluorescence (LIF) instrument which was installed on top of the airship. Together with a comprehensive set of trace gas (O3, CO, NO, NO2, HCHO, HONO, VOCs), photolysis frequencies and aerosol measurements as well as the measurement of meteorological parameters, these data provide the possibility to test the current understanding of the chemical processes in the planetary boundary layer (PBL) over different landscapes and in different chemical regimes. The unique flight performance of the Zeppelin NT allowed us to measure transects at a constant altitude as well as vertical profiles within the range of 80 m to 1000 m above ground. The transect flights show changes in the HOx distribution and kOH while crossing different chemical regimes on the way from Friedrichshafen, Germany to Jämijärvi, Finland over Germany, Denmark and Sweden. Vertical profile flights over the boreal forest close to Jämijärvi and Hyytiälä (both Finland) gave the opportunity to investigate the layering of the PBL and with that the vertical distribution of HOx and kOH with a high spatial and temporal resolution. Gradients in the HOx concentration and kOH were measured between the different layers during the early morning hours. The maximum radical concentrations found during the campaign were 1.0 x 107 cm-3 for OH and 1.0 x 109 cm-3 for HO2. The total OH reactivity measured in Finland was much lower than what was reported before in the literature from ground based measurements and ranged from 1 s-1 to 6 s-1. Acknowledgement: PEGASOS project funded by the European Commission under the Framework Programme 7 (FP7-ENV-2010-265148)

An Ancient Gene Network Is Co-opted for Teeth on Old and New Jaws

PubMed Central

Fraser, Gareth J; Hulsey, C. Darrin; Bloomquist, Ryan F; Uyesugi, Kristine; Manley, Nancy R; Streelman, J. Todd

2009-01-01

Vertebrate dentitions originated in the posterior pharynx of jawless fishes more than half a billion years ago. As gnathostomes (jawed vertebrates) evolved, teeth developed on oral jaws and helped to establish the dominance of this lineage on land and in the sea. The advent of oral jaws was facilitated, in part, by absence of hox gene expression in the first, most anterior, pharyngeal arch. Much later in evolutionary time, teleost fishes evolved a novel toothed jaw in the pharynx, the location of the first vertebrate teeth. To examine the evolutionary modularity of dentitions, we asked whether oral and pharyngeal teeth develop using common or independent gene regulatory pathways. First, we showed that tooth number is correlated on oral and pharyngeal jaws across species of cichlid fishes from Lake Malawi (East Africa), suggestive of common regulatory mechanisms for tooth initiation. Surprisingly, we found that cichlid pharyngeal dentitions develop in a region of dense hox gene expression. Thus, regulation of tooth number is conserved, despite distinct developmental environments of oral and pharyngeal jaws; pharyngeal jaws occupy hox-positive, endodermal sites, and oral jaws develop in hox-negative regions with ectodermal cell contributions. Next, we studied the expression of a dental gene network for tooth initiation, most genes of which are similarly deployed across the two disparate jaw sites. This collection of genes includes members of the ectodysplasin pathway, eda and edar, expressed identically during the patterning of oral and pharyngeal teeth. Taken together, these data suggest that pharyngeal teeth of jawless vertebrates utilized an ancient gene network before the origin of oral jaws, oral teeth, and ectodermal appendages. The first vertebrate dentition likely appeared in a hox-positive, endodermal environment and expressed a genetic program including ectodysplasin pathway genes. This ancient regulatory circuit was co-opted and modified for teeth in oral jaws of the first jawed vertebrate, and subsequently deployed as jaws enveloped teeth on novel pharyngeal jaws. Our data highlight an amazing modularity of jaws and teeth as they coevolved during the history of vertebrates. We exploit this diversity to infer a core dental gene network, common to the first tooth and all of its descendants. PMID:19215146

PROJECTING POPULATION-LEVEL RESPONSE OF PURPLE SEA URCHINS TO LEAD CONTAMINATION FOR AN ESTUARINE ECOLOGICAL RISK ASSESSMENT

EPA Science Inventory

As part of an ecological risk assessment case study at the Portsmouth naval Shipyard (PNS), Kittery, Maine, USA, the population level effects of lead exposure to purple sea urchin, Arbacia punctulata, were investigated using a stage-classified matrix population model. The model d...

50 CFR Table 2d to Part 679 - Species Codes-Non-FMP Species

Code of Federal Regulations, 2014 CFR

2014-10-01

... 217 GREENLING Kelp 194 Rock 191 Whitespot 192 Grenadier, giant 214 Grenadier (rattail) 213 Jellyfish..., Pacific (pilchard) 170 Sea cucumber, red 895 Shad 180 Skilfish 715 Snailfish, general (genus Liparis and... Snails 890 Urchin, green sea 893 Urchin, red sea 892 [76 FR 40636, July 11, 2011] ...

Cascading effects of fishing on Galapagos rocky reef communities: reanalysis using corrected data

USGS Publications Warehouse

Sonnenholzner, Jorge I.; Ladah, Lydia B.; Lafferty, Kevin D.

2009-01-01

This article replaces Sonnenholzner et al. (2007; Mar Ecol Prog Ser 343:77–85), which was retracted on September 19, 2007, due to errors in entry of data on sea urchins. We sampled 10 highly fished and 10 (putatively) lightly fished shallow rocky reefs in the southeastern area of the Galapagos Marine Reserve, Ecuador. After the correction, these are the new results: there was a negative association between slate-pencil urchins Eucidaris galapagensis and non-coralline algae. In addition, pencil urchins were less abundant where there were many predators. An indirect positive association between predators and non-coralline algae occurred. Fishing appeared to affect this trophic cascade. The spiny lobster Panulirus penicillatus, the slipper lobster Scyllarides astori, and the Mexican hogfish Bodianus diplotaenia were significantly less abundant at highly fished sites. Urchin density was higher at highly fished sites. Non-coralline algae were nearly absent from highly fished sites, where a continuous carpet of the anemone Aiptasia sp. was recorded, and the algal assemblage was mainly structured by encrusting coralline and articulated calcareous algae.

PI3K inhibitors block skeletogenesis but not patterning in sea urchin embryos.

PubMed

Bradham, C A; Miranda, E L; McClay, D R

2004-04-01

Skeletogenesis in the sea urchin embryo is a simple model of biomineralization, pattern formation, and cell-cell communication during embryonic development. The calcium carbonate skeletal spicules are secreted by primary mesenchyme cells (PMCs), but the skeletal pattern is dictated by the embryonic ectoderm. Although the process of skeletogenesis is well characterized, there is little molecular understanding of the basis of patterning within this system. In this study, we examined the contribution of phosphatidylinositide 3-kinase (PI3K)-mediated signaling to the skeletogenic process in sea urchin embryos by using the well-established PI3K inhibitors LY294002 and wortmannin. Our results show that PI3K inhibitors specifically and reversibly block skeletogenesis, and that this blockade occurs within the PMCs rather than in the ectoderm, because the inhibitors block spiculogenesis in cultured micromeres. Our results are consistent with a model in which PI3K signaling is required, not for pattern sensing or interpretation but rather for the biomineralization process itself in the sea urchin embryo. Copyright 2004 Wiley-Liss, Inc.

MnO2 prepared by hydrothermal method and electrochemical performance as anode for lithium-ion battery

PubMed Central

2014-01-01

Two α-MnO2 crystals with caddice-clew-like and urchin-like morphologies are prepared by the hydrothermal method, and their structure and electrochemical performance are characterized by scanning electron microscope (SEM), X-ray diffraction (XRD), galvanostatic cell cycling, cyclic voltammetry, and electrochemical impedance spectroscopy (EIS). The morphology of the MnO2 prepared under acidic condition is urchin-like, while the one prepared under neutral condition is caddice-clew-like. The identical crystalline phase of MnO2 crystals is essential to evaluate the relationship between electrochemical performances and morphologies for lithium-ion battery application. In this study, urchin-like α-MnO2 crystals with compact structure have better electrochemical performance due to the higher specific capacity and lower impedance. We find that the relationship between electrochemical performance and morphology is different when MnO2 material used as electrochemical supercapacitor or as anode of lithium-ion battery. For lithium-ion battery application, urchin-like MnO2 material has better electrochemical performance. PMID:24982603

Toxic Diatom Aldehydes Affect Defence Gene Networks in Sea Urchins

PubMed Central

Varrella, Stefano; Ruocco, Nadia; Ianora, Adrianna; Bentley, Matt G.; Costantini, Maria

2016-01-01

Marine organisms possess a series of cellular strategies to counteract the negative effects of toxic compounds, including the massive reorganization of gene expression networks. Here we report the modulated dose-dependent response of activated genes by diatom polyunsaturated aldehydes (PUAs) in the sea urchin Paracentrotus lividus. PUAs are secondary metabolites deriving from the oxidation of fatty acids, inducing deleterious effects on the reproduction and development of planktonic and benthic organisms that feed on these unicellular algae and with anti-cancer activity. Our previous results showed that PUAs target several genes, implicated in different functional processes in this sea urchin. Using interactomic Ingenuity Pathway Analysis we now show that the genes targeted by PUAs are correlated with four HUB genes, NF-κB, p53, δ-2-catenin and HIF1A, which have not been previously reported for P. lividus. We propose a working model describing hypothetical pathways potentially involved in toxic aldehyde stress response in sea urchins. This represents the first report on gene networks affected by PUAs, opening new perspectives in understanding the cellular mechanisms underlying the response of benthic organisms to diatom exposure. PMID:26914213

A Hox Gene, Antennapedia, Regulates Expression of Multiple Major Silk Protein Genes in the Silkworm Bombyx mori*

PubMed Central

Tsubota, Takuya; Tomita, Shuichiro; Uchino, Keiro; Kimoto, Mai; Takiya, Shigeharu; Kajiwara, Hideyuki; Yamazaki, Toshimasa; Sezutsu, Hideki

2016-01-01

Hox genes play a pivotal role in the determination of anteroposterior axis specificity during bilaterian animal development. They do so by acting as a master control and regulating the expression of genes important for development. Recently, however, we showed that Hox genes can also function in terminally differentiated tissue of the lepidopteran Bombyx mori. In this species, Antennapedia (Antp) regulates expression of sericin-1, a major silk protein gene, in the silk gland. Here, we investigated whether Antp can regulate expression of multiple genes in this tissue. By means of proteomic, RT-PCR, and in situ hybridization analyses, we demonstrate that misexpression of Antp in the posterior silk gland induced ectopic expression of major silk protein genes such as sericin-3, fhxh4, and fhxh5. These genes are normally expressed specifically in the middle silk gland as is Antp. Therefore, the evidence strongly suggests that Antp activates these silk protein genes in the middle silk gland. The putative sericin-1 activator complex (middle silk gland-intermolt-specific complex) can bind to the upstream regions of these genes, suggesting that Antp directly activates their expression. We also found that the pattern of gene expression was well conserved between B. mori and the wild species Bombyx mandarina, indicating that the gene regulation mechanism identified here is an evolutionarily conserved mechanism and not an artifact of the domestication of B. mori. We suggest that Hox genes have a role as a master control in terminally differentiated tissues, possibly acting as a primary regulator for a range of physiological processes. PMID:26814126

The expression of HoxB5 and SPC in neonatal rat lung after exposure to fluoxetine.

PubMed

Taghizadeh, Razieh; Taghipour, Zahra; Karimi, Akbar; Shamsizadeh, Ali; Taghavi, Mohammad Mohsen; Shariati, Mahdi; Shabanizadeh, Ahmad; Jafari Naveh, Hamid Reza; Bidaki, Reza; Aminzadeh, Fariba

2016-01-01

Approximately 10% of pregnant women suffer from pregnancy-associated depression. Fluoxetine, as a selective serotonin reuptake inhibitor, is being employed as a therapy for depressive disorders. The present study aimed to determine the effects of fluoxetine on neonatal lung development. Thirty pregnant Wistar rats (weighing 200-250 g) were treated daily with 7 mg/kg fluoxetine from gestation day 0 to gestation day 21, via gavage. The control group received a similar volume of distilled water only. Following delivery, the newborns and their lungs were immediately weighed in both of the groups. The right lung was fixed for histological assessments while the left lung was used for evaluation of the expression of SPC and HoxB5 by the real-time polymerase chain reaction method. Results have indicated that even though the body weight and the number of neonatal rats in both groups were the same, the lung weight of neonates exposed to fluoxetine was significantly different compared to the control group ( P <0.05). Expression of both genes was increased, nonetheless, only elevation of HoxB5 was significant ( P <0.05). Histological studies demonstrated that lung tissue in the fluoxetine treatment group morphologically appears to be similar to the pseudoglandular phase, whereas the control group lungs experienced more development. According to the upregulated expression of HoxB5 concerning histological findings, results of the present study showed that fluoxetine can influence lung growth and may in turn lead to delay in lung development. So establishment of studies to identify the effects of antidepressant drugs during pregnancy is deserved.

Re-expression of pro-fibrotic, embryonic preserved mediators in irradiated arterial vessels of the head and neck region.

PubMed

Möbius, Patrick; Preidl, Raimund H M; Weber, Manuel; Amann, Kerstin; Neukam, Friedrich W; Wehrhan, Falk

2017-11-01

Surgical treatment of head and neck malignancies frequently includes microvascular free tissue transfer. Preoperative radiotherapy increases postoperative fibrosis-related complications up to transplant loss. Fibrogenesis is associated with re-expression of embryonic preserved tissue developmental mediators: osteopontin (OPN), regulated by sex-determining region Y‑box 9 (Sox9), and homeobox A9 (HoxA9) play important roles in pathologic tissue remodeling and are upregulated in atherosclerotic vascular lesions; dickkopf-1 (DKK1) inhibits pro-fibrotic and atherogenic Wnt signaling. We evaluated the influence of irradiation on expression of these mediators in arteries of the head and neck region. DKK1, HoxA9, OPN, and Sox9 expression was examined immunohistochemically in 24 irradiated and 24 nonirradiated arteries of the lower head and neck region. The ratio of positive cells to total cell number (labeling index) in the investigated vessel walls was assessed semiquantitatively. DKK1 expression was significantly decreased, whereas HoxA9, OPN, and Sox9 expression were significantly increased in irradiated compared to nonirradiated arterial vessels. Preoperative radiotherapy induces re-expression of embryonic preserved mediators in arterial vessels and may thus contribute to enhanced activation of pro-fibrotic downstream signaling leading to media hypertrophy and intima degeneration comparable to fibrotic development steps in atherosclerosis. These histopathological changes may be promoted by HoxA9-, OPN-, and Sox9-related inflammation and vascular remodeling, supported by downregulation of anti-fibrotic DKK1. Future pharmaceutical strategies targeting these vessel alterations, e. g., bisphosphonates, might reduce postoperative complications in free tissue transfer.

Inhibitors of procollagen C-terminal proteinase block gastrulation and spicule elongation in the sea urchin embryo.

PubMed

Huggins, L G; Lennarz, W J

2001-08-01

In the sea urchin embryo, inhibition of collagen processing and deposition affects both gastrulation and embryonic skeleton (spicule) formation. It has been found that cell-free extracts of gastrula-stage embryos of Strongylocentrotus purpuratus contain a procollagen C-terminal proteinase (PCP) activity. A rationally designed non-peptidic organic hydroxamate, which is a potent and specific inhibitor of human recombinant PCP (FG-HL1), inhibited both the sea urchin PCP as well as purified chick embryo tendon PCP. In the sea urchin embryo, FG-HL1 inhibited gastrulation and blocked spicule elongation, but not spicule nucleation. A related compound with a terminal carboxylate rather than a hydroxamate (FG-HL2) did not inhibit either chick PCP or sea urchin PCP activity in a procollagen-cleavage assay. However, FG-HL2 did block spicule elongation without affecting spicule nucleation or gastrulation. Neither compound was toxic, because their effects were reversible on removal. It was shown that the inhibition of gastrulation and spicule elongation were independent of tissue specification events, because both the endoderm specific marker Endo1 and the primary mesenchyme cell specific marker SM50 were expressed in embryos treated with FG-HL1 and FG-HL2. These results suggest that disruption of the fibrillar collagen deposition in the blastocoele blocks the cell movements of gastrulation and may disrupt the positional information contained within the extracellular matrix, which is necessary for spicule formation.

Augmentative Biocontrol in Natural Marine Habitats: Persistence, Spread and Non-Target Effects of the Sea Urchin Evechinus chloroticus

PubMed Central

Atalah, Javier; Hopkins, Grant A.; Forrest, Barrie M.

2013-01-01

Augmentative biocontrol aims to control established pest populations through enhancement of their indigenous enemies. To our knowledge, this approach has not been applied at an operational scale in natural marine habitats, in part because of the perceived risk of adverse non-target effects on native ecosystems. In this paper, we focus on the persistence, spread and non-target effects of the sea urchin Evechinus chloroticus when used as biocontrol agent to eradicate an invasive kelp from Fiordland, New Zealand. Rocky reef macrobenthic assemblages were monitored over 17 months in areas where the indigenous algal canopy was either removed or left intact prior to the translocation of a large number of urchins (>50 ind.·m−2). Urchin densities in treated areas significantly declined ∼9 months after transplant, and began spreading to adjacent sites. At the end of the 17-month study, densities had declined to ∼5 ind.·m−2. Compared to controls, treatment sites showed persistent shifts from kelp forest to urchin barrens, which were accompanied by significant reductions in taxa richness. Although these non-target effects were pronounced, they were considered to be localised and reversible, and arguably outweigh the irreversible and more profound ecological impacts associated with the establishment of an invasive species in a region of high conservation value. Augmentative biocontrol, used in conjunction with traditional control methods, represents a promising tool for the integrated management of marine pests. PMID:24260376

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.

Toxicity of leather tanning wastewater effluents in sea urchin early development and in marine microalgae.

PubMed

Meriç, Süreyya; De Nicola, Elena; Iaccarino, Mario; Gallo, Marialuisa; Di Gennaro, Annamaria; Morrone, Gaetano; Warnau, Michel; Belgiorno, Vincenzo; Pagano, Giovanni

2005-10-01

This study was designed to investigate the composition and the toxicity of leather tanning wastewater and conditioned sludge collected at the leather tanning wastewater treatment plant (CODISO) located in Solofra, Avellino (Southern Italy). Samples were analyzed for their conventional parameters (COD, TSS, chromium and ammonia) and for metal content. Effluent samples included raw wastewater, and samples collected following coagulation/flocculation process and biological treatment. A set of toxicity endpoints were tested using sea urchin and marine microalgal bioassays by evaluating acute embryotoxicity, developmental defects, changes in sperm fertilization success and transmissible damage from sperm to the offspring, and changes in algal growth rate. Dose-related toxicity to sea urchin embryogenesis and sperm fertilization success was exerted by effluent or sludge samples according to the following rank: conditioned sludge > coagulated effluent > or = raw influent > effluent from biological treatment. Offspring quality was not affected by sperm exposure to any wastewater or to sludge samples. Algal growth was inhibited by raw or coagulated effluent to a similar extent and, again, the effluent from the biological treatment resulted in a decreased toxicity. The results suggest that coagulated effluent and conditioned sludge result in higher toxicity than raw influent in sea urchin embryos and sperm, whereas the biological wastewater treatment of coagulated effluent, in both sea urchins and algae, cause a substantial improvement of wastewater quality. Hence a final biological wastewater treatment should be operated to minimize any environmental damage from tannery wastewater.

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.

Controllable fabrication of urchin-like Co3O4 hollow spheres for high-performance supercapacitors and lithium-ion batteries.

PubMed

Chen, Fashen; Liu, Xiaohe; Zhang, Zhian; Zhang, Ning; Pan, Anqiang; Liang, Shuquan; Ma, Renzhi

2016-09-27

Urchin-like cobalt oxide (Co 3 O 4 ) hollow spheres can be successfully prepared by thermal decomposition of cobalt carbonate hydroxide hydrate (Co(CO 3 ) 0.5 (OH)·0.11H 2 O) obtained by template-assisted hydrothermal synthesis. The morphology, crystal structure evolution and thermal decomposition behaviors of the as-prepared products have been carefully investigated. A plausible formation mechanism of the urchin-like Co 3 O 4 hollow spheres in the presence of hexadecyl trimethyl ammonium bromide (CTAB) as the surfactant template is proposed. The urchin-like Co 3 O 4 hollow spheres are further constructed as electrode materials for high-performance supercapacitors with a high specific capacitance of 460 F g -1 at a current density of 4 A g -1 and excellent cycling stability. Furthermore, as anode materials for lithium-ion batteries (LIBs), superior lithium storage performance of 1342.2 mA h g -1 (0.1 C) and 1122.7 mA h g -1 (0.2 C) can also be achieved. The excellent performances can be ascribed to the unique hierarchical urchin-like hollow structure of the electrode materials, which offers a large specific surface area, short electron and ion diffusion paths and high permeability while being directly in contact with the electrolyte. Moreover, the hollow structure with sufficient internal void spaces can self-accommodate volume change during electrochemical reactions, which improves the structural stability and integrity.

A computational model for BMP movement in sea urchin embryos.

PubMed

van Heijster, Peter; Hardway, Heather; Kaper, Tasso J; Bradham, Cynthia A

2014-12-21

Bone morphogen proteins (BMPs) are distributed along a dorsal-ventral (DV) gradient in many developing embryos. The spatial distribution of this signaling ligand is critical for correct DV axis specification. In various species, BMP expression is spatially localized, and BMP gradient formation relies on BMP transport, which in turn requires interactions with the extracellular proteins Short gastrulation/Chordin (Chd) and Twisted gastrulation (Tsg). These binding interactions promote BMP movement and concomitantly inhibit BMP signaling. The protease Tolloid (Tld) cleaves Chd, which releases BMP from the complex and permits it to bind the BMP receptor and signal. In sea urchin embryos, BMP is produced in the ventral ectoderm, but signals in the dorsal ectoderm. The transport of BMP from the ventral ectoderm to the dorsal ectoderm in sea urchin embryos is not understood. Therefore, using information from a series of experiments, we adapt the mathematical model of Mizutani et al. (2005) and embed it as the reaction part of a one-dimensional reaction-diffusion model. We use it to study aspects of this transport process in sea urchin embryos. We demonstrate that the receptor-bound BMP concentration exhibits dorsally centered peaks of the same type as those observed experimentally when the ternary transport complex (Chd-Tsg-BMP) forms relatively quickly and BMP receptor binding is relatively slow. Similarly, dorsally centered peaks are created when the diffusivities of BMP, Chd, and Chd-Tsg are relatively low and that of Chd-Tsg-BMP is relatively high, and the model dynamics also suggest that Tld is a principal regulator of the system. At the end of this paper, we briefly compare the observed dynamics in the sea urchin model to a version that applies to the fly embryo, and we find that the same conditions can account for BMP transport in the two types of embryos only if Tld levels are reduced in sea urchin compared to fly. Copyright © 2014 Elsevier Ltd. All rights reserved.

Indirect food web interactions: Sea otters and kelp forest fishes in the Aleutian archipelago

USGS Publications Warehouse

Reisewitz, S.E.; Estes, J.A.; Simenstad, C.A.

2006-01-01

Although trophic cascades - the effect of apex predators on progressively lower trophic level species through top-down forcing - have been demonstrated in diverse ecosystems, the broader potential influences of trophic cascades on other species and ecosystem processes are not well studied. We used the overexploitation, recovery and subsequent collapse of sea otter (Enhydra lutris) populations in the Aleutian archipelago to explore if and how the abundance and diet of kelp forest fishes are influenced by a trophic cascade linking sea otters with sea urchins and fleshy macroalgae. We measured the abundance of sea urchins (biomass density), kelp (numerical density) and fish (Catch per unit effort) at four islands in the mid-1980s (when otters were abundant at two of the islands and rare at the two others) and in 2000 (after otters had become rare at all four islands). Our fish studies focused on rock greenling (Hexagrammos lagocephalus), the numerically dominant species in this region. In the mid-1980s, the two islands with high-density otter populations supported dense kelp forests, relatively few urchins, and abundant rock greenling whereas the opposite pattern (abundant urchins, sparse kelp forests, and relatively few rock greenling) occurred at islands where otters were rare. In the 2000, the abundances of urchins, kelp and greenling were grossly unchanged at islands where otters were initially rare but had shifted to the characteristic pattern of otter-free systems at islands where otters were initially abundant. Significant changes in greenling diet occurred between the mid-1980s and the 2000 although the reasons for these changes were difficult to assess because of strong island-specific effects. Whereas urchin-dominated communities supported more diverse fish assemblages than kelp-dominated communities, this was not a simple effect of the otter-induced trophic cascade because all islands supported more diverse fish assemblages in 2000 than in the mid-1980s. ?? Springer-Verlag 2005.

Welcome mats? The role of seagrass meadow structure in controlling post-settlement survival in a keystone sea-urchin species

NASA Astrophysics Data System (ADS)

Prado, Patricia; Romero, Javier; Alcoverro, Teresa

2009-11-01

Processes acting on the early-life histories of marine organisms can have important consequences for the structuring of benthic communities. In particular, the degree of coupling between larval supply and adult abundances can wield considerable influence on the strength of trophic interactions in the ecosystem. These processes have been relatively well described in rocky systems and soft-sediment communities, and it is clear that they are governed by very different bottlenecks. Seagrass meadows make interesting study systems because they bear structural affinities to both soft sediments as well as rocky substrates. We examined the early-life history of Paracentrotus lividus, one of the dominant herbivores in Mediterranean seagrass meadows, to identify the drivers of population dynamics in this species. We measured spatial and temporal variability in sea urchin post-settlement in 10 Posidonia oceanica meadows in the North-Western Mediterranean over a period of two years, and compared the numbers with the one-year old cohort a year later (i.e. the new population recruitment) as well as between successive size-age groups. Urchin post-settlers differed substantially between meadows but were present in both years in all meadows surveyed, suggesting that larval supply was not limiting for any of the studied sites. However, in six of the studied meadows, the one-year cohort of urchins was absent in both years, indicating that post-settlement processes strongly affected urchins in these meadows. In contrast, in four of the studied meadows, there was a strong coupling between post-settlers and one-year cohort individuals. These meadows were structurally different from the others in that they were characterised by an exposed matrix of rhizomes forming a dense seagrass mat. This mat apparently strongly mediates post-settlement mortality, and its presence or absence dictates the successful establishment of urchin populations in seagrass meadows. As the population aged, the relationship between size-age groups decreased evidencing the action of other processes. Yet, these results indicate that differences in physical structure are a vital bottleneck for sea urchin populations in seagrass meadows. Exploring the interaction between ecosystem structure and early-life history may provide a broader and more unified framework to understand the dynamics of a range of benthic habitats, including rocky substrates, soft sediments and seagrass meadows.

BCOR regulates myeloid cell proliferation and differentiation

PubMed Central

Cao, Qi; Gearhart, Micah D.; Gery, Sigal; Shojaee, Seyedmehdi; Yang, Henry; Sun, Haibo; Lin, De-chen; Bai, Jing-wen; Mead, Monica; Zhao, Zhiqiang; Chen, Qi; Chien, Wen-wen; Alkan, Serhan; Alpermann, Tamara; Haferlach, Torsten; Müschen, Markus; Bardwell, Vivian J.; Koeffler, H. Phillip

2016-01-01

BCOR is a component of a variant Polycomb group repressive complex 1 (PRC1). Recently, we and others reported recurrent somatic BCOR loss-of-function mutations in myelodysplastic syndrome and acute myelogenous leukaemia (AML). However, the role of BCOR in normal hematopoiesis is largely unknown. Here, we explored the function of BCOR in myeloid cells using myeloid murine models with Bcor conditional loss-of-function or overexpression alleles. Bcor mutant bone marrow cells showed significantly higher proliferation and differentiation rates with upregulated expression of Hox genes. Mutation of Bcor reduced protein levels of RING1B, an H2A ubiquitin ligase subunit of PRC1 family complexes and reduced H2AK119ub upstream of upregulated HoxA genes. Global RNA expression profiling in murine cells and AML patient samples with BCOR loss-of-function mutation suggested that loss of BCOR expression is associated with enhanced cell proliferation and myeloid differentiation. Our results strongly suggest that BCOR plays an indispensable role in hematopoiesis by inhibiting myeloid cell proliferation and differentiation and offer a mechanistic explanation for how BCOR regulates gene expression such as Hox genes. PMID:26847029

Insights into Hox protein function from a large scale combinatorial analysis of protein domains.

PubMed

Merabet, Samir; Litim-Mecheri, Isma; Karlsson, Daniel; Dixit, Richa; Saadaoui, Mehdi; Monier, Bruno; Brun, Christine; Thor, Stefan; Vijayraghavan, K; Perrin, Laurent; Pradel, Jacques; Graba, Yacine

2011-10-01

Protein function is encoded within protein sequence and protein domains. However, how protein domains cooperate within a protein to modulate overall activity and how this impacts functional diversification at the molecular and organism levels remains largely unaddressed. Focusing on three domains of the central class Drosophila Hox transcription factor AbdominalA (AbdA), we used combinatorial domain mutations and most known AbdA developmental functions as biological readouts to investigate how protein domains collectively shape protein activity. The results uncover redundancy, interactivity, and multifunctionality of protein domains as salient features underlying overall AbdA protein activity, providing means to apprehend functional diversity and accounting for the robustness of Hox-controlled developmental programs. Importantly, the results highlight context-dependency in protein domain usage and interaction, allowing major modifications in domains to be tolerated without general functional loss. The non-pleoitropic effect of domain mutation suggests that protein modification may contribute more broadly to molecular changes underlying morphological diversification during evolution, so far thought to rely largely on modification in gene cis-regulatory sequences.

Insights into Hox Protein Function from a Large Scale Combinatorial Analysis of Protein Domains

PubMed Central

Karlsson, Daniel; Dixit, Richa; Saadaoui, Mehdi; Monier, Bruno; Brun, Christine; Thor, Stefan; Vijayraghavan, K.; Perrin, Laurent; Pradel, Jacques; Graba, Yacine

2011-01-01

Protein function is encoded within protein sequence and protein domains. However, how protein domains cooperate within a protein to modulate overall activity and how this impacts functional diversification at the molecular and organism levels remains largely unaddressed. Focusing on three domains of the central class Drosophila Hox transcription factor AbdominalA (AbdA), we used combinatorial domain mutations and most known AbdA developmental functions as biological readouts to investigate how protein domains collectively shape protein activity. The results uncover redundancy, interactivity, and multifunctionality of protein domains as salient features underlying overall AbdA protein activity, providing means to apprehend functional diversity and accounting for the robustness of Hox-controlled developmental programs. Importantly, the results highlight context-dependency in protein domain usage and interaction, allowing major modifications in domains to be tolerated without general functional loss. The non-pleoitropic effect of domain mutation suggests that protein modification may contribute more broadly to molecular changes underlying morphological diversification during evolution, so far thought to rely largely on modification in gene cis-regulatory sequences. PMID:22046139

Stratospheric Ozone Variations Caused by Solar Proton Events between 1963 and 2005

NASA Technical Reports Server (NTRS)

Jackman, Charles H.; Fleming, Eric L.

2006-01-01

Solar proton fluxes have been measured by satellites for over forty years (1963-2005). Several satellites, including the NASA Interplanetary Monitoring Platforms (1963-1993) and the NOAA Geostationary Operational Environmental Satellites (1994-2005), have been used to compile this long-term dataset. Some solar eruptions lead to solar proton events (SPEs) at the Earth, which typically last a few days. High energy solar protons associated with SPEs precipitate on the Earth's atmosphere and cause increases in odd hydrogen (HOx) and odd nitrogen (NOy) in the polar cap regions (greater than 60 degrees geomagnetic). The enhanced HOx leads to short-lived ozone depletion (days) due to the short lifetime of HOx constituents. The enhanced NOy leads to long-lived ozone changes because of the long lifetime of the NOy family in the stratosphere and lower mesosphere. Very large SPEs occurred in 1972, 1989, 2000, 2001, and 2003 and were predicted to cause maximum total ozone depletions of 1-3%, which lasted for several months to years past the events. These long-term ozone changes caused by SPES are discussed.

[The role of developmental HOX genes in cervical cancer].

PubMed

López-Romero, Ricardo; Marrero-Rodríguez, Daniel; Romero-Morelos, Pablo; Villegas, Vanessa; Valdivia, Alejandra; Arreola, Hugo; Huerta-Padilla, Víctor; Salcedo, Mauricio

2015-01-01

Cervical cancer (CC) is a multifactorial disease associated to genetic, environmental and epigenetic factors, being the infection by human papillomavirus the main etiologic agent. Additionally, the alteration in the expression of transcription factors has been considered of importance for the development of this tumor. HOX genes encode a group of transcription factors involved in cellular proliferation and differentiation processes during the development of embryonic structures in vertebrates; their aberrant expression is associated with tumorigenesis and metastasis. A range of evidence suggests a role for HOX genes in the development of cervical neoplastic cell. Studies in CC cell lines, primary tumors and premalignant lesions have suggested the involvement of HOXA1, HOXC5, C6, C8 and C10, HOXD9 and HOXD13 in the process of cervical carcinogenesis. Also, the de novo expression of genes HOXB2, B4, B13 and HOXC11-C13 appears to be involved in the process of malignant transformation of cervical epithelial cell. These data would allow to open a field in search of new molecular markers in cervical cancer and the development of new therapeutic strategies for this malignancy.

Enhancing hydrogen production of Enterobacter aerogenes by heterologous expression of hydrogenase genes originated from Synechocystis sp.

PubMed

Song, Wenlu; Cheng, Jun; Zhao, Jinfang; Zhang, Chuanxi; Zhou, Junhu; Cen, Kefa

2016-09-01

The hydrogenase genes (hoxEFUYH) of Synechocystis sp. PCC 6803 were cloned and heterologously expressed in Enterobacter aerogenes ATCC13408 for the first time in this study, and the hydrogen yield was significantly enhanced using the recombinant strain. A recombinant plasmid containing the gene in-frame with Glutathione-S-Transferase (GST) gene was transformed into E. aerogenes ATCC13408 to produce a GST-fusion protein. SDS-PAGE and western blot analysis confirm the successful expression of the hox genes. The hydrogenase activity of the recombinant strain is 237.6±9.3ml/(g-DW·h), which is 152% higher than the wild strain. The hydrogen yield of the recombinant strain is 298.3ml/g-glucose, which is 88% higher than the wild strain. During hydrogen fermentation, the recombinant strain produces more acetate and butyrate, but less ethanol. This is corresponding to the NADH metabolism in the cell due to the higher hydrogenase activity with the heterologous expression of hox genes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Heterochronic shift in Hox-mediated activation of sonic hedgehog leads to morphological changes during fin development.

PubMed

Sakamoto, Koji; Onimaru, Koh; Munakata, Keijiro; Suda, Natsuno; Tamura, Mika; Ochi, Haruki; Tanaka, Mikiko

2009-01-01

We explored the molecular mechanisms of morphological transformations of vertebrate paired fin/limb evolution by comparative gene expression profiling and functional analyses. In this study, we focused on the temporal differences of the onset of Sonic hedgehog (Shh) expression in paired appendages among different vertebrates. In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, concomitant with Hoxd10 expression. In dogfish (Scyliorhinus canicula), however, we found that Shh was transcribed late in fin development, concomitant with Hoxd13 expression. We utilized zebrafish as a model to determine whether quantitative changes in hox expression alter the timing of shh expression in pectoral fins of zebrafish embryos. We found that the temporal shift of Shh activity altered the size of endoskeletal elements in paired fins of zebrafish and dogfish. Thus, a threshold level of hox expression determines the onset of shh expression, and the subsequent heterochronic shift of Shh activity can affect the size of the fin endoskeleton. This process may have facilitated major morphological changes in paired appendages during vertebrate limb evolution.

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.

Echinoid bioerosion and herbivory on Kenyan coral reefs: the role of protection from fishing.

PubMed

Carreiro-Silva, M; McClanahan, T R.

2001-07-30

During feeding, echinoids remove a large proportion of calcium carbonate in addition to the algae growing on dead coral and are consequently of importance in estimating the turnover of organic and inorganic carbon in coral reefs. Rates of herbivory and the erosion of dead coral substratum, referred to as bioerosion, by the most abundant echinoid species in Kenyan reefs, Echinothrix diadema (Linnaeus), Diadema setosum (Leske), D. savignyi (Michelin) and Echinometra mathaei (de Blainville), were compared in three different reef categories with different histories of fishing and its exclusion. These were reefs: (i) protected within Marine National Parks, which exclude all forms of fishing, coral and shell collection for more than 25 years; (ii) one reef within a Marine Park, which has received protection from fishing activities for 8 years (referred to as 'newly protected' reef); and (iii) unprotected reefs, which experience heavy fishing and some coral collection. The aim was to investigate the grazing and bioerosion activity by the above echinoid species in these reef categories. We surveyed sea urchin population densities and determined their rates of bioerosion and herbivory per individual and square meter. Individual rates of bioerosion and herbivory, of the species D. setosum, D. savignyi and E. diadema were estimated from laboratory gut content analysis and gut evacuation experiments in the field, using elevated underwater cages. Individual rates of bioerosion and herbivory of E. mathaei were obtained from a previous field study [J. Exp. Mar. Biol. Ecol. 147 (1991) 121]. Sea urchin bioerosion was greater than herbivory for all studied species and proportional to the body size of the sea urchin species. The large-bodied E. diadema exhibited the highest bioerosion and herbivory rates (5.5+/-0.9 and 2.2+/-0.3 g individual(-1) day(-1), respectively) followed by D. setosum (1.8+/-0.3 and 1.1+/-0.2 g individual(-1) day(-1)) and D. savignyi (0.7+/-0.2 and 0.4+/-0.1 g individual(-1) day(-1)). Highest sea urchin densities were recorded at unprotected reefs (6.2+/-1.5 individual m(-2)), and therefore, bioerosion and herbivory by sea urchins were also highest in this reef category (1180+/-230 g CaCO(3) m(-2) year(-1) and 450+/-77 g algae m(-2) year(-1)). Protected reefs recorded 20 times lower sea urchin bioerosion and herbivory rates (50.3+/-25.8 g CaCO(3) m(-2) year(-1) and 20.7+/-10.4 g algae m(-2) year(-1)), due to the low sea urchin population densities in these reefs (0.06+/-0.01 individual m(-2)). The newly protected reef, with intermediate number of sea urchins (1.2+/-0.1 individual m(-2)), had intermediate rates of sea urchin bioerosion and herbivory (711+/-157 g CaCO(3) m(-2) year(-1) and 299+/-63 g algae m(-2) year(-1)). These findings suggest that echinoids are important in the carbon cycle and reef development, and that fishing can influence these ecological processes.

Archaeological and Paleontological Salvage at Barbers Point, Oahu

DTIC Science & Technology

1978-03-01

Isognomon aalifo~iaum Pinatada galtsoffi TeUina ~ugosa ECHINODERMATA ( sea urchins ) Coloboaent~otus at~atus Eahinomet~a n~thaei Eahinot~ diadema...galtsoffi Tellina rugosa ECHINODERMATA ( sea urchins ) Coloboaentrotus atratus Eahinometra mathaei Eahinothrix diadema Heteroeentrotus mammillatus...Ewa Plain, a former coral-algae calcareous reef that emerged following the post-Pleistocene sea -level subsidence. The topography that usually results

EFFECTS OF TRIBUTYLTIN ON CA2+ HOMEOSTASIS AND MECHANISMS CONTROLLING CELL CYCLING IN SEA URCHIN EGGS (R823881)

EPA Science Inventory

Abstract

Tributyltin (TBT) is one of the widespread organotins in the marine environment: we have investigated its cellular targets in the eggs of the marine invertebrate sea urchin Paracentrotus lividus. TBT was used at concentrations ranging from 10^-9

Nuclear Test Summary - TRINITY-HARDTACK. Sanitized

DTIC Science & Technology

1962-08-15

8217 ’R iP,- Z Modal 1561 dcelgn nI~s11OII 8 anid Baractol Lan~h A66 in. W)8 .i,600 lW. 1MTION Urchin TOTIAL DEVICE WBIGNIi: - 10,000 lbs. . I~~~BMMU g wa...Deleted -44’ qOfl1UO5 don BI and Bararol D ee Length 128 in. Wolgt ś,600 lbs (t&clcar System) ICMfTIO-N: Urchin TOTAL DEVIC WEIGH1 10iO 500 ios ot whc-a A...MINfATIONM Urchin InLengt 1l2a in. ftWei&~1 ev7. 600 lbs (Nuclegr SYa~m TOTAL DEVICE WSICAMT M~ 1050 lbs Deleted F\\ T. I I- 7 /SPOti5O: LASL SHOT MNhSBR: 8

THE MEMBRANE CAPACITANCE OF THE SEA URCHIN EGG

PubMed Central

Rothschild, Lord

1957-01-01

1. The surface of the unfertilized sea urchin egg is folded and the folds are reversibly eliminated by exposing the egg to hypotonic sea water. If the plasma membrane is outside the layer of cortical granules, unfolding may explain why the membrane capacitance per unit area decreases (and does not increase) when a sea urchin egg is put into hypotonic sea water. 2. The degree of surface folding markedly increases after fertilization, which provides an explanation for the increase in membrane capacitance per unit area observed after fertilization. 3. The percentage reduction in membrane folding in fertilized eggs after immersion in hypotonic sea water is probably sufficient to explain the decrease in membrane capacitance per unit area observed in these conditions. PMID:13416315

Modularity and design principles in the sea urchin embryo gene regulatory network

PubMed Central

Peter, Isabelle S.; Davidson, Eric H.

2010-01-01

The gene regulatory network (GRN) established experimentally for the pre-gastrular sea urchin embryo provides causal explanations of the biological functions required for spatial specification of embryonic regulatory states. Here we focus on the structure of the GRN which controls the progressive increase in complexity of territorial regulatory states during embryogenesis; and on the types of modular subcircuits of which the GRN is composed. Each of these subcircuit topologies executes a particular operation of spatial information processing. The GRN architecture reflects the particular mode of embryogenesis represented by sea urchin development. Network structure not only specifies the linkages constituting the genomic regulatory code for development, but also indicates the various regulatory requirements of regional developmental processes. PMID:19932099

Micromechanics of Sea Urchin spines.

PubMed

Tsafnat, Naomi; Fitz Gerald, John D; Le, Hai N; Stachurski, Zbigniew H

2012-01-01

The endoskeletal structure of the Sea Urchin, Centrostephanus rodgersii, has numerous long spines whose known functions include locomotion, sensing, and protection against predators. These spines have a remarkable internal microstructure and are made of single-crystal calcite. A finite-element model of the spine's unique porous structure, based on micro-computed tomography (microCT) and incorporating anisotropic material properties, was developed to study its response to mechanical loading. Simulations show that high stress concentrations occur at certain points in the spine's architecture; brittle cracking would likely initiate in these regions. These analyses demonstrate that the organization of single-crystal calcite in the unique, intricate morphology of the sea urchin spine results in a strong, stiff and lightweight structure that enhances its strength despite the brittleness of its constituent material.

Euechinoidea and Cidaroidea respond differently to ocean acidification.

PubMed

Collard, Marie; Dery, Aurélie; Dehairs, Frank; Dubois, Philippe

2014-08-01

The impact of the chemical changes in the ocean waters due to the increasing atmospheric CO₂ depends on the ability of an organism to control extracellular pH. Among sea urchins, this seems specific to the Euechinoidea, sea urchins except Cidaroidea. However, Cidaroidea survived two ocean acidification periods: the Permian-Trias and the Cretaceous-Tertiary crises. We investigated the response of these two sea urchin groups to reduced seawater pH with the tropical cidaroid Eucidaris tribuloides, the sympatric euechinoid Tripneustes ventricosus and the temperate euechinoid Paracentrotus lividus. Both euechinoid showed a compensation of the coelomic fluid pH due to increased buffer capacity. This was linked to an increased concentration of DIC in the coelomic fluid and thus of bicarbonate ions (most probably originating from the surrounding seawater as isotopic signature of the carbon - δ¹³C - was similar). On the other hand, the cidaroid showed no changes within the coelomic fluid. Moreover, the δ¹³C of the coelomic fluid did not match that of the seawater and was not significantly different between the urchins from the different treatments. Feeding rate was not affected in any species. While euechinoids are able to regulate their extracellular acid-base balance, many questions are still unanswered on the costs of this capacity. On the contrary, cidaroids do not seem affected by a reduced seawater pH. Further investigations need to be undertaken to cover more species and physiological and metabolic parameters in order to determine if energy trade-offs occur and how this mechanism of compensation is distributed among sea urchins. Copyright © 2014 Elsevier Inc. All rights reserved.

Expression of two different sulfated fucans by females of Lytechinus variegatus may regulate the seasonal variation in the fertilization of the sea urchin.

PubMed

Cinelli, Leonardo P; Castro, Michelle O; Santos, Livia L; Garcia, Clarice R; Vilela-Silva, Ana-Cristina E S; Mourão, Paulo A S

2007-08-01

The egg jellies of sea urchins contain sulfated polysaccharides with unusual structures, composed of linear chains of l-fucose or l-galactose with well-defined repetitive units. The specific pattern of sulfation and the position of the glycosidic bond vary among sulfated polysaccharides from different species. These polysaccharides show species specificity in inducing the acrosome reaction, which is a critical event for fertilization. Females of the sea urchin Lytechinus variegatus spawn eggs containing a sulfated fucan with the repetitive sequence [3-alpha-L-Fucp-2(OSO(3))-1 --> 3-alpha-L-Fucp-4(OSO(3))-1 --> 3-alpha-L-Fucp-2,4(OSO(3))-1 --> 3-alpha-L-Fucp-2(OSO(3))-1](n). We now observe that, close to winter, a period of decreased fertility for the sea urchin, the females synthesize a distinct sulfated fucan with a simple structure, composed of 4-sulfated, 3-linked alpha-fucose residues. This sulfated fucan is inactive when tested in vitro for the acrosome reaction using homologous sperm. The amount of egg jellies spawned by females (and their constituent sulfated polysaccharides) varied greatly throughout the year. Apparently, there is a correlation between the temperature of the sea water and the expression of the 4-sulfated, 3-linked sulfated fucan. Overall, we described the occurrence of two isotypes of sulfated fucan in the egg jelly of the sea urchin L. variegatus, which differ in their biological activity and may be involved in the periodicity of the reproductive cycle of the invertebrate.

Comparison of the receptor FGFRL1 from sea urchins and humans illustrates evolution of a zinc binding motif in the intracellular domain

PubMed Central

2009-01-01

Background FGFRL1, the gene for the fifth member of the fibroblast growth factor receptor (FGFR) family, is found in all vertebrates from fish to man and in the cephalochordate amphioxus. Since it does not occur in more distantly related invertebrates such as insects and nematodes, we have speculated that FGFRL1 might have evolved just before branching of the vertebrate lineage from the other invertebrates (Beyeler and Trueb, 2006). Results We identified the gene for FGFRL1 also in the sea urchin Strongylocentrotus purpuratus and cloned its mRNA. The deduced amino acid sequence shares 62% sequence similarity with the human protein and shows conservation of all disulfides and N-linked carbohydrate attachment sites. Similar to the human protein, the S. purpuratus protein contains a histidine-rich motif at the C-terminus, but this motif is much shorter than the human counterpart. To analyze the function of the novel motif, recombinant fusion proteins were prepared in a bacterial expression system. The human fusion protein bound to nickel and zinc affinity columns, whereas the sea urchin protein barely interacted with such columns. Direct determination of metal ions by atomic absorption revealed 2.6 mole zinc/mole protein for human FGFRL1 and 1.7 mole zinc/mole protein for sea urchin FGFRL1. Conclusion The FGFRL1 gene has evolved much earlier than previously assumed. A comparison of the intracellular domain between sea urchin and human FGFRL1 provides interesting insights into the shaping of a novel zinc binding domain. PMID:20021659

Base excision DNA repair in the embryonic development of the sea urchin, Strongylocentrotus intermedius.

PubMed

Torgasheva, Natalya A; Menzorova, Natalya I; Sibirtsev, Yurii T; Rasskazov, Valery A; Zharkov, Dmitry O; Nevinsky, Georgy A

2016-06-21

In actively proliferating cells, such as the cells of the developing embryo, DNA repair is crucial for preventing the accumulation of mutations and synchronizing cell division. Sea urchin embryo growth was analyzed and extracts were prepared. The relative activity of DNA polymerase, apurinic/apyrimidinic (AP) endonuclease, uracil-DNA glycosylase, 8-oxoguanine-DNA glycosylase, and other glycosylases was analyzed using specific oligonucleotide substrates of these enzymes; the reaction products were resolved by denaturing 20% polyacrylamide gel electrophoresis. We have characterized the profile of several key base excision repair activities in the developing embryos (2 blastomers to mid-pluteus) of the grey sea urchin, Strongylocentrotus intermedius. The uracil-DNA glycosylase specific activity sharply increased after blastula hatching, whereas the specific activity of 8-oxoguanine-DNA glycosylase steadily decreased over the course of the development. The AP-endonuclease activity gradually increased but dropped at the last sampled stage (mid-pluteus 2). The DNA polymerase activity was high at the first cleavage division and then quickly decreased, showing a transient peak at blastula hatching. It seems that the developing sea urchin embryo encounters different DNA-damaging factors early in development within the protective envelope and later as a free-floating larva, with hatching necessitating adaptation to the shift in genotoxic stress conditions. No correlation was observed between the dynamics of the enzyme activities and published gene expression data from developing congeneric species, S. purpuratus. The results suggest that base excision repair enzymes may be regulated in the sea urchin embryos at the level of covalent modification or protein stability.