Why should we investigate the morphological disparity of plant clades?

PubMed

Oyston, Jack W; Hughes, Martin; Gerber, Sylvain; Wills, Matthew A

2016-04-01

Disparity refers to the morphological variation in a sample of taxa, and is distinct from diversity or taxonomic richness. Diversity and disparity are fundamentally decoupled; many groups attain high levels of disparity early in their evolution, while diversity is still comparatively low. Diversity may subsequently increase even in the face of static or declining disparity by increasingly fine sub-division of morphological 'design' space (morphospace). Many animal clades reached high levels of disparity early in their evolution, but there have been few comparable studies of plant clades, despite their profound ecological and evolutionary importance. This study offers a prospective and some preliminary macroevolutionary analyses. Classical morphometric methods are most suitable when there is reasonable conservation of form, but lose traction where morphological differences become greater (e.g. in comparisons across higher taxa). Discrete character matrices offer one means to compare a greater diversity of forms. This study explores morphospaces derived from eight discrete data sets for major plant clades, and discusses their macroevolutionary implications. Most of the plant clades in this study show initial, high levels of disparity that approach or attain the maximum levels reached subsequently. These plant clades are characterized by an initial phase of evolution during which most regions of their empirical morphospaces are colonized. Angiosperms, palms, pines and ferns show remarkably little variation in disparity through time. Conifers furnish the most marked exception, appearing at relatively low disparity in the latest Carboniferous, before expanding incrementally with the radiation of successive, tightly clustered constituent sub-clades. Many cladistic data sets can be repurposed for investigating the morphological disparity of plant clades through time, and offer insights that are complementary to more focused morphometric studies. The unique structural and

A new phylogeny-based tribal classification of subfamily Detarioideae, an early branching clade of florally diverse tropical arborescent legumes.

PubMed

de la Estrella, Manuel; Forest, Félix; Klitgård, Bente; Lewis, Gwilym P; Mackinder, Barbara A; de Queiroz, Luciano P; Wieringa, Jan J; Bruneau, Anne

2018-05-02

Detarioideae (81 genera, c. 760 species) is one of the six Leguminosae subfamilies recently reinstated by the Legume Phylogeny Working Group. This subfamily displays high morphological variability and is one of the early branching clades in the evolution of legumes. Using previously published and newly generated sequences from four loci (matK-trnK, rpL16, trnG-trnG2G and ITS), we develop a new densely sampled phylogeny to assess generic relationships and tribal delimitations within Detarioideae. The ITS phylogenetic trees are poorly resolved, but the plastid data recover several strongly supported clades, which also are supported in a concatenated plastid + ITS sequence analysis. We propose a new phylogeny-based tribal classification for Detarioideae that includes six tribes: re-circumscribed Detarieae and Amherstieae, and the four new tribes Afzelieae, Barnebydendreae, Saraceae and Schotieae. An identification key and descriptions for each of the tribes are also provided.

Anuran trypanosomes: phylogenetic evidence for new clades in Brazil.

PubMed

da S Ferreira, Juliana I G; da Costa, Andrea P; Ramirez, Diego; Roldan, Jairo A M; Saraiva, Danilo; da S Founier, Gislene F R; Sue, Ana; Zambelli, Erick R; Minervino, Antonio H H; Verdade, Vanessa K; Gennari, Solange M; Marcili, Arlei

2015-05-01

Trypanosomes of anurans and fish are grouped into the Aquatic Clade which includes species isolated from fish, amphibians, turtles and platypus, usually transmitted by leeches and phlebotomine sand flies. Trypanosomes from Brazilian frogs are grouped within the Aquatic Clade with other anuran trypanosome species, where there seems to be coevolutionary patterns with vertebrate hosts and association to Brazilian biomes (Atlantic Forest, Pantanal and Amazonia Rainforest). We characterised the anuran trypanosomes from two different areas of the Cerrado biome and examined their phylogenetic relationships based on the SSU rRNA gene. A total of 112 anurans of six species was analysed and trypanosome prevalence evaluated through haemoculture was found to be 7% (8 positive frogs). However, only three isolates (2.7%) from two anuran species were recovered and cryopreserved. Analysis including SSU rDNA sequences from previous studies segregated the anuran trypanosomes into six groups, the previously reported An01 to An04, and An05 and An06 reported herein. Clade An05 comprises the isolates from Leptodactylus latrans (Steffen) and Pristimantis sp. captured in the Cerrado biome and Trypanosoma chattoni Mathis & Leger, 1911. The inclusion of new isolates in the phylogenetic analyses provided evidence for a new group (An06) of parasites from phlebotomine hosts. Our results indicate that the diversity of trypanosome species is underestimated since studies conducted in Brazil and other regions of the world are still few.

Evidence that clade A and clade B head lice live in sympatry and recombine in Algeria.

PubMed

Boutellis, A; Bitam, I; Fekir, K; Mana, N; Raoult, D

2015-03-01

Pediculus humanus L. (Psocodea: Pediculidae) can be characterized into three deeply divergent lineages (clades) based on mitochondrial DNA. Clade A consists of both head lice and clothing lice and is distributed worldwide. Clade B consists of head lice only and is mainly found in North and Central America, and in western Europe and Australia. Clade C, which consists only of head lice, is found in Ethiopia, Nepal and Senegal. Twenty-six head lice collected from pupils at different elementary schools in two localities in Algiers (Algeria) were analysed using molecular methods for genotyping lice (cytochrome b and the multi-spacer typing (MST) method. For the first time, we found clade B head lice in Africa living in sympatry with clade A head lice. The phylogenetic analysis of the concatenated sequences of these populations of head lice showed that clade A and clade B head lice had recombined, suggesting that interbreeding occurs when lice live in sympatry. © 2014 The Royal Entomological Society.

Dynamics of clade diversification on the morphological hypercube

PubMed Central

Gavrilets, S.

1999-01-01

Understanding the relationship between taxonomic and morphological changes is important in identifying the reasons for accelerated morphological diversification early in the history of animal phyla. Here, a simple general model describing the joint dynamics of taxonomic diversity and morphological disparity is presented and applied to the data on the diversification of blastozoans. I show that the observed patterns of deceleration in clade diversification can be explicable in terms of the geometric structure of the morphospace and the effects of extinction and speciation on morphological disparity without invoking major declines in the size of morphological transitions or taxonomic turnover rates. The model allows testing of hypotheses about patterns of diversification and estimation of rates of morphological evolution. In the case of blastozoans, I find no evidence that major changes in evolutionary rates and mechanisms are responsible for the deceleration of morphological diversification seen during the period of this clade's expansion. At the same time, there is evidence for a moderate decline in overall rates of morphological diversification concordant with a major change (from positive to negative values) in the clade's growth rate.

Highly pathogenic avian influenza H5N1 clade 2.3.2.1 and clade 2.3.4 viruses do not induce a clade-specific phenotype in mallard ducks

PubMed Central

Crumpton, Jeri Carol; Rubrum, Adam; Phommachanh, Phouvong; Douangngeun, Bounlom; Peiris, Malik; Guan, Yi; Webster, Robert; Webby, Richard

2017-01-01

Among the diverse clades of highly pathogenic avian influenza (HPAI) H5N1 viruses of the goose/Guangdong lineage, only a few have been able to spread across continents: clade 2.2 viruses spread from China to Europe and into Africa in 2005–2006, clade 2.3.2.1 viruses spread from China to Eastern Europe in 2009–2010 and clade 2.3.4.4 viruses of the H5Nx subtype spread from China to Europe and North America in 2014/2015. While the poultry trade and wild-bird migration have been implicated in the spread of HPAI H5N1 viruses, it has been proposed that robust virus-shedding by wild ducks in the absence of overt clinical signs may have contributed to the wider dissemination of the clade 2.2, 2.3.2.1 and 2.3.4.4 viruses. Here we determined the phenotype of two divergent viruses from clade 2.3.2.1, a clade that spread widely, and two divergent viruses from clade 2.3.4, a clade that was constrained to Southeast Asia, in young (ducklings) and adult (juvenile) mallard ducks. We found that the virus-shedding magnitude and duration, transmission pattern and pathogenicity of the viruses in young and adult mallard ducks were largely independent of the virus clade. A clade-specific pattern could only be detected in terms of cumulative virus shedding, which was higher with clade 2.3.2.1 than with clade 2.3.4 viruses in juvenile mallards, but not in ducklings. The ability of clade 2.3.2.1c A/common buzzard/Bulgaria/38 WB/2010-like viruses to spread cross-continentally may, therefore, have been strain-specific or independent of phenotype in wild ducks. PMID:28631606

Origin and Dispersal History of Two Colonial Ascidian Clades in the Botryllus schlosseri Species Complex.

PubMed

Nydam, Marie L; Giesbrecht, Kirsten B; Stephenson, Emily E

2017-01-01

Human-induced global warming and species introductions are rapidly altering the composition and functioning of Earth's marine ecosystems. Ascidians (Phylum Chordata, Subphylum Tunicata, Class Ascidiacea) are likely to play an increasingly greater role in marine communities. The colonial ascidian B. schlosseri is a cryptic species complex comprising five genetically divergent clades (A-E). Clade A is a global species, and Clade E has so far been identified in European waters only. Using the largest mitochondrial cytochrome oxidase I datasets yet assembled, we determine the origin and dispersal history of these species. Nucleotide diversity and Approximate Bayesian Computation analyses support a Pacific origin for Clade A, with two likely dispersal scenarios that both show the northwestern Atlantic populations establishing early in the history of the species. Both Discrete Phylogeographic Analysis and Approximate Bayesian Computation support an origin of Clade E on the French side of the English Channel. An unsampled lineage evolved from the French lineage, which reflects the conclusion from the median joining network that not all Clade E lineages have been sampled. This unsampled lineage gave rise to the haplotypes on the English side of the English Channel, which were the ancestors to the Mediterranean and Bay of Biscay populations. Clade E has a wider geographic range than previously thought, and shows evidence of recent range expansion. Both Clade A and Clade E should be considered widespread species: Clade A globally and Clade E within Europe.

A revision of the Solanum elaeagnifolium clade (Elaeagnifolium clade; subgenus Leptostemonum, Solanaceae)

PubMed Central

Knapp, Sandra; Sagona, Eva; Carbonell, Anna K.Z.; Chiarini, Franco

2017-01-01

Abstract The Solanum elaeagnifolium clade (Elaeagnifolium clade) contains five species of small, often rhizomatous, shrubs from deserts and dry forests in North and South America. Members of the clade were previously classified in sections Leprophora, Nycterium and Lathyrocarpum, and were not thought to be closely related. The group is sister to the species-rich monophyletic Old World clade of spiny solanums. The species of the group have an amphitropical distribution, with three species in Mexico and the southwestern United States and three species in Argentina. Solanum elaeagnifolium occurs in both North and South America, and is a noxious invasive weed in dry areas worldwide. Members of the group are highly variable morphologically, and this variability has led to much synonymy, particularly in the widespread S. elaeagnifolium. We here review the taxonomic history, morphology, relationships and ecology of these species and provide keys for their identification, descriptions, full synonymy (including designations of lectotypes) and nomenclatural notes. Illustrations, distribution maps and preliminary conservation assessments are provided for all species. PMID:29033654

Overexpressed Proteins in Hypervirulent Clade 8 and Clade 6 Strains of Escherichia coli O157:H7 Compared to E. coli O157:H7 EDL933 Clade 3 Strain.

PubMed

Amigo, Natalia; Zhang, Qi; Amadio, Ariel; Zhang, Qunjie; Silva, Wanderson M; Cui, Baiyuan; Chen, Zhongjian; Larzabal, Mariano; Bei, Jinlong; Cataldi, Angel

2016-01-01

Escherichia coli O157:H7 is responsible for severe diarrhea and hemolytic uremic syndrome (HUS), and predominantly affects children under 5 years. The major virulence traits are Shiga toxins, necessary to develop HUS and the Type III Secretion System (T3SS) through which bacteria translocate effector proteins directly into the host cell. By SNPs typing, E. coli O157:H7 was separated into nine different clades. Clade 8 and clade 6 strains were more frequently associated with severe disease and HUS. In this study, we aimed to identify differentially expressed proteins in two strains of E. coli O157:H7 (clade 8 and clade 6), obtained from cattle and compared them with the well characterized reference EDL933 strain (clade 3). Clade 8 and clade 6 strains show enhanced pathogenicity in a mouse model and virulence-related properties. Proteins were extracted and analyzed using the TMT-6plex labeling strategy associated with two dimensional liquid chromatography and mass spectrometry in tandem. We detected 2241 proteins in the cell extract and 1787 proteins in the culture supernatants. Attention was focused on the proteins related to virulence, overexpressed in clade 6 and 8 strains compared to EDL933 strain. The proteins relevant overexpressed in clade 8 strain were the curli protein CsgC, a transcriptional activator (PchE), phage proteins, Stx2, FlgM and FlgD, a dienelactone hydrolase, CheW and CheY, and the SPATE protease EspP. For clade 6 strain, a high overexpression of phage proteins was detected, mostly from Stx2 encoding phage, including Stx2, flagellin and the protease TagA, EDL933_p0016, dienelactone hydrolase, and Haemolysin A, amongst others with unknown function. Some of these proteins were analyzed by RT-qPCR to corroborate the proteomic data. Clade 6 and clade 8 strains showed enhanced transcription of 10 out of 12 genes compared to EDL933. These results may provide new insights in E. coli O157:H7 mechanisms of pathogenesis.

The Genomic Basis of Parasitism in the Strongyloides Clade of Nematodes

PubMed Central

Hunt, Vicky L.; Tsai, Isheng J.; Coghlan, Avril; Reid, Adam J.; Holroyd, Nancy; Foth, Bernardo J.; Tracey, Alan; Cotton, James A.; Stanley, Eleanor J.; Beasley, Helen; Bennett, Hayley M.; Brooks, Karen; Harsha, Bhavana; Kajitani, Rei; Kulkarni, Arpita; Harbecke, Dorothee; Nagayasu, Eiji; Nichol, Sarah; Ogura, Yoshitoshi; Quail, Michael A.; Randle, Nadine; Xia, Dong; Brattig, Norbert W.; Soblik, Hanns; Ribeiro, Diogo M.; Sanchez-Flores, Alejandro; Hayashi, Tetsuya; Itoh, Takehiko; Denver, Dee R.; Grant, Warwick; Stoltzfus, Jonathan D.; Lok, James B.; Murayama, Haruhiko; Wastling, Jonathan; Streit, Adrian; Kikuchi, Taisei; Viney, Mark; Berriman, Matthew

2016-01-01

Soil transmitted nematodes, including Strongyloides, cause one of the most prevalent Neglected Tropical Diseases. Here we compare the genomes of four Strongyloides spp., including the human pathogen S. stercoralis, and their close relatives that are facultatively parasitic (Parastrongyloides trichosuri) and free-living (Rhabditophanes sp). A significant paralogous expansion of key gene families – astacin-like and SCP/TAPS coding gene families – is associated with the evolution of parasitism in this clade. Exploiting the unique Strongyloides life cycle we compare the transcriptome of its parasitic and free-living stages and find that these same genes are upregulated in the parasitic stages, underscoring their role in nematode parasitism. PMID:26829753

The spread of highly pathogenic avian influenza (subtype H5N1) clades in Bangladesh, 2010 and 2011.

PubMed

Osmani, Muzaffar G; Ward, Michael P; Giasuddin, Md; Islam, Md Rafiqul; Kalam, Abul

2014-04-01

Since the global spread of highly pathogenic avian influenza H5N1 during 2005-2006, control programs have been successfully implemented in most affected countries. HPAI H5N1 was first reported in Bangladesh in 2007, and since then 546 outbreaks have been reported to the OIE. The disease has apparently become endemic in Bangladesh. Spatio-temporal information on 177 outbreaks of HPAI H5N1 occurring between February 2010 and April 2011 in Bangladesh, and 37 of these outbreaks in which isolated H5N1 viruses were phylogenetically characterized to clade, were analyzed. Three clades were identified, 2.2 (21 cases), 2.3.4 (2 cases) and 2.3.2.1 (14 cases). Clade 2.2 was identified throughout the time period and was widely distributed in a southeast-northwest orientation. Clade 2.3.2.1 appeared later and was generally confined to central Bangladesh in a north-south orientation. Based on a direction test, clade 2.2 viruses spread in a southeast-to-northwest direction, whereas clade 2.3.2.1 spread west-to-east. The magnitude of spread of clade 2.3.2.1 was greater relative to clade 2.2 (angular concentration 0.2765 versus 0.1860). In both cases, the first outbreak(s) were identified as early outliers, but in addition, early outbreaks (one each) of clade 2.2 were also identified in central Bangladesh and in northwest Bangladesh, a considerable distance apart. The spread of highly pathogenic avian influenza H5N1 in Bangladesh is characterized by reported long-distance translocation events. This poses a challenge to disease control efforts. Increased enforcement of biosecurity and stronger control of movements between affected farms and susceptible farms, and better surveillance and reporting, is needed. Although the movement of poultry and equipment appears to be a more likely explanation for the patterns identified, the relative contribution of trade and the market chain versus wild birds in spreading the disease needs further investigation. Copyright © 2014 Elsevier B.V. All

Cranial base evolution within the hominin clade

PubMed Central

Nevell, L; Wood, B

2008-01-01

The base of the cranium (i.e. the basioccipital, the sphenoid and the temporal bones) is of particular interest because it undergoes significant morphological change within the hominin clade, and because basicranial morphology features in several hominin species diagnoses. We use a parsimony analysis of published cranial and dental data to predict the cranial base morphology expected in the hypothetical last common ancestor of the Pan–Homo clade. We also predict the primitive condition of the cranial base for the hominin clade, and document the evolution of the cranial base within the major subclades within the hominin clade. This analysis suggests that cranial base morphology has continued to evolve in the hominin clade, both before and after the emergence of the genus Homo. PMID:18380865

Evidence of Sympatry of Clade A and Clade B Head Lice in a Pre-Columbian Chilean Mummy from Camarones

PubMed Central

Boutellis, Amina; Drali, Rezak; Rivera, Mario A.; Mumcuoglu, Kosta Y.; Raoult, Didier

2013-01-01

Three different lineages of head lice are known to parasitize humans. Clade A, which is currently worldwide in distribution, was previously demonstrated to be present in the Americas before the time of Columbus. The two other types of head lice are geographically restricted to America and Australia for clade B and to Africa and Asia for clade C. In this study, we tested two operculated nits from a 4,000-year-old Chilean mummy of Camarones for the presence of the partial Cytb mitochondrial gene (270 bp). Our finding shows that clade B head lice were present in America before the arrival of the European colonists. PMID:24204678

Genome-Wide Comparison of Cowpox Viruses Reveals a New Clade Related to Variola Virus

PubMed Central

Kurth, Andreas; Nitsche, Andreas

2013-01-01

Zoonotic infections caused by several orthopoxviruses (OPV) like monkeypox virus or vaccinia virus have a significant impact on human health. In Europe, the number of diagnosed infections with cowpox viruses (CPXV) is increasing in animals as well as in humans. CPXV used to be enzootic in cattle; however, such infections were not being diagnosed over the last decades. Instead, individual cases of cowpox are being found in cats or exotic zoo animals that transmit the infection to humans. Both animals and humans reveal local exanthema on arms and legs or on the face. Although cowpox is generally regarded as a self-limiting disease, immunosuppressed patients can develop a lethal systemic disease resembling smallpox. To date, only limited information on the complex and, compared to other OPV, sparsely conserved CPXV genomes is available. Since CPXV displays the widest host range of all OPV known, it seems important to comprehend the genetic repertoire of CPXV which in turn may help elucidate specific mechanisms of CPXV pathogenesis and origin. Therefore, 22 genomes of independent CPXV strains from clinical cases, involving ten humans, four rats, two cats, two jaguarundis, one beaver, one elephant, one marah and one mongoose, were sequenced by using massive parallel pyrosequencing. The extensive phylogenetic analysis showed that the CPXV strains sequenced clearly cluster into several distinct clades, some of which are closely related to Vaccinia viruses while others represent different clades in a CPXV cluster. Particularly one CPXV clade is more closely related to Camelpox virus, Taterapox virus and Variola virus than to any other known OPV. These results support and extend recent data from other groups who postulate that CPXV does not form a monophyletic clade and should be divided into multiple lineages. PMID:24312452

Genome-wide comparison of cowpox viruses reveals a new clade related to Variola virus.

PubMed

Dabrowski, Piotr Wojtek; Radonić, Aleksandar; Kurth, Andreas; Nitsche, Andreas

2013-01-01

Zoonotic infections caused by several orthopoxviruses (OPV) like monkeypox virus or vaccinia virus have a significant impact on human health. In Europe, the number of diagnosed infections with cowpox viruses (CPXV) is increasing in animals as well as in humans. CPXV used to be enzootic in cattle; however, such infections were not being diagnosed over the last decades. Instead, individual cases of cowpox are being found in cats or exotic zoo animals that transmit the infection to humans. Both animals and humans reveal local exanthema on arms and legs or on the face. Although cowpox is generally regarded as a self-limiting disease, immunosuppressed patients can develop a lethal systemic disease resembling smallpox. To date, only limited information on the complex and, compared to other OPV, sparsely conserved CPXV genomes is available. Since CPXV displays the widest host range of all OPV known, it seems important to comprehend the genetic repertoire of CPXV which in turn may help elucidate specific mechanisms of CPXV pathogenesis and origin. Therefore, 22 genomes of independent CPXV strains from clinical cases, involving ten humans, four rats, two cats, two jaguarundis, one beaver, one elephant, one marah and one mongoose, were sequenced by using massive parallel pyrosequencing. The extensive phylogenetic analysis showed that the CPXV strains sequenced clearly cluster into several distinct clades, some of which are closely related to Vaccinia viruses while others represent different clades in a CPXV cluster. Particularly one CPXV clade is more closely related to Camelpox virus, Taterapox virus and Variola virus than to any other known OPV. These results support and extend recent data from other groups who postulate that CPXV does not form a monophyletic clade and should be divided into multiple lineages.

Field and experimental evidence of a new caiman trypanosome species closely phylogenetically related to fish trypanosomes and transmitted by leeches

PubMed Central

Fermino, Bruno R.; Paiva, Fernando; Soares, Priscilla; Tavares, Luiz Eduardo R.; Viola, Laerte B.; Ferreira, Robson C.; Botero-Arias, Robinson; de-Paula, Cátia D.; Campaner, Marta; Takata, Carmen S.A.; Teixeira, Marta M.G.; Camargo, Erney P.

2015-01-01

Trypanosoma terena and Trypanosoma ralphi are known species of the South American crocodilians Caiman crocodilus, Caiman yacare and Melanosuchus niger and are phylogenetically related to the tsetse-transmitted Trypanosoma grayi of the African Crocodylus niloticus. These trypanosomes form the Crocodilian clade of the terrestrial clade of the genus Trypanosoma. A PCR-survey for trypanosomes in caiman blood samples and in leeches taken from caimans revealed unknown trypanosome diversity and frequent mixed infections. Phylogenies based on SSU (small subunit) of rRNA and gGAPDH (glycosomal Glyceraldehyde Phosphate Dehydrogenase) gene sequences revealed a new trypanosome species clustering with T. terena and T. ralphi in the crocodilian clade and an additional new species nesting in the distant Aquatic clade of trypanosomes, which is herein named Trypanosoma clandestinus n. sp. This new species was found in Caiman yacare, Caiman crocodilus and M. niger from the Pantanal and Amazonian biomes in Brazil. Large numbers of dividing epimastigotes and unique thin and long trypomastigotes were found in the guts of leeches (Haementeria sp.) removed from the mouths of caimans. The trypanosomes recovered from the leeches had sequences identical to those of T. clandestinus of caiman blood samples. Experimental infestation of young caimans (Caiman yacare) with infected leeches resulted in long-lasting T. clandestinus infections that permitted us to delineate its life cycle. In contrast to T. terena, T. ralphi and T. grayi, which are detectable by hemoculturing, microscopy and standard PCR of caiman blood, T. clandestinus passes undetected by these methods due to very low parasitemia and could be detected solely by the more sensitive nested PCR method. T. clandestinus n. sp. is the first crocodilian trypanosome known to be transmitted by leeches and positioned in the aquatic clade closest to fish trypanosomes. Our data show that caimans can host trypanosomes of the aquatic or

Plastome phylogeny and early diversification of Brassicaceae.

PubMed

Guo, Xinyi; Liu, Jianquan; Hao, Guoqian; Zhang, Lei; Mao, Kangshan; Wang, Xiaojuan; Zhang, Dan; Ma, Tao; Hu, Quanjun; Al-Shehbaz, Ihsan A; Koch, Marcus A

2017-02-16

The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family. Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.

Evaluation of a fast single-photon avalanche photodiode for measurement of early transmitted photons through diffusive media.

PubMed

Mu, Ying; Valim, Niksa; Niedre, Mark

2013-06-15

We tested the performance of a fast single-photon avalanche photodiode (SPAD) in measurement of early transmitted photons through diffusive media. In combination with a femtosecond titanium:sapphire laser, the overall instrument temporal response time was 59 ps. Using two experimental models, we showed that the SPAD allowed measurement of photon-density sensitivity functions that were approximately 65% narrower than the ungated continuous wave case at very early times. This exceeds the performance that we have previously achieved with photomultiplier-tube-based systems and approaches the theoretical maximum predicted by time-resolved Monte Carlo simulations.

Understanding the link between early sexual initiation and later sexually transmitted infection: test and replication in two longitudinal studies.

PubMed

Epstein, Marina; Bailey, Jennifer A; Manhart, Lisa E; Hill, Karl G; Hawkins, J David; Haggerty, Kevin P; Catalano, Richard F

2014-04-01

Age at sexual initiation is strongly associated with sexually transmitted infections (STI); yet, prevention programs aiming to delay sexual initiation have shown mixed results in reducing STI. This study tested three explanatory mechanisms for the relationship between early sexual debut and STI: number of sexual partners, individual characteristics, and environmental antecedents. A test-and-replicate strategy was employed using two longitudinal studies: the Seattle Social Development Project (SSDP) and Raising Healthy Children (RHC). Childhood measures included pubertal age, behavioral disinhibition, and family, school, and peer influences. Alcohol use and age of sexual debut were measured during adolescence. Lifetime number of sexual partners and having sex under the influence were measured during young adulthood. Sexually transmitted infection diagnosis was self-reported at age 24. Early sex was defined as debut at <15 years. Path models were developed in SSDP evaluating relationships between measures, and were then tested in RHC. The relationship between early sex and STI was fully mediated by lifetime sex partners in SSDP, but only partially in RHC, after accounting for co-occurring factors. Behavioral disinhibition predicted early sex, early alcohol use, number of sexual partners, and sex under the influence, but had no direct effect on STI. Family management protected against early sex and early alcohol use, whereas antisocial peers exacerbated the risk. Early sexual initiation, a key mediator of STI, is driven by antecedents that influence multiple risk behaviors. Targeting co-occurring individual and environmental factors may be more effective than discouraging early sexual debut and may concomitantly improve other risk behaviors. Copyright © 2014 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C

PubMed Central

Ramos-González, Pedro Luis; Chabi-Jesus, Camila; Guerra-Peraza, Orlene; Breton, Michèle Claire; Arena, Gabriella Dias; Nunes, Maria Andreia; Kitajima, Elliot Watanabe; Machado, Marcos Antonio; Freitas-Astúa, Juliana

2016-01-01

Citrus leprosis virus C (CiLV-C) causes a severe disease affecting citrus orchards in the Western hemisphere. This study reveals the molecular variability of the virus by analyzing four genomic regions (p29, p15, MP and RNA2-intergenic region) distributed over its two RNAs. Nucleotide diversity (π) values were relatively low but statistically different over the analyzed genes and subpopulations, indicating their distinct evolutionary history. Values of πp29 and πMP were higher than those of πp15 and πRNA2–IR, whereas πMP was increased due to novel discovered isolates phylogenetically clustered in a divergent clade that we called SJP. Isolate BR_SP_SJP_01 RNA1 and RNA2 sequences, clade SJP, showed an identity of 85.6% and 88.4%, respectively, with those corresponding to CiLV-C, the type member of the genus Cilevirus, and its RNA2 5′-proximal region was revealed as a minor donor in a putative inter-clade recombination event. In addition to citrus, BR_SP_SJP_01 naturally infects the weed Commelina benghalensis and is efficiently transmitted by Brevipalpus yothersi mites. Our data demonstrated that negative selection was the major force operating in the evaluated viral coding regions and defined amino acids putatively relevant for the biological function of cilevirus proteins. This work provides molecular tools and sets up a framework for further epidemiological studies. PMID:27275832

Outbreaks among Wild Birds and Domestic Poultry Caused by Reassorted Influenza A(H5N8) Clade 2.3.4.4 Viruses, Germany, 2016.

PubMed

Pohlmann, Anne; Starick, Elke; Harder, Timm; Grund, Christian; Höper, Dirk; Globig, Anja; Staubach, Christoph; Dietze, Klaas; Strebelow, Günter; Ulrich, Reiner G; Schinköthe, Jan; Teifke, Jens P; Conraths, Franz J; Mettenleiter, Thomas C; Beer, Martin

2017-04-01

In November 2016, an influenza A(H5N8) outbreak caused deaths of wild birds and domestic poultry in Germany. Clade 2.3.4.4 virus was closely related to viruses detected at the Russia-Mongolia border in 2016 but had new polymerase acidic and nucleoprotein segments. These new strains may be more efficiently transmitted to and shed by birds.

The Association of Early Substance Use with Lifetime/Past Year Contraction of Sexually Transmitted Diseases: A National Study

ERIC Educational Resources Information Center

Merianos, Ashley L.; Rosen, Brittany L.; King, Keith A.; Vidourek, Rebecca A.; Fehr, Sara K.

2015-01-01

The study purpose is to examine the impact of early substance use on lifetime and past year contraction of sexually transmitted diseases (STDs), including chlamydia, gonorrhea, herpes, and syphilis. A secondary analysis of the 2012 National Survey on Drug Use and Health (N = 52,529) was conducted to determine if lifetime or past year STD…

Breadth of neutralizing antibodies elicited by stable, homogeneous clade A and clade C HIV-1 gp140 envelope trimers in guinea pigs.

PubMed

Nkolola, Joseph P; Peng, Hanqin; Settembre, Ethan C; Freeman, Michael; Grandpre, Lauren E; Devoy, Colleen; Lynch, Diana M; La Porte, Annalena; Simmons, Nathaniel L; Bradley, Ritu; Montefiori, David C; Seaman, Michael S; Chen, Bing; Barouch, Dan H

2010-04-01

The native envelope (Env) spike on the surface of human immunodeficiency virus type 1 (HIV-1) is trimeric, and thus trimeric Env vaccine immunogens are currently being explored in preclinical immunogenicity studies. Key challenges have included the production and purification of biochemically homogeneous and stable trimers and the evaluation of these immunogens utilizing standardized virus panels for neutralization assays. Here we report the binding and neutralizing antibody (NAb) responses elicited by clade A (92UG037.8) and clade C (CZA97.012) Env gp140 trimer immunogens in guinea pigs. These trimers have been selected and engineered for optimal biochemical stability and have defined antigenic properties. Purified gp140 trimers with Ribi adjuvant elicited potent, cross-clade NAb responses against tier 1 viruses as well as detectable but low-titer NAb responses against select tier 2 viruses from clades A, B, and C. In particular, the clade C trimer elicited NAbs that neutralized 27%, 20%, and 47% of tier 2 viruses from clades A, B, and C, respectively. Heterologous DNA prime, protein boost as well as DNA prime, recombinant adenovirus boost regimens expressing these antigens, however, did not result in an increased magnitude or breadth of NAb responses in this system. These data demonstrate the immunogenicity of stable, homogeneous clade A and clade C gp140 trimers and exemplify the utility of standardized tier 1 and tier 2 virus panels for assessing the NAb responses of candidate HIV-1 Env immunogens.

Repeated climate-linked host shifts have promoted diversification in a temperate clade of leaf-mining flies

PubMed Central

Winkler, Isaac S.; Mitter, Charles; Scheffer, Sonja J.

2009-01-01

A central but little-tested prediction of “escape and radiation” coevolution is that colonization of novel, chemically defended host plant clades accelerates insect herbivore diversification. That theory, in turn, exemplifies one side of a broader debate about the relative influence on clade dynamics of intrinsic (biotic) vs. extrinsic (physical-environmental) forces. Here, we use a fossil-calibrated molecular chronogram to compare the effects of a major biotic factor (repeated shift to a chemically divergent host plant clade) and a major abiotic factor (global climate change) on the macroevolutionary dynamics of a large Cenozoic radiation of phytophagous insects, the leaf-mining fly genus Phytomyza (Diptera: Agromyzidae). We find one of the first statistically supported examples of consistently elevated net diversification accompanying shift to new plant clades. In contrast, we detect no significant direct effect on diversification of major global climate events in the early and late Oligocene. The broader paleoclimatic context strongly suggests, however, that climate change has at times had a strong indirect influence through its effect on the biotic environment. Repeated rapid Miocene radiation of these flies on temperate herbaceous asterids closely corresponds to the dramatic, climate-driven expansion of seasonal, open habitats. PMID:19805134

Gastrointestinal Tract Colonization Dynamics by Different Enterococcus faecium Clades

PubMed Central

Montealegre, Maria Camila; Singh, Kavindra V.; Murray, Barbara E.

2016-01-01

Colonization of the gastrointestinal tract (GIT) generally precedes infection with antibiotic-resistant Enterococcus faecium. We used a mouse GIT colonization model to test differences in the colonization levels by strains from different E. faecium lineages: clade B, part of the healthy human microbiota; subclade A1, associated with infections; and subclade A2, primarily associated with animals. After mono-inoculation, there was no significant difference in colonization (measured as the geometric mean number of colony-forming units per gram) by the E. faecium clades at any time point (P > .05). However, in competition assays, with 6 of the 7 pairs, clade B strains outcompeted clade A strains in their ability to persist in the GIT; this difference was significant in some pairs by day 2 and in all pairs by day 14 (P < .0008–.0283). This observation may explain the predominance of clade B in the community and why antibiotic-resistant hospital-associated E. faecium are often replaced by clade B strains once patients leave the hospital. PMID:26671890

Adolescents' Sexually Transmitted Disease Protective Attitudes Predict Sexually Transmitted Disease Acquisition in Early Adulthood

ERIC Educational Resources Information Center

Crosby, Richard A.; Danner, Fred

2008-01-01

Background: Estimates suggest that about 48% of nearly 19 million cases of sexually transmitted diseases (STDs) occurring annually in the United States are acquired by persons aged 15-24 years. The purpose of this study was to test the hypothesis that adolescents' attitudes about protecting themselves from STDs predict their laboratory-confirmed…

Evolution of the intercontinental disjunctions in six continents in the Ampelopsis clade of the grape family (Vitaceae)

PubMed Central

2012-01-01

Background The Ampelopsis clade (Ampelopsis and its close allies) of the grape family Vitaceae contains ca. 43 species disjunctly distributed in Asia, Europe, North America, South America, Africa, and Australia, and is a rare example to study both the Northern and the Southern Hemisphere intercontinental disjunctions. We reconstruct the temporal and spatial diversification of the Ampelopsis clade to explore the evolutionary processes that have resulted in their intercontinental disjunctions in six continents. Results The Bayesian molecular clock dating and the likelihood ancestral area analyses suggest that the Ampelopsis clade most likely originated in North America with its crown group dated at 41.2 Ma (95% HPD 23.4 - 61.0 Ma) in the middle Eocene. Two independent Laurasian migrations into Eurasia are inferred to have occurred in the early Miocene via the North Atlantic land bridges. The ancestor of the Southern Hemisphere lineage migrated from North America to South America in the early Oligocene. The Gondwanan-like pattern of intercontinental disjunction is best explained by two long-distance dispersals: once from South America to Africa estimated at 30.5 Ma (95% HPD 16.9 - 45.9 Ma), and the other from South America to Australia dated to 19.2 Ma (95% HPD 6.7 - 22.3 Ma). Conclusions The global disjunctions in the Ampelopsis clade are best explained by a diversification model of North American origin, two Laurasian migrations, one migration into South America, and two post-Gondwanan long-distance dispersals. These findings highlight the importance of both vicariance and long distance dispersal in shaping intercontinental disjunctions of flowering plants. PMID:22316163

Variable depth distribution of Trichodesmium clades in the North Pacific Ocean.

PubMed

Rouco, Mónica; Haley, Sheean T; Alexander, Harriet; Wilson, Samuel T; Karl, David M; Dyhrman, Sonya T

2016-12-01

Populations of nitrogen-fixing cyanobacteria in the genus Trichodesmium are critical to ocean ecosystems, yet predicting patterns of Trichodesmium distribution and their role in ocean biogeochemistry is an ongoing challenge. This may, in part, be due to differences in the physiological ecology of Trichodesmium species, which are not typically considered independently in field studies. In this study, the abundance of the two dominant Trichodesmium clades (Clade I and Clade III) was investigated during a survey at Station ALOHA in the North Pacific Subtropical Gyre (NPSG) using a clade-specific qPCR approach. While Clade I dominated the Trichodesmium community, Clade III abundance was >50% in some NPSG samples, in contrast to the western North Atlantic where Clade III abundance was always <10%. Clade I populations were distributed down to depths >80 m, while Clade III populations were only observed in the mixed layer and found to be significantly correlated with depth and temperature. These data suggest active niche partitioning of Trichodesmium species from different clades, as has been observed in other cyanobacteria. Tracking the distribution and physiology of Trichodesmium spp. would contribute to better predictions of the physiological ecology of this biogeochemically important genus in the present and future ocean. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Symbiodinium Clade Affects Coral Skeletal Isotopic Ratio

NASA Astrophysics Data System (ADS)

Carilli, J.; Charles, C. D.; Garren, M.; McField, M.; Norris, R. D.

2011-12-01

The influence of different physiologies of Symbiodinium dinoflagellate symbiont clades on the skeletal chemistry of associated coral hosts has not previously been investigated. This is an important issue because coral skeletons are routinely used for tropical paleoclimatic reconstructions. We analyzed coral skeletal samples collected simultaneously from neighboring colonies off Belize and found that those harboring different clades of Symbiodinium displayed significantly different skeletal oxygen isotopic compositions. We also found evidence for mean shifts in skeletal oxygen isotopic composition after coral bleaching (the loss and potential exchange of symbionts) in two of four longer coral cores from the Mesoamerican Reef, though all experienced similar climatic conditions. Thus, we suggest that symbiont clade identity leaves a signature in the coral skeletal archive and that this influence must be considered for quantitative environmental reconstruction. In addition, we suggest that the skeletal isotopic signature may be used to identify changes in the dominant symbiont clade that have occurred in the past, to identify how common and widespread this phenomenon is--a potential adaptation to climate change.

Gastrointestinal Tract Colonization Dynamics by Different Enterococcus faecium Clades.

PubMed

Montealegre, Maria Camila; Singh, Kavindra V; Murray, Barbara E

2016-06-15

Colonization of the gastrointestinal tract (GIT) generally precedes infection with antibiotic-resistant Enterococcus faecium We used a mouse GIT colonization model to test differences in the colonization levels by strains from different E. faecium lineages: clade B, part of the healthy human microbiota; subclade A1, associated with infections; and subclade A2, primarily associated with animals. After mono-inoculation, there was no significant difference in colonization (measured as the geometric mean number of colony-forming units per gram) by the E. faecium clades at any time point (P > .05). However, in competition assays, with 6 of the 7 pairs, clade B strains outcompeted clade A strains in their ability to persist in the GIT; this difference was significant in some pairs by day 2 and in all pairs by day 14 (P < .0008-.0283). This observation may explain the predominance of clade B in the community and why antibiotic-resistant hospital-associated E. faecium are often replaced by clade B strains once patients leave the hospital. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Origin and Population Dynamics of a Novel HIV-1 Subtype G Clade Circulating in Cape Verde and Portugal

PubMed Central

Guimarães, Monick L.; Morgado, Mariza G.; Bello, Gonzalo

2015-01-01

The human immunodeficiency virus type 1 (HIV-1) subtype G is the most prevalent and second most prevalent HIV-1 clade in Cape Verde and Portugal, respectively; but there is no information about the origin and spatiotemporal dispersal pattern of this HIV-1 clade circulating in those countries. To this end, we used Maximum Likelihood and Bayesian coalescent-based methods to analyze a collection of 578 HIV-1 subtype G pol sequences sampled throughout Portugal, Cape Verde and 11 other countries from West and Central Africa over a period of 22 years (1992 to 2013). Our analyses indicate that most subtype G sequences from Cape Verde (80%) and Portugal (95%) branched together in a distinct monophyletic cluster (here called GCV-PT). The GCV-PT clade probably emerged after a single migration of the virus out of Central Africa into Cape Verde between the late 1970s and the middle 1980s, followed by a rapid dissemination to Portugal a couple of years later. Reconstruction of the demographic history of the GCV-PT clade circulating in Cape Verde and Portugal indicates that this viral clade displayed an initial phase of exponential growth during the 1980s and 1990s, followed by a decline in growth rate since the early 2000s. Our data also indicate that during the exponential growth phase the GCV-PT clade recombined with a preexisting subtype B viral strain circulating in Portugal, originating the CRF14_BG clade that was later disseminated to Spain and Cape Verde. Historical and recent human population movements between Angola, Cape Verde and Portugal probably played a key role in the origin and dispersal of the GCV-PT and CRF14_BG clades. PMID:25993094

Origin and Population Dynamics of a Novel HIV-1 Subtype G Clade Circulating in Cape Verde and Portugal.

PubMed

de Pina-Araujo, Isabel Inês M; Delatorre, Edson; Guimarães, Monick L; Morgado, Mariza G; Bello, Gonzalo

2015-01-01

The human immunodeficiency virus type 1 (HIV-1) subtype G is the most prevalent and second most prevalent HIV-1 clade in Cape Verde and Portugal, respectively; but there is no information about the origin and spatiotemporal dispersal pattern of this HIV-1 clade circulating in those countries. To this end, we used Maximum Likelihood and Bayesian coalescent-based methods to analyze a collection of 578 HIV-1 subtype G pol sequences sampled throughout Portugal, Cape Verde and 11 other countries from West and Central Africa over a period of 22 years (1992 to 2013). Our analyses indicate that most subtype G sequences from Cape Verde (80%) and Portugal (95%) branched together in a distinct monophyletic cluster (here called G(CV-PT)). The G(CV-PT) clade probably emerged after a single migration of the virus out of Central Africa into Cape Verde between the late 1970s and the middle 1980s, followed by a rapid dissemination to Portugal a couple of years later. Reconstruction of the demographic history of the G(CV-PT) clade circulating in Cape Verde and Portugal indicates that this viral clade displayed an initial phase of exponential growth during the 1980s and 1990s, followed by a decline in growth rate since the early 2000s. Our data also indicate that during the exponential growth phase the G(CV-PT) clade recombined with a preexisting subtype B viral strain circulating in Portugal, originating the CRF14_BG clade that was later disseminated to Spain and Cape Verde. Historical and recent human population movements between Angola, Cape Verde and Portugal probably played a key role in the origin and dispersal of the G(CV-PT )and CRF14_BG clades.

Clade 8 and Clade 6 Strains of Escherichia coli O157:H7 from Cattle in Argentina have Hypervirulent-Like Phenotypes

PubMed Central

Amigo, Natalia; Mercado, Elsa; Bentancor, Adriana; Singh, Pallavi; Vilte, Daniel; Gerhardt, Elisabeth; Zotta, Elsa; Ibarra, Cristina; Manning, Shannon D.; Larzábal, Mariano; Cataldi, Angel

2015-01-01

The hemolytic uremic syndrome (HUS) whose main causative agent is enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a disease that mainly affects children under 5 years of age. Argentina is the country with the highest incidence of HUS in the world. Cattle are a major reservoir and source of infection with E. coli O157:H7. To date, the epidemiological factors that contribute to its prevalence are poorly understood. Single nucleotide polymorphism (SNP) typing has helped to define nine E. coli O157:H7 clades and the clade 8 strains were associated with most of the cases of severe disease. In this study, eight randomly selected isolates of EHEC O157:H7 from cattle in Argentina were studied as well as two human isolates. Four of them were classified as clade 8 through the screening for 23 SNPs; the two human isolates grouped in this clade as well, while two strains were closely related to strains representing clade 6. To assess the pathogenicity of these strains, we assayed correlates of virulence. Shiga toxin production was determined by an ELISA kit. Four strains were high producers and one of these strains that belonged to a novel genotype showed high verocytotoxic activity in cultured cells. Also, these clade 8 and 6 strains showed high RBC lysis and adherence to epithelial cells. One of the clade 6 strains showed stronger inhibition of normal water absorption than E. coli O157:H7 EDL933 in human colonic explants. In addition, two of the strains showing high levels of Stx2 production and RBC lysis activity were associated with lethality and uremia in a mouse model. Consequently, circulation of such strains in cattle may partially contribute to the high incidence of HUS in Argentina. PMID:26030198

Spathaspora boniae sp. nov., a D-xylose-fermenting species in the Candida albicans/Lodderomyces clade.

PubMed

Morais, Camila G; Batista, Thiago M; Kominek, Jacek; Borelli, Beatriz M; Furtado, Carolina; Moreira, Rennan G; Franco, Gloria R; Rosa, Luiz H; Fonseca, César; Hittinger, Chris T; Lachance, Marc-André; Rosa, Carlos A

2017-10-01

Two yeast isolates producing asci-containing elongate ascospores with curved ends typical of the genus Spathaspora were isolated from rotting wood samples collected in an Atlantic rainforest ecosystem in Brazil. Phylogenetic analysis of the LSU rRNA gene D1/D2 domain sequences demonstrated that the strains represent a new species and placed it next to Candida blackwellae, in a clade that also contains Candida albicans and Candida dubliniensis. Other sequences of the ribosomal gene cluster supported same placementin the same clade, and a phylogenomic analysis placed this new species in an early emerging position relative to the larger C. albicans/Lodderomyces clade. One interpretation is that the genus Spathaspora is, in fact, paraphyletic. In conformity with this view, we propose the novel species Spathaspora boniae sp. nov. to accommodate the isolates. The type strain of Spathaspora boniae sp. nov. is UFMG-CM-Y306 T (=CBS 13262 T ). The MycoBank number is MB 821297. A detailed analysis of xylose metabolism was conducted for the new species.

Detection of bacterial pathogens in clade E head lice collected from Niger's refugees in Algeria.

PubMed

Louni, Meriem; Amanzougaghene, Nadia; Mana, Nassima; Fenollar, Florence; Raoult, Didier; Bitam, Idir; Mediannikov, Oleg

2018-06-15

findings from head lice collected on migrant and non-migrant population, our results show, for the first time, that head lice from Niger belong to haplogroup E, and confirm that the clade E had a west African distribution. We also detected, for the first time, the presence of C. burnetii and A. baumannii in these Nigerien head lice. Nevertheless, further studies are needed to determine whether the head lice can transmit these pathogenic bacteria from one person to another.

Phylogeny and biogeography of the most diverse clade of South American gymnophthalmid lizards (Squamata, Gymnophthalmidae, Cercosaurinae).

PubMed

Torres-Carvajal, Omar; Lobos, Simón E; Venegas, Pablo J; Chávez, Germán; Aguirre-Peñafiel, Vanessa; Zurita, Daniel; Echevarría, Lourdes Y

2016-06-01

Nearly 50% of the diversity of the speciose Neotropical lizard clade Gymnophthalmidae is nested within the subclade Cercosaurinae. The taxonomy of Cercosaurinae lizards has been historically confusing because many diagnostic characters of those clades traditionally ranked as genera do not represent true diagnostic apomorphies. Even though molecular phylogenies of several 'genera' have been presented in the last few years, some of them remain poorly sampled (e.g., Anadia, Echinosaura, Potamites, Riama). In this paper we present a more comprehensive phylogeny of Cercosaurinae lizards with emphasis on Andean taxa from Ecuador and Peru, as well as a time-calibrated phylogeny with reconstruction of ancestral areas. Our analysis includes 52% of all recognized species of Cercosaurinae (67 species) and 1914 characters including three mitochondrial and one nuclear gene. We find that Anadia, Echinosaura, Euspondylus, Potamites, Proctoporus, and Riama are not monophyletic: the Tepuian Anadia mcdiarmidi is not sister to Andean species of Anadia; Echinosaura sulcarostrum is not included in the same clade formed by other species of Echinosaura and their more recent common ancestor; Teuchocercus is nested within Echinosaura; species of Euspondylus included in this study are nested within Proctoporus; Riama laudahnae is included in Proctoporus; and Potamites is paraphyletic and split in two separate clades, one of which we name Gelanesaurus, also a new genus-group name. Within Potamites, P. ecpleopus is paraphyletic, and P. strangulatus strangulatus and P. strangulatus trachodus are recognized as two distinct species. We also identify three unnamed clades (i.e., not nested within any of the recognized 'genera') from Andean populations in Ecuador and Peru. The estimated age of the clade Cercosaurinae (∼60Ma) corresponds to the early stages of the northern Andes. Even though the distribution of the most recent common ancestor of Cercosaurinae remains equivocal, our analysis shows

The oldest platypus and its bearing on divergence timing of the platypus and echidna clades

PubMed Central

Rowe, Timothy; Rich, Thomas H.; Vickers-Rich, Patricia; Springer, Mark; Woodburne, Michael O.

2008-01-01

Monotremes have left a poor fossil record, and paleontology has been virtually mute during two decades of discussion about molecular clock estimates of the timing of divergence between the platypus and echidna clades. We describe evidence from high-resolution x-ray computed tomography indicating that Teinolophos, an Early Cretaceous fossil from Australia's Flat Rocks locality (121–112.5 Ma), lies within the crown clade Monotremata, as a basal platypus. Strict molecular clock estimates of the divergence between platypus and echidnas range from 17 to 80 Ma, but Teinolophos suggests that the two monotreme clades were already distinct in the Early Cretaceous, and that their divergence may predate even the oldest strict molecular estimates by at least 50%. We generated relaxed molecular clock models using three different data sets, but only one yielded a date overlapping with the age of Teinolophos. Morphology suggests that Teinolophos is a platypus in both phylogenetic and ecological aspects, and tends to contradict the popular view of rapid Cenozoic monotreme diversification. Whereas the monotreme fossil record is still sparse and open to interpretation, the new data are consistent with much slower ecological, morphological, and taxonomic diversification rates for monotremes than in their sister taxon, the therian mammals. This alternative view of a deep geological history for monotremes suggests that rate heterogeneities may have affected mammalian evolution in such a way as to defeat strict molecular clock models and to challenge even relaxed molecular clock models when applied to mammalian history at a deep temporal scale. PMID:18216270

The oldest platypus and its bearing on divergence timing of the platypus and echidna clades.

PubMed

Rowe, Timothy; Rich, Thomas H; Vickers-Rich, Patricia; Springer, Mark; Woodburne, Michael O

2008-01-29

Monotremes have left a poor fossil record, and paleontology has been virtually mute during two decades of discussion about molecular clock estimates of the timing of divergence between the platypus and echidna clades. We describe evidence from high-resolution x-ray computed tomography indicating that Teinolophos, an Early Cretaceous fossil from Australia's Flat Rocks locality (121-112.5 Ma), lies within the crown clade Monotremata, as a basal platypus. Strict molecular clock estimates of the divergence between platypus and echidnas range from 17 to 80 Ma, but Teinolophos suggests that the two monotreme clades were already distinct in the Early Cretaceous, and that their divergence may predate even the oldest strict molecular estimates by at least 50%. We generated relaxed molecular clock models using three different data sets, but only one yielded a date overlapping with the age of Teinolophos. Morphology suggests that Teinolophos is a platypus in both phylogenetic and ecological aspects, and tends to contradict the popular view of rapid Cenozoic monotreme diversification. Whereas the monotreme fossil record is still sparse and open to interpretation, the new data are consistent with much slower ecological, morphological, and taxonomic diversification rates for monotremes than in their sister taxon, the therian mammals. This alternative view of a deep geological history for monotremes suggests that rate heterogeneities may have affected mammalian evolution in such a way as to defeat strict molecular clock models and to challenge even relaxed molecular clock models when applied to mammalian history at a deep temporal scale.

Origin and Diversification of Major Clades in Parmelioid Lichens (Parmeliaceae, Ascomycota) during the Paleogene Inferred by Bayesian Analysis

PubMed Central

Amo de Paz, Guillermo; Cubas, Paloma; Divakar, Pradeep K.; Lumbsch, H. Thorsten; Crespo, Ana

2011-01-01

There is a long-standing debate on the extent of vicariance and long-distance dispersal events to explain the current distribution of organisms, especially in those with small diaspores potentially prone to long-distance dispersal. Age estimates of clades play a crucial role in evaluating the impact of these processes. The aim of this study is to understand the evolutionary history of the largest clade of macrolichens, the parmelioid lichens (Parmeliaceae, Lecanoromycetes, Ascomycota) by dating the origin of the group and its major lineages. They have a worldwide distribution with centers of distribution in the Neo- and Paleotropics, and semi-arid subtropical regions of the Southern Hemisphere. Phylogenetic analyses were performed using DNA sequences of nuLSU and mtSSU rDNA, and the protein-coding RPB1 gene. The three DNA regions had different evolutionary rates: RPB1 gave a rate two to four times higher than nuLSU and mtSSU. Divergence times of the major clades were estimated with partitioned BEAST analyses allowing different rates for each DNA region and using a relaxed clock model. Three calibrations points were used to date the tree: an inferred age at the stem of Lecanoromycetes, and two dated fossils: Parmelia in the parmelioid group, and Alectoria. Palaeoclimatic conditions and the palaeogeological area cladogram were compared to the dated phylogeny of parmelioid. The parmelioid group diversified around the K/T boundary, and the major clades diverged during the Eocene and Oligocene. The radiation of the genera occurred through globally changing climatic condition of the early Oligocene, Miocene and early Pliocene. The estimated divergence times are consistent with long-distance dispersal events being the major factor to explain the biogeographical distribution patterns of Southern Hemisphere parmelioids, especially for Africa-Australia disjunctions, because the sequential break-up of Gondwana started much earlier than the origin of these clades. However, our

Kretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade

PubMed Central

Abella, Juan; Alba, David M.; Robles, Josep M.; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raül; Montoya, Plinio; Morales, Jorge

2012-01-01

The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8–7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12–11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint. PMID:23155439

Kretzoiarctos gen. nov., the oldest member of the giant panda clade.

PubMed

Abella, Juan; Alba, David M; Robles, Josep M; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raül; Montoya, Plinio; Morales, Jorge

2012-01-01

The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8-7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12-11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint.

Rapid diversification and not clade age explains high diversity in neotropical Adelpha butterflies

PubMed Central

Mullen, Sean P.; Savage, Wesley K.; Wahlberg, Niklas; Willmott, Keith R.

2011-01-01

Latitudinal gradients in species richness are among the most well-known biogeographic patterns in nature, and yet there remains much debate and little consensus over the ecological and evolutionary causes of these gradients. Here, we evaluated whether two prominent alternative hypotheses (namely differences in diversification rate or clade age) could account for the latitudinal diversity gradient in one of the most speciose neotropical butterfly genera (Adelpha) and its close relatives. We generated a multilocus phylogeny of a diverse group of butterflies in the containing tribe Limenitidini, which has both temperate and tropical representatives. Our results suggest there is no relationship between clade age and species richness that could account for the diversity gradient, but that instead it could be explained by a significantly higher diversification rate within the predominantly tropical genus Adelpha. An apparent early larval host-plant shift to Rubiaceae and other plant families suggests that the availability of new potential host plants probably contributed to an increase in diversification of Adelpha in the lowland Neotropics. Collectively, our results support the hypothesis that the equatorial peak in species richness observed within Adelpha is the result of increased diversification rate in the last 10–15 Myr rather than a function of clade age, perhaps reflecting adaptive divergence in response to the dramatic host-plant diversity found within neotropical ecosystems. PMID:21106589

Expanding the World of Marine Bacterial and Archaeal Clades

PubMed Central

Yilmaz, Pelin; Yarza, Pablo; Rapp, Josephine Z.; Glöckner, Frank O.

2016-01-01

Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as

Preventing Sexually Transmitted Diseases

PubMed Central

Kieren, Dianne; Cumming, Ceinwen E.; Cumming, David C.

1992-01-01

The discouraging results of early efforts to educate the public about sexually transmitted diseases indicated that the goals of STD preventive action must be longer term and must change attitudes and behaviour as well as educate. They must also avoid an ostrich mentality about the sexual involvement of young people. This article examines more recent approaches to teaching about sexuality in general and STD prevention in particular. PMID:21221351

Nitrate competition in a coral symbiosis varies with temperature among Symbiodinium clades.

PubMed

Baker, David M; Andras, Jason P; Jordán-Garza, Adán Guillermo; Fogel, Marilyn L

2013-06-01

Many reef-building corals form symbioses with dinoflagellates from the diverse genus Symbiodinium. There is increasing evidence of functional significance to Symbiodinium diversity, which affects the coral holobiont's response to changing environmental conditions. For example, corals hosting Symbiodinium from the clade D taxon exhibit greater resistance to heat-induced coral bleaching than conspecifics hosting the more common clade C. Yet, the relatively low prevalence of clade D suggests that this trait is not advantageous in non-stressful environments. Thus, clade D may only be able to out-compete other Symbiodinium types within the host habitat when conditions are chronically stressful. Previous studies have observed enhanced photosynthesis and fitness by clade C holobionts at non-stressful temperatures, relative to clade D. Yet, carbon-centered metrics cannot account for enhanced growth rates and patterns of symbiont succession to other genetic types when nitrogen often limits reef productivity. To investigate the metabolic costs of hosting thermally tolerant symbionts, we examined the assimilation and translocation of inorganic (15)N and (13)C in the coral Acropora tenuis experimentally infected with either clade C (sub-type C1) or D Symbiodinium at 28 and 30 °C. We show that at 28 °C, C1 holobionts acquired 22% more (15)N than clade D. However, at 30 °C, C1 symbionts acquired equivalent nitrogen and 16% less carbon than D. We hypothesize that C1 competitively excludes clade D in hospite via enhanced nitrogen acquisition and thus dominates coral populations despite warming oceans.

Clade age and species richness are decoupled across the eukaryotic tree of life.

PubMed

Rabosky, Daniel L; Slater, Graham J; Alfaro, Michael E

2012-08-01

Explaining the dramatic variation in species richness across the tree of life remains a key challenge in evolutionary biology. At the largest phylogenetic scales, the extreme heterogeneity in species richness observed among different groups of organisms is almost certainly a function of many complex and interdependent factors. However, the most fundamental expectation in macroevolutionary studies is simply that species richness in extant clades should be correlated with clade age: all things being equal, older clades will have had more time for diversity to accumulate than younger clades. Here, we test the relationship between stem clade age and species richness across 1,397 major clades of multicellular eukaryotes that collectively account for more than 1.2 million described species. We find no evidence that clade age predicts species richness at this scale. We demonstrate that this decoupling of age and richness is unlikely to result from variation in net diversification rates among clades. At the largest phylogenetic scales, contemporary patterns of species richness are inconsistent with unbounded diversity increase through time. These results imply that a fundamentally different interpretative paradigm may be needed in the study of phylogenetic diversity patterns in many groups of organisms.

A new hypothesis of dinosaur relationships and early dinosaur evolution.

PubMed

Baron, Matthew G; Norman, David B; Barrett, Paul M

2017-03-22

For 130 years, dinosaurs have been divided into two distinct clades-Ornithischia and Saurischia. Here we present a hypothesis for the phylogenetic relationships of the major dinosaurian groups that challenges the current consensus concerning early dinosaur evolution and highlights problematic aspects of current cladistic definitions. Our study has found a sister-group relationship between Ornithischia and Theropoda (united in the new clade Ornithoscelida), with Sauropodomorpha and Herrerasauridae (as the redefined Saurischia) forming its monophyletic outgroup. This new tree topology requires redefinition and rediagnosis of Dinosauria and the subsidiary dinosaurian clades. In addition, it forces re-evaluations of early dinosaur cladogenesis and character evolution, suggests that hypercarnivory was acquired independently in herrerasaurids and theropods, and offers an explanation for many of the anatomical features previously regarded as notable convergences between theropods and early ornithischians.

Progress to extinction: increased specialisation causes the demise of animal clades.

PubMed

Raia, P; Carotenuto, F; Mondanaro, A; Castiglione, S; Passaro, F; Saggese, F; Melchionna, M; Serio, C; Alessio, L; Silvestro, D; Fortelius, M

2016-08-10

Animal clades tend to follow a predictable path of waxing and waning during their existence, regardless of their total species richness or geographic coverage. Clades begin small and undifferentiated, then expand to a peak in diversity and range, only to shift into a rarely broken decline towards extinction. While this trajectory is now well documented and broadly recognised, the reasons underlying it remain obscure. In particular, it is unknown why clade extinction is universal and occurs with such surprising regularity. Current explanations for paleontological extinctions call on the growing costs of biological interactions, geological accidents, evolutionary traps, and mass extinctions. While these are effective causes of extinction, they mainly apply to species, not clades. Although mass extinctions is the undeniable cause for the demise of a sizeable number of major taxa, we show here that clades escaping them go extinct because of the widespread tendency of evolution to produce increasingly specialised, sympatric, and geographically restricted species over time.

Progress to extinction: increased specialisation causes the demise of animal clades

NASA Astrophysics Data System (ADS)

Raia, P.; Carotenuto, F.; Mondanaro, A.; Castiglione, S.; Passaro, F.; Saggese, F.; Melchionna, M.; Serio, C.; Alessio, L.; Silvestro, D.; Fortelius, M.

2016-08-01

Animal clades tend to follow a predictable path of waxing and waning during their existence, regardless of their total species richness or geographic coverage. Clades begin small and undifferentiated, then expand to a peak in diversity and range, only to shift into a rarely broken decline towards extinction. While this trajectory is now well documented and broadly recognised, the reasons underlying it remain obscure. In particular, it is unknown why clade extinction is universal and occurs with such surprising regularity. Current explanations for paleontological extinctions call on the growing costs of biological interactions, geological accidents, evolutionary traps, and mass extinctions. While these are effective causes of extinction, they mainly apply to species, not clades. Although mass extinctions is the undeniable cause for the demise of a sizeable number of major taxa, we show here that clades escaping them go extinct because of the widespread tendency of evolution to produce increasingly specialised, sympatric, and geographically restricted species over time.

Rapid Differentiation between Livestock-Associated and Livestock-Independent Staphylococcus aureus CC398 Clades

PubMed Central

Larsen, Jesper; Soldanova, Katerina; Aziz, Maliha; Contente-Cuomo, Tania; Petersen, Andreas; Vandendriessche, Stien; Jiménez, Judy N.; Mammina, Caterina; van Belkum, Alex; Salmenlinna, Saara; Laurent, Frederic; Skov, Robert L.; Larsen, Anders R.; Andersen, Paal S.; Price, Lance B.

2013-01-01

Staphylococcus aureus clonal complex 398 (CC398) isolates cluster into two distinct phylogenetic clades based on single-nucleotide polymorphisms (SNPs) revealing a basal human clade and a more derived livestock clade. The scn and tet(M) genes are strongly associated with the human and the livestock clade, respectively, due to loss and acquisition of mobile genetic elements. We present canonical single-nucleotide polymorphism (canSNP) assays that differentiate the two major host-associated S. aureus CC398 clades and a duplex PCR assay for detection of scn and tet(M). The canSNP assays correctly placed 88 S. aureus CC398 isolates from a reference collection into the human and livestock clades and the duplex PCR assay correctly identified scn and tet(M). The assays were successfully applied to a geographically diverse collection of 272 human S. aureus CC398 isolates. The simple assays described here generate signals comparable to a whole-genome phylogeny for major clade assignment and are easily integrated into S. aureus CC398 surveillance programs and epidemiological studies. PMID:24244535

Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity.

PubMed

Krishnan, Arunkumar; Iyer, Lakshminarayan M; Holland, Stephen J; Boehm, Thomas; Aravind, L

2018-04-03

AID/APOBEC deaminases (AADs) convert cytidine to uridine in single-stranded nucleic acids. They are involved in numerous mutagenic processes, including those underpinning vertebrate innate and adaptive immunity. Using a multipronged sequence analysis strategy, we uncover several AADs across metazoa, dictyosteliida, and algae, including multiple previously unreported vertebrate clades, and versions from urochordates, nematodes, echinoderms, arthropods, lophotrochozoans, cnidarians, and porifera. Evolutionary analysis suggests a fundamental division of AADs early in metazoan evolution into secreted deaminases (SNADs) and classical AADs, followed by diversification into several clades driven by rapid-sequence evolution, gene loss, lineage-specific expansions, and lateral transfer to various algae. Most vertebrate AADs, including AID and APOBECs1-3, diversified in the vertebrates, whereas the APOBEC4-like clade has a deeper origin in metazoa. Positional entropy analysis suggests that several AAD clades are diversifying rapidly, especially in the positions predicted to interact with the nucleic acid target motif, and with potential viral inhibitors. Further, several AADs have evolved neomorphic metal-binding inserts, especially within loops predicted to interact with the target nucleic acid. We also observe polymorphisms, driven by alternative splicing, gene loss, and possibly intergenic recombination between paralogs. We propose that biological conflicts of AADs with viruses and genomic retroelements are drivers of rapid AAD evolution, suggesting a widespread presence of mutagenesis-based immune-defense systems. Deaminases like AID represent versions "institutionalized" from the broader array of AADs pitted in such arms races for mutagenesis of self-DNA, and similar recruitment might have independently occurred elsewhere in metazoa. Copyright © 2018 the Author(s). Published by PNAS.

The Longibrachiatum Clade of Trichoderma: a revision with new species

USDA-ARS?s Scientific Manuscript database

The Longibrachiatum Clade of Trichoderma is revised. Eight new species are described (T. aethiopicum, T. capillare, T. flagellatum, T. gillesii, T. gracile, T. pinnatum, T. saturnisporopsis, T. solani). The twenty-one species known to belong to the Longibrachiatum Clade are included in a synoptic ke...

Rapid Identification of Different Escherichia coli Sequence Type 131 Clades.

PubMed

Matsumura, Yasufumi; Pitout, Johann D D; Peirano, Gisele; DeVinney, Rebekah; Noguchi, Taro; Yamamoto, Masaki; Gomi, Ryota; Matsuda, Tomonari; Nakano, Satoshi; Nagao, Miki; Tanaka, Michio; Ichiyama, Satoshi

2017-08-01

Escherichia coli sequence type 131 (ST131) is a pandemic clonal lineage that is responsible for the global increase in fluoroquinolone resistance and extended-spectrum-β-lactamase (ESBL) producers. The members of ST131 clade C, especially subclades C2 and C1-M27, are associated with ESBLs. We developed a multiplex conventional PCR assay with the ability to detect all ST131 clades (A, B, and C), as well as C subclades (C1-M27, C1-nM27 [C1-non-M27], and C2). To validate the assay, we used 80 ST131 global isolates that had been fully sequenced. We then used the assay to define the prevalence of each clade in two Japanese collections consisting of 460 ESBL-producing E. coli ST131 (2001-12) and 329 E. coli isolates from extraintestinal sites (ExPEC) (2014). The assay correctly identified the different clades in all 80 global isolates: clades A ( n = 12), B ( n = 12), and C, including subclades C1-M27 ( n = 16), C1-nM27 ( n = 20), C2 ( n = 17), and other C ( n = 3). The assay also detected all 565 ST131 isolates in both collections without any false positives. Isolates from clades A ( n = 54), B ( n = 23), and C ( n = 483) corresponded to the O serotypes and the fimH types of O16-H41, O25b-H22, and O25b-H30, respectively. Of the 483 clade C isolates, C1-M27 was the most common subclade (36%), followed by C1-nM27 (32%) and C2 (15%). The C1-M27 subclade with bla CTX-M-27 became especially prominent after 2009. Our novel multiplex PCR assay revealed the predominance of the C1-M27 subclade in recent Japanese ESBL-producing E. coli isolates and is a promising tool for epidemiological studies of ST131. Copyright © 2017 American Society for Microbiology.

Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets.

PubMed

Herfst, Sander; Mok, Chris K P; van den Brand, Judith M A; van der Vliet, Stefan; Rosu, Miruna E; Spronken, Monique I; Yang, Zifeng; de Meulder, Dennis; Lexmond, Pascal; Bestebroer, Theo M; Peiris, J S Malik; Fouchier, Ron A M; Richard, Mathilde

2018-01-01

Since their emergence in 1997, A/H5N1 influenza viruses of the A/goose/Guangdong/1/96 lineage have diversified in multiple genetic and antigenic clades upon continued circulation in poultry in several countries in Eurasia and Africa. Since 2009, reassortant viruses carrying clade 2.3.4.4 hemagglutinin (HA) and internal and neuraminidase (NA) genes of influenza A viruses of different avian origin have been detected, yielding various HA-NA combinations, such as A/H5N1, A/H5N2, A/H5N3, A/H5N5, A/H5N6, and A/H5N8. Previous studies reported on the low pathogenicity and lack of airborne transmission of A/H5N2 and A/H5N8 viruses in the ferret model. However, although A/H5N6 viruses are the only clade 2.3.4.4 viruses that crossed the species barrier and infected humans, the risk they pose for human health remains poorly characterized. Here, the characterization of A/H5N6 A/Guangzhou/39715/2014 virus in vitro and in ferrets is described. This A/H5N6 virus possessed high polymerase activity, mediated by the E627K substitution in the PB2 protein, which corresponds to only one biological trait out of the three that were previously shown to confer airborne transmissibility to A/H5N1 viruses between ferrets. This might explain its lack of airborne transmission between ferrets. After intranasal inoculation, A/H5N6 virus replicated to high titers in the respiratory tracts of ferrets and was excreted for at least 6 days. Moreover, A/H5N6 virus caused severe pneumonia in ferrets upon intratracheal inoculation. Thus, A/H5N6 virus causes a more severe disease in ferrets than previously investigated clade 2.3.4.4 viruses, but our results demonstrate that the risk from airborne spread is currently low. IMPORTANCE Avian influenza A viruses are a threat to human health, as they cross the species barrier and infect humans occasionally, often with severe outcome. The antigenic and genetic diversity of A/H5 viruses from the A/goose/Guangdong/1/96 lineage is increasing, due to continued

Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets

PubMed Central

Mok, Chris K. P.; van den Brand, Judith M. A.; van der Vliet, Stefan; Rosu, Miruna E.; Spronken, Monique I.; Yang, Zifeng; de Meulder, Dennis; Lexmond, Pascal; Bestebroer, Theo M.; Peiris, J. S. Malik; Fouchier, Ron A. M.

2018-01-01

ABSTRACT Since their emergence in 1997, A/H5N1 influenza viruses of the A/goose/Guangdong/1/96 lineage have diversified in multiple genetic and antigenic clades upon continued circulation in poultry in several countries in Eurasia and Africa. Since 2009, reassortant viruses carrying clade 2.3.4.4 hemagglutinin (HA) and internal and neuraminidase (NA) genes of influenza A viruses of different avian origin have been detected, yielding various HA-NA combinations, such as A/H5N1, A/H5N2, A/H5N3, A/H5N5, A/H5N6, and A/H5N8. Previous studies reported on the low pathogenicity and lack of airborne transmission of A/H5N2 and A/H5N8 viruses in the ferret model. However, although A/H5N6 viruses are the only clade 2.3.4.4 viruses that crossed the species barrier and infected humans, the risk they pose for human health remains poorly characterized. Here, the characterization of A/H5N6 A/Guangzhou/39715/2014 virus in vitro and in ferrets is described. This A/H5N6 virus possessed high polymerase activity, mediated by the E627K substitution in the PB2 protein, which corresponds to only one biological trait out of the three that were previously shown to confer airborne transmissibility to A/H5N1 viruses between ferrets. This might explain its lack of airborne transmission between ferrets. After intranasal inoculation, A/H5N6 virus replicated to high titers in the respiratory tracts of ferrets and was excreted for at least 6 days. Moreover, A/H5N6 virus caused severe pneumonia in ferrets upon intratracheal inoculation. Thus, A/H5N6 virus causes a more severe disease in ferrets than previously investigated clade 2.3.4.4 viruses, but our results demonstrate that the risk from airborne spread is currently low. IMPORTANCE Avian influenza A viruses are a threat to human health, as they cross the species barrier and infect humans occasionally, often with severe outcome. The antigenic and genetic diversity of A/H5 viruses from the A/goose/Guangdong/1/96 lineage is increasing, due to

The Gondwana Breakup and the History of the Atlantic and Indian Oceans Unveils Two New Clades for Early Neobatrachian Diversification

PubMed Central

Frazão, Annelise; da Silva, Hélio Ricardo; Russo, Claudia Augusta de Moraes

2015-01-01

The largest anuran diversity belongs to the Neobatrachia, which harbor more than five thousand extant species. Here, we propose a new hypothesis for the historical aspects of the neobatrachian evolution with a formal biogeographical analysis. We selected 12 genes for 144 neobatrachian genera and four archaeobatrachian outgroups and performed a phylogenetic analysis using a maximum likelihood algorithm with the rapid bootstrap test. We also estimated divergence times for major lineages using a relaxed uncorrelated clock method. According to our time scale, the diversification of crown Neobatrachia began around the end of the Early Cretaceous. Our phylogenetic tree suggests that the first split of Neobatrachia is related to the geological events in the Atlantic and Indian Oceans. Hence, we propose names for these clades that indicate this connection, i.e., Atlanticanura and Indianura. The Atlanticanura is composed of three major neobatrachian lineages: Heleophrynidae, Australobatrachia and Nobleobatrachia. On the other hand, the Indianura consists of two major lineages: Sooglossoidea and Ranoides. The biogeographical analysis indicates that many neobatrachian splits occurred as a result of geological events such as the separation between South America and Africa, between India and the Seychelles, and between Australia and South America. PMID:26618546

Insights into the activity of maturation inhibitor PF-46396 on HIV-1 clade C.

PubMed

Ghimire, Dibya; Timilsina, Uddhav; Srivastava, Tryambak Pratap; Gaur, Ritu

2017-03-02

HIV maturation inhibitors are an emerging class of anti-retroviral compounds that inhibit the viral protease-mediated cleavage of the Gag, CA-SP1 (capsid-spacer peptide 1) peptide to mature CA. The first-in-class maturation inhibitor bevirimat (BVM) displayed potent activity against HIV-1 clade B but was ineffective against other HIV-1 clades including clade C. Another pyridone-based maturation inhibitor, PF-46396 displayed potent activity against HIV-1 clade B. In this study, we aimed at determining the activity of PF-46396 against HIV-1 clade C. We employed various biochemical and virological assays to demonstrate that PF-46396 is effective against HIV-1 clade C. We observed a dose dependent accumulation of CA-SP1 intermediate in presence of the compound. We carried out mutagenesis in the CA- SP1 region of HIV-1 clade C Gag and observed that the mutations conferred resistance against the compound. Many mutations inhibited Gag processing thereby reducing virus release in the absence of the compound. However, presence of PF-46396 rescued these defects and enhanced virus release, replication capacity and infectivity of HIV-1 clade C. These results put together identify PF-46396 as a broadly active maturation inhibitor against HIV-1 clade B and C and help in rational designing of novel analogs with reduced toxicity and increased efficacy for its potential use in clinics.

Unique clade of alphaproteobacterial endosymbionts induces complete cytoplasmic incompatibility in the coconut beetle

PubMed Central

Takano, Shun-ichiro; Tuda, Midori; Takasu, Keiji; Furuya, Naruto; Imamura, Yuya; Kim, Sangwan; Tashiro, Kosuke; Iiyama, Kazuhiro; Tavares, Matias; Amaral, Acacio Cardoso

2017-01-01

Maternally inherited bacterial endosymbionts in arthropods manipulate host reproduction to increase the fitness of infected females. Cytoplasmic incompatibility (CI) is one such manipulation, in which uninfected females produce few or no offspring when they mate with infected males. To date, two bacterial endosymbionts, Wolbachia and Cardinium, have been reported as CI inducers. Only Wolbachia induces complete CI, which causes 100% offspring mortality in incompatible crosses. Here we report a third CI inducer that belongs to a unique clade of Alphaproteobacteria detected within the coconut beetle, Brontispa longissima. This beetle comprises two cryptic species, the Asian clade and the Pacific clade, which show incompatibility in hybrid crosses. Different bacterial endosymbionts, a unique clade of Alphaproteobacteria in the Pacific clade and Wolbachia in the Asian clade, induced bidirectional CI between hosts. The former induced complete CI (100% mortality), whereas the latter induced partial CI (70% mortality). Illumina MiSeq sequencing and denaturing gradient gel electrophoresis patterns showed that the predominant bacterium detected in the Pacific clade of B. longissima was this unique clade of Alphaproteobacteria alone, indicating that this endosymbiont was responsible for the complete CI. Sex distortion did not occur in any of the tested crosses. The 1,160 bp of 16S rRNA gene sequence obtained for this endosymbiont had only 89.3% identity with that of Wolbachia, indicating that it can be recognized as a distinct species. We discuss the potential use of this bacterium as a biological control agent. PMID:28533374

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

PubMed Central

Nandi, Tannistha; Holden, Matthew T.G.; Didelot, Xavier; Mehershahi, Kurosh; Boddey, Justin A.; Beacham, Ifor; Peak, Ian; Harting, John; Baybayan, Primo; Guo, Yan; Wang, Susana; How, Lee Chee; Sim, Bernice; Essex-Lopresti, Angela; Sarkar-Tyson, Mitali; Nelson, Michelle; Smither, Sophie; Ong, Catherine; Aw, Lay Tin; Hoon, Chua Hui; Michell, Stephen; Studholme, David J.; Titball, Richard; Chen, Swaine L.; Parkhill, Julian

2015-01-01

Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed whole-genome sequencing (WGS) on 106 clinical, animal, and environmental strains from a restricted Asian locale. Whole-genome phylogenies resolved multiple genomic clades of Bp, largely congruent with multilocus sequence typing (MLST). We discovered widespread recombination in the Bp core genome, involving hundreds of regions associated with multiple haplotypes. Highly recombinant regions exhibited functional enrichments that may contribute to virulence. We observed clade-specific patterns of recombination and accessory gene exchange, and provide evidence that this is likely due to ongoing recombination between clade members. Reciprocally, interclade exchanges were rarely observed, suggesting mechanisms restricting gene flow between clades. Interrogation of accessory elements revealed that each clade harbored a distinct complement of restriction-modification (RM) systems, predicted to cause clade-specific patterns of DNA methylation. Using methylome sequencing, we confirmed that representative strains from separate clades indeed exhibit distinct methylation profiles. Finally, using an E. coli system, we demonstrate that Bp RM systems can inhibit uptake of non-self DNA. Our data suggest that RM systems borne on mobile elements, besides preventing foreign DNA invasion, may also contribute to limiting exchanges of genetic material between individuals of the same species. Genomic clades may thus represent functional units of genetic isolation in Bp, modulating intraspecies genetic diversity. PMID:25236617

Coupling molecules and morphology to discover new clades of ciliates.

NASA Astrophysics Data System (ADS)

Grattepanche, J. D.; Maurer-Alcalá, X. X.; Tucker, S. J.; McManus, G. B.; Katz, L. A.

2016-02-01

In a previous study using high-throughput sequencing (Grattepanche et al submitted, oral presentation?), we observe the presence of two clades of spirotrich ciliates mainly present in marine deep-water along the New England coast. These clades, clusters X1 and X2, are characterized by several deletions in their SSU-rDNA and have been observed elsewhere as both identical and similar sequences have been deposited on GenBank from other environmental studies, but lack morphological description. In order to link molecules (SSU-rDNA sequence) to their morphology, we sample below the photic zone (between 60 to 400m of depth) in the New England coast (Northeast Atlantic) in a transect crossing the continental shelf. We designed an oligonucleotide probe specific for choreotrich and oligotrich ciliates and another specific to clusters X1 and X2 to describe these clades through a combination of Fluorescence In Situ Hybridization (FISH) and light microscopy. Our aim is to increase our knowledge on the morphology of these `unknown' clades of ciliates, which will allow for future ecological studies.

Adolescent Sexuality: Pregnancy, Sexually Transmitted Diseases, and Prevention.

ERIC Educational Resources Information Center

Santelli, John S.; And Others

1992-01-01

Special edition discusses adolescent sexuality, focusing on pregnancy, sexually transmitted diseases, and prevention. The articles focus on demographics, risk factors, school-based risk reduction programs, contraception, early intervention, options, school-based prenatal and postpartum care programs, teenage parenting, abortion, HIV and AIDS,…

Herbivory increases diversification across insect clades

PubMed Central

Wiens, John J.; Lapoint, Richard T.; Whiteman, Noah K.

2015-01-01

Insects contain more than half of all living species, but the causes of their remarkable diversity remain poorly understood. Many authors have suggested that herbivory has accelerated diversification in many insect clades. However, others have questioned the role of herbivory in insect diversification. Here, we test the relationships between herbivory and insect diversification across multiple scales. We find a strong, positive relationship between herbivory and diversification among insect orders. However, herbivory explains less variation in diversification within some orders (Diptera, Hemiptera) or shows no significant relationship with diversification in others (Coleoptera, Hymenoptera, Orthoptera). Thus, we support the overall importance of herbivory for insect diversification, but also show that its impacts can vary across scales and clades. In summary, our results illuminate the causes of species richness patterns in a group containing most living species, and show the importance of ecological impacts on diversification in explaining the diversity of life. PMID:26399434

Herbivory increases diversification across insect clades.

PubMed

Wiens, John J; Lapoint, Richard T; Whiteman, Noah K

2015-09-24

Insects contain more than half of all living species, but the causes of their remarkable diversity remain poorly understood. Many authors have suggested that herbivory has accelerated diversification in many insect clades. However, others have questioned the role of herbivory in insect diversification. Here, we test the relationships between herbivory and insect diversification across multiple scales. We find a strong, positive relationship between herbivory and diversification among insect orders. However, herbivory explains less variation in diversification within some orders (Diptera, Hemiptera) or shows no significant relationship with diversification in others (Coleoptera, Hymenoptera, Orthoptera). Thus, we support the overall importance of herbivory for insect diversification, but also show that its impacts can vary across scales and clades. In summary, our results illuminate the causes of species richness patterns in a group containing most living species, and show the importance of ecological impacts on diversification in explaining the diversity of life.

Molecular diversity of early foraminifera

NASA Astrophysics Data System (ADS)

Holzmann, Maria; Pawlowski, Jan

2017-04-01

Monothalamid foraminifera are a diverse group that is characterized by single-chambered agglutinated or organic test. They occur in all marine habitats and are also present in terrestrial and freshwater environments. Monothalamids branch at the base of foraminiferal tree, as a paraphyletic group with some clades branching at the base of Globothalamea and Tubothalamea. We have currently more than 1500 sequences of monothalamids in our database that can be divided in at least 20 clades among which certain are particularly well presented by sequence numbers and/or number of different species. These are members of clade BM that contain Bathysiphon and Micrometula, clade C that contains among others xenophyophorans, saccaminids, and a large variety of organic-walled or agglutinated genera, clade E that contains the genera Psammophaga, Vellaria and Nellya and four clades that contain freshwater foraminifera. In general, the monothalamid clades comprise both agglutinated and organic-walled genera. Some common genera, such as Crithionina, Saccammina, Hippocrepina, are polyphyletic. Our results clearly show that monothalamids are highly diverse and their molecular diversity by far surpasses their morphological variety. Based on phylogenomic studies, monothalamids evolved early in the evolution of eukaryotes, as a part of the supergroup of Rhizaria, comprising also radiolarians and other amoeboid protists. The monothalamids have diverged from ancestral radiolarians, probably about 1000 million years ago, but the exact time is difficult to infer because of the uncertainties concerning a calibration of a eukaryotic phylogenomic tree.

Classification of Cowpox Viruses into Several Distinct Clades and Identification of a Novel Lineage

PubMed Central

Franke, Annika; Pfaff, Florian; Jenckel, Maria; Hoffmann, Bernd; Höper, Dirk; Antwerpen, Markus; Meyer, Hermann; Beer, Martin; Hoffmann, Donata

2017-01-01

Cowpox virus (CPXV) was considered as uniform species within the genus Orthopoxvirus (OPV). Previous phylogenetic analysis indicated that CPXV is polyphyletic and isolates may cluster into different clades with two of these clades showing genetic similarities to either variola (VARV) or vaccinia viruses (VACV). Further analyses were initiated to assess both the genetic diversity and the evolutionary background of circulating CPXVs. Here we report the full-length sequences of 20 CPXV strains isolated from different animal species and humans in Germany. A phylogenetic analysis of altogether 83 full-length OPV genomes confirmed the polyphyletic character of the species CPXV and suggested at least four different clades. The German isolates from this study mainly clustered into two CPXV-like clades, and VARV- and VACV-like strains were not observed. A single strain, isolated from a cotton-top tamarin, clustered distantly from all other CPXVs and might represent a novel and unique evolutionary lineage. The classification of CPXV strains into clades roughly followed their geographic origin, with the highest clade diversity so far observed for Germany. Furthermore, we found evidence for recombination between OPV clades without significant disruption of the observed clustering. In conclusion, this analysis markedly expands the number of available CPXV full-length sequences and confirms the co-circulation of several CPXV clades in Germany, and provides the first data about a new evolutionary CPXV lineage. PMID:28604604

Pathobiology of Clade 2.3.4.4 H5Nx High-Pathogenicity Avian Influenza Virus Infections in Minor Gallinaceous Poultry Supports Early Backyard Flock Introductions in the Western United States in 2014-2015

PubMed Central

Bertran, Kateri; Lee, Dong-Hun; Pantin-Jackwood, Mary J.; Spackman, Erica; Balzli, Charles; Suarez, David L.

2017-01-01

ABSTRACT In 2014 and 2015, the United States experienced an unprecedented outbreak of Eurasian clade 2.3.4.4 H5 highly pathogenic avian influenza (HPAI) virus. Initial cases affected mainly wild birds and mixed backyard poultry species, while later outbreaks affected mostly commercial chickens and turkeys. The pathogenesis, transmission, and intrahost evolutionary dynamics of initial Eurasian H5N8 and reassortant H5N2 clade 2.3.4.4 HPAI viruses in the United States were investigated in minor gallinaceous poultry species (i.e., species for which the U.S. commercial industries are small), namely, Japanese quail, bobwhite quail, pearl guinea fowl, chukar partridges, and ring-necked pheasants. Low mean bird infectious doses (<2 to 3.7 log10) support direct introduction and infection of these species as observed in mixed backyard poultry during the early outbreaks. Pathobiological features and systemic virus replication in all species tested were consistent with HPAI virus infection. Sustained virus shedding with transmission to contact-exposed birds, alongside long incubation periods, may enable unrecognized dissemination and adaptation to other gallinaceous species, such as chickens and turkeys. Genome sequencing of excreted viruses revealed numerous low-frequency polymorphisms and 20 consensus-level substitutions in all genes and species, but especially in Japanese quail and pearl guinea fowl and in internal proteins PB1 and PB2. This genomic flexibility after only one passage indicates that influenza viruses can continue to evolve in galliform species, increasing their opportunity to adapt to other species. Our findings suggest that these gallinaceous poultry are permissive for infection and sustainable transmissibility with the 2014 initial wild bird-adapted clade 2.3.4.4 virus, with potential acquisition of mutations leading to host range adaptation. IMPORTANCE The outbreak of clade 2.3.4.4 H5 highly pathogenic avian influenza (HPAI) virus that occurred in the

Photosynthetic pigments of oceanic Chlorophyta belonging to prasinophytes clade VII.

PubMed

Lopes Dos Santos, Adriana; Gourvil, Priscillia; Rodríguez, Francisco; Garrido, José Luis; Vaulot, Daniel

2016-02-01

The ecological importance and diversity of pico/nanoplanktonic algae remains poorly studied in marine waters, in part because many are tiny and without distinctive morphological features. Amongst green algae, Mamiellophyceae such as Micromonas or Bathycoccus are dominant in coastal waters while prasinophytes clade VII, yet not formerly described, appear to be major players in open oceanic waters. The pigment composition of 14 strains representative of different subclades of clade VII was analyzed using a method that improves the separation of loroxanthin and neoxanthin. All the prasinophytes clade VII analyzed here showed a pigment composition similar to that previously reported for RCC287 corresponding to pigment group prasino-2A. However, we detected in addition astaxanthin for which it is the first report in prasinophytes. Among the strains analyzed, the pigment signature is qualitatively similar within subclades A and B. By contrast, RCC3402 from subclade C (Picocystis) lacks loroxanthin, astaxanthin, and antheraxanthin but contains alloxanthin, diatoxanthin, and monadoxanthin that are usually found in diatoms or cryptophytes. For subclades A and B, loroxanthin was lowest at highest light irradiance suggesting a light-harvesting role of this pigment in clade VII as in Tetraselmis. © 2015 Phycological Society of America.

Phylogeny, evolutionary trends and classification of the Spathelia-Ptaeroxylon clade: morphological and molecular insights.

PubMed

Appelhans, M S; Smets, E; Razafimandimbison, S G; Haevermans, T; van Marle, E J; Couloux, A; Rabarison, H; Randrianarivelojosia, M; Kessler, P J A

2011-06-01

The Spathelia-Ptaeroxylon clade is a group of morphologically diverse plants that have been classified together as a result of molecular phylogenetic studies. The clade is currently included in Rutaceae and recognized at a subfamilial level (Spathelioideae) despite the fact that most of its genera have traditionally been associated with other families and that there are no obvious morphological synapomorphies for the clade. The aim of the present study is to construct phylogenetic trees for the Spathelia-Ptaeroxylon clade and to investigate anatomical characters in order to decide whether it should be kept in Rutaceae or recognized at the familial level. Anatomical characters were plotted on a cladogram to help explain character evolution within the group. Moreover, phylogenetic relationships and generic limits within the clade are also addressed. A species-level phylogenetic analysis of the Spathelia-Ptaeroxylon clade based on five plastid DNA regions (rbcL, atpB, trnL-trnF, rps16 and psbA-trnH) was conducted using Bayesian, maximum parsimony and maximum likelihood methods. Leaf and seed anatomical characters of all genera were (re)investigated by light and scanning electron microscopy. With the exception of Spathelia, all genera of the Spathelila-Ptaeroxylon clade are monophyletic. The typical leaf and seed anatomical characters of Rutaceae were found. Further, the presence of oil cells in the leaves provides a possible synapomorphy for the clade. The Spathelia-Ptaeroxylon clade is well placed in Rutaceae and it is reasonable to unite the genera into one subfamily (Spathelioideae). We propose a new tribal classification of Spathelioideae. A narrow circumscription of Spathelia is established to make the genus monophyletic, and Sohnreyia is resurrected to accommodate the South American species of Spathelia. The most recent common ancestor of Spathelioideae probably had leaves with secretory cavities and oil cells, haplostemonous flowers with appendaged staminal

Phylogenetic Clades 6 and 8 of Enterohemorrhagic Escherichia coli O157:H7 With Particular stx Subtypes are More Frequently Found in Isolates From Hemolytic Uremic Syndrome Patients Than From Asymptomatic Carriers

PubMed Central

Iyoda, Sunao; Manning, Shannon D.; Seto, Kazuko; Kimata, Keiko; Isobe, Junko; Etoh, Yoshiki; Ichihara, Sachiko; Migita, Yuji; Ogata, Kikuyo; Honda, Mikiko; Kubota, Tsutomu; Kawano, Kimiko; Matsumoto, Kazutoshi; Kudaka, Jun; Asai, Norio; Yabata, Junko; Tominaga, Kiyoshi; Terajima, Jun; Morita-Ishihara, Tomoko; Izumiya, Hidemasa; Ogura, Yoshitoshi; Saitoh, Takehito; Iguchi, Atsushi; Kobayashi, Hideki; Hara-Kudo, Yukiko; Ohnishi, Makoto; Arai, Reiko; Kawase, Masao; Asano, Yukiko; Asoshima, Nanami; Chiba, Kazuki; Furukawa, Ichiro; Kuroki, Toshiro; Hamada, Madoka; Harada, Seiya; Hatakeyama, Takashi; Hirochi, Takashi; Sakamoto, Yumiko; Hiroi, Midori; Takashi, Kanda; Horikawa, Kazumi; Iwabuchi, Kaori; Kameyama, Mitsuhiro; Kasahara, Hitomi; Kawanishi, Shinya; Kikuchi, Koji; Ueno, Hiroyuki; Kitahashi, Tomoko; Kojima, Yuka; Konishi, Noriko; Obata, Hiromi; Kai, Akemi; Kono, Tomomi; Kurazono, Takayuki; Matsumoto, Masakado; Matsumoto, Yuko; Nagai, Yuhki; Naitoh, Hideki; Nakajima, Hiroshi; Nakamura, Hiromi; Nakane, Kunihiko; Nishi, Keiko; Saitoh, Etsuko; Satoh, Hiroaki; Takamura, Mitsuteru; Shiraki, Yutaka; Tanabe, Junichi; Tanaka, Keiko; Tokoi, Yuki; Yatsuyanagi, Jun

2014-01-01

Background  Enterohemorrhagic Escherichia coli (EHEC) O157:H7 infection causes severe diseases such as bloody diarrhea and hemolytic uremic syndrome (HUS). Although EHEC O157:H7 strains have exhibited high genetic variability, their abilities to cause human diseases have not been fully examined. Methods  Clade typing and stx subtyping of EHEC O157:H7 strains, which were isolated in Japan during 1999–2011 from 269 HUS patients and 387 asymptomatic carriers (ACs) and showed distinct pulsed-field gel electrophoresis patterns, were performed to determine relationships between specific lineages and clinical presentation. Results  Clades 6 and 8 strains were more frequently found among the isolates from HUS cases than those from ACs (P = .00062 for clade 6, P < .0001 for clade 8). All clade 6 strains isolated from HUS patients harbored stx2a and/or stx2c, whereas all clade 8 strains harbored either stx2a or stx2a/stx2c. However, clade 7 strains were predominantly found among the AC isolates but less frequently found among the HUS isolates, suggesting a significant association between clade 7 and AC (P < .0001). Logistic regression analysis revealed that 0–9 year old age is a significant predictor of the association between clade 8 and HUS. We also found an intact norV gene, which encodes for a nitric oxide reductase that inhibits Shiga toxin activity under anaerobic condition, in all clades 1–3 isolates but not in clades 4–8 isolates. Conclusions  Early detection of EHEC O157:H7 strains that belonged to clades 6/8 and harbored specific stx subtypes may be important for defining the risk of disease progression in EHEC-infected 0- to 9-year-old children. PMID:25734131

Identification of potent maturation inhibitors against HIV-1 clade C.

PubMed

Timilsina, Uddhav; Ghimire, Dibya; Timalsina, Bivek; Nitz, Theodore J; Wild, Carl T; Freed, Eric O; Gaur, Ritu

2016-06-06

Antiretroviral therapy has led to a profound improvement in the clinical care of HIV-infected patients. However, drug tolerability and the evolution of drug resistance have limited treatment options for many patients. Maturation inhibitors are a new class of antiretroviral agents for treatment of HIV-1. They act by interfering with the maturation of the virus by blocking the last step in Gag processing: the cleavage of the capsid-spacer peptide 1 (CA-SP1) intermediate to mature CA by the viral protease (PR). The first-in-class maturation inhibitor bevirimat (BVM) failed against a subset of HIV-1 isolates in clinical trials due to polymorphisms present in the CA-SP1 region of the Gag protein. Sequence analysis indicated that these polymorphisms are more common in non-clade B strains of HIV-1 such as HIV-1 clade C. Indeed, BVM was found to be ineffective against HIV-1 clade C molecular clones tested in this study. A number of BVM analogs were synthesized by chemical modifications at the C-28 position to improve its activity. The new BVM analogs displayed potent activity against HIV-1 clade B and C and also reduced infectivity of the virus. This study identifies novel and broadly active BVM analogs that may ultimately demonstrate efficacy in the clinic.

Phylogeny, evolutionary trends and classification of the Spathelia–Ptaeroxylon clade: morphological and molecular insights

PubMed Central

Appelhans, M. S.; Smets, E.; Razafimandimbison, S. G.; Haevermans, T.; van Marle, E. J.; Couloux, A.; Rabarison, H.; Randrianarivelojosia, M.; Keßler, P. J. A.

2011-01-01

Background and Aims The Spathelia–Ptaeroxylon clade is a group of morphologically diverse plants that have been classified together as a result of molecular phylogenetic studies. The clade is currently included in Rutaceae and recognized at a subfamilial level (Spathelioideae) despite the fact that most of its genera have traditionally been associated with other families and that there are no obvious morphological synapomorphies for the clade. The aim of the present study is to construct phylogenetic trees for the Spathelia–Ptaeroxylon clade and to investigate anatomical characters in order to decide whether it should be kept in Rutaceae or recognized at the familial level. Anatomical characters were plotted on a cladogram to help explain character evolution within the group. Moreover, phylogenetic relationships and generic limits within the clade are also addressed. Methods A species-level phylogenetic analysis of the Spathelia–Ptaeroxylon clade based on five plastid DNA regions (rbcL, atpB, trnL–trnF, rps16 and psbA–trnH) was conducted using Bayesian, maximum parsimony and maximum likelihood methods. Leaf and seed anatomical characters of all genera were (re)investigated by light and scanning electron microscopy. Key Results With the exception of Spathelia, all genera of the Spathelila–Ptaeroxylon clade are monophyletic. The typical leaf and seed anatomical characters of Rutaceae were found. Further, the presence of oil cells in the leaves provides a possible synapomorphy for the clade. Conclusions The Spathelia–Ptaeroxylon clade is well placed in Rutaceae and it is reasonable to unite the genera into one subfamily (Spathelioideae). We propose a new tribal classification of Spathelioideae. A narrow circumscription of Spathelia is established to make the genus monophyletic, and Sohnreyia is resurrected to accommodate the South American species of Spathelia. The most recent common ancestor of Spathelioideae probably had leaves with secretory cavities

Trachyrhizium urniformis n. g., n. sp., a Novel Marine Filose Thecate Amoeba Related to a Cercozoan Environmental Clade (Novel Clade 4).

PubMed

Shiratori, Takashi; Ishida, Ken-Ichiro

2016-11-01

A novel cercozoan filose thecate amoeba, Trachyrhizium urniformis n. g., n. sp., was isolated from a marine sediment sample collected at Agenashiku Island, Okinawa, Japan. We performed light and electron microscopic observations, and a molecular phylogenetic analysis using the small subunit ribosomal RNA gene of the isolate. Cells of T. urniformis are spherical in shape and are covered by a thin theca possessing a wide rounded aperture. Branching and occasionally anastomosing filopodia with small granules emerge from the aperture. The granules are transported in the filopodia bidirectionally. Transmission electron microscopy showed that cells of T. urniformis possess nucleus with permanently condensed chromatin, Golgi apparatuses, microbodies, mitochondria with tubular cristae, and extrusomes. Several morphological and ultrastructural features of T. urniformis (the presence of thecae and nucleus with permanently condensed chromatin) show similarities with those of Thecofilosea. In a phylogenetic analysis, T. urniformis included in Thecofilosea with weak statistical supports and formed a clade with two sequences that constitutes a cercozoan environmental clade, novel clade 4. On the basis of morphological and ultrastructural information and the results of the phylogenetic analysis, we propose T. urniformis as a new member of class Thecofilosea. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis

PubMed Central

Malmstrom, Rex R; Rodrigue, Sébastien; Huang, Katherine H; Kelly, Libusha; Kern, Suzanne E; Thompson, Anne; Roggensack, Sara; Berube, Paul M; Henn, Matthew R; Chisholm, Sallie W

2013-01-01

Prochlorococcus is the numerically dominant photosynthetic organism throughout much of the world's oceans, yet little is known about the ecology and genetic diversity of populations inhabiting tropical waters. To help close this gap, we examined natural Prochlorococcus communities in the tropical Pacific Ocean using a single-cell whole-genome amplification and sequencing. Analysis of the gene content of just 10 single cells from these waters added 394 new genes to the Prochlorococcus pan-genome—that is, genes never before seen in a Prochlorococcus cell. Analysis of marker genes, including the ribosomal internal transcribed sequence, from dozens of individual cells revealed several representatives from two uncultivated clades of Prochlorococcus previously identified as HNLC1 and HNLC2. While the HNLC clades can dominate Prochlorococcus communities under certain conditions, their overall geographic distribution was highly restricted compared with other clades of Prochlorococcus. In the Atlantic and Pacific oceans, these clades were only found in warm waters with low Fe and high inorganic P levels. Genomic analysis suggests that at least one of these clades thrives in low Fe environments by scavenging organic-bound Fe, a process previously unknown in Prochlorococcus. Furthermore, the capacity to utilize organic-bound Fe appears to have been acquired horizontally and may be exchanged among other clades of Prochlorococcus. Finally, one of the single Prochlorococcus cells sequenced contained a partial genome of what appears to be a prophage integrated into the genome. PMID:22895163

Testing the link between population genetic differentiation and clade diversification in Costa Rican orchids.

PubMed

Kisel, Yael; Moreno-Letelier, Alejandra C; Bogarín, Diego; Powell, Martyn P; Chase, Mark W; Barraclough, Timothy G

2012-10-01

Species population genetics could be an important factor explaining variation in clade species richness. Here, we use newly generated amplified fragment length polymorphism (AFLP) data to test whether five pairs of sister clades of Costa Rican orchids that differ greatly in species richness also differ in average neutral genetic differentiation within species, expecting that if the strength of processes promoting differentiation within species is phylogenetically heritable, then clades with greater genetic differentiation should diversify more. Contrary to expectation, neutral genetic differentiation does not correlate directly with total diversification in the clades studied. Neutral genetic differentiation varies greatly among species and shows no heritability within clades. Half of the variation in neutral genetic differentiation among populations can be explained by ecological variables, and species-level traits explain the most variation. Unexpectedly, we find no isolation by distance in any species, but genetic differentiation is greater between populations occupying different niches. This pattern corresponds with those observed for microscopic eukaryotes and could reflect effective widespread dispersal of tiny and numerous orchid seeds. Although not providing a definitive answer to whether population genetics processes affect clade diversification, this work highlights the potential for addressing new macroevolutionary questions using a comparative population genetic approach. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Genetic tools for the investigation of Roseobacter clade bacteria

PubMed Central

2009-01-01

Background The Roseobacter clade represents one of the most abundant, metabolically versatile and ecologically important bacterial groups found in marine habitats. A detailed molecular investigation of the regulatory and metabolic networks of these organisms is currently limited for many strains by missing suitable genetic tools. Results Conjugation and electroporation methods for the efficient and stable genetic transformation of selected Roseobacter clade bacteria including Dinoroseobacter shibae, Oceanibulbus indolifex, Phaeobacter gallaeciensis, Phaeobacter inhibens, Roseobacter denitrificans and Roseobacter litoralis were tested. For this purpose an antibiotic resistance screening was performed and suitable genetic markers were selected. Based on these transformation protocols stably maintained plasmids were identified. A plasmid encoded oxygen-independent fluorescent system was established using the flavin mononucleotide-based fluorescent protein FbFP. Finally, a chromosomal gene knockout strategy was successfully employed for the inactivation of the anaerobic metabolism regulatory gene dnr from D. shibae DFL12T. Conclusion A genetic toolbox for members of the Roseobacter clade was established. This provides a solid methodical basis for the detailed elucidation of gene regulatory and metabolic networks underlying the ecological success of this group of marine bacteria. PMID:20021642

A functional genomic analysis of Arabidopsis thaliana PP2C clade D

USDA-ARS?s Scientific Manuscript database

In the reference dicot plant Arabidopsis thaliana, the PP2C family of P-protein phosphatases includes the products of 80 genes that have been separated into 10 multi-protein clades plus six singletons. Clade D includes the products of nine genes distributed among 3 chromosomes (PPD1, At3g12620; PPD2...

FISH-Flow: a quantitative molecular approach for describing mixed clade communities of Symbiodinium

NASA Astrophysics Data System (ADS)

McIlroy, S. E.; Smith, G. J.; Geller, J. B.

2014-03-01

Our understanding of reef corals and their fate in a changing climate is limited by our ability to monitor the diversity and abundance of the dinoflagellate endosymbionts that sustain them. This study combined two well-known methods in tandem: fluorescent in situ hybridization (FISH) for genotype-specific labeling of Symbiodinium and flow cytometry to quantify the abundance of each symbiont clade in a sample. This technique (FISH-Flow) was developed with cultured Symbiodinium representing four distinct clades (based on large subunit rDNA) and was used to distinguish and quantify these types with high efficiency and few false positives. This technique was also applied to freshly isolated symbionts of Orbicella faveolata and Orbicella annularis. Isolates from acutely bleached coral tissues had significantly lower labeling efficiency; however, isolates from healthy tissue had efficiencies comparable to cultured Symbiodinium trials. RNA degradation in bleaching samples may have interfered with labeling of cells. Nevertheless, we were able to determine that, with and without thermal stress, experimental columns of the coral O. annularis hosted a majority of clade B and B/C symbionts on the top and side of the coral column, respectively. We demonstrated that, for cultured Symbiodinium and Symbiodinium freshly isolated from healthy host tissues, the relative ratio of clades could be accurately determined for clades present at as low as 7 % relative abundance. While this method does not improve upon PCR-based techniques in identifying clades at background levels, FISH-Flow provides a high precision, flexible system for targeting, quantifying and isolating Symbiodinium genotypes of interest.

The Estimation of Tree Posterior Probabilities Using Conditional Clade Probability Distributions

PubMed Central

Larget, Bret

2013-01-01

In this article I introduce the idea of conditional independence of separated subtrees as a principle by which to estimate the posterior probability of trees using conditional clade probability distributions rather than simple sample relative frequencies. I describe an algorithm for these calculations and software which implements these ideas. I show that these alternative calculations are very similar to simple sample relative frequencies for high probability trees but are substantially more accurate for relatively low probability trees. The method allows the posterior probability of unsampled trees to be calculated when these trees contain only clades that are in other sampled trees. Furthermore, the method can be used to estimate the total probability of the set of sampled trees which provides a measure of the thoroughness of a posterior sample. [Bayesian phylogenetics; conditional clade distributions; improved accuracy; posterior probabilities of trees.] PMID:23479066

Benefits from living together? Clades whose species use similar habitats may persist as a result of eco-evolutionary feedbacks.

PubMed

Prinzing, Andreas; Ozinga, Wim A; Brändle, Martin; Courty, Pierre-Emmanuel; Hennion, Françoise; Labandeira, Conrad; Parisod, Christian; Pihain, Mickael; Bartish, Igor V

2017-01-01

Contents 66 I. 67 II. 68 III. 69 IV. 70 V. 73 VI. 75 VII. 77 78 References 78 SUMMARY: Recent decades have seen declines of entire plant clades while other clades persist despite changing environments. We suggest that one reason why some clades persist is that species within these clades use similar habitats, because such similarity may increase the degree of co-occurrence of species within clades. Traditionally, co-occurrence among clade members has been suggested to be disadvantageous because of increased competition and enemy pressure. Here, we hypothesize that increased co-occurrence among clade members promotes mutualist exchange, niche expansion or hybridization, thereby helping species avoid population decline from environmental change. We review the literature and analyse published data for hundreds of plant clades (genera) within a well-studied region and find major differences in the degree to which species within clades occupy similar habitats. We tentatively show that, in clades for which species occupy similar habitats, species tend to exhibit increased co-occurrence, mutualism, niche expansion, and hybridization - and rarely decline. Consistently, throughout the geological past, clades whose species occupied similar habitats often persisted through long time-spans. Overall, for many plant species, the occupation of similar habitats among fellow clade members apparently reduced their vulnerability to environmental change. Future research should identify when and how this previously unrecognized eco-evolutionary feedback operates. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Sequential and Simultaneous Immunization of Rabbits with HIV-1 Envelope Glycoprotein SOSIP.664 Trimers from Clades A, B and C

PubMed Central

Klasse, P. J.; Ozorowski, Gabriel; Cupo, Albert; Pugach, Pavel; Ringe, Rajesh P.; Golabek, Michael; van Gils, Marit J.; Guttman, Miklos; Lee, Kelly K.; Wilson, Ian A.; Butera, Salvatore T.; Ward, Andrew B.; Montefiori, David C.; Sanders, Rogier W.; Moore, John P.

2016-01-01

We have investigated the immunogenicity in rabbits of native-like, soluble, recombinant SOSIP.664 trimers based on the env genes of four isolates of human immunodeficiency virus type 1 (HIV-1); specifically BG505 (clade A), B41 (clade B), CZA97 (clade C) and DU422 (clade C). The various trimers were delivered either simultaneously (as a mixture of clade A + B trimers) or sequentially over a 73-week period. Autologous, Tier-2 neutralizing antibody (NAb) responses were generated to the clade A and clade B trimers in the bivalent mixture. When delivered as boosting immunogens to rabbits immunized with the clade A and/or clade B trimers, the clade C trimers also generated autologous Tier-2 NAb responses, the CZA97 trimers doing so more strongly and consistently than the DU422 trimers. The clade C trimers also cross-boosted the pre-existing NAb responses to clade A and B trimers. We observed heterologous Tier-2 NAb responses albeit inconsistently, and with limited overall breath. However, cross-neutralization of the clade A BG505.T332N virus was consistently observed in rabbits immunized only with clade B trimers and then boosted with clade C trimers. The autologous NAbs induced by the BG505, B41 and CZA97 trimers predominantly recognized specific holes in the glycan shields of the cognate virus. The shared location of some of these holes may account for the observed cross-boosting effects and the heterologous neutralization of the BG505.T332N virus. These findings will guide the design of further experiments to determine whether and how multiple Env trimers can together induce more broadly neutralizing antibody responses. PMID:27627672

Predicting Mycobacterium tuberculosis Complex Clades Using Knowledge-Based Bayesian Networks

PubMed Central

Bennett, Kristin P.

2014-01-01

We develop a novel approach for incorporating expert rules into Bayesian networks for classification of Mycobacterium tuberculosis complex (MTBC) clades. The proposed knowledge-based Bayesian network (KBBN) treats sets of expert rules as prior distributions on the classes. Unlike prior knowledge-based support vector machine approaches which require rules expressed as polyhedral sets, KBBN directly incorporates the rules without any modification. KBBN uses data to refine rule-based classifiers when the rule set is incomplete or ambiguous. We develop a predictive KBBN model for 69 MTBC clades found in the SITVIT international collection. We validate the approach using two testbeds that model knowledge of the MTBC obtained from two different experts and large DNA fingerprint databases to predict MTBC genetic clades and sublineages. These models represent strains of MTBC using high-throughput biomarkers called spacer oligonucleotide types (spoligotypes), since these are routinely gathered from MTBC isolates of tuberculosis (TB) patients. Results show that incorporating rules into problems can drastically increase classification accuracy if data alone are insufficient. The SITVIT KBBN is publicly available for use on the World Wide Web. PMID:24864238

When Can Clades Be Potentially Resolved with Morphology?

PubMed Central

Bapst, David W.

2013-01-01

Morphology-based phylogenetic analyses are the only option for reconstructing relationships among extinct lineages, but often find support for conflicting hypotheses of relationships. The resulting lack of phylogenetic resolution is generally explained in terms of data quality and methodological issues, such as character selection. A previous suggestion is that sampling ancestral morphotaxa or sampling multiple taxa descended from a long-lived, unchanging lineage can also yield clades which have no opportunity to share synapomorphies. This lack of character information leads to a lack of ‘intrinsic’ resolution, an issue that cannot be solved with additional morphological data. It is unclear how often we should expect clades to be intrinsically resolvable in realistic circumstances, as intrinsic resolution must increase as taxonomic sampling decreases. Using branching simulations, I quantify intrinsic resolution across several models of morphological differentiation and taxonomic sampling. Intrinsically unresolvable clades are found to be relatively frequent in simulations of both extinct and living taxa under realistic sampling scenarios, implying that intrinsic resolution is an issue for morphology-based analyses of phylogeny. Simulations which vary the rates of sampling and differentiation were tested for their agreement to observed distributions of durations from well-sampled fossil records and also having high intrinsic resolution. This combination only occurs in those datasets when differentiation and sampling rates are both unrealistically high relative to branching and extinction rates. Thus, the poor phylogenetic resolution occasionally observed in morphological phylogenetics may result from a lack of intrinsic resolvability within groups. PMID:23638034

Parallel Evolution of Two Clades of an Atlantic-Endemic Pathogenic Lineage of Vibrio parahaemolyticus by Independent Acquisition of Related Pathogenicity Islands

PubMed Central

Xu, Feng; Drees, Kevin P.; Sebra, Robert P.; Jones, Stephen H.

2017-01-01

ABSTRACT Shellfish-transmitted Vibrio parahaemolyticus infections have recently increased from locations with historically low disease incidence, such as the Northeast United States. This change coincided with a bacterial population shift toward human-pathogenic variants occurring in part through the introduction of several Pacific native lineages (ST36, ST43, and ST636) to nearshore areas off the Atlantic coast of the Northeast United States. Concomitantly, ST631 emerged as a major endemic pathogen. Phylogenetic trees of clinical and environmental isolates indicated that two clades diverged from a common ST631 ancestor, and in each of these clades, a human-pathogenic variant evolved independently through acquisition of distinct Vibrio pathogenicity islands (VPaI). These VPaI differ from each other and bear little resemblance to hemolysin-containing VPaI from isolates of the pandemic clonal complex. Clade I ST631 isolates either harbored no hemolysins or contained a chromosome I-inserted island we call VPaIβ that encodes a type 3 secretion system (T3SS2β) typical of Trh hemolysin producers. The more clinically prevalent and clonal ST631 clade II had an island we call VPaIγ that encodes both tdh and trh and that was inserted in chromosome II. VPaIγ was derived from VPaIβ but with some additional acquired elements in common with VPaI carried by pandemic isolates, exemplifying the mosaic nature of pathogenicity islands. Genomics comparisons and amplicon assays identified VPaIγ-type islands containing tdh inserted adjacent to the ure cluster in the three introduced Pacific and most other emergent lineages that collectively cause 67% of infections in the Northeast United States as of 2016. IMPORTANCE The availability of three different hemolysin genotypes in the ST631 lineage provided a unique opportunity to employ genome comparisons to further our understanding of the processes underlying pathogen evolution. The fact that two different pathogenic clades arose in

Transmitted drug resistance in patients with acute/recent HIV infection in Brazil.

PubMed

Ferreira, Ana Cristina G; Coelho, Lara E; Grinsztejn, Eduarda; Jesus, Carlos S de; Guimarães, Monick L; Veloso, Valdiléa G; Grinsztejn, Beatriz; Cardoso, Sandra W

The widespread use of antiretroviral therapy increased the transmission of antiretroviral resistant HIV strains. Antiretroviral therapy initiation during acute/recent HIV infection limits HIV reservoirs and improves immune response in HIV infected individuals. Transmitted drug resistance may jeopardize the early goals of early antiretroviral treatment among acute/recent HIV infected patients. Patients with acute/recent HIV infection who underwent resistance test before antiretroviral treatment initiation were included in this analysis. HIV-1 sequences were obtained using an in house protease/reverse transcriptase genotyping assay. Transmitted drug resistance was identified according to the Stanford HIV Database for Transmitted Drug Resistance Mutations, based on WHO 2009 surveillance list, and HIV-1 subtyping according to Rega HIV-1 subtyping tool. Comparison between patients with and without transmitted drug resistance was made using Kruskal-Wallis and Chi-square tests. Forty-three patients were included, 13 with acute HIV infection and 30 with recent HIV infection. The overall transmitted drug resistance prevalence was 16.3% (95% confidence interval [CI]: 8.1-30.0%). The highest prevalence of resistance (11.6%, 95% CI: 8.1-24.5) was against non-nucleoside reverse transcriptase inhibitors, and K103N was the most frequently identified mutation. The high prevalence of nonnucleoside reverse transcriptase inhibitors resistance indicates that efavirenz-based regimen without prior resistance testing is not ideal for acutely/recently HIV-infected individuals in our setting. In this context, the recent proposal of including integrase inhibitors as a first line regimen in Brazil could be an advantage for the treatment of newly HIV infected individuals. However, it also poses a new challenge, since integrase resistance test is not routinely performed for antiretroviral naive individuals. Further studies on transmitted drug resistance among acutely/recently HIV-infected are

Description of Teunomyces gen. nov. for the Candida kruisii clade, Suhomyces gen. nov. for the Candida tanzawaensis clade and Suhomyces kilbournensis sp. nov.

PubMed

Kurtzman, Cletus P; Robnett, Christie J; Blackwell, Meredith

2016-08-01

DNA sequence analysis has shown that species of the Candida kruisii clade and species of the C. tanzawaensis clade represent phylogenetically circumscribed genera, which are described as Teunomyces gen. nov., type species T kruisii, and Suhomyces gen. nov., type species S tanzawaensis Many of the species are distributed worldwide and they are often isolated from fungus-feeding insects and their habitats. Included is the description of S. kilbournensis (type strain NRRL Y-17864, CBS 14276), a species found almost exclusively on maize kernels (Zea mays) in IL, USA. Published by Oxford University Press on behalf of FEMS 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed.

PubMed

Tanaka, Mami; Endo, Shoko; Kotake, Fumihito; Al-Saari, Nurhidayu; Amin, A K M Rohul; Feng, Gao; Mino, Sayaka; Doi, Hidetaka; Ogura, Yoshitoshi; Hayashi, Tetsuya; Suda, Wataru; Hattori, Masahira; Yumoto, Isao; Sawabe, Toko; Sawabe, Tomoo; Araki, Toshiyoshi

2017-01-01

A novel strain Vibrio aphrogenes sp. nov. strain CA-1004T isolated from the surface of seaweed collected on the coast of Mie Prefecture in 1994 [1] was characterized using polyphasic taxonomy including multilocus sequence analysis (MLSA) and a genome based comparison. Both phylogenetic analyses on the basis of 16S rRNA gene sequences and MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the strain could be placed in the Rumoiensis clade in the genus Vibrio. Sequence similarities of the 16S rRNA gene and the multilocus genes against the Rumoiensis clade members, V. rumoiensis, V. algivorus, V. casei, and V. litoralis, were low enough to propose V. aphrogenes sp. nov. strain CA-1004T as a separate species. The experimental DNA-DNA hybridization data also revealed that the strain CA-1004T was separate from four known Rumoiensis clade species. The G+C content of the V. aphrogenes strain was determined as 42.1% based on the genome sequence. Major traits of the strain were non-motile, halophilic, fermentative, alginolytic, and gas production. A total of 27 traits (motility, growth temperature range, amylase, alginase and lipase productions, and assimilation of 19 carbon compounds) distinguished the strain from the other species in the Rumoiensis clade. The name V. aphrogenes sp. nov. is proposed for this species in the Rumoiensis clade, with CA-1004T as the type strain (JCM 31643T = DSM 103759T).

High Prevalence and Onward Transmission of Non-Pandemic HIV-1 Subtype B Clades in Northern and Northeastern Brazilian Regions

PubMed Central

Divino, Flavia; de Lima Guerra Corado, Andre; Gomes Naveca, Felipe; Stefani, Mariane M. A.; Bello, Gonzalo

2016-01-01

The Human immunodeficiency virus type-1 (HIV-1) epidemic in Brazil is mainly driven by the subtype B pandemic lineage (BPANDEMIC), while Caribbean non-pandemic subtype B clades (BCAR) seem to account for a very low fraction of HIV-infections in this country. The molecular characteristics of the HIV-1 subtype B strains disseminated in the Northern and Northeastern Brazilian regions, however, have not been explored so far. In this study, we estimate the prevalence of the HIV-1 BPANDEMIC and BCAR clades across different Brazilian regions and we reconstruct the spatiotemporal dynamics of dissemination of the major Brazilian BCAR clades. A total of 2,682 HIV-1 subtype B pol sequences collected from 21 different Brazilian states from the five country regions between 1998 and 2013 were analyzed. Maximum Likelihood phylogenetic analyses revealed that the BCAR strains reached 16 out 21 Brazilian states here analyzed. The BCAR clades comprise a low fraction (<10%) of subtype B infections in most Brazilian states analyzed, with exception of Roraima (41%), Amazonas (14%) and Maranhão (14%). Bayesian phylogeographic analyses indicate that BCAR strains originally from the Hispaniola and Trinidad and Tobago were introduced at multiple times into different states from all Brazilian regions and a few of those strains, probably introduced into Roraima, Maranhão and São Paulo between the late 1970s and the early 1980s, established secondary outbreaks in the Brazilian population. These results support that the HIV-1 subtype B epidemics in some Brazilian states from the Northern and Northeastern regions display a unique molecular pattern characterized by the high prevalence of BCAR lineages, which probably reflects a strong epidemiological link with the HIV-1 epidemics in the Caribbean region. PMID:27603317

Euryhaline ecology of early tetrapods revealed by stable isotopes.

PubMed

Goedert, Jean; Lécuyer, Christophe; Amiot, Romain; Arnaud-Godet, Florent; Wang, Xu; Cui, Linlin; Cuny, Gilles; Douay, Guillaume; Fourel, François; Panczer, Gérard; Simon, Laurent; Steyer, J-Sébastien; Zhu, Min

2018-06-01

The fish-to-tetrapod transition-followed later by terrestrialization-represented a major step in vertebrate evolution that gave rise to a successful clade that today contains more than 30,000 tetrapod species. The early tetrapod Ichthyostega was discovered in 1929 in the Devonian Old Red Sandstone sediments of East Greenland (dated to approximately 365 million years ago). Since then, our understanding of the fish-to-tetrapod transition has increased considerably, owing to the discovery of additional Devonian taxa that represent early tetrapods or groups evolutionarily close to them. However, the aquatic environment of early tetrapods and the vertebrate fauna associated with them has remained elusive and highly debated. Here we use a multi-stable isotope approach (δ 13 C, δ 18 O and δ 34 S) to show that some Devonian vertebrates, including early tetrapods, were euryhaline and inhabited transitional aquatic environments subject to high-magnitude, rapid changes in salinity, such as estuaries or deltas. Euryhalinity may have predisposed the early tetrapod clade to be able to survive Late Devonian biotic crises and then successfully colonize terrestrial environments.

Clades of Adeno-Associated Viruses Are Widely Disseminated in Human Tissues

PubMed Central

Gao, Guangping; Vandenberghe, Luk H.; Alvira, Mauricio R.; Lu, You; Calcedo, Roberto; Zhou, Xiangyang; Wilson, James M.

2004-01-01

The potential for using Adeno-associated virus (AAV) as a vector for human gene therapy has stimulated interest in the Dependovirus genus. Serologic data suggest that AAV infections are prevalent in humans, although analyses of viruses and viral sequences from clinical samples are extremely limited. Molecular techniques were used in this study to successfully detect endogenous AAV sequences in 18% of all human tissues screened, with the liver and bone marrow being the most predominant sites. Sequence characterization of rescued AAV DNAs indicated a diverse array of molecular forms which segregate into clades whose members share functional and serologic similarities. One of the most predominant human clades is a hybrid of two previously described AAV serotypes, while another clade was found in humans and several species of nonhuman primates, suggesting a cross-species transmission of this virus. These data provide important information regarding the biology of parvoviruses in humans and their use as gene therapy vectors. PMID:15163731

Clade perseverance from Mesozoic to present: a multidisciplinary approach to interpretation of pattern and process.

PubMed

Barnes, David K A

2002-10-01

Two clades of marine bryozoans, cyclostomes and cheilostomes, exemplify the benefits of applying a multidisciplinary approach to the interpretation of long-term evolutionary patterns. The cyclostome bryozoans were dominant in the Mesozoic; since that era, they have decreased in absolute terms and the cheilostomes have come to exceed them in both abundance and diversity. Many studies of living assemblages of the encrusting members of these two clades indicate that cheilostomes are superior space competitors, but paleontological studies suggest that competition between the two taxa has not been escalating over geological time. Both clades occur throughout the world's oceans and seas, and recent work in the geographical extremes has shown that the relative success of the clades varies markedly from place to place. In this study, the importance of differential patterns of recruitment and cumulative space occupation in the two clades was evaluated over four years and in two environments, one temperate and one polar. In both of these environments, peaks of recruitment and space occupation by the two clades were out of phase. The different strategies and outcomes of spatial competition are examined, largely using data from the literature. Only recently has it been realized that tied outcomes of competition are stable alternative results and not simply transitory phases. Many competitive encounters involving cyclostomes result in ties, implying that their strategy is based on persistence rather than dominance. When different indices and models are used to analyze competition data from the two clades, the interpretation varies markedly with methodology. The differences in patterns of recruitment, space occupation, and spatial competition have influenced both our understanding of how the two clades have persisted alongside each other and our perception of cheilostome superiority. Analysis of fluid dynamics has shown that small differences in the mechanical structure of

Phylogeny and taxonomy of the North American clade of the Ceratocystis fimbriata complex.

PubMed

Johnson, Jason A; Harrington, Thomas C; Engelbrecht, C J B

2005-01-01

Ceratocystis fimbriata is a widely distributed, plant pathogenic fungus that causes wilts and cankers on many woody hosts. Earlier phylogenetic analyses of DNA sequences revealed three geographic clades within the C. fimbriata complex that are centered respectively in North America, Latin America and Asia. This study looked for cryptic species within the North American clade. The internal transcribed spacer regions (ITS) of the rDNA were sequenced, and phylogenetic analysis indicated that most isolates from the North American clade group into four host-associated lineages, referred to as the aspen, hickory, oak and cherry lineages, which were isolated primarily from wounds or diseased trees of Populus, Carya, Quercus and Prunus, respectively. A single isolate collected from P. serotina in Wisconsin had a unique ITS sequence. Allozyme electromorphs also were highly polymorphic within the North American clade, and the inferred phylogenies from these data were congruent with the ITS-rDNA analyses. In pairing experiments isolates from the aspen, hickory, oak and cherry lineages were interfertile only with other isolates from their respective lineages. Inoculation experiments with isolates of the four host-associated groupings showed strong host specialization by isolates from the aspen and hickory lineages on Populus tremuloides and Carya illinoensis, respectively, but isolates from the oak and cherry lineages did not consistently reveal host specialization. Morphological features distinguish isolates in the North American clade from those of the Latin American clade (including C. fimbriata sensu stricto). Based on the phylogenetic evidence, interfertility, host specialization and morphology, the oak and cherry lineages are recognized as the earlier described C. variospora, the poplar lineage as C. populicola sp. nov., and the hickory lineage as C. caryae sp. nov. A new species associated with the bark beetle Scolytus quadrispinosus on Carya is closely related to C

Draft genome and sequence variant data of the oomycete Pythium insidiosum strain Pi45 from the phylogenetically-distinct Clade-III.

PubMed

Kittichotirat, Weerayuth; Patumcharoenpol, Preecha; Rujirawat, Thidarat; Lohnoo, Tassanee; Yingyong, Wanta; Krajaejun, Theerapong

2017-12-01

Pythium insidiosum is a unique oomycete microorganism, capable of infecting humans and animals. The organism can be phylogenetically categorized into three distinct clades: Clade-I (strains from the Americas); Clade-II (strains from Asia and Australia), and Clade-III (strains from Thailand and the United States). Two draft genomes of the P. insidiosum Clade-I strain CDC-B5653 and Clade-II strain Pi-S are available in the public domain. The genome of P. insidiosum from the distinct Clade-III, which is distantly-related to the other two clades, is lacking. Here, we report the draft genome sequence of the P. insidiosum strain Pi45 (also known as MCC13; isolated from a Thai patient with pythiosis; accession numbers BCFM01000001-BCFM01017277) as a representative strain of the phylogenetically-distinct Clade-III. We also report a genome-scale data set of sequence variants (i.e., SNPs and INDELs) found in P. insidiosum (accessible online at the Mendeley database: http://dx.doi.org/10.17632/r75799jy6c.1).

Mitogenomic circumscription of a novel percomorph fish clade mainly comprising "Syngnathoidei" (Teleostei).

PubMed

Song, Ha Yeun; Mabuchi, Kohji; Satoh, Takashi P; Moore, Jon A; Yamanoue, Yusuke; Miya, Masaki; Nishida, Mutsumi

2014-06-01

Percomorpha, comprising about 60% of modern teleost fishes, has been described as the "(unresolved) bush at the top" of the tree, with its intrarelationships still being ambiguous owing to huge diversity (>15,000 species). Recent molecular phylogenetic studies based on extensive taxon and character sampling, however, have revealed a number of unexpected clades of Percomorpha, and one of which is composed of Syngnathoidei (seahorses, pipefishes, and their relatives) plus several groups distributed across three different orders. To circumscribe the clade more definitely, we sampled several candidate taxa with reference to the previous studies and newly determined whole mitochondrial genome (mitogenome) sequences for 16 percomorph species across syngnathoids, dactylopterids, and their putatively closely-related fishes (Mullidae, Callionymoidei, Malacanthidae). Unambiguously aligned sequences (13,872 bp) from those 16 species plus 78 percomorphs and two outgroups (total 96 species) were subjected to partitioned Bayesian and maximum likelihood analyses. The resulting trees revealed a highly supported clade comprising seven families in Syngnathoidei (Gasterosteiformes), Dactylopteridae (Scorpaeniformes), Mullidae in Percoidei and two families in Callionymoidei (Perciformes). We herein proposed to call this clade "Syngnathiformes" following the latest nuclear DNA studies with some revisions on the included families. Copyright © 2014 Elsevier B.V. All rights reserved.

Revision of the Lima clade (Miconia sect. Lima, Miconieae, Melastomataceae) of the Greater Antilles

PubMed Central

Majure, Lucas C.; Bécquer, Eldis R.; Judd, Walter S.

2016-01-01

Abstract Miconia sect. Lima is an entirely Greater Antillean clade that consists of 19 known species of shrubs and small trees, which were previously recognized under the polyphyletic genera Leandra and Ossaea. The highest species richness in the clade is represented on Cuba (10 species), followed by Hispaniola (8 species) and then Jamaica (1 species). Here we present a taxonomic revision of the clade based on the study of species in the field, herbarium specimens, as well as a DNA-based phylogeny reconstruction. The Lima clade most likely originated on Cuba and then spread to Jamaica once and Hispaniola multiple times. Species of this clade can be recognized by the well developed bulla-based hairs of the adaxial leaf surface, as well as the clavate-dendritic hairs produced along the primary, secondary and tertiary veins of the adaxial leaf surface, mostly towards the leaf base, terminal inflorescences, acute petal apices, slightly bulla-based hairs produced subapically along the petal abaxial surface, and anthers with a dorso-basal appendage and a single, dorsally oriented pore. Descriptions, synonymies, along with distribution maps and illustrations/figures, are given for each species. Miconia pagnolensis sp. nov. is newly described in this revision. PMID:27829802

R5 clade C SHIV strains with tier 1 or 2 neutralization sensitivity: tools to dissect env evolution and to develop AIDS vaccines in primate models.

PubMed

Siddappa, Nagadenahalli B; Watkins, Jennifer D; Wassermann, Klemens J; Song, Ruijiang; Wang, Wendy; Kramer, Victor G; Lakhashe, Samir; Santosuosso, Michael; Poznansky, Mark C; Novembre, Francis J; Villinger, François; Else, James G; Montefiori, David C; Rasmussen, Robert A; Ruprecht, Ruth M

2010-07-21

HIV-1 clade C (HIV-C) predominates worldwide, and anti-HIV-C vaccines are urgently needed. Neutralizing antibody (nAb) responses are considered important but have proved difficult to elicit. Although some current immunogens elicit antibodies that neutralize highly neutralization-sensitive (tier 1) HIV strains, most circulating HIVs exhibiting a less sensitive (tier 2) phenotype are not neutralized. Thus, both tier 1 and 2 viruses are needed for vaccine discovery in nonhuman primate models. We constructed a tier 1 simian-human immunodeficiency virus, SHIV-1157ipEL, by inserting an "early," recently transmitted HIV-C env into the SHIV-1157ipd3N4 backbone [1] encoding a "late" form of the same env, which had evolved in a SHIV-infected rhesus monkey (RM) with AIDS. SHIV-1157ipEL was rapidly passaged to yield SHIV-1157ipEL-p, which remained exclusively R5-tropic and had a tier 1 phenotype, in contrast to "late" SHIV-1157ipd3N4 (tier 2). After 5 weekly low-dose intrarectal exposures, SHIV-1157ipEL-p systemically infected 16 out of 17 RM with high peak viral RNA loads and depleted gut CD4+ T cells. SHIV-1157ipEL-p and SHIV-1157ipd3N4 env genes diverge mostly in V1/V2. Molecular modeling revealed a possible mechanism for the increased neutralization resistance of SHIV-1157ipd3N4 Env: V2 loops hindering access to the CD4 binding site, shown experimentally with nAb b12. Similar mutations have been linked to decreased neutralization sensitivity in HIV-C strains isolated from humans over time, indicating parallel HIV-C Env evolution in humans and RM. SHIV-1157ipEL-p, the first tier 1 R5 clade C SHIV, and SHIV-1157ipd3N4, its tier 2 counterpart, represent biologically relevant tools for anti-HIV-C vaccine development in primates.

Postantifungal effect of caspofungin against the Candida albicans and Candida parapsilosis clades.

PubMed

Gil-Alonso, Sandra; Jauregizar, Nerea; Eraso, Elena; Quindós, Guillermo

2016-10-01

Killing and postantifungal effects could be relevant for the selection of optimal dosing schedules. This study aims to compare time-kill and postantifungal effects with caspofungin on Candida albicans (C. albicans, Candida dubliniensis, Candida africana) and Candida parapsilosis (C. parapsilosis, Candida metapsilosis, Candida orthopsilosis) clades. In the postantifungal effect experiments, strains were exposed to caspofungin for 1 h at concentrations 0.12-8 μg/mL. Time-kill experiments were conducted at the same concentrations. Caspofungin exhibited a significant and prolonged postantifungal effect (>37 h) with 2 μg/mL against the most strains of C. albicans clade. Against the C. parapsilosis clade, the postantifungal effect was <12 h at 8 μg/mL, except for two strains. Caspofungin was fungicidal against C. albicans, C. dubliniensis and C. metapsilosis. Copyright © 2016 Elsevier Inc. All rights reserved.

An Anti-HIV-1 V3 Loop Antibody Fully Protects Cross-Clade and Elicits T-Cell Immunity in Macaques Mucosally Challenged with an R5 Clade C SHIV

PubMed Central

Lakhashe, Samir K.; Humbert, Michael; Sholukh, Anton; Hemashettar, Girish; Wong, Yin Ling; Yoon, John K.; Wang, Wendy; Novembre, Francis J.; Villinger, Francois; Ibegbu, Chris; Patel, Kalpana; Corti, Davide; Agatic, Gloria; Vanzetta, Fabrizia; Bianchi, Siro; Heeney, Jonathan L.; Sallusto, Federica; Lanzavecchia, Antonio; Ruprecht, Ruth M.

2011-01-01

Neutralizing antibodies have been shown to protect macaques against SHIV challenge. However, genetically diverse HIV-1 clades have evolved, and a key question left unanswered is whether neutralizing antibodies can confer cross-clade protection in vivo. The novel human monoclonal antibody HGN194 was isolated from an individual infected with an HIV-1 clade AG recombinant circulating recombinant form (CRF). HGN194 targets an epitope in the third hypervariable loop (V3) of HIV-1 gp120 and neutralizes a range of relatively neutralization-sensitive and resistant viruses. We evaluated the potential of HGN194 to protect infant rhesus monkeys against a SHIV encoding a primary CCR5-tropic HIV-1 clade C envelope. After high-dose mucosal challenge, all untreated controls became highly viremic while all HGN194-treated animals (50 mg/kg) were completely protected. When HGN194 was given at 1 mg/kg, one out of two monkeys remained aviremic, whereas the other had delayed, lower peak viremia. Interestingly, all protected monkeys given high-dose HGN194 developed Gag-specific proliferative responses of both CD4+ and CD8+ T cells. To test whether generation of the latter involved cryptic infection, we ablated CD8+ cells after HGN194 clearance. No viremia was detected in any protected monkeys, thus ruling out virus reservoirs. Thus, induction of CD8 T-cell immunity may have resulted from transient “Hit and Run” infection or cross priming via Ag-Ab-mediated cross-presentation. Together, our data identified the HGN194 epitope as protective and provide proof-of-concept that this anti-V3 loop mAb can prevent infection with sterilizing immunity after challenge with virus of a different clade, implying that V3 is a potential vaccine target. PMID:21483815

Predictors of Self-reported Sexually Transmitted Diseases among Homeless and Runaway Adolescents

PubMed Central

Tyler, Kimberly A.; Whitbeck, Les B.; Hoyt, Dan R.; Yoder, Kevin A.

2009-01-01

Path analysis was used to investigate factors associated with self-reported sexually transmitted diseases among 569 homeless and runaway adolescents in four Midwestern states. Youth were interviewed by outreach workers directly on the streets, in shelters, and in drop-in centers. Results indicated that family abuse was positively related to substance use, affiliation with friends who sold sex, and time on own. Early family abuse indirectly increased the likelihood of self-reported sexually transmitted diseases through time on own, substance use, friends selling sex, and risky sexual behaviors. Finally, substance use and affiliation with friends who sold sex was positively associated with risky sexual behaviors, which in turn was related to self-reported sexually transmitted diseases. No significant gender interactions were found for this model. PMID:25125705

Greatly reduced phylogenetic structure in the cultivated potato clade of potatoes, Solanum section Petota

USDA-ARS?s Scientific Manuscript database

The species boundaries of wild and cultivated potatoes, Solanum section Petota, are controversial with most of the taxonomic problems in a clade containing cultivated potatoes. We here provide the first in-depth phylogenetic study of the cultivated potato clade to explore possible causes of these pr...

Ecological variation in South American geophagine cichlids arose during an early burst of adaptive morphological and functional evolution

PubMed Central

Arbour, Jessica Hilary; López-Fernández, Hernán

2013-01-01

Diversity and disparity are unequally distributed both phylogenetically and geographically. This uneven distribution may be owing to differences in diversification rates between clades resulting from processes such as adaptive radiation. We examined the rate and distribution of evolution in feeding biomechanics in the extremely diverse and continentally distributed South American geophagine cichlids. Evolutionary patterns in multivariate functional morphospace were examined using a phylomorphospace approach, disparity-through-time analyses and by comparing Brownian motion (BM) and adaptive peak evolutionary models using maximum likelihood. The most species-rich and functionally disparate clade (CAS) expanded more efficiently in morphospace and evolved more rapidly compared with both BM expectations and its sister clade (GGD). Members of the CAS clade also exhibited an early burst in functional evolution that corresponds to the development of modern ecological roles and may have been related to the colonization of a novel adaptive peak characterized by fast oral jaw mechanics. Furthermore, reduced ecological opportunity following this early burst may have restricted functional evolution in the GGD clade, which is less species-rich and more ecologically specialized. Patterns of evolution in ecologically important functional traits are consistent with a pattern of adaptive radiation within the most diverse clade of Geophagini. PMID:23740780

Major Clades of Australasian Rutoideae (Rutaceae) Based on rbcL and atpB Sequences

PubMed Central

Bayly, Michael J.; Holmes, Gareth D.; Forster, Paul I.; Cantrill, David J.; Ladiges, Pauline Y.

2013-01-01

Background Rutaceae subfamily Rutoideae (46 genera, c. 660 species) is diverse in both rainforests and sclerophyll vegetation of Australasia. Australia and New Caledonia are centres of endemism with a number of genera and species distributed disjunctly between the two regions. Our aim was to generate a high-level molecular phylogeny for the Australasian Rutoideae and identify major clades as a framework for assessing morphological and biogeographic patterns and taxonomy. Methodology/Principal Findings Phylogenetic analyses were based on chloroplast genes, rbcL and atpB, for 108 samples (78 new here), including 38 of 46 Australasian genera. Results were integrated with those from other molecular studies to produce a supertree for Rutaceae worldwide, including 115 of 154 genera. Australasian clades are poorly matched with existing tribal classifications, and genera Philotheca and Boronia are not monophyletic. Major sclerophyll lineages in Australia belong to two separate clades, each with an early divergence between rainforest and sclerophyll taxa. Dehiscent fruits with seeds ejected at maturity (often associated with myrmecochory) are inferred as ancestral; derived states include woody capsules with winged seeds, samaras, fleshy drupes, and retention and display of seeds in dehisced fruits (the last two states adaptations to bird dispersal, with multiple origins among rainforest genera). Patterns of relationship and levels of sequence divergence in some taxa, mostly species, with bird-dispersed (Acronychia, Sarcomelicope, Halfordia and Melicope) or winged (Flindersia) seeds are consistent with recent long-distance dispersal between Australia and New Caledonia. Other deeper Australian/New Caledonian divergences, some involving ant-dispersed taxa (e.g., Neoschmidia), suggest older vicariance. Conclusions/Significance This comprehensive molecular phylogeny of the Australasian Rutoideae gives a broad overview of the group’s evolutionary and biogeographic history

A diminutive perinate European Enantiornithes reveals an asynchronous ossification pattern in early birds.

PubMed

Knoll, Fabien; Chiappe, Luis M; Sanchez, Sophie; Garwood, Russell J; Edwards, Nicholas P; Wogelius, Roy A; Sellers, William I; Manning, Phillip L; Ortega, Francisco; Serrano, Francisco J; Marugán-Lobón, Jesús; Cuesta, Elena; Escaso, Fernando; Sanz, Jose Luis

2018-03-05

Fossils of juvenile Mesozoic birds provide insight into the early evolution of avian development, however such fossils are rare. The analysis of the ossification sequence in these early-branching birds has the potential to address important questions about their comparative developmental biology and to help understand their morphological evolution and ecological differentiation. Here we report on an early juvenile enantiornithine specimen from the Early Cretaceous of Europe, which sheds new light on the osteogenesis in this most species-rich clade of Mesozoic birds. Consisting of a nearly complete skeleton, it is amongst the smallest known Mesozoic avian fossils representing post-hatching stages of development. Comparisons between this new specimen and other known early juvenile enantiornithines support a clade-wide asynchronous pattern of osteogenesis in the sternum and the vertebral column, and strongly indicate that the hatchlings of these phylogenetically basal birds varied greatly in size and tempo of skeletal maturation.

Efficacy of clade 2.3.2 H5 commercial vaccines in protecting chickens from clade 2.3.4.4 H5N8 highly pathogenic avian influenza infection.

PubMed

Yuk, Seong-Su; Erdene-Ochir, T O; Kwon, Jung-Hoon; Noh, Jin-Yong; Hong, Woo-Tack; Jeong, Jei-Hyun; Jeong, Sol; Gwon, Gyeong-Bin; Shin, Jong-Il; Sur, Jung-Hyang; Song, Chang-Seon

2017-03-01

Emerging clade 2.3.4.4 of the highly pathogenic avian influenza (HPAI) virus strain H5N8, which had been detected sporadically in domestic poultry in China, started to affect wild birds and poultry in South Korea in 2014. The virus was spread to Germany, Italy, the Netherlands, United Kingdom, and even United States by migratory birds. Here, we tested currently used commercial clade 2.3.2 H5 vaccines to evaluate mortality, clinical signs, virus shedding, and histological damage after experimental infection of chickens with the clade 2.3.4.4 HPAI H5N8 virus. Although the vaccination protected chickens from death, it failed to prevent chickens from shedding the virus and from tissue damage according to histological examination. These results suggest that the use of appropriate vaccines that match the currently epidemic HPAI virus is recommended, and continuous HPAI surveillance and testing of currently used commercial vaccines should be performed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Temporal variability of coastal Planctomycetes clades at Kabeltonne station, North Sea.

PubMed

Pizzetti, Ilaria; Fuchs, Bernhard M; Gerdts, Gunnar; Wichels, Antje; Wiltshire, Karen H; Amann, Rudolf

2011-07-01

Members of the bacterial phylum Planctomycetes are reported in marine water samples worldwide, but quantitative information is scarce. Here we investigated the phylogenetic diversity, abundance, and distribution of Planctomycetes in surface waters off the German North Sea island Helgoland during different seasons by 16S rRNA gene analysis and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). Generally Planctomycetes are more abundant in samples collected in summer and autumn than in samples collected in winter and spring. Statistical analysis revealed that Planctomycetes abundance was correlated to the Centrales diatom bloom in spring 2007. The analysis of size-fractionated seawater samples and of macroaggregates showed that ~90% of the Planctomycetes reside in the >3-μm size fraction. Comparative sequence analysis of 184 almost full-length 16S rRNA genes revealed three dominant clades. The clades, named Planctomyces-related group A, uncultured Planctomycetes group B, and Pirellula-related group D, were monitored by CARD-FISH using newly developed oligonucleotide probes. All three clades showed recurrent abundance patterns during two annual sampling campaigns. Uncultured Planctomycetes group B was most abundant in autumn samples, while Planctomyces-related group A was present in high numbers only during late autumn and winter. The levels of Pirellula-related group D were more constant throughout the year, with elevated counts in summer. Our analyses suggest that the seasonal succession of the Planctomycetes is correlated with algal blooms. We hypothesize that the niche partitioning of the different clades might be caused by their algal substrates.

Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon

PubMed Central

Faria, Nuno Rodrigues; Suchard, Marc A; Abecasis, Ana; Sousa, J. D.; Ndembi, Nicaise; Camacho, R.J.; Vandamme, Anne-Mieke; Peeters, Martine; Lemey, Philippe

2015-01-01

Evolutionary analyses have revealed an origin of pandemic HIV-1 group M in the Congo River basin in the first part of the XXth century, but the patterns of historical viral spread in or around its epicentre remain largely unexplored. Here, we combine epidemiologic and molecular sequence data to investigate the spatiotemporal patterns of the CRF02_AG clade. By explicitly integrating prevalence counts and genetic population size estimates we date the epidemic emergence of CRF02_AG at 1973.1 (1972.1, 1975.3 95% CI). To infer their phylogeographic signature at a regional scale, we analyze pol and env time-stamped sequence data from 8 countries using a Bayesian phylogeographic approach based on a discrete asymmetric model. Our data confirms a spatial origin of this clade in the Democratic Republic of Congo (DRC) and suggests that viral dissemination to Cameroon occurred at an early stage of the evolutionary history of CRF02_AG. We find considerable support for epidemiological linkage between neighbour countries. Compilation of ethnographic data suggests that well-supported viral migration was related with chance exportation events rather than by sustained human migratory flows. Finally, using sequence data from 15 locations in Cameroon, we use relaxed random walk models to explore the spatiotemporal dynamics of CRF02_AG at a finer geographical detail. Phylogeographic dispersal in continuous space reveals that at least two distinct CRF02_AG lineages are circulating in overlapping regions that are evolving at different evolutionary and diffusion rates. Altogether, by combining molecular and epidemiological data, our results provide a time scale for CRF02_AG, place its spatial root within the putative root of group-M diversity and propose a scenario for the spatiotemporal patterns of a successful HIV-1 lineage both at a regional and country-scale. PMID:21565285

A jungle tale: Molecular phylogeny and divergence time estimates of the Desmopsis-Stenanona clade (Annonaceae) in Mesoamerica.

PubMed

Ortiz-Rodriguez, Andrés Ernesto; Ornelas, Juan Francisco; Ruiz-Sanchez, Eduardo

2018-05-01

The predominantly Asian tribe Miliuseae (Annonaceae) includes over 37 Neotropical species that are mainly distributed across Mesoamerica, from southern Mexico to northern Colombia. The tremendous ecological and morphological diversity of this clade, including ramiflory, cauliflory, flagelliflory, and clonality, suggests adaptive radiation. Despite the spectacular phenotypic divergence of this clade, little is known about its phylogenetic and evolutionary history. In this study we used a nuclear DNA marker and seven chloroplast markers, and maximum parsimony, maximum likelihood and Bayesian inference methods to reconstruct a comprehensive time-calibrated phylogeny of tribe Miliuseae, especially focusing on the Desmopsis-Stenanona clade. We also perform ancestral area reconstructions to infer the biogeographic history of this group. Finally, we use ecological niche modeling, lineage distribution models, and niche overlap tests to assess whether geographic isolation and ecological specialization influenced the diversification of lineages within this clade. We reconstructed a monophyletic Miliuseae that is divided into two strongly supported clades: (i) a Sapranthus-Tridimeris clade and (ii) a Desmopsis-Stenanona clade. The colonization of the Neotropics and subsequent diversification of Neotropical Miliuseae seems to have been associated with the expansion of the boreotropical forests during the late Eocene and their subsequent fragmentation and southern displacement. Further speciation within Neotropical Miliuseae out of the Maya block seems to have occurred during the last 15 million years. Lastly, the geographic structuring of major lineages of the Desmopsis-Stenanona clade seems to have followed a climatic gradient, supporting the hypothesis that morphological differentiation between closely related species resulted from both long-term isolation between geographic ranges and adaptation to environmental conditions. Copyright © 2018 Elsevier Inc. All rights

Characterization of humoral responses to soluble trimeric HIV gp140 from a clade A Ugandan field isolate

PubMed Central

2013-01-01

Trimeric soluble forms of HIV gp140 envelope glycoproteins represent one of the closest molecular structures compared to native spikes present on intact virus particles. Trimeric soluble gp140 have been generated by several groups and such molecules have been shown to induce antibodies with neutralizing activity against homologous and heterologous viruses. In the present study, we generated a recombinant trimeric soluble gp140, derived from a previously identified Ugandan A-clade HIV field isolate (gp14094UG018). Antibodies elicited in immunized rabbits show a broad binding pattern to HIV envelopes of different clades. An epitope mapping analysis reveals that, on average, the binding is mostly focused on the C1, C2, V3, V5 and C5 regions. Immune sera show neutralization activity to Tier 1 isolates of different clades, demonstrating cross clade neutralizing activity which needs to be further broadened by possible structural modifications of the clade A gp14094UG018. Our results provide a rationale for the design and evaluation of immunogens and the clade A gp14094UG018 shows promising characteristics for potential involvement in an effective HIV vaccine with broad activity. PMID:23835244

Characterization of humoral responses to soluble trimeric HIV gp140 from a clade A Ugandan field isolate.

PubMed

Visciano, Maria Luisa; Tagliamonte, Maria; Stewart-Jones, Guillaume; Heyndrickx, Leo; Vanham, Guido; Jansson, Marianne; Fomsgaard, Anders; Grevstad, Berit; Ramaswamy, Meghna; Buonaguro, Franco M; Tornesello, Maria Lina; Biswas, Priscilla; Scarlatti, Gabriella; Buonaguro, Luigi

2013-07-08

Trimeric soluble forms of HIV gp140 envelope glycoproteins represent one of the closest molecular structures compared to native spikes present on intact virus particles. Trimeric soluble gp140 have been generated by several groups and such molecules have been shown to induce antibodies with neutralizing activity against homologous and heterologous viruses. In the present study, we generated a recombinant trimeric soluble gp140, derived from a previously identified Ugandan A-clade HIV field isolate (gp14094UG018). Antibodies elicited in immunized rabbits show a broad binding pattern to HIV envelopes of different clades. An epitope mapping analysis reveals that, on average, the binding is mostly focused on the C1, C2, V3, V5 and C5 regions. Immune sera show neutralization activity to Tier 1 isolates of different clades, demonstrating cross clade neutralizing activity which needs to be further broadened by possible structural modifications of the clade A gp14094UG018. Our results provide a rationale for the design and evaluation of immunogens and the clade A gp14094UG018 shows promising characteristics for potential involvement in an effective HIV vaccine with broad activity.

Hymenochaetales: a molecular phylogeny for the hymenochaetoid clade

Treesearch

Karl-Henrik Larsson; Erast Parmasto; Michael Fischer; Ewald Langer; Karen K. Nakasone; Scott A. Redhead

2006-01-01

The hymenochaetoid clade is dominated by wood-decaying species previously classified in the artificial families Corticiaceae, Polyporaceae and Stereaceae. The majority of these species cause a white rot. The polypore Bridgeoporus and several corticioid species with inconspicuous basidiomata live in association with brown-rotted wood, but their nutritional strategy is...

HIV-1 Gp120 clade B/C induces a GRP78 driven cytoprotective mechanism in astrocytoma

PubMed Central

López, Sheila N.; Rodríguez-Valentín, Madeline; Rivera, Mariela; Rodríguez, Maridaliz; Babu, Mohan; Cubano, Luis A.; Xiong, Huangui; Wang, Guangdi; Kucheryavykh, Lilia; Boukli, Nawal M.

2017-01-01

HIV-1 clades are known to be one of the key factors implicated in modulating HIV-associated neurocognitive disorders. HIV-1 B and C clades account for the majority of HIV-1 infections, clade B being the most neuropathogenic. The mechanisms behind HIV-mediated neuropathogenesis remain the subject of active research. We hypothesized that HIV-1 gp120 clade B and C proteins may exert differential proliferation, cell survival and NeuroAIDS effects in human astrocytoma cells via the Unfolded Protein Response, an endoplasmic reticulum- based cytoprotective mechanism. The differential effect of gp120 clade B and C was evaluated using for the first time a Tandem Mass Tag isobaric labeling quantitative proteomic approach. Flow cytometry analyses were performed for cell cycle and cell death identification. Among the proteins differentiated by HIV-1 gp120 proteins figure cytoskeleton, oxidative stress, UPR markers and numerous glycolytic metabolism enzymes. Our results demonstrate that HIV-1 gp120 B induced migration, proliferative and protective responses granted by the expression of GRP78, while HIV-1 gp120 C induced the expression of key inflammatory and pro-apoptotic markers. These novel findings put forward the first evidence that GRP78 is a key player in HIV-1 clade B and C neuropathogenic discrepancies and can be used as a novel target for immunotherapies. PMID:28978127

Distinct SagA from Hospital-Associated Clade A1 Enterococcus faecium Strains Contributes to Biofilm Formation

PubMed Central

Paganelli, F. L.; de Been, M.; Braat, J. C.; Hoogenboezem, T.; Vink, C.; Bayjanov, J.; Rogers, M. R. C.; Huebner, J.; Bonten, M. J. M.; Willems, R. J. L.

2015-01-01

Enterococcus faecium is an important nosocomial pathogen causing biofilm-mediated infections. Elucidation of E. faecium biofilm pathogenesis is pivotal for the development of new strategies to treat these infections. In several bacteria, extracellular DNA (eDNA) and proteins act as matrix components contributing to biofilm development. In this study, we investigated biofilm formation capacity and the roles of eDNA and secreted proteins for 83 E. faecium strains with different phylogenetic origins that clustered in clade A1 and clade B. Although there was no significant difference in biofilm formation between E. faecium strains from these two clades, the addition of DNase I or proteinase K to biofilms demonstrated that eDNA is essential for biofilm formation in most E. faecium strains, whereas proteolysis impacted primarily biofilms of E. faecium clade A1 strains. Secreted antigen A (SagA) was the most abundant protein in biofilms from E. faecium clade A1 and B strains, although its localization differed between the two groups. sagA was present in all sequenced E. faecium strains, with a consistent difference in the repeat region between the clades, which correlated with the susceptibility of biofilms to proteinase K. This indicates an association between the SagA variable repeat profile and the localization and contribution of SagA in E. faecium biofilms. PMID:26209668

Distinct SagA from Hospital-Associated Clade A1 Enterococcus faecium Strains Contributes to Biofilm Formation.

PubMed

Paganelli, F L; de Been, M; Braat, J C; Hoogenboezem, T; Vink, C; Bayjanov, J; Rogers, M R C; Huebner, J; Bonten, M J M; Willems, R J L; Leavis, H L

2015-10-01

Enterococcus faecium is an important nosocomial pathogen causing biofilm-mediated infections. Elucidation of E. faecium biofilm pathogenesis is pivotal for the development of new strategies to treat these infections. In several bacteria, extracellular DNA (eDNA) and proteins act as matrix components contributing to biofilm development. In this study, we investigated biofilm formation capacity and the roles of eDNA and secreted proteins for 83 E. faecium strains with different phylogenetic origins that clustered in clade A1 and clade B. Although there was no significant difference in biofilm formation between E. faecium strains from these two clades, the addition of DNase I or proteinase K to biofilms demonstrated that eDNA is essential for biofilm formation in most E. faecium strains, whereas proteolysis impacted primarily biofilms of E. faecium clade A1 strains. Secreted antigen A (SagA) was the most abundant protein in biofilms from E. faecium clade A1 and B strains, although its localization differed between the two groups. sagA was present in all sequenced E. faecium strains, with a consistent difference in the repeat region between the clades, which correlated with the susceptibility of biofilms to proteinase K. This indicates an association between the SagA variable repeat profile and the localization and contribution of SagA in E. faecium biofilms. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Phylogeny of the Ampelocissus-Vitis clade in Vitaceae supports the New World origin of the grape genus.

PubMed

Liu, Xiu-Qun; Ickert-Bond, Stefanie M; Nie, Ze-Long; Zhou, Zhuo; Chen, Long-Qing; Wen, Jun

2016-02-01

The grapes and the close allies in Vitaceae are of great agronomic and economic importance. Our previous studies showed that the grape genus Vitis was closely related to three tropical genera, which formed the Ampelocissus-Vitis clade (including Vitis, Ampelocissus, Nothocissus and Pterisanthes). Yet the phylogenetic relationships of the four genera within this clade remain poorly resolved. Furthermore, the geographic origin of Vitis is still controversial, because the sampling of the close relatives of Vitis was too limited in the previous studies. This study reconstructs the phylogenetic relationships within the clade, and hypothesizes the origin of Vitis in a broader phylogenetic framework, using five plastid and two nuclear markers. The Ampelocissus-Vitis clade is supported to be composed of five main lineages. Vitis includes two described subgenera each as a monophyletic group. Ampelocissus is paraphyletic. The New World Ampelocissus does not form a clade and shows a complex phylogenetic relationship, with A. acapulcensis and A. javalensis forming a clade, and A. erdvendbergiana sister to Vitis. The majority of the Asian Ampelocissus species form a clade, within which Pterisanthes is nested. Pterisanthes is polyphyletic, suggesting that the lamellate inflorescence characteristic of the genus represents convergence. Nothocissus is sister to the clade of Asian Ampelocissus and Pterisanthes. The African Ampelocissus forms a clade with several Asian species. Based on the Bayesian dating and both the RASP and Lagrange analyses, Vitis is inferred to have originated in the New World during the late Eocene (39.4Ma, 95% HPD: 32.6-48.6Ma), then migrated to Eurasia in the late Eocene (37.3Ma, 95% HPD: 30.9-45.1Ma). The North Atlantic land bridges (NALB) are hypothesized to be the most plausible route for the Vitis migration from the New World to Eurasia, while intercontinental long distance dispersal (LDD) cannot be eliminated as a likely mechanism. Copyright © 2015

Plastid genome evolution across the genus Cuscuta (Convolvulaceae): two clades within subgenus Grammica exhibit extensive gene loss.

PubMed

Braukmann, Thomas; Kuzmina, Maria; Stefanovic, Sasa

2013-02-01

The genus Cuscuta (Convolvulaceae, the morning glory family) is one of the most intensely studied lineages of parasitic plants. Whole plastome sequencing of four Cuscuta species has demonstrated changes to both plastid gene content and structure. The presence of photosynthetic genes under purifying selection indicates that Cuscuta is cryptically photosynthetic. However, the tempo and mode of plastid genome evolution across the diversity of this group (~200 species) remain largely unknown. A comparative investigation of plastid genome content, grounded within a phylogenetic framework, was conducted using a slot-blot Southern hybridization approach. Cuscuta was extensively sampled (~56% of species), including groups previously suggested to possess more altered plastomes compared with other members of this genus. A total of 56 probes derived from all categories of protein-coding genes, typically found within the plastomes of flowering plants, were used. The results indicate that two clades within subgenus Grammica (clades 'O' and 'K') exhibit substantially more plastid gene loss relative to other members of Cuscuta. All surveyed members of the 'O' clade show extensive losses of plastid genes from every category of genes typically found in the plastome, including otherwise highly conserved small and large ribosomal subunits. The extent of plastid gene losses within this clade is similar in magnitude to that observed previously in some non-asterid holoparasites, in which the very presence of a plastome has been questioned. The 'K' clade also exhibits considerable loss of plastid genes. Unlike in the 'O' clade, in which all species seem to be affected, the losses in clade 'K' progress phylogenetically, following a pattern consistent with the Evolutionary Transition Series hypothesis. This clade presents an ideal opportunity to study the reduction of the plastome of parasites 'in action'. The widespread plastid gene loss in these two clades is hypothesized to be a

Trading Capsule for Increased Cytotoxin Production: Contribution to Virulence of a Newly Emerged Clade of emm89 Streptococcus pyogenes.

PubMed

Zhu, Luchang; Olsen, Randall J; Nasser, Waleed; de la Riva Morales, Ivan; Musser, James M

2015-10-06

Strains of emm89 Streptococcus pyogenes have become one of the major causes of invasive infections worldwide in the last 10 years. We recently sequenced the genome of 1,125 emm89 strains and identified three major phylogenetic groups, designated clade 1, clade 2, and the epidemic clade 3. Epidemic clade 3 strains, which now cause the great majority of infections, have two distinct genetic features compared to clade 1 and clade 2 strains. First, all clade 3 organisms have a variant 3 nga promoter region pattern, which is associated with increased production of secreted cytolytic toxins SPN (S. pyogenes NADase) and SLO (streptolysin O). Second, all clade 3 strains lack the hasABC locus mediating hyaluronic acid capsule synthesis, whereas this locus is intact in clade 1 and clade 2 strains. We constructed isogenic mutant strains that produce different levels of SPN and SLO toxins and capsule (none, low, or high). Here we report that emm89 strains with elevated toxin production are significantly more virulent than low-toxin producers. Importantly, we also show that capsule production is dispensable for virulence in strains that already produce high levels of SPN and SLO. Our results provide new understanding about the molecular mechanisms contributing to the rapid emergence and molecular pathogenesis of epidemic clade 3 emm89 S. pyogenes. S. pyogenes (group A streptococcus [GAS]) causes pharyngitis ("strep throat"), necrotizing fasciitis, and other human infections. Serious infections caused by emm89 S. pyogenes strains have recently increased in frequency in many countries. Based on whole-genome sequence analysis of 1,125 strains recovered from patients on two continents, we discovered that a new emm89 clone, termed clade 3, has two distinct genetic features compared to its predecessors: (i) absence of the genes encoding antiphagocytic hyaluronic acid capsule virulence factor and (ii) increased production of the secreted cytolytic toxins SPN and SLO. emm89 S

A diminutive perinate European Enantiornithes reveals an asynchronous ossification pattern in early birds

DOE PAGES

Knoll, Fabien; Chiappe, Luis M.; Sanchez, Sophie; ...

2018-03-05

Fossils of juvenile Mesozoic birds provide insight into the early evolution of avian development, however such fossils are rare. The analysis of the ossification sequence in these early-branching birds has the potential to address important questions about their comparative developmental biology and to help understand their morphological evolution and ecological differentiation. Here we report on an early juvenile enantiornithine specimen from the Early Cretaceous of Europe, which sheds new light on the osteogenesis in this most species-rich clade of Mesozoic birds. Consisting of a nearly complete skeleton, it is amongst the smallest known Mesozoic avian fossils representing post-hatching stages ofmore » development. Finally, comparisons between this new specimen and other known early juvenile enantiornithines support a clade-wide asynchronous pattern of osteogenesis in the sternum and the vertebral column, and strongly indicate that the hatchlings of these phylogenetically basal birds varied greatly in size and tempo of skeletal maturation.« less

A diminutive perinate European Enantiornithes reveals an asynchronous ossification pattern in early birds

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

Knoll, Fabien; Chiappe, Luis M.; Sanchez, Sophie

Fossils of juvenile Mesozoic birds provide insight into the early evolution of avian development, however such fossils are rare. The analysis of the ossification sequence in these early-branching birds has the potential to address important questions about their comparative developmental biology and to help understand their morphological evolution and ecological differentiation. Here we report on an early juvenile enantiornithine specimen from the Early Cretaceous of Europe, which sheds new light on the osteogenesis in this most species-rich clade of Mesozoic birds. Consisting of a nearly complete skeleton, it is amongst the smallest known Mesozoic avian fossils representing post-hatching stages ofmore » development. Finally, comparisons between this new specimen and other known early juvenile enantiornithines support a clade-wide asynchronous pattern of osteogenesis in the sternum and the vertebral column, and strongly indicate that the hatchlings of these phylogenetically basal birds varied greatly in size and tempo of skeletal maturation.« less

Corallite wall and septal microstructure in scleractinian reef corals: comparison of molecular clades within the family Faviidae.

PubMed

Budd, Ann F; Stolarski, Jarosław

2011-01-01

Recent molecular phylogenies conflict with traditional scleractinian classification at ranks ranging from suborder to genus, challenging morphologists to discover new characters that better agree with molecular data. Such characters are essential for including fossils in analyses and tracing evolutionary patterns through geologic time. We examine the skeletal morphology of 36 species belonging to the traditional families Faviidae, Merulinidae, Pectiniidae, and Trachyphylliidae (3 Atlantic, 14 Indo-Pacific, 2 cosmopolitan genera) at the macromorphological, micromorphological, and microstructural levels. Molecular analyses indicate that the families are not monophyletic groups, but consist of six family-level clades, four of which are examined [clade XV = Diploastrea heliopora; clade XVI = Montastraea cavernosa; clade XVII ("Pacific faviids") = Pacific faviids (part) + merulinids (part) + pectiniids (part) + M. annularis complex; clade XXI ("Atlantic faviids") = Atlantic faviids (part) + Atlantic mussids]. Comparisons among molecular clades indicate that micromorphological and microstructural characters (singly and in combination) are clade diagnostic, but with two exceptions, macromorphologic characters are not. The septal teeth of "Atlantic faviids" are paddle-shaped (strong secondary calcification axes) or blocky, whereas the septal teeth of "Pacific faviids" are spine-shaped or multidirectional. Corallite walls in "Atlantic faviids" are usually septothecal, with occasional trabeculothecal elements; whereas corallite walls in "Pacific faviids" are usually trabeculothecal or parathecal or they contain abortive septa. Exceptions include subclades of "Pacific faviids" consisting of a) Caulastraea and Oulophyllia (strong secondary axes) and b) Cyphastrea (septothecal walls). Diploastrea has a diagnostic synapticulothecal wall and thick triangular teeth; Montastraea cavernosa is also distinct, possessing both "Pacific faviid" (abortive septa) and "Atlantic faviid

Transmitted/Founder HIV-1 Subtype C Viruses Show Distinctive Signature Patterns in Vif, Vpr, and Vpu That Are Under Subsequent Immune Pressure During Early Infection.

PubMed

Rossenkhan, Raabya; MacLeod, Iain J; Brumme, Zabrina L; Magaret, Craig A; Sebunya, Theresa K; Musonda, Rosemary; Gashe, Berhanu A; Edlefsen, Paul T; Novitsky, Vlad; Essex, M

Viral variants that predominate during early infection may exhibit constrained diversity compared with those found during chronic infection and could contain amino acid signature patterns that may enhance transmission, establish productive infection, and influence early events that modulate the infection course. We compared amino acid distributions in 17 patients recently infected with HIV-1C with patients with chronic infection. We found significantly lower entropy in inferred transmitted/founder (t/f) compared with chronic viruses and identified signature patterns in Vif and Vpr from inferred t/f viruses. We investigated sequence evolution longitudinally up to 500 days postseroconversion and compared the impact of selected substitutions on predicted human leukocyte antigen (HLA) binding affinities of published and predicted cytotoxic T-lymphocyte epitopes. Polymorphisms in Vif and Vpr during early infection occurred more frequently at epitope-HLA anchor residues and significantly decreased predicted epitope-HLA binding. Transmission-associated sequence signatures may have implications for novel strategies to prevent HIV-1 transmission.

Transmitted/Founder HIV-1 Subtype C Viruses Show Distinctive Signature Patterns in Vif, Vpr, and Vpu That Are Under Subsequent Immune Pressure During Early Infection

PubMed Central

Rossenkhan, Raabya; MacLeod, Iain J.; Brumme, Zabrina L.; Magaret, Craig A.; Sebunya, Theresa K.; Musonda, Rosemary; Gashe, Berhanu A.; Edlefsen, Paul T.; Novitsky, Vlad

2016-01-01

Abstract Viral variants that predominate during early infection may exhibit constrained diversity compared with those found during chronic infection and could contain amino acid signature patterns that may enhance transmission, establish productive infection, and influence early events that modulate the infection course. We compared amino acid distributions in 17 patients recently infected with HIV-1C with patients with chronic infection. We found significantly lower entropy in inferred transmitted/founder (t/f) compared with chronic viruses and identified signature patterns in Vif and Vpr from inferred t/f viruses. We investigated sequence evolution longitudinally up to 500 days postseroconversion and compared the impact of selected substitutions on predicted human leukocyte antigen (HLA) binding affinities of published and predicted cytotoxic T-lymphocyte epitopes. Polymorphisms in Vif and Vpr during early infection occurred more frequently at epitope-HLA anchor residues and significantly decreased predicted epitope-HLA binding. Transmission-associated sequence signatures may have implications for novel strategies to prevent HIV-1 transmission. PMID:27349335

Unique Phylogenetic Lineage Found in the Fusarium-like Clade after Re-examining BCCM/IHEM Fungal Culture Collection Material

PubMed Central

De Cremer, Koen; Piérard, Denis; Hendrickx, Marijke

2016-01-01

Recently, the Fusarium genus has been narrowed based upon phylogenetic analyses and a Fusarium-like clade was adopted. The few species of the Fusarium-like clade were moved to new, re-installed or existing genera or provisionally retained as "Fusarium." Only a limited number of reference strains and DNA marker sequences are available for this clade and not much is known about its actual species diversity. Here, we report six strains, preserved by the Belgian fungal culture collection BCCM/IHEM as a Fusarium species, that belong to the Fusarium-like clade. They showed a slow growth and produced pionnotes, typical morphological characteristics of many Fusarium-like species. Multilocus sequencing with comparative sequence analyses in GenBank and phylogenetic analyses, using reference sequences of type material, confirmed that they were indeed member of the Fusarium-like clade. One strain was identified as "Fusarium" ciliatum whereas another strain was identified as Fusicolla merismoides. The four remaining strains were shown to represent a unique phylogenetic lineage in the Fusarium-like clade and were also found morphologically distinct from other members of the Fusarium-like clade. Based upon phylogenetic considerations, a new genus, Pseudofusicolla gen. nov., and a new species, Pseudofusicolla belgica sp. nov., were installed for this lineage. A formal description is provided in this study. Additional sampling will be required to gather isolates other than the historical strains presented in the present study as well as to further reveal the actual species diversity in the Fusarium-like clade. PMID:27790062

Cross-Border Sexual Transmission of the Newly Emerging HIV-1 Clade CRF51_01B

PubMed Central

Cheong, Hui Ting; Ng, Kim Tien; Ong, Lai Yee; Chook, Jack Bee; Chan, Kok Gan; Takebe, Yutaka; Kamarulzaman, Adeeba; Tee, Kok Keng

2014-01-01

A novel HIV-1 recombinant clade (CRF51_01B) was recently identified among men who have sex with men (MSM) in Singapore. As cases of sexually transmitted HIV-1 infection increase concurrently in two socioeconomically intimate countries such as Malaysia and Singapore, cross transmission of HIV-1 between said countries is highly probable. In order to investigate the timeline for the emergence of HIV-1 CRF51_01B in Singapore and its possible introduction into Malaysia, 595 HIV-positive subjects recruited in Kuala Lumpur from 2008 to 2012 were screened. Phylogenetic relationship of 485 amplified polymerase gene sequences was determined through neighbour-joining method. Next, near-full length sequences were amplified for genomic sequences inferred to be CRF51_01B and subjected to further analysis implemented through Bayesian Markov chain Monte Carlo (MCMC) sampling and maximum likelihood methods. Based on the near full length genomes, two isolates formed a phylogenetic cluster with CRF51_01B sequences of Singapore origin, sharing identical recombination structure. Spatial and temporal information from Bayesian MCMC coalescent and maximum likelihood analysis of the protease, gp120 and gp41 genes suggest that Singapore is probably the country of origin of CRF51_01B (as early as in the mid-1990s) and featured a Malaysian who acquired the infection through heterosexual contact as host for its ancestral lineages. CRF51_01B then spread rapidly among the MSM in Singapore and Malaysia. Although the importation of CRF51_01B from Singapore to Malaysia is supported by coalescence analysis, the narrow timeframe of the transmission event indicates a closely linked epidemic. Discrepancies in the estimated divergence times suggest that CRF51_01B may have arisen through multiple recombination events from more than one parental lineage. We report the cross transmission of a novel CRF51_01B lineage between countries that involved different sexual risk groups. Understanding the cross

Cross-border sexual transmission of the newly emerging HIV-1 clade CRF51_01B.

PubMed

Cheong, Hui Ting; Ng, Kim Tien; Ong, Lai Yee; Chook, Jack Bee; Chan, Kok Gan; Takebe, Yutaka; Kamarulzaman, Adeeba; Tee, Kok Keng

2014-01-01

A novel HIV-1 recombinant clade (CRF51_01B) was recently identified among men who have sex with men (MSM) in Singapore. As cases of sexually transmitted HIV-1 infection increase concurrently in two socioeconomically intimate countries such as Malaysia and Singapore, cross transmission of HIV-1 between said countries is highly probable. In order to investigate the timeline for the emergence of HIV-1 CRF51_01B in Singapore and its possible introduction into Malaysia, 595 HIV-positive subjects recruited in Kuala Lumpur from 2008 to 2012 were screened. Phylogenetic relationship of 485 amplified polymerase gene sequences was determined through neighbour-joining method. Next, near-full length sequences were amplified for genomic sequences inferred to be CRF51_01B and subjected to further analysis implemented through Bayesian Markov chain Monte Carlo (MCMC) sampling and maximum likelihood methods. Based on the near full length genomes, two isolates formed a phylogenetic cluster with CRF51_01B sequences of Singapore origin, sharing identical recombination structure. Spatial and temporal information from Bayesian MCMC coalescent and maximum likelihood analysis of the protease, gp120 and gp41 genes suggest that Singapore is probably the country of origin of CRF51_01B (as early as in the mid-1990s) and featured a Malaysian who acquired the infection through heterosexual contact as host for its ancestral lineages. CRF51_01B then spread rapidly among the MSM in Singapore and Malaysia. Although the importation of CRF51_01B from Singapore to Malaysia is supported by coalescence analysis, the narrow timeframe of the transmission event indicates a closely linked epidemic. Discrepancies in the estimated divergence times suggest that CRF51_01B may have arisen through multiple recombination events from more than one parental lineage. We report the cross transmission of a novel CRF51_01B lineage between countries that involved different sexual risk groups. Understanding the cross

Meiotic Clade AAA ATPases: Protein Polymer Disassembly Machines.

PubMed

Monroe, Nicole; Hill, Christopher P

2016-05-08

Meiotic clade AAA ATPases (ATPases associated with diverse cellular activities), which were initially grouped on the basis of phylogenetic classification of their AAA ATPase cassette, include four relatively well characterized family members, Vps4, spastin, katanin and fidgetin. These enzymes all function to disassemble specific polymeric protein structures, with Vps4 disassembling the ESCRT-III polymers that are central to the many membrane-remodeling activities of the ESCRT (endosomal sorting complexes required for transport) pathway and spastin, katanin p60 and fidgetin affecting multiple aspects of cellular dynamics by severing microtubules. They share a common domain architecture that features an N-terminal MIT (microtubule interacting and trafficking) domain followed by a single AAA ATPase cassette. Meiotic clade AAA ATPases function as hexamers that can cycle between the active assembly and inactive monomers/dimers in a regulated process, and they appear to disassemble their polymeric substrates by translocating subunits through the central pore of their hexameric ring. Recent studies with Vps4 have shown that nucleotide-induced asymmetry is a requirement for substrate binding to the pore loops and that recruitment to the protein lattice via MIT domains also relieves autoinhibition and primes the AAA ATPase cassettes for substrate binding. The most striking, unifying feature of meiotic clade AAA ATPases may be their MIT domain, which is a module that is found in a wide variety of proteins that localize to ESCRT-III polymers. Spastin also displays an adjacent microtubule binding sequence, and the presence of both ESCRT-III and microtubule binding elements may underlie the recent findings that the ESCRT-III disassembly function of Vps4 and the microtubule-severing function of spastin, as well as potentially katanin and fidgetin, are highly coordinated. Copyright © 2015 Elsevier Ltd. All rights reserved.

Culture and hybridization experiments on an ulva clade including the Qingdao strain blooming in the yellow sea.

PubMed

Hiraoka, Masanori; Ichihara, Kensuke; Zhu, Wenrong; Ma, Jiahai; Shimada, Satoshi

2011-05-05

In the summer of 2008, immediately prior to the Beijing Olympics, a massive green tide of the genus Ulva covered the Qingdao coast of the Yellow Sea in China. Based on molecular analyses using the nuclear encoded rDNA internal transcribed spacer (ITS) region, the Qingdao strains dominating the green tide were reported to be included in a single phylogenetic clade, currently regarded as a single species. On the other hand, our detailed phylogenetic analyses of the clade, using a higher resolution DNA marker, suggested that two genetically separate entities could be included within the clade. However, speciation within the Ulva clade has not yet been examined. We examined the occurrence of an intricate speciation within the clade, including the Qingdao strains, via combined studies of culture, hybridization and phylogenetic analysis. The two entities separated by our phylogenetic analyses of the clade were simply distinguished as U. linza and U. prolifera morphologically by the absence or presence of branches in cultured thalli. The inclusion of sexual strains and several asexual strains were found in each taxon. Hybridizations among the sexual strains also supported the separation by a partial gamete incompatibility. The sexually reproducing Qingdao strains crossed with U. prolifera without any reproductive boundary, but a complete reproductive isolation to U. linza occurred by gamete incompatibility. The results demonstrate that the U. prolifera group includes two types of sexual strains distinguishable by crossing affinity to U. linza. Species identification within the Ulva clade requires high resolution DNA markers and/or hybridization experiments and is not possible by reliance on the ITS markers alone.

Plastid genome evolution across the genus Cuscuta (Convolvulaceae): two clades within subgenus Grammica exhibit extensive gene loss

PubMed Central

Braukmann, Thomas

2013-01-01

The genus Cuscuta (Convolvulaceae, the morning glory family) is one of the most intensely studied lineages of parasitic plants. Whole plastome sequencing of four Cuscuta species has demonstrated changes to both plastid gene content and structure. The presence of photosynthetic genes under purifying selection indicates that Cuscuta is cryptically photosynthetic. However, the tempo and mode of plastid genome evolution across the diversity of this group (~200 species) remain largely unknown. A comparative investigation of plastid genome content, grounded within a phylogenetic framework, was conducted using a slot-blot Southern hybridization approach. Cuscuta was extensively sampled (~56% of species), including groups previously suggested to possess more altered plastomes compared with other members of this genus. A total of 56 probes derived from all categories of protein-coding genes, typically found within the plastomes of flowering plants, were used. The results indicate that two clades within subgenus Grammica (clades ‘O’ and ‘K’) exhibit substantially more plastid gene loss relative to other members of Cuscuta. All surveyed members of the ‘O’ clade show extensive losses of plastid genes from every category of genes typically found in the plastome, including otherwise highly conserved small and large ribosomal subunits. The extent of plastid gene losses within this clade is similar in magnitude to that observed previously in some non-asterid holoparasites, in which the very presence of a plastome has been questioned. The ‘K’ clade also exhibits considerable loss of plastid genes. Unlike in the ‘O’ clade, in which all species seem to be affected, the losses in clade ‘K’ progress phylogenetically, following a pattern consistent with the Evolutionary Transition Series hypothesis. This clade presents an ideal opportunity to study the reduction of the plastome of parasites ‘in action’. The widespread plastid gene loss in these two clades is

Juvenile skeletogenesis in anciently diverged sea urchin clades.

PubMed

Gao, Feng; Thompson, Jeffrey R; Petsios, Elizabeth; Erkenbrack, Eric; Moats, Rex A; Bottjer, David J; Davidson, Eric H

2015-04-01

Mechanistic understanding of evolutionary divergence in animal body plans devolves from analysis of those developmental processes that, in forms descendant from a common ancestor, are responsible for their morphological differences. The last common ancestor of the two extant subclasses of sea urchins, i.e., euechinoids and cidaroids, existed well before the Permian/Triassic extinction (252 mya). Subsequent evolutionary divergence of these clades offers in principle a rare opportunity to solve the developmental regulatory events underlying a defined evolutionary divergence process. Thus (i) there is an excellent and fairly dense (if yet incompletely analyzed) fossil record; (ii) cladistically confined features of the skeletal structures of modern euechinoid and cidaroid sea urchins are preserved in fossils of ancestral forms; (iii) euechinoids and cidaroids are among current laboratory model systems in molecular developmental biology (here Strongylocentrotus purpuratus [Sp] and Eucidaris tribuloides [Et]); (iv) skeletogenic specification in sea urchins is uncommonly well understood at the causal level of interactions of regulatory genes with one another, and with known skeletogenic effector genes, providing a ready arsenal of available molecular tools. Here we focus on differences in test and perignathic girdle skeletal morphology that distinguish all modern euechinoid from all modern cidaroid sea urchins. We demonstrate distinct canonical test and girdle morphologies in juveniles of both species by use of SEM and X-ray microtomography. Among the sharply distinct morphological features of these clades are the internal skeletal structures of the perignathic girdle to which attach homologous muscles utilized for retraction and protraction of Aristotles׳ lantern and its teeth. We demonstrate that these structures develop de novo between one and four weeks after metamorphosis. In order to study the underlying developmental processes, a method of section whole mount in

Phytomonas (Euglenozoa: Trypanosomatidae): Phylogenetic analyses support infrageneric lineages and a new species transmitted to Solanaceae fruits by a pentatomid hemipteran.

PubMed

Zanetti, Andernice; Ferreira, Robson C; Serrano, Myrna G; Takata, Carmen S A; Campaner, Marta; Attias, Marcia; de Souza, Wanderley; Teixeira, Marta M G; Camargo, Erney P

2016-10-01

The genus Phytomonas includes trypanosomatids transmitted to the fruits, latex, and phloem of vascular plants by hemipterans. We inferred the phylogenetic relationships of plant and insect isolates assigned to the previously defined genetic groups A-F and H of Phytomonas, particularly those from groups A, C and E comprising flagellates of Solanaceae fruits. Phylogenetic analyses using glycosomal Glyceraldehyde Phosphate Dehydrogenase (gGAPDH) and Small Subunit rRNA (SSU rRNA) genes strongly supported the monophyly of the genus Phytomonas and its division into seven main infrageneric phylogenetic lineages (Phy clades). Isolates from fruit or latex do not constitute monophyletic assemblages but disperse through more than one lineages. In this study, fruit flagellates were distributed in three clades: PhyA, formed by isolates from Solanaceae and phytophagous hemipterans; PhyC comprising flagellates from four plant families; and PhyE, which contains 15 fruit isolates from seven species of Solanaceae. The flagellates of PhyE are described as Phytomonas dolleti n. sp. according to their positioning in phylogenetic trees, complemented by data about their life cycle, and developmental and morphological characteristics in cultures, fruits of Solanum spp., and salivary glands of the vector, the phytophagous hemipteran Arvelius albopunctatus (Pentatomidae). Crown Copyright © 2016. Published by Elsevier GmbH. All rights reserved.

High throughput generation and characterization of replication-competent clade C transmitter-founder simian human immunodeficiency viruses

PubMed Central

Dutta, Debashis; Johnson, Samuel; Dalal, Alisha; Deymier, Martin J.; Hunter, Eric

2018-01-01

Traditional restriction endonuclease-based cloning has been routinely used to generate replication-competent simian-human immunodeficiency viruses (SHIV) and simian tropic HIV (stHIV). This approach requires the existence of suitable restriction sites or the introduction of nucleotide changes to create them. Here, using an In-Fusion cloning technique that involves homologous recombination, we generated SHIVs and stHIVs based on epidemiologically linked clade C transmitted/founder HIV molecular clones from Zambia. Replacing vif from these HIV molecular clones with vif of SIVmac239 resulted in chimeric genomes used to generate infectious stHIV viruses. Likewise, exchanging HIV env genes and introducing N375 mutations to enhance macaque CD4 binding site and cloned into a SHIVAD8-EO backbone. The generated SHIVs and stHIV were infectious in TZMbl and ZB5 cells, as well as macaque PBMCs. Therefore, this method can replace traditional methods and be a valuable tool for the rapid generation and testing of molecular clones of stHIV and SHIV based on primary clinical isolates will be valuable to generate rapid novel challenge viruses for HIV vaccine/cure studies. PMID:29758076

Taxonomic evaluation of species in the Streptomyces hirsutus clade using multi-locus sequence analysis and proposals to reclassify several species in this clade

USDA-ARS?s Scientific Manuscript database

Previous phylogenetic analyses of species of Streptomyces based on 16S rRNA gene sequences resulted in a statistically well-supported clade (100% bootstrap value) containing 8 species that exhibited very similar gross morphology in producing open looped (Retinaculum-Apertum) to spiral (Spira) chains...

[Sexually transmitted coinfections. HIV coinfections].

PubMed

Marschalkó, Márta; Pónyai, Katinka; Kárpáti, Sarolta

2015-01-04

Coinfections of sexually transmitted infections are frequent due to the same transmission routes which may facilitate the transmission of other sexually transmitted infections. Sexually transmitted coinfections are associated with atypical and generally more severe clinical features, more complications, resistency to treatment, unfavourable outcome, and worse prognosis. Sexually transmitted infections may increase the likelihood of acquiring and transmission of HIV infection. The authors summarize the most important characteristics of sexually transmitted infections (such as HIV and hepatitis B virus, HIV and hepatitis C virus, HIV and syphilis, HIV and gonorrhoeae, HIV and chlamydia coinfections). These infections are more frequent in HIV infected patients than in the normal population. The shared transmission routes, impairment of the immune response, elevated cytokine levels and the associated inflammatory milieu produce local tissue damage, breaches in mucosal epithelium, which increases the risk of human immunodeficiency virus infection. Regular screening for sexually transmitted infections, use of more sensitive diagnostic methods, improved reporting and avoidance of unsafe sexual behaviour among certain subpopulations as well as education are essential in the prevention of sexually transmitted coinfections.

Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades

PubMed Central

Blanga-Kanfi, Shani; Miranda, Hector; Penn, Osnat; Pupko, Tal; DeBry, Ronald W; Huchon, Dorothée

2009-01-01

Background Rodentia is the most diverse order of placental mammals, with extant rodent species representing about half of all placental diversity. In spite of many morphological and molecular studies, the family-level relationships among rodents and the location of the rodent root are still debated. Although various datasets have already been analyzed to solve rodent phylogeny at the family level, these are difficult to combine because they involve different taxa and genes. Results We present here the largest protein-coding dataset used to study rodent relationships. It comprises six nuclear genes, 41 rodent species, and eight outgroups. Our phylogenetic reconstructions strongly support the division of Rodentia into three clades: (1) a "squirrel-related clade", (2) a "mouse-related clade", and (3) Ctenohystrica. Almost all evolutionary relationships within these clades are also highly supported. The primary remaining uncertainty is the position of the root. The application of various models and techniques aimed to remove non-phylogenetic signal was unable to solve the basal rodent trifurcation. Conclusion Sequencing and analyzing a large sequence dataset enabled us to resolve most of the evolutionary relationships among Rodentia. Our findings suggest that the uncertainty regarding the position of the rodent root reflects the rapid rodent radiation that occurred in the Paleocene rather than the presence of conflicting phylogenetic and non-phylogenetic signals in the dataset. PMID:19341461

Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences.

PubMed

Söllinger, Andrea; Schwab, Clarissa; Weinmaier, Thomas; Loy, Alexander; Tveit, Alexander T; Schleper, Christa; Urich, Tim

2016-01-01

Methanogenic Thermoplasmata of the novel order Methanomassiliicoccales were recently discovered in human and animal gastro-intestinal tracts (GITs). However, their distribution in other methanogenic environments has not been addressed systematically. Here, we surveyed Methanomassiliicoccales presence in wetland soils, a globally important source of methane emissions to the atmosphere, and in the GITs of different animals by PCR targeting their 16S rRNA and methyl:coenzyme M reductase (α-subunit) genes. We detected Methanomassiliicoccales in all 16 peat soils investigated, indicating their wide distribution in these habitats. Additionally, we detected their genes in various animal faeces. Methanomassiliicoccales were subdivided in two broad phylogenetic clades designated 'environmental' and 'GIT' clades based on differential, although non-exclusive, habitat preferences of their members. A well-supported cluster within the environmental clade comprised more than 80% of all wetland 16S rRNA gene sequences. Metagenome assembly from bovine rumen fluid enrichments resulted in two almost complete genomes of both Methanomassiliicoccales clades. Comparative genomics revealed that members of the environmental clade contain larger genomes and a higher number of genes encoding anti-oxidative enzymes than animal GIT clade representatives. This study highlights the wide distribution of Methanomassiliicoccales in wetlands, which suggests that they contribute to methane emissions from these climate-relevant ecosystems. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Cross-reactivity of anti-HIV-1 T cell immune responses among the major HIV-1 clades in HIV-1-positive individuals from 4 continents.

PubMed

Coplan, Paul M; Gupta, Swati B; Dubey, Sheri A; Pitisuttithum, Punnee; Nikas, Alex; Mbewe, Bernard; Vardas, Efthyia; Schechter, Mauro; Kallas, Esper G; Freed, Dan C; Fu, Tong-Ming; Mast, Christopher T; Puthavathana, Pilaipan; Kublin, James; Brown Collins, Kelly; Chisi, John; Pendame, Richard; Thaler, Scott J; Gray, Glenda; Mcintyre, James; Straus, Walter L; Condra, Jon H; Mehrotra, Devan V; Guess, Harry A; Emini, Emilio A; Shiver, John W

2005-05-01

The genetic diversity of human immunodeficiency virus type 1 (HIV-1) raises the question of whether vaccines that include a component to elicit antiviral T cell immunity based on a single viral genetic clade could provide cellular immune protection against divergent HIV-1 clades. Therefore, we quantified the cross-clade reactivity, among unvaccinated individuals, of anti-HIV-1 T cell responses to the infecting HIV-1 clade relative to other major circulating clades. Cellular immune responses to HIV-1 clades A, B, and C were compared by standardized interferon- gamma enzyme-linked immunospot assays among 250 unvaccinated individuals, infected with diverse HIV-1 clades, from Brazil, Malawi, South Africa, Thailand, and the United States. Cross-clade reactivity was evaluated by use of the ratio of responses to heterologous versus homologous (infecting) clades of HIV-1. Cellular immune responses were predominantly focused on viral Gag and Nef proteins. Cross-clade reactivity of cellular immune responses to HIV-1 clade A, B, and C proteins was substantial for Nef proteins (ratio, 0.97 [95% confidence interval, 0.89-1.05]) and lower for Gag proteins (ratio, 0.67 [95% confidence interval, 0.62-0.73]). The difference in cross-clade reactivity to Nef and Gag proteins was significant (P<.0001). Cross-clade reactivity of cellular immune responses can be substantial but varies by viral protein.

Decoupled form and function in disparate herbivorous dinosaur clades

NASA Astrophysics Data System (ADS)

Lautenschlager, Stephan; Brassey, Charlotte A.; Button, David J.; Barrett, Paul M.

2016-05-01

Convergent evolution, the acquisition of morphologically similar traits in unrelated taxa due to similar functional demands or environmental factors, is a common phenomenon in the animal kingdom. Consequently, the occurrence of similar form is used routinely to address fundamental questions in morphofunctional research and to infer function in fossils. However, such qualitative assessments can be misleading and it is essential to test form/function relationships quantitatively. The parallel occurrence of a suite of morphologically convergent craniodental characteristics in three herbivorous, phylogenetically disparate dinosaur clades (Sauropodomorpha, Ornithischia, Theropoda) provides an ideal test case. A combination of computational biomechanical models (Finite Element Analysis, Multibody Dynamics Analysis) demonstrate that despite a high degree of morphological similarity between representative taxa (Plateosaurus engelhardti, Stegosaurus stenops, Erlikosaurus andrewsi) from these clades, their biomechanical behaviours are notably different and difficult to predict on the basis of form alone. These functional differences likely reflect dietary specialisations, demonstrating the value of quantitative biomechanical approaches when evaluating form/function relationships in extinct taxa.

Decoupled form and function in disparate herbivorous dinosaur clades.

PubMed

Lautenschlager, Stephan; Brassey, Charlotte A; Button, David J; Barrett, Paul M

2016-05-20

Convergent evolution, the acquisition of morphologically similar traits in unrelated taxa due to similar functional demands or environmental factors, is a common phenomenon in the animal kingdom. Consequently, the occurrence of similar form is used routinely to address fundamental questions in morphofunctional research and to infer function in fossils. However, such qualitative assessments can be misleading and it is essential to test form/function relationships quantitatively. The parallel occurrence of a suite of morphologically convergent craniodental characteristics in three herbivorous, phylogenetically disparate dinosaur clades (Sauropodomorpha, Ornithischia, Theropoda) provides an ideal test case. A combination of computational biomechanical models (Finite Element Analysis, Multibody Dynamics Analysis) demonstrate that despite a high degree of morphological similarity between representative taxa (Plateosaurus engelhardti, Stegosaurus stenops, Erlikosaurus andrewsi) from these clades, their biomechanical behaviours are notably different and difficult to predict on the basis of form alone. These functional differences likely reflect dietary specialisations, demonstrating the value of quantitative biomechanical approaches when evaluating form/function relationships in extinct taxa.

Major clades of Agaricales: a multilocus phylogenetic overview.

Treesearch

P. Brandon Matheny; Judd M. Curtis; Valerie Hofstetter; M. Catherine Aime; Jean-Marc Moncalvo; Zai-Wei Ge; Zhu-Liang Yang; Joseph F. Ammirati; Timothy J. Baroni; Neale L. Bougher; Karen W. Lodge Hughes; Richard W. Kerrigan; Michelle T. Seidl; Aanen; Matthew Duur K. DeNitis; Graciela M. Daniele; Dennis E. Desjardin; Bradley R. Kropp; Lorelei L. Norvell; Andrew Parker; Else C. Vellinga; Rytas Vilgalys; David S. Hibbett

2006-01-01

An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes recovered six major clades, which are recognized informally and labeled the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid,...

Characterization of Clade 7.2 H5 Avian Influenza Viruses That Continue To Circulate in Chickens in China

PubMed Central

Liu, Liling; Zeng, Xianying; Chen, Pucheng; Deng, Guohua; Li, Yanbing; Shi, Jianzhong; Gu, Chunyang; Kong, Huihui; Suzuki, Yasuo; Jiang, Yongping; Tian, Guobin

2016-01-01

ABSTRACT The H5N1 avian influenza viruses emerged in Southeast Asia in the late 20th century and have evolved into multiple phylogenetic clades based on their hemagglutinin (HA)-encoding genes. The clade 7.2 viruses were first detected in chickens in northern China in 2006, and vaccines specifically targeted to the clade were developed and have been used in poultry in China since 2006. During routine surveillance and disease diagnosis, we isolated seven H5 viruses between 2011 and 2014 that bear the clade 7.2 HA genes. Here, we performed extensive studies to understand how the clade 7.2 H5 viruses have evolved in chickens in China. Full genome sequence analysis revealed that the seven viruses formed two subtypes (four H5N1 viruses and three H5N2 viruses) and four genotypes by deriving genes from other influenza viruses. All of the viruses had antigenically drifted from the clade 7.2 viruses that were isolated in 2006. Pathogenicity studies of four viruses, one from each genotype, revealed that all of the viruses are highly pathogenic in chickens, but none of them could replicate in ducks. The four viruses exclusively bound to avian-type receptors and replicated only in the turbinates and/or lungs of mice; none of them were lethal to mice at a dosage of 106 50% egg infective doses (EID50). Our study indicates that although the clade 7.2 viruses have not been eradicated from poultry through vaccination, they have not become more dangerous to other animals (e.g., ducks and mice) and humans. IMPORTANCE Animal influenza viruses can acquire the ability to infect and kill humans. The H5N1 viruses have been a concern in recent decades because of their clear pandemic potential. We sorted H5N1 influenza viruses into different phylogenetic clades based on their HA genes. The clade 7.2 viruses were detected in chickens in several provinces of northern China in 2006. Vaccines for these viruses were subsequently developed and have been used ever since to control infection of

Characterization of Clade 7.2 H5 Avian Influenza Viruses That Continue To Circulate in Chickens in China.

PubMed

Liu, Liling; Zeng, Xianying; Chen, Pucheng; Deng, Guohua; Li, Yanbing; Shi, Jianzhong; Gu, Chunyang; Kong, Huihui; Suzuki, Yasuo; Jiang, Yongping; Tian, Guobin; Chen, Hualan

2016-11-01

The H5N1 avian influenza viruses emerged in Southeast Asia in the late 20th century and have evolved into multiple phylogenetic clades based on their hemagglutinin (HA)-encoding genes. The clade 7.2 viruses were first detected in chickens in northern China in 2006, and vaccines specifically targeted to the clade were developed and have been used in poultry in China since 2006. During routine surveillance and disease diagnosis, we isolated seven H5 viruses between 2011 and 2014 that bear the clade 7.2 HA genes. Here, we performed extensive studies to understand how the clade 7.2 H5 viruses have evolved in chickens in China. Full genome sequence analysis revealed that the seven viruses formed two subtypes (four H5N1 viruses and three H5N2 viruses) and four genotypes by deriving genes from other influenza viruses. All of the viruses had antigenically drifted from the clade 7.2 viruses that were isolated in 2006. Pathogenicity studies of four viruses, one from each genotype, revealed that all of the viruses are highly pathogenic in chickens, but none of them could replicate in ducks. The four viruses exclusively bound to avian-type receptors and replicated only in the turbinates and/or lungs of mice; none of them were lethal to mice at a dosage of 10 6 50% egg infective doses (EID 50 ). Our study indicates that although the clade 7.2 viruses have not been eradicated from poultry through vaccination, they have not become more dangerous to other animals (e.g., ducks and mice) and humans. Animal influenza viruses can acquire the ability to infect and kill humans. The H5N1 viruses have been a concern in recent decades because of their clear pandemic potential. We sorted H5N1 influenza viruses into different phylogenetic clades based on their HA genes. The clade 7.2 viruses were detected in chickens in several provinces of northern China in 2006. Vaccines for these viruses were subsequently developed and have been used ever since to control infection of poultry. Here, we

[Comparative foliar anatomy and systematics of the Trichocentrum-clade with emphasis in Cohniella (Asparagales: Orchidaceae)].

PubMed

Cetzal-Ix, William; Noguera-Savelli, Eliana; Jáuregui, Damelis; Carnevali, Germáin

2013-12-01

The genera Cohniella, Lophiarella, Lophiaris, and Trichocentrum are included in the Trichocentrum-clade. These genera are distributed from Florida and Northern Mexico to Southern Brazil and Northern Argentina, growing in tropical deciduous forests or tropical rain forests and thorn scrub forests to pine-oak forest, from sea level to 1700 m. The leaf anatomical structure of 23 members of the Trichocentrum-clade was explored as a source of taxonomic and phylogenetic characters. A total of 11 species of Cohniella, three species of Lophiarella, seven species of Lophiaris, two species of Trichocentrum, and other four species were included as outgroup. Anatomical characters were studied by cross sections and paradermic observations of the middle portion of fresh leaves. Although anatomical characters were fairly homogeneous throughout the clade, twelve vegetative anatomical, phylogenetically informative characters were selected and coded for an analysis that was performed using an exhaustive search (implicit enumeration) implemented through TNT. The strict consensus of 2692 most parsimonious trees resulted in a poorly resolved polytomy, which however recovers the Trichocentrum-clade with a monophyletic, strongly supported Cohniella nested within it with unifacial leaves and the presence of cellular inclusions in the epidermis as synapomorphies. We concluded that the anatomy characters alone are insufficient to assess the relationships amongst the genera of the Trichocentrum-clade. However, the two synapomorphies recovered for Cohniella strongly support its monophyly when these are analyzed in conjunction with other data sources (e.g., molecular and morphological characters).

Decoupled evolution of floral traits and climatic preferences in a clade of Neotropical Gesneriaceae.

PubMed

Serrano-Serrano, Martha Liliana; Perret, Mathieu; Guignard, Maïté; Chautems, Alain; Silvestro, Daniele; Salamin, Nicolas

2015-11-10

Major factors influencing the phenotypic diversity of a lineage can be recognized by characterizing the extent and mode of trait evolution between related species. Here, we compared the evolutionary dynamics of traits associated with floral morphology and climatic preferences in a clade composed of the genera Codonanthopsis, Codonanthe and Nematanthus (Gesneriaceae). To test the mode and specific components that lead to phenotypic diversity in this group, we performed a Bayesian phylogenetic analysis of combined nuclear and plastid DNA sequences and modeled the evolution of quantitative traits related to flower shape and size and to climatic preferences. We propose an alternative approach to display graphically the complex dynamics of trait evolution along a phylogenetic tree using a wide range of evolutionary scenarios. Our results demonstrated heterogeneous trait evolution. Floral shapes displaced into separate regimes selected by the different pollinator types (hummingbirds versus insects), while floral size underwent a clade-specific evolution. Rates of evolution were higher for the clade that is hummingbird pollinated and experienced flower resupination, compared with species pollinated by bees, suggesting a relevant role of plant-pollinator interactions in lowland rainforest. The evolution of temperature preferences is best explained by a model with distinct selective regimes between the Brazilian Atlantic Forest and the other biomes, whereas differentiation along the precipitation axis was characterized by higher rates, compared with temperature, and no regime or clade-specific patterns. Our study shows different selective regimes and clade-specific patterns in the evolution of morphological and climatic components during the diversification of Neotropical species. Our new graphical visualization tool allows the representation of trait trajectories under parameter-rich models, thus contributing to a better understanding of complex evolutionary dynamics.

Soil-Transmitted Helminth Infections

MedlinePlus

... 1.5 billion people, or 24% of the world’s population, are infected with soil-transmitted helminth infections worldwide. ... 1.5 billion people, or 24% of the world’s population, are infected with soil-transmitted helminth infections worldwide. ...

EveryBody[TM]: Preventing HIV and Other Sexually Transmitted Diseases among Young Teens.

ERIC Educational Resources Information Center

Schoeberlein, Deborah

EveryBody is a curriculum that emphasizes prevention of human immunodeficiency virus (HIV) and other sexually transmitted diseases (STDs) among early adolescents. It fosters active learning and facilitates communication about HIV/STD prevention and promotes safer behaviors. EveryBody incorporates current research on adolescent development so it…

Is Amazonia a 'museum' for Neotropical trees? The evolution of the Brownea clade (Detarioideae, Leguminosae).

PubMed

Schley, Rowan J; de la Estrella, Manuel; Pérez-Escobar, Oscar Alejandro; Bruneau, Anne; Barraclough, Timothy; Forest, Félix; Klitgård, Bente

2018-09-01

The flora of the Neotropics is unmatched in its diversity, however the mechanisms by which diversity has accumulated are debated and largely unclear. The Brownea clade (Leguminosae) is a characteristic component of the Neotropical flora, and the species within it are diverse in their floral morphology, attracting a wide variety of pollinators. This investigation aimed to estimate species divergence times and infer relationships within the group, in order to test whether the Brownea clade followed the 'cradle' or 'museum' model of diversification, i.e. whether species evolved rapidly over a short time period, or gradually over many millions of years. We also aimed to trace the spatio-temporal evolution of the clade by estimating ancestral biogeographical patterns in the group. We used BEAST to build a dated phylogeny of 73 Brownea clade species using three molecular markers (ITS, trnK and psbA-trnH), resulting in well-resolved phylogenetic relationships within the clade, as well as robust divergence time estimates from which we inferred diversification rates and ancestral biogeography. Our analyses revealed an Eocene origin for the group, after which the majority of diversification happened in Amazonia during the Miocene, most likely concurrent with climatic and geological changes caused by the rise of the Andes. We found no shifts in diversification rate over time, suggesting a gradual accumulation of lineages with low extinction rates. These results may help to understand why Amazonia is host to the highest diversity of tree species on Earth. Copyright © 2018 Elsevier Inc. All rights reserved.

High Ancient Genetic Diversity of Human Lice, Pediculus humanus, from Israel Reveals New Insights into the Origin of Clade B Lice.

PubMed

Amanzougaghene, Nadia; Mumcuoglu, Kosta Y; Fenollar, Florence; Alfi, Shir; Yesilyurt, Gonca; Raoult, Didier; Mediannikov, Oleg

2016-01-01

The human head louse, Pediculus humanus capitis, is subdivided into several significantly divergent mitochondrial haplogroups, each with particular geographical distributions. Historically, they are among the oldest human parasites, representing an excellent marker for tracking older events in human evolutionary history. In this study, ancient DNA analysis using real-time polymerase chain reaction (qPCR), combined with conventional PCR, was applied to the remains of twenty-four ancient head lice and their eggs from the Roman period which were recovered from Israel. The lice and eggs were found in three combs, one of which was recovered from archaeological excavations in the Hatzeva area of the Judean desert, and two of which found in Moa, in the Arava region, close to the Dead Sea. Results show that the head lice remains dating approximately to 2,000 years old have a cytb haplogroup A, which is worldwide in distribution, and haplogroup B, which has thus far only been found in contemporary lice from America, Europe, Australia and, most recently, Africa. More specifically, this haplogroup B has a B36 haplotype, the most common among B haplogroups, and has been present in America for at least 4,000 years. The present findings confirm that clade B lice existed, at least in the Middle East, prior to contacts between Native Americans and Europeans. These results support a Middle Eastern origin for clade B followed by its introduction into the New World with the early peoples. Lastly, the presence of Acinetobacter baumannii DNA was demonstrated by qPCR and sequencing in four head lice remains belonging to clade A.

Dengue virus type 1 clade replacement in recurring homotypic outbreaks

PubMed Central

2013-01-01

Background Recurring dengue outbreaks occur in cyclical pattern in most endemic countries. The recurrences of dengue virus (DENV) infection predispose the population to increased risk of contracting the severe forms of dengue. Understanding the DENV evolutionary mechanism underlying the recurring dengue outbreaks has important implications for epidemic prediction and disease control. Results We used a set of viral envelope (E) gene to reconstruct the phylogeny of DENV-1 isolated between the periods of 1987–2011 in Malaysia. Phylogenetic analysis of DENV-1 E gene revealed that genotype I virus clade replacements were associated with the cyclical pattern of major DENV-1 outbreaks in Malaysia. A total of 9 non-conservative amino acid substitutions in the DENV-1 E gene consensus were identified; 4 in domain I, 3 in domain II and 2 in domain III. Selection pressure analyses did not reveal any positively selected codon site within the full length E gene sequences (1485 nt, 495 codons). A total of 183 (mean dN/dS = 0.0413) negatively selected sites were found within the Malaysian isolates; neither positive nor negative selection was noted for the remaining 312 codons. All the viruses were cross-neutralized by the respective patient sera suggesting no strong support for immunological advantage of any of the amino acid substitutions. Conclusion DENV-1 clade replacement is associated with recurrences of major DENV-1 outbreaks in Malaysia. Our findings are consistent with those of other studies that the DENV-1 clade replacement is a stochastic event independent of positive selection. PMID:24073945

Molecular phylogeny of the Acre clade (Crassulaceae): dealing with the lack of definitions for Echeveria and Sedum.

PubMed

Carrillo-Reyes, Pablo; Sosa, Victoria; Mort, Mark E

2009-10-01

The phylogenetic relationships within many clades of the Crassulaceae are still uncertain, therefore in this study attention was focused on the "Acre clade", a group comprised of approximately 526 species in eight genera that include many Asian and Mediterranean species of Sedum and the majority of the American genera (Echeveria, Graptopetalum, Lenophyllum, Pachyphytum, Villadia, and Thompsonella). Parsimony and Bayesian analyses were conducted with 133 species based on nuclear (ETS, ITS) and chloroplast DNA regions (rpS16, matK). Our analyses retrieved four major clades within the Acre clade. Two of these were in a grade and corresponded to Asian species of Sedum, the rest corresponded to a European-Macaronesian group and to an American group. The American group included all taxa that were formerly placed in the Echeverioideae and the majority of the American Sedoideae. Our analyses support the monophyly of three genera--Lenophyllum, Thompsonella, and Pachyphytum; however, the relationships among Echeveria, Sedum and the various segregates of Sedum are largely unresolved. Our analyses represents the first broad phylogenetic framework for Acre clade, but further studies are necessary on the groups poorly represented here, such as the European and Asian species of Sedum and the Central and South American species of Echeveria.

Diversity of pollination ecology in the Schismatoglottis Calyptrata Complex Clade (Araceae).

PubMed

Hoe, Y C; Gibernau, M; Wong, S Y

2018-05-01

Field studies integrating pollination investigations with an assessment of floral scent composition and thermogenesis in tropical aroids are rather few. Thus, this study aimed to investigate the pollination biology of nine species belonging to Schismatoglottis Calyptrata Complex Clade. The flowering mechanism, visiting insect activities, reproductive system, thermogenesis and floral scent composition were examined. Anthesis for all species started at dawn and lasted 25-29 h. Colocasiomyia (Diptera, Drosophilidae) are considered the main pollinators for all the investigated species. Cycreon (Coleoptera, Hydrophilidae) are considered secondary pollinators as they are only present in seven of the nine host plants, despite the fact that they are the most effective pollen carrier, carrying up to 15 times more pollen grains than Colocasiomyia flies. However, the number of Colocasiomyia individuals was six times higher than Cycreon beetles. Chaloenus (Chrysomelidae, Galeuricinae) appeared to be an inadvertent pollinator. Atheta (Coleoptera, Staphylinidae) is considered a floral visitor in most investigated species of the Calyptrata Complex Clade in Sarawak, but a possible pollinator in S. muluensis. Chironomidae midges and pteromalid wasps are considered visitors in S. calyptrata. Thermogenesis in a biphasic pattern was observed in inflorescences of S. adducta, S. calyptrata, S. giamensis, S. pseudoniahensis and S. roh. The first peak occurred during pistillate anthesis; the second peak during staminate anthesis. Inflorescences of all investigated species of Calyptrata Complex Clade emitted four types of ester compound, with methyl ester-3-methyl-3-butenoic acid as a single major VOC (volatile organic compound). The appendix, pistillate zone, staminate zone and spathe emitted all these compounds. A mixed fly-beetle pollination system is considered an ancestral trait in the Calyptrata Complex Clade, persisting in Sarawak taxa, whereas the marked reduction of

A phylogenetic overview of the antrodia clade (Basidiomycota, Polyporales)

Treesearch

Beatriz Ortiz-Santana; Daniel L. Lindner; Otto Miettinen; Alfredo Justo; David S. Hibbett

2013-01-01

Phylogenetic relationships among members of the antrodia clade were investigated with molecular data from two nuclear ribosomal DNA regions, LSU and ITS. A total of 123 species representing 26 genera producing a brown rot were included in the present study. Three DNA datasets (combined LSU-ITS dataset, LSU dataset, ITS dataset) comprising sequences of 449 isolates were...

The estimation of tree posterior probabilities using conditional clade probability distributions.

PubMed

Larget, Bret

2013-07-01

In this article I introduce the idea of conditional independence of separated subtrees as a principle by which to estimate the posterior probability of trees using conditional clade probability distributions rather than simple sample relative frequencies. I describe an algorithm for these calculations and software which implements these ideas. I show that these alternative calculations are very similar to simple sample relative frequencies for high probability trees but are substantially more accurate for relatively low probability trees. The method allows the posterior probability of unsampled trees to be calculated when these trees contain only clades that are in other sampled trees. Furthermore, the method can be used to estimate the total probability of the set of sampled trees which provides a measure of the thoroughness of a posterior sample.

The influence of sexual activity on the vaginal microbiota and Gardnerella vaginalis clade diversity in young women

PubMed Central

Garland, Suzanne M.; Fairley, Christopher K.; Hocking, Jane S.; Law, Matthew G.; Plummer, Erica L.; Fethers, Katherine A.; Chow, Eric P. F.; Tabrizi, Sepehr N.; Bradshaw, Catriona S.

2017-01-01

Objectives To examine the influence of sexual activity on the composition and consistency of the vaginal microbiota over time, and distribution of Gardnerella vaginalis clades in young women. Methods Fifty-two participants from a university cohort were selected. Vaginal swabs were self-collected every 3-months for up to 12 months with 184 specimens analysed. The vaginal microbiota was characterised using Roche 454 V3/4 region 16S rRNA sequencing, and G.vaginalis clade typing by qPCR. Results A Lactobacillus crispatus dominated vaginal microbiota was associated with Caucasian ethnicity (adjusted relative risk ratio[ARRR] = 7.28, 95%CI:1.37,38.57,p = 0.020). An L.iners (ARRR = 17.51, 95%CI:2.18,140.33,p = 0.007) or G.vaginalis (ARRR = 14.03, 95%CI:1.22,160.69, p = 0.034) dominated microbiota was associated with engaging in penile-vaginal sex. Microbiota dominated by L.crispatus, L.iners or other lactobacilli exhibited greater longitudinal consistency of the bacterial communities present compared to ones dominated by heterogeneous non-lactobacilli (p<0.030); sexual activity did not influence consistency. Women who developed BV were more likely to have clade GV4 compared to those reporting no sex/practiced non-coital activities (OR = 11.82, 95%CI:1.87,74.82,p = 0.009). Specimens were more likely to contain multiple G.vaginalis clades rather than a single clade if women engaged in penile-vaginal sex (RRR = 9.55, 95%CI:1.33,68.38,p = 0.025) or were diagnosed with BV (RRR = 31.5, 95%CI:1.69,586.87,p = 0.021). Conclusions Sexual activity and ethnicity influenced the composition of the vaginal microbiota of these young, relatively sexually inexperienced women. Women had consistent vaginal microbiota over time if lactobacilli were the dominant spp. present. Penile-vaginal sex did not alter the consistency of microbial communities but increased G.vaginalis clade diversity in young women with and without BV, suggesting sexual transmission of commensal and potentially

The influence of sexual activity on the vaginal microbiota and Gardnerella vaginalis clade diversity in young women.

PubMed

Vodstrcil, Lenka A; Twin, Jimmy; Garland, Suzanne M; Fairley, Christopher K; Hocking, Jane S; Law, Matthew G; Plummer, Erica L; Fethers, Katherine A; Chow, Eric P F; Tabrizi, Sepehr N; Bradshaw, Catriona S

2017-01-01

To examine the influence of sexual activity on the composition and consistency of the vaginal microbiota over time, and distribution of Gardnerella vaginalis clades in young women. Fifty-two participants from a university cohort were selected. Vaginal swabs were self-collected every 3-months for up to 12 months with 184 specimens analysed. The vaginal microbiota was characterised using Roche 454 V3/4 region 16S rRNA sequencing, and G.vaginalis clade typing by qPCR. A Lactobacillus crispatus dominated vaginal microbiota was associated with Caucasian ethnicity (adjusted relative risk ratio[ARRR] = 7.28, 95%CI:1.37,38.57,p = 0.020). An L.iners (ARRR = 17.51, 95%CI:2.18,140.33,p = 0.007) or G.vaginalis (ARRR = 14.03, 95%CI:1.22,160.69, p = 0.034) dominated microbiota was associated with engaging in penile-vaginal sex. Microbiota dominated by L.crispatus, L.iners or other lactobacilli exhibited greater longitudinal consistency of the bacterial communities present compared to ones dominated by heterogeneous non-lactobacilli (p<0.030); sexual activity did not influence consistency. Women who developed BV were more likely to have clade GV4 compared to those reporting no sex/practiced non-coital activities (OR = 11.82, 95%CI:1.87,74.82,p = 0.009). Specimens were more likely to contain multiple G.vaginalis clades rather than a single clade if women engaged in penile-vaginal sex (RRR = 9.55, 95%CI:1.33,68.38,p = 0.025) or were diagnosed with BV (RRR = 31.5, 95%CI:1.69,586.87,p = 0.021). Sexual activity and ethnicity influenced the composition of the vaginal microbiota of these young, relatively sexually inexperienced women. Women had consistent vaginal microbiota over time if lactobacilli were the dominant spp. present. Penile-vaginal sex did not alter the consistency of microbial communities but increased G.vaginalis clade diversity in young women with and without BV, suggesting sexual transmission of commensal and potentially pathogenic clades.

SRP-2 is a cross-class inhibitor that participates in postembryonic development of the nematode Caenorhabditis elegans: initial characterization of the clade L serpins.

PubMed

Pak, Stephen C; Kumar, Vasantha; Tsu, Christopher; Luke, Cliff J; Askew, Yuko S; Askew, David J; Mills, David R; Brömme, Dieter; Silverman, Gary A

2004-04-09

High molecular weight serpins are members of a large superfamily of structurally conserved proteins that inactivate target proteinases by a suicide substrate-like mechanism. In vertebrates, different clades of serpins distribute predominantly to either the intracellular or extracellular space. Although much is known about the function, structure, and inhibitory mechanism of circulating serpins such as alpha(1)-antitrypsin (SERPINA1) and antithrombin III (SERPINC1), relatively little is known about the function of the vertebrate intracellular (clade B) serpins. To gain a better understanding of the biology of the intracellular serpins, we initiated a comparative genomics study using Caenorhabditis elegans as a model system. A screen of the C. elegans genomic and cDNA databases revealed nine serpin genes, tandemly arrayed on chromosome V. Although the C. elegans serpins represent a unique clade (L), they share significant functional homology with members of the clade B group of intracellular serpins, since they lack typical N-terminal signal peptides and reside intracellularly. To determine whether nematode serpins function as proteinase inhibitors, one family member, srp-2, was chosen for further characterization. Biochemical analysis of recombinant SRP-2 protein revealed SRP-2 to be a dual cross-class inhibitor of the apoptosis-related serine proteinase, granzyme B, and the lysosomal cysteine proteinases, cathepsins K, L, S, and V. Analysis of temporal and spatial expression indicated that SRP-2 was present during early embryonic development and highly expressed in the intestine and hypoderm of larval and adult worms. Transgenic animals engineered to overexpress SRP-2 were slow growing and/or arrested at the first, second, or third larval stages. These data suggest that perturbations of serpin-proteinase balance are critical for correct postembryonic development in C. elegans.

The oldest known primate skeleton and early haplorhine evolution.

PubMed

Ni, Xijun; Gebo, Daniel L; Dagosto, Marian; Meng, Jin; Tafforeau, Paul; Flynn, John J; Beard, K Christopher

2013-06-06

Reconstructing the earliest phases of primate evolution has been impeded by gaps in the fossil record, so that disagreements persist regarding the palaeobiology and phylogenetic relationships of the earliest primates. Here we report the discovery of a nearly complete and partly articulated skeleton of a primitive haplorhine primate from the early Eocene of China, about 55 million years ago, the oldest fossil primate of this quality ever recovered. Coupled with detailed morphological examination using propagation phase contrast X-ray synchrotron microtomography, our phylogenetic analysis based on total available evidence indicates that this fossil is the most basal known member of the tarsiiform clade. In addition to providing further support for an early dichotomy between the strepsirrhine and haplorhine clades, this new primate further constrains the age of divergence between tarsiiforms and anthropoids. It also strengthens the hypothesis that the earliest primates were probably diurnal, arboreal and primarily insectivorous mammals the size of modern pygmy mouse lemurs.

Testing Evolutionary Hypotheses in the Classroom with MacClade Software.

ERIC Educational Resources Information Center

Codella, Sylvio G.

2002-01-01

Introduces MacClade which is a Macintosh-based software package that uses the techniques of cladistic analysis to explore evolutionary patterns. Describes a novel and effective exercise that allows undergraduate biology majors to test a hypothesis about behavioral evolution in insects. (Contains 13 references.) (Author/YDS)

The Three Clades of the Telomere-Associated TLO Gene Family of Candida albicans Have Different Splicing, Localization, and Expression Features

PubMed Central

Anderson, Matthew Z.; Baller, Joshua A.; Dulmage, Keely; Wigen, Lauren

2012-01-01

Candida albicans grows within a wide range of host niches, and this adaptability enhances its success as a commensal and as a pathogen. The telomere-associated TLO gene family underwent a recent expansion from one or two copies in other CUG clade members to 14 expressed copies in C. albicans. This correlates with increased virulence and clinical prevalence relative to those of other Candida clade species. The 14 expressed TLO gene family members have a conserved Med2 domain at the N terminus, suggesting a role in general transcription. The C-terminal half is more divergent, distinguishing three clades: clade α and clade β have no introns and encode proteins that localize primarily to the nucleus; clade γ sometimes undergoes splicing, and the gene products localize within the mitochondria as well as the nuclei. Additionally, TLOα genes are generally expressed at much higher levels than are TLOγ genes. We propose that expansion of the TLO gene family and the predicted role of Tlo proteins in transcription regulation provide C. albicans with the ability to adapt rapidly to the broad range of different environmental niches within the human host. PMID:22923044

Quantifying variation in speciation and extinction rates with clade data.

PubMed

Paradis, Emmanuel; Tedesco, Pablo A; Hugueny, Bernard

2013-12-01

High-level phylogenies are very common in evolutionary analyses, although they are often treated as incomplete data. Here, we provide statistical tools to analyze what we name "clade data," which are the ages of clades together with their numbers of species. We develop a general approach for the statistical modeling of variation in speciation and extinction rates, including temporal variation, unknown variation, and linear and nonlinear modeling. We show how this approach can be generalized to a wide range of situations, including testing the effects of life-history traits and environmental variables on diversification rates. We report the results of an extensive simulation study to assess the performance of some statistical tests presented here as well as of the estimators of speciation and extinction rates. These latter results suggest the possibility to estimate correctly extinction rate in the absence of fossils. An example with data on fish is presented. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Revision of the Maddenia clade of Prunus (Rosaceae)

PubMed Central

Wen, Jun; Shi, Wenting

2012-01-01

Abstract The Maddenia clade of Prunus L. is monographed based on herbarium and field studies. Four species are currently accepted in this group: Prunus himalayana J.Wen, Prunus hypoleuca (Koehne) J.Wen, Prunus hypoxantha (Koehne) J.Wen, and Prunus gongshanensis J.Wen, with the last described herein as a new species. Maddenia fujianensis Y.T.Chang and Maddenia incisoserrata T.T.Yü & T.C.Ku are treated as synonyms of Prunus hypoleuca. PMID:22577333

Dinoflagellate phylogeny revisited: Using ribosomal proteins to resolve deep branching dinoflagellate clades

PubMed Central

Bachvaroff, Tsvetan R.; Gornik, Sebastian G.; Concepcion, Gregory T.; Waller, Ross F.; Mendez, Gregory S.; Lippmeier, J. Casey; Delwiche, Charles F.

2014-01-01

The alveolates are composed of three major lineages, the ciliates, dinoflagellates, and apicomplexans. Together these ‘protist’ taxa play key roles in primary production and ecology, as well as in illness of humans and other animals. The interface between the dinoflagellate and apicomplexan clades has been an area of recent discovery, blurring the distinction between these two clades. Moreover, phylogenetic analysis has yet to determine the position of basal dinoflagellate clades hence the deepest branches of the dinoflagellate tree currently remain unresolved. Large-scale mRNA sequencing was applied to 11 species of dinoflagellates, including strains of the syndinean genera Hematodinium and Amoebophrya, parasites of crustaceans and dinoflagellates, respectively, to optimize and update the dinoflagellate tree. From the transcriptome-scale data a total of 73 ribosomal protein-coding genes were selected for phylogeny. After individual gene orthology assessment, the genes were concatenated into a >15,000 amino acid alignment with 76 taxa from dinoflagellates, apicomplexans, ciliates, and the outgroup heterokonts. Overall the tree was well resolved and supported, when the data was subsampled with gblocks or constraint trees were tested with the approximately unbiased test. The deepest branches of the dinoflagellate tree can now be resolved with strong support, and provides a clearer view of the evolution of the distinctive traits of dinoflagellates. PMID:24135237

Deciphering and dating the red panda's ancestry and early adaptive radiation of Musteloidea.

PubMed

Sato, Jun J; Wolsan, Mieczyslaw; Minami, Shinji; Hosoda, Tetsuji; Sinaga, Martua H; Hiyama, Kozue; Yamaguchi, Yasunori; Suzuki, Hitoshi

2009-12-01

information from all sampled genes yielded a approximately 42-Myr timescale to caniform evolution and provided evidence of five periods of increased diversification. The red panda's lineage and those of other extant musteloid families are estimated to have diverged during a 3-Myr interval from the mid-Early Oligocene to near the Early/Late Oligocene boundary. We present fossil evidence that extends the early adaptive radiation of the total clade of musteloids to the Eocene-Oligocene transition and also suggests Asia as a center of this radiation.

Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae).

PubMed

Fonseca, Luiz Henrique M; Lohmann, Lúcia G

2018-06-01

Combining high-throughput sequencing data with amplicon sequences allows the reconstruction of robust phylogenies based on comprehensive sampling of characters and taxa. Here, we combine Next Generation Sequencing (NGS) and Sanger sequencing data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae), a diverse lineage of Neotropical plants, using Maximum Likelihood and Bayesian approaches. We used NGS to obtain complete or nearly-complete plastomes of members of this clade, leading to a final dataset with 54 individuals, representing 44 members of ingroup and 10 outgroups. In addition, we obtained Sanger sequences of two plastid markers (ndhF and rpl32-trnL) for 44 individuals (43 ingroup and 1 outgroup) and the nuclear PepC for 64 individuals (63 ingroup and 1 outgroup). Our final dataset includes 87 individuals of members of the "Adenocalymma-Neojobertia" clade, representing 66 species (ca. 90% of the diversity), plus 11 outgroups. Plastid and nuclear datasets recovered congruent topologies and were combined. The combined analysis recovered a monophyletic "Adenocalymma-Neojobertia" clade and a paraphyletic Adenocalymma that also contained a monophyletic Neojobertia plus Pleonotoma albiflora. Relationships are strongly supported in all analyses, with most lineages within the "Adenocalymma-Neojobertia" clade receiving maximum posterior probabilities. Ancestral character state reconstructions using Bayesian approaches identified six morphological synapomorphies of clades namely, prophyll type, petiole and petiolule articulation, tendril ramification, inflorescence ramification, calyx shape, and fruit wings. Other characters such as habit, calyx cupular trichomes, corolla color, and corolla shape evolved multiple times. These characters are putatively related with the clade diversification and can be further explored in diversification studies. Copyright © 2018 Elsevier Inc. All rights reserved.

Antigenic diversity of H5 highly pathogenic avian influenza viruses of clade 2.3.4.4 isolated in Asia.

PubMed

Ohkawara, Ayako; Okamatsu, Masatoshi; Ozawa, Makoto; Chu, Duc-Huy; Nguyen, Lam Thanh; Hiono, Takahiro; Matsuno, Keita; Kida, Hiroshi; Sakoda, Yoshihiro

2017-05-01

H5 highly pathogenic avian influenza viruses (HPAIV) have spread in both poultry and wild birds since late 2003. Continued circulation of HPAIV in poultry in several regions of the world has led to antigenic drift. In the present study, we analyzed the antigenic properties of H5 HPAIV isolated in Asia using four neutralizing mAbs recognizing hemagglutinin, which were established using A/chicken/Kumamoto/1-7/2014 (H5N8), belonging to clade 2.3.4.4 and also using polyclonal antibodies. Viruses of clades 1.1, 2.3.2.1, 2.3.4, and 2.3.4.4 had different reactivity patterns to the panel of mAbs, thereby indicating that the antigenicity of the viruses of clade 2.3.4.4 were similar but differed from the other clades. In particular, the antigenicity of the viruses of clade 2.3.4.4 differed from those of the viruses of clades 2.3.4 and 2.3.2.1, which suggests that the recent H5 HPAIV have further evolved antigenically divergent. In addition, reactivity of antiserum suggests that the antigenicity of viruses of clade 2.3.4.4 differed slightly among groups A, B, and C. Vaccines are still used in poultry in endemic countries, so the antigenicity of H5 HPAIV should be monitored continually to facilitate control of avian influenza. The panel of mAbs established in the present study will be useful for detecting antigenic drift in the H5 viruses that emerge from the current strains. © 2017 The Societies and John Wiley & Sons Australia, Ltd.

Enhanced virulence of clade 2.3.2.1 highly pathogenic avian influenza A H5N1 viruses in ferrets.

PubMed

Pearce, Melissa B; Pappas, Claudia; Gustin, Kortney M; Davis, C Todd; Pantin-Jackwood, Mary J; Swayne, David E; Maines, Taronna R; Belser, Jessica A; Tumpey, Terrence M

2017-02-01

Sporadic avian to human transmission of highly pathogenic avian influenza (HPAI) A(H5N1) viruses necessitates the analysis of currently circulating and evolving clades to assess their potential risk. Following the spread and sustained circulation of clade 2 viruses across multiple continents, numerous subclades and genotypes have been described. To better understand the pathogenesis associated with the continued diversification of clade 2A(H5N1) influenza viruses, we investigated the relative virulence of eleven human and poultry isolates collected from 2006 to 2013 by determining their ability to cause disease in the ferret model. Numerous clade 2 viruses, including a clade 2.2 avian isolate, a 2.2.2.1 human isolate, and two 2.2.1 human isolates, were found to be of low virulence in the ferret model, though lethality was detected following infection with one 2.2.1 human isolate. In contrast, three of six clade 2.3.2.1 avian isolates tested led to severe disease and death among infected ferrets. Clade 2.3.2.1b and 2.3.2.1c isolates, but not 2.3.2.1a isolates, were associated with ferret lethality. All A(H5N1) viruses replicated efficiently in the respiratory tract of ferrets regardless of their virulence and lethality. However, lethal isolates were characterized by systemic viral dissemination, including detection in the brain and enhanced histopathology in lung tissues. The finding of disparate virulence phenotypes between clade 2A(H5N1) viruses, notably differences between subclades of 2.3.2.1 viruses, suggests there are distinct molecular determinants present within the established subclades, the identification of which will assist in molecular-based surveillance and public health efforts against A(H5N1) viruses. Published by Elsevier Inc.

Enhanced virulence of clade 2.3.2.1 highly pathogenic avian influenza A H5N1 viruses in ferrets

PubMed Central

Pearce, Melissa B.; Pappas, Claudia; Gustin, Kortney M.; Davis, C. Todd; Pantin-Jackwood, Mary J.; Swayne, David E.; Maines, Taronna R.; Belser, Jessica A.; Tumpey, Terrence M.

2017-01-01

Sporadic avian to human transmission of highly pathogenic avian influenza (HPAI) A(H5N1) viruses necessitates the analysis of currently circulating and evolving clades to assess their potential risk. Following the spread and sustained circulation of clade 2 viruses across multiple continents, numerous subclades and genotypes have been described. To better understand the pathogenesis associated with the continued diversification of clade 2 A(H5N1) influenza viruses, we investigated the relative virulence of eleven human and poultry isolates collected from 2006 to 2013 by determining their ability to cause disease in the ferret model. Numerous clade 2 viruses, including a clade 2.2 avian isolate, a 2.2.2.1 human isolate, and two 2.2.1 human isolates, were found to be of low virulence in the ferret model, though lethality was detected following infection with one 2.2.1 human isolate. In contrast, three of six clade 2.3.2.1 avian isolates tested led to severe disease and death among infected ferrets. Clade 2.3.2.1b and 2.3.2.1c isolates, but not 2.3.2.1a isolates, were associated with ferret lethality. All A(H5N1) viruses replicated efficiently in the respiratory tract of ferrets regardless of their virulence and lethality. However, lethal isolates were characterized by systemic viral dissemination, including detection in the brain and enhanced histopathology in lung tissues. The finding of disparate virulence phenotypes between clade 2 A(H5N1) viruses, notably differences between subclades of 2.3.2.1 viruses, suggests there are distinct molecular determinants present within the established subclades, the identification of which will assist in molecular-based surveillance and public health efforts against A(H5N1) viruses. PMID:28038412

Sexually transmitted diseases among adults who had been abused and neglected as children: a 30-year prospective study.

PubMed

Wilson, Helen W; Widom, Cathy S

2009-04-01

We examined associations between childhood abuse and neglect and the risk in adulthood for sexually transmitted diseases. In a prospective cohort design, we matched children aged 0 to 11 years with documented cases of abuse or neglect during 1967 to 1971 with a control group of children who had not been maltreated (754 participants in all) and followed them into adulthood. Information about lifetime history of sexually transmitted diseases was collected as part of a medical status examination when participants were approximately 41 years old. Childhood sexual abuse increased risk for any sexually transmitted disease (odds ratio [OR] = 1.94; 95% confidence interval [CI] = 1.00, 3.77; P = .05) and more than 1 type of sexually transmitted disease (OR = 3.33; 95% CI = 1.33, 8.22; P = .01). Physical abuse increased risk for more than 1 type of sexually transmitted disease (OR = 3.61; 95% CI = 1.39, 9.38; P = .009). Our results provided the first prospective evidence that child physical and sexual abuse increases risk for sexually transmitted diseases. Early screening and interventions are needed to identify and prevent sexually transmitted diseases among child abuse victims.

Distinct Processes Drive Diversification in Different Clades of Gesneriaceae.

PubMed

Roalson, Eric H; Roberts, Wade R

2016-07-01

Using a time-calibrated phylogenetic hypothesis including 768 Gesneriaceae species (out of [Formula: see text]3300 species) and more than 29,000 aligned bases from 26 gene regions, we test Gesneriaceae for diversification rate shifts and the possible proximal drivers of these shifts: geographic distributions, growth forms, and pollination syndromes. Bayesian Analysis of Macroevolutionary Mixtures analyses found five significant rate shifts in Beslerieae, core Nematanthus, core Columneinae, core Streptocarpus, and Pacific Cyrtandra These rate shifts correspond with shifts in diversification rates, as inferred by Binary State Speciation and Extinction Model and Geographic State Speciation and Extinction model, associated with hummingbird pollination, epiphytism, unifoliate growth, and geographic area. Our results suggest that diversification processes are extremely variable across Gesneriaceae clades with different combinations of characters influencing diversification rates in different clades. Diversification patterns between New and Old World lineages show dramatic differences, suggesting that the processes of diversification in Gesneriaceae are very different in these two geographic regions. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

High Ancient Genetic Diversity of Human Lice, Pediculus humanus, from Israel Reveals New Insights into the Origin of Clade B Lice

PubMed Central

Amanzougaghene, Nadia; Mumcuoglu, Kosta Y.; Fenollar, Florence; Alfi, Shir; Yesilyurt, Gonca; Raoult, Didier; Mediannikov, Oleg

2016-01-01

The human head louse, Pediculus humanus capitis, is subdivided into several significantly divergent mitochondrial haplogroups, each with particular geographical distributions. Historically, they are among the oldest human parasites, representing an excellent marker for tracking older events in human evolutionary history. In this study, ancient DNA analysis using real-time polymerase chain reaction (qPCR), combined with conventional PCR, was applied to the remains of twenty-four ancient head lice and their eggs from the Roman period which were recovered from Israel. The lice and eggs were found in three combs, one of which was recovered from archaeological excavations in the Hatzeva area of the Judean desert, and two of which found in Moa, in the Arava region, close to the Dead Sea. Results show that the head lice remains dating approximately to 2,000 years old have a cytb haplogroup A, which is worldwide in distribution, and haplogroup B, which has thus far only been found in contemporary lice from America, Europe, Australia and, most recently, Africa. More specifically, this haplogroup B has a B36 haplotype, the most common among B haplogroups, and has been present in America for at least 4,000 years. The present findings confirm that clade B lice existed, at least in the Middle East, prior to contacts between Native Americans and Europeans. These results support a Middle Eastern origin for clade B followed by its introduction into the New World with the early peoples. Lastly, the presence of Acinetobacter baumannii DNA was demonstrated by qPCR and sequencing in four head lice remains belonging to clade A. PMID:27741281

Clade 2.3.4.4 avian influenza A (H5N8) outbreak in commercial poultry, Iran, 2016: the first report and update data.

PubMed

Ghafouri, Seyed Ali; GhalyanchiLangeroudi, Arash; Maghsoudloo, Hossein; Kh Farahani, Reza; Abdollahi, Hamed; Tehrani, Farshad; Fallah, Mohammad Hossein

2017-06-01

In 2010, H5N8 highly pathogenic avian influenza (HPAI) viruses of the A/Goose/Guangdong/1/1996 lineage dramatically affected poultry and wild birds in Asia, Europe, and North America. In November 2016, HPAI H5N8 was detected in a commercial layer farm in Tehran province. The diagnosis was based on real-time reverse transcriptase PCR (RRT-PCR) and sequencing of haemaglutinin (HA) and neuraminidase (NA) genes from suspected samples. Genetic and phylogenetic analysis of the HA gene demonstrated that the Iranian HPAI H5N8 viruses belong to the HPAI H5 virus clade 2.3.4.4 and cluster within group B (Gochang-like). In particular, the highest similarity was found with the sequences of the HPAI H5N8 identified in Russia in 2016. To our knowledge, this clade has not been previously detected in Iran. Previous HPAI A (H5) epidemic in Iran occurred in 2015 and involved exclusively viruses of clade 2.3.2.1c. These findings indicate that Iran is at high risk of introduction of HPAI H5 of the A/Goose/Guangdong/1/1996 lineage from East Asia and highlight the need to maintain adequate monitoring activities in target wild and domestic bird species for HPAI early detection. This study is useful for better understanding the genetic and antigenic evolution of H5 HPAI viruses in the region and the world.

Protein evolution in two co-occurring types of Symbiodinium: an exploration into the genetic basis of thermal tolerance in Symbiodinium clade D

PubMed Central

2012-01-01

Background The symbiosis between reef-building corals and photosynthetic dinoflagellates (Symbiodinium) is an integral part of the coral reef ecosystem, as corals are dependent on Symbiodinium for the majority of their energy needs. However, this partnership is increasingly at risk due to changing climatic conditions. It is thought that functional diversity within Symbiodinium may allow some corals to rapidly adapt to different environments by changing the type of Symbiodinium with which they partner; however, very little is known about the molecular basis of the functional differences among symbiont groups. One group of Symbiodinium that is hypothesized to be important for the future of reefs is clade D, which, in general, seems to provide the coral holobiont (i.e., coral host and associated symbiont community) with elevated thermal tolerance. Using high-throughput sequencing data from field-collected corals we assembled, de novo, draft transcriptomes for Symbiodinium clades C and D. We then explore the functional basis of thermal tolerance in clade D by comparing rates of coding sequence evolution among the four clades of Symbiodinium most commonly found in reef-building corals (A-D). Results We are able to highlight a number of genes and functional categories as candidates for involvement in the increased thermal tolerance of clade D. These include a fatty acid desaturase, molecular chaperones and proteins involved in photosynthesis and the thylakoid membrane. We also demonstrate that clades C and D co-occur within most of the sampled colonies of Acropora hyacinthus, suggesting widespread potential for this coral species to acclimatize to changing thermal conditions via ‘shuffling’ the proportions of these two clades from within their current symbiont communities. Conclusions Transcriptome-wide analysis confirms that the four main Symbiodinium clades found within corals exhibit extensive evolutionary divergence (18.5-27.3% avg. pairwise nucleotide difference

Differential Penicillin-Binding Protein 5 (PBP5) Levels in the Enterococcus faecium Clades with Different Levels of Ampicillin Resistance.

PubMed

Montealegre, Maria Camila; Roh, Jung Hyeob; Rae, Meredith; Davlieva, Milya G; Singh, Kavindra V; Shamoo, Yousif; Murray, Barbara E

2017-01-01

Ampicillin resistance in Enterococcus faecium is a serious concern worldwide, complicating the treatment of E. faecium infections. Penicillin-binding protein 5 (PBP5) is considered the main ampicillin resistance determinant in E. faecium The three known E. faecium clades showed sequence variations in the pbp5 gene that are associated with their ampicillin resistance phenotype; however, these changes alone do not explain the array of resistance levels observed among E. faecium clinical strains. We aimed to determine if the levels of PBP5 are differentially regulated between the E. faecium clades, with the hypothesis that variations in PBP5 levels could help account for the spectrum of ampicillin MICs seen in E. faecium We studied pbp5 mRNA levels and PBP5 protein levels as well as the genetic environment upstream of pbp5 in 16 E. faecium strains that belong to the different E. faecium clades and for which the ampicillin MICs covered a wide range. Our results found that pbp5 and PBP5 levels are increased in subclade A1 and A2 ampicillin-resistant strains compared to those in clade B and subclade A2 ampicillin-susceptible strains. Furthermore, we found evidence of major clade-associated rearrangements in the region upstream of pbp5, including large DNA fragment insertions, deletions, and single nucleotide polymorphisms, that may be associated with the differential regulation of PBP5 levels between the E. faecium clades. Overall, these findings highlight the contribution of the clade background to the regulation of PBP5 abundance and point to differences in the region upstream of pbp5 as likely contributors to the differential expression of ampicillin resistance. Copyright © 2016 American Society for Microbiology.

Novel H5N8 clade 2.3.4.4 highly pathogenic avian influenza virus in wild awuatic birds, Russia, 2016

USDA-ARS?s Scientific Manuscript database

H5N1 high pathogenicity avian influenza virus (HPAIV) emerged in 1996 in Guangdong China (Gs/GD) and has evolved into multiple genetic clades. Since 2008, HPAIV H5 clade 2.3.4 with N2, N5 and N8 neuraminidase subtypes have been identified in mainland China and outbreak of HPAIV H5N8 clade 2.3.4.4 ou...

TRANSMIT system evaluation : final report

DOT National Transportation Integrated Search

1998-06-30

This report presents the evaluation results of TRANSCOMs System for Managing Incidents and Traffic (TRANSMIT). The TRANSMIT system utilizes Electronic Toll and Traffic Management (ETTM) equipment, which is compatible with the E-Z Pass system, for ...

The microsporidium Nosema disstriae (Thomson 1959): Fine structure and phylogenetic position within the N. bombycis clade.

PubMed

Kyei-Poku, George; Sokolova, Yuliya Y

2017-02-01

A microsporidium Nosema disstriae (Thomson) is a parasite of the forest tent caterpillar Malacasoma disstria (Lepidoptera: Lasiocampidae), a notable defoliator of deciduous trees in North America. The goal of this paper was to demonstrate the ultrastructure of N. disstriae and to determine the position of this microsporidium within the N. bombycis clade (NBC) using comparative morphology and multiple molecular phylogenetic markers: RPB1, LSU-, ITS- and SSU-rDNA. As a part of this goal, the revision of the described members of the NBC has been performed. The ultrastructure of proliferating stages and spores of N. disstriae were similar to previously described Nosema spp. parasitizing lepidopteran species. Meronts produced tubular-like structures on their surfaces and exhibited a tight association with host mitochondria. All stages were diplokaryotic and developed without interfacial envelopes. Disporoblastic sporogony produced typical Nosema-type spores with 9-12 polar filament coils. A vesicle with immature spores was once recognized on sections, concordant with the previous record of octosporous sporogony in the N. disstriae life cycle. Rarely, spores with thinner envelopes and large posterior vacuoles were seen in the midgut. Tracheae were most heavily infected. Midgut, surrounding muscles, haemocytes and fat body also contained microsporidia. SSUrRNA-inferred phylogenies were consistent with previously published articles and did not resolve the relation within the NBC clade. The RPB1-inferred trees and concatenated RPB1 and LSU-ITS-SSUrDNA-based trees demonstrated clustering of N. disstriae with N. antheraeae as early divergent species within the NBC. Copyright © 2016 Elsevier Inc. All rights reserved.

Statistics, Uncertainty, and Transmitted Variation

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

Wendelberger, Joanne Roth

2014-11-05

The field of Statistics provides methods for modeling and understanding data and making decisions in the presence of uncertainty. When examining response functions, variation present in the input variables will be transmitted via the response function to the output variables. This phenomenon can potentially have significant impacts on the uncertainty associated with results from subsequent analysis. This presentation will examine the concept of transmitted variation, its impact on designed experiments, and a method for identifying and estimating sources of transmitted variation in certain settings.

The origin and early evolution of metatherian mammals: the Cretaceous record.

PubMed

Williamson, Thomas E; Brusatte, Stephen L; Wilson, Gregory P

2014-01-01

Metatherians, which comprise marsupials and their closest fossil relatives, were one of the most dominant clades of mammals during the Cretaceous and are the most diverse clade of living mammals after Placentalia. Our understanding of this group has increased greatly over the past 20 years, with the discovery of new specimens and the application of new analytical tools. Here we provide a review of the phylogenetic relationships of metatherians with respect to other mammals, discuss the taxonomic definition and diagnosis of Metatheria, outline the Cretaceous history of major metatherian clades, describe the paleobiology, biogeography, and macroevolution of Cretaceous metatherians, and provide a physical and climatic background of Cretaceous metatherian faunas. Metatherians are a clade of boreosphendian mammals that must have originated by the Late Jurassic, but the first unequivocal metatherian fossil is from the Early Cretaceous of Asia. Metatherians have the distinctive tightly interlocking occlusal molar pattern of tribosphenic mammals, but differ from Eutheria in their dental formula and tooth replacement pattern, which may be related to the metatherian reproductive process which includes an extended period of lactation followed by birth of extremely altricial young. Metatherians were widespread over Laurasia during the Cretaceous, with members present in Asia, Europe, and North America by the early Late Cretaceous. In particular, they were taxonomically and morphologically diverse and relatively abundant in the Late Cretaceous of western North America, where they have been used to examine patterns of biogeography, macroevolution, diversification, and extinction through the Late Cretaceous and across the Cretaceous-Paleogene (K-Pg) boundary. Metatherian diversification patterns suggest that they were not strongly affected by a Cretaceous Terrestrial Revolution, but they clearly underwent a severe extinction across the K-Pg boundary.

Limits to Forecasting Precision for Outbreaks of Directly Transmitted Diseases

PubMed Central

Drake, John M

2006-01-01

Background Early warning systems for outbreaks of infectious diseases are an important application of the ecological theory of epidemics. A key variable predicted by early warning systems is the final outbreak size. However, for directly transmitted diseases, the stochastic contact process by which outbreaks develop entails fundamental limits to the precision with which the final size can be predicted. Methods and Findings I studied how the expected final outbreak size and the coefficient of variation in the final size of outbreaks scale with control effectiveness and the rate of infectious contacts in the simple stochastic epidemic. As examples, I parameterized this model with data on observed ranges for the basic reproductive ratio (R 0) of nine directly transmitted diseases. I also present results from a new model, the simple stochastic epidemic with delayed-onset intervention, in which an initially supercritical outbreak (R 0 > 1) is brought under control after a delay. Conclusion The coefficient of variation of final outbreak size in the subcritical case (R 0 < 1) will be greater than one for any outbreak in which the removal rate is less than approximately 2.41 times the rate of infectious contacts, implying that for many transmissible diseases precise forecasts of the final outbreak size will be unattainable. In the delayed-onset model, the coefficient of variation (CV) was generally large (CV > 1) and increased with the delay between the start of the epidemic and intervention, and with the average outbreak size. These results suggest that early warning systems for infectious diseases should not focus exclusively on predicting outbreak size but should consider other characteristics of outbreaks such as the timing of disease emergence. PMID:16435887

Use of matrix-assisted laser desorption ionization-time of flight mass spectrometry to identify MLST clade 4 Clostridium difficile isolates.

PubMed

Cheng, Jing-Wei; Liu, Chang; Kudinha, Timothy; Xiao, Meng; Yu, Shu-Ying; Yang, Chun-Xia; Wei, Ming; Liang, Guo-Wei; Shao, Dong-Hua; Kong, Fanrong; Tong, Zhao-Hui; Xu, Ying-Chun

2018-04-26

Clostridium difficile is the leading cause of health care-associated infections. Previous studies suggest that C. difficile MLST clade 4 strains with higher drug resistance rates constitute the major clone spreading in China. Thus development of a rapid and accurate typing method for these strains is needed to monitor the epidemiology of this clone and to guide clinical treatment. A total of 160 non-duplicate C. difficile isolates recovered from three large teaching hospitals in Beijing were studied. All the 41 clade 4 C. difficile isolates clustered together on the PCA dendrogram. Spectra peak statistics revealed that five markers (2691.43Da, 2704.91Da, 2711.93Da, 3247.27Da and 3290.76Da) can easily and reliably distinguish between clade 4 and non-clade 4 isolates, with area under the curve (AUC) values of 0.991, 0.997, 0.973, 1 and 1, respectively. In conclusion, MALDI-TOF MS is a very simple and accurate method for identifying C. difficile MLST clade 4 strains. Copyright © 2018 Elsevier Inc. All rights reserved.

Molecular phylogeny of the spider family Sparassidae with focus on the genus Eusparassus and notes on the RTA-clade and 'Laterigradae'.

PubMed

Moradmand, Majid; Schönhofer, Axel L; Jäger, Peter

2014-05-01

The phylogeny of the spider family Sparassidae is comprehensively investigated using four molecular markers (mitochondrial COI and 16S; nuclear H3 and 28S). Sparassidae was recovered as monophyletic and as most basal group within the RTA-clade. The higher-level clade Dionycha was not but monophyly of RTA-clade was supported. No affiliation of Sparassidae to other members of the 'Laterigradae' (Philodromidae, Selenopidae and Thomisidae) was observed, and the crab-like posture of this group assumed a result of convergent evolution. Only Philodromidae and Selenopidae were found members of a supported clade, but together with Salticidae and Corinnidae, while Thomisidae was nested within the higher Lycosoidea. Within Sparassidae monophyly of the subfamilies Heteropodinae sensu stricto, Palystinae and Deleninae was recovered. Sparianthinae was supported as the most basal clade within Sparassidae. Sparassinae and the genus Olios were found each to be polyphyletic. Eusparassinae was not recovered monophyletic, with the two original genera Eusparassus and Pseudomicrommata in separate clades and only the latter clustered with most other assumed Eusparassinae, here termed the "African clade". Further focus was on the monophyletic genus Eusparassus and its proposed species groups, of which the dufouri-, walckenaeri- and doriae-group were confirmed as monophyletic with the two latter groups more closely related. According to molecular clock analyses, the divergence time of Sparassidae and Eusparassus was estimated with 186 and 70 million years ago respectively. Copyright © 2014 Elsevier Inc. All rights reserved.

[Infectious pathology: vulvovaginitis, sexually transmitted diseases, pelvic inflammatory disease, tubo-ovarian abscesses].

PubMed

Ibarrola Vidaurre, M; Benito, J; Azcona, B; Zubeldía, N

2009-01-01

Sexually transmitted diseases are those where the principal path of infection is through intimate contact. Numerous patients attend Accidents and emergencies for this reason, both because of the clinical features and because of social implications. The most frequent symptoms are lower abdominal pain, vaginal bleeding or excessive or troubling vaginal flow. Vulvovaginites are one of the principal problems in the everyday clinical practice of gynaecology. A genital ulcer whose principal aetiology is herpes, followed by syphilis and chancroid, increases the risk of contracting HIV infection and alters the course of other sexually transmitted diseases. Inflammatory pelvic disease encompasses infections of the upper female genital tract. The importance of early diagnosis and suitable treatment is both due to the complications in its acute phase and to its sequels, which include chronic pain and sterility.

Stockpiled pre-pandemic H5N1 influenza virus vaccines with AS03 adjuvant provide cross-protection from H5N2 clade 2.3.4.4 virus challenge in ferrets

PubMed Central

Sun, Xiangjie; Belser, Jessica A.; Pulit-Penaloza, Joanna A.; Creager, Hannah M.; Guo, Zhu; Jefferson, Stacie N.; Liu, Feng; York, Ian A.; Stevens, James; Maines, Taronna R.; Jernigan, Daniel B.; Katz, Jacqueline M.; Levine, Min Z.; Tumpey, Terrence M.

2018-01-01

Avian influenza viruses, notably H5 subtype viruses, pose a continuous threat to public health due to their pandemic potential. In recent years, influenza virus H5 subtype split vaccines with novel oil-in-water emulsion based adjuvants (e.g. AS03, MF59) have been shown to be safe, immunogenic, and able to induce broad immune responses in clinical trials, providing strong scientific support for vaccine stockpiling. However, whether such vaccines can provide protection from infection with emerging, antigenically distinct clades of H5 viruses has not been adequately addressed. Here, we selected two AS03-adjuvanted H5N1 vaccines from the US national prepandemic influenza vaccine stockpile and assessed whether the 2004–05 vaccines could provide protection against a 2014 highly pathogenic avian influenza (HPAI) H5N2 virus (A/northern pintail/Washington/40964/2014), a clade 2.3.4.4 virus responsible for mass culling of poultry in North America. Ferrets received two doses of adjuvanted vaccine containing 7.5 μg of hemagglutinin (HA) from A/Vietnam/1203/2004 (clade 1) or A/Anhui/1/2005 (clade 2.3.4) virus either in a homologous or heterologous prime-boost vaccination regime. We found that both vaccination regimens elicited robust antibody responses against the 2004–05 vaccine viruses and could reduce virus-induced morbidity and viral replication in the lower respiratory tract upon heterologous challenge despite the low level of cross-reactive antibody titers to the challenge H5N2 virus. This study supports the value of existing stockpiled 2004–05 influenza H5N1 vaccines, combined with AS03-adjuvant for early use in the event of an emerging pandemic with H5N2-like clade 2.3.4.4 viruses. PMID:28554058

The other epidemics. Sexually transmitted diseases.

PubMed

Jacobson, J L

1993-01-01

Around 70% of female infertility in developing countries is caused by sexually transmitted diseases (STDs) that can be traced back to husbands or partners. STDs and reproductive tract infections cause 750,000 deaths and 75 million illnesses among women each year worldwide, and these deaths may more than double by the year 2000. Death rates are rising fastest in Africa, followed by Asia and Latin America. About 450,000 cases of potentially fatal reproductive tract cancers are diagnosed annually: an estimated 354,000 occur in Third World women, virtually all of whom die. Worldwide, roughly 250 million new infections of chlamydia, gonorrhea, and the human papillomavirus are sexually transmitted each year. Chlamydia and the human papillomavirus account for 50 million and 30 million new cases per year, respectively. The human immunodeficiency virus (HIV) infected 1 million people worldwide between April and December 1991, according to the World Health Organization. A study in the Indian state of Maharashtra revealed that 92% of the 650 rural women examined had an average of 3.6 infections of gynecological type or sexually transmitted type per women. Another study in 2 rural Egyptian villages found that half of 509 nonpregnant women aged 20 to 60 years had infections. Only 2 facilities for the diagnosis and treatment of STDs exist in all of Kenya. In Ibadan, Nigeria, with a population of 2 million, there is only 1 recognized STD clinic. The physical consequences of several STDs have been linked to increased risks of AIDS transmission. Early recognition and treatment of STDs in pregnant women would cut infant mortality. Maternal infections with chlamydia, gonorrhea, or herpes are transferred to infants at birth 25% to 50% of the time. In Africa, infant blindness caused by gonorrhea infection is 50 times more common than in industrial countries. The International Women's Health Coalition's March 1992 meeting of more than 50 Third World scientists, health advocates, and

2012 Sexually Transmitted Diseases Surveillance, Other Sexually Transmitted Diseases

MedlinePlus

... 2012 Sexually Transmitted Diseases Surveillance Table of Contents Introductory Section Foreword Preface Acronyms Figures- National Profile Figures - ... GISP Profiles Related Links STD Home STD Data & Statistics NCHHSTP Atlas Interactive STD Data - 1996-2013 STD ...

A history of sexually transmitted diseases in Thailand: policy and politics.

PubMed

Bamber, S D; Hewison, K J; Underwood, P J

1993-04-01

This paper provides a brief history of sexually transmitted diseases (STDs) in Thailand. The presentation is divided into three main sections: the period up to the 1930s; the period from the 1930s until the end of the early 1980s; and the period from the early 1980s until the present, the so-called 'AIDS Era'. The discussion in each of these sections focuses, as far as sources permit, on the epidemiological picture, as well as describing public and official responses to these diseases. In the final part of the paper consideration is given to these findings in relation to the present situation in Thailand regarding the HIV/AIDS epidemic.

Mosaic clade M human immunodeficiency virus type 1 (HIV-1) envelope immunogens

DOEpatents

Korber, Bette T [Los Alamos, NM; Fischer, William [Los Alamos, NM; Liao, Hua-Xin [Durham, NC; Haynes, Barton F [Durham, NC; Letvin, Norman [Boston, MA; Hahn,; Beatrice, H [Birmingham, AL

2011-05-31

The present invention relates to mosaic clade M HIV-1 Env polypeptides and to compositions comprising same. The polypeptides of the invention are suitable for use in inducing an immune response to HIV-1 in a human.

Development of Clade-Specific and Broadly Reactive Live Attenuated Influenza Virus Vaccines against Rapidly Evolving H5 Subtype Viruses

PubMed Central

Boonnak, Kobporn; Matsuoka, Yumiko; Wang, Weijia; Suguitan, Amorsolo L.; Chen, Zhongying; Paskel, Myeisha; Baz, Mariana; Moore, Ian; Jin, Hong

2017-01-01

ABSTRACT We have developed pandemic live attenuated influenza vaccines (pLAIVs) against clade 1 H5N1 viruses on an Ann Arbor cold-adapted (ca) backbone that induced long-term immune memory. In 2015, many human infections caused by a new clade (clade 2.2.1.1) of goose/Guangdong (gs/GD) lineage H5N1 viruses were reported in Egypt, which prompted updating of the H5N1 pLAIV. We explored two strategies to generate suitable pLAIVs. The first approach was to modify the hemagglutinin gene of a highly pathogenic wild-type (wt) clade 2.2.1.1 virus, A/Egypt/N03434/2009 (Egy/09) (H5N1), with its unmodified neuraminidase (NA) gene; this virus was designated Egy/09 ca. The second approach was to select a low-pathogenicity avian influenza H5 virus that elicited antibodies that cross-reacted with a broad range of H5 viruses, including the Egypt H5N1 viruses, and contained a novel NA subtype for humans. We selected the low-pathogenicity A/duck/Hokkaido/69/2000 (H5N3) (dk/Hok/00) virus for this purpose. Both candidate vaccines were attenuated and immunogenic in ferrets, inducing antibodies that neutralized homologous and heterologous H5 viruses with different degrees of cross-reactivity; Egy/09 ca vaccine antisera were more specific for the gs/GD lineage viruses but did not neutralize recent North American isolates (clade 2.3.4.4), whereas antisera from dk/Hok/69 ca-vaccinated ferrets cross-reacted with clade 2.3.4.4 and 2.2.1 viruses but not clade 1 or 2.1 viruses. When vaccinated ferrets were challenged with homologous and heterologous H5 viruses, challenge virus replication was reduced in the respiratory tract. Thus, the two H5 pLAIV candidates are suitable for clinical development to protect humans from infection with different clades of H5 viruses. IMPORTANCE In response to the continuing evolution of H5N1 avian influenza viruses and human infections, new candidate H5 live attenuated vaccines were developed by using two different approaches: one targeted a specific circulating

Development of Clade-Specific and Broadly Reactive Live Attenuated Influenza Virus Vaccines against Rapidly Evolving H5 Subtype Viruses.

PubMed

Boonnak, Kobporn; Matsuoka, Yumiko; Wang, Weijia; Suguitan, Amorsolo L; Chen, Zhongying; Paskel, Myeisha; Baz, Mariana; Moore, Ian; Jin, Hong; Subbarao, Kanta

2017-08-01

We have developed pandemic live attenuated influenza vaccines (pLAIVs) against clade 1 H5N1 viruses on an Ann Arbor cold-adapted ( ca ) backbone that induced long-term immune memory. In 2015, many human infections caused by a new clade (clade 2.2.1.1) of goose/Guangdong (gs/GD) lineage H5N1 viruses were reported in Egypt, which prompted updating of the H5N1 pLAIV. We explored two strategies to generate suitable pLAIVs. The first approach was to modify the hemagglutinin gene of a highly pathogenic wild-type ( wt ) clade 2.2.1.1 virus, A/Egypt/N03434/2009 (Egy/09) (H5N1), with its unmodified neuraminidase (NA) gene; this virus was designated Egy/09 ca The second approach was to select a low-pathogenicity avian influenza H5 virus that elicited antibodies that cross-reacted with a broad range of H5 viruses, including the Egypt H5N1 viruses, and contained a novel NA subtype for humans. We selected the low-pathogenicity A/duck/Hokkaido/69/2000 (H5N3) (dk/Hok/00) virus for this purpose. Both candidate vaccines were attenuated and immunogenic in ferrets, inducing antibodies that neutralized homologous and heterologous H5 viruses with different degrees of cross-reactivity; Egy/09 ca vaccine antisera were more specific for the gs/GD lineage viruses but did not neutralize recent North American isolates (clade 2.3.4.4), whereas antisera from dk/Hok/69 ca -vaccinated ferrets cross-reacted with clade 2.3.4.4 and 2.2.1 viruses but not clade 1 or 2.1 viruses. When vaccinated ferrets were challenged with homologous and heterologous H5 viruses, challenge virus replication was reduced in the respiratory tract. Thus, the two H5 pLAIV candidates are suitable for clinical development to protect humans from infection with different clades of H5 viruses. IMPORTANCE In response to the continuing evolution of H5N1 avian influenza viruses and human infections, new candidate H5 live attenuated vaccines were developed by using two different approaches: one targeted a specific circulating

Insights on the evolutionary origin of Detarioideae, a clade of ecologically dominant tropical African trees.

PubMed

de la Estrella, Manuel; Forest, Félix; Wieringa, Jan J; Fougère-Danezan, Marie; Bruneau, Anne

2017-06-01

African tropical forests are generally considered less diverse than their Neotropical and Asian counterparts. By contrast, the Detarioideae is much more diverse in Africa than in South America and Asia. To better understand the evolution of this contrasting diversity pattern, we investigated the biogeographical and ecological origin of this subfamily, testing whether they originated in dry biomes surrounding the Tethys Seaway as currently hypothesized for many groups of Leguminosae. We constructed the largest time-calibrated phylogeny for the subfamily to date, reconstructed ancestral states for geography and biome/habitat, estimated diversification and extinction rates, and evaluated biome/habitat and geographic shifts in Detarioideae. The ancestral habitat of Detarioideae is postulated to be a primary forest (terra firme) originated in Africa-South America, in the early Palaeocene, after which several biome/habitat and geographic shifts occurred. The origin of Detarioideae is older than previous estimates, which postulated a dry (succulent) biome origin according to the Tethys Seaway hypothesis, and instead we reveal a post Gondwana and terra firme origin for this early branching clade of legumes. Detarioideae include some of the most dominant trees in evergreen forests and have likely played a pivotal role in shaping continental African forest diversity. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Polyphyletic origin of MERS coronaviruses and isolation of a novel clade A strain from dromedary camels in the United Arab Emirates

PubMed Central

Lau, Susanna K P; Wernery, Renate; Wong, Emily Y M; Joseph, Sunitha; Tsang, Alan K L; Patteril, Nissy Annie Georgy; Elizabeth, Shyna K; Chan, Kwok-Hung; Muhammed, Rubeena; Kinne, Jöerg; Yuen, Kwok-Yung; Wernery, Ulrich; Woo, Patrick C Y

2016-01-01

Little is known regarding the molecular epidemiology of Middle East respiratory syndrome coronavirus (MERS-CoV) circulating in dromedaries outside Saudi Arabia. To address this knowledge gap, we sequenced 10 complete genomes of MERS-CoVs isolated from 2 live and 8 dead dromedaries from different regions in the United Arab Emirates (UAE). Phylogenetic analysis revealed one novel clade A strain, the first detected in the UAE, and nine clade B strains. Strain D998/15 had a distinct phylogenetic position within clade A, being more closely related to the dromedary isolate NRCE-HKU205 from Egypt than to the human isolates EMC/2012 and Jordan-N3/2012. A comparison of predicted protein sequences also demonstrated the existence of two clade A lineages with unique amino acid substitutions, A1 (EMC/2012 and Jordan-N3/2012) and A2 (D998/15 and NRCE-HKU205), circulating in humans and camels, respectively. The nine clade B isolates belong to three distinct lineages: B1, B3 and B5. Two B3 strains, D1271/15 and D1189.1/15, showed evidence of recombination between lineages B4 and B5 in ORF1ab. Molecular clock analysis dated the time of the most recent common ancestor (tMRCA) of clade A to March 2011 and that of clade B to November 2011. Our data support a polyphyletic origin of MERS-CoV in dromedaries and the co-circulation of diverse MERS-CoVs including recombinant strains in the UAE. PMID:27999424

Characterization of the Transmitted Virus in an Ongoing HIV-1 Epidemic Driven by Injecting Drug Use.

PubMed

Dukhovlinova, Elena; Masharsky, Alexey; Vasileva, Aleksandra; Porrello, Alessandro; Zhou, Shuntai; Toussova, Olga; Verevochkin, Sergei; Akulova, Ekaterina; Frishman, Dmitrij; Montefiori, David; Labranche, Celia; Hoffman, Irving; Miller, William; Cohen, Myron S; Kozlov, Andrei; Swanstrom, Ronald

2018-05-14

Understanding features of the HIV-1 transmission process have the potential to inform biological interventions for prevention. We have examined the transmitted virus in a cohort of people who inject drugs and who are at risk of HIV-1 infection through blood contamination when injecting in a group. This study focused on seven newly infected participants in St. Petersburg, Russia, who were in acute or early infection. We used end-point dilution PCR to amplify single viral genomes to assess the complexity of the transmitted virus. We also used deep sequencing to further assess the complexity of the virus. We interpret the results as indicating that a single viral variant was transmitted in each case, consistent with a model where the exposure to virus during transmission was limiting. We also looked at phenotypic properties of the viral Env protein in isolates from acute and chronic infection. Although differences were noted, there was no consistent pattern that distinguished the transmitted variants. Similarly, in spite of the reduced genetic heterogeneity of the more recent subtype A HIV-1 epidemic in St. Petersburg, we did not see reduced variance in the neutralization properties compared to isolates from the more mature subtype C HIV-1 epidemic. Finally, in looking at members of injecting groups related to the AHI/early subjects we found examples of sequence linkage consistent with ongoing and rapid spread of HIV-1 in these groups. These studies emphasize the dynamic nature of this epidemic and reinforce the idea that improved prevention methods are needed.

Complete genome sequence of Campylobacter jejuni strain 12567 a livestock-associated clade representative

USDA-ARS?s Scientific Manuscript database

We report the complete genome sequence of the Campylobacter jejuni strain 12567, a member of a C. jejuni livestock-associated clade that expresses glycoconjugates linked to improved gastrointestinal tract persistence....

Dobrogeria aegyssensis, a new early Spathian (Early Triassic) coelacanth from North Dobrogea (Romania)

NASA Astrophysics Data System (ADS)

Cavin, Lionel; Grădinaru, Eugen

2014-06-01

The Early Triassic witnessed the highest taxic diversity of coelacanths (or Actinistia), a clade with a single living genus today. This peak of diversity is accentuated here with the description of a new coelacanth discovered in the lower Spathian (Upper Olenekian, Lower Triassic) cropping out in the Tulcea Veche (Old Tulcea) promontory, in the city of Tulcea, in North Dobrogea, Romania. The bone remains were preserved in a block of limestone, which was chemically dissolved. The resulting 3D and matrix-free ossifications correspond mostly to elements of the skull and branchial apparatus. Posterior parietals, postparietal with associated prootic and basisphenoid allow a precise description of the neurocranium. Ossifications of the lower jaw, together with branchial and pectoral elements, complete the description of this coelacanth and support the coining of a new generic and specific name, Dobrogeria aegyssensis. A phylogenetic analysis of actinistians with the new species recovers clades which were found in most recent analyses, i.e. the Sasseniidae, the Laugiidae, the Coelacanthiformes, the Latimerioidei, the Mawsoniidae and the Latimeriidae, and identifies the new taxon as a non-latimerioid coelacanthiform.

Phytophthora borealis and Phytophthora riparia , new species in Phytophthora ITS Clade 6

Treesearch

Everrett Hansen; Paul Reeser; Wendy Sutton

2012-01-01

Phytopthora borealis and Phytophthora riparia were identified in recent Phytophthora surveys in forest streams in Oregon, California and Alaska are described as new species in Phytophthora ITS Clade 6. They are similar in growth form and morphology to P. gonapodyides...

The origin and early evolution of metatherian mammals: the Cretaceous record

PubMed Central

Williamson, Thomas E.; Brusatte, Stephen L.; Wilson, Gregory P.

2014-01-01

Abstract Metatherians, which comprise marsupials and their closest fossil relatives, were one of the most dominant clades of mammals during the Cretaceous and are the most diverse clade of living mammals after Placentalia. Our understanding of this group has increased greatly over the past 20 years, with the discovery of new specimens and the application of new analytical tools. Here we provide a review of the phylogenetic relationships of metatherians with respect to other mammals, discuss the taxonomic definition and diagnosis of Metatheria, outline the Cretaceous history of major metatherian clades, describe the paleobiology, biogeography, and macroevolution of Cretaceous metatherians, and provide a physical and climatic background of Cretaceous metatherian faunas. Metatherians are a clade of boreosphendian mammals that must have originated by the Late Jurassic, but the first unequivocal metatherian fossil is from the Early Cretaceous of Asia. Metatherians have the distinctive tightly interlocking occlusal molar pattern of tribosphenic mammals, but differ from Eutheria in their dental formula and tooth replacement pattern, which may be related to the metatherian reproductive process which includes an extended period of lactation followed by birth of extremely altricial young. Metatherians were widespread over Laurasia during the Cretaceous, with members present in Asia, Europe, and North America by the early Late Cretaceous. In particular, they were taxonomically and morphologically diverse and relatively abundant in the Late Cretaceous of western North America, where they have been used to examine patterns of biogeography, macroevolution, diversification, and extinction through the Late Cretaceous and across the Cretaceous-Paleogene (K-Pg) boundary. Metatherian diversification patterns suggest that they were not strongly affected by a Cretaceous Terrestrial Revolution, but they clearly underwent a severe extinction across the K-Pg boundary. PMID:25589872

Revisiting the phylogeny of Bombacoideae (Malvaceae): Novel relationships, morphologically cohesive clades, and a new tribal classification based on multilocus phylogenetic analyses.

PubMed

Carvalho-Sobrinho, Jefferson G; Alverson, William S; Alcantara, Suzana; Queiroz, Luciano P; Mota, Aline C; Baum, David A

2016-08-01

Bombacoideae (Malvaceae) is a clade of deciduous trees with a marked dominance in many forests, especially in the Neotropics. The historical lack of a well-resolved phylogenetic framework for Bombacoideae hinders studies in this ecologically important group. We reexamined phylogenetic relationships in this clade based on a matrix of 6465 nuclear (ETS, ITS) and plastid (matK, trnL-trnF, trnS-trnG) DNA characters. We used maximum parsimony, maximum likelihood, and Bayesian inference to infer relationships among 108 species (∼70% of the total number of known species). We analyzed the evolution of selected morphological traits: trunk or branch prickles, calyx shape, endocarp type, seed shape, and seed number per fruit, using ML reconstructions of their ancestral states to identify possible synapomorphies for major clades. Novel phylogenetic relationships emerged from our analyses, including three major lineages marked by fruit or seed traits: the winged-seed clade (Bernoullia, Gyranthera, and Huberodendron), the spongy endocarp clade (Adansonia, Aguiaria, Catostemma, Cavanillesia, and Scleronema), and the Kapok clade (Bombax, Ceiba, Eriotheca, Neobuchia, Pachira, Pseudobombax, Rhodognaphalon, and Spirotheca). The Kapok clade, the most diverse lineage of the subfamily, includes sister relationships (i) between Pseudobombax and "Pochota fendleri" a historically incertae sedis taxon, and (ii) between the Paleotropical genera Bombax and Rhodognaphalon, implying just two bombacoid dispersals to the Old World, the other one involving Adansonia. This new phylogenetic framework offers new insights and a promising avenue for further evolutionary studies. In view of this information, we present a new tribal classification of the subfamily, accompanied by an identification key. Copyright © 2016 Elsevier Inc. All rights reserved.

Comparative Ability of Oropsylla montana and Xenopsylla cheopis Fleas to Transmit Yersinia pestis by Two Different Mechanisms

PubMed Central

Bland, David M.; Bosio, Christopher F.; Jarrett, Clayton O.

2017-01-01

Background Transmission of Yersinia pestis by flea bite can occur by two mechanisms. After taking a blood meal from a bacteremic mammal, fleas have the potential to transmit the very next time they feed. This early-phase transmission resembles mechanical transmission in some respects, but the mechanism is unknown. Thereafter, transmission occurs after Yersinia pestis forms a biofilm in the proventricular valve in the flea foregut. The biofilm can impede and sometimes completely block the ingestion of blood, resulting in regurgitative transmission of bacteria into the bite site. In this study, we compared the relative efficiency of the two modes of transmission for Xenopsylla cheopis, a flea known to become completely blocked at a high rate, and Oropsylla montana, a flea that has been considered to rarely develop proventricular blockage. Methodology/Principal findings Fleas that took an infectious blood meal containing Y. pestis were maintained and monitored for four weeks for infection and proventricular blockage. The number of Y. pestis transmitted by groups of fleas by the two modes of transmission was also determined. O. montana readily developed complete proventricular blockage, and large numbers of Y. pestis were transmitted by that mechanism both by it and by X. cheopis, a flea known to block at a high rate. In contrast, few bacteria were transmitted in the early phase by either species. Conclusions A model system incorporating standardized experimental conditions and viability controls was developed to more reliably compare the infection, proventricular blockage and transmission dynamics of different flea vectors, and was used to resolve a long-standing uncertainty concerning the vector competence of O. montana. Both X. cheopis and O. montana are fully capable of transmitting Y. pestis by the proventricular biofilm-dependent mechanism. PMID:28081130

A dinosaur missing-link? Chilesaurus and the early evolution of ornithischian dinosaurs.

PubMed

Baron, Matthew G; Barrett, Paul M

2017-08-01

The enigmatic dinosaur taxon Chilesaurus diegosuarezi was originally described as a tetanuran theropod, but this species possesses a highly unusual combination of features that could provide evidence of alternative phylogenetic positions within the clade. In order to test the relationships of Chilesaurus , we added it to a new dataset of early dinosaurs and other dinosauromorphs. Our analyses recover Chilesaurus in a novel position, as the earliest diverging member of Ornithischia, rather than a tetanuran theropod. The basal position of Chilesaurus within the clade and its suite of anatomical characters suggest that it might represent a 'transitional' taxon, bridging the morphological gap between Theropoda and Ornithischia, thereby offering potential insights into the earliest stages of ornithischian evolution, which were previously obscure. For example, our results suggest that pubic retroversion occurred prior to some of the craniodental and postcranial modifications that previously diagnosed the clade (e.g. the presence of a predentary bone and ossified tendons). © 2017 The Author(s).

Qualitative Evaluation of Historical and Relational Factors Influencing Pregnancy and Sexually Transmitted Infection Risks in Foster Youth

PubMed Central

Ahrens, Kym R.; Spencer, Renee; Bonnar, Mavis; Coatney, Alexis; Hall, Tyson

2016-01-01

Purpose To explore how attitudes, norms, behaviors, responses to early life experiences, and protective factors influence pregnancy and sexually transmitted infection risks from the perspectives of current and former foster youth to inform the development of prevention strategies. Methods We conducted semi-structured individual qualitative interviews with a diverse sample of 22 current/former foster youth aged 15–21 years (63% female; average age = 18.6 years). We then used Theoretical Thematic Analysis to systematically analyze the data for key themes related to sexual health in four categories: 1) norms and attitudes, 2) responses to early life experiences, 3) protective factors, and 4) youth-driven intervention ideas. Results Participants reported a range of sexual experience levels, varied sexual orientations, and also reported varied life experiences prior to and during foster care. We detected several norms and attitudes that likely contribute to risks of early pregnancies and sexually transmitted infections. These included that one can tell by looking whether a partner is trustworthy or has a sexually transmitted infection, that condoms aren’t necessary with long-term or infrequent partners or if birth control is used, and that teen pregnancy is an inevitable event. With respect to responses to early life experiences, youth frequently described difficulties dealing with strong emotions in the context of romantic and/or sexual relationships; many attributed these difficulties to early experiences with biological family members or in foster care. Participants linked emotion regulation difficulties with struggles in trust appraisal, effective communication, and impulsive behaviors. Youth also described a variety of protective factors that they felt helped them prevent sexual risk behaviors or improved their lives in other respects. Finally, participants endorsed factors likely to improve intervention acceptability and efficacy, including an open, non

Repeated evolution of vertebrate pollination syndromes in a recently diverged Andean plant clade.

PubMed

Lagomarsino, Laura P; Forrestel, Elisabeth J; Muchhala, Nathan; Davis, Charles C

2017-08-01

Although specialized interactions, including those involving plants and their pollinators, are often invoked to explain high species diversity, they are rarely explored at macroevolutionary scales. We investigate the dynamic evolution of hummingbird and bat pollination syndromes in the centropogonid clade (Lobelioideae: Campanulaceae), an Andean-centered group of ∼550 angiosperm species. We demonstrate that flowers hypothesized to be adapted to different pollinators based on flower color fall into distinct regions of morphospace, and this is validated by morphology of species with known pollinators. This supports the existence of pollination syndromes in the centropogonids, an idea corroborated by ecological studies. We further demonstrate that hummingbird pollination is ancestral, and that bat pollination has evolved ∼13 times independently, with ∼11 reversals. This convergence is associated with correlated evolution of floral traits within selective regimes corresponding to pollination syndrome. Collectively, our results suggest that floral morphological diversity is extremely labile, likely resulting from selection imposed by pollinators. Finally, even though this clade's rapid diversification is partially attributed to their association with vertebrate pollinators, we detect no difference in diversification rates between hummingbird- and bat-pollinated lineages. Our study demonstrates the utility of pollination syndromes as a proxy for ecological relationships in macroevolutionary studies of certain species-rich clades. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Global cooling as a driver of diversification in a major marine clade

NASA Astrophysics Data System (ADS)

Davis, Katie E.; Hill, Jon; Astrop, Tim I.; Wills, Matthew A.

2016-10-01

Climate is a strong driver of global diversity and will become increasingly important as human influences drive temperature changes at unprecedented rates. Here we investigate diversification and speciation trends within a diverse group of aquatic crustaceans, the Anomura. We use a phylogenetic framework to demonstrate that speciation rate is correlated with global cooling across the entire tree, in contrast to previous studies. Additionally, we find that marine clades continue to show evidence of increased speciation rates with cooler global temperatures, while the single freshwater clade shows the opposite trend with speciation rates positively correlated to global warming. Our findings suggest that both global cooling and warming lead to diversification and that habitat plays a role in the responses of species to climate change. These results have important implications for our understanding of how extant biota respond to ongoing climate change and are of particular importance for conservation planning of marine ecosystems.

Enhanced virulence of clade 2.3.2.1 highly pathogenic avian influenza A(H5N1) viruses in ferrets

USDA-ARS?s Scientific Manuscript database

Sporadic avian to human transmission of highly pathogenic avian influenza (HPAI) A (H5N1) viruses necessitates the analysis of currently circulating and evolving clades to assess their potential risk. Following the spread and sustained circulation of clade 2 viruses across multiple continents, num...

Evolution, global spread, and pathogenicity of highly pathogenic avian influenza H5Nx clade 2.3.4.4

PubMed Central

Lee, Dong-Hun; Bertran, Kateri; Kwon, Jung-Hoon

2017-01-01

Novel subtypes of Asian-origin (Goose/Guangdong lineage) H5 highly pathogenic avian influenza (HPAI) viruses belonging to clade 2.3.4, such as H5N2, H5N5, H5N6, and H5N8, have been identified in China since 2008 and have since evolved into four genetically distinct clade 2.3.4.4 groups (A–D). Since 2014, HPAI clade 2.3.4.4 viruses have spread rapidly via migratory wild aquatic birds and have evolved through reassortment with prevailing local low pathogenicity avian influenza viruses. Group A H5N8 viruses and its reassortant viruses caused outbreaks in wide geographic regions (Asia, Europe, and North America) during 2014–2015. Novel reassortant Group B H5N8 viruses caused outbreaks in Asia, Europe, and Africa during 2016–2017. Novel reassortant Group C H5N6 viruses caused outbreaks in Korea and Japan during the 2016–2017 winter season. Group D H5N6 viruses caused outbreaks in China and Vietnam. A wide range of avian species, including wild and domestic waterfowl, domestic poultry, and even zoo birds, seem to be permissive for infection by and/or transmission of clade 2.3.4.4 HPAI viruses. Further, compared to previous H5N1 HPAI viruses, these reassortant viruses show altered pathogenicity in birds. In this review, we discuss the evolution, global spread, and pathogenicity of H5 clade 2.3.4.4 HPAI viruses. PMID:28859267

Crimean-Congo Hemorrhagic Fever Virus Clade IV (Asia 1) in Ticks of Western Iran.

PubMed

Kayedi, Mohammad Hassan; Chinikar, Sadegh; Mostafavi, Ehsan; Khakifirouz, Sahar; Jalali, Tahmineh; Hosseini-Chegeni, Asadolah; Naghizadeh, Ali; Niedrig, Matthias; Fooks, Anthony R; Shahhosseini, Nariman

2015-09-01

Crimean-Congo Hemorrhagic Fever virus (CCHFV) is transmitted through the bite of an infected tick, or by direct contact with CCHFV-infected patients' blood or the products of infected livestock. In 2012, ticks were collected in eight regions of Lorestan Province, Iran. In total, 434 ticks were collected. Reverse transcriptase polymerase chain reaction was used for the detection of CCHFV RNA. Of 434 ticks, 419 (96.6%) ticks were from the family Ixodidae (hard ticks) and 15 (3.5%) ticks were from the family Argasidae (soft ticks). The presence of CCHFV RNA was detected in 29 (6.7%) of 434 ticks. The infected tick species include Hyalomma asiaticum (n = 7, 7.4%), Hyalomma anatolicum (n = 12, 13.2%), Hyalomma marginatum (n = 1, 16.7%), and Rhipicephalus sanguineus (n = 9, 4.3%). These empirical data demonstrated that the majority of CCHFV-positive ticks belonged to the Ixodidae. None of the Argasidae and Haemaphysalis sulcata species was infected with CCHFV. The phylogenetic analyses of the tick-derived CCHFV strains revealed that all 29 viral strains fell in clade IV (Asia 1). The most abundant species of tick collected in this study was R. sanguineus followed by different species of Hyalomma. Given the infection rate among collected ticks, H. marginatum was the most abundant infected tick species (16.7%) followed by H. anatolicum (13.2%), H. asiaticum (7.4%), and R. sanguineus (4.3%). © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Evolution, global spread, and pathogenicity of highly pathogenic avian influenza H5Nx clade 2.3.4.4

USDA-ARS?s Scientific Manuscript database

Novel subtypes of Eurasian-origin (Goose/Guangdong lineage) H5 highly pathogenic avian influenza (HPAI) viruses belonging to clade 2.3.4 such as H5N2, H5N5, H5N6, and H5N8 have been identified in China since 2008 and subsequently evolved into four genetically distinct groups (A – D) of clade 2.3.4.4...

A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers

PubMed Central

Gladyshev, Eugene A.; Meselson, Matthew; Arkhipova, Irina R.

2007-01-01

Rotifers of class Bdelloidea, a group of aquatic invertebrates in which males and meiosis have never been documented, are also unusual in their lack of multicopy LINE-like and gypsy-like retrotransposons, groups inhabiting the genomes of nearly all other metazoans. Bdelloids do contain numerous DNA transposons, both intact and decayed, and domesticated Penelope-like retroelements Athena, concentrated at telomeric regions. Here we describe two LTR retrotransposons, each found at low copy number in a different bdelloid species, which define a clade different from previously known clades of LTR retrotransposons. Like bdelloid DNA transposons and Athena, these elements have been found preferentially in telomeric regions. Unlike bdelloid DNA transposons, many of which are decayed, the newly described elements, named Vesta and Juno, inhabiting the genomes of Philodina roseola and Adineta vaga, respectively, appear to be intact and to represent recent insertions, possibly from an exogenous source. We describe the retrovirus-like structure of the new elements, containing gag, pol, and env-like open reading frames, and discuss their possible origins, transmission, and behavior in bdelloid genomes. PMID:17129685

Sexually Transmitted Infections, Pregnancy, and Breastfeeding

MedlinePlus

... email updates Submit Sexually transmitted infections, pregnancy, and breastfeeding Sexually transmitted infections (STIs) are also called sexually ... away. Are STI treatments safe to use while breastfeeding? If you are being treated for an STI, ...

A New Clade of African Body and Head Lice Infected by Bartonella quintana and Yersinia pestis-Democratic Republic of the Congo.

PubMed

Drali, Rezak; Shako, Jean-Christophe; Davoust, Bernard; Diatta, Georges; Raoult, Didier

2015-11-01

The human body louse is known as a vector for the transmission of three serious diseases-specifically, epidemic typhus, trench fever, and relapsing fever caused by Rickettsia prowazekii, Bartonella quintana, and Borrelia recurrentis, respectively-that have killed millions of people. It is also suspected in the transmission of a fourth pathogen, Yersinia pestis, which is the etiologic agent of plague. To date, human lice belonging to the genus Pediculus have been classified into three mitochondrial clades: A, B, and C. Here, we describe a fourth mitochondrial clade, Clade D, comprising head and body lice. Clade D may be a vector of B. quintana and Y. pestis, which is prevalent in a highly plague-endemic area near the Rethy Health District, Orientale Province, Democratic Republic of the Congo. © The American Society of Tropical Medicine and Hygiene.

Taxonomy of the ant genus Proceratium Roger (Hymenoptera, Formicidae) in the Afrotropical region with a revision of the P.arnoldi clade and description of four new species.

PubMed

Hita Garcia, Francisco; Hawkes, Peter G; Alpert, Gary D

2014-01-01

The taxonomy of the genus Proceratium Roger is updated for the Afrotropical region. We give an overview of the genus in the region, provide an illustrated identification key to the three clades (Proceratiumarnoldi, Proceratiumstictum and Proceratiumtoschii clades) and revise the Proceratiumarnoldi clade. Four new species from the Proceratiumarnoldi clade are described as new: Proceratiumsokoke sp. n. from Kenya, Proceratiumcarri sp. n. from Mozambique, and Proceratiumnilo sp. n. and Proceratiumsali sp. n. from Tanzania. In order to integrate the new species into the existing taxonomic system we present an illustrated identification key to distinguish the seven Afrotropical species of the Proceratiumarnoldi clade. In addition, we provide accounts for all members of the Proceratiumarnoldi clade including detailed descriptions, diagnoses, taxonomic discussions, distribution data and high quality montage images.

A 12-year molecular survey of clinical herpes simplex virus type 2 isolates demonstrates the circulation of clade A and B strains in Germany.

PubMed

Schmidt-Chanasit, Jonas; Bialonski, Alexandra; Heinemann, Patrick; Ulrich, Rainer G; Günther, Stephan; Rabenau, Holger F; Doerr, Hans Wilhelm

2010-07-01

Recently two different herpes simplex virus type 2 (HSV-2) clades (A and B) were described on DNA sequence data of the glycoprotein E (gE), G (gG) and I (gI) genes. To type the circulating HSV-2 wild-type strains in Germany by a novel approach and to monitor potential changes in the molecular epidemiology between 1997 and 2008. A total of 64 clinical HSV-2 isolates were analyzed by a novel approach using the DNA sequences of the complete open reading frames of glycoprotein B (gB) and gG. Recombination analysis of the gB and gG gene sequences was performed to reveal intragenic recombinants. Based on the phylogenetic analysis of the gB coding DNA sequence 8 of 64 (12%) isolates were classified as clade A strains and 56 of 64 (88%) isolates were classified as clade B strains. Analysis of the gG coding DNA sequence classified 4 (6%) isolates as clade A strains and 60 (94%) isolates as clade B strains. In comparison, the 8 isolates classified as clade A strains using the gB sequence data were classified as clade B strains when using the gG coding DNA sequence, suggesting intergenic recombination events. Intragenic recombination events were not detected. The first molecular survey of clinical HSV-2 isolates from Germany demonstrated the circulation of clade A and B strains and of intergenic recombinants over a period of 12 years. Copyright (c) 2010 Elsevier B.V. All rights reserved.

47 CFR 95.135 - Maximum authorized transmitting power.

Code of Federal Regulations, 2010 CFR

2010-10-01

... transmitting power. (a) No station may transmit with more than 50 watts output power. (b) [Reserved] (c) A small control station at a point north of Line A or east of Line C must transmit with no more than 5 watts ERP. (d) A fixed station must transmit with no more than 15 watts output power. (e) A small base...

Two distinct phylogenetic clades of infectious hematopoietic necrosis virus overlap within the Columbia River basin

USGS Publications Warehouse

Garver, K.A.; Troyer, R.M.; Kurath, G.

2003-01-01

Infectious hematopoietic necrosis virus (IHNV), an aquatic rhabdovirus, causes a highly lethal disease of salmonid fish in North America. To evaluate the genetic diversity of IHNV from throughout the Columbia River basin, excluding the Hagerman Valley, Idaho, the sequences of a 303 nt region of the glycoprotein gene (mid-G) of 120 virus isolates were determined. Sequence comparisons revealed 30 different sequence types, with a maximum nucleotide diversity of 7.3% (22 mismatches) and an intrapopulational nucleotide diversity of 0.018. This indicates that the genetic diversity of IHNV within the Columbia River basin is 3-fold higher than in Alaska, but 2-fold lower than in the Hagerman Valley, Idaho. Phylogenetic analyses separated the Columbia River basin IHNV isolates into 2 major clades, designated U and M. The 2 clades geographically overlapped within the lower Columbia River basin and in the lower Snake River and tributaries, while the upper Columbia River basin had only U clade and the upper Snake River basin had only M clade virus types. These results suggest that there are co-circulating lineages of IHNV present within specific areas of the Columbia River basin. The epidemiological significance of these findings provided insight into viral traffic patterns exhibited by IHNV in the Columbia River basin, with specific relevance to how the Columbia River basin IHNV types were related to those in the Hagerman Valley. These analyses indicate that there have likely been 2 historical events in which Hagerman Valley IHNV types were introduced and became established in the lower Columbia River basin. However, the data also clearly indicates that the Hagerman Valley is not a continuous source of waterborne virus infecting salmonid stocks downstream.

Global cooling as a driver of diversification in a major marine clade

PubMed Central

Davis, Katie E.; Hill, Jon; Astrop, Tim I.; Wills, Matthew A.

2016-01-01

Climate is a strong driver of global diversity and will become increasingly important as human influences drive temperature changes at unprecedented rates. Here we investigate diversification and speciation trends within a diverse group of aquatic crustaceans, the Anomura. We use a phylogenetic framework to demonstrate that speciation rate is correlated with global cooling across the entire tree, in contrast to previous studies. Additionally, we find that marine clades continue to show evidence of increased speciation rates with cooler global temperatures, while the single freshwater clade shows the opposite trend with speciation rates positively correlated to global warming. Our findings suggest that both global cooling and warming lead to diversification and that habitat plays a role in the responses of species to climate change. These results have important implications for our understanding of how extant biota respond to ongoing climate change and are of particular importance for conservation planning of marine ecosystems. PMID:27701377

New clades of euthyneuran gastropods (Mollusca) from 28S rRNA sequences.

PubMed

Dayrat, B; Tillier, A; Lecointre, G; Tillier, S

2001-05-01

Recent morphological and molecular results on phylogeny of euthyneuran gastropods, which include opisthobranchs and pulmonates, have greatly diminished previous supposed resolution of their phylogenetic relationships. In addition to recent morphological results, sequences of the D1 and D2 domains of the 28S rRNA are here analyzed by parsimony for 31 euthyneuran species. The molecular and previous morphological data sets were not congruent according to an ILD test, and morphological and molecular data could not be analyzed simultaneously. Consequently Bremer's Combinable Component Consensus was used to obtain a new tree, with the following supported molecular results: monophyly of a new clade of opisthobranchs including actively swimming Euthyneura, i.e., pelagic Gymnosomata and Thecosomata plus benthic Anaspidea; first molecular confirmation of monophylies of Hygrophila, including Chilina, Acteonoidea, and Sacoglossa, which include both shell-bearing species and slugs; and new confirmation of the monophyly of Stylommatophora. Morphological characters which support the new clades obtained here are discussed. Copyright 2001 Academic Press.

Differential Th17 response induced by the two clades of the pandemic ST258 Klebsiella pneumoniae clonal lineages producing KPC-type carbapenemase

PubMed Central

Clemente, Ann Maria; Castronovo, Giuseppe; Antonelli, Alberto; D’Andrea, Marco Maria; Tanturli, Michele; Perissi, Eloisa; Paccosi, Sara; Parenti, Astrid; Cozzolino, Federico; Rossolini, Gian Maria

2017-01-01

The spread of KPC-type carbapenemases is mainly attributed to the global dissemination of Klebsiella pneumoniae (KP) strains belonging to the clonal group (CG) 258, including sequence type (ST) 258 and other related STs. Two distinct clades of CG258-KP have evolved, which differ mainly for the composition of their capsular polysaccharides, and recent studies indicate that clade 1 evolved from an ancestor of clade 2 by recombination of a genomic fragment carrying the capsular polysaccharide (cps) locus. In this paper, we investigated the ability of two ST258-KP strains, KKBO-1 and KK207-1, selected as representatives of ST258-KP clade 2 and clade 1, respectively, to activate an adaptive immune response using ex vivo-stimulation of PBMC from normal donors as an experimental model. Our data showed that KKBO-1 (clade 2) induces a Th17 response more efficiently than KK207-1 (clade 1): the percentage of CD4+IL17+ cells and the production of IL-17A were significantly higher in cultures with KKBO-1 compared to cultures with KK207-1. While no differences in the rate of bacterial internalization or in the bacteria-induced expression of CD86 and HLA-DR by monocytes and myeloid dendritic cells were revealed, we found that the two strains significantly differ in inducing the production of cytokines involved in the adaptive immune response, as IL-1β, IL-23 and TNF-α, by antigen-presenting cells, with KKBO-1 being a more efficient inducer than KK207-1. The immune responses elicited by KK207-1 were comparable to those elicited by CIP 52.145, a highly virulent K. pneumoniae reference strain known to escape immune-inflammatory responses. Altogether, present results suggest that CG258-KP of the two clades are capable of inducing a different response of adaptive immunity in the human host. PMID:28586386

A revision of the Dulcamaroid Clade of  Solanum L. (Solanaceae)

PubMed Central

Knapp, Sandra

2013-01-01

Abstract The Dulcamaroid clade of Solanum contains 45 species of mostly vining or weakly scandent species, including the common circumboreal weed Solanum dulcamara L. The group comprises members of the previously recognised infrageneric groupings sect. Andropedas Rusby, sect. Californisolanum A. Child, sect. Dulcamara (Moench) Dumort., sect. Holophylla (G.Don) Walp., sect. Jasminosolanum (Bitter) Seithe, sect.Lysiphellos (Bitter) Seithe, subsect. Nitidum A.Child and sect. Subdulcamara Dunal. These infrageneric groups are not monophyletic as traditionally recognised, and the complex history of the classification of the dulcamaroid solanums is reviewed. Many of the species in the clade are quite variable morphologically; plants are shrubs, herbaceous vines or woody canopy lianas, and habits can vary between these states in a single locality. Variation in leaf shape and pubescence density and type is also extreme and has lead to the description of many minor morphological variants as distinct species. The flowers of members of the group are generally very showy, and several species (e.g., Solanum crispum Ruiz & Pav., Solanum laxum Spreng., Solanum seaforthianum Andrews) are popular ornamental plants that have occasionally escaped from cultivation and become naturalised. The clade is here divided into five morphologically and geographically delimited species groups to facilitate further study. One new species from southern Ecuador, Solanum agnoston S.Knapp sp. nov., is described here. Full descriptions and synonymies (including designations of lectotypes or neotypes), preliminary conservation assessments, illustrations, distribution maps, and an extensive list of localities are provided for all species. PMID:23794937

An outbreak of enterically transmitted non-A, non-B hepatitis in Pakistan.

PubMed

Iqbal, M; Ahmed, A; Qamar, A; Dixon, K; Duncan, J F; Islam, N U; Rauf, A; Bryan, J P; Malik, I A; Legters, L J

1989-04-01

An epidemic of enterically transmitted non-A, non-B hepatitis occurred at a college in Sargodha, Pakistan in early 1987. There were 133 clinical cases, an attack rate of approximately 20%. Though the disease was relatively mild, all clinical cases required hospitalization and prolonged convalescence. Nearly all cases were associated with a single water source. The epidemic ended when the water supply was improved. This is the 4th described epidemic of non-A, non-B hepatitis in Pakistan.

Sexually transmitted diseases in Poland in 2011.

PubMed

Majewski, Sławomir; Rudnicka, Iwona

2013-01-01

Was to assess epidemiological situation of sexually transmitted diseases in Poland in 2011. Analysis of the data on prevalence of syphilis, gonorrhoea, non-gonococcal urethritis, genital herpes and genital warts was gathered from yearly reports MZ-14 from several didtricts. In 2011 there were 841 reported cases of all types of syphilis, which was higher by 24 than in 2010. Within the reported cases, 554 cases were of early syphilis, 274 cases of late syphilis, and 11 cases of congenital syphilis. Syphilis during pregnancy and childbirth was reported in 13 women. The highest incidence of syphilis in 2011, similarly to previous years was in Mazowieckie district (4.7/100,000) and the lowest in Swietokrzyskie district (0.2/100,000), the average in a whole country accounted to 2.2/100,000. In 2011 there were 351 cases of gonorrhoea reported, which was higher by 77 cases than reported in the previous year. The highest incidence was reported in Mazowieckie voivodeship. Non-gonococcal urethritis -NGU was identified in 484 persons; this was less by 294 cases than reported in the previous year. The highest incidence rate was reported in Dolnoślaskie voivodeship 9.6/100,000. There were 428 cases of genital warts reported which was less by 174 cases than reported in 2010. The highest incidence rate was reported in Mazowieckie voivodeship, Warminsko- Mazurskie voivodeship and Kujawsko-Pomorskie voivodeship. As in previous years the most unfavourable epidemiological situation in terms of all registered sexually transmitted diseases was in Mazowieckie voivodeship. In 2011 among sexually transmitted diseases NGU and genital warts were reported in lower numbers then in previous year. In the same time numbers of reported cases of gonorrhoea and syphilis increased. There is a continued decrease in the number of serological tests done for syphilis. Epidemiological indicators of treatment for gonorrhoea and syphilis are very low for number of years. The epidemiological data is

Balance between transmitted HLA preadapted and nonassociated polymorphisms is a major determinant of HIV-1 disease progression.

PubMed

Mónaco, Daniela C; Dilernia, Dario A; Fiore-Gartland, Andrew; Yu, Tianwei; Prince, Jessica L; Dennis, Kristine K; Qin, Kai; Schaefer, Malinda; Claiborne, Daniel T; Kilembe, William; Tang, Jianming; Price, Matt A; Farmer, Paul; Gilmour, Jill; Bansal, Anju; Allen, Susan; Goepfert, Paul; Hunter, Eric

2016-09-19

HIV-1 adapts to a new host through mutations that facilitate immune escape. Here, we evaluate the impact on viral control and disease progression of transmitted polymorphisms that were either preadapted to or nonassociated with the new host's HLA. In a cohort of 169 Zambian heterosexual transmission pairs, we found that almost one-third of possible HLA-linked target sites in the transmitted virus Gag protein are already adapted, and that this transmitted preadaptation significantly reduced early immune recognition of epitopes. Transmitted preadapted and nonassociated polymorphisms showed opposing effects on set-point VL and the balance between the two was significantly associated with higher set-point VLs in a multivariable model including other risk factors. Transmitted preadaptation was also significantly associated with faster CD4 decline (<350 cells/µl) and this association was stronger after accounting for nonassociated polymorphisms, which were linked with slower CD4 decline. Overall, the relative ratio of the two classes of polymorphisms was found to be the major determinant of CD4 decline in a multivariable model including other risk factors. This study reveals that, even before an immune response is mounted in the new host, the balance of these opposing factors can significantly influence the outcome of HIV-1 infection. © 2016 Mónaco et al.

Neuroimaging abnormalities in clade C HIV are independent of Tat genetic diversity.

PubMed

Paul, Robert H; Phillips, Sarah; Hoare, Jacqueline; Laidlaw, David H; Cabeen, Ryan; Olbricht, Gayla R; Su, Yuqing; Stein, Dan J; Engelbrecht, Susan; Seedat, Soraya; Salminen, Lauren E; Baker, Laurie M; Heaps, Jodi; Joska, John

2017-04-01

Controversy remains regarding the neurotoxicity of clade C human immunodeficiency virus (HIV-C). When examined in preclinical studies, a cysteine to serine substitution in the C31 dicysteine motif of the HIV-C Tat protein (C31S) results in less severe brain injury compared to other viral clades. By contrast, patient cohort studies identify significant neuropsychological impairment among HIV-C individuals independent of Tat variability. The present study clarified this discrepancy by examining neuroimaging markers of brain integrity among HIV-C individuals with and without the Tat substitution. Thirty-seven HIV-C individuals with the Tat C31S substitution, 109 HIV-C individuals without the Tat substitution (C31C), and 34 HIV- controls underwent 3T structural magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI). Volumes were determined for the caudate, putamen, thalamus, corpus callosum, total gray matter, and total white matter. DTI metrics included fractional anisotropy (FA), radial diffusivity (RD), and axial diffusivity (AD). Tracts of interest included the anterior thalamic radiation (ATR), cingulum bundle (CING), uncinate fasciculus (UNC), and corpus callosum (CC). HIV+ individuals exhibited smaller volumes in subcortical gray matter, total gray matter and total white matter compared to HIV- controls. HIV+ individuals also exhibited DTI abnormalities across multiple tracts compared to HIV- controls. By contrast, neither volumetric nor diffusion indices differed significantly between the Tat C31S and C31C groups. Tat C31S status is not a sufficient biomarker of HIV-related brain integrity in patient populations. Clinical attention directed at brain health is warranted for all HIV+ individuals, independent of Tat C31S or clade C status.

Taxonomy of the ant genus Proceratium Roger (Hymenoptera, Formicidae) in the Afrotropical region with a revision of the P. arnoldi clade and description of four new species

PubMed Central

Hita Garcia, Francisco; Hawkes, Peter G.; Alpert, Gary D.

2014-01-01

Abstract The taxonomy of the genus Proceratium Roger is updated for the Afrotropical region. We give an overview of the genus in the region, provide an illustrated identification key to the three clades (Proceratium arnoldi, Proceratium stictum and Proceratium toschii clades) and revise the Proceratium arnoldi clade. Four new species from the Proceratium arnoldi clade are described as new: Proceratium sokoke sp. n. from Kenya, Proceratium carri sp. n. from Mozambique, and Proceratium nilo sp. n. and Proceratium sali sp. n. from Tanzania. In order to integrate the new species into the existing taxonomic system we present an illustrated identification key to distinguish the seven Afrotropical species of the Proceratium arnoldi clade. In addition, we provide accounts for all members of the Proceratium arnoldi clade including detailed descriptions, diagnoses, taxonomic discussions, distribution data and high quality montage images. PMID:25349516

Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family.

PubMed

Alnajar, Seema; Gupta, Radhey S

2017-10-01

The family Enterobacteriaceae harbors many important pathogens, however it has proven difficult to reliably distinguish different members of this family or discern their interrelationships. To understand the interrelationships among the Enterobacteriaceae species, we have constructed two comprehensive phylogenetic trees for 78 genome-sequenced Enterobacteriaceae species based on 2487 core genome proteins, and another set of 118 conserved proteins. The genome sequences of Enterobacteriaceae species were also analyzed for genetic relatedness based on average amino acid identity and 16S rRNA sequence similarity. In parallel, comparative genomic studies on protein sequences from the Enterobacteriaceae have identified 88 molecular markers in the form of conserved signature indels (CSIs) that are uniquely shared by specific members of the family. All of these multiple lines of investigations provide consistent evidence that most of the species/genera within the family can be assigned to 6 different subfamily level clades which are designated as the "Escherichia clade", "Klebsiella clade", "Enterobacter clade", "Kosakonia clade", "Cronobacter clade" and "Cedecea clade". The members of the six described clades, in addition to their distinct branching in phylogenetic trees, can now be reliably demarcated in molecular terms on the basis of multiple identified CSIs that are exclusively shared by the group members. Several additional CSIs identified in this work that are either specific for individual genera (viz. Kosakonia, Kluyvera and Escherichia-Shigella), or are present at various taxonomic depths, offer information regarding the interrelationships among the different clades. The described molecular markers provide novel means for diagnostic as well as genetic and biochemical studies on the Enterobacteriaceae species and for resolving the polyphyly of its several genera viz. Escherichia, Enterobacter and Kluyvera. On the bases of our results, we are proposing the

Phylogeography of ostreopsis along west Pacific coast, with special reference to a novel clade from Japan.

PubMed

Sato, Shinya; Nishimura, Tomohiro; Uehara, Keita; Sakanari, Hiroshi; Tawong, Wittaya; Hariganeya, Naohito; Smith, Kirsty; Rhodes, Lesley; Yasumoto, Takeshi; Taira, Yosuke; Suda, Shoichiro; Yamaguchi, Haruo; Adachi, Masao

2011-01-01

A dinoflagellate genus Ostreopsis is known as a potential producer of Palytoxin derivatives. Palytoxin is the most potent non-proteinaceous compound reported so far. There has been a growing number of reports on palytoxin-like poisonings in southern areas of Japan; however, the distribution of Ostreopsis has not been investigated so far. Morphological plasticity of Ostreopsis makes reliable microscopic identification difficult so the employment of molecular tools was desirable. In total 223 clones were examined from samples mainly collected from southern areas of Japan. The D8-D10 region of the nuclear large subunit rDNA (D8-D10) was selected as a genetic marker and phylogenetic analyses were conducted. Although most of the clones were unable to be identified, there potentially 8 putative species established during this study. Among them, Ostreopsis sp. 1-5 did not belong to any known clade, and each of them formed its own clade. The dominant species was Ostreopsis sp. 1, which accounted for more than half of the clones and which was highly toxic and only distributed along the Japanese coast. Comparisons between the D8-D10 and the Internal Transcribed Spacer (ITS) region of the nuclear rDNA, which has widely been used for phylogenetic/phylogeographic studies in Ostreopsis, revealed that the D8-D10 was less variable than the ITS, making consistent and reliable phylogenetic reconstruction possible. This study unveiled a surprisingly diverse and widespread distribution of Japanese Ostreopsis. Further study will be required to better understand the phylogeography of the genus. Our results posed the urgent need for the development of the early detection/warning systems for Ostreopsis, particularly for the widely distributed and strongly toxic Ostreopsis sp. 1. The D8-D10 marker will be suitable for these purposes.

Detection and Characterization of Clade 1 Reassortant H5N1 Viruses Isolated from Human Cases in Vietnam during 2013

PubMed Central

Balish, Amanda; Hoang, Anh Nguyen; Gustin, Kortney M.; Nhung, Pham Thi; Jones, Joyce; Thu, Ngoc Nguyen; Davis, William; Ngoc, Thao Nguyen Thi; Jang, Yunho; Sleeman, Katrina; Villanueva, Julie; Kile, James; Gubareva, Larisa V.; Lindstrom, Stephen; Tumpey, Terrence M.; Davis, C. Todd; Long, Nguyen Thanh

2015-01-01

Highly pathogenic avian influenza (HPAI) H5N1 is endemic in Vietnamese poultry and has caused sporadic human infection in Vietnam since 2003. Human infections with HPAI H5N1 are of concern due to a high mortality rate and the potential for the emergence of pandemic viruses with sustained human-to-human transmission. Viruses isolated from humans in southern Vietnam have been classified as clade 1 with a single genome constellation (VN3) since their earliest detection in 2003. This is consistent with detection of this clade/genotype in poultry viruses endemic to the Mekong River Delta and surrounding regions. Comparison of H5N1 viruses detected in humans from southern Vietnamese provinces during 2012 and 2013 revealed the emergence of a 2013 reassortant virus with clade 1.1.2 hemagglutinin (HA) and neuraminidase (NA) surface protein genes but internal genes derived from clade 2.3.2.1a viruses (A/Hubei/1/2010-like; VN12). Closer analysis revealed mutations in multiple genes of this novel genotype (referred to as VN49) previously associated with increased virulence in animal models and other markers of adaptation to mammalian hosts. Despite the changes identified between the 2012 and 2013 genotypes analyzed, their virulence in a ferret model was similar. Antigenically, the 2013 viruses were less cross-reactive with ferret antiserum produced to the clade 1 progenitor virus, A/Vietnam/1203/2004, but reacted with antiserum produced against a new clade 1.1.2 WHO candidate vaccine virus (A/Cambodia/W0526301/2012) with comparable hemagglutination inhibition titers as the homologous antigen. Together, these results indicate changes to both surface and internal protein genes of H5N1 viruses circulating in southern Vietnam compared to 2012 and earlier viruses. PMID:26244768

Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae.

PubMed

Straub, Shannon C K; Moore, Michael J; Soltis, Pamela S; Soltis, Douglas E; Liston, Aaron; Livshultz, Tatyana

2014-11-01

Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way polytomy, leaving ambiguous the homology of aggregated pollen in two major lineages, the Periplocoideae, which possess pollen tetrads, and the milkweeds (Secamonoideae plus Asclepiadoideae), which possess pollinia. To assess whether greatly increased character sampling would resolve these relationships, a plastome sequence data matrix was assembled for 13 taxa of Apocynaceae, including nine newly generated complete plastomes, one partial new plastome, and three previously reported plastomes, collectively representing all primary crown clade lineages and outgroups. The effects of phylogenetic noise, long-branch attraction, and model selection (linked versus unlinked branch lengths among data partitions) were evaluated in a hypothesis-testing framework based on Shimodaira-Hasegawa tests. Discrimination among alternative crown clade resolutions was affected by all three factors. Exclusion of the noisiest alignment positions and topologies influenced by long-branch attraction resulted in a trichotomy along the spine of the crown clade consisting of Rhabdadenia+the Asian clade, Baisseeae+milkweeds, and Periplocoideae+the New World clade. Parsimony reconstruction on all optimal topologies after noise exclusion unambiguously supports parallel evolution of aggregated pollen in Periplocoideae (tetrads) and milkweeds (pollinia). Our phylogenomic approach has greatly advanced the resolution of one of the most perplexing radiations in Apocynaceae, providing the

Phylogeny of Elatinaceae and the Tropical Gondwanan Origin of the Centroplacaceae(Malpighiaceae, Elatinaceae) Clade

PubMed Central

Xi, Zhenxiang; Peterson, Kylee; Rushworth, Catherine; Beaulieu, Jeremy; Davis, Charles C.

2016-01-01

The flowering plant family Elatinaceae is a widespread aquatic lineage inhabiting temperate and tropical latitudes, including ∼35(-50) species. Its phylogeny remains largely unknown, compromising our understanding of its systematics. Moreover, this group is particularly in need of attention because the biogeography of most aquatic plant clades has yet to be investigated, resulting in uncertainty about whether aquatic plants show histories that deviate from terrestrial plants. We inferred the phylogeny of Elatinaceae from four DNA regions spanning 59 accessions across the family. An expanded sampling was used for molecular divergence time estimation and ancestral area reconstruction to infer the biogeography of Elatinaceae and their closest terrestrial relatives, Malpighiaceae and Centroplacaceae. The two genera of Elatinaceae, Bergia and Elatine, are monophyletic, but several traditionally recognized groups within the family are non-monophyletic. Our results suggest two ancient biogeographic events in the Centroplacaceae(Malpighiaceae, Elatinaceae) clade involving western Gondwana, while Elatinaceae shows a more complicated biogeographic history with a high degree of continental endemicity. Our results indicate the need for further taxonomic investigation of Elatinaceae. Further, our study is one of few to implicate ancient Gondwanan biogeography in extant angiosperms, especially significant given the Centroplacaceae(Malpighiaceae, Elatinaceae) clade's largely tropical distribution. Finally, Elatinaceae demonstrates long-term continental in situ diversification, which argues against recent dispersal as a universal explanation commonly invoked for aquatic plant distributions. PMID:27684711

Sexually transmitted diseases in Indonesia.

PubMed

Harahap, M

1980-10-01

Epidemiological factors and changing ecological conditions have greatly facilitated the spread of sexually transmitted diseases and led to their rising incidence in Indonesia. Gonorrhoea is at present very prevalent, and drug resistance among circulating strains of gonococci is a contributing factor. Despite medical advances in both diagnosis and treatment of sexually transmitted diseases, these are becoming commoner; unlike other communicable diseases they have so far defied efforts to control them.

Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

PubMed Central

Gao, Beile

2012-01-01

Summary: The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria. PMID:22390973

Experimental infection of H5N1 and H5N8 highly pathogenic avian influenza viruses in Northern Pintail (Anas acuta).

PubMed

Kwon, J-H; Lee, D-H; Swayne, D E; Noh, J-Y; Yuk, S-S; Jeong, S; Lee, S-H; Woo, C; Shin, J-H; Song, C-S

2018-05-04

The wide geographic spread of Eurasian Goose/Guangdong lineage highly pathogenic avian influenza (HPAI) clade 2.3.4.4 viruses by wild birds is of great concern. In December 2014, an H5N8 HPAI clade 2.3.4.4 Group A (2.3.4.4A) virus was introduced to North America. Long-distance migratory wild aquatic birds between East Asia and North America, such as Northern Pintail (Anas acuta), were strongly suspected of being a source of intercontinental transmission. In this study, we evaluated the pathogenicity, infectivity and transmissibility of an H5N8 HPAI clade 2.3.4.4A virus in Northern Pintails and compared the results to that of an H5N1 HPAI clade 2.3.2.1 virus. All of Northern Pintails infected with either H5N1 or H5N8 virus lacked clinical signs and mortality, but the H5N8 clade 2.3.4.4 virus was more efficient at replicating within and transmitting between Northern Pintails than the H5N1 clade 2.3.2.1 virus. The H5N8-infected birds shed high titre of viruses from oropharynx and cloaca, which in the field supported virus transmission and spread. This study highlights the role of wild waterfowl in the intercontinental spread of some HPAI viruses. Migratory aquatic birds should be carefully monitored for the early detection of H5 clade 2.3.4.4 and other HPAI viruses. © 2018 Blackwell Verlag GmbH.

Sexually Transmitted Diseases

MedlinePlus

Sexually transmitted diseases (STDs) are infections that are passed from one person to another through sexual contact. The causes of STDs ... often help with the symptoms and keep the disease under control. Correct usage of latex condoms greatly ...

Macroevolutionary dynamics in the early diversification of Asteraceae.

PubMed

Panero, Jose L; Crozier, Bonnie S

2016-06-01

Spatial and temporal differences in ecological opportunity can result in disparity of net species diversification rates and consequently uneven distribution of taxon richness across the tree of life. The largest eudicotyledonous plant family Asteraceae has a global distribution and at least 460 times more species than its South American endemic sister family Calyceraceae. In this study, diversification rate dynamics across Asteraceae are examined in light of the several hypothesized causes for the family's evolutionary success that could be responsible for rate change. The innovations of racemose capitulum and pappus, and a whole genome duplication event occurred near the origin of the family, yet we found the basal lineages of Asteraceae that evolved in South America share background diversification rates with Calyceraceae and their Australasian sister Goodeniaceae. Instead we found diversification rates increased gradually from the origin of Asteraceae approximately 69.5Ma in the late Cretaceous through the Early Eocene Climatic Optimum at least. In contrast to earlier studies, significant rate shifts were not strongly correlated with intercontinental dispersals or polyploidization. The difference is due primarily to sampling more backbone nodes, as well as calibrations placed internally in Asteraceae that resulted in earlier divergence times than those found in most previous relaxed clock studies. Two clades identified as having transformed rate processes are the Vernonioid Clade and a clade within the Heliantheae alliance characterized by phytomelanic fruit (PF Clade) that represents an American radiation. In Africa, subfamilies Carduoideae, Pertyoideae, Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae diverged in a relatively short span of only 6.5millionyears during the Middle Eocene. Copyright © 2016 Elsevier Inc. All rights reserved.

The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation

PubMed Central

Yang, Guan-Dong; Agapow, Paul-Michael

2017-01-01

The kind and duration of phylogenetic topological “signatures” left in the wake of macroevolutionary events remain poorly understood. To this end, we examined a broad range of simulated phylogenies generated using trait-biased, heritable speciation probabilities and mass extinction that could be either random or selective on trait value, but also using background extinction and diversity-dependence to constrain clade sizes. In keeping with prior results, random mass extinction increased imbalance of clades that recovered to pre-extinction size, but was a relatively weak effect. Mass extinction that was selective on trait values tended to produce clades of similar or greater balance compared to random extinction or controls. Allowing evolution to continue past the point of clade-size recovery resulted in erosion and eventual erasure of this signal, with all treatments converging on similar values of imbalance, except for very intense extinction regimes targeted at taxa with high speciation rates. Return to a more balanced state with extended post-extinction evolution was also associated with loss of the previous phylogenetic root in most treatments. These results further demonstrate that while a mass extinction event can produce a recognizable phylogenetic signal, its effects become increasingly obscured the further an evolving clade gets from that event, with any sharp imbalance due to unrelated evolutionary factors. PMID:28644846

The effect of abortion legalization on sexual behavior: evidence from sexually transmitted diseases.

PubMed

Klick, Jonathan; Stratmann, Thomas

2003-06-01

Unwanted pregnancy represents a major cost of sexual activity. When abortion was legalized in a number of states in 1969 and 1970 (and nationally in 1973), this cost was reduced. We predict that abortion legalization generated incentives leading to an increase in sexual activity, accompanied by an increase in sexually transmitted diseases (STDs). Using Centers for Disease Control data on the incidence of gonorrhea and syphilis by state, we test the hypothesis that abortion legalization led to an increase in sexually transmitted diseases. We find that gonorrhea and syphilis incidences are significantly and positively correlated with abortion legalization. Further, we find a divergence in STD rates among early legalizing states and late legalizing states starting in 1970 and a subsequent convergence after the Roe v. Wade decision, indicating that the relation between STDs and abortion is casual. Abortion legalization accounts for about one-fourth of the average disease incidence.

Vaginal microbiota and viral sexually transmitted diseases.

PubMed

Nardis, C; Mosca, L; Mastromarino, P

2013-01-01

Healthy vaginal microbiota is an important biological barrier to pathogenic microorganisms. When this predominantly Lactobacillus community is disrupted, decreased in abundance and replaced by different anaerobes, bacterial vaginosis (BV) may occur. BV is associated with prevalence and incidence of several sexually transmitted infections. This review provides background on BV, discusses the epidemiologic data to support a role of altered vaginal microbiota for acquisition of sexually transmitted diseases and analyzes mechanisms by which lactobacilli could counteract sexually transmitted viral infections.

Shifting Clade Distribution, Reassortment, and Emergence of New Subtypes of Highly Pathogenic Avian Influenza A(H5) Viruses Collected from Vietnamese Poultry from 2012 to 2015

PubMed Central

Jang, Yunho; Nguyen, Tho D.; Jones, Joyce; Shepard, Samuel S.; Yang, Hua; Gerloff, Nancy; Nguyen, Long V.; Inui, Ken; Yang, Genyan; Creanga, Adrian; Wang, Li; Mai, Duong T.; Thor, Sharmi; Stevens, James; To, Thanh L.; Wentworth, David E.; Nguyen, Tung; Pham, Dong V.; Bryant, Juliet E.

2016-01-01

ABSTRACT Whole-genome sequences of representative highly pathogenic avian influenza A(H5) viruses from Vietnam were generated, comprising samples from poultry outbreaks and active market surveillance collected from January 2012 to August 2015. Six hemagglutinin gene clades were characterized. Clade 1.1.2 was predominant in southern Mekong provinces throughout 2012 and 2013 but gradually disappeared and was not detected after April 2014. Clade 2.3.2.1c viruses spread rapidly during 2012 and were detected in the south and center of the country. A number of clade 1.1.2 and 2.3.2.1c interclade reassortant viruses were detected with different combinations of internal genes derived from 2.3.2.1a and 2.3.2.1b viruses, indicating extensive cocirculation. Although reassortment generated genetic diversity at the genotype level, there was relatively little genetic drift within the individual gene segments, suggesting genetic stasis over recent years. Antigenically, clade 1.1.2, 2.3.2.1a, 2.3.2.1b, and 2.3.2.1c viruses remained related to earlier viruses and WHO-recommended prepandemic vaccine strains representing these clades. Clade 7.2 viruses, although detected in only low numbers, were the exception, as indicated by introduction of a genetically and antigenically diverse strain in 2013. Clade 2.3.4.4 viruses (H5N1 and H5N6) were likely introduced in April 2014 and appeared to gain dominance across northern and central regions. Antigenic analyses of clade 2.3.4.4 viruses compared to existing clade 2.3.4 candidate vaccine viruses (CVV) indicated the need for an updated vaccine virus. A/Sichuan/26221/2014 (H5N6) virus was developed, and ferret antisera generated against this virus were demonstrated to inhibit some but not all clade 2.3.4.4 viruses, suggesting consideration of alternative clade 2.3.4.4 CVVs. IMPORTANCE Highly pathogenic avian influenza (HPAI) A(H5) viruses have circulated continuously in Vietnam since 2003, resulting in hundreds of poultry outbreaks and

Dynamic facial expressions of emotion transmit an evolving hierarchy of signals over time.

PubMed

Jack, Rachael E; Garrod, Oliver G B; Schyns, Philippe G

2014-01-20

Designed by biological and social evolutionary pressures, facial expressions of emotion comprise specific facial movements to support a near-optimal system of signaling and decoding. Although highly dynamical, little is known about the form and function of facial expression temporal dynamics. Do facial expressions transmit diagnostic signals simultaneously to optimize categorization of the six classic emotions, or sequentially to support a more complex communication system of successive categorizations over time? Our data support the latter. Using a combination of perceptual expectation modeling, information theory, and Bayesian classifiers, we show that dynamic facial expressions of emotion transmit an evolving hierarchy of "biologically basic to socially specific" information over time. Early in the signaling dynamics, facial expressions systematically transmit few, biologically rooted face signals supporting the categorization of fewer elementary categories (e.g., approach/avoidance). Later transmissions comprise more complex signals that support categorization of a larger number of socially specific categories (i.e., the six classic emotions). Here, we show that dynamic facial expressions of emotion provide a sophisticated signaling system, questioning the widely accepted notion that emotion communication is comprised of six basic (i.e., psychologically irreducible) categories, and instead suggesting four. Copyright © 2014 Elsevier Ltd. All rights reserved.

Cytogeography of the Humifusa clade of Opuntia s.s. Mill. 1754 (Cactaceae, Opuntioideae, Opuntieae): correlations with pleistocene refugia and morphological traits in a polyploid complex

PubMed Central

Majure, Lucas C.; Judd, Walter S.; Soltis, Pamela S.; Soltis, Douglas E.

2012-01-01

Abstract Ploidy has been well studied and used extensively in the genus Opuntia to determine species boundaries, detect evidence of hybridization, and infer evolutionary patterns. We carried out chromosome counts for all members of the Humifusa clade to ascertain whether geographic patterns are associated with differences in ploidy. We then related chromosomal data to observed morphological variability, polyploid formation, and consequently the evolutionary history of the clade. We counted chromosomes of 277 individuals from throughout the ranges of taxa included within the Humifusa clade, with emphasis placed on the widely distributed species, Opuntia humifusa (Raf.) Raf., 1820 s.l. and Opuntia macrorhiza Engelm., 1850 s.l. We also compiled previous counts made for species in the clade along with our new counts to plot geographic distributions of the polyploid and diploid taxa. A phylogeny using nuclear ribosomal ITS sequence data was reconstructed to determine whether ploidal variation is consistent with cladogenesis. We discovered that diploids of the Humifusa clade are restricted to the southeastern United States (U.S.), eastern Texas, and southeastern New Mexico. Polyploid members of the clade, however, are much more widely distributed, occurring as far north as the upper midwestern U.S. (e.g., Michigan, Minnesota, Wisconsin). Morphological differentiation, although sometimes cryptic, is commonly observed among diploid and polyploid cytotypes, and such morphological distinctions may be useful in diagnosing possible cryptic species. Certain polyploid populations of Opuntia humifusa s.l. and Opuntia macrorhiza s.l., however, exhibit introgressive morphological characters, complicating species delineations. Phylogenetically, the Humifusa clade forms two subclades that are distributed, respectively, in the southeastern U.S. (including all southeastern U.S. diploids, polyploid Opuntia abjecta Small, 1923, and polyploid Opuntia pusilla (Haw.) Haw., 1812) and the

Sexually transmitted diseases among psychiatric patients in Brazil.

PubMed

Dutra, Maria Rita Teixeira; Campos, Lorenza Nogueira; Guimarães, Mark Drew Crosland

2014-01-01

Sexually transmitted diseases are still highly prevalent worldwide and represent an important public health problem. Psychiatric patients are at increased risk of sexually transmitted diseases but there are scarce published studies with representative data of this population. We sought to estimate the prevalence and correlates of self-reported sexually transmitted diseases among patients with mental illnesses under care in a national representative sample in Brazil (n=2145). More than one quarter of the sample (25.8%) reported a lifetime history of sexually transmitted disease. Multivariate analyses showed that patients with a lifetime sexually transmitted disease history were older, had history of homelessness, used more alcohol and illicit drugs, suffered violence, perceived themselves to be at greater risk for HIV and had high risk sexual behavioral: practised unprotected sex, started sexual life earlier, had more than ten sexual partners, exchanged money and/or drugs for sex and had a partner that refused to use condom. Our findings indicate a high prevalence of self-reported sexually transmitted diseases among psychiatric patients in Brazil, and emphasize the need for implementing sexually transmitted diseases prevention programs in psychiatric settings, including screening, treatment, and behavioral modification interventions. Copyright © 2013 Elsevier Editora Ltda. All rights reserved.

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

PubMed Central

2011-01-01

Background Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families. Results Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans. Conclusions The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation.

PubMed

Nakatani, Masanori; Miya, Masaki; Mabuchi, Kohji; Saitoh, Kenji; Nishida, Mutsumi

2011-06-22

Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families. Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans. The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100-112 Ma, creating an over 100

Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade

PubMed Central

Lo, Pei-Chun; Liu, Shu-Hui; Nor, Siti Azizah Mohd

2017-01-01

The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene—Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a

Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade.

PubMed

Lo, Pei-Chun; Liu, Shu-Hui; Nor, Siti Azizah Mohd; Chen, Wei-Jen

2017-01-01

The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a

Characterization of cross-clade monoclonal antibodies against H5N1 highly pathogenic avian influenza virus and their application to the antigenic analysis of diverse H5 subtype viruses.

PubMed

Gronsang, Dulyatad; Bui, Anh N; Trinh, Dai Q; Bui, Vuong N; Nguyen, Khong V; Can, Minh X; Omatsu, Tsutomu; Mizutani, Tetsuya; Nagai, Makoto; Katayama, Yukie; Thampaisarn, Rapeewan; Ogawa, Haruko; Imai, Kunitoshi

2017-08-01

H5N1 highly pathogenic avian influenza viruses (HPAIVs) are a threat to both animal and public health and require specific and rapid detection for prompt disease control. We produced three neutralizing anti-hemagglutinin (HA) monoclonal antibodies (mAbs) using two clades (2.2 and 2.5) of the H5N1 HPAIV isolated in Japan. Blocking immunofluorescence tests showed that each mAb recognized different epitopes; 3B5.1 and 3B5.2 mAbs against the clade 2.5 virus showed cross-clade reactivity to all 26 strains from clades 1, 2.2, 2.3.2.1, 2.3.2.1a, b, c and 2.3.4, suggesting that the epitope(s) recognized are conserved. Conversely, the 1G5 mAb against the clade 2.2 virus showed reactivity to only clades 1, 2.3.4 and 2.5 strains. An analysis of escape mutants, and some clades of the H5N1 viruses recognized by 3B5.1 and 3B5.2 mAbs, suggested that the mAbs bind to an epitope, including amino acid residues at position 162 in the HA1 protein (R162 and K162). Unexpectedly, however, when five Eurasian-origin H5 low-pathogenic AIV (LPAIV) strains with R162 were examined (EA-nonGsGD clade) as well as two American-origin strains (Am-nonGsGD clade), the mAb recognized only EA-nonGsGD clade strains. The R162 and K162 residues in the HA1 protein were highly conserved among 36 of the 43 H5N1 clades reported, including clades 2.3.2.1a and 2.3.2.1c that are currently circulating in Asia, Africa and Europe. The amino acid residues (158-PTIKRSYNNTNQE-170) in the HA1 protein are probably an epitope responsible for the cross-clade reactivity of the mAbs, considering the epitopes reported elsewhere. The 3B5.1 and 3B5.2 mAbs may be useful for the specific detection of H5N1 HPAIVs circulating in the field.

A multiplex PCR method discriminating between the TYLCV and TYLCV-Mld clades of tomato yellow leaf curl virus.

PubMed

Lefeuvre, P; Hoareau, M; Delatte, H; Reynaud, B; Lett, J-M

2007-09-01

Tomato yellow leaf curl virus (TYLCV) is one of the causal agents of tomato yellow leaf curl disease (TYLCD) and can cause up to 100% yield losses in tomato fields. As TYLCV continues to spread, many isolates have been described in different parts of the world. Recently two closely related but distinct TYLCV clades, called TYLCV and TYLCV-Mld, have been identified. Isolates from those two clades differ mainly in the nucleotide sequences of their replication associated protein genes but do not display significantly different symptomatology. In order to improve monitoring of the rapidly expanding worldwide TYLCD epidemic, a multiplex polymerase chain reaction assay (mPCR) was developed. A set of three primers were designed to detect and characterize the TYLCV and TYLCV-Mld clade isolates. The specificity and sensitivity of the mPCR were validated on TYLCV infected tomato plants and Bemisia tabaci whiteflies. Being cheap, fast and highly sensitive this new diagnostic tool should greatly simplify efforts to trace the global spread of TYLCV.

Estimating growth rates of uncultivated clades of archaea and bacteria in marine sediments

NASA Astrophysics Data System (ADS)

Lloyd, K. G.

2016-12-01

The vast majority of microbes present in marine sediments have never been cultivated in laboratory conditions. It is therefore difficult to estimate the growth rates of these organisms in situ. Quantitative PCR (qPCR) and 16S rRNA gene libraries from sediments below 10 cm show very little change in abundance of these organisms with depth or with redox conditions. Therefore, we hypothesized that uncultivated clades of bacteria and archaea that are ubiquitous in marine sediments, actually grow in the upper 10 cm of marine sediments. We collected sediment cores from the White Oak River estuary, sectioned them in 1 cm intervals, and examined the changes in abundance of uncultivated microbes with depth using 16S rRNA gene libraries and qPCR. We found that some of the key clades associated with the deep subsurface microbiome, such as Bathyarchaeota and MBG-D, increase in abundance with depth, demonstrating extremely slow growth in these shallow subsurface sediments.

Molecular phylogeny and ecological diversification in a clade of New World songbirds (genus Vireo).

PubMed

Cicero, C; Johnson, N K

1998-10-01

We constructed a molecular phylogeny for a clade of eye-ringed vireos (Vireo flavifrons and the V. solitarius complex) to examine existing hypotheses of speciation and ecological diversification. Complete sequences of the mtDNA cytochrome b gene were obtained from 47 individuals of this group plus four vireonid outgroups. Mean levels of sequence divergence in the clade varied from 0.29% to 5.7%. Differences were greatest between V. flavifrons and four taxa of 'V. solitarius'. The latter separated into three taxonomic, geographical and ecological groups: V. plumbeus plumbeus, V. cassinii cassinii, and V. solitarius solitarius plus V. solitarius alticola. These differed by an average of 2.6-3.2%. Populations within each group revealed low levels of sequence variation (x = 0.20%) and little geographical structuring. The mtDNA data generally corroborate results from allozymes. V. plumbeus shows a loss of yellow-green carotenoid pigmentation from the ancestral condition. The occupancy of relatively dry habitats by this species and V. cassinii represents a derived ecological shift from more-humid environments occupied by other species of vireonids. Ecological divergence in this clade occurred in allopatry and is associated with generic-level stability in morphometrics and foraging styles. Migratory behaviour and seasonal habitat shifts apparently evolved multiple times in vireos breeding in temperate environments. Present geographical and ecological distributions, and low levels of intrataxon genetic divergence, are hypothesized to be the result of postglacial regionalization of climate-plant associations and rapid northward expansion of breeding ranges.

Photovoltaic device having light transmitting electrically conductive stacked films

DOEpatents

Weber, Michael F.; Tran, Nang T.; Jeffrey, Frank R.; Gilbert, James R.; Aspen, Frank E.

1990-07-10

A light transmitting electrically conductive stacked film, useful as a light transmitting electrode, including a first light transmitting electrically conductive layer, having a first optical thickness, a second light transmitting layer, having a second optical thickness different from the optical thickness of the first layer, and an electrically conductive metallic layer interposed between and in initimate contact with the first and second layers.

Sexually transmitted infections and risk of prostate cancer: review of historical and emerging hypotheses.

PubMed

Sutcliffe, Siobhan

2010-08-01

Since the early 1950s when sexually transmitted infections (STIs) were first proposed as a possible risk factor for prostate cancer, numerous epidemiologic studies have been conducted. Initially, these studies were primarily small case-control studies with retrospective, self-reported assessments of a narrow range of STIs, typically either any STIs, or gonorrhea and syphilis. However, as new STIs have been discovered/recognized, new and better tests to detect histories of STIs have been developed, and new resources for prostate cancer research have been created, epidemiologic studies have expanded to include a wide range of STIs, and have moved towards more rigorous, prospective study designs and serological assessment of STI histories. The results of these studies are reviewed and discussed, as well as possible new avenues of research, such as Trichomonas vaginalis infection and infections not typically considered to be sexually transmitted.

Highly pathogenic avian influenza H5N1 Clade 2.3.2.1c virus in migratory birds, 2014-2015.

PubMed

Bi, Yuhai; Chen, Jianjun; Zhang, Zhenjie; Li, Mingxin; Cai, Tianlong; Sharshov, Kirill; Susloparov, Ivan; Shestopalov, Alexander; Wong, Gary; He, Yubang; Xing, Zhi; Sun, Jianqing; Liu, Di; Liu, Yingxia; Liu, Lei; Liu, Wenjun; Lei, Fumin; Shi, Weifeng; Gao, George F

2016-08-01

A novel Clade 2.3.2.1c H5N1 reassortant virus caused several outbreaks in wild birds in some regions of China from late 2014 to 2015. Based on the genetic and phylogenetic analyses, the viruses possess a stable gene constellation with a Clade 2.3.2.1c HA, a H9N2-derived PB2 gene and the other six genes of Asian H5N1-origin. The Clade 2.3.2.1c H5N1 reassortants displayed a high genetic relationship to a human H5N1 strain (A/Alberta/01/2014). Further analysis showed that similar viruses have been circulating in wild birds in China, Russia, Dubai (Western Asia), Bulgaria and Romania (Europe), as well as domestic poultry in some regions of Africa. The affected areas include the Central Asian, East Asian-Australasian, West Asian-East African, and Black Sea/Mediterranean flyways. These results show that the novel Clade 2.3.2.1c reassortant viruses are circulating worldwide and may have gained a selective advantage in migratory birds, thus posing a serious threat to wild birds and potentially humans.

Detection and Genomic Characterization of Motility in Lactobacillus curvatus: Confirmation of Motility in a Species outside the Lactobacillus salivarius Clade

PubMed Central

Cousin, Fabien J.; Lynch, Shónagh M.; Harris, Hugh M. B.; McCann, Angela; Lynch, Denise B.; Neville, B. Anne; Irisawa, Tomohiro; Okada, Sanae; Endo, Akihito

2014-01-01

Lactobacillus is the largest genus within the lactic acid bacteria (LAB), with almost 180 species currently identified. Motility has been reported for at least 13 Lactobacillus species, all belonging to the Lactobacillus salivarius clade. Motility in lactobacilli is poorly characterized. It probably confers competitive advantages, such as superior nutrient acquisition and niche colonization, but it could also play an important role in innate immune system activation through flagellin–Toll-like receptor 5 (TLR5) interaction. We now report strong evidence of motility in a species outside the L. salivarius clade, Lactobacillus curvatus (strain NRIC 0822). The motility of L. curvatus NRIC 0822 was revealed by phase-contrast microscopy and soft-agar motility assays. Strain NRIC 0822 was motile at temperatures between 15°C and 37°C, with a range of different carbohydrates, and under varying atmospheric conditions. We sequenced the L. curvatus NRIC 0822 genome, which revealed that the motility genes are organized in a single operon and that the products are very similar (>98.5% amino acid similarity over >11,000 amino acids) to those encoded by the motility operon of Lactobacillus acidipiscis KCTC 13900 (shown for the first time to be motile also). Moreover, the presence of a large number of mobile genetic elements within and flanking the motility operon of L. curvatus suggests recent horizontal transfer between members of two distinct Lactobacillus clades: L. acidipiscis in the L. salivarius clade and L. curvatus in the L. sakei clade. This study provides novel phenotypic, genetic, and phylogenetic insights into flagellum-mediated motility in lactobacilli. PMID:25501479

Detection and genomic characterization of motility in Lactobacillus curvatus: confirmation of motility in a species outside the Lactobacillus salivarius clade.

PubMed

Cousin, Fabien J; Lynch, Shónagh M; Harris, Hugh M B; McCann, Angela; Lynch, Denise B; Neville, B Anne; Irisawa, Tomohiro; Okada, Sanae; Endo, Akihito; O'Toole, Paul W

2015-02-01

Lactobacillus is the largest genus within the lactic acid bacteria (LAB), with almost 180 species currently identified. Motility has been reported for at least 13 Lactobacillus species, all belonging to the Lactobacillus salivarius clade. Motility in lactobacilli is poorly characterized. It probably confers competitive advantages, such as superior nutrient acquisition and niche colonization, but it could also play an important role in innate immune system activation through flagellin–Toll-like receptor 5 (TLR5) interaction. We now report strong evidence of motility in a species outside the L. salivarius clade, Lactobacillus curvatus (strain NRIC0822). The motility of L. curvatus NRIC 0822 was revealed by phase-contrast microscopy and soft-agar motility assays. Strain NRIC 0822 was motile at temperatures between 15 °C and 37 °C, with a range of different carbohydrates, and under varying atmospheric conditions. We sequenced the L. curvatus NRIC 0822 genome, which revealed that the motility genes are organized in a single operon and that the products are very similar (>98.5% amino acid similarity over >11,000 amino acids) to those encoded by the motility operon of Lactobacillus acidipiscis KCTC 13900 (shown for the first time to be motile also). Moreover, the presence of a large number of mobile genetic elements within and flanking the motility operon of L. curvatus suggests recent horizontal transfer between members of two distinct Lactobacillus clades: L. acidipiscis in the L. salivarius clade and L. curvatus inthe L. sakei clade. This study provides novel phenotypic, genetic, and phylogenetic insights into flagellum-mediated motility in lactobacilli.

Wavelet Compression of Satellite-Transmitted Digital Mammograms

NASA Technical Reports Server (NTRS)

Zheng, Yuan F.

2001-01-01

Breast cancer is one of the major causes of cancer death in women in the United States. The most effective way to treat breast cancer is to detect it at an early stage by screening patients periodically. Conventional film-screening mammography uses X-ray films which are effective in detecting early abnormalities of the breast. Direct digital mammography has the potential to improve the image quality and to take advantages of convenient storage, efficient transmission, and powerful computer-aided diagnosis, etc. One effective alternative to direct digital imaging is secondary digitization of X-ray films. This technique may not provide as high an image quality as the direct digital approach, but definitely have other advantages inherent to digital images. One of them is the usage of satellite-transmission technique for transferring digital mammograms between a remote image-acquisition site and a central image-reading site. This technique can benefit a large population of women who reside in remote areas where major screening and diagnosing facilities are not available. The NASA-Lewis Research Center (LeRC), in collaboration with the Cleveland Clinic Foundation (CCF), has begun a pilot study to investigate the application of the Advanced Communications Technology Satellite (ACTS) network to telemammography. The bandwidth of the T1 transmission is limited (1.544 Mbps) while the size of a mammographic image is huge. It takes a long time to transmit a single mammogram. For example, a mammogram of 4k by 4k pixels with 16 bits per pixel needs more than 4 minutes to transmit. Four images for a typical screening exam would take more than 16 minutes. This is too long a time period for a convenient screening. Consequently, compression is necessary for making satellite-transmission of mammographic images practically possible. The Wavelet Research Group of the Department of Electrical Engineering at The Ohio State University (OSU) participated in the LeRC-CCF collaboration by

A Single Early Introduction of HIV-1 Subtype B into Central America Accounts for Most Current Cases

PubMed Central

Murillo, Wendy; Veras, Nazle; Prosperi, Mattia; de Rivera, Ivette Lorenzana; Paz-Bailey, Gabriela; Morales-Miranda, Sonia; Juarez, Sandra I.; Yang, Chunfu; DeVos, Joshua; Marín, José Pablo; Mild, Mattias; Albert, Jan

2013-01-01

Human immunodeficiency virus type 1 (HIV-1) variants show considerable geographical separation across the world, but there is limited information from Central America. We provide the first detailed investigation of the genetic diversity and molecular epidemiology of HIV-1 in six Central American countries. Phylogenetic analysis was performed on 625 HIV-1 pol gene sequences collected between 2002 and 2010 in Honduras, El Salvador, Nicaragua, Costa Rica, Panama, and Belize. Published sequences from neighboring countries (n = 57) and the rest of the world (n = 740) were included as controls. Maximum likelihood methods were used to explore phylogenetic relationships. Bayesian coalescence-based methods were used to time HIV-1 introductions. Nearly all (98.9%) Central American sequences were of subtype B. Phylogenetic analysis revealed that 437 (70%) sequences clustered within five significantly supported monophyletic clades formed essentially by Central American sequences. One clade contained 386 (62%) sequences from all six countries; the other four clades were smaller and more country specific, suggesting discrete subepidemics. The existence of one large well-supported Central American clade provides evidence that a single introduction of HIV-1 subtype B in Central America accounts for most current cases. An introduction during the early phase of the HIV-1 pandemic may explain its epidemiological success. Moreover, the smaller clades suggest a subsequent regional spread related to specific transmission networks within each country. PMID:23616665

Impacts of Abstinence Education on Teen Sexual Activity, Risk of Pregnancy, and Risk of Sexually Transmitted Diseases

ERIC Educational Resources Information Center

Trenholm, Christopher; Devaney, Barbara; Fortson, Kenneth; Clark, Melissa; Bridgespan, Lisa Quay; Wheeler, Justin

2008-01-01

This paper examines the impacts of four abstinence-only education programs on adolescent sexual activity and risks of pregnancy and sexually transmitted diseases (STDs). Based on an experimental design, the impact analysis uses survey data collected in 2005 and early 2006 from more than 2,000 teens who had been randomly assigned to either a…

Challenges for accurate and prompt molecular diagnosis of clades of highly pathogenic avian influenza H5N1 viruses emerging in Vietnam.

PubMed

Slomka, Marek J; To, Thanh L; Tong, Hien H; Coward, Vivien J; Hanna, Amanda; Shell, Wendy; Pavlidis, Theo; Densham, Anstice L E; Kargiolakis, Georgios; Arnold, Mark E; Banks, Jill; Brown, Ian H

2012-01-01

Forty-six chickens and 48 ducks were sampled from four Vietnamese poultry premises in 2009 infected with H5N1 highly pathogenic avian influenza (HPAI) clade 2.3.2 and 2.3.4 viruses, which also differed by cleavage site (CS) sequences in their haemagglutinin (HA) genes. All clinical specimens (n=282), namely tracheal and cloacal swabs plus feathers, were tested by five Eurasian reverse-transcriptase AI RealTime polymerase chain reaction (RRT-PCR) methods. Bayesian modelling showed similar high sensitivity for the validated H5 HA2 RRT-PCR and a new modified M-gene RRT-PCR that utilizes lyophilized reagents. Both were more sensitive than the validated "wet" M-gene RRT-PCR. Another RRT-PCR, which targeted the H5-gene CS region, was effective for clade 2.3.4 detection, but severely compromised for clade 2.3.2 viruses. Reduced sensitivity of the H5 CS and "wet" M-gene RRT-PCRs correlated with mismatches between the target and the primer and/or probe sequences. However, the H5 HA2 RRT-PCR sensitively detected both clade 2.3.2 and 2.3.4 viruses, and agreed with N1 RRT-PCR results. Feather testing from diseased chicken and duck flocks by AI RRT-PCRs resulted in the most sensitive identification of H5N1 HPAI-infected birds. Evolution of new H5N1 HPAI clades remains a concern for currently affected Asian countries, but also for more distant regions where it is important to be prepared for new incursions of H5N1 HPAI viruses. Genetic evidence for adamantane resistance and sensitivity was also observed in isolates from both clades.

Glucosylation and other biotransformations of T-2 toxin by yeasts of the Trichomonascus clade

USDA-ARS?s Scientific Manuscript database

Twenty-five yeasts assigned to the Trichomonascus clade (Saccharomycotina, Ascomycota), including three Trichomonascus species and 22 anamorphic species presently classified in Blastobotrys, were tested for their ability to convert T-2 toxin, a Fusarium trichothecene mycotoxin, to less toxic product...

Developing Clade-Specific Microsatellite Markers: A Case Study in the Filamentous Fungal Genus Aspergillus

USDA-ARS?s Scientific Manuscript database

Microsatellite markers are highly variable and very commonly used in population genetics studies. However, microsatellite loci are typically poorly conserved and cannot be used in distant related species. Thus, development of clade-specific microsatellite markers would increase efficiency and allow ...

Cable Modems' Transmitted RF: A Study of SNR, Error Rates, Transmit Levels, and Trouble Call Metrics

ERIC Educational Resources Information Center

Tebbetts, Jo A.

2013-01-01

Hypotheses were developed and tested to measure the cable modems operational metrics response to a reconfiguration of the cable modems' transmitted RF applied to the CMTS. The purpose of this experiment was to compare two groups on the use of non-federal RF spectrum to determine if configuring the cable modems' transmitted RF from 25.2…

Shifting Clade Distribution, Reassortment, and Emergence of New Subtypes of Highly Pathogenic Avian Influenza A(H5) Viruses Collected from Vietnamese Poultry from 2012 to 2015.

PubMed

Nguyen, Diep T; Jang, Yunho; Nguyen, Tho D; Jones, Joyce; Shepard, Samuel S; Yang, Hua; Gerloff, Nancy; Fabrizio, Thomas; Nguyen, Long V; Inui, Ken; Yang, Genyan; Creanga, Adrian; Wang, Li; Mai, Duong T; Thor, Sharmi; Stevens, James; To, Thanh L; Wentworth, David E; Nguyen, Tung; Pham, Dong V; Bryant, Juliet E; Davis, C Todd

2017-03-01

Whole-genome sequences of representative highly pathogenic avian influenza A(H5) viruses from Vietnam were generated, comprising samples from poultry outbreaks and active market surveillance collected from January 2012 to August 2015. Six hemagglutinin gene clades were characterized. Clade 1.1.2 was predominant in southern Mekong provinces throughout 2012 and 2013 but gradually disappeared and was not detected after April 2014. Clade 2.3.2.1c viruses spread rapidly during 2012 and were detected in the south and center of the country. A number of clade 1.1.2 and 2.3.2.1c interclade reassortant viruses were detected with different combinations of internal genes derived from 2.3.2.1a and 2.3.2.1b viruses, indicating extensive cocirculation. Although reassortment generated genetic diversity at the genotype level, there was relatively little genetic drift within the individual gene segments, suggesting genetic stasis over recent years. Antigenically, clade 1.1.2, 2.3.2.1a, 2.3.2.1b, and 2.3.2.1c viruses remained related to earlier viruses and WHO-recommended prepandemic vaccine strains representing these clades. Clade 7.2 viruses, although detected in only low numbers, were the exception, as indicated by introduction of a genetically and antigenically diverse strain in 2013. Clade 2.3.4.4 viruses (H5N1 and H5N6) were likely introduced in April 2014 and appeared to gain dominance across northern and central regions. Antigenic analyses of clade 2.3.4.4 viruses compared to existing clade 2.3.4 candidate vaccine viruses (CVV) indicated the need for an updated vaccine virus. A/Sichuan/26221/2014 (H5N6) virus was developed, and ferret antisera generated against this virus were demonstrated to inhibit some but not all clade 2.3.4.4 viruses, suggesting consideration of alternative clade 2.3.4.4 CVVs. IMPORTANCE Highly pathogenic avian influenza (HPAI) A(H5) viruses have circulated continuously in Vietnam since 2003, resulting in hundreds of poultry outbreaks and sporadic human

Full-Genome Sequence of a Novel Varicella-Zoster Virus Clade Isolated in Mexico

PubMed Central

Rodríguez-Castillo, Araceli; Ortiz-Alcántara, Joanna María; Gonzalez-Durán, Elizabeth; Segura-Candelas, José Miguel; Pérez-Agüeros, Sandra Ivette; Escobar-Escamilla, Noé; Méndez-Tenorio, Alfonso; Diaz-Quiñonez, José Alberto

2015-01-01

Varicella-zoster virus (VZV) is a member of the Herpesviridae family, which causes varicella (chicken pox) and herpes zoster (shingles) in humans. Here, we report the complete genome sequence of varicella-zoster virus, isolated from a vesicular fluid sample, revealing the circulation of VZV clade VIII in Mexico. PMID:26159533

Using the urtA Gene to Profile Nitrogen Stress Adaptation and Spatio-Temporal Abundance of Synechococcus Clades in the California Current System

NASA Astrophysics Data System (ADS)

Chatterjee, T.; Shilova, I. N.; Zehr, J. P.

2015-12-01

Among the planet's most abundant photosynthetic groups, the picocyanobacteria Synechococcus contributes nearly a quarter of our global oxygen supply. Urea, from both natural and anthropogenic sources, is an important alternative to the preferred yet limited sources of reduced nitrogen for cyanobacteria in the marine environment. While urea uptake activity has been observed during nitrogen (N) limitation, this stress adaptation is not well-studied in natural habitats. We propose the urtAgene, which encodes the substrate-binding subunit of the urea-uptake ABC transporter, as a molecular marker to profile cell abundance and stress response in relation to N fluctuation. Strains prevalent in temperate waters of the California Current System - Synechococcus CC9311 (clade I), CC9605 (clade II) and CC9902/BL107 (clade IV) - were targeted by clade-specific qPCR assays to measure urtA gene copy abundance in samples from different geographical stations and a time-series. Spatial and seasonal patterns in clade abundance resembled those previously reported by studies using other Synechococcus marker genes, thus validating urtA as a strong marker. Synechococcus clades I and IV were most abundant in coastal and transitional stations, while the more oligotrophic clade II was detected near open waters. Synechococcus abundances were highest before and after the annual upwelling season, as supported by a non clade-specific rbcL-qPCR assay. A lack of correlation between abundance and nitrate availability indicated utilization of alternative nitrogen sources like urea, which was further evidenced by the detection of clade IV urtA transcripts at the station closest to shore. Urea concentrations tend to be highest in coastal environments due to fertilizer runoff, which can stimulate phytoplankton blooms including harmful algal blooms. This study adds to insight on how such environmental factors are related to N-cycling and patterns of urea-assimilating microbial populations like

Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities.

PubMed

Nagy, László G; Riley, Robert; Tritt, Andrew; Adam, Catherine; Daum, Chris; Floudas, Dimitrios; Sun, Hui; Yadav, Jagjit S; Pangilinan, Jasmyn; Larsson, Karl-Henrik; Matsuura, Kenji; Barry, Kerrie; Labutti, Kurt; Kuo, Rita; Ohm, Robin A; Bhattacharya, Sukanta S; Shirouzu, Takashi; Yoshinaga, Yuko; Martin, Francis M; Grigoriev, Igor V; Hibbett, David S

2016-04-01

Evolution of lignocellulose decomposition was one of the most ecologically important innovations in fungi. White-rot fungi in the Agaricomycetes (mushrooms and relatives) are the most effective microorganisms in degrading both cellulose and lignin components of woody plant cell walls (PCW). However, the precise evolutionary origins of lignocellulose decomposition are poorly understood, largely because certain early-diverging clades of Agaricomycetes and its sister group, the Dacrymycetes, have yet to be sampled, or have been undersampled, in comparative genomic studies. Here, we present new genome sequences of ten saprotrophic fungi, including members of the Dacrymycetes and early-diverging clades of Agaricomycetes (Cantharellales, Sebacinales, Auriculariales, and Trechisporales), which we use to refine the origins and evolutionary history of the enzymatic toolkit of lignocellulose decomposition. We reconstructed the origin of ligninolytic enzymes, focusing on class II peroxidases (AA2), as well as enzymes that attack crystalline cellulose. Despite previous reports of white rot appearing as early as the Dacrymycetes, our results suggest that white-rot fungi evolved later in the Agaricomycetes, with the first class II peroxidases reconstructed in the ancestor of the Auriculariales and residual Agaricomycetes. The exemplars of the most ancient clades of Agaricomycetes that we sampled all lack class II peroxidases, and are thus concluded to use a combination of plesiomorphic and derived PCW degrading enzymes that predate the evolution of white rot. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Partitioning Nitrification Between Specific Archaeal and Bacterial Clades in a Large, Nitrogen-Rich Estuary (San Francisco Bay, CA)

NASA Astrophysics Data System (ADS)

Damashek, J.; Casciotti, K. L.; Francis, C. A.

2014-12-01

Nitrification is the sole link between nitrogen inputs and losses in marine ecosystems, and understanding the microbial ecology and biogeochemistry of nitrification is therefore crucial for understanding how aquatic ecosystems process nitrogen. Recently-discovered ammonia-oxidizing archaea (AOA), rather than ammonia-oxidizing bacteria (AOB), appear to drive ammonia oxidation in many ecosystems, including much of the ocean. However, few studies have investigated these microbes in estuary waters, despite the fact nitrogen concentrations in estuaries are often far higher than the ocean, and can cause drastic ecological harm. We sought to determine the roles of AOA and AOB in driving pelagic nitrification throughout San Francisco Bay, by combining biogeochemical rate measurements with a suite of measurements of the abundance and diversity of AOA and AOB. It addition to traditional functional gene analyses and high-throughput 16S amplicon sequencing, we developed novel qPCR assays to selectively target the ammonia-oxidizing clades found in this estuary, which gave insights into clade-specific distributional patterns. Our biogeochemical data suggest a sizable fraction of ammonium in the bay is oxidized in the water column, likely by AOA, with nitrification in bottom waters also oxidizing a substantial portion of the ammonium exuded by sediments. Generally, Sacramento River waters and Suisun Bay bottom waters had the highest nitrification rates. AOA outnumbered AOB at most stations, and were present in high abundance at both the marine and freshwater ends of the estuary, while AOB abundance was highest in the low-salinity, brackish regions. Different archaeal clades were found at either end of the estuary, suggesting strong niche partitioning along the salinity gradient, with a third clade present largely in brackish waters. This work helps to assess the ability of ammonia-oxidizing microbes in estuaries to transform nitrogen prior to water discharge into the sea, and

Advertisement call of Scinax camposseabrai (Bokermann, 1968) (Anura: Hylidae), with comments on the call of three species of the Scinax ruber clade.

PubMed

Novaes, Gabriel; Zina, Juliana

2016-02-25

Scinax camposseabrai was allocated into the Scinax ruber clade by Caramaschi & Cardoso (2006) by overall similarities as snout not pointed, breeding in open areas, and an advertisement calls with multipulsed notes. This assumption about the call was based solely on an onomatopoeia provided by Bokermann (1968). Herein we provide a formal description of the advertisement call of S. camposseabrai and compare it with described calls of other S. ruber clade species. Additionally, we provide descriptions of the advertisement calls of three sympatric species of the S. ruber clade: S. eurydice (Bokermann), S. pachycrus (Miranda-Ribeiro) and S. cf. x-signatus.

Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core

PubMed Central

Leite, Deborah C. A.; Leão, Pedro; Garrido, Amana G.; Lins, Ulysses; Santos, Henrique F.; Pires, Débora O.; Castro, Clovis B.; van Elsas, Jan D.; Zilberberg, Carla; Rosado, Alexandre S.; Peixoto, Raquel S.

2017-01-01

The hologenome theory of evolution (HTE), which is under fierce debate, presupposes that parts of the microbiome are transmitted from one generation to the next [vertical transmission (VT)], which may also influence the evolution of the holobiont. Even though bacteria have previously been described in early life stages of corals, these early life stages (larvae) could have been inoculated in the water and not inside the parental colony (through gametes) carrying the parental microbiome. How Symbiodinium is transmitted to offspring is also not clear, as only one study has described this mechanism in spawners. All other studies refer to incubators. To explore the VT hypothesis and the key components being transferred, colonies of the broadcast spawner species Mussismilia hispida were kept in nurseries until spawning. Gamete bundles, larvae and adult corals were analyzed to identify their associated microbiota with respect to composition and location. Symbiodinium and bacteria were detected by sequencing in gametes and coral planula larvae. However, no cells were detected using microscopy at the gamete stage, which could be related to the absence of those cells inside the oocytes/dispersed in the mucus or to a low resolution of our approach. A preliminary survey of Symbiodinium diversity indicated that parental colonies harbored Symbiodinium clades B, C and G, whereas only clade B was found in oocytes and planula larvae [5 days after fertilization (a.f.)]. The core bacterial populations found in the bundles, planula larvae and parental colonies were identified as members of the genera Burkholderia, Pseudomonas, Acinetobacter, Ralstonia, Inquilinus and Bacillus, suggesting that these populations could be vertically transferred through the mucus. The collective data suggest that spawner corals, such as M. hispida, can transmit Symbiodinium cells and the bacterial core to their offspring by a coral gamete (and that this gamete, with its bacterial load, is released into

Digital media and sexually transmitted infections.

PubMed

Gilliam, Melissa; Chor, Julie; Hill, Brandon

2014-10-01

Digital media, including the Internet, social networking sites, text messaging, and mobile applications, are ubiquitous among adolescents and young adults. These platforms enable users to obtain important information on a multitude of health topics, they may facilitate risk-taking behaviors, and they can be key components of health interventions. The purpose of this article is to review the recent literature on digital media and sexually transmitted infections, discussing their role in potentiating and reducing risk. This review demonstrates adolescents' use of digital media to gather information on health topics and discusses significant privacy concerns regarding using media to explore sexual health information. Although several studies demonstrate an association between social media and increased sexual risk-taking behaviors, this relationship is not fully understood. Digital media-based interventions are increasingly being developed to either reduce risk or improve management of sexually transmitted infections. As greater numbers of adolescents use digital media, the potential for these platforms to influence sexual risk-taking behaviors is significant. Additional research is needed to better understand the impact of digital media on sexually transmitted infection risk and to develop social media-based interventions to improve sexually transmitted infection outcomes.

Group delay variations of GPS transmitting and receiving antennas

NASA Astrophysics Data System (ADS)

Wanninger, Lambert; Sumaya, Hael; Beer, Susanne

2017-09-01

GPS code pseudorange measurements exhibit group delay variations at the transmitting and the receiving antenna. We calibrated C1 and P2 delay variations with respect to dual-frequency carrier phase observations and obtained nadir-dependent corrections for 32 satellites of the GPS constellation in early 2015 as well as elevation-dependent corrections for 13 receiving antenna models. The combined delay variations reach up to 1.0 m (3.3 ns) in the ionosphere-free linear combination for specific pairs of satellite and receiving antennas. Applying these corrections to the code measurements improves code/carrier single-frequency precise point positioning, ambiguity fixing based on the Melbourne-Wübbena linear combination, and determination of ionospheric total electron content. It also affects fractional cycle biases and differential code biases.

Sexually transmitted diseases during pregnancy: a synthesis of particularities.

PubMed

Costa, Mariana Carvalho; Bornhausen Demarch, Eduardo; Azulay, David Rubem; Périssé, André Reynaldo Santos; Dias, Maria Fernanda Reis Gavazzoni; Nery, José Augusto da Costa

2010-01-01

Sexually transmitted diseases (STDs) have a significant prevalence in both the general population and pregnant women. Accordingly, we consider the physiological changes of the maternal organism that can alter the clinical course of these diseases. In addition, obstetric and neonatal complications may occur, resulting in increased maternal and infant morbidity and mortality. We explore features of the natural course and treatment during pregnancy of the major STDs: soft chancre, donovanosis, gonorrhea, chlamydia, viral hepatitis, genital herpes, human papillomavirus (HPV) infection, lymphogranuloma venereum, syphilis, and vulvovaginitis. We believe that health professionals should pay careful attention to STDs, particularly in relation to early diagnosis and precautions on the use of drugs during pregnancy. Prevention and partner treatment to achieve effective results are also extremely relevant.

Ichthyophonus parasite phylogeny based on ITS rDNA structure prediction and alignment identifies six clades, with a single dominant marine type

USGS Publications Warehouse

Gregg, Jacob; Thompson, Rachel L.; Purcell, Maureen; Friedman, Carolyn S.; Hershberger, Paul

2016-01-01

Despite their widespread, global impact in both wild and cultured fishes, little is known of the diversity, transmission patterns, and phylogeography of parasites generally identified as Ichthyophonus. This study constructed a phylogeny based on the structural alignment of internal transcribed spacer (ITS) rDNA sequences to compare Ichthyophonus isolates from fish hosts in the Atlantic and Pacific oceans, and several rivers and aquaculture sites in North America, Europe, and Japan. Structure of the Ichthyophonus ITS1–5.8S–ITS2 transcript exhibited several homologies with other eukaryotes, and 6 distinct clades were identified within Ichthyophonus. A single clade contained a majority (71 of 98) of parasite isolations. This ubiquitous Ichthyophonus type occurred in 13 marine and anadromous hosts and was associated with epizootics in Atlantic herring, Chinook salmon, and American shad. A second clade contained all isolates from aquaculture, despite great geographic separation of the freshwater hosts. Each of the 4 remaining clades contained isolates from single host species. This study is the first to evaluate the genetic relationships among Ichthyophonus species across a significant portion of their host and geographic range. Additionally, parasite infection prevalence is reported in 16 fish species.

47 CFR 64.3001 - Obligation to transmit 911 calls.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Obligation to transmit 911 calls. 64.3001 Section 64.3001 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES... Obligation to transmit 911 calls. All telecommunications carriers shall transmit all 911 calls to a PSAP, to...

47 CFR 64.3001 - Obligation to transmit 911 calls.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 3 2012-10-01 2012-10-01 false Obligation to transmit 911 calls. 64.3001 Section 64.3001 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES... Obligation to transmit 911 calls. All telecommunications carriers shall transmit all 911 calls to a PSAP, to...

47 CFR 64.3001 - Obligation to transmit 911 calls.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 3 2013-10-01 2013-10-01 false Obligation to transmit 911 calls. 64.3001 Section 64.3001 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES... Obligation to transmit 911 calls. All telecommunications carriers shall transmit all 911 calls to a PSAP, to...

47 CFR 64.3001 - Obligation to transmit 911 calls.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 3 2014-10-01 2014-10-01 false Obligation to transmit 911 calls. 64.3001 Section 64.3001 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES... Obligation to transmit 911 calls. All telecommunications carriers shall transmit all 911 calls to a PSAP, to...

47 CFR 64.3001 - Obligation to transmit 911 calls.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 3 2011-10-01 2011-10-01 false Obligation to transmit 911 calls. 64.3001 Section 64.3001 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES... Obligation to transmit 911 calls. All telecommunications carriers shall transmit all 911 calls to a PSAP, to...

Ocular Manifestations of Mosquito-Transmitted Diseases.

PubMed

Karesh, James W; Mazzoli, Robert A; Heintz, Shannon K

2018-03-01

Of the 3,548 known mosquito species, about 100 transmit human diseases. Mosquitoes are distributed globally throughout tropical and temperate regions where standing water sources are available for egg laying and the maturation of larva. Female mosquitoes require blood meals for egg production. This is the main pathway for disease transmission. Mosquitoes carry several pathogenic organisms responsible for significant ocular pathology and vision loss including West Nile, Rift Valley, chikungunya, dengue viruses, various encephalitis viruses, malarial parasites, Francisella tularensis, microfilarial parasites, including Dirofilaria, Wuchereria, and Brugia spp., and human botfly larvae. Health care providers may not be familiar with many of these mosquito-transmitted diseases or their associated ocular findings delaying diagnosis, treatment, and recovery of visual function. This article aims to provide an overview of the ocular manifestations associated with mosquito-transmitted diseases.

High Local Diversity of Trypanosoma in a Common Bat Species, and Implications for the Biogeography and Taxonomy of the T. cruzi Clade

PubMed Central

Kalko, Elisabeth K. V.; Cottontail, Iain; Wellinghausen, Nele; Tschapka, Marco; Perkins, Susan L.

2014-01-01

The Trypanosoma cruzi clade is a group of parasites that comprises T. cruzi sensu lato and its closest relatives. Although several species have been confirmed phylogenetically to belong to this clade, it is uncertain how many more species can be expected to belong into this group. Here, we present the results of a survey of trypanosome parasites of the bat Artibeus jamaicensis from the Panamá Canal Zone, an important seed disperser. Using a genealogical species delimitation approach, the Poisson tree processes (PTP), we tentatively identified five species of trypanosomes – all belonging to the T. cruzi clade. A small monophyletic group of three putative Trypanosoma species places at the base of the clade phylogeny, providing evidence for at least five independent colonization events of these parasites into the New World. Artibeus jamaicensis presents a high diversity of these blood parasites and is the vertebrate with the highest number of putative trypanosome species reported from a single locality. Our results emphasize the need for continued efforts to survey mammalian trypanosomes. PMID:25268381

Can treefrog phylogeographical clades and species' phylogenetic topologies be recovered by bioacoustical analyses?

PubMed

Forti, Lucas Rodriguez; Lingnau, Rodrigo; Encarnação, Lais Carvalho; Bertoluci, Jaime; Toledo, Luís Felipe

2017-01-01

Phenotypic traits, such as the frog advertisement call, are generally correlated with interspecific genetic variation, and, as a consequence of strong sexual selection, these behaviors may carry a phylogenetic signal. However, variation in acoustic traits is not always correlated with genetic differences between populations (intraspecific variation); phenotypic plasticity and environmental variables may explain part of such variation. For example, local processes can affect acoustic properties in different lineages due to differences in physical structure, climatic conditions, and biotic interactions, particularly when populations are isolated. However, acoustic traits can be used to test phylogenetic hypotheses. We analyzed the advertisement calls of Dendropsophus elegans males from 18 sites and compared them with those of four closely related congeneric species, in order to test for differences between inter and intraspecific variation. We analyzed 451 calls of 45 males of these five species. Because males from distant sites were grouped together without population congruence, differences found in advertisement calls among individuals were not correlated with phylogeographical clades. Phylogenetic and cluster analyses of the D. elegans clades and those of closely related species grouped all five species into the same topology, as reported by previous molecular and morphological phylogenies. However, the topology of the D. elegans phylogeographical clades did not match the topology previously reported. Acoustic communication in D. elegans seems to be conserved among populations, and the phylogeographical history of the species does not explain the variation among lineages in call properties, despite some congruent phylogenetic signals evident at the species level. Based on molecular clocks retrieved from the literature, it seems that more than 6.5 million years of divergence (late Miocene) are necessary to allow significant changes to occur in the acoustic

Can treefrog phylogeographical clades and species’ phylogenetic topologies be recovered by bioacoustical analyses?

PubMed Central

Forti, Lucas Rodriguez; Lingnau, Rodrigo; Encarnação, Lais Carvalho; Bertoluci, Jaime; Toledo, Luís Felipe

2017-01-01

Phenotypic traits, such as the frog advertisement call, are generally correlated with interspecific genetic variation, and, as a consequence of strong sexual selection, these behaviors may carry a phylogenetic signal. However, variation in acoustic traits is not always correlated with genetic differences between populations (intraspecific variation); phenotypic plasticity and environmental variables may explain part of such variation. For example, local processes can affect acoustic properties in different lineages due to differences in physical structure, climatic conditions, and biotic interactions, particularly when populations are isolated. However, acoustic traits can be used to test phylogenetic hypotheses. We analyzed the advertisement calls of Dendropsophus elegans males from 18 sites and compared them with those of four closely related congeneric species, in order to test for differences between inter and intraspecific variation. We analyzed 451 calls of 45 males of these five species. Because males from distant sites were grouped together without population congruence, differences found in advertisement calls among individuals were not correlated with phylogeographical clades. Phylogenetic and cluster analyses of the D. elegans clades and those of closely related species grouped all five species into the same topology, as reported by previous molecular and morphological phylogenies. However, the topology of the D. elegans phylogeographical clades did not match the topology previously reported. Acoustic communication in D. elegans seems to be conserved among populations, and the phylogeographical history of the species does not explain the variation among lineages in call properties, despite some congruent phylogenetic signals evident at the species level. Based on molecular clocks retrieved from the literature, it seems that more than 6.5 million years of divergence (late Miocene) are necessary to allow significant changes to occur in the acoustic

A revision of the “African Non-Spiny” Clade of Solanum L. (Solanum sections Afrosolanum Bitter, Benderianum Bitter, Lemurisolanum Bitter, Lyciosolanum Bitter, Macronesiotes Bitter, and Quadrangulare Bitter: Solanaceae)

PubMed Central

Knapp, Sandra; Vorontsova, Maria S.

2016-01-01

Abstract The African Non-Spiny (ANS) clade contains 14 species of mostly large canopy lianas or scandent shrubs confined to Madagascar (10) and continental Africa (4, with with one species reaching the southern Arabian peninsula). Members of the clade were previously classified in sections Afrosolanum Bitter, Benderianum Bitter, Lemurisolanum Bitter, Macronesiotes Bitter and Quadrangulare Bitter, and were throught to be related to a variety of New World groups. The group is an early-branching lineage of non-spiny solanums and characters shared with other vining New World solanums are homoplastic. The 14 species of the group occupy a wide range of habitats, from wet forests in western Africa to savanna and dry forests of southern Madagascar and dune habitats in South Africa. Many members of the group are highly variable morphologically, and habit can vary between shrub and canopy vine in a single locality. We here review the taxonomic history, morphology, potential relationships and ecology of these species; we provide keys for their identification, descriptions, full synonymy (including designations of lectotypes and neotypes) and nomenclatural notes. Illustrations, distribution maps and preliminary conservation assessments are provided for all species. PMID:27489494

Soil transmitted helminths and schistosoma mansoni infections among school children in Zarima town, northwest Ethiopia.

PubMed

Alemu, Abebe; Atnafu, Asmamaw; Addis, Zelalem; Shiferaw, Yitayal; Teklu, Takele; Mathewos, Biniam; Birhan, Wubet; Gebretsadik, Simon; Gelaw, Baye

2011-07-09

In Ethiopia, because of low quality drinking water supply and latrine coverage, helminths infections are the second most predominant causes of outpatient morbidity. Indeed, there is a scarcity of information on the prevalence of soil transmitted helminths and Schistosomiasis in Ethiopia, special in study area. Therefore, the aim of this study was to determine the prevalence and associated risk factors of soil transmitted helminths and intestinal Schistosomiasis. Cross-sectional study was conducted among 319 school children of Zarima town from April 1 to May 25, 2009. A pre-tested structured questionnaire was used to collect socio-demographic data and possible risk factors exposure. Early morning stool samples were collected and a Kato Katz semi concentration technique was used to examine and count parasitic load by compound light microscope. Data entry and analysis was done using SPSS-15 version and p-value < 0.05 considered statistically significant. Out of 319 study subjects, 263 (82.4%) of the study participants infected with one or more parasites. From soil transmitted helminths, Ascaris lumbricoides was the predominant isolate (22%) followed by Hookworms (19%) and Trichuris trichiura (2.5%). Schistosoma mansoni was also isolated in 37.9% of the study participants. Hookworm and S. mansoni infections showed statistically significant associations with shoe wearing and swimming habit of school children, respectively. Prevalence of soil transmitted helminths (STH) and S.mansoni was high and the diseases were still major health problem in the study area which alerts public health intervention as soon as possible.

Changes in adaptation of H5N2 highly pathogenic avian influenza H5 clade 2.3.4.4 viruses in chickens and mallards

PubMed Central

DeJesus, Eric; Costa-Hurtado, Mar; Smith, Diane; Lee, Dong-Hun; Spackman, Erica; Kapczynski, Darrell R.; Torchetti, Mia Kim; Killian, Mary Lea; Suarez, David L.; Swayne, David E.; Pantin-Jackwood, Mary J.

2016-01-01

H5N2 highly pathogenic avian influenza (HPAI) viruses caused a severe poultry outbreak in the United States (U.S.) during 2015. In order to examine changes in adaptation of this viral lineage, the infectivity, pathogenesis and transmission of poultry H5N2 viruses were investigated in chickens and mallards in comparison to the wild duck 2014 U.S. index H5N2 virus. The four poultry isolates examined had a lower mean bird infectious dose than the index virus but still transmitted poorly to direct contacts. In mallards, two of the H5N2 poultry isolates had similar high infectivity and transmissibility as the index H5N2 virus, the H5N8 U.S. index virus, and a 2005 H5N1 clade 2.2 virus. Mortality occurred with the H5N1 virus and, interestingly, with one of two poultry H5N2 isolates. Increased virus adaptation to chickens was observed with the poultry H5N2 viruses; however these viruses retained high adaptation to mallards but pathogenicity was differently affected. PMID:27632565

A novel Haemosporida clade at the rank of genus in North American cranes (Aves: Gruiformes).

PubMed

Bertram, Miranda R; Hamer, Sarah A; Hartup, Barry K; Snowden, Karen F; Medeiros, Matthew C; Outlaw, Diana C; Hamer, Gabriel L

2017-04-01

The unicellular blood parasites in the order Haemosporida are highly diverse, infect many vertebrates, are responsible for a large disease burden among humans and animals, and have reemerged as an important model system to understand the evolutionary and ecological dynamics of host-parasite interactions. The phylogenetics and systematics of Haemosporida are limited by poor sampling of different vertebrate host taxa. We surveyed the Haemosporida of wild whooping cranes (Grus americana) and sandhill cranes (Grus canadensis) (Aves: Gruiformes) using a combination of morphological and molecular approaches. We identified Haemoproteus antigonis in blood smears based on published morphological descriptions. Phylogenetic analysis based on partial cytochrome b (cytb) and cytochrome oxidase (coI) sequences placed H. antigonis parasites in a novel clade, distinct from all avian Haemosporida genera for which cytb and/or coI sequences are available. Molecular clock and divergence estimates suggest this crane clade may represent a new genus. This is the first molecular description of H. antigonis and the first report of H. antigonis in wild whooping cranes, an endangered bird in North America. Further sampling of Haemosporida, especially from hosts of the Gruiformes and other poorly sampled orders, will help to resolve the relationship of the H. antigonis clade to other avian Haemosporida genera. Our study highlights the potential of sampling neglected host species to discover novel lineages of diverse parasite groups. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments

USGS Publications Warehouse

Holmes, Dawn E.; O'Neil, Regina A.; Vrionis, Helen A.; N'Guessan, Lucie A.; Ortiz-Bernad, Irene; Larrahondo, Maria J.; Adams, Lorrie A.; Ward, Joy A.; Nicoll , Julie S.; Nevin, Kelly P.; Chavan, Milind A.; Johnson, Jessica P.; Long, Philip E.; Lovely, Derek R.

2007-01-01

There are distinct differences in the physiology of Geobacter species available in pure culture. Therefore, to understand the ecology of Geobacter species in subsurface environments, it is important to know which species predominate. Clone libraries were assembled with 16S rRNA genes and transcripts amplified from three subsurface environments in which Geobacter species are known to be important members of the microbial community: (1) a uranium-contaminated aquifer located in Rifle, CO, USA undergoing in situ bioremediation; (2) an acetate-impacted aquifer that serves as an analog for the long-term acetate amendments proposed for in situ uranium bioremediation and (3) a petroleum-contaminated aquifer in which Geobacter species play a role in the oxidation of aromatic hydrocarbons coupled with the reduction of Fe(III). The majority of Geobacteraceae 16S rRNA sequences found in these environments clustered in a phylogenetically coherent subsurface clade, which also contains a number of Geobacter species isolated from subsurface environments. Concatamers constructed with 43 Geobacter genes amplified from these sites also clustered within this subsurface clade. 16S rRNA transcript and gene sequences in the sediments and groundwater at the Rifle site were highly similar, suggesting that sampling groundwater via monitoring wells can recover the most active Geobacter species. These results suggest that further study of Geobacter species in the subsurface clade is necessary to accurately model the behavior of Geobacter species during subsurface bioremediation of metal and organic contaminants.

47 CFR 22.809 - Transmitting power limits.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Transmitting power limits. The transmitting power of ground and airborne mobile transmitters operating on the... Watts, except as provided in § 22.811. (b) Airborne mobile transmitters. The transmitter power output of airborne mobile transmitters must not exceed 25 Watts and must not be less than 4 Watts. ...

Root evolution at the base of the lycophyte clade: insights from an Early Devonian lycophyte

PubMed Central

Matsunaga, Kelly K. S.; Tomescu, Alexandru M. F.

2016-01-01

Background and Aims The evolution of complex rooting systems during the Devonian had significant impacts on global terrestrial ecosystems and the evolution of plant body plans. However, detailed understanding of the pathways of root evolution and the architecture of early rooting systems is currently lacking. We describe the architecture and resolve the structural homology of the rooting system of an Early Devonian basal lycophyte. Insights gained from these fossils are used to address lycophyte root evolution and homology. Methods Plant fossils are preserved as carbonaceous compressions at Cottonwood Canyon (Wyoming), in the Lochkovian–Pragian (∼411 Ma; Early Devonian) Beartooth Butte Formation. We analysed 177 rock specimens and documented morphology, cuticular anatomy and structural relationships, as well as stratigraphic position and taphonomic conditions. Key Results The rooting system of the Cottonwood Canyon lycophyte is composed of modified stems that bear fine, dichotomously branching lateral roots. These modified stems, referred to as root-bearing axes, are produced at branching points of the above-ground shoot system. Root-bearing axes preserved in growth position exhibit evidence of positive gravitropism, whereas the lateral roots extend horizontally. Consistent recurrence of these features in successive populations of the plant preserved in situ demonstrates that they represent constitutive structural traits and not opportunistic responses of a flexible developmental programme. Conclusions This is the oldest direct evidence for a rooting system preserved in growth position. These rooting systems, which can be traced to a parent plant, include some of the earliest roots known to date and demonstrate that substantial plant–substrate interactions were under way by Early Devonian time. The morphological relationships between stems, root-bearing axes and roots corroborate evidence that positive gravitropism and root identity were evolutionarily

Root evolution at the base of the lycophyte clade: insights from an Early Devonian lycophyte.

PubMed

Matsunaga, Kelly K S; Tomescu, Alexandru M F

2016-04-01

The evolution of complex rooting systems during the Devonian had significant impacts on global terrestrial ecosystems and the evolution of plant body plans. However, detailed understanding of the pathways of root evolution and the architecture of early rooting systems is currently lacking. We describe the architecture and resolve the structural homology of the rooting system of an Early Devonian basal lycophyte. Insights gained from these fossils are used to address lycophyte root evolution and homology. Plant fossils are preserved as carbonaceous compressions at Cottonwood Canyon (Wyoming), in the Lochkovian-Pragian (∼411 Ma; Early Devonian) Beartooth Butte Formation. We analysed 177 rock specimens and documented morphology, cuticular anatomy and structural relationships, as well as stratigraphic position and taphonomic conditions. The rooting system of the Cottonwood Canyon lycophyte is composed of modified stems that bear fine, dichotomously branching lateral roots. These modified stems, referred to as root-bearing axes, are produced at branching points of the above-ground shoot system. Root-bearing axes preserved in growth position exhibit evidence of positive gravitropism, whereas the lateral roots extend horizontally. Consistent recurrence of these features in successive populations of the plant preserved in situ demonstrates that they represent constitutive structural traits and not opportunistic responses of a flexible developmental programme. This is the oldest direct evidence for a rooting system preserved in growth position. These rooting systems, which can be traced to a parent plant, include some of the earliest roots known to date and demonstrate that substantial plant-substrate interactions were under way by Early Devonian time. The morphological relationships between stems, root-bearing axes and roots corroborate evidence that positive gravitropism and root identity were evolutionarily uncoupled in lycophytes, and challenge the hypothesis that

Full-Genome Sequence of a Novel Varicella-Zoster Virus Clade Isolated in Mexico.

PubMed

Garcés-Ayala, Fabiola; Rodríguez-Castillo, Araceli; Ortiz-Alcántara, Joanna María; Gonzalez-Durán, Elizabeth; Segura-Candelas, José Miguel; Pérez-Agüeros, Sandra Ivette; Escobar-Escamilla, Noé; Méndez-Tenorio, Alfonso; Diaz-Quiñonez, José Alberto; Ramirez-González, José Ernesto

2015-07-09

Varicella-zoster virus (VZV) is a member of the Herpesviridae family, which causes varicella (chicken pox) and herpes zoster (shingles) in humans. Here, we report the complete genome sequence of varicella-zoster virus, isolated from a vesicular fluid sample, revealing the circulation of VZV clade VIII in Mexico. Copyright © 2015 Garcés-Ayala et al.

Multilocus molecular phylogeny of the ornamental wood-eating catfishes (Siluriformes, Loricariidae, Panaqolus and Panaque) reveals undescribed diversity and parapatric clades.

PubMed

Lujan, Nathan K; Cramer, Christian A; Covain, Raphael; Fisch-Muller, Sonia; López-Fernández, Hernán

2017-04-01

Approximately two-dozen species in three genera of the Neotropical suckermouth armored catfish family Loricariidae are the only described fishes known to specialize on diets consisting largely of wood. We conducted a molecular phylogenetic analysis of 10 described species and 14 undescribed species or morphotypes assigned to the wood-eating catfish genus Panaqolus, and four described species and three undescribed species or morphotypes assigned to the distantly related wood-eating catfish genus Panaque. Our analyses included individuals and species from both genera that are broadly distributed throughout tropical South America east of the Andes Mountains and 13 additional genera hypothesized to have also descended from the most recent common ancestor of Panaqolus and Panaque. Bayesian and maximum likelihood analyses of two mitochondrial and three nuclear loci totaling 4293bp confirmed respective monophyly of Panaqolus, exclusive of the putative congener 'Panaqolus' koko, and Panaque. Members of Panaqolus sensu stricto were distributed across three strongly monophyletic clades: a clade of 10 generally darkly colored, lyretail species distributed across western headwaters of the Amazon Basin, a clade of three irregularly and narrowly banded species from the western Orinoco Basin, and a clade of 11 generally brown, broadly banded species that are widely distributed throughout the Amazon Basin. We erect new subgenera for each of these clades and a new genus for the morphologically, biogeographically and ecologically distinct species 'Panaqolus' koko. Our finding that perhaps half of the species-level diversity in the widespread genus Panaqolus remains undescribed illustrates the extent to which total taxonomic diversity of small and philopatric, yet apparently widely distributed, Amazonian fishes may remain underestimated. Ranges for two Panaqolus subgenera and the genus Panaque overlap with the wood-eating genus Cochliodon in central Andean tributaries of the upper

[Correlation between soil-transmitted nematode infections and children's growth].

PubMed

Wang, Xiao-Bing; Wang, Guo-Fei; Zhang, Lin-Xiu; Luo, Ren-Fu; Wang, Ju-Jun; Medina, Alexis; Eggleston, Karen; Rozelle, Scott; Smith, Scott

2013-06-01

To understand the infection status of soil-transmitted nematodes in southwest China and the correlation between soil-transmitted nematode infections and children's growth. The prevalence of soil-transmitted nematode infections was determined by Kato-Katz technique, and in part of the children, the examination of Enterobius vermicularis eggs was performed by using the cellophane swab method. The influencing factors were surveyed by using a standardized questionnaire. The relationship between soil-transmitted nematode infections and children's growth was analyzed by the ordinary least square (OLS) method. A total of 1 707 children were examined, with a soil-transmitted nematode infection rate of 22.2%. The results of OLS analysis showed that there existed the negative correlation between soil-transmitted nematode infections and the indexes of children's growth including BMI, the weight-for-age Z score and height-for-age Z score. Furthermore, other correlated variables included the age, gender, educational level of mother and raising livestock and poultry, etc. Children' s retardation is still a serious issue in the southwest poor areas of China and correlated with the infections of soil-transmitted nematodes. For improving children's growth, it is greatly significant to enhance the deworming and health education about parasitic diseases in mothers.

Novel reassortant clade 2.3.4.4 avian influenza A (H5N8) virus in a grey heron in South Korea in 2017.

PubMed

Woo, Chanjin; Kwon, Jung-Hoon; Lee, Dong-Hun; Kim, Youngsik; Lee, Kwanghee; Jo, Seong-Deok; Son, Ki Dong; Oem, Jae-Ku; Wang, Seung-Jun; Kim, Yongkwan; Shin, Jeonghwa; Song, Chang-Seon; Jheong, Weonhwa; Jeong, Jipseol

2017-12-01

We report the identification of a novel reassortant clade 2.3.4.4 H5N8 virus from a dead grey heron in Korea in 2017. Outbreaks of clade 2.3.4.4 H5 HPAIVs have been reported worldwide, and they have evolved into multiple genotypes among wild birds. Phylogenetic analysis indicated that this virus likely originated from Qinghai Lake and Western Siberia and further evolved through reassortment with Eurasian LPAI during the 2016 fall migration of wild birds. Enhanced surveillance and comparative genetic analysis will help to monitor the further evolution and dissemination of clade 2.3.4.4 HPAIVs.

The evolutionary dynamics of highly pathogenic avian influenza H5N1 in south-central Vietnam reveals multiple clades evolving from Chinese and Cambodian viruses.

PubMed

Nguyen, Tinh Huu; Than, Van Thai; Thanh, Hien Dang; Nguyen, Van Quang; Nguyen, Kim Hue; Nguyen, Duc Tan; Park, Jong-Hwa; Chung, In Sik; Jeong, Dae Gwin; Chang, Kyu-Tae; Oh, Tae Kwang; Kim, Wonyong

2015-10-01

In Vietnam, highly pathogenic avian influenza (HPAI), such as that caused by H5N1 viruses, is the most highly contagious infectious disease that has been affecting domestic poultry in recent years. Vietnam might be an evolutionary hotspot and a potential source of globally pandemic strains. However, few studies have reported viruses circulating in the south-central region of Vietnam. In the present study, 47 H5N1-positive samples were collected from both vaccinated and unvaccinated poultry farms in the South Central Coast region of Vietnam during 2013-2014, and their genetic diversity was analyzed. A common sequence motif for HPAI virus was identified at HA-cleavage sites in all samples: either RERRRKR/G (clades 2.3.2.1c and 2.3.2.1a) or REGRRKKR/G (clade 1.1.2). Phylogenetic analysis of HA genes identified three clades of HPAI H5N1: 1.1.2 (n=1), 2.3.2.1a (n=1), and 2.3.2.1c (n=45). The phylogenetic analysis indicated that these Vietnamese clades may have evolved from Chinese and Cambodian virus clades isolated in 2012-2013 but are less closely related to the clades detected from the Tyva Republic, Bulgaria, Mongolia, Japan, and Korea in 2009-2011. Detection of the coexistence of virus clades 2.3.2.1 and the very virulent 1.1.2 in the south-central regions suggests their local importance and highlights concerns regarding their spread, both northwards and southwards, as well as the potential for reassortment. The obtained data highlight the importance of regular identification of viral evolution and the development and use of region-specific vaccines. Copyright © 2015 Elsevier Ltd. All rights reserved.

Pathobiology of clade 2.3.4.4 H5Nx high pathogenicity avian influenza virus infections in minor gallinaceous poultry supports early backyard flock introductions in the Western United States in 2014-2015

USDA-ARS?s Scientific Manuscript database

In 2014 and 2015, the United States experienced an unprecedented outbreak of Eurasian clade 2.3.4.4 H5 highly pathogenic avian influenza (HPAI) virus. Initial cases affected mainly wild birds and mixed backyard poultry species, while later outbreaks affected mostly commercial chickens and turkeys. T...

ArxA, a new clade of arsenite oxidase within the DMSO reductase family of molybdenum oxidoreductases

USGS Publications Warehouse

Zargar, Kamrun; Conrad, Alison; Bernick, David L.; Lowe, Todd M.; Stolc, Viktor; Hoeft, Shelley; Oremland, Ronald S.; Stolz, John; Saltikov, Chad W.

2012-01-01

Arsenotrophy, growth coupled to autotrophic arsenite oxidation or arsenate respiratory reduction, occurs only in the prokaryotic domain of life. The enzymes responsible for arsenotrophy belong to distinct clades within the DMSO reductase family of molybdenum-containing oxidoreductases: specifically arsenate respiratory reductase, ArrA, and arsenite oxidase, AioA (formerly referred to as AroA and AoxB). A new arsenite oxidase clade, ArxA, represented by the haloalkaliphilic bacterium Alkalilimnicola ehrlichii strain MLHE-1 was also identified in the photosynthetic purple sulfur bacterium Ectothiorhodospira sp. strain PHS-1. A draft genome sequence of PHS-1 was completed and an arx operon similar to MLHE-1 was identified. Gene expression studies showed that arxA was strongly induced with arsenite. Microbial ecology investigation led to the identification of additional arxA-like sequences in Mono Lake and Hot Creek sediments, both arsenic-rich environments in California. Phylogenetic analyses placed these sequences as distinct members of the ArxA clade of arsenite oxidases. ArxA-like sequences were also identified in metagenome sequences of several alkaline microbial mat environments of Yellowstone National Park hot springs. These results suggest that ArxA-type arsenite oxidases appear to be widely distributed in the environment presenting an opportunity for further investigations of the contribution of Arx-dependent arsenotrophy to the arsenic biogeochemical cycle.

Evidence of a Native Northwest Atlantic COI Haplotype Clade in the Cryptogenic Colonial Ascidian Botryllus schlosseri.

PubMed

Yund, Philip O; Collins, Catherine; Johnson, Sheri L

2015-06-01

The colonial ascidian Botryllus schlosseri should be considered cryptogenic (i.e., not definitively classified as either native or introduced) in the Northwest Atlantic. Although all the evidence is quite circumstantial, over the last 15 years most research groups have accepted the scenario of human-mediated dispersal and classified B. schlosseri as introduced; others have continued to consider it native or cryptogenic. We address the invasion status of this species by adding 174 sequences to the growing worldwide database for the mitochondrial gene cytochrome c oxidase subunit I (COI) and analyzing 1077 sequences to compare genetic diversity of one clade of haplotypes in the Northwest Atlantic with two hypothesized source regions (the Northeast Atlantic and Mediterranean). Our results lead us to reject the prevailing view of the directionality of transport across the Atlantic. We argue that the genetic diversity patterns at COI are far more consistent with the existence of at least one haplotype clade in the Northwest Atlantic (and possibly a second) that substantially pre-dates human colonization from Europe, with this native North American clade subsequently introduced to three sites in Northeast Atlantic and Mediterranean waters. However, we agree with past researchers that some sites in the Northwest Atlantic have more recently been invaded by alien haplotypes, so that some populations are currently composed of a mixture of native and invader haplotypes. © 2015 Marine Biological Laboratory.

Early Homo and the role of the genus in paleoanthropology.

PubMed

Villmoare, Brian

2018-01-01

The history of the discovery of early fossils attributed to the genus Homo has been contentious, with scholars disagreeing over the generic assignment of fossils proposed as members of our genus. In this manuscript I review the history of discovery and debate over early Homo and evaluate the various taxonomic hypotheses for the genus. To get a sense of how hominin taxonomy compares to taxonomic practice outside paleoanthropology, I compare the diversity of Homo to genera in other vertebrate clades. Finally, I propose a taxonomic model that hews closely to current models for hominin phylogeny and is consistent with taxonomic practice across evolutionary biology. © 2018 American Association of Physical Anthropologists.

Optimisation approaches for concurrent transmitted light imaging during confocal microscopy.

PubMed

Collings, David A

2015-01-01

The transmitted light detectors present on most modern confocal microscopes are an under-utilised tool for the live imaging of plant cells. As the light forming the image in this detector is not passed through a pinhole, out-of-focus light is not removed. It is this extended focus that allows the transmitted light image to provide cellular and organismal context for fluorescence optical sections generated confocally. More importantly, the transmitted light detector provides images that have spatial and temporal registration with the fluorescence images, unlike images taken with a separately-mounted camera. Because plants often provide difficulties for taking transmitted light images, with the presence of pigments and air pockets in leaves, this study documents several approaches to improving transmitted light images beginning with ensuring that the light paths through the microscope are correctly aligned (Köhler illumination). Pigmented samples can be imaged in real colour using sequential scanning with red, green and blue lasers. The resulting transmitted light images can be optimised and merged in ImageJ to generate colour images that maintain registration with concurrent fluorescence images. For faster imaging of pigmented samples, transmitted light images can be formed with non-absorbed wavelengths. Transmitted light images of Arabidopsis leaves expressing GFP can be improved by concurrent illumination with green and blue light. If the blue light used for YFP excitation is blocked from the transmitted light detector with a cheap, coloured glass filters, the non-absorbed green light will form an improved transmitted light image. Changes in sample colour can be quantified by transmitted light imaging. This has been documented in red onion epidermal cells where changes in vacuolar pH triggered by the weak base methylamine result in measurable colour changes in the vacuolar anthocyanin. Many plant cells contain visible levels of pigment. The transmitted light

A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae): robust support for interfamilial relationships and molecular synapomorphies define major clades.

PubMed

Cameron, Stephen L; Lo, Nathan; Bourguignon, Thomas; Svenson, Gavin J; Evans, Theodore A

2012-10-01

Despite their ecological significance as decomposers and their evolutionary significance as the most speciose eusocial insect group outside the Hymenoptera, termite (Blattodea: Termitoidae or Isoptera) evolutionary relationships have yet to be well resolved. Previous morphological and molecular analyses strongly conflict at the family level and are marked by poor support for backbone nodes. A mitochondrial (mt) genome phylogeny of termites was produced to test relationships between the recognised termite families, improve nodal support and test the phylogenetic utility of rare genomic changes found in the termite mt genome. Complete mt genomes were sequenced for 7 of the 9 extant termite families with additional representatives of each of the two most speciose families Rhinotermitidae (3 of 7 subfamilies) and Termitidae (3 of 8 subfamilies). The mt genome of the well supported sister-group of termites, the subsocial cockroach Cryptocercus, was also sequenced. A highly supported tree of termite relationships was produced by all analytical methods and data treatment approaches, however the relationship of the termites+Cryptocercus clade to other cockroach lineages was highly affected by the strong nucleotide compositional bias found in termites relative to other dictyopterans. The phylogeny supports previously proposed suprafamilial termite lineages, the Euisoptera and Neoisoptera, a later derived Kalotermitidae as sister group of the Neoisoptera and a monophyletic clade of dampwood (Stolotermitidae, Archotermopsidae) and harvester termites (Hodotermitidae). In contrast to previous termite phylogenetic studies, nodal supports were very high for family-level relationships within termites. Two rare genomic changes in the mt genome control region were found to be molecular synapomorphies for major clades. An elongated stem-loop structure defined the clade Polyphagidae + (Cryptocercus+termites), and a further series of compensatory base changes in this stem-loop is

MOLECULAR PHYLOGENY AND TAXONOMY OF THE AEGAGROPILA CLADE (CLADOPHORALES, ULVOPHYCEAE), INCLUDING THE DESCRIPTION OF AEGAGROPILOPSIS GEN. NOV. AND PSEUDOCLADOPHORA GEN. NOV.(1).

PubMed

Boedeker, Christian; O'Kelly, Charles J; Star, Wim; Leliaert, Frederik

2012-06-01

The Aegagropila clade represents a unique group of cladophoralean green algae occurring mainly in brackish and freshwater environments. The clade is sister to the species-rich and primarily marine Cladophora and Siphonocladus lineages. Phylogenetic analyses of partial LSU and SSU nrDNA sequences reveal four main lineages within the Aegagropila clade, and allow a taxonomic reassessment. One lineage consists of two marine 'Cladophora' species, for which the new genus Pseudocladophora and the new family Pseudocladophoraceae are proposed. For the other lineages, the family name Pithophoraceae is reinstated. Within the Pithophoraceae, the earliest diverging lineage includes Wittrockiella and Cladophorella calcicola, occurring mainly in brackish and subaerial habitats. The two other lineages are restricted to freshwater. One of them shows a strong tendency for epizoism, and consists of Basicladia species and Arnoldiella conchophila. The other lineage includes Aegagropila, Pithophora and a small number of tropical 'Cladophora' species. The latter are transferred to the new genus Aegagropilopsis. Previously, polypyramidal pyrenoids had been suggested to be apomorphous for this clade, but we report the finding of both polypyramidal and bilenticular pyrenoids in members of the Pithophoraceae, and thus show that this character has no diagnostic value. © 2012 Phycological Society of America.

An updated assessment of Symbiodinium spp. that associate with common scleractinian corals from Moorea (French Polynesia) reveals high diversity among background symbionts and a novel finding of clade B.

PubMed

Rouzé, Héloïse; Lecellier, Gaël J; Saulnier, Denis; Planes, Serge; Gueguen, Yannick; Wirshing, Herman H; Berteaux-Lecellier, Véronique

2017-01-01

The adaptative bleaching hypothesis (ABH) states that, depending on the symbiotic flexibility of coral hosts (i.e., the ability of corals to "switch" or "shuffle" their algal symbionts), coral bleaching can lead to a change in the composition of their associated Symbiodinium community and, thus, contribute to the coral's overall survival. In order to determine the flexibility of corals, molecular tools are required to provide accurate species delineations and to detect low levels of coral-associated Symbiodinium . Here, we used highly sensitive quantitative (real-time) PCR (qPCR) technology to analyse five common coral species from Moorea (French Polynesia), previously screened using only traditional molecular methods, to assess the presence of low-abundance (background) Symbiodinium spp. Similar to other studies, each coral species exhibited a strong specificity to a particular clade, irrespective of the environment. In addition, however, each of the five species harboured at least one additional Symbiodinium clade, among clades A-D, at background levels. Unexpectedly, and for the first time in French Polynesia, clade B was detected as a coral symbiont. These results increase the number of known coral- Symbiodinium associations from corals found in French Polynesia, and likely indicate an underestimation of the ability of the corals in this region to associate with and/or "shuffle" different Symbiodinium clades. Altogether our data suggest that corals from French Polynesia may favor a trade-off between optimizing symbioses with a specific Symbiodinium clade(s), maintaining associations with particular background clades that may play a role in the ability of corals to respond to environmental change.

Nematode infections: soil-transmitted helminths and trichinella.

PubMed

Knopp, Stefanie; Steinmann, Peter; Keiser, Jennifer; Utzinger, Jürg

2012-06-01

Infection with soil-transmitted helminths occurs via ingestion of nematode eggs with contaminated food and water, via hands, or inhalation of dust, or by penetration of larvae through the skin. Trichinella infections are caused by the ingestion of larvae contained in undercooked meat. In highly endemic areas, preventive chemotherapy (ie, regular administration of anthelmintic drugs to at-risk populations) is the key strategy against soil-transmitted helminthiasis. Integrated control approaches, including improved hygiene, sanitation, and water, are required for lasting effects. Because of growing tourism, travel, and migration, clinicians and specialized travel clinics must remain aware of the diagnosis, prevention, and treatment of soil-transmitted helminth and Trichinella infections. Copyright © 2012 Elsevier Inc. All rights reserved.

Nucleic acids encoding mosaic clade M human immunodeficiency virus type 1 (HIV-1) envelope immunogens

DOEpatents

Korber, Bette T; Fischer, William; Liao, Hua-Xin; Haynes, Barton F; Letvin, Norman; Hahn, Beatrice H

2015-04-21

The present invention relates to nucleic acids encoding mosaic clade M HIV-1 Env polypeptides and to compositions and vectors comprising same. The nucleic acids of the invention are suitable for use in inducing an immune response to HIV-1 in a human.

Revision of the Middle American clade of the ant genus Stenamma Westwood (Hymenoptera, Formicidae, Myrmicinae)

PubMed Central

Branstetter, Michael G.

2013-01-01

Abstract Stenamma is a cryptic “leaf-litter” ant genus that occurs in mesic forest habitats throughout the Holarctic region, Central America, and part of northwestern South America (Colombia and Ecuador). The genus was thought to be restricted primarily to the temperate zone, but recent collecting efforts have uncovered a large radiation of Neotropical forms, which rival the Holarctic species in terms of morphological and behavioral diversity. By inferring a broad-scale molecular phylogeny of Stenamma, Branstetter (2012) showed that all Neotropical species belong to a diverse Middle American clade (MAC), and that this clade is sister to an almost completely geographically separated Holarctic clade (HOC). Here, the Middle American clade of Stenamma is revised to recognize 40 species, of which 33 are described as new. Included in the revision are a key to species based on the worker caste, and for each species where possible, descriptions and images of workers and queens, images of males, information on geographic distribution, descriptions of intraspecific variation, and notes on natural history. Several species groups are defined, but the majority of species remain unassigned due to a lack of diagnostic morphological character states for most molecular clades. The following species are redescribed: Stenamma alas Longino, Stenamma diversum Mann, Stenamma expolitum Smith, Stenamma felixi Mann, Stenamma huachucanum Smith, Stenamma manni Wheeler, and Stenamma schmidti Menozzi. The following are described as new: Stenamma andersoni sp. n., Stenamma atribellum sp. n., Stenamma brujita sp. n., Stenamma callipygium sp. n., Stenamma catracho sp. n., Stenamma connectum sp. n., Stenamma crypticum sp. n., Stenamma cusuco sp. n., Stenamma excisum sp. n., Stenamma expolitico sp. n., Stenamma hojarasca sp. n., Stenamma ignotum sp. n., Stenamma lagunum sp. n., Stenamma llama sp. n., Stenamma leptospinum sp. n., Stenamma lobinodus sp. n., Stenamma longinoi sp. n., Stenamma

Evolutionary clade affects resistance of Clostridium difficile spores to Cold Atmospheric Plasma

NASA Astrophysics Data System (ADS)

Connor, Mairéad; Flynn, Padrig B.; Fairley, Derek J.; Marks, Nikki; Manesiotis, Panagiotis; Graham, William G.; Gilmore, Brendan F.; McGrath, John W.

2017-02-01

Clostridium difficile is a spore forming bacterium and the leading cause of colitis and antibiotic associated diarrhoea in the developed world. Spores produced by C. difficile are robust and can remain viable for months, leading to prolonged healthcare-associated outbreaks with high mortality. Exposure of C. difficile spores to a novel, non-thermal atmospheric pressure gas plasma was assessed. Factors affecting sporicidal efficacy, including percentage of oxygen in the helium carrier gas admixture, and the effect on spores from different strains representing the five evolutionary C. difficile clades was investigated. Strains from different clades displayed varying resistance to cold plasma. Strain R20291, representing the globally epidemic ribotype 027 type, was the most resistant. However all tested strains displayed a ~3 log reduction in viable spore counts after plasma treatment for 5 minutes. Inactivation of a ribotype 078 strain, the most prevalent clinical type seen in Northern Ireland, was further assessed with respect to surface decontamination, pH, and hydrogen peroxide concentration. Environmental factors affected plasma activity, with dry spores without the presence of organic matter being most susceptible. This study demonstrates that cold atmospheric plasma can effectively inactivate C. difficile spores, and highlights factors that can affect sporicidal activity.

Infectivity, transmission and pathogenicity of H5 highly pathogenic avian influenza clade 2.3.4.4 (H5N8 and H5N2) United States index viruses in Pekin ducks and Chinese geese.

PubMed

Pantin-Jackwood, Mary J; Costa-Hurtado, Mar; Bertran, Kateri; DeJesus, Eric; Smith, Diane; Swayne, David E

2017-06-07

In late 2014, a H5N8 highly pathogenic avian influenza (HPAI) virus, clade 2.3.4.4, spread by migratory waterfowl into North America reassorting with low pathogenicity AI viruses to produce a H5N2 HPAI virus. Since domestic waterfowl are common backyard poultry frequently in contact with wild waterfowl, the infectivity, transmissibility, and pathogenicity of the United States H5 HPAI index viruses (H5N8 and H5N2) was investigated in domestic ducks and geese. Ducks infected with the viruses had an increase in body temperature but no or mild clinical signs. Infected geese did not show increase in body temperature and most only had mild clinical signs; however, some geese presented severe neurological signs. Ducks became infected and transmitted the viruses to contacts when inoculated with high virus doses [(10 4 and 10 6 50% embryo infective dose (EID 50 )], but not with a lower dose (10 2 EID 50 ). Geese inoculated with the H5N8 virus became infected regardless of the virus dose given, and transmitted the virus to direct contacts. Only geese inoculated with the higher doses of the H5N2 and their contacts became infected, indicating differences in infectivity between the two viruses and the two waterfowl species. Geese shed higher titers of virus and for a longer period of time than ducks. In conclusion, the H5 HPAI viruses can infect domestic waterfowl and easily transmit to contact birds, with geese being more susceptible to infection and disease than ducks. The disease is mostly asymptomatic, but infected birds shed virus for several days representing a risk to other poultry species.

GNSS satellite transmit power and its impact on orbit determination

NASA Astrophysics Data System (ADS)

Steigenberger, Peter; Thoelert, Steffen; Montenbruck, Oliver

2018-06-01

Antenna thrust is a small acceleration acting on Global Navigation Satellite System satellites caused by the transmission of radio navigation signals. Knowledge about the transmit power and the mass of the satellites is required for the computation of this effect. The actual transmit power can be obtained from measurements with a high-gain antenna and knowledge about the properties of the transmit and receive antennas as well as losses along the propagation path. Transmit power measurements for different types of GPS, GLONASS, Galileo, and BeiDou-2 satellites were taken with a 30-m dish antenna of the German Aerospace Center (DLR) located at its ground station in Weilheim. For GPS, total L-band transmit power levels of 50-240 W were obtained, 20-135 W for GLONASS, 95-265 W for Galileo, and 130-185 W for BeiDou-2. The transmit power differs usually only slightly for individual spacecraft within one satellite block. An exception are the GLONASS-M satellites where six subgroups with different transmit power levels could be identified. Considering the antenna thrust in precise orbit determination of GNSS satellites decreases the orbital radius by 1-27 mm depending on the transmit power, the satellite mass, and the orbital period.

Soil transmitted helminths and schistosoma mansoni infections among school children in zarima town, northwest Ethiopia

PubMed Central

2011-01-01

Background In Ethiopia, because of low quality drinking water supply and latrine coverage, helminths infections are the second most predominant causes of outpatient morbidity. Indeed, there is a scarcity of information on the prevalence of soil transmitted helminths and Schistosomiasis in Ethiopia, special in study area. Therefore, the aim of this study was to determine the prevalence and associated risk factors of soil transmitted helminths and intestinal Schistosomiasis. Methods Cross-sectional study was conducted among 319 school children of Zarima town from April 1 to May 25, 2009. A pre-tested structured questionnaire was used to collect socio-demographic data and possible risk factors exposure. Early morning stool samples were collected and a Kato Katz semi concentration technique was used to examine and count parasitic load by compound light microscope. Data entry and analysis was done using SPSS-15 version and p-value < 0.05 considered statistically significant. Results Out of 319 study subjects, 263 (82.4%) of the study participants infected with one or more parasites. From soil transmitted helminths, Ascaris lumbricoides was the predominant isolate (22%) followed by Hookworms (19%) and Trichuris trichiura (2.5%). Schistosoma mansoni was also isolated in 37.9% of the study participants. Hookworm and S. mansoni infections showed statistically significant associations with shoe wearing and swimming habit of school children, respectively. Conclusion Prevalence of soil transmitted helminths (STH) and S.mansoni was high and the diseases were still major health problem in the study area which alerts public health intervention as soon as possible. PMID:21740589

Diversification in an Afro-Asian songbird clade (Erythropygia-Copsychus) reveals founder-event speciation via trans-oceanic dispersals and a southern to northern colonization pattern in Africa.

PubMed

Voelker, Gary; Peñalba, Joshua V; Huntley, Jerry W; Bowie, Rauri C K

2014-04-01

Erythropygia scrub-robins and their allies are distributed throughout Africa, Europe, Southeast Asia, India, Madagascar and the Seychelles. This broad distribution, as well as the distribution of Erythropygia taxa across Africa, presents an interesting opportunity to explore the mechanisms by which this biogeographic distribution was achieved. Multilocus sequence data (3310 base pairs from two mitochondrial and two nuclear genes) were generated for all species of Erythropygia and Cercotrichas scrub-robins, as well as from genera previously shown to render Erythropygia paraphyletic. Using model-based phylogenetic methods and molecular clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the lineage. Ancestral area reconstructions were performed on the phylogeny using probabilistic approaches implemented in LaGrange and BioGeoBEARS. Our results confirm that Erythropygia is not monophyletic, and that one of the two Erythropygia clades is more closely related to a clade of Asian and Indian Ocean islands distributed species. Overall, the Erythropygia and allies clade originated in Africa in the late Miocene c. 6.9 Ma. Subsequently, a number of overwater dispersals occurred to include an initial colonization of Southeast Asia, and an ensuing progression of colonizations from Southeast Asia to the Seychelles, from there to Madagascar, and from these Indian Ocean islands back to Southeast Asia. Within the two clades of Erythropygia, ancestral area reconstructions within Africa indicate a Southern Africa origin, with subsequent lineage divergence in each clade indicating northward colonization. Overall, this clade of non-migratory songbirds shows a remarkable number of trans-oceanic colonization events, that were possibly facilitated by wind-driven dispersal; repeated Africa to Asia colonizations, two of which occur in this clade, are exceptionally rare in birds. Also rare is our finding that colonization patterns in Africa indicate a

Skull ontogeny: developmental patterns of fishes conserved across major tetrapod clades.

PubMed

Schoch, Rainer R

2006-01-01

In vertebrates, the ontogeny of the bony skull forms a particularly complex part of embryonic development. Although this area used to be restricted to neontology, recent discoveries of fossil ontogenies provide an additional source of data. One of the most detailed ossification sequences is known from Permo-Carboniferous amphibians, the branchiosaurids. These temnospondyls form a near-perfect link between the piscine osteichthyans and the various clades of extant tetrapods, retaining a full complement of dermal bones in the skull. For the first time, the broader evolutionary significance of these event sequences is analyzed, focusing on the identification of sequence heterochronies. A set of 120 event pairs was analyzed by event pair cracking, which helped identify active movers. A cladistic analysis of the event pair data was also carried out, highlighting some shared patterns between widely divergent clades of tetrapods. The analyses revealed an unexpected degree of similarity between the widely divergent taxa. Most interesting is the apparently modular composition of the cranial sequence: five clusters of bones were discovered in each of which the elements form in the same time window: (1) jaw bones, (2) marginal palatal elements, (3) circumorbital bones, (4) skull roof elements, and (5) neurocranial ossifications. In the studied taxa, these "modules" have in most cases been shifted fore and back on the trajectory relative to the Amia sequence, but did not disintegrate. Such "modules" might indicate a high degree of evolutionary limitation (constraint).

47 CFR 95.135 - Maximum authorized transmitting power.

Code of Federal Regulations, 2011 CFR

2011-10-01

... watts ERP. (d) A fixed station must transmit with no more than 15 watts output power. (e) A small base station must transmit with no more than 5 watts ERP. [48 FR 35237, Aug. 3, 1983, as amended at 53 FR 47717...

Spatio-temporal niche partitioning of closely related picocyanobacteria clades and phycocyanin pigment types in Lake Constance (Germany).

PubMed

Becker, Sven; Sánchez-Baracaldo, Patricia; Singh, Arvind K; Hayes, Paul K

2012-05-01

We found that the clade-specific abundance dynamics of Synechococcus type picocyanobacteria in the pelagic and littoral zone macro-habitats of Lake Constance (Germany) challenge the hypothesis of a regular annual succession of picocyanobacteria genotypes in temperate zone lakes. Methods used in this study were quantitative Taq nuclease assays (TNA), denaturing gradient gel electrophoresis (DGGE), a 19-month time series analysis (with two isothermal and two stratified periods) and genotyping of a new littoral phycocyanin (PC)-rich Synechococcus strain collection. The recorded differences between the two macro-habitats and between seasons or years, and the observed effect of water column mixis in winter on the inversion of clade-specific dominance ratios in Lake Constance might explain the known inter-annual differences in abundance and dynamics of the autotrophic picoplankton (APP) in lakes. The APP in Lake Constance shows a high genetic diversity with a low overall abundance, similar to the APP in the Baltic Sea, but different from Lake Biwa in Japan or lakes in the UK. Our results indicate that APP bloom events in both macro-habitats of Lake Constance are driven by phycoerythrin-rich Synechococcus genotypes of the Subalpine Cluster I. DGGE revealed the presence of a diverse periphyton (biofilm) community of the PC-rich Synechococcus pigment type in the littoral zone in early spring, when no such community was detectable in the pelagic habitat. A more sensitive and quantitative approach with TNA, however, revealed an intermittent presence of one PC-rich genotype in the plankton. We discuss the seasonal development of the pelagic and littoral PC-rich community, and while we cannot rule out a strain isolation bias, we found that isolated PC-rich strains from the pelagic habitat have different genotypes when compared to new littoral strains. We also observed littoral substrates colonized by specific PC-rich Synechococcus genotypes. © 2012 Federation of European

Transmit beamforming for optimal second-harmonic generation.

PubMed

Hoilund-Kaupang, Halvard; Masoy, Svein-Erik

2011-08-01

A simulation study of transmit ultrasound beams from several transducer configurations is conducted to compare second-harmonic imaging at 3.5 MHz and 11 MHz. Second- harmonic generation and the ability to suppress near field echoes are compared. Each transducer configuration is defined by a chosen f-number and focal depth, and the transmit pressure is estimated to not exceed a mechanical index of 1.2. The medium resembles homogeneous muscle tissue with nonlinear elasticity and power-law attenuation. To improve computational efficiency, the KZK equation is utilized, and all transducers are circular-symmetric. Previous literature shows that second-harmonic generation is proportional to the square of the transmit pressure, and that transducer configurations with different transmit frequencies, but equal aperture and focal depth in terms of wavelengths, generate identical second-harmonic fields in terms of shape. Results verify this for a medium with attenuation f1. For attenuation f1.1, deviations are found, and the high frequency subsequently performs worse than the low frequency. The results suggest that high frequencies are less able to suppress near-field echoes in the presence of a heterogeneous body wall than low frequencies.

Seven wood-inhabiting new species of the genus Trichoderma (Fungi, Ascomycota) in Viride clade

PubMed Central

Qin, Wen-Tao; Zhuang, Wen-Ying

2016-01-01

More than 200 recent collections of Trichoderma from China were examined and 16 species belonging to the Viride clade were identified based on integrated studies of phenotypic and molecular data. Among them, seven wood-inhabiting new species, T. albofulvopsis, T. densum, T. laevisporum, T. sinokoningii, T. sparsum, T. sphaerosporum and T. subviride, are found. They form trichoderma- to verticillium-like conidiophores, lageniform to subulate phialides and globose to ellipsoidal conidia, but vary greatly in colony features, growth rates, and sizes of phialides and conidia. To explore their taxonomic positions, the phylogenetic tree including all the known species of the Viride clade is constructed based on sequence analyses of the combined RNA polymerase II subunit b and translation elongation factor 1 alpha exon genes. Our results indicated that the seven new species were well-located in the Koningii, Rogersonii and Neorufum subclades as well as a few independent terminal branches. They are clearly distinguishable from any existing species. Morphological distinctions and sequence divergences between the new species and their close relatives were discussed. PMID:27245694

Seven wood-inhabiting new species of the genus Trichoderma (Fungi, Ascomycota) in Viride clade.

PubMed

Qin, Wen-Tao; Zhuang, Wen-Ying

2016-06-01

More than 200 recent collections of Trichoderma from China were examined and 16 species belonging to the Viride clade were identified based on integrated studies of phenotypic and molecular data. Among them, seven wood-inhabiting new species, T. albofulvopsis, T. densum, T. laevisporum, T. sinokoningii, T. sparsum, T. sphaerosporum and T. subviride, are found. They form trichoderma- to verticillium-like conidiophores, lageniform to subulate phialides and globose to ellipsoidal conidia, but vary greatly in colony features, growth rates, and sizes of phialides and conidia. To explore their taxonomic positions, the phylogenetic tree including all the known species of the Viride clade is constructed based on sequence analyses of the combined RNA polymerase II subunit b and translation elongation factor 1 alpha exon genes. Our results indicated that the seven new species were well-located in the Koningii, Rogersonii and Neorufum subclades as well as a few independent terminal branches. They are clearly distinguishable from any existing species. Morphological distinctions and sequence divergences between the new species and their close relatives were discussed.

Biogeography of a novel clade of Ensifer meliloti associated with the Australian legume Trigonella suavissima

USDA-ARS?s Scientific Manuscript database

Here we describe a novel clade within Ensifer meliloti and consider how geographic and ecological isolation contributed to the limited distribution of this group. Members of the genus Ensifer are best known for their ability to form nitrogen-fixing symbioses with forage legumes of three related gene...

Computational analysis of antibody dynamics identifies recent HIV-1 infection.

PubMed

Seaton, Kelly E; Vandergrift, Nathan A; Deal, Aaron W; Rountree, Wes; Bainbridge, John; Grebe, Eduard; Anderson, David A; Sawant, Sheetal; Shen, Xiaoying; Yates, Nicole L; Denny, Thomas N; Liao, Hua-Xin; Haynes, Barton F; Robb, Merlin L; Parkin, Neil; Santos, Breno R; Garrett, Nigel; Price, Matthew A; Naniche, Denise; Duerr, Ann C; Keating, Sheila; Hampton, Dylan; Facente, Shelley; Marson, Kara; Welte, Alex; Pilcher, Christopher D; Cohen, Myron S; Tomaras, Georgia D

2017-12-21

Accurate HIV-1 incidence estimation is critical to the success of HIV-1 prevention strategies. Current assays are limited by high false recent rates (FRRs) in certain populations and a short mean duration of recent infection (MDRI). Dynamic early HIV-1 antibody response kinetics were harnessed to identify biomarkers for improved incidence assays. We conducted retrospective analyses on circulating antibodies from known recent and longstanding infections and evaluated binding and avidity measurements of Env and non-Env antigens and multiple antibody forms (i.e., IgG, IgA, IgG3, IgG4, dIgA, and IgM) in a diverse panel of 164 HIV-1-infected participants (clades A, B, C). Discriminant function analysis identified an optimal set of measurements that were subsequently evaluated in a 324-specimen blinded biomarker validation panel. These biomarkers included clade C gp140 IgG3, transmitted/founder clade C gp140 IgG4 avidity, clade B gp140 IgG4 avidity, and gp41 immunodominant region IgG avidity. MDRI was estimated at 215 day or alternatively, 267 days. FRRs in untreated and treated subjects were 5.0% and 3.6%, respectively. Thus, computational analysis of dynamic HIV-1 antibody isotype and antigen interactions during infection enabled design of a promising HIV-1 recency assay for improved cross-sectional incidence estimation.

Computational analysis of antibody dynamics identifies recent HIV-1 infection

PubMed Central

Seaton, Kelly E.; Vandergrift, Nathan A.; Deal, Aaron W.; Rountree, Wes; Anderson, David A.; Sawant, Sheetal; Shen, Xiaoying; Yates, Nicole L.; Denny, Thomas N.; Haynes, Barton F.; Robb, Merlin L.; Parkin, Neil; Santos, Breno R.; Price, Matthew A.; Naniche, Denise; Duerr, Ann C.; Hampton, Dylan; Facente, Shelley; Marson, Kara; Welte, Alex; Pilcher, Christopher D.; Cohen, Myron S.

2017-01-01

Accurate HIV-1 incidence estimation is critical to the success of HIV-1 prevention strategies. Current assays are limited by high false recent rates (FRRs) in certain populations and a short mean duration of recent infection (MDRI). Dynamic early HIV-1 antibody response kinetics were harnessed to identify biomarkers for improved incidence assays. We conducted retrospective analyses on circulating antibodies from known recent and longstanding infections and evaluated binding and avidity measurements of Env and non-Env antigens and multiple antibody forms (i.e., IgG, IgA, IgG3, IgG4, dIgA, and IgM) in a diverse panel of 164 HIV-1–infected participants (clades A, B, C). Discriminant function analysis identified an optimal set of measurements that were subsequently evaluated in a 324-specimen blinded biomarker validation panel. These biomarkers included clade C gp140 IgG3, transmitted/founder clade C gp140 IgG4 avidity, clade B gp140 IgG4 avidity, and gp41 immunodominant region IgG avidity. MDRI was estimated at 215 day or alternatively, 267 days. FRRs in untreated and treated subjects were 5.0% and 3.6%, respectively. Thus, computational analysis of dynamic HIV-1 antibody isotype and antigen interactions during infection enabled design of a promising HIV-1 recency assay for improved cross-sectional incidence estimation. PMID:29263306

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data

PubMed Central

Hipp, Andrew L.; Eaton, Deren A. R.; Cavender-Bares, Jeannine; Fitzek, Elisabeth; Nipper, Rick; Manos, Paul S.

2014-01-01

Previous phylogenetic studies in oaks (Quercus, Fagaceae) have failed to resolve the backbone topology of the genus with strong support. Here, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23–33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.40 E06 aligned nucleotides, constituting 27,727 sequence clusters. RAD-Seq data were readily combined across runs, with no difference in phylogenetic placement between technical replicates, which overlapped by only 43–64% in locus coverage. 17% (4,715) of the loci we analyzed could be mapped with high confidence to one or more expressed sequence tags in NCBI Genbank. A concatenated matrix of the loci that BLAST to at least one EST sequence provides approximately half as many variable or parsimony-informative characters as equal-sized datasets from the non-EST loci. The EST-associated matrix is more complete (fewer missing loci) and has slightly lower homoplasy than non-EST subsampled matrices of the same size, but there is no difference in phylogenetic support or relative attribution of base substitutions to internal versus terminal branches of the phylogeny. We introduce a partitioned RAD visualization method (implemented in the R package RADami; http://cran.r-project.org/web/packages/RADami) to investigate the possibility that suboptimal topologies supported by large numbers of loci—due, for example, to reticulate evolution or lineage sorting—are masked by the globally optimal tree. We find no evidence for strongly-supported alternative topologies in our study, suggesting that the phylogeny we recover is a robust estimate of large-scale phylogenetic patterns in the American oak clade. Our study is one of the first to demonstrate the utility of RAD-Seq data for inferring phylogeny in a 23–33

Trypanosoma livingstonei: a new species from African bats supports the bat seeding hypothesis for the Trypanosoma cruzi clade

PubMed Central

2013-01-01

Background Bat trypanosomes have been implicated in the evolutionary history of the T. cruzi clade, which comprises species from a wide geographic and host range in South America, Africa and Europe, including bat-restricted species and the generalist agents of human American trypanosomosis T. cruzi and T. rangeli. Methods Trypanosomes from bats (Rhinolophus landeri and Hipposideros caffer) captured in Mozambique, southeast Africa, were isolated by hemoculture. Barcoding was carried out through the V7V8 region of Small Subunit (SSU) rRNA and Fluorescent Fragment Length barcoding (FFLB). Phylogenetic inferences were based on SSU rRNA, glyceraldehyde phosphate dehydrogenase (gGAPDH) and Spliced Leader (SL) genes. Morphological characterization included light, scanning and transmission electron microscopy. Results New trypanosomes from bats clustered together forming a clade basal to a larger assemblage called the T. cruzi clade. Barcoding, phylogenetic analyses and genetic distances based on SSU rRNA and gGAPDH supported these trypanosomes as a new species, which we named Trypanosoma livingstonei n. sp. The large and highly polymorphic SL gene repeats of this species showed a copy of the 5S ribosomal RNA into the intergenic region. Unique morphological (large and broad blood trypomastigotes compatible to species of the subgenus Megatrypanum and cultures showing highly pleomorphic epimastigotes and long and slender trypomastigotes) and ultrastructural (cytostome and reservosomes) features and growth behaviour (when co-cultivated with HeLa cells at 37°C differentiated into trypomastigotes resembling the blood forms and do not invaded the cells) complemented the description of this species. Conclusion Phylogenetic inferences supported the hypothesis that Trypanosoma livingstonei n. sp. diverged from a common ancestral bat trypanosome that evolved exclusively in Chiroptera or switched at independent opportunities to mammals of several orders forming the clade T. cruzi

Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms.

PubMed

Anderson, Frank E; Williams, Bronwyn W; Horn, Kevin M; Erséus, Christer; Halanych, Kenneth M; Santos, Scott R; James, Samuel W

2017-05-30

Earthworms (Crassiclitellata) are a diverse group of annelids of substantial ecological and economic importance. Earthworms are primarily terrestrial infaunal animals, and as such are probably rather poor natural dispersers. Therefore, the near global distribution of earthworms reflects an old and likely complex evolutionary history. Despite a long-standing interest in Crassiclitellata, relationships among and within major clades remain unresolved. In this study, we evaluate crassiclitellate phylogenetic relationships using 38 new transcriptomes in combination with publicly available transcriptome data. Our data include representatives of nearly all extant earthworm families and a representative of Moniligastridae, another terrestrial annelid group thought to be closely related to Crassiclitellata. We use a series of differentially filtered data matrices and analyses to examine the effects of data partitioning, missing data, compositional and branch-length heterogeneity, and outgroup inclusion. We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology. The topology supports two major earthworm clades, each of which consists of a Northern Hemisphere subclade and a Southern Hemisphere subclade. Divergence time analysis results are concordant with the hypothesis that these north-south splits are the result of the breakup of the supercontinent Pangaea. These results support several recently proposed revisions to the classical understanding of earthworm phylogeny, reveal two major clades that seem to reflect Pangaean distributions, and raise new questions about earthworm evolutionary relationships.

Structural basis of clade-specific HIV-1 neutralization by humanized anti-V3 monoclonal antibody KD-247.

PubMed

Kirby, Karen A; Ong, Yee Tsuey; Hachiya, Atsuko; Laughlin, Thomas G; Chiang, Leslie A; Pan, Yun; Moran, Jennifer L; Marchand, Bruno; Singh, Kamalendra; Gallazzi, Fabio; Quinn, Thomas P; Yoshimura, Kazuhisa; Murakami, Toshio; Matsushita, Shuzo; Sarafianos, Stefan G

2015-01-01

Humanized monoclonal antibody KD-247 targets the Gly(312)-Pro(313)-Gly(314)-Arg(315) arch of the third hypervariable (V3) loop of the HIV-1 surface glycoprotein. It potently neutralizes many HIV-1 clade B isolates, but not of other clades. To understand the molecular basis of this specificity, we solved a high-resolution (1.55 Å) crystal structure of the KD-247 antigen binding fragment and examined the potential interactions with various V3 loop targets. Unlike most antibodies, KD-247 appears to interact with its target primarily through light chain residues. Several of these interactions involve Arg(315) of the V3 loop. To evaluate the role of light chain residues in the recognition of the V3 loop, we generated 20 variants of KD-247 single-chain variable fragments with mutations in the antigen-binding site. Purified proteins were assessed for V3 loop binding using AlphaScreen technology and for HIV-1 neutralization. Our data revealed that recognition of the clade-specificity defining residue Arg(315) of the V3 loop is based on a network of interactions that involve Tyr(L32), Tyr(L92), and Asn(L27d) that directly interact with Arg(315), thus elucidating the molecular interactions of KD-247 with its V3 loop target. © FASEB.

Adsorption to Fish Sperm of Vertically Transmitted Fish Viruses

NASA Astrophysics Data System (ADS)

Mulcahy, Dan; Pascho, Ronald J.

1984-07-01

More than 99 percent of a vertically transmitted fish rhabdovirus, infectious hematopoietic necrosis virus, was removed from suspension in less than 1 minute by adsorption to the surface membrane of sperm from two genera of salmonid fishes. The vertically transmitted, infectious pancreatic necrosis virus adsorbed to a lesser degree, but no adsorption occurred with a second fish rhabdovirus that is not vertically transmitted. Such adsorption may be involved in vertical transmission of these viruses.

Adsorption to fish sperm of vertically transmitted fish viruses

USGS Publications Warehouse

Mulcahy, D.; Pascho, R.J.

1984-01-01

More than 99 percent of a vertically transmitted fish rhabdovirus, infectious hematopoietic necrosis virus, was removed from suspension in less than 1 minute by adsorption to the surface membrane of sperm from two genera of salmonid fishes. The vertically transmitted, infectious pancreatic necrosis virus adsorbed to a lesser degree, but no adsorption occurred with a second fish rhabdovirus that is not vertically transmitted. Such adsorption may be involved in vertical transmission of these viruses.

Evolutionary origin and early biogeography of otophysan fishes (Ostariophysi: Teleostei).

PubMed

Chen, Wei-Jen; Lavoué, Sébastien; Mayden, Richard L

2013-08-01

The biogeography of the mega-diverse, freshwater, and globally distributed Otophysi has received considerable attention. This attraction largely stems from assumptions as to their ancient origin, the clade being almost exclusively freshwater, and their suitability as to explanations of trans-oceanic distributions. Despite multiple hypotheses explaining present-day distributions, problems remain, precluding more parsimonious explanations. Underlying previous hypotheses are alternative phylogenies for Otophysi, uncertainties as to temporal diversification and assumptions integral to various explanations. We reexamine the origin and early diversification of this clade based on a comprehensive time-calibrated, molecular-based phylogenetic analysis and event-based approaches for ancestral range inference of lineages. Our results do not corroborate current phylogenetic classifications of otophysans. We demonstrate Siluriformes are never sister to Gymnotiformes and Characiformes are most likely nonmonophyletic. Divergence time estimates specify a split between Cypriniformes and Characiphysi with the fragmentation of Pangea. The early diversification of characiphysans either predated, or was contemporary with, the separation of Africa and South America, and involved a combination of within- and between-continental divergence events for these lineages. The intercontinental diversification of siluroids and characoids postdated major intercontinental tectonic fragmentations (<90 Mya). Post-tectonic drift dispersal events are hypothesized to account for their current distribution patterns. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Alternate pathways of body shape evolution translate into common patterns of locomotor evolution in two clades of lizards.

PubMed

Bergmann, Philip J; Irschick, Duncan J

2010-06-01

Body shape has a fundamental impact on organismal function, but it is unknown how functional morphology and locomotor performance and kinematics relate across a diverse array of body shapes. We showed that although patterns of body shape evolution differed considerably between lizards of the Phrynosomatinae and Lerista, patterns of locomotor evolution coincided between clades. Specifically, we found that the phrynosomatines evolved a stocky phenotype through body widening and limb shortening, whereas Lerista evolved elongation through body lengthening and limb shortening. In both clades, relative limb length played a key role in locomotor evolution and kinematic strategies, with long-limbed species moving faster and taking longer strides. In Lerista, the body axis also influenced locomotor evolution. Similar patterns of locomotor evolution were likely due to constraints on how the body can move. However, these common patterns of locomotor evolution between the two clades resulted in different kinematic strategies and levels of performance among species because of their morphological differences. Furthermore, we found no evidence that distinct body shapes are adaptations to different substrates, as locomotor kinematics did not change on loose or solid substrates. Our findings illustrate the importance of studying kinematics to understand the mechanisms of locomotor evolution and phenotype-function relationships.

Diversification into novel habitats in the Africa clade of Dioscorea (Dioscoreaceae): erect habit and elephant's foot tubers.

PubMed

Maurin, Olivier; Muasya, A Muthama; Catalan, Pilar; Shongwe, Eugene Z; Viruel, Juan; Wilkin, Paul; van der Bank, Michelle

2016-11-08

Dioscorea is a widely distributed and highly diversified genus in tropical regions where it is represented by ten main clades, one of which diversified exclusively in Africa. In southern Africa it is characterised by a distinct group of species with a pachycaul or "elephant's foot" structure that is partially to fully exposed above the substrate. In contrast to African representatives of the genus from other clades, occurring mainly in forest or woodland, the pachycaul taxa and their southern African relatives occur in diverse habitats ranging from woodland to open vegetation. Here we investigate patterns of diversification in the African clade, time of transition from forest to more open habitat, and morphological traits associated with each habitat and evaluate if such transitions have led to modification of reproductive organs and mode of dispersal. The Africa clade originated in the Oligocene and comprises four subclades. The Dioscorea buchananii subclade (southeastern tropical Africa and South Africa) is sister to the East African subclade, which is respectively sister to the recently evolved sister South African (e. g., Cape and Pachycaul) subclades. The Cape and Pachycaul subclades diversified in the east of the Cape Peninsula in the mid Miocene, in an area with complex geomorphology and climate, where the fynbos, thicket, succulent karoo and forest biomes meet. Diversification out of forest is associated with major shifts in morphology of the perennial tuber (specifically an increase in size and orientation which presumably led them to become pachycaul) and rotation of stem (from twining to non-twining). The iconic elephant's foot morphology, observed in grasslands and thicket biomes, where its corky bark may offer protection against fire and herbivory, evolved since mid Miocene. A shift in pollination trait is observed within the forest, but entry into open habitat does not show association with reproductive morphology, except in the seed wing, which has

Robust regression and posterior predictive simulation increase power to detect early bursts of trait evolution.

PubMed

Slater, Graham J; Pennell, Matthew W

2014-05-01

A central prediction of much theory on adaptive radiations is that traits should evolve rapidly during the early stages of a clade's history and subsequently slowdown in rate as niches become saturated--a so-called "Early Burst." Although a common pattern in the fossil record, evidence for early bursts of trait evolution in phylogenetic comparative data has been equivocal at best. We show here that this may not necessarily be due to the absence of this pattern in nature. Rather, commonly used methods to infer its presence perform poorly when when the strength of the burst--the rate at which phenotypic evolution declines--is small, and when some morphological convergence is present within the clade. We present two modifications to existing comparative methods that allow greater power to detect early bursts in simulated datasets. First, we develop posterior predictive simulation approaches and show that they outperform maximum likelihood approaches at identifying early bursts at moderate strength. Second, we use a robust regression procedure that allows for the identification and down-weighting of convergent taxa, leading to moderate increases in method performance. We demonstrate the utility and power of these approach by investigating the evolution of body size in cetaceans. Model fitting using maximum likelihood is equivocal with regards the mode of cetacean body size evolution. However, posterior predictive simulation combined with a robust node height test return low support for Brownian motion or rate shift models, but not the early burst model. While the jury is still out on whether early bursts are actually common in nature, our approach will hopefully facilitate more robust testing of this hypothesis. We advocate the adoption of similar posterior predictive approaches to improve the fit and to assess the adequacy of macroevolutionary models in general.

Molecular-based rapid inventories of sympatric diversity: a comparison of DNA barcode clustering methods applied to geography-based vs clade-based sampling of amphibians.

PubMed

Paz, Andrea; Crawford, Andrew J

2012-11-01

Molecular markers offer a universal source of data for quantifying biodiversity. DNA barcoding uses a standardized genetic marker and a curated reference database to identify known species and to reveal cryptic diversity within wellsampled clades. Rapid biological inventories, e.g. rapid assessment programs (RAPs), unlike most barcoding campaigns, are focused on particular geographic localities rather than on clades. Because of the potentially sparse phylogenetic sampling, the addition of DNA barcoding to RAPs may present a greater challenge for the identification of named species or for revealing cryptic diversity. In this article we evaluate the use of DNA barcoding for quantifying lineage diversity within a single sampling site as compared to clade-based sampling, and present examples from amphibians. We compared algorithms for identifying DNA barcode clusters (e.g. species, cryptic species or Evolutionary Significant Units) using previously published DNA barcode data obtained from geography-based sampling at a site in Central Panama, and from clade-based sampling in Madagascar. We found that clustering algorithms based on genetic distance performed similarly on sympatric as well as clade-based barcode data, while a promising coalescent-based method performed poorly on sympatric data. The various clustering algorithms were also compared in terms of speed and software implementation. Although each method has its shortcomings in certain contexts, we recommend the use of the ABGD method, which not only performs fairly well under either sampling method, but does so in a few seconds and with a user-friendly Web interface.

Production of three symbiosis-related fatty acids by Symbiodinium types in clades A-F associated with marine invertebrate larvae

NASA Astrophysics Data System (ADS)

Mies, M.; Chaves-Filho, A. B.; Miyamoto, S.; Güth, A. Z.; Tenório, A. A.; Castro, C. B.; Pires, D. O.; Calderon, E. N.; Sumida, P. Y. G.

2017-12-01

Symbiodinium are dinoflagellates engaged in a mutualistic symbiosis with multiple coral reef taxa. They are divided in nine different clades (A-I), which typically associate with different hosts. However, very little information is available on metabolic differences in Symbiodinium types, especially when associated with metazoan larvae. We tested whether three ω3 fatty acids (stearidonic acid, SDA; docosapentaenoic acid, DPA; and docosahexaenoic acid, DHA) that are typically translocated from Symbiodinium to its host are produced by Symbiodinium types within clades A-F associated with Mussismilia hispida (scleractinian coral), Berghia stephanieae (nudibranch), and Tridacna crocea (giant clam) larvae. We acquired and spawned broodstock for each host, cultured their larvae, and offered Symbiodinium types belonging to clades A-F. Samples were taken during a 72-h window after the offer of Symbiodinium, and fatty acids were extracted and analyzed by gas chromatography. The concentrations of SDA and DPA for all host larvae-dinoflagellate associations were low and variable, without trends. However, M. hispida planula larvae associated with Symbiodinium A1 and C1 had a statistically significant higher amount of DHA. The veliger larvae of B. stephanieae digested the Symbiodinium, and the amount of DHA remained constant throughout the experiment. The veliger larvae of T. crocea associated with Symbiodinium A1 and C1 also presented a higher amount of DHA, although not statistically different from the other types. These results show that Symbiodinium A1 and C1, in the case of M. hispida and T. crocea (which usually harbor strains within clades A and C), may contribute a small amount of DHA to the larvae of these organisms and form a stronger mutualism than other strains.

USACE AIS Transmit Technical Support Summary Report

DTIC Science & Technology

2014-09-01

the TAG block for the correct transmitters, and then send to the USACE AIS network. B. Outbound openings in the USCG firewall for the USCG Message...USACE AIS Transmit Technical Support Summary Report Distribution Statement A: Approved for public release; distribution is unlimited...September 2014 Report No. CD-D-09-15 USACE AIS Transmit Technical Support Summary Report ii UNCLAS//Public | CG-926 RDC | I. Gonin et al. Public

Nomenclature updates resulting from the evolution of avian influenza A(H5) virus clades 2.1.3.2a, 2.2.1, and 2.3.4 during 2013-2014.

PubMed

Smith, Gavin J D; Donis, Ruben O

2015-09-01

The A/goose/Guangdong/1/96-like hemagglutinin (HA) genes of highly pathogenic avian influenza (HPAI) A(H5) viruses have continued to rapidly evolve since the most recent update to the H5 clade nomenclature by the WHO/OIE/FAO H5N1 Evolution Working Group. New clades diverging beyond established boundaries need to be identified and designated accordingly. Hemagglutinin sequences deposited in publicly accessible databases up to December 31, 2014, were analyzed by phylogenetic and average pairwise distance methods to identify new clades that merit nomenclature changes. Three new clade designations were recommended based on division of clade 2·1·3·2a (Indonesia), 2·2·1 (Egypt), and 2·3·4 (widespread detection in Asia, Europe, and North America) that includes newly emergent HPAI virus subtypes H5N2, H5N3, H5N5, H5N6, and H5N8. Continued global surveillance for HPAI A(H5) viruses in all host species and timely reporting of sequence data will be critical to quickly identify new clades and assess their potential impact on human and animal health. © 2015 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

Differential niche dynamics among major marine invertebrate clades

PubMed Central

Hopkins, Melanie J; Simpson, Carl; Kiessling, Wolfgang

2014-01-01

The degree to which organisms retain their environmental preferences is of utmost importance in predicting their fate in a world of rapid climate change. Notably, marine invertebrates frequently show strong affinities for either carbonate or terrigenous clastic environments. This affinity is due to characteristics of the sediments as well as correlated environmental factors. We assessed the conservatism of substrate affinities of marine invertebrates over geological timescales, and found that niche conservatism is prevalent in the oceans, and largely determined by the strength of initial habitat preference. There is substantial variation in niche conservatism among major clades with corals and sponges being among the most conservative. Time-series analysis suggests that niche conservatism is enhanced during times of elevated nutrient flux, whereas niche evolution tends to occur after mass extinctions. Niche evolution is not necessarily elevated in genera exhibiting higher turnover in species composition. PMID:24313951

Phylodynamics of avian influenza clade 2.2.1 H5N1 viruses in Egypt.

PubMed

Arafa, Abdelsatar; El-Masry, Ihab; Kholosy, Shereen; Hassan, Mohammed K; Dauphin, Gwenaelle; Lubroth, Juan; Makonnen, Yilma J

2016-03-22

Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are widely distributed within poultry populations in Egypt and have caused multiple human infections. Linking the epidemiological and sequence data is important to understand the transmission, persistence and evolution of the virus. This work describes the phylogenetic dynamics of H5N1 based on molecular characterization of the hemagglutinin (HA) gene of isolates collected from February 2006 to May 2014. Full-length HA sequences of 368 H5N1 viruses were generated and were genetically analysed to study their genetic evolution. They were collected from different poultry species, production sectors, and geographic locations in Egypt. The Bayesian Markov Chain Monte Carlo (BMCMC) method was applied to estimate the evolutionary rates among different virus clusters; additionally, an analysis of selection pressures in the HA gene was performed using the Single Likelihood Ancestor Counting (SLAC) method. The phylogenetic analysis of the H5 gene from 2006-14 indicated the presence of one virus introduction of the classic clade (2.2.1) from which two main subgroups were originated, the variant subgroup which was further subdivided into 2 sub-divisions (2.2.1.1 and 2.2.1.1a) and the endemic subgroup (2.2.1.2). The clade 2.2.1.2 showed a high evolution rate over a period of 6 years (6.9 × 10(-3) sub/site/year) in comparison to the 2.2.1.1a variant cluster (7.2 × 10(-3) over a period of 4 years). Those two clusters are under positive selection as they possess 5 distinct positively selected sites in the HA gene. The mutations at 120, 154, and 162 HA antigenic sites and the other two mutations (129∆, I151T) that occurred from 2009-14 were found to be stable in the 2.2.1.2 clade. Additionally, 13 groups of H5N1 HPAI viruses were identified based on their amino acid sequences at the cleavage site and "EKRRKKR" became the dominant pattern beginning in 2013. Continuous evolution of H5N1 HPAI viruses in Egypt has

The Early Origin of the Antarctic Marine Fauna and Its Evolutionary Implications.

PubMed

Crame, J Alistair; Beu, Alan G; Ineson, Jon R; Francis, Jane E; Whittle, Rowan J; Bowman, Vanessa C

2014-01-01

The extensive Late Cretaceous - Early Paleogene sedimentary succession of Seymour Island, N.E. Antarctic Peninsula offers an unparalleled opportunity to examine the evolutionary origins of a modern polar marine fauna. Some 38 modern Southern Ocean molluscan genera (26 gastropods and 12 bivalves), representing approximately 18% of the total modern benthic molluscan fauna, can now be traced back through at least part of this sequence. As noted elsewhere in the world, the balance of the molluscan fauna changes sharply across the Cretaceous - Paleogene (K/Pg) boundary, with gastropods subsequently becoming more diverse than bivalves. A major reason for this is a significant radiation of the Neogastropoda, which today forms one of the most diverse clades in the sea. Buccinoidea is the dominant neogastropod superfamily in both the Paleocene Sobral Formation (SF) (56% of neogastropod genera) and Early - Middle Eocene La Meseta Formation (LMF) (47%), with the Conoidea (25%) being prominent for the first time in the latter. This radiation of Neogastropoda is linked to a significant pulse of global warming that reached at least 65°S, and terminates abruptly in the upper LMF in an extinction event that most likely heralds the onset of global cooling. It is also possible that the marked Early Paleogene expansion of neogastropods in Antarctica is in part due to a global increase in rates of origination following the K/Pg mass extinction event. The radiation of this and other clades at ∼65°S indicates that Antarctica was not necessarily an evolutionary refugium, or sink, in the Early - Middle Eocene. Evolutionary source - sink dynamics may have been significantly different between the Paleogene greenhouse and Neogene icehouse worlds.

The oldest ionoscopiform from China sheds new light on the early evolution of halecomorph fishes

PubMed Central

Xu, Guang-Hui; Zhao, Li-Jun; Coates, Michael I.

2014-01-01

The Halecomorphi are a major subdivision of the ray-finned fishes. Although living halecomorphs are represented solely by the freshwater bowfin, Amia calva, this clade has a rich fossil history, and the resolution of interrelationships among extinct members is central to the problem of understanding the origin of the Teleostei, the largest clade of extant vertebrates. The Ionoscopiformes are extinct marine halecomorphs that were inferred to have originated in the Late Jurassic of Europe, and subsequently dispersed to the Early Cretaceous of the New World. Here, we report the discovery of a new ionoscopiform, Robustichthys luopingensis gen. et sp. nov., based on eight well-preserved specimens from the Anisian (242–247 Ma), Middle Triassic marine deposits of Luoping, eastern Yunnan Province, China. The new species documents the oldest known ionoscopiform, extending the stratigraphic range of this group by approximately 90 Ma, and the geographical distribution of this group into the Middle Triassic of South China, a part of eastern Palaeotethys Ocean. These new data provide a minimum estimate for the split of Ionoscopiformes from its sister clade Amiiformes and shed new light on the origin of ionoscopiform fishes. PMID:24872460

Early bursts of body size and shape evolution are rare in comparative data.

PubMed

Harmon, Luke J; Losos, Jonathan B; Jonathan Davies, T; Gillespie, Rosemary G; Gittleman, John L; Bryan Jennings, W; Kozak, Kenneth H; McPeek, Mark A; Moreno-Roark, Franck; Near, Thomas J; Purvis, Andy; Ricklefs, Robert E; Schluter, Dolph; Schulte Ii, James A; Seehausen, Ole; Sidlauskas, Brian L; Torres-Carvajal, Omar; Weir, Jason T; Mooers, Arne Ø

2010-08-01

George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations-more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed by relative stasis. We compared the fit of this model to both single selective peak and random walk models. We found little support for the early-burst model of adaptive radiation, whereas both other models, particularly that of selective peaks, were commonly supported. In addition, we found that the net rate of morphological evolution varied inversely with clade age. The youngest clades appear to evolve most rapidly because long-term change typically does not attain the amount of divergence predicted from rates measured over short time scales. Across our entire analysis, the dominant pattern was one of constraints shaping evolution continually through time rather than rapid evolution followed by stasis. We suggest that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data.

Broad Antibody Mediated Cross-Neutralization and Preclinical Immunogenicity of New Codon-Optimized HIV-1 Clade CRF02_AG and G Primary Isolates

PubMed Central

Agwale, Simon M.; Forbi, Joseph C.; Notka, Frank; Wrin, Terri; Wild, Jens; Wagner, Ralf; Wolf, Hans

2011-01-01

Creation of an effective vaccine for HIV has been an elusive goal of the scientific community for almost 30 years. Neutralizing antibodies are assumed to be pivotal to the success of a prophylactic vaccine but previous attempts to make an immunogen capable of generating neutralizing antibodies to primary “street strain” isolates have resulted in responses of very limited breadth and potency. The objective of the study was to determine the breadth and strength of neutralizing antibodies against autologous and heterologous primary isolates in a cohort of HIV-1 infected Nigerians and to characterize envelopes from subjects with particularly broad or strong immune responses for possible use as vaccine candidates in regions predominated by HIV-1 CRF02_AG and G subtypes. Envelope vectors from a panel of primary Nigerian isolates were constructed and tested with plasma/sera from the same cohort using the PhenoSense HIV neutralizing antibody assay (Monogram Biosciences Inc, USA) to assess the breadth and potency of neutralizing antibodies. The immediate goal of this study was realized by the recognition of three broadly cross-neutralizing sera: (NG2-clade CRF02_AG, NG3-clade CRF02_AG and NG9- clade G). Based on these findings, envelope gp140 sequences from NG2 and NG9, complemented with a gag sequence (Clade G) and consensus tat (CRF02_AG and G) antigens have been codon-optimized, synthesized, cloned and evaluated in BALB/c mice. The intramuscular administration of these plasmid DNA constructs, followed by two booster DNA immunizations, induced substantial specific humoral response against all constructs and strong cellular responses against the gag and tat constructs. These preclinical findings provide a framework for the design of candidate vaccine for use in regions where the HIV-1 epidemic is driven by clades CRF02_AG and G. PMID:21829720

Broad antibody mediated cross-neutralization and preclinical immunogenicity of new codon-optimized HIV-1 clade CRF02_AG and G primary isolates.

PubMed

Agwale, Simon M; Forbi, Joseph C; Notka, Frank; Wrin, Terri; Wild, Jens; Wagner, Ralf; Wolf, Hans

2011-01-01

Creation of an effective vaccine for HIV has been an elusive goal of the scientific community for almost 30 years. Neutralizing antibodies are assumed to be pivotal to the success of a prophylactic vaccine but previous attempts to make an immunogen capable of generating neutralizing antibodies to primary "street strain" isolates have resulted in responses of very limited breadth and potency. The objective of the study was to determine the breadth and strength of neutralizing antibodies against autologous and heterologous primary isolates in a cohort of HIV-1 infected Nigerians and to characterize envelopes from subjects with particularly broad or strong immune responses for possible use as vaccine candidates in regions predominated by HIV-1 CRF02_AG and G subtypes. Envelope vectors from a panel of primary Nigerian isolates were constructed and tested with plasma/sera from the same cohort using the PhenoSense HIV neutralizing antibody assay (Monogram Biosciences Inc, USA) to assess the breadth and potency of neutralizing antibodies. The immediate goal of this study was realized by the recognition of three broadly cross-neutralizing sera: (NG2-clade CRF02_AG, NG3-clade CRF02_AG and NG9- clade G). Based on these findings, envelope gp140 sequences from NG2 and NG9, complemented with a gag sequence (Clade G) and consensus tat (CRF02_AG and G) antigens have been codon-optimized, synthesized, cloned and evaluated in BALB/c mice. The intramuscular administration of these plasmid DNA constructs, followed by two booster DNA immunizations, induced substantial specific humoral response against all constructs and strong cellular responses against the gag and tat constructs. These preclinical findings provide a framework for the design of candidate vaccine for use in regions where the HIV-1 epidemic is driven by clades CRF02_AG and G.

Sex workers and the control of sexually transmitted disease.

PubMed

Day, S; Ward, H

1997-06-01

To describe and assess measures to control sexually transmitted diseases (STDs) among sex workers and their partners. A review of medical, historical and social literature, focusing on selected cases. Measures to control disease in sex workers today are often prompted by concerns about HIV transmission. However, the literature shows that prostitution varies from one place and time to another, together with the risk of sexually transmitted disease. A broad social definition of prostitution rather than a narrow reference to levels of sexual activity is important for effective disease control, as an understanding of the relation between social disadvantage and sexual activity enables the provision of occupational services that sex workers actually want and use. Social prejudice and legal sanctions cause some sex workers and their partners to avoid even the most appropriate and accessible specialist services. Therefore targeted programmes can only complement, and not replace, general measures to control STDs, which are developed for other social groups or the local population as a whole. Sex workers and sex work differ from one place to another and so a single model for STD control is inappropriate. None the less, occupational health risks suggest a general need for specialist services. Where these do not compound the disadvantages that sex workers already suffer, medical services are likely to offer significant benefits in prevention, early diagnosis, and treatment of STDs. As the stigma of prostitution leads many people to remain invisible to services, a general health infrastructure and anti-discriminatory measures will be equally important to effective disease control.

Sex workers and the control of sexually transmitted disease.

PubMed Central

Day, S; Ward, H

1997-01-01

OBJECTIVES: To describe and assess measures to control sexually transmitted diseases (STDs) among sex workers and their partners. METHODS: A review of medical, historical and social literature, focusing on selected cases. RESULTS: Measures to control disease in sex workers today are often prompted by concerns about HIV transmission. However, the literature shows that prostitution varies from one place and time to another, together with the risk of sexually transmitted disease. A broad social definition of prostitution rather than a narrow reference to levels of sexual activity is important for effective disease control, as an understanding of the relation between social disadvantage and sexual activity enables the provision of occupational services that sex workers actually want and use. Social prejudice and legal sanctions cause some sex workers and their partners to avoid even the most appropriate and accessible specialist services. Therefore targeted programmes can only complement, and not replace, general measures to control STDs, which are developed for other social groups or the local population as a whole. CONCLUSIONS: Sex workers and sex work differ from one place to another and so a single model for STD control is inappropriate. None the less, occupational health risks suggest a general need for specialist services. Where these do not compound the disadvantages that sex workers already suffer, medical services are likely to offer significant benefits in prevention, early diagnosis, and treatment of STDs. As the stigma of prostitution leads many people to remain invisible to services, a general health infrastructure and anti-discriminatory measures will be equally important to effective disease control. PMID:9306894

Inter-Clade Protection Offered by Mw-Adjuvanted Recombinant HA, NP Proteins, and M2e Peptide Combination Vaccine in Mice Correlates with Cellular Immune Response.

PubMed

Ingle, Nilesh B; Virkar, Rashmi G; Arankalle, Vidya A

2016-01-01

We documented earlier that Mw (heat-killed suspension of Mycobacterium indicus pranii ) adjuvant when used with conserved antigens, nucleoprotein (NP), and ectodomain of matrix (M2) protein (M2e) provided complete protection against homologous (clade 2.2) virus challenge in mice. The present study extends these observations to inter-clade challenge (clade 2.3.2.1) H5N1 virus and attempts to understand preliminary immunologic basis for the observed protection. Female BALB/c mice immunized with a single or two doses of vaccine formulations (clade 2.2 antigens) were challenged with 100LD50 homologous or heterologous (clade 2.3.2.1) virus. To understand the preliminary immunologic mechanism, we studied proportions of selected immune cell types, immune response gene expression, and Th1/Th2 cytokines induced by antigen-stimulated splenocytes from immunized mice, at different time points. Complete protection was conferred by Mw-HA, Mw-HA + NP, and Mw-HA + NP + M2e against homologous challenge. The protection correlated with IgG2a antibody titers indicating important role of Th1 response. Despite high inter-cladal antigenic differences, complete protection against the heterologous strain was achieved with Mw-HA + NP + M2e. Of note, a single dose with higher antigen concentrations (50 µg HA + 50 μg NP + 50 μg M2e) led to 80% protection against clade 2.3.2.1 strain. The protection conferred by Mw-HNM correlated with induction of IFN-γ, CD8 + T cytotoxic cells, and CD4 + T helper cells. Mw-adjuvanted HA + NP + M2e combination represents a promising vaccine candidate deserving further evaluation.

Novel Multistatic Adaptive Microwave Imaging Methods for Early Breast Cancer Detection

NASA Astrophysics Data System (ADS)

Xie, Yao; Guo, Bin; Li, Jian; Stoica, Petre

2006-12-01

Multistatic adaptive microwave imaging (MAMI) methods are presented and compared for early breast cancer detection. Due to the significant contrast between the dielectric properties of normal and malignant breast tissues, developing microwave imaging techniques for early breast cancer detection has attracted much interest lately. MAMI is one of the microwave imaging modalities and employs multiple antennas that take turns to transmit ultra-wideband (UWB) pulses while all antennas are used to receive the reflected signals. MAMI can be considered as a special case of the multi-input multi-output (MIMO) radar with the multiple transmitted waveforms being either UWB pulses or zeros. Since the UWB pulses transmitted by different antennas are displaced in time, the multiple transmitted waveforms are orthogonal to each other. The challenge to microwave imaging is to improve resolution and suppress strong interferences caused by the breast skin, nipple, and so forth. The MAMI methods we investigate herein utilize the data-adaptive robust Capon beamformer (RCB) to achieve high resolution and interference suppression. We will demonstrate the effectiveness of our proposed methods for breast cancer detection via numerical examples with data simulated using the finite-difference time-domain method based on a 3D realistic breast model.

Emergence of multiple clade 2.3.2.1 influenza A (H5N1) virus subgroups in Vietnam and detection of novel reassortants.

PubMed

Creanga, Adrian; Thi Nguyen, Diep; Gerloff, Nancy; Thi Do, Hoa; Balish, Amanda; Dang Nguyen, Hoang; Jang, Yunho; Thi Dam, Vui; Thor, Sharmi; Jones, Joyce; Simpson, Natosha; Shu, Bo; Emery, Shannon; Berman, LaShondra; Nguyen, Ha T; Bryant, Juliet E; Lindstrom, Steve; Klimov, Alexander; Donis, Ruben O; Davis, C Todd; Nguyen, Tung

2013-09-01

Phylogenetic analyses of 169 influenza A(H5N1) virus genomes were conducted for samples collected through active surveillance and outbreak responses in Vietnam between September 2010 and September 2012. While clade 1.1 viruses persisted in southern regions, three genetically distinct subgroups of clade 2.3.2.1 were found in northern and central Vietnam. The identification of each subgroup corresponded with detection of novel reassortants, likely due to their overlapping circulation throughout the country. While the previously identified clade 1.1 and A/Hubei/1/2010-like 2.3.2.1 genotypes remained the predominant viruses detected, four viruses were found to be reassortants between A/Hubei/1/2010-like (HA, NA, PB2, PB1, PA, NP) and A/duck/Vietnam/NCVD-885/2010-like (M, NS) viruses and one virus was identified as having A/duck/Vietnam/NCVD-885/2010-like HA, NA, PB1, and NP with A/Hubei/1/2010-like PB2 and PA genes. Additionally, clade 2.3.2.1 A/Hong Kong/6841/2010-like viruses, first detected in mid-2012, were identified as reassortants comprised of A/Hubei/1/2010-like PB2 and PA and A/duck/Vietnam/NCVD-885/2010-like PB1, NP, NA, M, NS genes. Published by Elsevier Inc.

Note on transmitted complexity for quantum dynamical systems

NASA Astrophysics Data System (ADS)

Watanabe, Noboru; Muto, Masahiro

2017-10-01

Transmitted complexity (mutual entropy) is one of the important measures for quantum information theory developed recently in several ways. We will review the fundamental concepts of the Kossakowski, Ohya and Watanabe entropy and define a transmitted complexity for quantum dynamical systems. This article is part of the themed issue `Second quantum revolution: foundational questions'.

Stigma and stereotypes: women and sexually transmitted infections.

PubMed

East, Leah; Jackson, Debra; O'Brien, Louise; Peters, Kathleen

2012-01-01

Sexually transmitted infections have long been associated with stigma and stereotypes due to their very nature. Throughout history sexually transmitted infections have been associated with female prostitution and deviant immoral behaviour making women who contract these infections particularly vulnerable to being stigmatised and stereotyped. Although the stigma attached to such infections has previously been documented in the literature, the aim of this research was to gain in depth insight into young Australian women's experiences of having a sexually transmitted infection from a feminist perspective. Findings from this study provide insight into the onerous effects stigma can have on women with these infections and sheds light on how these effects can influence self-perceptions, fear of rejection and feelings of unworthiness. These findings can provide nurses with greater understanding and insight into the effects of stigma on women's experiences of having a sexually transmitted infection. Having this understanding and insight has the potential to promote therapeutic care and minimise the stigma that may be felt among women who have contracted this type of infection.

Emergence and dissemination of clade 2.3.4.4 H5Nx influenza viruses-how is the Asian HPAI H5 lineage maintained.

PubMed

Claes, Filip; Morzaria, Subhash P; Donis, Ruben O

2016-02-01

Highly pathogenic avian influenza (HPAI) A(H5N1) viruses containing the A/goose/Guangdong/96-like (GD/96) HA genes circulated in birds from four continents in the course of 2015 (Jan to Sept). A new HA clade, termed 2.3.4.4, emerged around 2010-2011 in China and revealed a novel propensity to reassort with NA subtypes other than N1, unlike dozens of earlier clades. Two subtypes, H5N6 and H5N8, have spread to countries in Asia (H5N6), Europe and North America (H5N8). Infections by clade 2.3.4.4 viruses are characterized by low virulence in poultry and some wild birds, contributing to wide geographical dissemination of the viruses via poultry trade and wild bird migration. Copyright © 2016. Published by Elsevier B.V.

Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades

PubMed Central

2012-01-01

Background Coffee trees (Rubiaceae) and tomato (Solanaceae) belong to the Asterid clade, while grapevine (Vitaceae) belongs to the Rosid clade. Coffee and tomato separated from grapevine 125 million years ago, while coffee and tomato diverged 83-89 million years ago. These long periods of divergent evolution should have permitted the genomes to reorganize significantly. So far, very few comparative mappings have been performed between very distantly related species belonging to different clades. We report the first multiple comparison between species from Asterid and Rosid clades, to examine both macro-and microsynteny relationships. Results Thanks to a set of 867 COSII markers, macrosynteny was detected between coffee, tomato and grapevine. While coffee and tomato genomes share 318 orthologous markers and 27 conserved syntenic segments (CSSs), coffee and grapevine also share a similar number of syntenic markers and CSSs: 299 and 29 respectively. Despite large genome macrostructure reorganization, several large chromosome segments showed outstanding macrosynteny shedding new insights into chromosome evolution between Asterids and Rosids. We also analyzed a sequence of 174 kb containing the ovate gene, conserved in a syntenic block between coffee, tomato and grapevine that showed a high-level of microstructure conservation. A higher level of conservation was observed between coffee and grapevine, both woody and long life-cycle plants, than between coffee and tomato. Out of 16 coffee genes of this syntenic segment, 7 and 14 showed complete synteny between coffee and tomato or grapevine, respectively. Conclusions These results show that significant conservation is found between distantly related species from the Asterid (Coffea canephora and Solanum sp.) and Rosid (Vitis vinifera) clades, at the genome macrostructure and microstructure levels. At the ovate locus, conservation did not decline in relation to increasing phylogenetic distance, suggesting that the time

Phylogenetic analysis of canine distemper virus in South America clade 1 reveals unique molecular signatures of the local epidemic.

PubMed

Fischer, Cristine D B; Gräf, Tiago; Ikuta, Nilo; Lehmann, Fernanda K M; Passos, Daniel T; Makiejczuk, Aline; Silveira, Marcos A T; Fonseca, André S K; Canal, Cláudio W; Lunge, Vagner R

2016-07-01

Canine distemper virus (CDV) is a highly contagious pathogen for domestic dogs and several wild carnivore species. In Brazil, natural infection of CDV in dogs is very high due to the large non-vaccinated dog population, a scenario that calls for new studies on the molecular epidemiology. This study investigates the phylodynamics and amino-acid signatures of CDV epidemic in South America by analyzing a large dataset compiled from publicly available sequences and also by collecting new samples from Brazil. A population of 175 dogs with canine distemper (CD) signs was sampled, from which 89 were positive for CDV, generating 42 new CDV sequences. Phylogenetic analysis of the new and publicly available sequences revealed that Brazilian sequences mainly clustered in South America 1 (SA1) clade, which has its origin estimated to the late 1980's. The reconstruction of the demographic history in SA1 clade showed an epidemic expanding until the recent years, doubling in size every nine years. SA1 clade epidemic distinguished from the world CDV epidemic by the emergence of the R580Q strain, a very rare and potentially detrimental substitution in the viral genome. The R580Q substitution was estimated to have happened in one single evolutionary step in the epidemic history in SA1 clade, emerging shortly after introduction to the continent. Moreover, a high prevalence (11.9%) of the Y549H mutation was observed among the domestic dogs sampled here. This finding was associated (p<0.05) with outcome-death and higher frequency in mixed-breed dogs, the later being an indicator of a continuous exchange of CDV strains circulating among wild carnivores and domestic dogs. The results reported here highlight the diversity of the worldwide CDV epidemic and reveal local features that can be valuable for combating the disease. Copyright © 2016 Elsevier B.V. All rights reserved.

A Middle Jurassic abelisaurid from Patagonia and the early diversification of theropod dinosaurs.

PubMed

Pol, Diego; Rauhut, Oliver W M

2012-08-22

Abelisaurids are a clade of large, bizarre predatory dinosaurs, most notable for their high, short skulls and extremely reduced forelimbs. They were common in Gondwana during the Cretaceous, but exceedingly rare in the Northern Hemisphere. The oldest definitive abelisaurids so far come from the late Early Cretaceous of South America and Africa, and the early evolutionary history of the clade is still poorly known. Here, we report a new abelisaurid from the Middle Jurassic of Patagonia, Eoabelisaurus mefi gen. et sp. nov., which predates the so far oldest known secure member of this lineage by more than 40 Myr. The almost complete skeleton reveals the earliest evolutionary stages of the distinctive features of abelisaurids, such as the modification of the forelimb, which started with a reduction of the distal elements. The find underlines the explosive radiation of theropod dinosaurs in the Middle Jurassic and indicates an unexpected diversity of ceratosaurs at that time. The apparent endemism of abelisauroids to southern Gondwana during Pangean times might be due to the presence of a large, central Gondwanan desert. This indicates that, apart from continent-scale geography, aspects such as regional geography and climate are important to reconstruct the biogeographical history of Mesozoic vertebrates.

A Middle Jurassic abelisaurid from Patagonia and the early diversification of theropod dinosaurs

PubMed Central

Pol, Diego; Rauhut, Oliver W. M.

2012-01-01

Abelisaurids are a clade of large, bizarre predatory dinosaurs, most notable for their high, short skulls and extremely reduced forelimbs. They were common in Gondwana during the Cretaceous, but exceedingly rare in the Northern Hemisphere. The oldest definitive abelisaurids so far come from the late Early Cretaceous of South America and Africa, and the early evolutionary history of the clade is still poorly known. Here, we report a new abelisaurid from the Middle Jurassic of Patagonia, Eoabelisaurus mefi gen. et sp. nov., which predates the so far oldest known secure member of this lineage by more than 40 Myr. The almost complete skeleton reveals the earliest evolutionary stages of the distinctive features of abelisaurids, such as the modification of the forelimb, which started with a reduction of the distal elements. The find underlines the explosive radiation of theropod dinosaurs in the Middle Jurassic and indicates an unexpected diversity of ceratosaurs at that time. The apparent endemism of abelisauroids to southern Gondwana during Pangean times might be due to the presence of a large, central Gondwanan desert. This indicates that, apart from continent-scale geography, aspects such as regional geography and climate are important to reconstruct the biogeographical history of Mesozoic vertebrates. PMID:22628475

Complete genome sequences of two novel European clade bovine foamy viruses from Germany and Poland.

PubMed

Hechler, Torsten; Materniak, Magdalena; Kehl, Timo; Kuzmak, Jacek; Löchelt, Martin

2012-10-01

Bovine foamy virus (BFV), or bovine spumaretrovirus, is an infectious agent of cattle with no obvious disease association but high prevalence in its host. Here, we report two complete BFV sequences, BFV-Riems, isolated in 1978 in East Germany, and BFV100, isolated in 2005 in Poland. Both new BFV isolates share the overall genetic makeup of other foamy viruses (FV). Although isolated almost 25 years apart and propagated in either bovine (BFV-Riems) or nonbovine (BFV100) cells, both viruses are highly related, forming the European BFV clade. Despite clear differences, BFV-Riems and BFV100 are still very similar to BFV isolates from China and the United States, comprising the non-European BFV clade. The genomic sequences presented here confirm the concept of high sequence conservation across most of the FV genome. Analyses of cell culture-derived genomes reveal that proviral DNA may specifically lack introns in the env-bel coding region. The spacing of the splice sites in this region suggests that BFV has developed a novel mode to express a secretory but nonfunctional Env protein.

Complete Genome Sequences of Two Novel European Clade Bovine Foamy Viruses from Germany and Poland

PubMed Central

Hechler, Torsten; Materniak, Magdalena; Kehl, Timo; Kuzmak, Jacek

2012-01-01

Bovine foamy virus (BFV), or bovine spumaretrovirus, is an infectious agent of cattle with no obvious disease association but high prevalence in its host. Here, we report two complete BFV sequences, BFV-Riems, isolated in 1978 in East Germany, and BFV100, isolated in 2005 in Poland. Both new BFV isolates share the overall genetic makeup of other foamy viruses (FV). Although isolated almost 25 years apart and propagated in either bovine (BFV-Riems) or nonbovine (BFV100) cells, both viruses are highly related, forming the European BFV clade. Despite clear differences, BFV-Riems and BFV100 are still very similar to BFV isolates from China and the United States, comprising the non-European BFV clade. The genomic sequences presented here confirm the concept of high sequence conservation across most of the FV genome. Analyses of cell culture-derived genomes reveal that proviral DNA may specifically lack introns in the env-bel coding region. The spacing of the splice sites in this region suggests that BFV has developed a novel mode to express a secretory but nonfunctional Env protein. PMID:22966195

High-Frame-Rate Doppler Ultrasound Using a Repeated Transmit Sequence

PubMed Central

Podkowa, Anthony S.; Oelze, Michael L.; Ketterling, Jeffrey A.

2018-01-01

The maximum detectable velocity of high-frame-rate color flow Doppler ultrasound is limited by the imaging frame rate when using coherent compounding techniques. Traditionally, high quality ultrasonic images are produced at a high frame rate via coherent compounding of steered plane wave reconstructions. However, this compounding operation results in an effective downsampling of the slow-time signal, thereby artificially reducing the frame rate. To alleviate this effect, a new transmit sequence is introduced where each transmit angle is repeated in succession. This transmit sequence allows for direct comparison between low resolution, pre-compounded frames at a short time interval in ways that are resistent to sidelobe motion. Use of this transmit sequence increases the maximum detectable velocity by a scale factor of the transmit sequence length. The performance of this new transmit sequence was evaluated using a rotating cylindrical phantom and compared with traditional methods using a 15-MHz linear array transducer. Axial velocity estimates were recorded for a range of ±300 mm/s and compared to the known ground truth. Using these new techniques, the root mean square error was reduced from over 400 mm/s to below 50 mm/s in the high-velocity regime compared to traditional techniques. The standard deviation of the velocity estimate in the same velocity range was reduced from 250 mm/s to 30 mm/s. This result demonstrates the viability of the repeated transmit sequence methods in detecting and quantifying high-velocity flow. PMID:29910966

Examining mediators of child sexual abuse and sexually transmitted infections.

PubMed

Sutherland, Melissa A

2011-01-01

Interpersonal violence has increasingly been identified as a risk factor for sexually transmitted infections. Understanding the pathways between violence and sexually transmitted infections is essential to designing effective interventions. The aim of this study was to examine dissociative symptoms, alcohol use, and intimate partner physical violence and sexual coercion as mediators of child sexual abuse and lifetime sexually transmitted infection diagnosis among a sample of women. A convenience sample of 202 women was recruited from healthcare settings, with 189 complete cases for analysis. A multiple mediation model tested the proposed mediators of child sexual abuse and lifetime sexually transmitted infection diagnosis. Bootstrapping, a resampling method, was used to test for mediation. Key variables included child sexual abuse, dissociative symptoms, alcohol use, and intimate partner violence. Child sexual abuse was reported by 46% of the study participants (n = 93). Child sexual abuse was found to have an indirect effect on lifetime sexually transmitted infection diagnosis, with the effect occurring through dissociative symptoms (95% confidence interval = 0.0033-0.4714) and sexual coercion (95% confidence interval = 0.0359-0.7694). Alcohol use and physical violence were not found to be significant mediators. This study suggests that dissociation and intimate partner sexual coercion are important mediators of child sexual abuse and sexually transmitted infection diagnosis. Therefore, interventions that consider the roles of dissociative symptoms and interpersonal violence may be effective in preventing sexually transmitted infections among women.

Pre-Clinical Development of a Recombinant, Replication-Competent Adenovirus Serotype 4 Vector Vaccine Expressing HIV-1 Envelope 1086 Clade C

PubMed Central

Alexander, Jeff; Mendy, Jason; Vang, Lo; Avanzini, Jenny B.; Garduno, Fermin; Manayani, Darly J.; Ishioka, Glenn; Farness, Peggy; Ping, Li-Hua; Swanstrom, Ronald; Parks, Robert; Liao, Hua-Xin; Haynes, Barton F.; Montefiori, David C.; LaBranche, Celia; Smith, Jonathan; Gurwith, Marc; Mayall, Tim

2013-01-01

Background There is a well-acknowledged need for an effective AIDS vaccine that protects against HIV-1 infection or limits in vivo viral replication. The objective of these studies is to develop a replication-competent, vaccine vector based on the adenovirus serotype 4 (Ad4) virus expressing HIV-1 envelope (Env) 1086 clade C glycoprotein. Ad4 recombinant vectors expressing Env gp160 (Ad4Env160), Env gp140 (Ad4Env140), and Env gp120 (Ad4Env120) were evaluated. Methods The recombinant Ad4 vectors were generated with a full deletion of the E3 region of Ad4 to accommodate the env gene sequences. The vaccine candidates were assessed in vitro following infection of A549 cells for Env-specific protein expression and for posttranslational transport to the cell surface as monitored by the binding of broadly neutralizing antibodies (bNAbs). The capacity of the Ad4Env vaccines to induce humoral immunity was evaluated in rabbits for Env gp140 and V1V2-specific binding antibodies, and HIV-1 pseudovirus neutralization. Mice immunized with the Ad4Env160 vaccine were assessed for IFNγ T cell responses specific for overlapping Env peptide sets. Results Robust Env protein expression was confirmed by western blot analysis and recognition of cell surface Env gp160 by multiple bNAbs. Ad4Env vaccines induced humoral immune responses in rabbits that recognized Env 1086 gp140 and V1V2 polypeptide sequences derived from 1086 clade C, A244 clade AE, and gp70 V1V2 CASE A2 clade B fusion protein. The immune sera efficiently neutralized tier 1 clade C pseudovirus MW965.26 and neutralized the homologous and heterologous tier 2 pseudoviruses to a lesser extent. Env-specific T cell responses were also induced in mice following Ad4Env160 vector immunization. Conclusions The Ad4Env vaccine vectors express high levels of Env glycoprotein and induce both Env-specific humoral and cellular immunity thus supporting further development of this new Ad4 HIV-1 Env vaccine platform in Phase 1 clinical

[Diseases transmitted by ticks locally and abroad].

PubMed

Gétaz, L; Loutan, L; Mezger, N

2012-05-09

This article provides a brief overview of some diseases transmitted by ticks. These vectors do not transmit only Lyme disease and tickborne-encephalitis, even in Switzerland. Several tick-borne diseases cause nonspecific flu-like symptoms. Nevertheless sometimes severe, some of these diseases can be treated with specific treatments. Repellents, appropriate clothes impregnated with permethrine and prompt removal of the tick are effective preventive measures to limit the risk of infection. There is an effective vaccine which protects against tick-borne encephalitis.

Development and validation of broad-range qualitative and clade-specific quantitative molecular probes for assessing mercury methylation in the environment

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

Christensen, Geoff A.; Wymore, Ann M.; King, Andrew J.

Two genes, hgcA and hgcB, are essential for microbial mercury (Hg)-methylation. Detection and estimation of their abundance, in conjunction with Hg concentration, bioavailability and biogeochemistry is critical in determining potential hot spots of methylmercury (MeHg) generation in at-risk environments. We developed broad-range degenerate PCR primers spanning known hgcAB genes to determine the presence of both genes in diverse environments. These primers were tested against an extensive set of pure cultures with published genomes, including 13 Deltaproteobacteria, nine Firmicutes, and nine methanogenic Archaea. A distinct PCR product at the expected size was confirmed for all hgcAB+ strains tested via Sanger sequencing.more » Additionally, we developed clade-specific degenerate quantitative primers (qPCR) that targeted hgcA for each of the three dominant Hg-methylating clades. The clade-specific qPCR primers amplified hgcA from 64%, 88% and 86% of tested pure cultures of Deltaproteobacteria, Firmicutes and Archaea, respectively, and were highly specific for each clade. Amplification efficiencies and detection limits were quantified for each organism. Primer sensitivity varied among species based on sequence conservation. Finally, to begin to evaluate the utility of our primer sets in nature, we tested hgcA and hgcAB recovery from pure cultures spiked into sand and soil. These novel quantitative molecular tools designed in this study will allow for more accurate identification and quantification of the individual Hg-methylating groups of microorganisms in the environment. Here, the resulting data will be essential in developing accurate and robust predictive models of Hg-methylation potential, ideally integrating the geochemistry of Hg methylation to the microbiology and genetics of hgcAB.« less

Development and validation of broad-range qualitative and clade-specific quantitative molecular probes for assessing mercury methylation in the environment

DOE PAGES

Christensen, Geoff A.; Wymore, Ann M.; King, Andrew J.; ...

2016-07-15

Two genes, hgcA and hgcB, are essential for microbial mercury (Hg)-methylation. Detection and estimation of their abundance, in conjunction with Hg concentration, bioavailability and biogeochemistry is critical in determining potential hot spots of methylmercury (MeHg) generation in at-risk environments. We developed broad-range degenerate PCR primers spanning known hgcAB genes to determine the presence of both genes in diverse environments. These primers were tested against an extensive set of pure cultures with published genomes, including 13 Deltaproteobacteria, nine Firmicutes, and nine methanogenic Archaea. A distinct PCR product at the expected size was confirmed for all hgcAB+ strains tested via Sanger sequencing.more » Additionally, we developed clade-specific degenerate quantitative primers (qPCR) that targeted hgcA for each of the three dominant Hg-methylating clades. The clade-specific qPCR primers amplified hgcA from 64%, 88% and 86% of tested pure cultures of Deltaproteobacteria, Firmicutes and Archaea, respectively, and were highly specific for each clade. Amplification efficiencies and detection limits were quantified for each organism. Primer sensitivity varied among species based on sequence conservation. Finally, to begin to evaluate the utility of our primer sets in nature, we tested hgcA and hgcAB recovery from pure cultures spiked into sand and soil. These novel quantitative molecular tools designed in this study will allow for more accurate identification and quantification of the individual Hg-methylating groups of microorganisms in the environment. Here, the resulting data will be essential in developing accurate and robust predictive models of Hg-methylation potential, ideally integrating the geochemistry of Hg methylation to the microbiology and genetics of hgcAB.« less

Evolutionary History of LINE-1 in the Major Clades of Placental Mammals

PubMed Central

Waters, Paul D.; Dobigny, Gauthier; Waddell, Peter J.; Robinson, Terence J.

2007-01-01

Background LINE-1 constitutes an important component of mammalian genomes. It has a dynamic evolutionary history characterized by the rise, fall and replacement of subfamilies. Most data concerning LINE-1 biology and evolution are derived from the human and mouse genomes and are often assumed to hold for all placentals. Methodology To examine LINE-1 relationships, sequences from the 3′ region of the reverse transcriptase from 21 species (representing 13 orders across Afrotheria, Xenarthra, Supraprimates and Laurasiatheria) were obtained from whole genome sequence assemblies, or by PCR with degenerate primers. These sequences were aligned and analysed. Principal Findings Our analysis reflects accepted placental relationships suggesting mostly lineage-specific LINE-1 families. The data provide clear support for several clades including Glires, Supraprimates, Laurasiatheria, Boreoeutheria, Xenarthra and Afrotheria. Within the afrotherian LINE-1 (AfroLINE) clade, our tree supports Paenungulata, Afroinsectivora and Afroinsectiphillia. Xenarthran LINE-1 (XenaLINE) falls sister to AfroLINE, providing some support for the Atlantogenata (Xenarthra+Afrotheria) hypothesis. Significance LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics. Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches) such as that to marsupials are shortened and/or broken up. Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent. PMID:17225861

Marine bacteria from the Roseobacter clade produce sulfur volatiles via amino acid and dimethylsulfoniopropionate catabolism.

PubMed

Brock, Nelson L; Menke, Markus; Klapschinski, Tim A; Dickschat, Jeroen S

2014-07-07

Dimethylsulfoniopropionate (DMSP) is a versatile sulfur source for the production of sulfur-containing secondary metabolites by marine bacteria from the Roseobacter clade. (34)S-labelled DMSP and cysteine, and several DMSP derivatives with modified S-alkyl groups were synthesised and used in feeding experiments that gave insights into the biosynthesis of sulfur volatiles from these bacteria.

22 CFR 1203.735-214 - Transmitting communications and gifts.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 22 Foreign Relations 2 2010-04-01 2010-04-01 true Transmitting communications and gifts. 1203.735-214 Section 1203.735-214 Foreign Relations UNITED STATES INTERNATIONAL DEVELOPMENT COOPERATION AGENCY....735-214 Transmitting communications and gifts. (a) Correspondence. In corresponding with anyone other...

Tip of the clade on the top of the World—the first fossil Lophopidae (Hemiptera: Fulgoromorpha) from the Palaeocene of Tibet

NASA Astrophysics Data System (ADS)

Szwedo, Jacek; Stroiński, Adam; Lin, Qibin

2015-06-01

Lophopidae is a family of planthoppers (Hemiptera: Fulgoromorpha) present today in tropical and subtropical zones of the Old World. The most recent taxonomic studies and phylogeny of these insects do not include the extinct representatives. Therefore, each new discovery of a fossil lophopid is of high interest, giving new insights to their evolutionary history and enabling to test the proposed relationships. The recent findings of extinct Lophopidae in Europe, in various Palaeogene deposits, put in doubts their proposed evolutionary and biogeographic scenario. The new fossil from the Palaeocene of Northern Tibet is related to one of the Lophopidae clades, Apia+ group, believed to be the most advanced one, and recently distributed in the recent Sundaland-New Guinea-Queensland area. A new genus and species Gesaris gnapo gen. et sp. n. provide information on early lophopids diversity and relationships and demonstrates the necessity for a revision of the existing hypotheses for the initial diversification and distributional pattern of the Lophopidae.

Decoupled temporal patterns of evolution and ecology in two post-Paleozoic clades

NASA Technical Reports Server (NTRS)

McKinney, F. K.; Lidgard, S.; Sepkoski, J. J. Jr; Taylor, P. D.

1998-01-01

Counts of taxonomic diversity are the prevailing standards for documenting large-scale patterns of evolution in the fossil record. However, the secular pattern of relative ecological importance between the bryozoan clades Cyclostomata and Cheilostomata is not reflected fully in compilations of generic diversity or within-fauna species richness, and the delayed ecological recovery of the Cheilostomata after the mass extinction at the Cretaceous-Tertiary boundary is missed entirely. These observations demonstrate that evolutionary success and ecological dominance can be decoupled and profoundly different, even over tens of millions of years.

Analysis of Ecological Distribution and Genomic Content from a Clade of Bacteroidetes Endemic to Sulfidic Environments

NASA Astrophysics Data System (ADS)

Zhou, K.; Sylvan, J. B.; Hallam, S. J.

2017-12-01

The Bacteroidetes are a ubiquitous phylum of bacteria found in a wide variety of habitats. Marine Bacteroidetes are known to utilize complex carbohydrates and have a potentially important role in the global carbon cycle through processing these compounds, which are not digestible by many other microbes. Some members of the phylum are known to perform denitrification and are facultative anaerobes, but Bacteroidetes are not known to participate in sulfur redox cycling. Recently, it was shown that a clade of uncultured Bacteroidetes, including the VC2.1_Bac22 group, appears to be endemic to sulfidic environments, including hydrothermal vent sulfide chimneys, sediments and marine water column oxygen minimum zones (OMZs). This clade, dubbed the Sulfiphilic Bacteroidetes, is not detected in 16S rRNA amplicon studies from non-sulfidic environments. To test the hypothesis that the Sulphiphilic Bacteroidetes are involved in sulfur redox chemistry, we updated our meta-analysis of the clade using 16s rRNA sequences from public databases and employed single-cell genomics to survey their genomic potential using 19 single amplified genomes (SAGs) isolated from the seasonally anoxic Saanich Inlet, a seasonally hypoxic basin in British Columbia. Initial analysis of these SAGs indicates the Sulphiphilic Bacteroidetes may perform sulfur redox reactions using a three gene psrABC operon encoding the polysulfide reductase enzyme complex with a thiosulfate sulfurtransferase (rhodanese), which putatively uses cyanide to convert thiosulfate to sulfite, just upstream. Interestingly, this is the same configuration as discovered recently in some Marine Group A bacteria. Further aspects of the Sulphiphilic Bacteroidetes' genomic potential will be presented in light of their presence in sulfidic environments.

33 CFR 169.215 - How must a ship transmit position reports?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false How must a ship transmit position... SECURITY (CONTINUED) PORTS AND WATERWAYS SAFETY SHIP REPORTING SYSTEMS Transmission of Long Range Identification and Tracking Information § 169.215 How must a ship transmit position reports? A ship must transmit...

33 CFR 169.215 - How must a ship transmit position reports?

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false How must a ship transmit position... SECURITY (CONTINUED) PORTS AND WATERWAYS SAFETY SHIP REPORTING SYSTEMS Transmission of Long Range Identification and Tracking Information § 169.215 How must a ship transmit position reports? A ship must transmit...

33 CFR 169.215 - How must a ship transmit position reports?

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false How must a ship transmit position... SECURITY (CONTINUED) PORTS AND WATERWAYS SAFETY SHIP REPORTING SYSTEMS Transmission of Long Range Identification and Tracking Information § 169.215 How must a ship transmit position reports? A ship must transmit...

The Early Origin of the Antarctic Marine Fauna and Its Evolutionary Implications

PubMed Central

Crame, J. Alistair; Beu, Alan G.; Ineson, Jon R.; Francis, Jane E.; Whittle, Rowan J.; Bowman, Vanessa C.

2014-01-01

The extensive Late Cretaceous – Early Paleogene sedimentary succession of Seymour Island, N.E. Antarctic Peninsula offers an unparalleled opportunity to examine the evolutionary origins of a modern polar marine fauna. Some 38 modern Southern Ocean molluscan genera (26 gastropods and 12 bivalves), representing approximately 18% of the total modern benthic molluscan fauna, can now be traced back through at least part of this sequence. As noted elsewhere in the world, the balance of the molluscan fauna changes sharply across the Cretaceous – Paleogene (K/Pg) boundary, with gastropods subsequently becoming more diverse than bivalves. A major reason for this is a significant radiation of the Neogastropoda, which today forms one of the most diverse clades in the sea. Buccinoidea is the dominant neogastropod superfamily in both the Paleocene Sobral Formation (SF) (56% of neogastropod genera) and Early - Middle Eocene La Meseta Formation (LMF) (47%), with the Conoidea (25%) being prominent for the first time in the latter. This radiation of Neogastropoda is linked to a significant pulse of global warming that reached at least 65°S, and terminates abruptly in the upper LMF in an extinction event that most likely heralds the onset of global cooling. It is also possible that the marked Early Paleogene expansion of neogastropods in Antarctica is in part due to a global increase in rates of origination following the K/Pg mass extinction event. The radiation of this and other clades at ∼65°S indicates that Antarctica was not necessarily an evolutionary refugium, or sink, in the Early – Middle Eocene. Evolutionary source – sink dynamics may have been significantly different between the Paleogene greenhouse and Neogene icehouse worlds. PMID:25493546

Male germline transmits fetal alcohol epigenetic marks for multiple generations: a review.

PubMed

Sarkar, Dipak K

2016-01-01

Alcohol exposure during fetal and early postnatal development can lead to an increased incidence of later life adult-onset diseases. Examples include central nervous system dysfunction, depression, anxiety, hyperactivity, and an inability to deal with stressful situations, increased infection and cancer. Direct effects of alcohol leading to developmental abnormalities often involve epigenetic modifications of genes that regulate cellular functions. Epigenetic marks carried over from the parents are known to undergo molecular programming events that happen early in embryonic development by a wave of DNA demethylation, which leaves the embryo with a fresh genomic composition. The proopiomelanocortin (Pomc) gene controls neuroendocrine-immune functions and is imprinted by fetal alcohol exposure. Recently, this gene has been shown to be hypermethylated through three generations. Additionally, the alcohol epigenetic marks on the Pomc gene are maintained in the male but not in the female germline during this transgenerational transmission. These data suggest that the male-specific chromosome might be involved in transmitting alcohol epigenetic marks through multiple generations. © 2015 Society for the Study of Addiction.

46 CFR 111.79-9 - Transmitting power between receptacles.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 4 2011-10-01 2011-10-01 false Transmitting power between receptacles. 111.79-9 Section 111.79-9 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) ELECTRICAL ENGINEERING ELECTRIC SYSTEMS-GENERAL REQUIREMENTS Receptacles § 111.79-9 Transmitting power between receptacles. (a) If...

46 CFR 111.79-9 - Transmitting power between receptacles.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 4 2013-10-01 2013-10-01 false Transmitting power between receptacles. 111.79-9 Section 111.79-9 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) ELECTRICAL ENGINEERING ELECTRIC SYSTEMS-GENERAL REQUIREMENTS Receptacles § 111.79-9 Transmitting power between receptacles. (a) If...

46 CFR 111.79-9 - Transmitting power between receptacles.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 4 2014-10-01 2014-10-01 false Transmitting power between receptacles. 111.79-9 Section 111.79-9 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) ELECTRICAL ENGINEERING ELECTRIC SYSTEMS-GENERAL REQUIREMENTS Receptacles § 111.79-9 Transmitting power between receptacles. (a) If...

46 CFR 111.79-9 - Transmitting power between receptacles.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 4 2012-10-01 2012-10-01 false Transmitting power between receptacles. 111.79-9 Section 111.79-9 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) ELECTRICAL ENGINEERING ELECTRIC SYSTEMS-GENERAL REQUIREMENTS Receptacles § 111.79-9 Transmitting power between receptacles. (a) If...

46 CFR 111.79-9 - Transmitting power between receptacles.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 4 2010-10-01 2010-10-01 false Transmitting power between receptacles. 111.79-9 Section 111.79-9 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) ELECTRICAL ENGINEERING ELECTRIC SYSTEMS-GENERAL REQUIREMENTS Receptacles § 111.79-9 Transmitting power between receptacles. (a) If...

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

PubMed Central

Feng, Yan-Jie; Liang, Dan; Hillis, David M.; Cannatella, David C.; Zhang, Peng

2017-01-01

Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous–Paleogene (K–Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K–Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation. PMID:28673970

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous-Paleogene boundary.

PubMed

Feng, Yan-Jie; Blackburn, David C; Liang, Dan; Hillis, David M; Wake, David B; Cannatella, David C; Zhang, Peng

2017-07-18

Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous-Paleogene (K-Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K-Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation.

Functional anatomy reveals secretory activity in papillose anthers of a buzz-pollinated Solanum species (Cyphomandra clade - Solanaceae).

PubMed

Falcão, B F; Stehmann, J R

2018-03-30

Pollination in Solanum (Solanaceae) species is commonly performed by female bees, which vibrate anthers to extract pollen. Another pollen removal type is by male euglossine bees, milking the anthers when searching for floral scents produced by secretory tissues (osmophorous) at the swollen connective of the anthers of species in the Cyphomandra clade. Some species of this clade, however, are buzz-pollinated and present papillate anthers that should also have secretory activity, a hypothesis here tested. The anthers of Solanum luridifuscescens were fixed at different stages of development and analysed under light microscopy, SEM and TEM. Histochemical tests for the detection of starch and lipids were done. Epidermal cells of the abaxial surface of the anthers were visibly papillose, had large nuclei and dense cytoplasm rich in organelles such as mitochondria and plastids, typical features of secretory tissues. In this site, lipid droplets were detected, concomitantly with starch consumption, compatible with the secretory process in osmophores. No exudate or accumulation of substances was seen on the surface; in agreement with a previous pollination study performed in field conditions, where no pollinators were observed collecting floral scents, only pollen. The histochemical and structural analyses have evidenced the lipidic composition of the secretion, strongly pointing to terpenes as the secreted compounds. Ours findings show that papillae of the anthers have secretory activities that produce lipophilic compounds. This does not result in resources for bees, but could be an evolutionary step to the development of more specialised anthers in the Cyphomandra clade. © 2018 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

Highly rearranged and size-variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers.

PubMed

Wu, Chung-Shien; Chaw, Shu-Miaw

2014-04-01

Although conifers are of immense ecological and economic value, bioengineering of their chloroplasts remains undeveloped. Understanding the chloroplast genomic organization of conifers can facilitate their bioengineering. Members of the conifer II clade (or cupressophytes) are highly diverse in both morphologic features and chloroplast genomic organization. We compared six cupressophyte chloroplast genomes (cpDNAs) that represent four of the five cupressophyte families, including three genomes that are first reported here (Agathis dammara, Calocedrus formosana and Nageia nagi). The six cupressophyte cpDNAs have lost a pair of large inverted repeats (IRs) and vary greatly in size, organization and tRNA copies. We demonstrate that cupressophyte cpDNAs have evolved towards reduced size, largely due to shrunken intergenic spacers. In cupressophytes, cpDNA rearrangements are capable of extending intergenic spacers, and synonymous mutations are negatively associated with the size and frequency of rearrangements. The variable cpDNA sizes of cupressophytes may have been shaped by mutational burden and genomic rearrangements. On the basis of cpDNA organization, our analyses revealed that in gymnosperms, cpDNA rearrangements are phylogenetically informative, which supports the 'gnepines' clade. In addition, removal of a specific IR influences the minimal rearrangements required for the gnepines and cupressophyte clades, whereby Pinaceae favours the removal of IRB but cupressophytes exclusion of IRA. This result strongly suggests that different IR copies have been lost from conifers I and II. Our data help understand the complexity and evolution of cupressophyte cpDNAs. © 2013 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology, The Association of Applied Biologists and John Wiley & Sons Ltd.

HIV-Tat immunization induces cross-clade neutralizing antibodies and CD4(+) T cell increases in antiretroviral-treated South African volunteers: a randomized phase II clinical trial.

PubMed

Ensoli, Barbara; Nchabeleng, Maphoshane; Ensoli, Fabrizio; Tripiciano, Antonella; Bellino, Stefania; Picconi, Orietta; Sgadari, Cecilia; Longo, Olimpia; Tavoschi, Lara; Joffe, Daniel; Cafaro, Aurelio; Francavilla, Vittorio; Moretti, Sonia; Pavone Cossut, Maria Rosaria; Collacchi, Barbara; Arancio, Angela; Paniccia, Giovanni; Casabianca, Anna; Magnani, Mauro; Buttò, Stefano; Levendal, Elise; Ndimande, John Velaphi; Asia, Bennett; Pillay, Yogan; Garaci, Enrico; Monini, Paolo

2016-06-09

Although combined antiretroviral therapy (cART) has saved millions of lives, it is incapable of full immune reconstitution and virus eradication. The transactivator of transcription (Tat) protein is a key human immunodeficiency virus (HIV) virulence factor required for virus replication and transmission. Tat is expressed and released extracellularly by infected cells also under cART and in this form induces immune dysregulation, and promotes virus reactivation, entry and spreading. Of note, anti-Tat antibodies are rare in natural infection and, when present, correlate with asymptomatic state and reduced disease progression. This suggested that induction of anti-Tat antibodies represents a pathogenesis-driven intervention to block progression and to intensify cART. Indeed Tat-based vaccination was safe, immunogenic and capable of immune restoration in an open-label, randomized phase II clinical trial conducted in 168 cART-treated volunteers in Italy. To assess whether B-clade Tat immunization would be effective also in patients with different genetic background and infecting virus, a phase II trial was conducted in South Africa. The ISS T-003 was a 48-week randomised, double-blinded, placebo-controlled trial to evaluate immunogenicity (primary endpoint) and safety (secondary endpoint) of B-clade Tat (30 μg) given intradermally, three times at 4-week intervals, in 200 HIV-infected adults on effective cART (randomised 1:1) with CD4(+) T-cell counts ≥200 cells/µL. Study outcomes also included cross-clade anti-Tat antibodies, neutralization, CD4(+) T-cell counts and therapy compliance. Immunization was safe and well-tolerated and induced durable, high titers anti-Tat B-clade antibodies in 97 % vaccinees. Anti-Tat antibodies were cross-clade (all vaccinees tested) and neutralized Tat-mediated entry of oligomeric B-clade and C-clade envelope in dendritic cells (24 participants tested). Anti-Tat antibody titers correlated positively with neutralization. Tat

Unique Phenotypic Characteristics of Recently Transmitted HIV-1 Subtype C Envelope Glycoprotein gp120: Use of CXCR6 Coreceptor by Transmitted Founder Viruses.

PubMed

Ashokkumar, Manickam; Aralaguppe, Shambhu G; Tripathy, Srikanth P; Hanna, Luke Elizabeth; Neogi, Ujjwal

2018-05-01

Adequate information on the precise molecular and biological composition of the viral strains that establish HIV infection in the human host will provide effective means of immunization against HIV infection. In an attempt to identify the transmitted founder (TF) virus and differentiate the biological properties and infectious potential of the TF virus from those of the population of the early transmitted viruses, 250 patient-derived gp120 envelope glycoproteins were cloned in pMN-K7-Luc-IRESs-NefΔgp120 to obtain chimeric viruses. Samples were obtained from eight infants who had recently become infected with HIV through mother-to-child transmission (MTCT) and two adults who acquired infection through the heterosexual route and were in the chronic stage of infection. Among the 250 clones tested, 65 chimeric viruses were infectious, and all belonged to HIV-1 subtype C. The 65 clones were analyzed for molecular features of the envelope, per-infectious-particle infectivity, coreceptor tropism, drug sensitivity, and sensitivity to broadly neutralizing antibodies. Based on genotypic and phenotypic analysis of the viral clones, we identified 10 TF viruses from the eight infants. The TF viruses were characterized by shorter V1V2 regions, a reduced number of potential N-linked glycosylation sites, and a higher infectivity titer compared to the virus variants from the adults in the chronic stage of infection. CXCR6 coreceptor usage, in addition to that of the CCR5 coreceptor, which was used by all 65 chimeric viruses, was identified in 13 viruses. The sensitivity of the TF variants to maraviroc and a standard panel of neutralizing monoclonal antibodies (VRC01, PG09, PG16, and PGT121) was found to be much lower than that of the virus variants from the adults in the chronic stage of infection. IMPORTANCE Tremendous progress has been made during the last three and half decades of HIV research, but some significant gaps continue to exist. One of the frontier areas of HIV

Sexually Transmitted Diseases and Infertility

PubMed Central

TSEVAT, Danielle G.; WIESENFELD, Harold C.; Parks, Caitlin; PEIPERT, Jeffrey F.

2016-01-01

Female infertility, including tubal factor infertility, is a major public health concern worldwide. Most cases of tubal factor infertility are attributable to untreated sexually transmitted diseases that ascend along the reproductive tract and are capable of causing tubal inflammation, damage, and scarring. Evidence has consistently demonstrated the effects of Chlamydia trachomatis and Neisseria gonorrhoeae as pathogenic bacteria involved in reproductive tract morbidities including tubal factor infertility and pelvic inflammatory disease. There is limited evidence in the medical literature that other sexually transmitted organisms, including Mycoplasma genitalium, Trichomonas vaginalis, and other microorganisms within the vaginal microbiome may be important factors involved in the pathology of infertility. Further investigation into the vaginal microbiome and other potential pathogens is necessary in order to identify preventable causes of tubal factor infertility. Improved clinical screening and prevention of ascending infection may provide a solution to the persistent burden of infertility. PMID:28007229

vasa and piwi are required for mitotic integrity in early embryogenesis in the spider Parasteatoda tepidariorum.

PubMed

Schwager, Evelyn E; Meng, Yue; Extavour, Cassandra G

2015-06-15

Studies in vertebrate and invertebrate model organisms on the molecular basis of primordial germ cell (PGC) specification have revealed that metazoans can specify their germ line either early in development by maternally transmitted cytoplasmic factors (inheritance), or later in development by signaling factors from neighboring tissues (induction). Regardless of the mode of PGC specification, once animal germ cells are specified, they invariably express a number of highly conserved genes. These include vasa and piwi, which can play essential roles in any or all of PGC specification, development, or gametogenesis. Although the arthropods are the most speciose animal phylum, to date there have been no functional studies of conserved germ line genes in species of the most basally branching arthropod clade, the chelicerates (which includes spiders, scorpions, and horseshoe crabs). Here we present the first such study by using molecular and functional tools to examine germ line development and the roles of vasa and piwi orthologues in the common house spider Parasteatoda (formerly Achaearanea) tepidariorum. We use transcript and protein expression patterns of Pt-vasa and Pt-piwi to show that primordial germ cells (PGCs) in the spider arise during late embryogenesis. Neither Pt-vasa nor Pt-piwi gene products are localized asymmetrically to any embryonic region before PGCs emerge as paired segmental clusters in opisthosomal segments 2-6 at late germ band stages. RNA interference studies reveal that both genes are required maternally for egg laying, mitotic progression in early embryos, and embryonic survival. Our results add to the growing body of evidence that vasa and piwi can play important roles in somatic development, and provide evidence for a previously hypothesized conserved role for vasa in cell cycle progression. Copyright © 2014 Elsevier Inc. All rights reserved.

Toward a comprehensive phylogenetic reconstruction of the evolutionary history of mitogen-activated protein kinases in the plant kingdom.

PubMed

Janitza, Philipp; Ullrich, Kristian Karsten; Quint, Marcel

2012-01-01

The mitogen-activated protein kinase (MAPK) pathway is a three-tier signaling cascade that transmits cellular information from the plasma membrane to the cytoplasm where it triggers downstream responses. The MAPKs represent the last step in this cascade and are activated when both tyrosine and threonine residues in a conserved TxY motif are phosphorylated by MAPK kinases, which in turn are themselves activated by phosphorylation by MAPK kinase kinases. To understand the molecular evolution of MAPKs in the plant kingdom, we systematically conducted a Hidden-Markov-Model based screen to identify MAPKs in 13 completely sequenced plant genomes. In this analysis, we included green algae, bryophytes, lycophytes, and several mono- and eudicotyledonous species covering >800 million years of evolution. The phylogenetic relationships of the 204 identified MAPKs based on Bayesian inference facilitated the retraction of the sequence of emergence of the four major clades that are characterized by the presence of a TDY or TEY-A/TEY-B/TEY-C type kinase activation loop. We present evidence that after the split of TDY- and TEY-type MAPKs, initially the TEY-C clade emerged. This was followed by the TEY-B clade in early land plants until the TEY-A clade finally emerged in flowering plants. In addition to these well characterized clades, we identified another highly conserved clade of 45 MAPK-likes, members of which were previously described as Mak-homologous kinases. In agreement with their essential functions, molecular population genetic analysis of MAPK genes in Arabidopsis thaliana accessions reveal that purifying selection drove the evolution of the MAPK family, implying strong functional constraints on MAPK genes. Closely related MAPKs most likely subfunctionalized, a process in which differential transcriptional regulation of duplicates may be involved.

An Early Miocene bumble bee from northern Bohemia (Hymenoptera, Apidae).

PubMed

Prokop, Jakub; Dehon, Manuel; Michez, Denis; Engel, Michael S

2017-01-01

A new species of fossil bumble bee (Apinae: Bombini) is described and figured from Early Miocene (Burdigalian) deposits of the Most Basin at the Bílina Mine, Czech Republic. Bombus trophonius sp. n. , is placed within the subgenus Cullumanobombus Vogt and distinguished from the several species groups therein. The species is apparently most similar to the Nearctic B. (Cullumanobombus) rufocinctus Cresson, the earliest-diverging species within the clade and the two may be related only by symplesiomorphies. The age of the fossil is in rough accordance with divergence estimations for Cullumanobombus .

HIV Controllers Exhibit Enhanced Frequencies of Major Histocompatibility Complex Class II Tetramer+ Gag-Specific CD4+ T Cells in Chronic Clade C HIV-1 Infection.

PubMed

Laher, Faatima; Ranasinghe, Srinika; Porichis, Filippos; Mewalal, Nikoshia; Pretorius, Karyn; Ismail, Nasreen; Buus, Søren; Stryhn, Anette; Carrington, Mary; Walker, Bruce D; Ndung'u, Thumbi; Ndhlovu, Zaza M

2017-04-01

Immune control of viral infections is heavily dependent on helper CD4 + T cell function. However, the understanding of the contribution of HIV-specific CD4 + T cell responses to immune protection against HIV-1, particularly in clade C infection, remains incomplete. Recently, major histocompatibility complex (MHC) class II tetramers have emerged as a powerful tool for interrogating antigen-specific CD4 + T cells without relying on effector functions. Here, we defined the MHC class II alleles for immunodominant Gag CD4 + T cell epitopes in clade C virus infection, constructed MHC class II tetramers, and then used these to define the magnitude, function, and relation to the viral load of HIV-specific CD4 + T cell responses in a cohort of untreated HIV clade C-infected persons. We observed significantly higher frequencies of MHC class II tetramer-positive CD4 + T cells in HIV controllers than progressors ( P = 0.0001), and these expanded Gag-specific CD4 + T cells in HIV controllers showed higher levels of expression of the cytolytic proteins granzymes A and B. Importantly, targeting of the immunodominant Gag41 peptide in the context of HLA class II DRB1*1101 was associated with HIV control ( r = -0.5, P = 0.02). These data identify an association between HIV-specific CD4 + T cell targeting of immunodominant Gag epitopes and immune control, particularly the contribution of a single class II MHC-peptide complex to the immune response against HIV-1 infection. Furthermore, these results highlight the advantage of the use of class II tetramers in evaluating HIV-specific CD4 + T cell responses in natural infections. IMPORTANCE Increasing evidence suggests that virus-specific CD4 + T cells contribute to the immune-mediated control of clade B HIV-1 infection, yet there remains a relative paucity of data regarding the role of HIV-specific CD4 + T cells in shaping adaptive immune responses in individuals infected with clade C, which is responsible for the majority of HIV

HIV Controllers Exhibit Enhanced Frequencies of Major Histocompatibility Complex Class II Tetramer+ Gag-Specific CD4+ T Cells in Chronic Clade C HIV-1 Infection

PubMed Central

Laher, Faatima; Ranasinghe, Srinika; Porichis, Filippos; Mewalal, Nikoshia; Pretorius, Karyn; Ismail, Nasreen; Buus, Søren; Stryhn, Anette; Carrington, Mary; Walker, Bruce D.; Ndung'u, Thumbi

2017-01-01

ABSTRACT Immune control of viral infections is heavily dependent on helper CD4+ T cell function. However, the understanding of the contribution of HIV-specific CD4+ T cell responses to immune protection against HIV-1, particularly in clade C infection, remains incomplete. Recently, major histocompatibility complex (MHC) class II tetramers have emerged as a powerful tool for interrogating antigen-specific CD4+ T cells without relying on effector functions. Here, we defined the MHC class II alleles for immunodominant Gag CD4+ T cell epitopes in clade C virus infection, constructed MHC class II tetramers, and then used these to define the magnitude, function, and relation to the viral load of HIV-specific CD4+ T cell responses in a cohort of untreated HIV clade C-infected persons. We observed significantly higher frequencies of MHC class II tetramer-positive CD4+ T cells in HIV controllers than progressors (P = 0.0001), and these expanded Gag-specific CD4+ T cells in HIV controllers showed higher levels of expression of the cytolytic proteins granzymes A and B. Importantly, targeting of the immunodominant Gag41 peptide in the context of HLA class II DRB1*1101 was associated with HIV control (r = −0.5, P = 0.02). These data identify an association between HIV-specific CD4+ T cell targeting of immunodominant Gag epitopes and immune control, particularly the contribution of a single class II MHC-peptide complex to the immune response against HIV-1 infection. Furthermore, these results highlight the advantage of the use of class II tetramers in evaluating HIV-specific CD4+ T cell responses in natural infections. IMPORTANCE Increasing evidence suggests that virus-specific CD4+ T cells contribute to the immune-mediated control of clade B HIV-1 infection, yet there remains a relative paucity of data regarding the role of HIV-specific CD4+ T cells in shaping adaptive immune responses in individuals infected with clade C, which is responsible for the majority of HIV

Sexually-Transmitted/Founder HIV-1 Cannot Be Directly Predicted from Plasma or PBMC-Derived Viral Quasispecies in the Transmitting Partner

PubMed Central

Frange, Pierre; Meyer, Laurence; Jung, Matthieu; Goujard, Cecile; Zucman, David; Abel, Sylvie; Hochedez, Patrick; Gousset, Marine; Gascuel, Olivier; Rouzioux, Christine; Chaix, Marie-Laure

2013-01-01

Objective Characterization of HIV-1 sequences in newly infected individuals is important for elucidating the mechanisms of viral sexual transmission. We report the identification of transmitted/founder viruses in eight pairs of HIV-1 sexually-infected patients enrolled at the time of primary infection (“recipients”) and their transmitting partners (“donors”). Methods Using a single genome-amplification approach, we compared quasispecies in donors and recipients on the basis of 316 and 376 C2V5 env sequences amplified from plasma viral RNA and PBMC-associated DNA, respectively. Results Both DNA and RNA sequences indicated very homogeneous viral populations in all recipients, suggesting transmission of a single variant, even in cases of recent sexually transmitted infections (STIs) in donors (n = 2) or recipients (n = 3). In all pairs, the transmitted/founder virus was derived from an infrequent variant population within the blood of the donor. The donor variant sequences most closely related to the recipient sequences were found in plasma samples in 3/8 cases and/or in PBMC samples in 6/8 cases. Although donors were exclusively (n = 4) or predominantly (n = 4) infected by CCR5-tropic (R5) strains, two recipients were infected with highly homogeneous CXCR4/dual-mixed-tropic (X4/DM) viral populations, identified in both DNA and RNA. The proportion of X4/DM quasispecies in donors was higher in cases of X4/DM than R5 HIV transmission (16.7–22.0% versus 0–2.6%), suggesting that X4/DM transmission may be associated with a threshold population of X4/DM circulating quasispecies in donors. Conclusions These suggest that a severe genetic bottleneck occurs during subtype B HIV-1 heterosexual and homosexual transmission. Sexually-transmitted/founder virus cannot be directly predicted by analysis of the donor’s quasispecies in plasma and/or PBMC. Additional studies are required to fully understand the traits that confer the capacity to transmit and

The oldest ionoscopiform from China sheds new light on the early evolution of halecomorph fishes.

PubMed

Xu, Guang-Hui; Zhao, Li-Jun; Coates, Michael I

2014-05-01

The Halecomorphi are a major subdivision of the ray-finned fishes. Although living halecomorphs are represented solely by the freshwater bowfin, Amia calva, this clade has a rich fossil history, and the resolution of interrelationships among extinct members is central to the problem of understanding the origin of the Teleostei, the largest clade of extant vertebrates. The Ionoscopiformes are extinct marine halecomorphs that were inferred to have originated in the Late Jurassic of Europe, and subsequently dispersed to the Early Cretaceous of the New World. Here, we report the discovery of a new ionoscopiform, Robustichthys luopingensis gen. et sp. nov., based on eight well-preserved specimens from the Anisian (242-247 Ma), Middle Triassic marine deposits of Luoping, eastern Yunnan Province, China. The new species documents the oldest known ionoscopiform, extending the stratigraphic range of this group by approximately 90 Ma, and the geographical distribution of this group into the Middle Triassic of South China, a part of eastern Palaeotethys Ocean. These new data provide a minimum estimate for the split of Ionoscopiformes from its sister clade Amiiformes and shed new light on the origin of ionoscopiform fishes. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Eight channel transmit array volume coil using on-coil radiofrequency current sources

PubMed Central

Kurpad, Krishna N.; Boskamp, Eddy B.

2014-01-01

Background At imaging frequencies associated with high-field MRI, the combined effects of increased load-coil interaction and shortened wavelength results in degradation of circular polarization and B1 field homogeneity in the imaging volume. Radio frequency (RF) shimming is known to mitigate the problem of B1 field inhomogeneity. Transmit arrays with well decoupled transmitting elements enable accurate B1 field pattern control using simple, non-iterative algorithms. Methods An eight channel transmit array was constructed. Each channel consisted of a transmitting element driven by a dedicated on-coil RF current source. The coil current distributions of characteristic transverse electromagnetic (TEM) coil resonant modes were non-iteratively set up on each transmitting element and 3T MRI images of a mineral oil phantom were obtained. Results B1 field patterns of several linear and quadrature TEM coil resonant modes that typically occur at different resonant frequencies were replicated at 128 MHz without having to retune the transmit array. The generated B1 field patterns agreed well with simulation in most cases. Conclusions Independent control of current amplitude and phase on each transmitting element was demonstrated. The transmit array with on-coil RF current sources enables B1 field shimming in a simple and predictable manner. PMID:24834418

A Theater-Based Approach to Primary Prevention of Sexual Behavior for Early Adolescents

ERIC Educational Resources Information Center

Lieberman, Lisa D.; Berlin, Cydelle; Palen, Lori-Ann; Ashley, Olivia Silber

2012-01-01

Early adolescence is a crucial period for preventing teen pregnancy and sexually transmitted infections. This study evaluated STAR LO, a theater-based intervention designed to affect antecedents of sexual activity among urban early adolescents (N = 1,143). Public elementary/middle schools received the intervention or served as a wait-listed…

Reintroduction of highly pathogenic avian influenza A/H5N8 virus of clade 2.3.4.4. in Russia.

PubMed

Marchenko, Vasiliy Y; Susloparov, Ivan M; Komissarov, Andrey B; Fadeev, Artem; Goncharova, Nataliya I; Shipovalov, Andrey V; Svyatchenko, Svetlana V; Durymanov, Alexander G; Ilyicheva, Tatyana N; Salchak, Lyudmila K; Svintitskaya, Elena P; Mikheev, Valeriy N; Ryzhikov, Alexander B

2017-05-01

In the spring of 2016, a loss of wild birds was observed during the monitoring of avian influenza virus activity in the Republic of Tyva. That outbreak was caused by influenza H5N8 virus of clade 2.3.4.4. In the fall, viruses of H5N8 clade 2.3.4.4 were propagated in European countries. This paper presents some results of analysis of the virus strains isolated during the spring and fall seasons in 2016 in the Russian Federation. The investigated strains were highly pathogenic for mice, and some of their antigenic and genetic features differed from those of an H5N8 strain that circulated in 2014 in Russia.

Characterization of clade 2.3.4.4 highly pathogenic H5 avian influenza viruses in ducks and chickens.

PubMed

Sun, Honglei; Pu, Juan; Hu, Jiao; Liu, Litao; Xu, Guanlong; Gao, George F; Liu, Xiufan; Liu, Jinhua

2016-01-01

Worldwide dissemination of reassortant variants of H5 clade 2.3.4.4 highly pathogenic avian influenza (HPAI) viruses has posed a great threat to the poultry industry. Here, we systematically characterized the H5N2, H5N6 and H5N8 influenza viruses in poultry and compared them with those of previous clade 2.3.4 H5N1 virus. All the three H5 subtype reassortants caused systematic infection in ducks, and exhibited efficient direct transmission in ducks. All of them were highly pathogenic in chickens; however, the H5 reassortants have reduced virulence compared to the parental H5N1 virus. Antigenicity analysis revealed that the current vaccines that are widely used in China may fail to confer protection against the H5 reassortants. Copyright © 2015 Elsevier B.V. All rights reserved.

Early Cenozoic radiations in the Antarctic marine realm and their evolutionary implications

NASA Astrophysics Data System (ADS)

Crame, Alistair

2014-05-01

The extensive and very well exposed Late Cretaceous - Early Paleogene sedimentary succession of Seymour Island, NE Antarctic Peninsula presents a unique opportunity to examine Early Cenozoic evolutionary radiations in a variety of macrofaunal taxa. Building on the extensive pioneer studies by US and Argentinian palaeontologists, recent investigations have focused on refining litho-, bio- and chronostratigraphies, and taxonomic revisions to a number of key groups. Within the numerically dominant Mollusca, the balance of faunas changes significantly across the Cretaceous/Paleogene boundary, with gastropods becoming numerically dominant for the first time in the Early Paleocene Sobral Formation (SF). At this level seven of the 31 gastropod genera present (= 23%) can be referred to modern Southern Ocean taxa and the same figure is maintained in the Early Eocene La Meseta Formation (LMF) where 21 of 63 genera are modern. A major reason for the rise of the gastropods in the earliest Cenozoic of Antarctica is a significant radiation of the Neogastropoda, which today forms one of the largest clades in the sea. 50% of the SF gastropod fauna and 53% of the LMF at the species level are neogastropods. This important burst of speciation is linked to a major pulse of global warming from ~63 - 43Ma when warm temperate conditions prevailed for long intervals of time at 65ºS. The marked Early Paleogene radiation of neogastropods in Antarctica represents a distinct pulse of southern high-latitude taxa that was coeval with similar tropical/subtropical radiations in localities such as the US Gulf Coast and NW Europe. Thus it would appear that the Early Cenozoic radiation of this major taxon was truly global in scale and not just confined to one latitudinal belt. Whereas it is possible to regard a significant proportion of the modern bivalve fauna as relicts, and thus Antarctica as an evolutionary refugium, or sink, it is much less easy to do so for the Neogastropoda. At least in the

The mystery of clade X: Orciraptor gen. nov. and Viridiraptor gen. nov. are highly specialised, algivorous amoeboflagellates (Glissomonadida, Cercozoa).

PubMed

Hess, Sebastian; Melkonian, Michael

2013-09-01

In freshwater ecosystems a vast diversity of elusive protists exists that specifically feed on microalgae. Due to difficulties in isolation and long-term maintenance, most of these are still poorly known. In this study stable, bacteria-free cultures of several limnetic, algivorous amoeboflagellates were investigated by light microscopy and molecular phylogenetic analyses. All strains represent naked, biflagellate cells, either occurring as rigid flagellates or as surface-attached amoebae. They perforate cell walls of certain Zygnematophyceae and Chlorophyceae (Viridiplantae) and phagocytose algal cell contents. Time-lapse microscopy revealed the feeding behaviour, locomotional processes and life histories of the amoeboflagellates. Clear differences in cell morphology and food range specificity led to the description of two new, monotypic genera Orciraptor and Viridiraptor, which occupy similar, but distinct ecological niches in aquatic ecosystems as 'necrophytophagous' and 'parasitoid' protists, respectively. Molecular phylogenetic analyses based on 18S rDNA sequence data demonstrated that Orciraptor and Viridiraptor belonged to 'clade X' within the order Glissomonadida (Cercozoa, Rhizaria). In conclusion, we established the phenotypic identity of a clade, which until now was exclusively known from environmental sequences, and erect the new family Viridiraptoridae for 'clade X'. Its algivorous members are compared with other glissomonads and nomenclatural, methodological and ecological aspects of these novel 'raptorial' amoeboflagellates are discussed. Copyright © 2013 Elsevier GmbH. All rights reserved.

Absence of clinical disease and contact transmission of HPAI H5NX clade 2.3.4.4 from North America in experimentally infected pigs.

PubMed

Kaplan, Bryan S; Torchetti, Mia K; Lager, Kelly M; Webby, Richard J; Vincent, Amy L

2017-09-01

In the fall of 2014, highly pathogenic avian influenza (HPAI) subtype H5N8 clade 2.3.4.4 was introduced into North America by migrating waterfowl from Asia where, through reassortment, novel HPAI H5N2 and H5N1 viruses emerged. Assess the susceptibility of pigs to HPAI H5N1, H5N2, and H5N8 clade 2.3.3.3 from North America. Pigs and trachea explants were inoculated with a representative panel of H5NX clade 2.3.4.4 HPAI viruses from North America. Nasal swabs, BALF, and sera were collected to assess replication and transmission in challenged and direct contact pigs by RRT-PCR, virus isolation, hemagglutination inhibition, and ELISA. Limited virus replication was restricted to the lower respiratory tract of challenged pigs, though absent in the nasal passages and trachea cultures, as determined by RRT-PCR in all samples. Seroconversion of inoculated pigs was detected by NP ELISA but was not reliably detected by antigen-specific hemagglutination inhibition. Boost with adjuvanted virus was required for the production of neutralizing antibodies to assess cross-reactivity between wild-type avian strains. All RRT-PCR and serology tests were negative for contact animals indicating a failure of transmission from primary inoculated pigs. H5NX clade 2.3.4.4 strains can replicate in the lower respiratory tract of swine upon high titer inoculation, though appear to be incapable of replication in swine nasal epithelium in vivo or ex vivo in trachea explants in culture. Infected pigs did not produce high levels of serum antibodies following infection. Collectively, our data show HPAI H5NX clade 2.3.4.4 viruses to be poorly adapted for replication and transmission in swine. © 2017 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

Biting midges (Culicoides, Diptera) transmit Haemoproteus parasites of owls: evidence from sporogony and molecular phylogeny.

PubMed

Bukauskaitė, Dovilė; Žiegytė, Rita; Palinauskas, Vaidas; Iezhova, Tatjana A; Dimitrov, Dimitar; Ilgūnas, Mikas; Bernotienė, Rasa; Markovets, Mikhail Yu; Valkiūnas, Gediminas

2015-06-04

analysis placed both parasite lineages in a clade of Culicoides spp.-transmitted avian Haemoproteus (Parahaemoproteus) spp. Culicoides nubeculosus and C. impunctatus are vectors of H. noctuae and H. syrnii. Phylogenies based on cytochrome b gene indicate parasite-vector relationships, and we recommend using them in predicting possible parasite-vector relationships and planning research on avian Haemoproteus spp. vectors in wildlife.

The glycoprotein TRP36 of Ehrlichia sp. UFMG-EV and related cattle pathogen Ehrlichia sp. UFMT-BV evolved from a highly variable clade of E. canis under adaptive diversifying selection.

PubMed

Cabezas-Cruz, Alejandro; Valdés, James J; de la Fuente, José

2014-12-10

A new species of Ehrlichia, phylogenetically distant from E. ruminantium, was found in 2010 infecting cattle in Canada. In 2012 and 2013, we reported the in vitro propagation, molecular and ultrastructural characterization of Ehrlichia sp. UFMG-EV (E. mineirensis), a new species of Ehrlichia isolated from the haemolymph of Brazilian Rhipicephalus (Boophilus) microplus ticks. A new organism, named Ehrlichia sp. UFMT-BV, closely related to Ehrlichia sp. UFMG-EV, was recently described in Brazil and after experimental infection it was shown to be pathogenic for cattle. This new emerging clade of cattle Ehrlichia pathogens is closely related to E. canis. The major immunogenic Tandem Repeat Protein (TRP36; also known as gp36) is extensively used to characterize the genetic diversity of E. canis. Homologs of TRP36 were found in both Ehrlichia sp. UFMG-EV and Ehrlichia sp. UFMT-BV. Herein, we characterized the evolution of this new Ehrlichia clade using TRP36 sequences. Our working hypothesis is that Ehrlichia sp. UFMG-EV and related microorganisms evolved from a highly variable E. canis clade. In support of our hypothesis we found that Ehrlichia sp. UFMG-EV and Ehrlichia sp. UFMT-BV TRP36 evolved from a highly divergent and variable clade within E. canis and this clade evolved under episodic diversifying selection with a high proportion of sites under positive selection. Our results suggest that Ehrlichia sp. UFMG-EV and Ehrlichia sp. UFMT-BV evolved from a variable clade within E. canis.

Transfusion-transmitted CMV infection - current knowledge and future perspectives.

PubMed

Ziemann, M; Thiele, T

2017-08-01

Transmission of human cytomegalovirus (CMV) via transfusion (TT-CMV) may still occur and remains a challenge in the treatment of immunocompromised CMV-seronegative patients, e.g. after stem cell transplantation, and for low birthweight infants. Measures to reduce the risk of TT-CMV have been evaluated in clinical studies, including leucocyte depletion of cellular blood products and/or the selection of CMV-IgG-negative donations. Studies in large blood donor cohorts indicate that donations from newly CMV-IgG-positive donors should bear the highest risk for transmitting CMV infections because they contain the highest levels of CMV-DNA, and early CMV antibodies cannot neutralise CMV. Based on this knowledge, rational strategies to reduce the residual risk of TT-CMV using leucoreduced blood products could be designed. However, there is a lack of evidence that CMV is still transmitted by transfusion of leucoreduced units. In low birthweight infants, most (if not all) CMV infections are caused by breast milk feeding or congenital transmission rather than by transfusion of leucoreduced blood products. For other patients at risk, no definitive data exist about the relative importance of alternative transmission routes of CMV compared to blood transfusion. As a result, only the conduction of well-designed studies addressing strategies to prevent TT-CMV and the thorough examination of presumed cases of TT-CMV will achieve guidance for the best transfusion regimen in patients at risk. © 2017 British Blood Transfusion Society.

Testing the SI × SC rule: Pollen-pistil interactions in interspecific crosses between members of the tomato clade (Solanum section Lycopersicon, Solanaceae).

PubMed

Baek, You Soon; Covey, Paul A; Petersen, Jennifer J; Chetelat, Roger T; McClure, Bruce; Bedinger, Patricia A

2015-02-01

Interspecific reproductive barriers (IRBs) act to ensure species integrity by preventing hybridization. Previous studies on interspecific crosses in the tomato clade have focused on the success of fruit and seed set. The SI × SC rule (SI species × SC species crosses are incompatible, but the reciprocal crosses are compatible) often applies to interspecific crosses. Because SI systems in the Solanaceae affect pollen tube growth, we focused on this process in a comprehensive study of interspecific crosses in the tomato clade to test whether the SI × SC rule was always followed. Pollen tube growth was assessed in reciprocal crosses between all 13 species of the tomato clade using fluorescence microscopy. In crosses between SC and SI species, pollen tube growth follows the SI × SC rule: interspecific pollen tube rejection occurs when SI species are pollinated by SC species, but in the reciprocal crosses (SC × SI), pollen tubes reach ovaries. However, pollen tube rejection occurred in some crosses between pairs of SC species, demonstrating that a fully functional SI system is not necessary for pollen tube rejection in interspecific crosses. Further, gradations in the strength of both pistil and pollen IRBs were revealed in interspecific crosses using SC populations of generally SI species. The SI × SC rule explains many of the compatibility relations in the tomato clade, but exceptions occur with more recently evolved SC species and accessions, revealing differences in strength of both pistil and pollen IRBs. © 2015 Botanical Society of America, Inc.

A distributed transmit beamforming synchronization strategy for multi-element radar systems

NASA Astrophysics Data System (ADS)

Xiao, Manlin; Li, Xingwen; Xu, Jikang

2017-02-01

The distributed transmit beamforming has recently been discussed as an energy-effective technique in wireless communication systems. A common ground of various techniques is that the destination node transmits a beacon signal or feedback to assist source nodes to synchronize signals. However, this approach is not appropriate for a radar system since the destination is a non-cooperative target of an unknown location. In our paper, we propose a novel synchronization strategy for a distributed multiple-element beamfoming radar system. Source nodes estimate parameters of beacon signals transmitted from others to get their local synchronization information. The channel information of the phase propagation delay is transmitted to nodes via the reflected beacon signals as well. Next, each node generates appropriate parameters to form a beamforming signal at the target. Transmit beamforming signals of all nodes will combine coherently at the target compensating for different propagation delay. We analyse the influence of the local oscillation accuracy and the parameter estimation errors on the performance of the proposed synchronization scheme. The results of numerical simulations illustrate that this synchronization scheme is effective to enable the transmit beamforming in a distributed multi-element radar system.

Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach

PubMed Central

Choi, Young-Joon; Klosterman, Steven J.; Kummer, Volker; Voglmayr, Hermann; Shin, Hyeon-Dong; Thines, Marco

2017-01-01

Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants. PMID:25772799

Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach.

PubMed

Choi, Young-Joon; Klosterman, Steven J; Kummer, Volker; Voglmayr, Hermann; Shin, Hyeon-Dong; Thines, Marco

2015-05-01

Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants. Copyright © 2015 Elsevier Inc. All rights reserved.

Early detection and treatment of sexually transmitted disease in pregnant adolescents of low socioeconomic status.

PubMed

Matson, S C; Pomeranz, A J; Kamps, K A

1993-10-01

This study evaluated the prevalence of sexually transmitted disease (STD) in adolescents presenting to a primary pediatric care clinic (PPCC) for the diagnosis of pregnancy and our ability to eradicate identified infections. We followed 168 pregnant adolescents of low socioeconomic status from their original pregnancy diagnosis until their first prenatal clinic visit. We collected screening cervical cultures for Neisseria gonorrhoeae and Chlamydia trachomatis by completing a pelvic examination on 91 patients at our PPCC. At the PPCC visit, 29% were positive for gonorrhea, chlamydia, or both. Screening tests for these infections were collected on all patients at the initial prenatal clinic visit. The risk for presenting to the prenatal clinic with a STD was significantly greater in patients not screened and treated for STD at the PPCC. Average delay from diagnosis to first prenatal clinic visit was 35.7 days. Thus, in this adolescent population, primary care providers are missing an important therapeutic opportunity by failing to identify and treat STD at initial diagnosis of pregnancy.

Transmit: An Advanced Traffic Management System

DOT National Transportation Integrated Search

1995-11-27

TRANSCOM'S SYSTEM FOR MANAGING INCIDENTS AND TRAFFIC, KNOWN AS TRANSMIT, WAS INITIATED TO ESTABLISH THE FEASIBILITY OF USING AUTOMATIC VEHICLE IDENTIFICATION (AVI) EQUIPMENT FOR TRAFFIC MANAGEMENT AND SURVEILLANCE APPLICATIONS. AVI TECHNOLOGY SYSTEMS...

Vaccine protection of poultry against H5 clade 2.3.4.4 highly pathogenic avian influenza

USDA-ARS?s Scientific Manuscript database

Following the 2014-2015 outbreaks of H5N2 and H5N8 (clade 2.3.4.4) highly pathogenic avian influenza (HPAI) in the U.S., studies were performed to identify vaccines with potential to be used as a control mechanism in the event of future outbreaks. We tested both inactivated and recombinant vaccine...

Pelagic larval duration predicts extinction risk in a freshwater fish clade.

PubMed

Douglas, Morgan; Keck, Benjamin P; Ruble, Crystal; Petty, Melissa; Shute, J R; Rakes, Patrick; Hulsey, C Darrin

2013-01-01

Pelagic larval duration (PLD) can influence evolutionary processes ranging from dispersal to extinction in aquatic organisms. Using estimates of PLD obtained from species of North American darters (Percidae: Etheostomatinae), we demonstrate that this freshwater fish clade exhibits surprising variation in PLD. Comparative analyses provide some evidence that higher stream gradients favour the evolution of shorter PLD. Additionally, similar to patterns in the marine fossil record in which lower PLD is associated with greater extinction probability, we found a reduced PLD in darter lineages was evolutionarily associated with extinction risk. Understanding the causes and consequences of PLD length could lead to better management and conservation of organisms in our increasingly imperiled aquatic environments.

Complex patterns of divergence among green-sensitive (RH2a) African cichlid opsins revealed by Clade model analyses

PubMed Central

2012-01-01

Background Gene duplications play an important role in the evolution of functional protein diversity. Some models of duplicate gene evolution predict complex forms of paralog divergence; orthologous proteins may diverge as well, further complicating patterns of divergence among and within gene families. Consequently, studying the link between protein sequence evolution and duplication requires the use of flexible substitution models that can accommodate multiple shifts in selection across a phylogeny. Here, we employed a variety of codon substitution models, primarily Clade models, to explore how selective constraint evolved following the duplication of a green-sensitive (RH2a) visual pigment protein (opsin) in African cichlids. Past studies have linked opsin divergence to ecological and sexual divergence within the African cichlid adaptive radiation. Furthermore, biochemical and regulatory differences between the RH2aα and RH2aβ paralogs have been documented. It thus seems likely that selection varies in complex ways throughout this gene family. Results Clade model analysis of African cichlid RH2a opsins revealed a large increase in the nonsynonymous-to-synonymous substitution rate ratio (ω) following the duplication, as well as an even larger increase, one consistent with positive selection, for Lake Tanganyikan cichlid RH2aβ opsins. Analysis using the popular Branch-site models, by contrast, revealed no such alteration of constraint. Several amino acid sites known to influence spectral and non-spectral aspects of opsin biochemistry were found to be evolving divergently, suggesting that orthologous RH2a opsins may vary in terms of spectral sensitivity and response kinetics. Divergence appears to be occurring despite intronic gene conversion among the tandemly-arranged duplicates. Conclusions Our findings indicate that variation in selective constraint is associated with both gene duplication and divergence among orthologs in African cichlid RH2a opsins. At

Head-to-Head Comparison of Poxvirus NYVAC and ALVAC Vectors Expressing Identical HIV-1 Clade C Immunogens in Prime-Boost Combination with Env Protein in Nonhuman Primates

PubMed Central

García-Arriaza, Juan; Perdiguero, Beatriz; Heeney, Jonathan; Seaman, Michael; Montefiori, David C.; Labranche, Celia; Yates, Nicole L.; Shen, Xiaoying; Tomaras, Georgia D.; Ferrari, Guido; Foulds, Kathryn E.; McDermott, Adrian; Kao, Shing-Fen; Roederer, Mario; Hawkins, Natalie; Self, Steve; Yao, Jiansheng; Farrell, Patrick; Phogat, Sanjay; Tartaglia, Jim; Barnett, Susan W.; Burke, Brian; Cristillo, Anthony; Weiss, Deborah; Lee, Carter; Kibler, Karen; Jacobs, Bert; Asbach, Benedikt; Wagner, Ralf; Ding, Song; Pantaleo, Giuseppe

2015-01-01

ABSTRACT We compared the HIV-1-specific cellular and humoral immune responses elicited in rhesus macaques immunized with two poxvirus vectors (NYVAC and ALVAC) expressing the same HIV-1 antigens from clade C, Env gp140 as a trimeric cell-released protein and a Gag-Pol-Nef polyprotein as Gag-induced virus-like particles (VLPs) (referred to as NYVAC-C and ALVAC-C). The immunization protocol consisted of two doses of the corresponding poxvirus vector plus two doses of a combination of the poxvirus vector and a purified HIV-1 gp120 protein from clade C. This immunogenicity profile was also compared to that elicited by vaccine regimens consisting of two doses of the ALVAC vector expressing HIV-1 antigens from clades B/E (ALVAC-vCP1521) plus two doses of a combination of ALVAC-vCP1521 and HIV-1 gp120 protein from clades B/E (similar to the RV144 trial regimen) or clade C. The results showed that immunization of macaques with NYVAC-C stimulated at different times more potent HIV-1-specific CD4+ T-cell responses and induced a trend toward higher-magnitude HIV-1-specific CD8+ T-cell immune responses than did ALVAC-C. Furthermore, NYVAC-C induced a trend toward higher levels of binding IgG antibodies against clade C HIV-1 gp140, gp120, or murine leukemia virus (MuLV) gp70-scaffolded V1/V2 and toward best cross-clade-binding IgG responses against HIV-1 gp140 from clades A, B, and group M consensus, than did ALVAC-C. Of the linear binding IgG responses, most were directed against the V3 loop in all immunization groups. Additionally, NYVAC-C and ALVAC-C also induced similar levels of HIV-1-neutralizing antibodies and antibody-dependent cellular cytotoxicity (ADCC) responses. Interestingly, binding IgA antibody levels against HIV-1 gp120 or MuLV gp70-scaffolded V1/V2 were absent or very low in all immunization groups. Overall, these results provide a comprehensive survey of the immunogenicity of NYVAC versus ALVAC expressing HIV-1 antigens in nonhuman primates and indicate that

Signaling Architectures that Transmit Unidirectional Information Despite Retroactivity.

PubMed

Shah, Rushina; Del Vecchio, Domitilla

2017-08-08

A signaling pathway transmits information from an upstream system to downstream systems, ideally in a unidirectional fashion. A key obstacle to unidirectional transmission is retroactivity, the additional reaction flux that affects a system once its species interact with those of downstream systems. This raises the fundamental question of whether signaling pathways have developed specialized architectures that overcome retroactivity and transmit unidirectional signals. Here, we propose a general procedure based on mathematical analysis that provides an answer to this question. Using this procedure, we analyze the ability of a variety of signaling architectures to transmit one-way (from upstream to downstream) signals, as key biological parameters are tuned. We find that single stage phosphorylation and phosphotransfer systems that transmit signals from a kinase show a stringent design tradeoff that hampers their ability to overcome retroactivity. Interestingly, cascades of these architectures, which are highly represented in nature, can overcome this tradeoff and thus enable unidirectional transmission. By contrast, phosphotransfer systems, and single and double phosphorylation cycles that transmit signals from a substrate, are unable to mitigate retroactivity effects, even when cascaded, and hence are not well suited for unidirectional information transmission. These results are largely independent of the specific reaction-rate constant values, and depend on the topology of the architectures. Our results therefore identify signaling architectures that, allowing unidirectional transmission of signals, embody modular processes that conserve their input/output behavior across multiple contexts. These findings can be used to decompose natural signal transduction networks into modules, and at the same time, they establish a library of devices that can be used in synthetic biology to facilitate modular circuit design. Copyright © 2017 Biophysical Society. Published by

An early geikiid dicynodont from the Tropidostoma Assemblage Zone (late Permian) of South Africa

PubMed Central

Smith, Roger M.H.

2017-01-01

Based on specimens previously identified as Tropidostoma, a new taxon of dicynodont (Bulbasaurus phylloxyron gen. et sp. nov.) from the Karoo Basin of South Africa is described. Bulbasaurus is a medium-sized dicynodont (maximum dorsal skull length 16.0 cm) restricted to the Tropidostoma Assemblage Zone (early Lopingian) of the Beaufort Group. Bulbasaurus can be distinguished from Tropidostoma by an array of characters including the presence of a tall, sharp premaxillary ridge, large, rugose, nearly-confluent nasal bosses, a nasofrontal ridge, massive tusks, robust pterygoids, prominently twisted subtemporal bar, and absence of a distinct postfrontal. Inclusion of Bulbasaurus in a phylogenetic analysis of anomodont therapsids recovers it as a member of Geikiidae, a clade of otherwise later Permian dicynodonts such as Aulacephalodon and Pelanomodon. Bulbasaurus exhibits many of the characters typical of adult Aulacephalodon, but at substantially smaller skull size (these characters are absent in comparably-sized Aulacephalodon juveniles), suggesting that the evolution of typical geikiid morphology preceded gigantism in the clade. Bulbasaurus is the earliest known geikiid and the only member of the group known from the Tropidostoma Assemblage Zone; discovery of this taxon shortens a perplexing ghost lineage and indicates that abundant clades from the later Permian of South Africa (e.g., Geikiidae, Dicynodontoidea) may have originated as rare components of earlier Karoo assemblage zones. PMID:28168104

Spatial distribution of soil-transmitted helminths, including Strongyloides stercoralis, among children in Zanzibar.

PubMed

Knopp, Stefanie; Mohammed, Khalfan A; Simba Khamis, I; Mgeni, Ali F; Stothard, J Russell; Rollinson, David; Marti, Hanspeter; Utzinger, Jürg

2008-11-01

A programme periodically distributing anthelminthic drugs to school-aged children for the control of soiltransmitted helminthiasis was launched in Zanzibar in the early 1990s. We investigated the spatial distribution of soiltransmitted helminth infections, including Strongyloides stercoralis, in 336 children from six districts in Unguja, Zanzibar, in 2007. One stool sample per child was examined with the Kato-Katz, Koga agar plate and Baermann methods. The point prevalence of the different helminth infections was compared to the geological characteristics of the study sites. The observed prevalences for Trichuris trichiura, Ascaris lumbricoides, hookworm and S. stercoralis were 35.5%, 12.2%, 11.9% and 2.2%, respectively, with considerable spatial heterogeneity. Whilst T. trichiura and hookworm infections were found in all six districts, no A. lumbricoides infections were recorded in the urban setting and only a low prevalence (2.2%) was observed in the South district. S. stercoralis infections were found in four districts with the highest prevalence (4.0%) in the West district. The prevalence of infection with any soil-transmitted helminth was highest in the North A district (69.6%) and lowest in the urban setting (22.4%). A. lumbricoides, hookworm and, with the exception of the North B district, S. stercoralis infections were observed to be more prevalent in the settings north of Zanzibar Town, which are characterized by alluvial clayey soils, moist forest regions and a higher precipitation. After a decade of large-scale administration of anthelminthic drugs, the prevalence of soil-transmitted helminth infections across Unguja is still considerable. Hence, additional measures, such as improving access to adequate sanitation and clean water and continued health education, are warranted to successfully control soil-transmitted helminthiasis in Zanzibar.

Earliest known unequivocal rhinocerotoid sheds new light on the origin of Giant Rhinos and phylogeny of early rhinocerotoids.

PubMed

Wang, Haibing; Bai, Bin; Meng, Jin; Wang, Yuanqing

2016-12-21

Forstercooperiines are a group of primitive rhinocerotoids with a relatively large body size in the Eocene, and normally considered to be closely related to Giant Rhinos. Here we report a new forstercooperiine, Pappaceras meiomenus sp. nov., from the late Early Eocene Arshanto Formation, Erlian Basin, Nei Mongol, China. Pappaceras is the earliest known unequivocal rhinocerotoid, and the holotype of the new species, represented by the most complete cranium of forstercooperiines known to date, shows the earliest evidence of reduction of the first upper premolar in rhinocerotoids, and resembles paraceratheriine Juxia in basicranial features, supporting the interpretation that the forstercooperiine clade is ancestral to paraceratheriines. The new species also displays some similarities with amynodontids in craniodental structures. Phylogenetic analysis identifies P. meiomenus as a basal taxon of the monophyletic forstercooperiines. It also reveals novel phylogenetic relationships of early rhinocerotoids that indicates Uintaceras is the sister group of paraceratheriids, to which amynodontids are more closely related than to any other group of rhinocerotoids. Furthermore, the eggysodontid clade is excluded from hyracodontids and placed as the sister group of rhinocerotids. Hyracodontidae, excluding paraceratheriids and eggysodontids, is placed as the most basal group of the rhinocerotoids.

[Occupational exposure to hand-transmitted vibration in Poland].

PubMed

Harazin, Barbara; Zieliński, Grzegorz

2004-01-01

Occupational exposure to hand transmitted vibration may cause disorders in upper extremities known as hand-arm vibration syndrome. Therefore it is essential to know the sources of vibration, occupational groups exposed to vibration and the number of exposed workers. The aim of the study was to estimate the number of men and women exposed to hand-transmitted vibration in Poland. The completed questionnaires were obtained from 265 (80%) sanitary inspection stations. They included questions on: the name of workplaces, the name and the type of vibration sources, workers' gender, the number of workers exposed to vibration, indicating the extent of exposure measured against the three threshold limit values (< 0.5 TLV; 0.5 < TLV < 1 and > 1 TLV), and the number of workers exposed to hand-transmitted vibration not documented by measurements in a particular workplaces, indicating one of the three possible kinds of exposure (occasional, periodical and constant). The questionnaire data were based on measurements and analyses performed in 1997-2000. The results of the study showed that vibrating tools used by grinders, fitters, locksmiths, rammers, road workers, carpenters and smiths proved to be the most frequent sources of hand-transmitted vibration. It was revealed that 78.6% of operators of these tools were exposed to vibration exceeding 1 TLV. The study also indicated that 17,000 workers, including 1700 women, were exposed to vibration exceeding the threshold limit values.

The Australasian frog family Ceratobatrachidae in China, Myanmar and Thailand: discovery of a new Himalayan forest frog clade

PubMed Central

YAN, Fang; JIANG, Ke; WANG, Kai; JIN, Jie-Qiong; SUWANNAPOOM, Chatmongkon; LI, Cheng; Jens, V. VINDUM; Rafe, M. BROWN; CHE, Jing

2016-01-01

In an effort to study the systematic affinities and specieslevel phylogenetic relationships of the enigmatic anurans variably assigned to the genera Ingerana or Limnonectes (family Dicroglossidae), we collected new molecular sequence data for five species including four Himalayan taxa, Limnonectes xizangensis, Lim. medogensis, Lim. alpine, Ingerana borealis and one southeast Asian species, I. tasanae, and analyzed these together with data from previous studies involving other ostensibly related taxa. Our surprising results demonstrate unequivocally that Lim. xizangensis, Lim. medogensis and Lim. alpine form a strongly supported clade, the sister-group of the family Australasian forest frog family Ceratobatrachidae. This discovery requires an expansion of the definition of Ceratobatrachidae and represents the first record of this family in China. These three species are distinguished from the species of Ingerana and Limnonectes by the: (1) absence of interdigital webbing of the foot, (2) absence of terminal discs on fingers and toes, (3) absence of circumarginal grooves on the fingers and toes, and (4) absence of tarsal folds. Given their phylogenetic and morphological distinctiveness, we assign them to the oldest available generic name for this clade, Liurana Dubois 1987, and transfer Liurana from Dicroglossidae to the family Ceratobatrachidae. In contrast, Ingerana tasanae was found to be clustered with strong support with the recently described genus Alcalus (Ceratobatrachidae), a small clade of otherwise Sundaic species; this constitutes a new record of the family Ceratobatrachidae for Myanmar and Thailand. Finally, Ingerana borealis clustered with the "true" Ingerana (family Dicroglossidae), for which the type species is I. tenasserimensis. PMID:26828029

Vaccination with virus-like particles containing H5 antigens from three H5N1 clades protects chickens from H5N1 and H5N8 influenza viruses

PubMed Central

Kapczynski, Darrell R.; Tumpey, Terrence M.; Hidajat, Rachmat; Zsak, Aniko; Chrzastek, Klaudia; Tretyakova, Irina; Pushko, Peter

2016-01-01

Highly pathogenic avian influenza (HPAI) viruses, especially H5N1 strains, represent a public health threat and cause widespread morbidity and mortality in domestic poultry. Recombinant virus-like particles (VLPs) represent a promising novel vaccine approach to control avian influenza including HPAI strains. Influenza VLPs contain viral hemagglutinin (HA), which can be expressed in cell culture within highly immunogenic VLPs that morphologically and antigenically resemble influenza virions, except VLPs are non-infectious. Here we describe a recombinant VLP containing HA proteins derived from three distinct clades of H5N1 viruses as an experimental, broadly protective H5 avian influenza vaccine. A baculovirus vector was configured to co-express the H5 genes from recent H5N1 HPAI isolates A/chicken/Germany/2014 (clade 2.3.4.4), A/chicken/West Java/Subang/29/2007 (clade 2.1.3) and A/chicken/Egypt/121/2012 (clade 2.2.1). Co-expression of these genes in Sf9 cells along with influenza neuraminidase (NA) and retrovirus gag genes resulted in production of triple-clade H555 VLPs that exhibited hemagglutination activity and morphologically resembled influenza virions. Vaccination of chickens with these VLPs resulted in induction of serum antibody responses and efficient protection against experimental challenges with three different viruses including the recent U.S. H5N8 HPAI isolate. We conclude that these novel triple-clade VLPs represent a feasible strategy for simultaneously evoking protective antibodies against multiple variants of H5 influenza virus. PMID:26868083

Tahitian tree snail mitochondrial clades survived recent mass extirpation.

PubMed

Lee, Taehwan; Burch, John B; Jung, Younghun; Coote, Trevor; Pearce-Kelly, Paul; O Foighil, Diarmaid

2007-07-03

Oceanic islands frequently support endemic faunal radiations that are highly vulnerable to introduced predators [1]. This vulnerability is epitomized by the rapid extinction in the wild of all but five of 61 described Society Islands partulid tree snails [2], following the deliberate introduction of an alien biological control agent: the carnivorous snail Euglandina rosea[3]. Tahiti's tree snail populations have been almost completely extirpated and three of the island's eight endemic Partula species are officially extinct, a fourth persisting only in captivity [2]. We report a molecular phylogenetic estimate of Tahitian Partula mitochondrial lineage survival calibrated with a 1970 reference museum collection that pre-dates the predator's 1974 introduction to the island [4]. Although severe winnowing of lineage diversity has occurred, none of the five primary Tahitian Partula clades present in the museum samples is extinct. Targeted conservation measures, especially of montane refuge populations, may yet preserve a representative sub-sample of Tahiti's endemic tree snail genetic diversity in the wild.

Modelling the geographical distribution of soil-transmitted helminth infections in Bolivia.

PubMed

Chammartin, Frédérique; Scholte, Ronaldo G C; Malone, John B; Bavia, Mara E; Nieto, Prixia; Utzinger, Jürg; Vounatsou, Penelope

2013-05-25

The prevalence of infection with the three common soil-transmitted helminths (i.e. Ascaris lumbricoides, Trichuris trichiura, and hookworm) in Bolivia is among the highest in Latin America. However, the spatial distribution and burden of soil-transmitted helminthiasis are poorly documented. We analysed historical survey data using Bayesian geostatistical models to identify determinants of the distribution of soil-transmitted helminth infections, predict the geographical distribution of infection risk, and assess treatment needs and costs in the frame of preventive chemotherapy. Rigorous geostatistical variable selection identified the most important predictors of A. lumbricoides, T. trichiura, and hookworm transmission. Results show that precipitation during the wettest quarter above 400 mm favours the distribution of A. lumbricoides. Altitude has a negative effect on T. trichiura. Hookworm is sensitive to temperature during the coldest month. We estimate that 38.0%, 19.3%, and 11.4% of the Bolivian population is infected with A. lumbricoides, T. trichiura, and hookworm, respectively. Assuming independence of the three infections, 48.4% of the population is infected with any soil-transmitted helminth. Empirical-based estimates, according to treatment recommendations by the World Health Organization, suggest a total of 2.9 million annualised treatments for the control of soil-transmitted helminthiasis in Bolivia. We provide estimates of soil-transmitted helminth infections in Bolivia based on high-resolution spatial prediction and an innovative variable selection approach. However, the scarcity of the data suggests that a national survey is required for more accurate mapping that will govern spatial targeting of soil-transmitted helminthiasis control.

Sexually transmitted diseases and the mobility explosion

PubMed Central

Catterall, R. D.

1975-01-01

The very great increase in the tourist industry during the past 20 years is described. This has occurred at a time when there has been an unprecedented rise in the incidence of sexually transmitted diseases. Evidence is presented that there is a relationship between the number of tourists and other travellers and the prevalence of sexually transmitted diseases. Case histories from three different categories of tourist are described and the impact of tourism on the spread of disease is stressed. It is suggested that health authorities throughout the world should give further consideration to plans to meet the challenge of the mobility explosion. PMID:1243165

Developing ribonucleic acid interference technology to manage whitefly-transmitted begomoviruses

USDA-ARS?s Scientific Manuscript database

Of nearly 300 viruses transmitted by the whitefly (Bemisia tabaci), 90% of them belong to the genus Begomovirus. Begomoviruses are efficiently transmitted by whiteflies to a range of agricultural crops. This results in billions of dollars lost annually, while jeopardizing food security worldwide. Se...

Sexually Transmitted Diseases Surveillance, 2014: Syphilis

MedlinePlus

... 2014 Sexually Transmitted Diseases Surveillance Table of Contents Introductory Section Foreword Preface Acronyms Figures- National Profile Figures – ... GISP Profiles Related Links STD Home STD Data & Statistics NCHHSTP Atlas Interactive STD Data – 1996-2013 STD ...

Selective wave-transmitting electromagnetic absorber through composite metasurface

NASA Astrophysics Data System (ADS)

Sun, Zhiwei; Zhao, Junming; Zhu, Bo; Jiang, Tian; Feng, Yijun

2017-11-01

Selective wave-transmitting absorbers which have one or more narrow transmission bands inside a wide absorption band are often demanded in wireless communication and radome applications for reducing the coupling between different systems, improving anti-jamming capability, and reducing antennas' radar cross section. Here we propose a feasible method that utilizing composite of two metasurfaces with different polarization dependent characteristics, one works as electromagnetic polarization rotator and the other as a wideband polarization dependent electromagnetic wave absorber. The polarization rotator produces a cross polarization output in the wave-transmitting band, while preserves the polarization of the incidence outside the band. The metasurface absorber works for certain linear polarization with a much wider absorption band covering the wave-transmitting frequency. When combining these two metasurfaces properly, the whole structure behaves as a wideband absorber with a certain frequency transmission window. The proposal may be applied in radome designs to reduce the radar cross section of antenna or improving the electromagnetic compatibility in communication devices.

Sexually Transmitted Diseases: Teens at Risk.

ERIC Educational Resources Information Center

Mascola, Laurene

1987-01-01

Parents of preteens need to be aware of the rapidly increasing incidence of sexually transmitted diseases among teenagers and to begin talking to their preteens to help prevent or modify risky sexual experimentation during middle adolescence. (MT)

Differing Roles of the Face and Voice in Early Human Communication: Roots of Language in Multimodal Expression

PubMed Central

Jhang, Yuna; Franklin, Beau; Ramsdell-Hudock, Heather L.; Oller, D. Kimbrough

2017-01-01

Seeking roots of language, we probed infant facial expressions and vocalizations. Both have roles in language, but the voice plays an especially flexible role, expressing a variety of functions and affect conditions with the same vocal categories—a word can be produced with many different affective flavors. This requirement of language is seen in very early infant vocalizations. We examined the extent to which affect is transmitted by early vocal categories termed “protophones” (squeals, vowel-like sounds, and growls) and by their co-occurring facial expressions, and similarly the extent to which vocal type is transmitted by the voice and co-occurring facial expressions. Our coder agreement data suggest infant affect during protophones was most reliably transmitted by the face (judged in video-only), while vocal type was transmitted most reliably by the voice (judged in audio-only). Voice alone transmitted negative affect more reliably than neutral or positive affect, suggesting infant protophones may be used especially to call for attention when the infant is in distress. By contrast, the face alone provided no significant information about protophone categories. Indeed coders in VID could scarcely recognize the difference between silence and voice when coding protophones in VID. The results suggest that partial decoupling of communicative roles for face and voice occurs even in the first months of life. Affect in infancy appears to be transmitted in a way that audio and video aspects are flexibly interwoven, as in mature language. PMID:29423398

Differing Roles of the Face and Voice in Early Human Communication: Roots of Language in Multimodal Expression.

PubMed

Jhang, Yuna; Franklin, Beau; Ramsdell-Hudock, Heather L; Oller, D Kimbrough

2017-01-01

Seeking roots of language, we probed infant facial expressions and vocalizations. Both have roles in language, but the voice plays an especially flexible role, expressing a variety of functions and affect conditions with the same vocal categories-a word can be produced with many different affective flavors. This requirement of language is seen in very early infant vocalizations. We examined the extent to which affect is transmitted by early vocal categories termed "protophones" (squeals, vowel-like sounds, and growls) and by their co-occurring facial expressions, and similarly the extent to which vocal type is transmitted by the voice and co-occurring facial expressions. Our coder agreement data suggest infant affect during protophones was most reliably transmitted by the face (judged in video-only), while vocal type was transmitted most reliably by the voice (judged in audio-only). Voice alone transmitted negative affect more reliably than neutral or positive affect, suggesting infant protophones may be used especially to call for attention when the infant is in distress. By contrast, the face alone provided no significant information about protophone categories. Indeed coders in VID could scarcely recognize the difference between silence and voice when coding protophones in VID. The results suggest that partial decoupling of communicative roles for face and voice occurs even in the first months of life. Affect in infancy appears to be transmitted in a way that audio and video aspects are flexibly interwoven, as in mature language.

Cytomegalovirus infection in preterm triplets transmitted via breast milk.

PubMed

Demirel, Gamze; Celik, Istemi Han; Canpolat, Fuat Emre; Dilmen, Ugur

2014-04-01

Cytomegalovirus (CMV) may transmit perinatally or from breast milk. The risk for development of symptomatic CMV disease in very-low-birth-weight premature infants after transmission from maternal breast milk is not clear. There are scarce data in the literature about congenital CMV infection in multiple pregnancies, being mostly with twin gestations. Here we present a unique case of triplets with CMV infection transmitted via breast milk.

[Evaluation on effectiveness of comprehensive control model for soil-transmitted nematodiasis].

PubMed

Hong-Chun, Tian; Meng, Tang; Hong, Xie; Han-Gang, Li; Xiao-Ke, Zhou; Chang-Hua, Liu; De-Fu, Zheng; Zhong-Jiu, Tang; Ming-Hui, Li; Cheng-Yu, Wu; Yi-Zhu, Ren

2011-10-01

To evaluate the effect of a comprehensive control model for soil-transmitted nematodiasis. Danling County was selected as a demonstration county carrying out the comprehensive prevention model centering on health education, nematode deworming, and drinking water and lavatories changing. On the other side, Hejiang was selected as a control. The effects were evaluated by comparing some indicators such as the infection rates of soil-transmitted nematodiasis and so on. The infection rates of soil-transmitted nematodiasis declined obviously from 2006 to 2009 in the demonstration county. The infection rates of Ascaris lumbricoides, hookworms, Trichiuris trichiura decreased by 91.14%, 81.65% and 65.77%. In the control county, those rates did not have downward tendency. In 2006, those rates in the demonstration county were higher than those in the control, but in 2009 those rates in the demonstration county were lower than those in the control. Through the three-year comprehensive prevention, the infection rates of soil-transmitted nematodiasis declined obviously in the demonstration county. The epidemic situation of soil-transmitted nematodiasis could be controlled effectively by the comprehensive prevention model.

Circumcision and risk of sexually transmitted infections in a birth cohort.

PubMed

Dickson, Nigel P; van Roode, Thea; Herbison, Peter; Paul, Charlotte

2008-03-01

To determine the impact of early childhood circumcision on sexually transmitted infection (STI) acquisition to age 32 years. The circumcision status of a cohort of children born in 1972 and 1973 in Dunedin, New Zealand was sought at age 3 years. Information about STIs was obtained at ages 21, 26, and 32 years. The incidence rates of STI acquisition were calculated, taking into account timing of first sex, and comparisons were made between the circumcised men and uncircumcised men. Adjustments were made for potential socioeconomic and sexual behavior confounding factors where appropriate. Of the 499 men studied, 201 (40.3%) had been circumcised by age 3 years. The circumcised and uncircumcised groups differed little in socioeconomic characteristics and sexual behavior. Overall, up to age 32 years, the incidence rates for all STIs were not statistically significantly different-23.4 and 24.4 per 1000 person-years for the uncircumcised and circumcised men, respectively. This was not affected by adjusting for any of the socioeconomic or sexual behavior characteristics. These findings are consistent with recent population-based cross-sectional studies in developed countries, which found that early childhood circumcision does not markedly reduce the risk of the common STIs in the general population in such countries.

Molecular phylogenetics and morphological reappraisal of the Platanthera clade (Orchidaceae: Orchidinae) prompts expansion of the generic limits of Galearis and Platanthera

PubMed Central

Bateman, Richard M.; James, Karen E.; Luo, Yi-Bo; Lauri, Robert K.; Fulcher, Timothy; Cribb, Phillip J.; Chase, Mark W.

2009-01-01

Background and Aims The Platanthera clade dominates the North American orchid flora and is well represented in eastern Asia. It has also generated some classic studies of speciation in Platanthera sections Platanthera and Limnorchis. However, it has proved rich in taxonomic controversy and near-monotypic genera. The clade is reviewed via a new molecular phylogenetic analysis and those results are combined with brief reconsideration of morphology in the group, aiming to rationalize the species into a smaller number of larger monophyletic genera and sections. Methods Nuclear ribosomal internal transcribed spacer (ITS) sequences were obtained from 86 accessions of 35 named taxa, supplemented from GenBank with five accessions encompassing a further two named taxa. Key Results Using Pseudorchis as outgroup, and scoring indels, the data matrix generated 30 most-parsimonious trees that differed in the placement of two major groups plus two closely related species. Several other internal nodes also attracted only indifferent statistical support. Nonetheless, by combining implicit assessment of morphological divergence with explicit assessment of molecular divergence (when available), nine former genera can be rationalized into four revised genera by sinking the monotypic Amerorchis, together with Aceratorchis and Chondradenia (neither yet sequenced), into Galearis, and by amalgamating Piperia, Diphylax and the monotypic Tsaiorchis into the former Platanthera section Platanthera. After further species sampling, this section will require sub-division into at least three sections. The present nomenclatural adjustments prompt five new combinations. Conclusions Resolution of major groups should facilitate future species-level research on the Platanthera clade. Recent evidence suggests that ITS sequence divergence characterizes most species other than the P. bifolia group. The floral differences that distinguished Piperia, Diphylax and Tsaiorchis from Platanthera, and

A novel thymidylate synthase from the Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) clade with altered nucleotide and folate binding sites.

PubMed

Lopez-Zavala, Alonso A; Guevara-Hernandez, Eduardo; Vazquez-Lujan, Luz H; Sanchez-Paz, Arturo; Garcia-Orozco, Karina D; Contreras-Vergara, Carmen A; Lopez-Leal, Gamaliel; Arvizu-Flores, Aldo A; Ochoa-Leyva, Adrian; Sotelo-Mundo, Rogerio R

2018-01-01

Thymidylate synthase (TS, E.C. 2.1.1.45) is a crucial enzyme for de novo deoxythymidine monophosphate (dTMP) biosynthesis. The gene for this enzyme is thyA , which encodes the folate-dependent TS that converts deoxyuridine monophosphate group (dUMP) into (dTMP) using the cofactor 5,10-methylenetetrahydrofolate (mTHF) as a carbon donor. We identified the thyA gene in the genome of the Vibrio parahaemolyticus strain FIM-S1708+ that is innocuous to humans but pathogenic to crustaceans. Surprisingly, we found changes in the residues that bind the substrate dUMP and mTHF, previously postulated as invariant among all TSs known (Finer-Moore, Santi & Stroud, 2003). Interestingly, those amino acid changes were also found in a clade of microorganisms that contains Vibrionales , Alteromonadales , Aeromonadales , and Pasteurellales (VAAP) from the Gammaproteobacteria class. In this work, we studied the biochemical properties of recombinant TS from V. parahemolyticus FIM-S1708+ (VpTS) to address the natural changes in the TS amino acid sequence of the VAAP clade. Interestingly, the K m for dUMP was 27.3 ± 4.3 µM, about one-fold larger compared to other TSs. The K m for mTHF was 96.3 ± 18 µM, about three- to five-fold larger compared to other species, suggesting also loss of affinity. Thus, the catalytic efficiency was between one or two orders of magnitude smaller for both substrates. We used trimethoprim, a common antibiotic that targets both TS and DHFR for inhibition studies. The IC 50 values obtained were high compared to other results in the literature. Nonetheless, this molecule could be a lead for the design antibiotics towards pathogens from the VAAP clade. Overall, the experimental results also suggest that in the VAAP clade the nucleotide salvage pathway is important and should be investigated, since the de novo dTMP synthesis appears to be compromised by a less efficient thymidylate synthase.

15 CFR 30.9 - Transmitting and correcting Electronic Export Information.

Code of Federal Regulations, 2012 CFR

2012-01-01

... in the AES and transmitting any changes to that information as soon as they are known. Corrections, cancellations, or amendments to that information shall be electronically identified and transmitted to the AES... authorized agent has received an error message from AES, the corrections shall take place as required. Fatal...

15 CFR 30.9 - Transmitting and correcting Electronic Export Information.

Code of Federal Regulations, 2014 CFR

2014-01-01

... in the AES and transmitting any changes to that information as soon as they are known. Corrections, cancellations, or amendments to that information shall be electronically identified and transmitted to the AES... authorized agent has received an error message from AES, the corrections shall take place as required. Fatal...

15 CFR 30.9 - Transmitting and correcting Electronic Export Information.

Code of Federal Regulations, 2011 CFR

2011-01-01

... in the AES and transmitting any changes to that information as soon as they are known. Corrections, cancellations, or amendments to that information shall be electronically identified and transmitted to the AES... authorized agent has received an error message from AES, the corrections shall take place as required. Fatal...

15 CFR 30.9 - Transmitting and correcting Electronic Export Information.

Code of Federal Regulations, 2013 CFR

2013-01-01

... in the AES and transmitting any changes to that information as soon as they are known. Corrections, cancellations, or amendments to that information shall be electronically identified and transmitted to the AES... authorized agent has received an error message from AES, the corrections shall take place as required. Fatal...

Why do leafcutter bees cut leaves? New insights into the early evolution of bees.

PubMed

Litman, Jessica R; Danforth, Bryan N; Eardley, Connal D; Praz, Christophe J

2011-12-07

Stark contrasts in clade species diversity are reported across the tree of life and are especially conspicuous when observed in closely related lineages. The explanation for such disparity has often been attributed to the evolution of key innovations that facilitate colonization of new ecological niches. The factors underlying diversification in bees remain poorly explored. Bees are thought to have originated from apoid wasps during the Mid-Cretaceous, a period that coincides with the appearance of angiosperm eudicot pollen grains in the fossil record. The reliance of bees on angiosperm pollen and their fundamental role as angiosperm pollinators have contributed to the idea that both groups may have undergone simultaneous radiations. We demonstrate that one key innovation--the inclusion of foreign material in nest construction--underlies both a massive range expansion and a significant increase in the rate of diversification within the second largest bee family, Megachilidae. Basal clades within the family are restricted to deserts and exhibit plesiomorphic features rarely observed among modern bees, but prevalent among apoid wasps. Our results suggest that early bees inherited a suite of behavioural traits that acted as powerful evolutionary constraints. While the transition to pollen as a larval food source opened an enormous ecological niche for the early bees, the exploitation of this niche and the subsequent diversification of bees only became possible after bees had evolved adaptations to overcome these constraints.

New euprimate postcrania from the early Eocene of Gujarat, India, and the strepsirrhine-haplorhine divergence.

PubMed

Dunn, Rachel H; Rose, Kenneth D; Rana, Rajendra S; Kumar, Kishor; Sahni, Ashok; Smith, Thierry

2016-10-01

The oldest primates of modern aspect (euprimates) appear abruptly on the Holarctic continents during a brief episode of global warming known as the Paleocene-Eocene Thermal Maximum, at the beginning of the Eocene (∼56 Ma). When they first appear in the fossil record, they are already divided into two distinct clades, Adapoidea (basal members of Strepsirrhini, which includes extant lemurs, lorises, and bushbabies) and Omomyidae (basal Haplorhini, which comprises living tarsiers, monkeys, and apes). Both groups have recently been discovered in the early Eocene Cambay Shale Formation of Vastan lignite mine, Gujarat, India, where they are known mainly from teeth and jaws. The Vastan fossils are dated at ∼54.5 Myr based on associated dinoflagellates and isotope stratigraphy. Here, we describe new, exquisitely preserved limb bones of these Indian primates that reveal more primitive postcranial characteristics than have been previously documented for either clade, and differences between them are so minor that in many cases we cannot be certain to which group they belong. Nevertheless, the small distinctions observed in some elements foreshadow postcranial traits that distinguish the groups by the middle Eocene, suggesting that the Vastan primates-though slightly younger than the oldest known euprimates-may represent the most primitive known remnants of the divergence between the two great primate clades. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mechanisms and consequences of paternally transmitted chromosomal abnormalities

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

Marchetti, F; Wyrobek, A J

Paternally transmitted chromosomal damage has been associated with pregnancy loss, developmental and morphological defects, infant mortality, infertility, and genetic diseases in the offspring including cancer. There is epidemiological evidence linking paternal exposure to occupational or environmental agents with an increased risk of abnormal reproductive outcomes. There is also a large body of literature on germ cell mutagenesis in rodents showing that treatment of male germ cells with mutagens has dramatic consequences on reproduction producing effects such as those observed in human epidemiological studies. However, we know very little about the etiology, transmission and early embryonic consequences of paternally-derived chromosomal abnormalities.more » The available evidence suggests that: (1) there are distinct patterns of germ cell-stage differences in the sensitivity of induction of transmissible genetic damage with male postmeiotic cells being the most sensitive; (2) cytogenetic abnormalities at first metaphase after fertilization are critical intermediates between paternal exposure and abnormal reproductive outcomes; and, (3) there are maternally susceptibility factors that may have profound effects on the amount of sperm DNA damage that is converted into chromosomal aberrations in the zygote and directly affect the risk for abnormal reproductive outcomes.« less

The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes

PubMed Central

Danchin, Etienne G.J.; Perfus-Barbeoch, Laetitia; Rancurel, Corinne; Thorpe, Peter; Da Rocha, Martine; Bajew, Simon; Neilson, Roy; Sokolova (Guzeeva), Elena; Da Silva, Corinne; Guy, Julie; Labadie, Karine; Esmenjaud, Daniel; Helder, Johannes; Jones, John T.

2017-01-01

Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq) to generate reference transcriptomes for two economically important nematode species, Xiphinema index and Longidorus elongatus, representative of two genera within the early-branching Clade 2 of the phylum Nematoda. We used a transcriptome-wide analysis to identify putative horizontal gene transfer events. This represents the first in-depth transcriptome analysis from any plant-parasitic nematode of this clade. For each species, we assembled ~30 million Illumina reads into a reference transcriptome. We identified 62 and 104 transcripts, from X. index and L. elongatus, respectively, that were putatively acquired via horizontal gene transfer. By cross-referencing horizontal gene transfer prediction with a phylum-wide analysis of Pfam domains, we identified Clade 2-specific events. Of these, a GH12 cellulase from X. index was analysed phylogenetically and biochemically, revealing a likely bacterial origin and canonical enzymatic function. Horizontal gene transfer was previously shown to be a phenomenon that has contributed to the evolution of plant parasitism among nematodes. Our findings underline the importance and the extensiveness of this phenomenon in the evolution of plant-parasitic life styles in this speciose and widespread animal phylum. PMID:29065523

The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes.

PubMed

Danchin, Etienne G J; Perfus-Barbeoch, Laetitia; Rancurel, Corinne; Thorpe, Peter; Da Rocha, Martine; Bajew, Simon; Neilson, Roy; Guzeeva, Elena Sokolova; Da Silva, Corinne; Guy, Julie; Labadie, Karine; Esmenjaud, Daniel; Helder, Johannes; Jones, John T; den Akker, Sebastian Eves-van

2017-10-23

Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq) to generate reference transcriptomes for two economically important nematode species, Xiphinema index and Longidorus elongatus , representative of two genera within the early-branching Clade 2 of the phylum Nematoda. We used a transcriptome-wide analysis to identify putative horizontal gene transfer events. This represents the first in-depth transcriptome analysis from any plant-parasitic nematode of this clade. For each species, we assembled ~30 million Illumina reads into a reference transcriptome. We identified 62 and 104 transcripts, from X. index and L. elongatus , respectively, that were putatively acquired via horizontal gene transfer. By cross-referencing horizontal gene transfer prediction with a phylum-wide analysis of Pfam domains, we identified Clade 2-specific events. Of these, a GH12 cellulase from X. index was analysed phylogenetically and biochemically, revealing a likely bacterial origin and canonical enzymatic function. Horizontal gene transfer was previously shown to be a phenomenon that has contributed to the evolution of plant parasitism among nematodes. Our findings underline the importance and the extensiveness of this phenomenon in the evolution of plant-parasitic life styles in this speciose and widespread animal phylum.

Simultaneous Transmit and Receive Performance of an 8-channel Digital Phased Array

DTIC Science & Technology

2017-01-16

Lincoln Laboratory Lexington, Massachusetts, USA Abstract—The Aperture- Level Simultaneous Transmit and Re- ceive (ALSTAR) architecture enables extremely...In [1], the Aperture- Level Simultaneous Transmit and Receive (ALSTAR) architecture was proposed for achieving STAR using a fully digital phased array...Aperture- Level Simultaneous Transmit and Receive (ALSTAR) architecture enables STAR functionality in a digital phased array without the use of specialized

SU-E-I-71: KVp Dependence of Transmitted Exposure for a Radiography Unit

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

Liang, Y; Lynch, D; So, J

2014-06-01

Purpose: To investigate the kVp dependence of the transmitted exposure for a radiography x-ray unit. Methods: The study used a GE DiscoveryTM XR656 DR unit, a 30 (L) × 30 (W) × 25 cm thick Lucite phantom, two anthropomorphic phantoms (an Alderson RS-310 chest phantom and a 3M skull phantom), an Unfors detector, and a Radcal 10x9-6 ion chamber. We measured the entrance exposure and transmitted exposure of each phantom at 60, 70, 80, 90, 100, 110, 120 kVp for mAs range from 2.5 to 200 mAs, without any additional filter. The FOV is 30×30 cm for the Lucite andmore » chest phantom (AP view), and 20×20 cm for skull phantom (Lateral view). The transmitted exposure was measured at the phantom center of the x-ray exit side. For chest phantom, the transmitted exposures at 3 inch upper right and upper left from the center were also measured. We also checked the reproducibility and accuracy of the DR unit. Results: For each phantom, at every kVp and mAs setting, the transmitted exposure per mAs was calculated and normalized by the relative entrance exposure; the averaged transmitted exposure per mAs at each specific kVp was then determined. For chest phantom, the mean transmitted exposure per mAs was the average of three exit locations. The averaged transmitted exposure per mAs was fit as a power function of kVp. The result showed the transmitted exposure per mAs was approximately proportional to third power of the kVp for two anthropomorphic phantoms and forth power of the kVp for the Lucite phantom. Conclusion: The traditional assumption of fifth power kVp dependence to the transmitted exposure is inaccurate. At the normal radiography kVp range, the transmitted exposure is approximately proportional to third power of the kVp for a typical patient and up to forth power of the kVp for a large patient.« less

Inductive Reasoning about Causally Transmitted Properties

ERIC Educational Resources Information Center

Shafto, Patrick; Kemp, Charles; Bonawitz, Elizabeth Baraff; Coley, John D.; Tenenbaum, Joshua B.

2008-01-01

Different intuitive theories constrain and guide inferences in different contexts. Formalizing simple intuitive theories as probabilistic processes operating over structured representations, we present a new computational model of category-based induction about causally transmitted properties. A first experiment demonstrates undergraduates'…

Sexually transmitted diseases in pregnant women in Lusaka.

PubMed

Ratnam, A V; Chatterjee, T K; Mulenga, R C

1980-01-01

The prevalance of sexually transmitted diseases has been known to be high in many African countries and preliminary investigations in Lusaka revealed a similar trend in Zambia. This paper presents an analysis of diagnoses made in 170 symptomatic pregnant women referred to the sexually transmitted diseases clinic and the screening results of 163 pregnant women in a routine antenatal examination. A high prevalance of gonococcal infection as well as syphilis was discovered in pregnant women. The implications of these findings on the possible complications and outcome of pregnancy are discussed and remedial measures suggested.

Characterization of clade 2.3.4.4 H5N8 highly pathogenic avian influenza viruses from wild birds possessing atypical hemagglutinin polybasic cleavage sites.

PubMed

Usui, Tatsufumi; Soda, Kosuke; Tomioka, Yukiko; Ito, Hiroshi; Yabuta, Toshiyo; Takakuwa, Hiroki; Otsuki, Koichi; Ito, Toshihiro; Yamaguchi, Tsuyoshi

2017-02-01

Since 2014, clade 2.3.4.4 H5 subtype highly pathogenic avian influenza viruses (HPAIVs) have been distributed worldwide. These viruses, which were reported to be highly virulent in chickens by intravenous inoculation, have a consensus HPAI motif PLRERRRKR at the HA cleavage site. However, two-clade 2.3.4.4 H5N8 viruses which we isolated from wild migratory birds in late 2014 in Japan possessed atypical HA cleavage sequences. A swan isolate, Tottori/C6, had a novel polybasic cleavage sequence, PLGERRRKR, and another isolate from a dead mandarin duck, Gifu/01, had a heterogeneous mixture of consensus PLRERRRKR and variant PLRERRRRKR sequences. The polybasic HA cleavage site is the prime virulence determinant of AIVs. Therefore, in the present study, we examined the pathogenicity of these H5N8 isolates in chickens by intravenous inoculation. When 10 6 EID 50 of these viruses were intravenously inoculated into chickens, the mean death time associated with Tottori/C6 was substantially longer (>6.1 days) than that associated with Gifu/01 (2.5 days). These viruses had comparable abilities to replicate in tissue culture cells in the presence and absence of exogenous trypsin, but the growth of Tottori/C6 was hampered. These results indicate that the novel cleavage motif of Tottori/C6 did not directly affect the infectivity of the virus, but Tottori/C6 caused attenuated pathogenicity in chickens because of hampered replication efficiency. It is important to test for the emergence of diversified HPAIVs, because introduction of HPAIVs with a lower virulence like Tottori/C6 might hinder early detection of affected birds in poultry farms.

Sexually Transmitted Infections and Male Circumcision: A Systematic Review and Meta-Analysis

PubMed Central

Van Howe, Robert S.

2013-01-01

The claim that circumcision reduces the risk of sexually transmitted infections has been repeated so frequently that many believe it is true. A systematic review and meta-analyses were performed on studies of genital discharge syndrome versus genital ulcerative disease, genital discharge syndrome, nonspecific urethritis, gonorrhea, chlamydia, genital ulcerative disease, chancroid, syphilis, herpes simplex virus, human papillomavirus, and contracting a sexually transmitted infection of any type. Chlamydia, gonorrhea, genital herpes, and human papillomavirus are not significantly impacted by circumcision. Syphilis showed mixed results with studies of prevalence suggesting intact men were at great risk and studies of incidence suggesting the opposite. Intact men appear to be of greater risk for genital ulcerative disease while at lower risk for genital discharge syndrome, nonspecific urethritis, genital warts, and the overall risk of any sexually transmitted infection. In studies of general populations, there is no clear or consistent positive impact of circumcision on the risk of individual sexually transmitted infections. Consequently, the prevention of sexually transmitted infections cannot rationally be interpreted as a benefit of circumcision, and any policy of circumcision for the general population to prevent sexually transmitted infections is not supported by the evidence in the medical literature. PMID:23710368

Avoiding sexually transmitted diseases.

PubMed

Stone, K M

1990-12-01

As the spectrum of sexually transmitted diseases (STDs) has broadened to include many infections that are not readily cured, prevention of STDs has become more important than ever. Primary prevention methods include abstinence, careful selection of sexual partners, condoms, vaginal spermicides, and a vaccine for hepatitis B. Condoms will protect against STDs only if they are used consistently and correctly; vaginal spermicides may also reduce risk of certain STDs. Health care providers should routinely counsel women on methods to reduce risk of STDs.

UWB multi-burst transmit driver for averaging receivers

DOEpatents

Dallum, Gregory E

2012-11-20

A multi-burst transmitter for ultra-wideband (UWB) communication systems generates a sequence of precisely spaced RF bursts from a single trigger event. There are two oscillators in the transmitter circuit, a gated burst rate oscillator and a gated RF burst or RF power output oscillator. The burst rate oscillator produces a relatively low frequency, i.e., MHz, square wave output for a selected transmit cycle, and drives the RF burst oscillator, which produces RF bursts of much higher frequency, i.e., GHz, during the transmit cycle. The frequency of the burst rate oscillator sets the spacing of the RF burst packets. The first oscillator output passes through a bias driver to the second oscillator. The bias driver conditions, e.g., level shifts, the signal from the first oscillator for input into the second oscillator, and also controls the length of each RF burst. A trigger pulse actuates a timing circuit, formed of a flip-flop and associated reset time delay circuit, that controls the operation of the first oscillator, i.e., how long it oscillates (which defines the transmit cycle).

Spreading of sexually transmitted diseases in heterosexual populations

PubMed Central

Gómez-Gardeñes, Jesús; Latora, Vito; Moreno, Yamir; Profumo, Elio

2008-01-01

The spread of sexually transmitted diseases (e.g., chlamydia, syphilis, gonorrhea, HIV, etc.) across populations is a major concern for scientists and health agencies. In this context, both the data collection on sexual contact networks and the modeling of disease spreading are intensive contributions to the search for effective immunization policies. Here, the spreading of sexually transmitted diseases on bipartite scale-free graphs, representing heterosexual contact networks, is considered. We analytically derive the expression for the epidemic threshold and its dependence with the system size in finite populations. We show that the epidemic outbreak in bipartite populations, with number of sexual partners distributed as in empirical observations from national sex surveys, takes place for larger spreading rates than for the case in which the bipartite nature of the network is not taken into account. Numerical simulations confirm the validity of the theoretical results. Our findings indicate that the restriction to crossed infections between the two classes of individuals (males and females) has to be taken into account in the design of efficient immunization strategies for sexually transmitted diseases. PMID:18212127

Adjacency Matrix-Based Transmit Power Allocation Strategies in Wireless Sensor Networks

PubMed Central

Consolini, Luca; Medagliani, Paolo; Ferrari, Gianluigi

2009-01-01

In this paper, we present an innovative transmit power control scheme, based on optimization theory, for wireless sensor networks (WSNs) which use carrier sense multiple access (CSMA) with collision avoidance (CA) as medium access control (MAC) protocol. In particular, we focus on schemes where several remote nodes send data directly to a common access point (AP). Under the assumption of finite overall network transmit power and low traffic load, we derive the optimal transmit power allocation strategy that minimizes the packet error rate (PER) at the AP. This approach is based on modeling the CSMA/CA MAC protocol through a finite state machine and takes into account the network adjacency matrix, depending on the transmit power distribution and determining the network connectivity. It will be then shown that the transmit power allocation problem reduces to a convex constrained minimization problem. Our results show that, under the assumption of low traffic load, the power allocation strategy, which guarantees minimal delay, requires the maximization of network connectivity, which can be equivalently interpreted as the maximization of the number of non-zero entries of the adjacency matrix. The obtained theoretical results are confirmed by simulations for unslotted Zigbee WSNs. PMID:22346705

A Diplodocid Sauropod Survivor from the Early Cretaceous of South America

PubMed Central

Gallina, Pablo A.; Apesteguía, Sebastián; Haluza, Alejandro; Canale, Juan I.

2014-01-01

Diplodocids are by far the most emblematic sauropod dinosaurs. They are part of Diplodocoidea, a vast clade whose other members are well-known from Jurassic and Cretaceous strata in Africa, Europe, North and South America. However, Diplodocids were never certainly recognized from the Cretaceous or in any other southern land mass besides Africa. Here we report a new sauropod, Leikupal laticauda gen. et sp. nov., from the early Lower Cretaceous (Bajada Colorada Formation) of Neuquén Province, Patagonia, Argentina. This taxon differs from any other sauropod by the presence of anterior caudal transverse process extremely developed with lateroventral expansions reinforced by robust dorsal and ventral bars, very robust centroprezygapophyseal lamina in anterior caudal vertebra and paired pneumatic fossae on the postzygapophyses in anterior-most caudal vertebra. The phylogenetic analyses support its position not only within Diplodocidae but also as a member of Diplodocinae, clustering together with the African form Tornieria, pushing the origin of Diplodocoidea to the Middle Jurassic or even earlier. The new discovery represents the first record of a diplodocid for South America and the stratigraphically youngest record of this clade anywhere. PMID:24828328

A diplodocid sauropod survivor from the early cretaceous of South America.

PubMed

Gallina, Pablo A; Apesteguía, Sebastián; Haluza, Alejandro; Canale, Juan I

2014-01-01

Diplodocids are by far the most emblematic sauropod dinosaurs. They are part of Diplodocoidea, a vast clade whose other members are well-known from Jurassic and Cretaceous strata in Africa, Europe, North and South America. However, Diplodocids were never certainly recognized from the Cretaceous or in any other southern land mass besides Africa. Here we report a new sauropod, Leikupal laticauda gen. et sp. nov., from the early Lower Cretaceous (Bajada Colorada Formation) of Neuquén Province, Patagonia, Argentina. This taxon differs from any other sauropod by the presence of anterior caudal transverse process extremely developed with lateroventral expansions reinforced by robust dorsal and ventral bars, very robust centroprezygapophyseal lamina in anterior caudal vertebra and paired pneumatic fossae on the postzygapophyses in anterior-most caudal vertebra. The phylogenetic analyses support its position not only within Diplodocidae but also as a member of Diplodocinae, clustering together with the African form Tornieria, pushing the origin of Diplodocoidea to the Middle Jurassic or even earlier. The new discovery represents the first record of a diplodocid for South America and the stratigraphically youngest record of this clade anywhere.

Major transitions in the evolution of early land plants: a bryological perspective

PubMed Central

Ligrone, Roberto; Duckett, Jeffrey G.; Renzaglia, Karen S.

2012-01-01

Background Molecular phylogeny has resolved the liverworts as the earliest-divergent clade of land plants and mosses as the sister group to hornworts plus tracheophytes, with alternative topologies resolving the hornworts as sister to mosses plus tracheophytes less well supported. The tracheophytes plus fossil plants putatively lacking lignified vascular tissue form the polysporangiophyte clade. Scope This paper reviews phylogenetic, developmental, anatomical, genetic and paleontological data with the aim of reconstructing the succession of events that shaped major land plant lineages. Conclusions Fundamental land plant characters primarily evolved in the bryophyte grade, and hence the key to a better understanding of the early evolution of land plants is in bryophytes. The last common ancestor of land plants was probably a leafless axial gametophyte bearing simple unisporangiate sporophytes. Water-conducting tissue, if present, was restricted to the gametophyte and presumably consisted of perforate cells similar to those in the early-divergent bryophytes Haplomitrium and Takakia. Stomata were a sporophyte innovation with the possible ancestral functions of producing a transpiration-driven flow of water and solutes from the parental gametophyte and facilitating spore separation before release. Stomata in mosses, hornworts and polysporangiophytes are viewed as homologous, and hence these three lineages are collectively referred to as the ‘stomatophytes’. An indeterminate sporophyte body (the sporophyte shoot) developing from an apical meristem was the key innovation in polysporangiophytes. Poikilohydry is the ancestral condition in land plants; homoiohydry evolved in the sporophyte of polysporangiophytes. Fungal symbiotic associations ancestral to modern arbuscular mycorrhizas evolved in the gametophytic generation before the separation of major present-living lineages. Hydroids are imperforate water-conducting cells specific to advanced mosses. Xylem vascular

Early Communication System (ECOMM) for ISS

NASA Technical Reports Server (NTRS)

Gaylor, Kent; Tu, Kwei

1999-01-01

The International Space Station (ISS) Early Communications System (ECOMM) was a Johnson Space Center (JSC) Avionic Systems Division (ASD) in-house developed communication system to provide early communications between the ISS and the Mission Control Center-Houston (MCC-H). This system allows for low rate commands (link rate of 6 kbps) to be transmitted through the Tracking and Data Relay Satellite System (TDRSS) from MCC-H to the ISS using TDRSS's S-band Single Access Forward (SSA/) link service. This system also allows for low rate telemetry (link rate of 20.48 kbps) to be transmitted from ISS to MCC-H through the TDRSS using TDRSS's S-band Single Access Return (SSAR) link service. In addition this system supports a JSC developed Onboard Communications Adapter (OCA) that allows for a two-way data exchange of 128 kbps between MCC-H and the ISS through TDRSS. This OCA data can be digital video/audio (two-way videoconference), and/or file transfers, and/or "white board". The key components of the system, the data formats used by the system to insure compatibility with the future ISS S-Band System, as well as how other vehicles may be able to use this system for their needs are discussed in this paper.

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.

PubMed

Saarela, Jeffery M; Wysocki, William P; Barrett, Craig F; Soreng, Robert J; Davis, Jerrold I; Clark, Lynn G; Kelchner, Scot A; Pires, J Chris; Edger, Patrick P; Mayfield, Dustin R; Duvall, Melvin R

2015-05-04

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes

PubMed Central

Saarela, Jeffery M.; Wysocki, William P.; Barrett, Craig F.; Soreng, Robert J.; Davis, Jerrold I.; Clark, Lynn G.; Kelchner, Scot A.; Pires, J. Chris; Edger, Patrick P.; Mayfield, Dustin R.; Duvall, Melvin R.

2015-01-01

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some ‘early-diverging’ tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae–Meliceae and Ampelodesmeae–Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae–Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae–Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a

Vector-transmitted disease vaccines: targeting salivary proteins in transmission (SPIT).

PubMed

McDowell, Mary Ann

2015-08-01

More than half the population of the world is at risk for morbidity and mortality from vector-transmitted diseases, and emerging vector-transmitted infections are threatening new populations. Rising insecticide resistance and lack of efficacious vaccines highlight the need for novel control measures. One such approach is targeting the vector-host interface by incorporating vector salivary proteins in anti-pathogen vaccines. Debate remains about whether vector saliva exposure exacerbates or protects against more severe clinical manifestations, induces immunity through natural exposure or extends to all vector species and associated pathogens. Nevertheless, exploiting this unique biology holds promise as a viable strategy for the development of vaccines against vector-transmitted diseases. Copyright © 2015 Elsevier Ltd. All rights reserved.

A new clade of Asian late Cretaceous long-snouted tyrannosaurids.

PubMed

Lü, Junchang; Yi, Laiping; Brusatte, Stephen L; Yang, Ling; Li, Hua; Chen, Liu

2014-05-07

The iconic tyrannosaurids were top predators in Asia and North America during the latest Cretaceous, and most species had deep skulls that allowed them to generate extreme bite forces. Two unusual specimens of Alioramus from Mongolia seem to indicate a divergent long-snouted body plan among some derived tyrannosaurids, but the rarity and juvenile nature of these fossils leaves many questions unanswered. Here, we describe a remarkable new species of long-snouted tyrannosaurid from the Maastrichtian of southeastern China, Qianzhousaurus sinensis. Phylogenetic analysis places Qianzhousaurus with both species of Alioramus in a novel longirostrine clade, which was geographically widespread across latest Cretaceous Asia and formed an important component of terrestrial ecosystems during this time. The new specimen is approximately twice the size as both Alioramus individuals, showing that the long-snouted morphology was not a transient juvenile condition of deep-snouted species, but a characteristic of a major tyrannosaurid subgroup.

Advances in understanding paternally transmitted Chromosomal Abnormalities

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

Marchetti, F; Sloter, E; Wyrobek, A J

2001-03-01

Multicolor FISH has been adapted for detecting the major types of chromosomal abnormalities in human sperm including aneuploidies for clinically-relevant chromosomes, chromosomal aberrations including breaks and rearrangements, and other numerical abnormalities. The various sperm FISH assays have been used to evaluate healthy men, men of advanced age, and men who have received mutagenic cancer therapy. The mouse has also been used as a model to investigate the mechanism of paternally transmitted genetic damage. Sperm FISH for the mouse has been used to detect chromosomally abnormal mouse sperm, while the PAINT/DAPI analysis of mouse zygotes has been used to evaluate themore » types of chromosomal defects that can be paternally transmitted to the embryo and their effects on embryonic development.« less

New species of Liolaemus (Reptilia, Squamata, Liolaemini) of the Liolaemus donosobarrosi clade from northwestern Patagonia, Neuquén province, Argentina.

PubMed

Avila, Luciano Javier; Perez, Cristian Hernán Fulvio; Minoli, Ignacio; Medina, Cintia Debora; Sites, Jack W Jr; Morando, Mariana

2017-12-07

Two new species of the Liolaemus donosobarrosi clade are described. Liolaemus tirantii sp. nov. and Liolaemus calliston sp. nov. differ from other members of their clade by a combination of coloration characters, morphometric and molecular traits. Liolaemus tirantii sp. nov. is known from three localities separated only a few kilometers from each other and Liolaemus calliston sp. nov. is known only from the type locality. Both species inhabit a region strongly impacted by oil and gas extraction but their conservation status is unknown.

New species, additions and a key to the Brazilian species of the Geminata clade of Solanum L. (Solanaceae) in Brazil

PubMed Central

Knapp, Sandra; Stehmann, João Renato; Giacomin, Leandro L.

2015-01-01

Abstract Two additions and four new species are described from Brazil for the large Geminata clade (Solanum: Solanaceae) bringing the total diversity in the group to 149 species, with 44 of these occurring in Brazil. New species are described from Brazil: Solanum amorimii S.Knapp & Giacomin, sp. nov. from Bahia and adjacent Minas Gerais states, Solanum filirhachis Giacomin & Stehmann, sp. nov. from Espirito Santo, Solanum psilophyllum Stehmann & Giacomin, sp. nov. from Minas Gerais and Solanum verticillatum S.Knapp & Stehmann, sp. nov. from São Paulo, Rio de Janeiro and Minas Gerais. Modern character-rich descriptions and lectotypifications are provided for Solanum apiahyense Witasek and Solanum lacteum Vell. All are illustrated, mapped and assessed for conservation status. We also provide a brief analysis of the diversity and endemism of the Geminata clade in Brazil and a key to all 44 Brazilian species. PMID:25878553

Paper area density measurement from forward transmitted scattered light

DOEpatents

Koo, Jackson C.

2001-01-01

A method whereby the average paper fiber area density (weight per unit area) can be directly calculated from the intensity of transmitted, scattered light at two different wavelengths, one being a non-absorpted wavelength. Also, the method makes it possible to derive the water percentage per fiber area density from a two-wavelength measurement. In the optical measuring technique optical transmitted intensity, for example, at 2.1 microns cellulose absorption line is measured and compared with another scattered, optical transmitted intensity reference in the nearby spectrum region, such as 1.68 microns, where there is no absorption. From the ratio of these two intensities, one can calculate the scattering absorption coefficient at 2.1 microns. This absorption coefficient at this wavelength is, then, experimentally correlated to the paper fiber area density. The water percentage per fiber area density can be derived from this two-wavelength measurement approach.

Analytical Model and Optimized Design of Power Transmitting Coil for Inductively Coupled Endoscope Robot.

PubMed

Ke, Quan; Luo, Weijie; Yan, Guozheng; Yang, Kai

2016-04-01

A wireless power transfer system based on the weakly inductive coupling makes it possible to provide the endoscope microrobot (EMR) with infinite power. To facilitate the patients' inspection with the EMR system, the diameter of the transmitting coil is enlarged to 69 cm. Due to the large transmitting range, a high quality factor of the Litz-wire transmitting coil is a necessity to ensure the intensity of magnetic field generated efficiently. Thus, this paper builds an analytical model of the transmitting coil, and then, optimizes the parameters of the coil by enlarging the quality factor. The lumped model of the transmitting coil includes three parameters: ac resistance, self-inductance, and stray capacitance. Based on the exact two-dimension solution, the accurate analytical expression of ac resistance is derived. Several transmitting coils of different specifications are utilized to verify this analytical expression, being in good agreements with the measured results except the coils with a large number of strands. Then, the quality factor of transmitting coils can be well predicted with the available analytical expressions of self- inductance and stray capacitance. Owing to the exact estimation of quality factor, the appropriate coil turns of the transmitting coil is set to 18-40 within the restrictions of transmitting circuit and human tissue issues. To supply enough energy for the next generation of the EMR equipped with a Ø9.5×10.1 mm receiving coil, the coil turns of the transmitting coil is optimally set to 28, which can transfer a maximum power of 750 mW with the remarkable delivering efficiency of 3.55%.

Imaging Arrays With Improved Transmit Power Capability

PubMed Central

Zipparo, Michael J.; Bing, Kristin F.; Nightingale, Kathy R.

2010-01-01

Bonded multilayer ceramics and composites incorporating low-loss piezoceramics have been applied to arrays for ultrasound imaging to improve acoustic transmit power levels and to reduce internal heating. Commercially available hard PZT from multiple vendors has been characterized for microstructure, ability to be processed, and electroacoustic properties. Multilayers using the best materials demonstrate the tradeoffs compared with the softer PZT5-H typically used for imaging arrays. Three-layer PZT4 composites exhibit an effective dielectric constant that is three times that of single layer PZT5H, a 50% higher mechanical Q, a 30% lower acoustic impedance, and only a 10% lower coupling coefficient. Application of low-loss multilayers to linear phased and large curved arrays results in equivalent or better element performance. A 3-layer PZT4 composite array achieved the same transmit intensity at 40% lower transmit voltage and with a 35% lower face temperature increase than the PZT-5 control. Although B-mode images show similar quality, acoustic radiation force impulse (ARFI) images show increased displacement for a given drive voltage. An increased failure rate for the multilayers following extended operation indicates that further development of the bond process will be necessary. In conclusion, bonded multilayer ceramics and composites allow additional design freedom to optimize arrays and improve the overall performance for increased acoustic output while maintaining image quality. PMID:20875996

A Quasi-Optical Transmit/Receive Switch for the Goldstone Solar System Radar

NASA Technical Reports Server (NTRS)

Bhanji, Al

1997-01-01

A novel quasi-optical transmit/receive switch design for use with a high transmit power, low receive noise planetary imaging radar system is described. Design tradeoffs and implementation are discussed.