Description and genomic characterization of Massiliimalia massiliensis gen. nov., sp. nov., and Massiliimalia timonensis gen. nov., sp. nov., two new members of the family Ruminococcaceae isolated from the human gut

2019 ◽  
Vol 112 (6) ◽  
pp. 905-918 ◽  
Author(s):  
Pamela Afouda ◽  
Sory Ibrahima Traore ◽  
Niokhor Dione ◽  
Claudia Andrieu ◽  
Enora Tomei ◽  
...  
Keyword(s):  
Human Gut ◽  
New Members ◽  
The Family ◽  
Genomic Characterization

scholarly journals Changes in reflectin protein phosphorylation are associated with dynamic iridescence in squid

2009 ◽  
Vol 7 (44) ◽  
pp. 549-560 ◽  
Author(s):  
Michi Izumi ◽  
Alison M. Sweeney ◽  
Daniel DeMartini ◽  
James C. Weaver ◽  
Meghan L. Powers ◽  
...  
Keyword(s):  
Cholinergic System ◽  
Protein Tyrosine Kinase ◽  
Kinase Inhibitor ◽  
Light Organ ◽  
Complex Dynamic ◽  
New Members ◽  
The Family ◽  
Muscarinic Cholinergic ◽  
Dynamic Camouflage

Many cephalopods exhibit remarkable dermal iridescence, a component of their complex, dynamic camouflage and communication. In the species Euprymna scolopes , the light-organ iridescence is static and is due to reflectin protein-based platelets assembled into lamellar thin-film reflectors called iridosomes, contained within iridescent cells called iridocytes. Squid in the family Loliginidae appear to be unique in which the dermis possesses a dynamic iridescent component with reflective, coloured structures that are assembled and disassembled under the control of the muscarinic cholinergic system and the associated neurotransmitter acetylcholine (ACh). Here we present the sequences and characterization of three new members of the reflectin family associated with the dynamically changeable iridescence in Loligo and not found in static Euprymna iridophores. In addition, we show that application of genistein, a protein tyrosine kinase inhibitor, suppresses ACh- and calcium-induced iridescence in Loligo . We further demonstrate that two of these novel reflectins are extensively phosphorylated in concert with the activation of iridescence by exogenous ACh. This phosphorylation and the correlated iridescence can be blocked with genistein. Our results suggest that tyrosine phosphorylation of reflectin proteins is involved in the regulation of dynamic iridescence in Loligo .

scholarly journals Rediscovery and genomic characterization of bovine astroviruses

2011 ◽  
Vol 92 (8) ◽  
pp. 1888-1898 ◽  
Author(s):  
Herman Tse ◽  
Wan-Mui Chan ◽  
Hoi-Wah Tsoi ◽  
Rachel Y. Y. Fan ◽  
Candy C. Y. Lau ◽  
...  
Keyword(s):  
Roe Deer ◽  
Mammalian Species ◽  
Capreolus Capreolus ◽  
Genetic Distances ◽  
Genome Sequences ◽  
Sea Lions ◽  
The Family ◽  
Genomic Characterization ◽  
Similar Organization

The genus Mamastrovirus belongs to the family Astroviridae and consists of at least six members infecting different mammalian hosts, including humans, cattle and pigs. In recent years, novel astroviruses have been identified in other mammalian species like roe deer, bats and sea lions. While the bovine astrovirus was one of the earliest astroviruses to have been studied, no further research has been performed recently and its genome sequence remains uncharacterized. In this report, we describe the detection and genomic characterization of astroviruses in bovine faecal specimens obtained in Hong Kong. Five of 209 specimens were found to be positive for astrovirus by RT-PCR. Two of the positive specimens were found to contain sequences from two different astrovirus strains. Complete genome sequences of approximately 6.3 kb in length were obtained for four strains, which showed similar organization of the genome compared to other astroviruses. Phylogenetic analysis confirmed their identities as members of the genus Mamastrovirus, and showed them to be most closely related to the Capreolus capreolus astrovirus. Based on the pairwise genetic distances among their full-length ORF2 sequences, these bovine astroviruses may be assigned into at least three different genotype species. Sequence analysis revealed evidence of potential recombination in ORF2. In summary, we report the first genome sequences of bovine astroviruses and clearly establish the species status of the virus. Additionally, our study is among the first to report co-infection by different astrovirus genotypes in the same host, which is an essential step for recombination to occur.

scholarly journals New Member of the V1V2-Directed CAP256-VRC26 Lineage That Shows Increased Breadth and Exceptional Potency

2015 ◽  
Vol 90 (1) ◽  
pp. 76-91 ◽  
Author(s):  
Nicole A. Doria-Rose ◽  
Jinal N. Bhiman ◽  
Ryan S. Roark ◽  
Chaim A. Schramm ◽  
Jason Gorman ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Broadly Neutralizing Antibodies ◽  
New Members ◽  
Isolation And Characterization ◽  
The Family ◽  
Clade C ◽  
Potential Clinical Utility ◽  
Hiv 1 ◽  
Viral Isolates

ABSTRACT The epitopes defined by HIV-1 broadly neutralizing antibodies (bNAbs) are valuable templates for vaccine design, and studies of the immunological development of these antibodies are providing insights for vaccination strategies. In addition, the most potent and broadly reactive of these bNAbs have potential for clinical use. We previously described a family of 12 V1V2-directed neutralizing antibodies, CAP256-VRC26, isolated from an HIV-1 clade C-infected donor at years 1, 2, and 4 of infection (N. A. Doria-Rose et al., Nature 509:55–62, 2014, http://dx.doi.org/10.1038/nature13036 ). Here, we report on the isolation and characterization of new members of the family mostly obtained at time points of peak serum neutralization breadth and potency. Thirteen antibodies were isolated from B cell culture, and eight were isolated using trimeric envelope probes for differential single B cell sorting. One of the new antibodies displayed a 10-fold greater neutralization potency than previously published lineage members. This antibody, CAP256-VRC26.25, neutralized 57% of diverse clade viral isolates and 70% of clade C isolates with remarkable potency. Among the viruses neutralized, the median 50% inhibitory concentration was 0.001 μg/ml. All 33 lineage members targeted a quaternary epitope focused on V2. While all known bNAbs targeting the V1V2 region interact with the N160 glycan, the CAP256-VRC26 antibodies showed an inverse correlation of neutralization potency with dependence on this glycan. Overall, our results highlight the ongoing evolution within a single antibody lineage and describe more potent and broadly neutralizing members with potential clinical utility, particularly in areas where clade C is prevalent. IMPORTANCE Studies of HIV-1 broadly neutralizing antibodies (bNAbs) provide valuable information for vaccine design, and the most potent and broadly reactive of these bNAbs have potential for clinical use. We previously described a family of V1V2-directed neutralizing antibodies from an HIV-1 clade C-infected donor. Here, we report on the isolation and characterization of new members of the family mostly obtained at time points of peak serum neutralization breadth and potency. One of the new antibodies, CAP256-VRC26.25, displayed a 10-fold greater neutralization potency than previously described lineage members. It neutralized 57% of diverse clade viral isolates and 70% of clade C isolates with remarkable potency: the median 50% inhibitory concentration was 0.001 μg/ml. Our results highlight the ongoing evolution within a single antibody lineage and describe more potent and broadly neutralizing members with potential clinical utility, particularly in areas where clade C is prevalent.

Genomic characterization of covert mortality nodavirus from farming shrimp: Evidence for a new species within the family Nodaviridae

2020 ◽  
Vol 286 ◽  
pp. 198092
Author(s):  
Tingting Xu ◽  
Shuang Liu ◽  
Xiaoping Li ◽  
Qingli Zhang
Keyword(s):  
New Species ◽  
The Family ◽  
Genomic Characterization ◽  
A New Species

Genomic characterization of Ralstonia solanacearum phage ϕRS138 of the family Siphoviridae

2015 ◽  
Vol 161 (2) ◽  
pp. 483-486 ◽  
Author(s):  
Bich Van Truong Thi ◽  
Nguyen Huan Pham Khanh ◽  
Ryuta Namikawa ◽  
Kaito Miki ◽  
Akihiro Kondo ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
The Family ◽  
Genomic Characterization

scholarly journals Genomic characterization of the unclassified bovine enteric virus Newbury agent-1 (Newbury1) endorses a new genus in the family Caliciviridae

Virology ◽  
2006 ◽  
Vol 350 (1) ◽  
pp. 240-250 ◽  
Author(s):  
S.L. Oliver ◽  
E. Asobayire ◽  
A.M. Dastjerdi ◽  
J.C. Bridger
Keyword(s):  
New Genus ◽  
Enteric Virus ◽  
The Family ◽  
Genomic Characterization

Identification, transmission and genomic characterization of a new member of the family Caulimoviridae causing a flower distortion disease of Rudbeckia hirta

2017 ◽  
Vol 241 ◽  
pp. 62-67 ◽  
Author(s):  
Benham Lockhart ◽  
Dimitre Mollov ◽  
Neil Olszewski ◽  
Nicholas Goldsmith
Keyword(s):  
Rudbeckia Hirta ◽  
The Family ◽  
Genomic Characterization

scholarly journals Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial ‘dark matter’

2020 ◽  
Vol 12 (11) ◽  
pp. 263-274
Author(s):  
James Y Tan ◽  
Sida Wang ◽  
Gregory J Dick ◽  
Vincent B Young ◽  
David H Sherman ◽  
...  
Keyword(s):  
Dark Matter ◽  
Microbial Communities ◽  
Ecological Interactions ◽  
Healthy Human ◽  
Encapsulated Cells ◽  
Microfluidic Droplets ◽  
The Family ◽  
Culture Independent ◽  
Genomic Characterization

Abstract While the ‘unculturable’ majority of the bacterial world is accessible with culture-independent tools, the inability to study these bacteria using culture-dependent approaches has severely limited our understanding of their ecological roles and interactions. To circumvent cultivation barriers, we utilize microfluidic droplets as localized, nanoliter-size bioreactors to co-cultivate subsets of microbial communities. This co-localization can support ecological interactions between a reduced number of encapsulated cells. We demonstrated the utility of this approach in the encapsulation and co-cultivation of droplet sub-communities from a fecal sample collected from a healthy human subject. With the whole genome amplification and metagenomic shotgun sequencing of co-cultivated sub-communities from 22 droplets, we observed that this approach provides accessibility to uncharacterized gut commensals for study. The recovery of metagenome-assembled genomes from one droplet sub-community demonstrated the capability to dissect the sub-communities with high-genomic resolution. In particular, genomic characterization of one novel member of the family Neisseriaceae revealed implications regarding its participation in fatty acid degradation and production of atherogenic intermediates in the human gut. The demonstrated genomic resolution and accessibility to the microbial ‘dark matter’ with this methodology can be applied to study the interactions of rare or previously uncultivated members of microbial communities.

Identification and genomic characterization of a novel fish reovirus, Hubei grass carp disease reovirus, isolated in 2009 in China

2013 ◽  
Vol 94 (10) ◽  
pp. 2266-2277 ◽  
Author(s):  
Yuding Fan ◽  
Shujing Rao ◽  
Lingbing Zeng ◽  
Jie Ma ◽  
Yong Zhou ◽  
...  
Keyword(s):  
Amino Acid ◽  
Grass Carp ◽  
Sequence Similarity ◽  
Amino Acid Level ◽  
Amino Acid Sequences ◽  
Full Genome Sequence ◽  
Total Size ◽  
The Family ◽  
Genomic Characterization

A novel fish reovirus, Hubei grass carp disease reovirus (HGDRV; formerly grass carp reovirus strain 104, GCRV104), was isolated from diseased grass carp in China in 2009 and the full genome sequence was determined. This reovirus was propagated in a grass carp kidney cell line with a typical cytopathic effect. The total size of the genome was 23 706 bp with a 51 mol% G+C content, and the 11 dsRNA segments encoded 12 proteins (two proteins encoded by segment 11). A nucleotide sequence similarity search using blastn found no significant matches except for segment 2, which partially matched that of the RNA-dependent RNA polymerase (RdRp) from several viruses in the genera Aquareovirus and Orthoreovirus of the family Reoviridae. At the amino acid level, seven segments (Seg-1 to Seg-6, and Seg-8) matched with species in the genera Aquareovirus (15–46 % identities) and Orthoreovirus (12–44 % identities), while for four segments (Seg-7, Seg-9, Seg-10 and Seg-11) no similarities in these genera were found. Conserved terminal sequences, 5′-GAAUU----UCAUC-3′, were found in each HGDRV segment at the 5′ and 3′ ends, and the 5′-terminal nucleotides were different from any known species in the genus Aquareovirus. Phylogenetic analysis based on RdRp amino acid sequences from members of the family Reoviridae showed that HGDRV clustered with aquareoviruses prior to joining a branch common with orthoreoviruses. Based on these observations, we propose that HGDRV is a new species in the genus Aquareovirus that is distantly related to any known species within this genus.

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