Conserved spatially interacting motifs of protein superfamilies: Application to fold recognition and function annotation of genome data

2004 ◽  
Vol 54 (4) ◽  
pp. 657-670 ◽  
Author(s):  
Anirban Bhaduri ◽  
R. Ravishankar ◽  
R. Sowdhamini
Keyword(s):  
Fold Recognition ◽  
Function Annotation ◽  
Protein Superfamilies ◽  
Genome Data ◽  
And Function

Identification and function annotation of long intervening noncoding RNAs

2016 ◽  
pp. bbw046 ◽  
Author(s):  
Haitao Luo ◽  
Dechao Bu ◽  
Liang Sun ◽  
Shuangsang Fang ◽  
Zhiyong Liu ◽  
...  
Keyword(s):  
Noncoding Rnas ◽  
Function Annotation ◽  
And Function

scholarly journals Ancestry of the AUTS2 family–A novel group of polycomb-complex proteins involved in human neurological disease

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0232101
Author(s):  
Robert A. Sellers ◽  
David L. Robertson ◽  
May Tassabehji
Keyword(s):  
Autosomal Dominant ◽  
Large Population ◽  
Evolutionary Analysis ◽  
Genome Data ◽  
High Prevalence ◽  
And Function ◽  
Polycomb Complex ◽  
Putative Domain ◽  
Human Specific

Autism susceptibility candidate 2 (AUTS2) is a neurodevelopmental regulator associated with an autosomal dominant intellectual disability syndrome, AUTS2 syndrome, and is implicated as an important gene in human-specific evolution. AUTS2 exists as part of a tripartite gene family, the AUTS2 family, which includes two relatively undefined proteins, Fibrosin (FBRS) and Fibrosin-like protein 1 (FBRSL1). Evolutionary ancestors of AUTS2 have not been formally identified outside of the Animalia clade. A Drosophila melanogaster protein, Tay bridge, with a role in neurodevelopment, has been shown to display limited similarity to the C-terminal of AUTS2, suggesting that evolutionary ancestors of the AUTS2 family may exist within other Protostome lineages. Here we present an evolutionary analysis of the AUTS2 family, which highlights ancestral homologs of AUTS2 in multiple Protostome species, implicates AUTS2 as the closest human relative to the progenitor of the AUTS2 family, and demonstrates that Tay bridge is a divergent ortholog of the ancestral AUTS2 progenitor gene. We also define regions of high relative sequence identity, with potential functional significance, shared by the extended AUTS2 protein family. Using structural predictions coupled with sequence conservation and human variant data from 15,708 individuals, a putative domain structure for AUTS2 was produced that can be used to aid interpretation of the consequences of nucleotide variation on protein structure and function in human disease. To assess the role of AUTS2 in human-specific evolution, we recalculated allele frequencies at previously identified human derived sites using large population genome data, and show a high prevalence of ancestral alleles, suggesting that AUTS2 may not be a rapidly evolving gene, as previously thought.

scholarly journals Recent selection of candidate genes for mammal domestication in Europeans and language change in Europe: a hypothesis

2019 ◽  
Author(s):  
Antonio Benítez-Burraco ◽  
Evgeny Chekalin ◽  
Sergey Bruskin ◽  
Irina Morozova
Keyword(s):  
Bronze Age ◽  
Language Change ◽  
Brain Size ◽  
Human Cognition ◽  
Nucleotide Polymorphisms ◽  
Late Neolithic ◽  
Single Nucleotide ◽  
Genome Data ◽  
And Function ◽  
And Behavior

AbstractHuman evolution resulted from changes in our biology, behavior, and culture. One source of these changes has been hypothesized to be our self-domestication (that is, the development in humans of features commonly found in domesticated strains of mammals, seemingly as a result of selection for reduced aggression). Signals of domestication, notably brain size reduction, have increased in recent times. In this paper we compare whole-genome data between Late Neolithic/Bronze Age individuals and modern Europeans and show that genes associated with mammal domestication and with neural crest development and function are significantly differently enriched in nonsynonymous single nucleotide polymorphisms between these two groups. We hypothesize how these changes might account for the increased features of self-domestication in modern humans and ultimately, for subtle recent changes in human cognition and behavior, including language.

scholarly journals Analysis of Ficus hirta Fig Endosymbionts Diversity and Species Composition

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 636
Author(s):  
Yifeng Liu ◽  
Songle Fan ◽  
Hui Yu
Keyword(s):  
High Throughput Sequencing ◽  
Biological Database ◽  
Fig Wasp ◽  
Fig Wasps ◽  
Function Annotation ◽  
History Of ◽  
Ficus Hirta ◽  
Bacteria And Fungi ◽  
And Function ◽  
Confined Environment

Endosymbionts living in plants and insects are pervasive. Ficus (Moraceae) has very special inflorescences (which we also call figs) enclosed like an urn, and such inflorescence is usually parasitized by fig wasps. Ficus breeds fig wasp larvae in its figs and adult fig wasps pollinate for Ficus, Ficus and its obligated pollinator formed fig-fig wasp mutualism. Previous studies have found that this confined environment in figs may have provided protection for fig wasps and that this has left some imprints on the genome of fig wasps during the coevolution history of figs and fig wasps. Research on the diversity of both bacteria and fungi in figs are fewer. Our study explored the diversity of endosymbionts in Ficus hirta figs. We utilized high-throughput sequencing and biological database to identify the specific microorganism in figs, then conducted microorganism communities’ diversity analysis and function annotation analysis. As a result, we identified the dominant endosymbionts in figs, mainly some insect internal parasitic bacteria and fungi, plant pathogen, endophytes, and saprotroph. Then we also found bacteria in Ficus hirta figs were more diversified than fungi, and bacteria communities in female figs and functional male figs were different. These findings may give us more insight into the coevolution and interaction among endosymbiont, fig, and fig wasp.

scholarly journals Advances in long noncoding RNAs: identification, structure prediction and function annotation

2015 ◽  
Vol 15 (1) ◽  
pp. 38-46 ◽  
Author(s):  
Xingli Guo ◽  
Lin Gao ◽  
Yu Wang ◽  
David K. Y. Chiu ◽  
Tong Wang ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Function Annotation ◽  
And Function

scholarly journals The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation

2018 ◽  
Vol 9 ◽  
Author(s):  
Ali H. A. Elbehery ◽  
Judith Feichtmayer ◽  
Dave Singh ◽  
Christian Griebler ◽  
Li Deng
Keyword(s):  
Function Annotation ◽  
Protein Cluster ◽  
And Function ◽  
Cluster Database

scholarly journals In silico sequence analysis, homology modeling and function annotation of leishmanolysin from Leishmania donovani

2015 ◽  
Vol 40 (4) ◽  
pp. 1266-1269 ◽  
Author(s):  
Somnath Waghmare ◽  
Abhishek Buxi ◽  
Yogesh Nandurkar ◽  
Anil Shelke ◽  
Ramrao Chavan
Keyword(s):  
Sequence Analysis ◽  
Homology Modeling ◽  
In Silico ◽  
Leishmania Donovani ◽  
Function Annotation ◽  
And Function
Sign in / Sign up

Export Citation Format

Share Document