BackgroundHaving conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group.ResultsHere we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000 Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats.ConclusionsOur findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5163-2) contains supplementary material, which is available to authorized users.
Tuberculosis (TB), a global disease mainly infected by Mycobacterium tuberculosis, remains leading public health problem worldwide. Suppressors of cytokine signaling (SOCSs) play important roles in the protection against microbial infection. However, the relationship between members of the SOCS family and tuberculosis infection remains unclear. Using peripheral blood mononuclear cells, we investigated the mRNA expression profiles of SOCS subfamilies among active TB, latent tuberculosis infection (LTBI), and healthy individuals. Our results showed that active tuberculosis subjects had higher levels of SOCS-3 mRNA, lower expressions of SOCS-2, -4, -5, -6, -7, and cytokine-inducible SH2-containing protein-1 (CIS-1) mRNAs, but not SOCS-1 mRNA than healthy and LTBI subjects. In men, LTBI patients had lower SOCS-3 than healthy subjects, and active TB patients had lower levels of SOCS-4, -5, and CIS-1 mRNAs but higher levels of SOCS-3 mRNA than healthy subjects. In women, LTBI patients had lower SOCS-3 mRNA level than healthy subjects, and active TB patients had lower CIS-1 mRNA level than healthy subjects. In non-aged adults (< 65 years old), TB patients had higher SOCS-3 mRNA and lower levels of SOCS-2, -4, -5, -6, -7, and CIS-1 mRNAs; whereas, aged TB patients (≥ 65 years old) had lower levels of SOCS-5 and CIS-1 mRNAs. These data suggest that particular SOCS members and their correlative relationships allow discrimination of active TB from healthy and LTBI subjects.
It is now widely believed that low-frequency variants may play an important role in cancers. In addition, low-frequency variants are usually closely related to populations. To identify the disease-associated variants, several projects are now underway to build a reference of genetic variations from different populations. Furthermore, massive tools and databases are available to compare the dynamic gene expression among different organs and predict functional effects of genetic variants. These resources aid to identify genetic roots of cancers in populations easier. Despite the existence of population allele frequency information, gene expression databases and functional effects of protein mutations, a comprehensive platform providing an integrated annotation database in human genetic variants, is still lacking. In the study, we proposed a web-based database to determine potential variations in cancers with collected variant information from current common databases and integrated those data to provide comprehensive analyses. The web-site offers a function to upload a variant call format (VCF) files for variants annotation. Importantly, we integrated population allele frequency information from NHBI GO Exome Sequencing Project (ESP), 1000 Genomes Project and Tohoku Medical Megabank Project to help users figure out the correlation between disease and population. Additionally, we also collected gene expression profiles from The Human Protein Atlas, Expression Atlas and NCBI SRA in different organs of human, mouse, and zebrafish respectively to reflect the relationship between gene expression and genetic variations in a specific organ. Overall, the database aids to predict protein functions in mutations, analyze population allele frequency and gene expression information from provided variants of diseases. In the result, we use three EGFR mutations to display the proposed system. A recent study has reported that Asian patients with non-small cell lung cancer (NSCLC) carrying a higher rate of EGFR mutations than non-Asian patients. These mutations, such as chr7:55241708G>C (G719A), chr7:55249005G>T (S768I) and chr7:55259515T>G (L858R), are found approximately in 30% of Asian (Japanese) patients. In functional prediction results, these sites are exonic and nonsynonymous mutations. The REVEL scores of three EGFR mutations are 0.824, 0.765 and 0.961, and gerp++ scores are 5.5, 5.85 and 5.71, respectively. Both REVEL and gerp++ show high scores for severe damage of protein structure in the mutations. According to the results, researchers can infer that the three mutations are pathogenic variants implying the nucleotide positions with a higher constraint. Citation Format: Li Mei Chiang, Chien Yueh Lee, Liang Chuan Lai, Mong Hsun Tsai, Tzu Pin Lu, Eric Y. Chuang. VariED: an integrated database of variants and gene expression profiles for genetic diseases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3573. doi:10.1158/1538-7445.AM2017-3573
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