Genomes and Genes
Summary: Genotypic differences observed among individuals in a population.
- Eilbeck K, QUINLAN A, Yandell M. Settling the score: variant prioritization and Mendelian disease. Nat Rev Genet. 2017;18:599-612 pubmed publisher..We place variant prioritization in the wider context of gene prioritization, burden testing and genotype-phenotype association, and we discuss opportunities and challenges introduced by whole-genome sequencing. ..
- Dolka B, Chrobak Chmiel D, Czopowicz M, Szeleszczuk P. Characterization of pathogenic Enterococcus cecorum from different poultry groups: Broiler chickens, layers, turkeys, and waterfowl. PLoS ONE. 2017;12:e0185199 pubmed publisher..The study provides a new insight into EC as pathogen of different bird species. The obtained data may be useful in further studies on EC-infections more focused on a specific type of poultry...
- Dario M, Moratelli R, Schwabl P, Jansen A, Llewellyn M. Small subunit ribosomal metabarcoding reveals extraordinary trypanosomatid diversity in Brazilian bats. PLoS Negl Trop Dis. 2017;11:e0005790 pubmed publisher..Our results highlight bats as a long-standing nexus among host-parasite interactions of multiple niches, sustained in part by opportunistic and incidental infections of consequence to evolutionary theory as much as to public health. ..
- Pereira G, Pinho R, Pinho E, Pires L, Bernardo Junior L, Pereira J, et al. Selection of maize inbred lines and gene expression for resistance to ear rot. Genet Mol Res. 2017;16: pubmed publisher..Thus, the genes LOX8 and Hsp82 are potential molecular markers for selection of maize inbred lines resistant to F. verticillioides. ..
- Zhu T, Liang C, Meng Z, Sun G, Meng Z, Guo S, et al. CottonFGD: an integrated functional genomics database for cotton. BMC Plant Biol. 2017;17:101 pubmed publisher..Equipped with specialized functional modules and modernized visualization tools, and populated with multiple kinds of -omics data, CottonFGD provides a quick and easy-to-use data analysis platform for cotton researchers worldwide. ..
- Doyle S, Bourguinat C, Nana Djeunga H, Kengne Ouafo J, Pion S, Bopda J, et al. Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity. PLoS Negl Trop Dis. 2017;11:e0005816 pubmed publisher..Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR) and sub-optimal responder (SOR) parasites...
- Lin N, Fu W, Zhao C, Li B, Yan X, Li Y. Biologico-clinical significance of DNMT3A variants expression in acute myeloid leukemia. Biochem Biophys Res Commun. 2017;494:270-277 pubmed publisher..These findings suggest that DNMT3A1 and DNMT3A2V are the main variants in acute myeloid leukemia with different clinical association, and might play important roles in the pathophysiology of acute myeloid leukemia...
- Kapatai G, Sheppard C, Troxler L, Litt D, Furrer J, Hilty M, et al. Pneumococcal 23B Molecular Subtype Identified Using Whole Genome Sequencing. Genome Biol Evol. 2017;9:2122-2135 pubmed publisher..Structural and antigenic variation of capsular types is the result of genetic variation within the capsular polysaccharide synthesis (CPS) locus; however, genetic variation may not always result ..
- Gopalan S, Carja O, Fagny M, Patin E, Myrick J, McEwen L, et al. Trends in DNA Methylation with Age Replicate Across Diverse Human Populations. Genetics. 2017;206:1659-1674 pubmed publisher..While many age-related CpG sites replicate across populations, we show that considering common genetic variation at meQTLs further improves our ability to detect previously identified age associations.
- Scott D, Zhang F. Implications of human genetic variation in CRISPR-based therapeutic genome editing. Nat Med. 2017;23:1095-1101 pubmed publisher..individual patients, treatment at the genomic level must contend with substantial inter-individual natural genetic variation. Here we analyze the recently released ExAC and 1000 Genomes data sets to determine how human genetic ..
- Yu C, Ang G, Subramaniam V, Johari James R, Ahmad A, Abdul Rahman T, et al. Inference of the Genetic Polymorphisms of CYP2D6 in Six Subtribes of the Malaysian Orang Asli from Whole-Genome Sequencing Data. Genet Test Mol Biomarkers. 2017;21:409-415 pubmed publisher..The findings in this study provide insights into the genetic polymorphisms of CYP2D6 in the Orang Asli of Peninsular Malaysia. ..
- Wheeler E, Leong A, Liu C, Hivert M, Strawbridge R, Podmore C, et al. Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis. PLoS Med. 2017;14:e1002383 pubmed publisher..Screening with direct glucose measurements, or genetically-informed HbA1c diagnostic thresholds in people with G6PD deficiency, may be required to avoid missed or delayed diagnoses. ..
- Hilmarsson H, Hytönen T, Isobe S, Goransson M, Toivainen T, Hallsson J. Population genetic analysis of a global collection of Fragaria vesca using microsatellite markers. PLoS ONE. 2017;12:e0183384 pubmed publisher..bracteata. In addition, F. vesca subsp. vesca forms a single global population with evidence that the Icelandic group is a separate cluster from the main Eurasian population. ..
- Richards A, Watza D, Findley A, Alazizi A, Wen X, Pai A, et al. Environmental perturbations lead to extensive directional shifts in RNA processing. PLoS Genet. 2017;13:e1006995 pubmed publisher..Together, these results demonstrate that RNA processing is dramatically changed in response to environmental perturbations through specific mechanisms regulated by trans factors...
- Okuhara D, Furutani S, Ito K, Ihara M, Matsuda K. Splice Variants of pH-Sensitive Chloride Channel Identify a Key Determinant of Ivermectin Sensitivity in the Larvae of the Silkworm Bombyx mori. Mol Pharmacol. 2017;92:491-499 pubmed publisher..This interaction is likely to prevent ivermectin-induced opening of the channel, accounting, at least partially, for the differential macrolide action on the two variants. ..
- Lau J, Kim Y, Murphy R, Newman R, Yang X, Zody M, et al. Deep sequencing of RSV from an adult challenge study and from naturally infected infants reveals heterogeneous diversification dynamics. Virology. 2017;510:289-296 pubmed publisher..In contrast, infant infections showed much less viral diversity. Our findings suggest multiple overlapping mechanisms for early control of acute viral infections, which may differ between age groups and host immune responses. ..
- Wang H, Tang X, Su Y, Chen J, Yan J. Characterization of clinical Vibrio parahaemolyticus strains in Zhoushan, China, from 2013 to 2014. PLoS ONE. 2017;12:e0180335 pubmed publisher..We conclude that continuous surveillance of V. parahaemolyticus in diarrhea patients is a public health priority and is useful for conducting risk assessment of foodborne illnesses caused by V. parahaemolyticus. ..
- Blasco A, MartÃnez Ãlvaro M, GarcÃa M, IbÃ¡Ã±ez Escriche N, Argente M. Selection for environmental variance of litter size in rabbits. Genet Sel Evol. 2017;49:48 pubmed publisher..We also conclude that selection for reduced environmental variance of litter size does not depress litter size. ..
- Wang Y, Hu Y, He D, Chen S, Li S, Lan D, et al. Contribution of both positive selection and relaxation of selective constraints to degeneration of flyability during geese domestication. PLoS ONE. 2017;12:e0185328 pubmed publisher..In addition, both positive artificial selection and the relaxation of functional constraints appeared to play important roles in the degeneration of flyability in domestic geese. ..
- Espínola S, Cancela M, Brisolara CorrÃªa L, Zaha A. Evolutionary fates of universal stress protein paralogs in Platyhelminthes. BMC Evol Biol. 2018;18:10 pubmed publisher..This framework aims to explain the sequence and functional diversity of this gene family, providing a foundation for future studies in other taxa in which USPs occur. ..
- Yildirim G, Attar R, Gulec Yilmaz S, Duman S, Isbir T. Association of CCR2 (+190 G/A) Gene Variants and Ovarian Cancer Severity. Genet Test Mol Biomarkers. 2017;21:512-515 pubmed publisher..The CCR2 (+190 G/A) GG genotype may be a potential risk factor for the severe forms of ovarian cancer and the A allele may be a risk-reducing factor for severe ovarian cancer. ..
- Montenegro M, Cuervo C, Cárdenas C, Duarte S, Díaz J, Thomas M, et al. Identification of a type I nitroreductase gene in non-virulent Trypanosoma rangeli. Mem Inst Oswaldo Cruz. 2017;112:504-509 pubmed publisher..In addition, T. rangeli was shown to be sensitive to benznidazole and nifurtimox in a concentration-dependent manner. In summary, T. rangeli appears to have a newly discovered functional type I NTR. ..
- Mostafavi H, Berisa T, Day F, Perry J, Przeworski M, Pickrell J. Identifying genetic variants that affect viability in large cohorts. PLoS Biol. 2017;15:e2002458 pubmed publisher..Beyond our findings, the analysis serves as a proof of principle for how upcoming biomedical data sets can be used to learn about selection effects in contemporary humans. ..
- Al Aama J, Shaik N, Banaganapalli B, Salama M, Rashidi O, Sahly A, et al. Whole exome sequencing of a consanguineous family identifies the possible modifying effect of a globally rare AK5 allelic variant in celiac disease development among Saudi patients. PLoS ONE. 2017;12:e0176664 pubmed publisher..Our study underlines the need to have population-specific genome databases to avoid false leads and to identify true candidate causal genes for the familial form of celiac disease. ..
- Sato K, Sakamoto H, Hirata M, Kidokoro Kobayashi M, Ozaki M, Higashi S, et al. Relationship Among Establishment Durations, Kin Relatedness, Aggressiveness, and Distance Between Populations of Eight Invasive Argentine Ant (Hymenoptera: Formicidae) Supercolonies in Japan. J Econ Entomol. 2017;110:1676-1684 pubmed publisher..After 15?yr, eradication will be more difficult, but it is preferable to just monitor the impact for a nonnative ecosystem. ..
- Stanisic L, Aleksic J, Dimitrijević V, Simeunovic P, Glavinic U, Stevanovic J, et al. New insights into the origin and the genetic status of the Balkan donkey from Serbia. Anim Genet. 2017;48:580-590 pubmed publisher..Clade 2 donkeys probably appeared in Greece prior to those belonging to Clade 1, whereas expansion and diversification of Clade 1 donkeys within the Balkans predated that of Clade 2 donkeys...
- Kamidi C, Saarman N, Dion K, Mireji P, Ouma C, Murilla G, et al. Multiple evolutionary origins of Trypanosoma evansi in Kenya. PLoS Negl Trop Dis. 2017;11:e0005895 pubmed publisher..brucei strains from different genetic backgrounds can become either causative agents of a dangerous, cosmopolitan livestock disease or of a lethal human disease, like for T. b. rhodesiense...
- Salehipour P, Nematzadeh M, Mobasheri M, Afsharpad M, Mansouri K, Modarressi M. Identification of new TSGA10 transcript variants in human testis with conserved regulatory RNA elements in 5'untranslated region and distinct expression in breast cancer. Biochim Biophys Acta Gene Regul Mech. 2017;1860:973-982 pubmed publisher
- Laggis A, Baxevanis A, Charalampidou A, Maniatsi S, Triantafyllidis A, Abatzopoulos T. Microevolution of the noble crayfish (Astacus astacus) in the Southern Balkan Peninsula. BMC Evol Biol. 2017;17:122 pubmed publisher..astacus. Such refugia have served as centres of expansion to northern regions. Recent history of the noble crayfish in southern Balkans reveals the influence of environmental (climate, geology and/or topology) and anthropogenic factors. ..
- Persyn E, Karakachoff M, Le Scouarnec S, Le Clézio C, Campion D, Consortium F, et al. DoEstRare: A statistical test to identify local enrichments in rare genomic variants associated with disease. PLoS ONE. 2017;12:e0179364 pubmed publisher..DoEstRare, by integrating variant position information, gives new opportunities to explain disease susceptibility. DoEstRare is implemented in a user-friendly R package. ..
- Balazik M, Farrae D, Darden T, Garman G. Genetic differentiation of spring-spawning and fall-spawning male Atlantic sturgeon in the James River, Virginia. PLoS ONE. 2017;12:e0179661 pubmed publisher..S. Atlantic coast, suggesting that current reference population database should be updated to incorporate both new samples and our increased understanding of Atlantic sturgeon life history. ..
- Baier F, Schmitz A, Sauer Gürth H, Wink M. Pre-Quaternary divergence and subsequent radiation explain longitudinal patterns of genetic and morphological variation in the striped skink, Heremites vittatus. BMC Evol Biol. 2017;17:132 pubmed publisher..Consistent with the genetic variation, our morphological analysis revealed that the majority of morphological traits show significant mean ..
- Kittichai V, Koepfli C, Nguitragool W, Sattabongkot J, Cui L. Substantial population structure of Plasmodium vivax in Thailand facilitates identification of the sources of residual transmission. PLoS Negl Trop Dis. 2017;11:e0005930 pubmed publisher..Understanding the genetic relationship of residual parasite populations can help track the origins of the parasites that are reintroduced into malaria-free regions within the country...
- de Oliveira G, Vieira V, Ávila E, Finger Jardim F, Caldeira T, Gatti F, et al. Human papillomavirus type distribution and HPV16 intratype diversity in southern Brazil in women with and without cervical lesions. Mem Inst Oswaldo Cruz. 2017;112:492-498 pubmed publisher..This study identified a high frequency of European and North American HPV16 lineages, consistent with the genetic background of the human population in southern Brazil. ..
- Pellegrinelli L, Bubba L, Galli C, Anselmi G, Primache V, Binda S, et al. Epidemiology and molecular characterization of influenza viruses, human parechoviruses and enteroviruses in children up to 5 years with influenza-like illness in Northern Italy during seven consecutive winter seasons (2010-2017). J Gen Virol. 2017;98:2699-2711 pubmed publisher..Influenza surveillance samples could provide us with valuable insight into the epidemiological features of viruses involved in ILI...
- Thieme F, Ludwig K. The Role of Noncoding Genetic Variation in Isolated Orofacial Clefts. J Dent Res. 2017;96:1238-1247 pubmed publisher..This review also highlights the role of the emerging research field "functional genomics" and its increasing contribution to our biological understanding of nsOFC. ..
- Abalde S, Tenorio M, Afonso C, Uribe J, Echeverry A, Zardoya R. Phylogenetic relationships of cone snails endemic to Cabo Verde based on mitochondrial genomes. BMC Evol Biol. 2017;17:231 pubmed publisher..Our study confirms the diversity of cone endemic to Cabo Verde but significantly reduces the number of valid species. Applying a sequence divergence threshold, the number of valid species within the sampled Africonus is reduced to half. ..
- Costa S, Fumian T, Lima I, Siqueira J, Silva L, Hernandez J, et al. High prevalence of norovirus in children with sporadic acute gastroenteritis in Manaus, Amazon Region, northern Brazil. Mem Inst Oswaldo Cruz. 2017;112:391-395 pubmed publisher..7 and GII.3. This research revealed a high circulation of NoV GII.4 in Manaus and contributed to the understanding of the importance of this virus in the aetiology of AGE cases, especially in a region with such few studies available. ..
- Taliercio E, Eickholt D, Rouf R, Carter T. Changes in gene expression between a soybean F1 hybrid and its parents are associated with agronomically valuable traits. PLoS ONE. 2017;12:e0177225 pubmed publisher..We propose that changes in gene expression, both additive and non-additive, and changes in allele specific expression bias may explain agronomic traits, and be valuable tools for plant breeders in the assessment of breeding populations. ..
- Mascagni F, Cavallini A, Giordani T, Natali L. Different histories of two highly variable LTR retrotransposons in sunflower species. Gene. 2017;634:5-14 pubmed publisher..In general, these two retrotransposon families differentially contributed to interspecific variability, emphasising the need to refer to specific families when studying genome evolution. ..
- Dawson N, Levings M. Antigen-specific regulatory T cells: are police CARs the answer?. Transl Res. 2017;187:53-58 pubmed publisher..Here, we discuss the progress in this field and highlight the major outstanding questions that remain to be addressed as this approach moves toward clinical applications. ..
- Kawasaki K, Mikami M, Nakatomi M, Braasch I, Batzel P, H Postlethwait J, et al. SCPP Genes and Their Relatives in Gar: Rapid Expansion of Mineralization Genes in Osteichthyans. J Exp Zool B Mol Dev Evol. 2017;328:645-665 pubmed publisher..Furthermore, the absence of acidic SCPP genes in chondrichthyans might be explained by the secondary loss of earliest acidic genes. It appears that many SCPP genes expanded rapidly in stem osteichthyans and in basal actinopterygians. ..
- Liu J, Shi Z, Lian Z, Chen H, Zhang Q, Feng H, et al. Association of CD58 gene polymorphisms with NMO spectrum disorders in a Han Chinese population. J Neuroimmunol. 2017;309:23-30 pubmed publisher..In conclusion, this study identified a new NMOSD susceptibility variant, rs56302466, and suggested that CD58 polymorphisms are associated with the risk of NMOSD in Han Chinese. ..
- Hundie G, Raj V, Gebremichael D, Pas S, Haagmans B. Genetic diversity of hepatitis C virus in Ethiopia. PLoS ONE. 2017;12:e0179064 pubmed publisher..This genotype is considered to be difficult to treat, thus, our finding has an important impact on the development of treatment strategies and patient management in Ethiopia. ..
- Behera V, Evans P, Face C, Hamagami N, Sankaranarayanan L, Keller C, et al. Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility. Nat Commun. 2018;9:782 pubmed publisher..Combined, our approaches reveal insights into the genetic basis of TF occupancy and their interplay with chromatin features. ..
- Converse P, Kuchta S, Hauswaldt J, Roosenburg W. Turtle soup, Prohibition, and the population genetic structure of Diamondback Terrapins (Malaclemys terrapin). PLoS ONE. 2017;12:e0181898 pubmed publisher..In addition, our study shows that population genetic tools can elucidate metapopulation dynamics in taxa with complex genetic histories impacted by anthropogenic activities. ..