Genomes and Genes
molecular sequence data
Summary: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
- Wang X, Tang Y, Lu J, Shao Y, Qin X, Li Y, et al. Characterization of novel cytochrome P450 2E1 knockout rat model generated by CRISPR/Cas9. Biochem Pharmacol. 2016;105:80-90 pubmed publisher..The Cyp2e1 KO rats as a novel and available rodent animal model provide a powerful tool for the study of CYP2E1 in the chemical metabolism, toxicity, carcinogenicity, and its core factor in drug-drug interactions. ..
- Liu Y, Petrovic A, Rombaut P, Mosalaganti S, Keller J, Raunser S, et al. Insights from the reconstitution of the divergent outer kinetochore of Drosophila melanogaster. Open Biol. 2016;6:150236 pubmed publisher..Our studies shed light on the structural and functional organization of a highly divergent kinetochore particle. ..
- Gu C, Zhang X, Chen S, Li T, Chen Y, Jiang J, et al. Isolation and characterization of the Chrysanthemum nitrate transporter CmNRT1. Genet Mol Res. 2016;15: pubmed publisher..Root (15)N influx in wild-type and transgenic A. thaliana lines under 10 or 0.2 mM (15)NO3 was tested. Our results indicate that CmNRT1 encodes a constitutive component for a low-affinity transporter. ..
- Zhou X, Ren W, Bharath S, Tang X, He Y, Chen C, et al. Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1. Cell Rep. 2016;14:2030-9 pubmed publisher..The conformational snapshots of BaPif1 provide insights into the mechanism governing the helicase activity of Pif1. ..
- Sreevidya M, Gopalakrishnan S, Kudapa H, Varshney R. Exploring plant growth-promotion actinomycetes from vermicompost and rhizosphere soil for yield enhancement in chickpea. Braz J Microbiol. 2016;47:85-95 pubmed publisher..The actinomycetes were identified as Streptomyces but different species in the 16S rDNA analysis. It was concluded that the selected actinomycetes have good plant growth-promotion and biocontrol potentials on chickpea. ..
- Wang Y, Ma L, Mao Y, Jiang X, Xia Y, Yu K, et al. Comammox in drinking water systems. Water Res. 2017;116:332-341 pubmed publisher..The findings of MAGs and the occurrences of AOM in different drinking water systems provided a significant clue that comammox are widely distributed in drinking water systems. ..
- Kamanina Y, Klimanova E, Dergousova E, Petrushanko I, Lopina O. Identification of a Region of the Polypeptide Chain of Na,K-ATPase ?-Subunit Interacting with 67-kDa Melittin-Like Protein. Biochemistry (Mosc). 2016;81:249-54 pubmed publisher..It was shown earlier that this motif of H,K-ATPase from gastric mucosa binds to melittin. We suggest that namely this motif of P-type ATPases is able to interact with proteins containing melittin-like modules. ..
- Ibaba J, Laing M, Gubba A. Zucchini shoestring virus: a distinct potyvirus in the papaya ringspot virus cluster. Arch Virol. 2016;161:2321-3 pubmed publisher..ZSSV is the second cucurbit-infecting virus in the PRSV cluster present in RSA. ..
- Honda S, Wakita S, Sugahara Y, Kawakita M, Oyama F, Sakaguchi M. Characterization of two Listeria innocua chitinases of different sizes that were expressed in Escherichia coli. Appl Microbiol Biotechnol. 2016;100:8031-41 pubmed publisher..The structure-function relationships of these chitinases are discussed in reference to other bacterial chitinases. ..
- Fikru R, Matetovici I, RogÃ© S, Merga B, Goddeeris B, BÃ¼scher P, et al. Ribosomal DNA analysis of tsetse and non-tsetse transmitted Ethiopian Trypanosoma vivax strains in view of improved molecular diagnosis. Vet Parasitol. 2016;220:15-22 pubmed publisher..The high GC content of T. vivax DNA renders accurate diagnosis of all pathogenic animal trypanosomes with one single PCR problematic. ..
- Woo C, Bertozzi C. Isotope Targeted Glycoproteomics (IsoTaG) to Characterize Intact, Metabolically Labeled Glycopeptides from Complex Proteomes. Curr Protoc Chem Biol. 2016;8:59-82 pubmed publisher..The outlined procedure is well defined in cell culture and has been executed with over 15 cell lines. ..
- Yoshida S, Hiraga K, Takehana T, Taniguchi I, Yamaji H, Maeda Y, et al. A bacterium that degrades and assimilates poly(ethylene terephthalate). Science. 2016;351:1196-9 pubmed publisher..Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol. ..
- Bahr L, Castelli M, Barolo M, Ruiz Mostacero N, Tosello M, LÃ³pez S. Ascochyta blight: isolation, characterization, and development of a rapid method to detect inhibitors of the chickpea fungal pathogen Ascochyta rabiei. Fungal Biol. 2016;120:424-32 pubmed publisher..rabiei from natural sources, a bioautographic method was developed. From the screening method developed, we found that extracts from cultures of Aspergillus parasiticus are active against A. rabiei. ..
- Gurdziel K, Vogt K, Schneider G, Richards N, Gumucio D. Computational prediction and experimental validation of novel Hedgehog-responsive enhancers linked to genes of the Hedgehog pathway. BMC Dev Biol. 2016;16:4 pubmed publisher..Additionally, the library of enriched GLI binding motifs that we have identified may allow improved identification of functional GLI binding sites. ..
- Liu B, Huang Y, Aronstam R, Lee H. Identification of a Short Cell-Penetrating Peptide from Bovine Lactoferricin for Intracellular Delivery of DNA in Human A549 Cells. PLoS ONE. 2016;11:e0150439 pubmed publisher..The L5a and L5a/DNA complexes were not cytotoxic. This biomimetic LFcin L5a represents one of the shortest effective CPPs and could be a promising lead peptide with less immunogenic for DNA delivery in gene therapy. ..
- de Breuil S, Canizares J, Blanca J, Bejerman N, Trucco V, Giolitti F, et al. Analysis of the coding-complete genomic sequence of groundnut ringspot virus suggests a common ancestor with tomato chlorotic spot virus. Arch Virol. 2016;161:2311-6 pubmed publisher..The high level of sequence similarity between GRSV and TCSV (over 90 % identity) observed in the genes and proteins encoded in the M RNA support previous results indicating that these viruses probably have a common ancestor. ..
- Ali M, el Shesheny R, Kandeil A, Shehata M, Elsokary B, Gomaa M, et al. Cross-sectional surveillance of Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels and other mammals in Egypt, August 2015 to January 2016. Euro Surveill. 2017;22: pubmed publisher..The presence of neutralising antibodies in one sheep apparently in contact with seropositive camels calls for further studies on domestic animals in contact with camels. ..
- Yue Y, Meng Y, Ma H, Hou S, Cao G, Hong W, et al. A large family of Dscam genes with tandemly arrayed 5' cassettes in Chelicerata. Nat Commun. 2016;7:11252 pubmed publisher..Hence, our findings have important implications for understanding the functional similarities between Drosophila Dscam1 and vertebrate Pcdhs, and may provide further mechanistic insights into the regulation of isoform diversity. ..
- Estep J, Sternburg E, Sanchez G, Karginov F. Immunoblot screening of CRISPR/Cas9-mediated gene knockouts without selection. BMC Mol Biol. 2016;17:9 pubmed publisher..Clonal screening for CRISPR/Cas9-mediated editing events using dot immunoblot is a straightforward and efficient approach that facilitates rapid generation of genomic mutants to study gene function. ..
- Frączyk M, Woźniakowski G, Kowalczyk A, Niemczuk K, Pejsak Z. Development of cross-priming amplification for direct detection of the African Swine Fever Virus, in pig and wild boar blood and sera samples. Lett Appl Microbiol. 2016;62:386-91 pubmed publisher..It has been shown that CPA is a rapid, sensitive and specific isothermal method for the detection of ASFV DNA, in directly collected blood or sera from pigs and wild boars. ..
- Xiang Y, Li H, Xu X, Xu C, Chen C, Lin X, et al. [Mutation analysis and prenatal diagnosis for 12 families affected with hereditary hearing loss and enlarged vestibular aqueduct]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2017;34:336-341 pubmed publisher..Such mutations can be found in most families affected with hearing loss and enlarged vestibular aqueduct, which may facilitate genetic counseling and prenatal diagnosis for such families. ..
- Liang F, Kroon G, McAvoy C, Chi C, Wright P, Shan S. Conformational dynamics of a membrane protein chaperone enables spatially regulated substrate capture and release. Proc Natl Acad Sci U S A. 2016;113:E1615-24 pubmed publisher..Our work demonstrates how the intrinsic conformational dynamics of a chaperone enables spatially coordinated substrate capture and release, which may be general to other ATP-independent chaperone systems. ..
- Han H, Zhang G, Wu M, Wang G. Identification and characterization of the Populus trichocarpa CLE family. BMC Genomics. 2016;17:174 pubmed publisher..Transcriptional profiling provided further insights into possible functional divergence, evidenced by differential expression patterns of various PtCLE genes. ..
- Marthaler A, Schmid B, Tubsuwan A, Poulsen U, Engelbrecht A, Mau Holzmann U, et al. Generation of an isogenic, gene-corrected control cell line of the spinocerebellar ataxia type 2 patient-derived iPSC line H271. Stem Cell Res. 2016;16:180-3 pubmed publisher..This gene corrected cell line will provide the ideal control to model SCA2 by iPSC technology. ..
- Li J, Liu Y, Zhu H, Zhang K. Phylogenic analysis of adhesion related genes Mad1 revealed a positive selection for the evolution of trapping devices of nematode-trapping fungi. Sci Rep. 2016;6:22609 pubmed publisher..Our study provides new insights into the evolution of trapping devices of nematode-trapping fungi and also contributes to understanding the importance of adhesions during the evolution of nematode-trapping fungi. ..
- Suntravat M, Uzcategui N, Atphaisit C, Helmke T, Lucena S, SÃ¡nchez E, et al. Gene expression profiling of the venom gland from the Venezuelan mapanare (Bothrops colombiensis) using expressed sequence tags (ESTs). BMC Mol Biol. 2016;17:7 pubmed publisher..This study represents the analysis of transcript expressions and provides a physical resource of unique genes for further study of gene function and the development of novel molecules for medical applications. ..
- Colabroy K. Tearing down to build up: Metalloenzymes in the biosynthesis lincomycin, hormaomycin and the pyrrolo [1,4]benzodiazepines. Biochim Biophys Acta. 2016;1864:724-737 pubmed publisher..This mini-pathway demonstrates the use of metal-dependent chemistry typically associated with natural product degradation in order to build a compact, functionalized building block for larger, bioactive molecules. ..
- Zhu Z, Meng M, Sun H, Li Y, Yu N, Zhang Y. Structural analysis and immunostimulatory activity of glycopeptides from Paecilomyces sinensis. Food Funct. 2016;7:1593-600 pubmed publisher..Cell proliferation assay and morphological observations indicated that in a certain range of concentrations and time, CPS-II can significantly improve the proliferation activity of RAW264.7 cells. ..
- Dimitrov I, Doytchinova I. Associations between Milk and Egg Allergens and the HLA-DRB1/DQ Polymorphism: A Bioinformatics Approach. Int Arch Allergy Immunol. 2016;169:33-9 pubmed publisher..The alleles DRB1*01:01, DQ4, DQ7 and DQ8 are considered as susceptible to egg allergy and DRB1*03:01, DRB1*04:04 and DRB1*12:01 as protective. Protective DQs against egg allergy were not revealed in this study. ..
- Huang K, Zhang J, O Neill K, Gurumurthy C, Quadros R, Tu Y, et al. Cleavage by Caspase 8 and Mitochondrial Membrane Association Activate the BH3-only Protein Bid during TRAIL-induced Apoptosis. J Biol Chem. 2016;291:11843-51 pubmed publisher..Together, these results for the first time establish that cleavage by caspase 8 and the subsequent association with the outer mitochondrial membrane are two critical events that activate Bid during death receptor-mediated apoptosis. ..
- Liu Y, Priscu J, Xiong J, Conrad R, Vick Majors T, Chu H, et al. Salinity drives archaeal distribution patterns in high altitude lake sediments on the Tibetan Plateau. FEMS Microbiol Ecol. 2016;92: pubmed publisher..Our results show that salinity is a key factor controlling archaeal community diversity and composition in lake sediments on a spatial scale that spans nearly 2000 km on the Tibetan Plateau. ..
- Viereck J, Kumarswamy R, Foinquinos A, Xiao K, Avramopoulos P, Kunz M, et al. Long noncoding RNA Chast promotes cardiac remodeling. Sci Transl Med. 2016;8:326ra22 pubmed publisher..These results indicate that Chast can be a potential target to prevent cardiac remodeling and highlight a general role of lncRNAs in heart diseases. ..
- Lo N, Tong K, Rose H, Ho S, Beninati T, Low D, et al. Multiple evolutionary origins of Australian soil-burrowing cockroaches driven by climate change in the Neogene. Proc Biol Sci. 2016;283:20152869 pubmed publisher..These transitions appear to have been driven by periods of aridification during the Miocene and Pliocene across eastern Australia. Our results provide an illuminating example of climate-driven parallel evolution among species. ..
- Friese A, Faesen A, Huis In t Veld P, Fischböck J, Prumbaum D, Petrovic A, et al. Molecular requirements for the inter-subunit interaction and kinetochore recruitment of SKAP and Astrin. Nat Commun. 2016;7:11407 pubmed publisher..Collectively, our studies represent the first thorough mechanistic analysis of SKAP and Astrin, and significantly advance our functional understanding of these important mitotic proteins. ..
- Zhai L, Feng L, Xia L, Yin H, Xiang S. Crystal structure of glycogen debranching enzyme and insights into its catalysis and disease-causing mutations. Nat Commun. 2016;7:11229 pubmed publisher..Combining the understanding of the GDE catalysis and functional characterizations of its disease-causing mutations provides molecular insights into GSDIII. ..
- Lei M, Li Z, Wang J, Fu Y, Ao M, Xu L. AfAP2-1, An Age-Dependent Gene of Aechmea fasciata, Responds to Exogenous Ethylene Treatment. Int J Mol Sci. 2016;17:303 pubmed publisher..Overexpression of AfAP2-1 in Arabidopsis thaliana results in an extremely delayed flowering phenotype. These results suggested that AfAP2-1 responds to ethylene and is a putative age-dependent flowering regulator in A. fasciata. ..
- Gustafsson T, Osman H, Werngren J, Hoffner S, Engman L, Holmgren A. Ebselen and analogs as inhibitors of Bacillus anthracis thioredoxin reductase and bactericidal antibacterials targeting Bacillus species, Staphylococcus aureus and Mycobacterium tuberculosis. Biochim Biophys Acta. 2016;1860:1265-71 pubmed publisher..We have characterized the thioredoxin system from B. anthracis as a novel drug target and ebselen and analogs thereof as a potential new class of antibiotics targeting several important human pathogens. ..
- Parra G, Sosnovtsev S, Abente E, Sandoval Jaime C, Bok K, Dolan M, et al. Mapping and modeling of a strain-specific epitope in the Norwalk virus capsid inner shell. Virology. 2016;492:232-41 pubmed publisher..The S domain, like the P domain, contains strain-specific epitopes that contribute to the antigenic diversity among the noroviruses. ..
- Barbera M, Martinez Torres D. Identification of the prothoracicotropic hormone (Ptth) coding gene and localization of its site of expression in the pea aphid Acyrthosiphon pisum. Insect Mol Biol. 2017;26:654-664 pubmed publisher..Here we report on the first identification of the aphid PTTH coding gene and the neuroanatomical localization of its expression in the aphid brain. ..
- Yan B, Sun W, Yan L, Zhang L, Zheng Y, Zeng Y, et al. Structural and functional characterisation of FOXO/Acan-DAF-16 from the parasitic nematode Angiostrongylus cantonensis. Acta Trop. 2016;164:125-136 pubmed publisher..These findings provide further evidence of the functional conservation of DAF-16s between parasitic nematodes and the free-living nematode C. elegans. ..
- Bird J, Zhang Y, Tian Y, Panova N, Barvik I, Greene L, et al. The mechanism of RNA 5? capping with NAD+, NADH and desphospho-CoA. Nature. 2016;535:444-7 pubmed..Our results define the mechanism and structural basis of NCIN capping, and suggest that NCIN-mediated ‘ab initio capping’ may occur in all organisms. ..
- Gharat S, Shaw B. Computational prediction and experimental validation of a novel miRNA in Suaeda maritima, a halophyte. Genet Mol Res. 2016;15: pubmed publisher..Thus, sma-miR1867 could be an essential component of salt resistance in halophytes. ..
- Leke W, Khatabi B, Mignouna D, Brown J, Fondong V. Complete genome sequence of a new bipartite begomovirus infecting cotton in the Republic of Benin in West Africa. Arch Virol. 2016;161:2329-33 pubmed publisher..This previously undescribed begomovirus is herein named "cotton yellow mosaic virus" (CYMV). ..
- de Souza W, Acrani G, Romeiro M, Júnior O, Tolardo A, de Andrade A, et al. Complete genome sequence of Piry vesiculovirus. Arch Virol. 2016;161:2325-8 pubmed publisher..Phylogenetic analysis confirmed that PIRYV is most closely related to Perinet virus and clustered in the same clade as Chandipura and Isfahan vesiculoviruses. ..
- Chen W, Weng Y, He W, Zhu Y, Zhang Y, Huang M, et al. [Molecular epidemiology of hand-foot-mouth disease associated pathogen Coxsackievirus A10 identified in Fujian province, 2011-2014]. Zhonghua Liu Xing Bing Xue Za Zhi. 2016;37:563-7 pubmed publisher..Cox A10 remained one of the predominant serotypes of HFMD in Fujian province. Cox A10 isolates identified in Fujian province were co-circulating and co-evolving with other domestic strains. ..
- Boyer S, Biswas D, Kumar Soshee A, Scaramozzino N, Nizak C, Rivoire O. Hierarchy and extremes in selections from pools of randomized proteins. Proc Natl Acad Sci U S A. 2016;113:3482-7 pubmed publisher..e., the potential for future evolution). ..
- Miles M, Shekhar T, Hall N, Hawkins C. TRAIL causes deletions at the HPRT and TK1 loci of clonogenically competent cells. Mutat Res. 2016;787:15-31 pubmed publisher..These data suggest that TRAIL too may provoke oncogenic damage to the genomes of surviving cells. ..
- Yin Z, Dong X, Dong D, Ma Y. Association of MYF5 and KLF15 gene polymorphisms with carcass traits in domestic pigeons (Columba livia). Br Poult Sci. 2016;57:612-618 pubmed..The BB genotype of the C5084T and T5127A SNPs could be a potential candidate genetic marker for marker-assisted selection in pigeon. ..
- Wei Y, Yang H, Luan Y, Long R, Wu Y, Wang Z. Isolation, identification and fibrolytic characteristics of rumen fungi grown with indigenous methanogen from yaks (Bos grunniens) grazing on the Qinghai-Tibetan Plateau. J Appl Microbiol. 2016;120:571-87 pubmed publisher..The N. frontalis with M. ruminantium co-cultures from yaks grazing on the Qinghai-Tibetan Plateau present great potential in lignocellulose biodegradation industry. ..
- Echeverry D, Deason N, Davidson J, Makuru V, Xiao H, Niedbalski J, et al. Human malaria diagnosis using a single-step direct-PCR based on the Plasmodium cytochrome oxidase III gene. Malar J. 2016;15:128 pubmed publisher..This PCR does not require DNA isolation, is sensitive, quick, produces confident/clear results, identifies all the Plasmodium species infecting humans, and is cost-effective. ..