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    Recurrent emergence of structural variants of LTR retrotransposon CsRn1 evolving novel expression strategy and their selective expansion in a carcinogenic liver fluke, Clonorchis sinensis.
    Mol Biochem Parasitol 2017 Mar 16. Epub 2017 Mar 16.
    Department of Microbiology, College of Medicine, Gachon University, 191 Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea. Electronic address:
    Autonomous retrotransposons, in which replication and transcription are coupled, encode the essential gag and pol genes as a fusion or separate overlapping form(s) that are expressed in single transcripts regulated by a common upstream promoter. The element-specific expression strategies have driven development of relevant translational recoding mechanisms including ribosomal frameshifting to satisfy the protein stoichiometry critical for the assembly of infectious virus-like particles. Retrotransposons with different recoding strategies exhibit a mosaic distribution pattern across the diverse families of reverse transcribing elements, even though their respective distributions are substantially skewed towards certain family groups. Read More

    Molecular analysis of norovirus in specimens from children enrolled in a 1982-1986 study in Belém, Brazil: A community-based longitudinal study.
    J Med Virol 2017 Mar 20. Epub 2017 Mar 20.
    Virology Section, Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health. Ananindeua, Pará, 67030-000, Brazil.
    Fecal specimens were collected during a longitudinal, community-based study in the city of Belém, North Brazil, that was conducted over 3 years (October 1982 to March 1986), in which 20 children were included from birth to 3 years of age. A total of 229 fecal samples were screened by real time RT-PCR targeting the junction region (ORF 1/2) of the norovirus (NoV) genome. NoV-positive samples were subjected to PCR and sequencing of the viral polymerase (ORF1) and viral protein 1 (VP1) genes (ORF2). Read More

    Identification of an archaeal maltooligosyltrehalose trehalohydrolase encoded by an interrupted gene.
    Extremophiles 2017 Mar 21. Epub 2017 Mar 21.
    Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China.
    Complete genome analysis of the thermoacidophilic Archaeon Sulfolobus tokodaii strain 7 revealed two open reading frames (ORF), namely, ST0926 and ST0927. These ORFs are interrupted by two putative insertions and encode for the N- and C-terminal fragments, respectively, of a putative Sulfolobus sp. maltooligosyltrehalose trehalohydrolase (StMTHase). Read More

    Tumor necrosis factor receptor-associated factor 6 (TRAF6) participates in peroxinectin gene expression in Fenneropenaeus penicillatus.
    Fish Shellfish Immunol 2017 Mar 14;64:193-201. Epub 2017 Mar 14.
    Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou University, Qinzhou, China. Electronic address:
    Tumor necrosis factor receptor-associated factor 6 (TRAF6) is an important cytoplasm signal adaptor that mediates signals activated by tumor necrosis factor receptor (TNFR) superfamily and the Interleukin-1 receptor/Toll-like receptor (IL-1/TLR) superfamily. In the study, the full-length cDNA of a TRAF6 homolog (FpTRAF6) was identified from Fenneropenaeus penicillatus. The full-length cDNA of FpTRAF6 is 2033 bp long, with an open reading frame (ORF) encoding a putative protein of 594 amino acids, including a RING type Zinc finger, two TRAF-type Zinc fingers, and a conserved C-terminal meprin and TRAF homology (MATH) domain. Read More

    Transposon insertion resulted in the silencing of Wx-B1n in Chinese wheat landraces.
    Theor Appl Genet 2017 Mar 17. Epub 2017 Mar 17.
    Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
    Key Message: A novel Wx-B1 allele was characterized; a transposon insertion resulted in the loss of its function, which is different from the previously reported gene silencing mechanisms at the Wx-B1 locus. The waxy protein composition of 53 Chinese wheat landraces was analyzed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional gel electrophoresis; of these, 10 did not show the expression of Wx-A1 (four accession) or Wx-B1 (six accessions) protein. The results of molecular marker detection revealed that the Wx-B1 allele (Wx-B1n) showed normal expression, inconsistent with the findings of SDS-PAGE for the Xiaobaipi accession. Read More

    Cloning and characterization of squalene synthase and cycloartenol synthase from Siraitia grosvenorii.
    Acta Pharm Sin B 2017 Mar 23;7(2):215-222. Epub 2016 Aug 23.
    The Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100194, China.
    Mogrosides and steroid saponins are tetracyclic triterpenoids found in Siraitia grosvenorii. Squalene synthase (SQS) and cycloartenol synthase (CAS) are key enzymes in triterpenoid and steroid biosynthesis. In this study, full-length cDNAs of SgSQS and SgCAS were cloned by a rapid amplification of cDNA-ends with polymerase chain reaction (RACE-PCR) approach. Read More

    Molecular cloning and functional identification of a cDNA encoding 4-hydroxy-3-methylbut-2-enyl diphosphate reductase from Tripterygium wilfordii.
    Acta Pharm Sin B 2017 Mar 22;7(2):208-214. Epub 2017 Jan 22.
    National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China.
    The 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR) is the last step key enzyme of the methylerythritol phosphate (MEP) pathway, synthesizing isopentenyl diphosphate and its allyl isomer dimethylallyl diphosphate, which is important for regulation of isoprenoid biosynthesis. Here the full-length cDNA of HDR, designated TwHDR (GenBank Accession No. KJ933412. Read More

    Molecular Characterization of Hemorrhagic Enteritis Viruses (HEV) Detected in HEV-Vaccinated Commercial Turkey Flocks in Germany.
    Avian Dis 2017 Mar;61(1):96-101
    A Clinic for Poultry, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany.
    Despite the application of live hemorrhagic enteritis virus (HEV) vaccines, HEV field outbreaks are suspected to still occur in turkey flocks in Germany. Increasing secondary bacterial infections in HEV-vaccinated flocks suggest that vaccines may be losing efficacy or, possibly, that vaccine strains are causing disease. Thus, the goal of the current study was to investigate the diversity of HEV isolates from fattening turkey flocks between 2008 and 2012 by characterizing the open reading frame (ORF)1 gene at its 5' and 3' ends. Read More

    Characterization of a new badnavirus from Wisteria sinensis.
    Arch Virol 2017 Mar 15. Epub 2017 Mar 15.
    Chinese Society of Inspection and Quarantine, Beijing, 101312, China.
    The complete genome sequence of a previously undescribed badnavirus isolated from a wisteria plant exhibiting mosaic and crinkle symptoms in Beijing, China, was determined. The circular double-stranded DNA genome of this virus was 7362 bp in size with four open reading frames (ORFs 1 to 4) on the plus strand. Sequence analysis showed that this virus shared the highest (69%) nucleotide (nt) sequence identity with pagoda yellow mosaic associated virus (PYMAV). Read More

    Characterization of bafilomycin biosynthesis in Kitasatospora setae KM-6054 and comparative analysis of gene clusters in Actinomycetales microorganisms.
    J Antibiot (Tokyo) 2017 Mar 15. Epub 2017 Mar 15.
    Kitasato Institute for Life Sciences, Kitasato University, Kanagawa, Japan.
    Bafilomycins A1, C1 and B1 (setamycin) produced by Kitasatospora setae KM-6054 belong to the plecomacrolide family, which exhibit antibacterial, antifungal, antineoplastic and immunosuppressive activities. An analysis of gene clusters from K. setae KM-6054 governing the biosynthesis of bafilomycins revealed that it contains five large open reading frames (ORFs) encoding the multifunctional polypeptides of bafilomycin polyketide synthases (PKSs). Read More

    Characterization and functional analysis of a novel C-type lectin from the swimming crab Portunus trituberculatus.
    Fish Shellfish Immunol 2017 Mar 10;64:185-192. Epub 2017 Mar 10.
    Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo 315211, China.
    C-type lectins (CTLs) are a family of calcium-dependent carbohydrate-binding proteins. In the present study, a novel C-type lectin (designated as PtCTL1) was identified and characterized from Portunus trituberculatus. The full-length cDNA of PtCTL1 was of 702 bp, containing a 5' untranslated region (UTR) of 91 bp, a 3' UTR of 110 bp with a poly (A) tail, and an open reading frame (ORF) of 501 bp encoding a polypeptide of 166 amino acids with a putative signaling peptide of 21 amino acids. Read More

    Identification and Characterization of two putative microRNAs encoded by Bombyx mori cypovirus.
    Virus Res 2017 Mar 7. Epub 2017 Mar 7.
    School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China. Electronic address:
    Viral microRNAs (miRNAs) have been demonstrated to play important roles in virus-host interactions. Some RNA virus-encoded miRNAs have been reported to promote viral replication and may be used as potential drug targets. Bombyx mori cypovirus (BmCPV), an important pathogen of silkworm, is a double-stranded RNA virus frequently causing serious damages in sericulture. Read More

    Biochemical properties and vaccine effect of recombinant TPx-3 from Schistosoma japonicum.
    Parasitol Res 2017 Apr 11;116(4):1361-1372. Epub 2017 Mar 11.
    Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, 200241, People's Republic of China.
    Thioredoxin peroxidases (TPxs) play an important role in maintaining redox homeostasis and in protecting organisms from the accumulation of toxic reactive oxygen species (ROS). In this study, we isolated the thioredoxin peroxidase-3 gene of Schistosoma japonicum, SjTPx-3. The open reading frame (ORF) of SjTPx-3 was 663 bp encoding 220 amino acids with a molecular weight of 24. Read More

    Identification of a novel species of papillomavirus in giraffe lesions using nanopore sequencing.
    Vet Microbiol 2017 Mar 30;201:26-31. Epub 2016 Dec 30.
    KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Herestraat 49/Box 1040, BE3000 Leuven, Belgium. Electronic address:
    Papillomaviridae form a large family of viruses that are known to infect a variety of vertebrates, including mammals, reptiles, birds and fish. Infections usually give rise to minor skin lesions but can in some cases lead to the development of malignant neoplasia. In this study, we identified a novel species of papillomavirus (PV), isolated from warts of four giraffes (Giraffa camelopardalis). Read More

    Possible chromosomal and germline integration of human herpesvirus 7.
    J Gen Virol 2017 Feb;98(2):266-274
    4​HHV-6 Foundation, Santa Barbara, CA 93101, USA.
    Human herpesvirus 7 (HHV-7) is a betaherpesvirus, and is phylogenetically related to both HHV-6A and HHV-6B. The presence of telomeric repeat sequences at both ends of its genome should make it equally likely to integrate into the human telomere as HHV-6. However, numerous studies have failed to detect germline integration of HHV-7, suggesting an important difference between the HHV-6A/-6B and HHV-7 genomes. Read More

    Designing of a Recombinant Agip Bacmid Construct with Infectious Properties Against Black Cutworm Agrotis ipsilon Larvae.
    Appl Biochem Biotechnol 2017 Mar 10. Epub 2017 Mar 10.
    Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt.
    In this study, Agrotis ipsilon nucleopolyhedrovirus bacmid has been constructed as an infectious bacmid in an attempt to allow genome recombination and generation of virus mutants. Since the FseI, a unique restriction site, is located in a viral coding region (ORF_119), PCR was performed to partially amplify the ORF_119 fragment containing the FseI site to facilitate the bacmid construction in a proper way without interrupting the ORF expression. Construction with repeated fragments at the end of the cloned viral was carried out in an attempt to facilitate circulation during infection in insect cells. Read More

    Molecular identification and functional analysis of CTRP9 in Epinephelus coioides.
    J Mol Endocrinol 2017 Mar 10. Epub 2017 Mar 10.
    W Li, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
    CTRP9 is a member of the C1q/TNF-related protein (CTRP) superfamily and has been studied in mammals, while the comparative studies of CTRP9 in non-mammalian species are still absent. In this study, CTRP9 was isolated and characterized from the orange-spotted grouper (Epinephelus coioides). The full length cDNA of CTRP9 was 1378 bp in size with ORF (open reading frame) of 1020 bp which encods a 339 amino acids preprohormone. Read More

    Identification of a small pacifastin protease inhibitor from Nasonia vitripennis venom that inhibits humoral immunity of host (Musca domestica).
    Toxicon 2017 Mar 7. Epub 2017 Mar 7.
    College of Life Sciences, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, PR China. Electronic address:
    Nasonia vitripennis is an important natural enemy of many flies. Pacifastin protease inhibitors (PPIs) play an important role in development and innate immunity of insects. In this study, cDNA sequences of a small pacifastin protease inhibitor in N. Read More

    Identification and characterization of a novel conserved 46 kD maltoporin of Aeromonas hydrophila as a versatile vaccine candidate in European eel (Anguilla anguilla).
    Fish Shellfish Immunol 2017 Mar 6;64:93-103. Epub 2017 Mar 6.
    College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
    European eel (Anguilla anguilla) is a crucial economic fish that has been plagued by Aeromonas hydrophila infections for many years. Vaccines that are cross-protective against multiple serotypes could provide an effective control against A. hydrophila-mediated diseases. Read More

    Constitutively-stressed yeast strains are high-yielding for recombinant Fps1: implications for the translational regulation of an aquaporin.
    Microb Cell Fact 2017 Mar 9;16(1):41. Epub 2017 Mar 9.
    School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
    Background: We previously selected four strains of Saccharomyces cerevisiae for their ability to produce the aquaporin Fps1 in sufficient yield for further study. Yields from the yeast strains spt3Δ, srb5Δ, gcn5Δ and yTHCBMS1 (supplemented with 0.5 μg/mL doxycycline) that had been transformed with an expression plasmid containing 249 base pairs of 5' untranslated region (UTR) in addition to the primary FPS1 open reading frame (ORF) were 10-80 times higher than yields from wild-type cells expressing the same plasmid. Read More

    Variation in the level of detail in pediatric voiding cystourethrogram reports.
    J Pediatr Urol 2016 Oct 8. Epub 2016 Oct 8.
    Department of Urology, Boston Children's Hospital, Boston, MA, USA.
    Introduction: Voiding cystourethrogram (VCUG) provides a wealth of data on urinary tract function and anatomy, but few standards exist for reporting VCUG findings.

    Objective: We aimed to assess variability in VCUG reports and to test our hypothesis that VCUG reports from pediatric facilities and pediatric radiologists are more complete than those performed at other facilities or by non-pediatric radiologists.

    Study Design: We analyzed original VCUG reports from children enrolled in the Randomized Intervention for Children with Vesicoureteral Reflux (RIVUR) trial. Read More

    Cloning and functional analysis of two sterol-C24-methyltransferase 1 (SMT1) genes from Paris polyphylla.
    J Asian Nat Prod Res 2017 Feb 23:1-10. Epub 2017 Feb 23.
    b Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences , Beijing 100700 , China.
    The biosynthetic pathways of phytosterols and steroidal saponins are located in two adjacent branches which share cycloartenol as substrate. The rate-limiting enzyme S-adenosyl-L-methionine-sterol-C24-methyltransferase 1 (SMT1) facilitates the metabolic flux toward phytosterols. It catalyzes the methylation of the cycloartenol in the side chain of the C24-alkyl group, to generate 24(28)-methylene cycloartenol. Read More

    A Family 13 thioesterase isolated from an activated sludge metagenome: Insights into aromatic compounds metabolism.
    Proteins 2017 Mar 9. Epub 2017 Mar 9.
    Centro de Investigación en Biotecnología, UAEM, Ave. Universidad 1001. Colonia Chamilpa, CP 62209, Cuernavaca, Morelos, Mexico.
    Activated sludge is produced during the treatment of sewage and industrial wastewaters. Its diverse chemical composition allows growth of a large collection of microbial phylotypes with very different physiologic and metabolic profiles. Thus, activated sludge is considered as an excellent environment to discover novel enzymes through functional metagenomics, especially activities related with degradation of environmental pollutants. Read More

    Dietary Risk Assessment of v-ATPase A dsRNAs on Monarch Butterfly Larvae.
    Front Plant Sci 2017 22;8:242. Epub 2017 Feb 22.
    Department of Entomology, University of Kentucky Lexington, KY, USA.
    By suppressing the expression of genes with essential biological functions, in planta RNAi can negatively affect the development and survival of target pests. As a part of a concerted effort to assess the risks of RNAi transgenic crops on non-target organisms, we developed an in vivo toxicity assay to examine the impacts of ingested dsRNAs incurred to the monarch butterfly, Danaus plexippus (L.), an iconic eco-indicator in North America. Read More

    Suppressor analysis of eepR mutant defects reveals coordinate regulation of secondary metabolites and serralysin biosynthesis by EepR and HexS.
    Microbiology 2017 Feb;163(2):280-288
    2​Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
    The EepR transcription factor positively regulates secondary metabolites and tissue-damaging metalloproteases. To gain insight into mechanisms by which EepR regulates pigment and co-regulated factors, genetic suppressor analysis was performed. Suppressor mutations that restored pigment to the non-pigmented ∆eepR mutant mapped to the hexS ORF. Read More

    YLL056C from Saccharomyces cerevisiae encodes a novel protein with aldehyde reductase activity.
    Appl Microbiol Biotechnol 2017 Mar 6. Epub 2017 Mar 6.
    Institute of Natural Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Sichuan, 611130, People's Republic of China.
    The short-chain dehydrogenase/reductase (SDR) family, the largest family in dehydrogenase/reductase superfamily, is divided into "classical," "extended," "intermediate," "divergent," "complex," and "atypical" groups. Recently, several open reading frames (ORFs) were characterized as intermediate SDR aldehyde reductase genes in Saccharomyces cerevisiae. However, no functional protein in the atypical group has been characterized in S. Read More

    Ctenopharyngodon idella IRF2 and ATF4 down-regulate the transcriptional level of PRKRA.
    Fish Shellfish Immunol 2017 Mar 2;64:155-164. Epub 2017 Mar 2.
    College of Life Science, Key Lab of Aquatic Resources and Utilization of Jiangxi Province, Nanchang University, Nanchang 330031, China. Electronic address:
    PRKRA (interferon-inducible double-stranded RNA-dependent protein kinase activator A) is a protective protein which regulates the adaptation of cells to ER stress and virus-stimulated signaling pathways by activating PKR. In the present study, a grass carp (Ctenopharyngodon idella) PRKRA full-length cDNA (named CiPRKRA, KT891991) was cloned and identified. The full-length cDNA is comprised of a 5' UTR (36 bp), a 3' UTR (350 bp) and the longest ORF (882 bp) encoding a polypeptide of 293 amino acids. Read More

    A CGMMV genome-replicon vector with partial sequences of coat protein gene efficiently expresses GFP in Nicotiana benthamiana.
    Virus Res 2017 Mar 2. Epub 2017 Mar 2.
    Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India. Electronic address:
    A highly infectious clone of Cucumber green mottle mosaic virus (CGMMV), a cucurbit-infecting tobamovirus was utilized for designing of gene expression vectors. Two versions of vector were examined for their efficacy in expressing the green fluorescent protein (GFP) in Nicotiana benthamiana. When the GFP gene was inserted at the stop codon of coat protein (CP) gene of the CGMMV genome without any read-through codon, systemic expression of GFP, as well as virion formation and systemic symptoms expression were obtained in N. Read More

    Molecular characterization and expression analysis of toll-like receptors 5 and 22 from natural triploid Carassius auratus.
    Fish Shellfish Immunol 2017 Mar 2;64:1-13. Epub 2017 Mar 2.
    College of Fisheries, Henan Normal University, Xinxiang 453007, PR China.
    Innate immunity, as the most primitive and universal host defense in fish, constitutes an efficient first line of defense to combat invading microbes. Toll-like receptors (TLRs) play essential roles in the innate immunity, and TLR5 and TLR22 are two important TLRs that can recognize flagellin and double stranded RNA (dsRNA), respectively. In this study, we identified and characterized two TLRs genes of Qihe crucian carp (Carassius auratus) (designated as CaTLR5 and CaTLR22). Read More

    Isolation and functional characterization of a methyl jasmonate-responsive 3-carene synthase from Lavandula x intermedia.
    Plant Mol Biol 2017 Apr 3;93(6):641-657. Epub 2017 Mar 3.
    Department of Biology, University of British Columbia, 1177 Research Rd, Kelowna, BC. V1V 1V7, Canada.
    Key Message: A methyl jasmonate responsive 3-carene synthase (Li3CARS) gene was isolated from Lavandula x intermedia and functionally characterized in vitro. Lavenders produce essential oils consisting mainly of monoterpenes, including the potent antimicrobial and insecticidal monoterpene 3-carene. In this study we isolated and functionally characterized a leaf-specific, methyl jasmonate (MeJA)-responsive monoterpene synthase (Li3CARS) from Lavandula x intermedia. Read More

    Molecular characterization of Pacific white shrimp (Litopenaeus vannamei) sodium bicarbonate cotransporter (NBC) and its role in response to pH stress.
    Fish Shellfish Immunol 2017 Feb 28;64:226-233. Epub 2017 Feb 28.
    CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China. Electronic address:
    The sodium bicarbonate cotransporter (NBC) is an integral membrane ion transporter that can transport HCO3(-) (or a related species, such as CO3(2-)) across the plasma membrane. Previous researches revealed that NBC might play an important role in the regulation of intracellular pH in vertebrates. In the present study, an NBC cDNA was identified from Pacific white shrimp (Litopenaeus vannamei) and designated as Lv-NBC. Read More

    Seroprevalence of Kaposi's sarcoma-associated herpesvirus among HIV-infected Uygurs in Xinjiang, China.
    J Med Virol 2017 Mar 2. Epub 2017 Mar 2.
    Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.
    Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma (KS), which primarily affects human immunodeficiency virus (HIV)-infected adults with advanced immunodeficiency. Xinjiang province in China is an endemic area for Kaposi's sarcoma (KS), however, currently, only limited prevalence data for KSHV infection in HIV-infected individuals living in this endemic area is available. A cross-sectional study of 86 HIV positive participants was conducted in Xinjiang, China from 2014 through 2015. Read More

    Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP.
    BMC Genomics 2017 Feb 28;18(1):216. Epub 2017 Feb 28.
    Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising, Germany.
    Background: While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribosomal footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. Read More

    A new genome-mining tool redefines the lasso peptide biosynthetic landscape.
    Nat Chem Biol 2017 Feb 28. Epub 2017 Feb 28.
    Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
    Ribosomally synthesized and post-translationally modified peptide (RiPP) natural products are attractive for genome-driven discovery and re-engineering, but limitations in bioinformatic methods and exponentially increasing genomic data make large-scale mining of RiPP data difficult. We report RODEO (Rapid ORF Description and Evaluation Online), which combines hidden-Markov-model-based analysis, heuristic scoring, and machine learning to identify biosynthetic gene clusters and predict RiPP precursor peptides. We initially focused on lasso peptides, which display intriguing physicochemical properties and bioactivities, but their hypervariability renders them challenging prospects for automated mining. Read More

    Potential contributions of heat shock proteins and related genes in sexual differentiation in yellow catfish (Pelteobagrus fulvidraco).
    Fish Physiol Biochem 2017 Feb 28. Epub 2017 Feb 28.
    College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China.
    Sex determination and differentiation in ectotherms are very complicated affairs and usually affected by both genetic and environmental factors. Because of their temperature-sensitive expression, heat shock proteins (HSPs) are good candidates for temperature-dependent sex determination (TSD). Similar to most thermosensitive fish species, the male to female ratio increases with temperature in yellow catfish (Pelteobagrus fulvidraco). Read More

    A new putative alphapartitivirus recovered from the powdery mildew fungus Erysiphe palczewskii.
    Virus Genes 2017 Feb 27. Epub 2017 Feb 27.
    State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crop, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
    Two double-stranded RNAs (dsRNA) likely representing the genome of a novel alphapartitivirus which we provisionally named Erysiphe palczewskii alphapartitivirus 1 (EpV1) were recovered from the powdery mildew fungus E. palczewskii infecting Sophora japonica in Jingzhou, Hubei province of China. The two dsRNAs, 1955 (dsRNA1) and 1917 (dsRNA2) bp in size, respectively, each contains a single open reading frame (ORF) encoding a 585- and 528-aa protein, respectively. Read More

    MSMEG_5684 down-regulation in Mycobacterium smegmatis affects its permeability, survival under stress and persistence.
    Tuberculosis (Edinb) 2017 Mar 19;103:61-70. Epub 2017 Jan 19.
    Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India. Electronic address:
    The Mycobacterium tuberculosis (Mtb) genome sequence and annotation details have been available for a long time; however physiological relevance of many ORFs remains poorly described. Mtb is a pathogenic strain; hence, surrogate strains such as Mycobacterium bovis BCG and Mycobacterium smegmatis (Msmeg) have also been studied to gain an understanding of mycobacterial physiology and metabolism. The Mycobacterium smegmatis mc(2) 155 ORF MSMEG_5684 is annotated as a part of serine biosynthetic pathway, however, its physiological significance remains to be established experimentally. Read More

    Molecular cloning and expression analysis of Megalobrama amblycephala transferrin gene and effects of exposure to iron and infection with Aeromonas hydrophila.
    Fish Physiol Biochem 2017 Feb 24. Epub 2017 Feb 24.
    Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
    Transferrin (Tf) plays an important function in iron homeostasis and metabolism of organisms. In this study, we identified and characterized the Tf gene in Megalobrama amblycephala and evaluated its expression in basal conditions as well as after iron overload and experimental infection with Aeromonas hydrophila. Furthermore, we studied the iron binding properties of recombinant Tf. Read More

    Molecular cloning of the MARCH family in grass carp (Ctenopharyngodon idellus) and their response to grass carp reovirus challenge.
    Fish Shellfish Immunol 2017 Apr 20;63:480-490. Epub 2017 Feb 20.
    State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. Electronic address:
    Grass carp (Ctenopharyngodon idellus) is an economical aquaculture species in China, and the Grass Carp Reovirus (GCRV) that causes hemorrhagic disease seriously affects the grass carp cultivation industry. Substantial evidence indicates that there is an association between the membrane-associated RING-CH family of E3 ligase (MARCH) family and immune defense in mammals, while functional studies on non-mammalian MARCH proteins are limited. In order to know the characteristics of the MARCH genes in C. Read More

    A thioredoxin from antarctic microcrustacean (Euphausia superba): Cloning and functional characterization.
    Fish Shellfish Immunol 2017 Apr 20;63:376-383. Epub 2017 Feb 20.
    Qingdao University of Science and Technology, Qingdao 266042, China.
    Thioredoxins, with a dithiol/disulfide active site (CGPC) are major highly conserved and ubiquitous proteins that are involved in protecting organisms against various oxidative stresses. In the present study, a novel thioredoxin gene was identified in antarctic microcrustacean, Euphausia superba (designated as EsTrx1). The full-length cDNA sequences of EsTrx1 was of 621 bp, containing a 5' untranslated region (UTR) of 45 bp, a 3' UTR of 276 bp and an open reading frame (ORF) of 303 bp encoding a putative protein of 100 amino acids. Read More

    Bioinformatic Analysis Reveals Archaeal tRNA(Tyr) and tRNA(Trp) Identities in Bacteria.
    Life (Basel) 2017 Feb 21;7(1). Epub 2017 Feb 21.
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
    The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNA(Tyr) and tRNA(Trp) genes reveal bacterial or archaeal origins. Read More

    Hepatitis E Virus Detection and Quantification by an RT-qPCR Assay calibrated to the World Health Organization Standard for HEV RNA.
    J Clin Microbiol 2017 Feb 22. Epub 2017 Feb 22.
    Dept. of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, U.S.A.
    Hepatitis E virus (HEV) has emerged as a cause of chronic hepatitis among immunocompromised patients. Molecular assays have become important tools for the diagnosis and management of these chronically-infected patients. A reverse transcription, real-time PCR (RT-qPCR) assay utilizing Pleiades probe chemistry and an RNA internal control for simultaneous detection and quantification of HEV RNA in human serum was developed based on adaptation of a previously described and broadly reactive primer set targeting the overlapping open reading frame (ORF) 2/3 nucleotide sequence of HEV. Read More

    H2A and Ca-L-hipposin gene: Characteristic analysis and expression responses to Aeromonas hydrophila infection in Carassius aurutus.
    Fish Shellfish Immunol 2017 Apr 20;63:344-352. Epub 2017 Feb 20.
    College of Fisheries, Henan Normal University, Xinxiang 453007, China.
    Antimicrobial peptide is an important component of the host innate immune system and thus serves a crucial function in host defense against microbial invasion. In this study, H2A and derived antimicrobial peptide Ca-L-hipposin were cloned and characterized in Carassius aurutus. The gene H2A full-length cDNA is 908 bp and includes a 5'-terminal untranslated region (UTR) of 55 bp and a 3'-terminal UTR of 466 bp with a canonical polyadenylation signal sequence AATAA, as well as an open reading frame (ORF) of 387 bp encoding a polypeptide of 128 amino acids, with a molecular weight of 13. Read More

    A ThDREB gene from Tamarix hispida improved the salt and drought tolerance of transgenic tobacco and T. hispida.
    Plant Physiol Biochem 2017 Apr 10;113:187-197. Epub 2017 Feb 10.
    State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, 150040 Harbin, China. Electronic address:
    Dehydration-responsive element-binding (DREB) transcription factors are important abiotic stress tolerance related genes, and some reports on the roles of DREB have primarily addressed herbal plants. To explore the abiotic stress tolerance role of DREB (ThDREB) from Tamarix hispida, a ThDREB gene with a complete ORF of 783 bp that encodes a 28.74 kDa protein with 260 amino acids, was isolated and functionally annotated. Read More

    Reevaluating species number, distribution and endemism of the coral genus Pocillopora Lamarck, 1816 using species delimitation methods and microsatellites.
    Mol Phylogenet Evol 2017 Feb 17;109:430-446. Epub 2017 Feb 17.
    UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Laboratoire d'excellence-CORAIL, Faculté des Sciences et Technologies, 15 Bd René Cassin, CS 92003, 97744 St Denis Cedex 09, La Réunion, France. Electronic address:
    Species delimitation methods based on genetic information, notably using single locus data, have been proposed as means of increasing the rate of biodiversity description, but can also be used to clarify complex taxonomies. In this study, we explore the species diversity within the cnidarian genus Pocillopora, widely distributed in the tropical belt of the Indo-Pacific Ocean. From 943 Pocillopora colonies sampled in the Western Indian Ocean, the Tropical Southwestern Pacific and Southeast Polynesia, representing a huge variety of morphotypes, we delineated Primary Species Hypotheses (PSH) applying the Automatic Barcode Gap Discovery method, the Poisson Tree Processes algorithm and the Generalized mixed Yule-coalescent model on two mitochondrial markers (Open Reading Frame and Dloop) and reconstructing a haploweb using one nuclear marker (Internal Transcribed Spacer 2). Read More

    A novel HRM assay for the simultaneous detection and differentiation of eight poxviruses of medical and veterinary importance.
    Sci Rep 2017 Feb 20;7:42892. Epub 2017 Feb 20.
    Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, A-1400 Vienna, Austria.
    Poxviruses belonging to the Orthopoxvirus, Capripoxvirus and Parapoxvirus genera share common host species and create a challenge for diagnosis. Here, we developed a novel multiplex PCR method for the simultaneous detection and differentiation of eight poxviruses, belonging to three genera: cowpox virus (CPXV) and camelpox virus (CMLV) [genus Orthopoxvirus]; goatpox virus (GTPV), sheeppox virus (SPPV) and lumpy skin disease virus (LSDV) [genus Capripoxvirus]; orf virus (ORFV), pseudocowpox virus (PCPV) and bovine papular stomatitis virus (BPSV) [genus Parapoxvirus]. The assay is based on high-resolution melting curve analysis (HRMCA) of PCR amplicons produced using genus specific primer pairs and dsDNA binding dye. Read More

    cDNA cloning and expression analysis of a phosphopyruvate hydratase gene from the chinese shrimp Fenneropenaeus chinensis.
    Fish Shellfish Immunol 2017 Apr 13;63:173-180. Epub 2017 Feb 13.
    Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266300, PR China. Electronic address:
    In the present study a cDNA encoding a phosphopyruvate hydratase (enolase) was cloned from the muscle of the Chinese shrimp (Fenneropenaeus chinensis) and named as FcEnolase. The cDNA of FcEnolase encoded a protein of 434 amino acid residues with a molecular mass 47.22 kDa. Read More

    A NLRC3-like gene from blunt snout bream (Megalobrama amblycephala): Molecular characterization, expression and association with resistance to Aeromonas hydrophila infection.
    Fish Shellfish Immunol 2017 Apr 20;63:213-219. Epub 2017 Feb 20.
    College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, PR China; Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Hunan University of Arts and Science, Changde 415000, PR China. Electronic address:
    NLRC (the nucleotide-oligomerization domain (NOD)-like receptor subfamily C) consists of teleost-specific NLRs (NOD-like receptors) and plays pivotal roles in microbial recognition and regulation of innate immune response. In this study, we cloned and characterized a NLRC3-like gene (MamNLRC3-like) from blunt snout bream (Megalobrama amblycephala) by using the quantitative real-time PCR method, and analyzed the correlation between its polymorphisms and resistance to Aeromonas hydrophila infection. The full length cDNA of MamNLRC3-like was 2863 bp, with a 5'-UTR of 169 bp, ORF of 2301 bp and 3'-UTR of 393 bp, encoding 766 amino acid residues. Read More

    HcToll3 was involved in anti-Vibrio defense in freshwater pearl mussel, Hyriopsis cumingii.
    Fish Shellfish Immunol 2017 Apr 16;63:189-195. Epub 2017 Feb 16.
    College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China. Electronic address:
    Toll-like receptors (TLRs) play an important role in the activation of innate immune response but their functions in bivalves remain largely unknown. In this study, we identified a TLR from the freshwater pearl mussel Hyriopsis cumingii (HcToll3) and investigated its functions in immunity. The full-length cDNA of HcToll3 is 3852 bp and includes an open reading frame (ORF) of 3228 bp that encodes a polypeptide of 1075 amino acids. Read More

    Autochthonous sporadic acute hepatitis E caused by two distinct subgenotype 3b hepatitis E virus strains with only 90% nucleotide identity.
    Clin J Gastroenterol 2017 Apr 15;10(2):168-173. Epub 2017 Feb 15.
    Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-Shi, Tochigi, 329-0498, Japan.
    Hepatitis E, which is caused by hepatitis E virus (HEV), is a public health concern in Japan, where the zoonotic food-borne transmission of HEV from domestic pigs and wild boars plays an important role. A 44-year-old Japanese man with autochthonous sporadic acute hepatitis E was admitted with general fatigue and moderate liver dysfunction. In the present study, two distinct HEV strains were recovered from the patient, who had consumed the raw or undercooked pig liver and intestine two or three times per week for 3 months before the disease onset. Read More

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