16,245 results match your criteria Orf


Molecular Characterization and Tissue Distribution of Mitochondrial Ca -Dependent Solute Carrier Protein during Prevention of Diapause by HCl Treatment in the Silkworm, Bombyx mori.

Zoolog Sci 2018 Dec;35(6):487-493

1 Department of Biosciences, College of Humanities and Sciences, Nihon University, Sakurajosui 3-25-40, Setagaya-ku, Tokyo 156-8550, Japan.

To clarify the molecular mechanism of prevention of entry into diapause in Bombyx mori by HCl treatment, we biochemically analyzed mitochondrial Ca -dependent solute carrier protein (MCSC) in diapause eggs treated with HCl solution. Our previous studies revealed that HCl treatment causes Ca to efflux from diapause eggs. Therefore, we attempted to analyze MCSC, which is known to associate with Ca . Read More

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December 2018

Molecular characterization, expression analysis, and ontogeny of complement component C9 in southern catfish (Silurus meridionalis).

Fish Shellfish Immunol 2018 Nov 30. Epub 2018 Nov 30.

Institute of Hydrobiology, Jinan University, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering Ministry of Education, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, West 601 Huangpu Avenue, Tianhe District, Guangzhou, 510632, People's Republic of China.

The complement system plays an important role in host defense against invading microorganisms. Complement component C9 is the last component that is involved in the formation of the membrane attack complex (MAC) on the surface of target cells. In the present study, the full length C9 cDNA sequence of 1984 bp with an open reading frame (ORF) of 1809 bp was cloned from southern catfish (Silurus meridionalis). Read More

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November 2018

Complete nucleotide sequence analysis of a novel Bacillus subtilis-infecting phage, BSP38, possibly belonging to a new genus in the subfamily Spounavirinae.

Arch Virol 2018 Dec 1. Epub 2018 Dec 1.

Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.

Bacillus subtilis-infecting phage BSP38 was isolated from a sewage sample. Morphologically, BSP38 was found to be similar to members of the subfamily Spounavirinae, family Myoviridae. Its genome is 153,268 bp long with 41. Read More

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December 2018

Generation of Stable Expression Mammalian Cell Lines Using Lentivirus.

Bio Protoc 2018 Nov;8(21)

Department of Radiation Oncology, Stanford University, Stanford, CA, USA.

Lentiviruses are used very widely to generate stable expression mammalian cell lines. They are used for both gene down-regulation (by using shRNA) or for gene up-regulation (by using ORF of gene of interest). The technique of generating stable cell lines using 3 generation lentivirus is very robust and it typically takes about 1-2 weeks to get stable expression for most mammalian cell lines. Read More

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November 2018

The enzymatic biosynthesis of acylated steroidal glycosides and their cytotoxic activity.

Acta Pharm Sin B 2018 Oct 1;8(6):981-994. Epub 2018 May 1.

State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.

Herein we describe the discovery and functional characterization of a steroidal glycosyltransferase (SGT) from and a steroidal glycoside acyltransferase (SGA) from and their application in the biosynthesis of acylated steroidal glycosides (ASGs). Initially, an gene, designated as OsSGT1, was isolated from . OsSGT1-containing cell free extract was then used as the biocatalyst to react with 49 structurally diverse drug-like compounds. Read More

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October 2018
2 Reads

Comparative proteomics of Tobacco mosaic virus-infected Nicotiana tabacum plants identified major host proteins involved in photosystems and plant defence.

J Proteomics 2018 Nov 29. Epub 2018 Nov 29.

Department of Biological Sciences, National University of Singapore (NUS), 14 Science Drive 4, 117543, Singapore; Temasek Life Sciences Laboratory, 1 Research Link, 117604, Singapore; National University of Singapore Suzhou Research Institute, Suzhou, Jiangsu 215123, China. Electronic address:

Tobacco mosaic virus (TMV) is a positive single-stranded RNA virus. Its 5' end ORF codes for the replicase proteins, namely 126 kDa and 183 kDa, respectively. These proteins interact with many host proteins to form a virus replication complex (VRC). Read More

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November 2018

Genome-Wide Quantitation of Protein Synthesis Rates in Bacteria.

Methods Enzymol 2018 22;612:225-249. Epub 2018 Sep 22.

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States. Electronic address:

Bacteria produce different amounts of their proteins in response to different conditions. The ability to accurately quantitate the rates of protein synthesis across the genome is an important step toward understanding both underlying regulation and bacterial physiology at a systems level. Ribosome profiling (deep sequencing of ribosome-protected mRNA fragments) enables accurate and high-throughput measurement of such synthesis rates. Read More

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September 2018

Molecular cloning, expression pattern of β-carotene 15,15-dioxygenase gene and association analysis with total carotenoid content in pearl oyster Pinctada fucata martensii.

Comp Biochem Physiol B Biochem Mol Biol 2018 Nov 28. Epub 2018 Nov 28.

Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; Pearl Breeding and Processing Engineering Technology, Research Center of Guangdong Province, Zhanjiang 524088, China. Electronic address:

β-carotene-15,15-dioxygenase is an enzyme involved in carotenoid metabolism to catalyze oxidative cleavage of β-carotene at its central double bond to two molecules of retinal in intestinal cells of vertebrate. In this study, we cloned and characterized β-carotene-15,15-dioxygenase in pearl oyster Pinctada fucata martensii (PmβCDOX). The full length of PmβCDOX gene was 1802 bp, including 1554 bp of the open reading frame (ORF) that encoded 517 amino acids, a 5'UTR of 134 bp and a 3' UTR of 114 bp. Read More

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November 2018

Varicella-zoster virus clades circulating in Spain over two decades.

J Clin Virol 2018 Nov 28;110:17-21. Epub 2018 Nov 28.

Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Spain. Electronic address:

Background: Despite childhood universal VZV immunization was introduced in 2015, there are no data on VZV clade distribution in Spain.

Objectives: To characterize the varicella-zoster virus strains circulating in Spain between 1997 and 2016.

Study Design: In this retrospective study, we determined the VZV clades in 294 patients with different pathologies (mainly encephalitis, zoster and varicella) by sequencing three fragments within ORF 22, ORF 21 and ORF 50 and, subsequently analyzing 7 relevant SNPs. Read More

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November 2018
1 Read

The genetic divergences of codon usage shed new lights on transmission of hepatitis E virus from swine to human.

Infect Genet Evol 2018 Dec 2. Epub 2018 Dec 2.

Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Room Na-1011, s-Gravendijkwal 230, NL-3015 CE, Rotterdam, the Netherlands. Electronic address:

Hepatitis E virus (HEV) is an important pathogen causing public health burden. Swine has been recognized as a main reservoir. Interestingly, genotype 1 HEV only infects human; whereas genotype 3 and 4 are zoonotic. Read More

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December 2018

Challenging SNP impact on caspofungin resistance by full-length FKS1 allele replacement in Candida lusitaniae.

J Antimicrob Chemother 2018 Dec 4. Epub 2018 Dec 4.

Univ. Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, 33000 Bordeaux, France.

Objectives: A strain of the opportunistic pathogenic yeast Candida lusitaniae was genetically engineered for full-length replacement of the FKS1 gene encoding the target of echinocandin antifungals in order to assess the impact of FKS mutations on echinocandin resistance and reduced echinocandin susceptibility (RES).

Methods: FKS1 allelic exchange was achieved by transforming C. lusitaniae with two DNA fragments covering the entire FKS1 ORF. Read More

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December 2018

Isolation and expression analysis of a candidate gametophyte sex determination gene (sjhmg) of kelp (Saccharina japonica).

J Phycol 2018 Dec 5. Epub 2018 Dec 5.

Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China.

Saccharina japonica undergoes an alternating life cycle during which the diploid sporophyte generation alternates with the monoploid gametophyte generation. Saccharina japonica uses the UV sex determination system to determine the sex of its haploid gametophytes. However, the sex-determining genes and the sex-determining mechanisms of kelp gametophytes have not been thoroughly elucidated to date. Read More

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December 2018

Identification of a Novel Partitivirus of NFCF319 and Evidence for the Related Antifungal Activity.

Front Plant Sci 2018 20;9:1699. Epub 2018 Nov 20.

Institute for Molecular Biology and Genetics, Chonbuk National University, Jeonju, South Korea.

We have reported 15 agarose gel band patterns of double-stranded RNA (dsRNA) from spp. We describe herein that band pattern IX in NFCF319, which appeared to be a single band but consisted of two dsRNAs of similar size, was identified as a novel mycovirus, designated partitivirus 1 (ThPV1). The larger segment (dsRNA1) of the ThPV1 genome comprised 2,289 bp and contained a single open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRp). Read More

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November 2018

Genomic characterisation of Cuiaba and Charleville viruses: arboviruses (family Rhabdoviridae, genus Sripuvirus) infecting reptiles and amphibians.

Virus Genes 2018 Dec 3. Epub 2018 Dec 3.

School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia.

Viruses in the family Rhabdoviridae are ecologically very diverse, infecting mammals, birds, reptiles, fish, plants and a wide range of other terrestrial and aquatic invertebrates. The genus Sripuvirus currently comprises five viruses that appear to circulate in transmission cycles involving reptiles and sandflies. Here, we report an analysis of the complete coding sequences of Cuiaba virus (CUIV), isolated from an amphibian (Bufo marinus) collected in Brazil, and Charleville virus (CHVV), isolated from sandflies (Phlebotomus sp. Read More

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December 2018

Clinical Manifestation, Dermoscopy, and Scanning Electron Microscopy in Two Cases of Contagious Ecthyma (Orf Nodule).

Case Rep Dermatol Med 2018 29;2018:2094086. Epub 2018 Oct 29.

Dermatology Division, Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.

Orf is a highly contagious skin disease commonly seen in goats and sheep that can be transmitted to people who have direct contact with infected animals. Here, we report the clinical manifestation, dermoscopy, and scanning electron microscopy in two women who developed skin lesions on their hands after handling goats with wounds in the udders. Human orf is usually self-limiting and no specific treatment is needed. Read More

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October 2018
1 Read

Chilo iridescent virus encodes two functional metalloproteases.

Arch Virol 2018 Nov 29. Epub 2018 Nov 29.

Department of Biology, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey.

The genome of Chilo iridescent virus (CIV) has two open reading frames (ORFs) with matrix metalloprotease (MMP) domains. The protein encoded by ORF 136R contains 178 amino acids with over 40% amino acid sequence identity to hypothetical metalloproteases of other viruses, and the protein 165R contains 264 amino acids with over 40% amino acid sequence identity to metalloproteases of a large group of organisms, primarily including a variety of Drosophila species. These proteins possess conserved zinc-binding motifs in their catalytic domains. Read More

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November 2018
1 Read

A simple method to estimate the linear length of the orbital floor in complex orbital surgery.

J Craniomaxillofac Surg 2018 Nov 9. Epub 2018 Nov 9.

OMFS-IMPATH Research Group Department of Imaging and Pathology, (Chairperson: Professor Dr. C. Politis), Belgium; Department of Oral and Maxillofacial Surgery, Hasselt University, Diepenbeek, Belgium.

Background: The orbital floor (OrF) and infraorbital rim (IOR) repair in cases of complete destruction is challenging mainly due to the fact that the defect length cannot be measured. The aim of the current study is to develop a method of calculating the Orf length by using the gender and the lengths of the medial, superior and lateral orbital walls (OrW) of the same orbit.

Material And Methods: Ninety-seven (59 male and 38 female) European adult dry skulls were classified according to age: 20-39, 40-59 and 60 years and above. Read More

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November 2018

C-type lectin 17A and macrophage-expressed receptor genes are magnified by fungal β-glucan after Vibrio parahaemolyticus infection in Totoaba macdonaldi cells.

Immunobiology 2018 Oct 18. Epub 2018 Oct 18.

Immunology & Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, B.C.S, 23096, Mexico. Electronic address:

C-type lectins are a principal carbohydrate recognition mechanism as glucans on cell surfaces. This study identified and investigated molecular characterization and immune roles of a novel c-type lectin 17A from Totoaba macdonaldi (TmCLEC17A), which were described in head-kidney leukocytes after immunostimulation with fungal β-glucan 197A and Vibrio parahaemolyticus infection. This nucleotide sequence from totoaba was acquired using NGS and bioinformatics tools. Read More

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October 2018

Heterologous expression and biochemical characterization of a novel cold-active α-amylase from the Antarctic bacteria Pseudoalteromonas sp. 2-3.

Protein Expr Purif 2018 Nov 27;155:78-85. Epub 2018 Nov 27.

Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile. Electronic address:

α-Amylase is an endo-acting enzyme which catalyzes random hydrolysis of starch. These enzymes are used in various biotechnological processes including the textile, paper, food, biofuels, detergents and pharmaceutical industries. The use of active enzymes at low temperatures has a high potential because these enzymes would avoid the demand for heating during the process thereby reducing costs. Read More

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November 2018

Identification and genomic sequence analysis of a new Spodoptera exigua multiple nucleopolyhedrovirus, SeMNPV-QD, isolated from Qingdao, China.

J Invertebr Pathol 2018 Nov 26;160:8-17. Epub 2018 Nov 26.

Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, PR China. Electronic address:

A new beet armyworm (Spodoptera exigua) multiple nucleopolyhedrovirus SeMNPV-QD was isolated from dead larvae in the field in Qingdao, Shandong, China. The virus has a polyhedron size of 1.39 ± 0. Read More

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November 2018

SIRT-3 Modulation by Resveratrol Improves Mitochondrial Oxidative Phosphorylation in Diabetic Heart through Deacetylation of TFAM.

Cells 2018 Nov 28;7(12). Epub 2018 Nov 28.

Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad 121001, India.

Background And Purpose: Mitochondrial dysfunction remains the crucial cause for many heart diseases including diabetic cardiomyopathy (DCM). Sirtuin-3 (SIRT-3) is a protein deacetylase localized in the mitochondria and regulates mitochondrial function. Being a noteworthy mitochondrial protein deacetylase enzyme, the role of SIRT-3 in DCM is yet to be explored. Read More

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November 2018

Molecular characterization and expression analysis of T cell receptor (TCR) γ and δ genes in dojo loach (Misgurnus anguillicaudatus) in response to bacterial, parasitic and fungal challenge.

Fish Shellfish Immunol 2018 Nov 25. Epub 2018 Nov 25.

Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, Hubei, 430070, China; Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, 415000, China. Electronic address:

In mammalian, T-cell receptors (TCRs) play a key role in recognizing the presented antigen from external to protect organisms against environmental pathogens. To understand the potential roles of TCRγ and TCRδ in dojo loach (Misgurnus anguillicaudatus), Ma-TCRγ and Ma-TCRδ cDNAs were cloned and their gene expression profiles were investigated after bacterial, parasitic and fungal challenge. The open reading frame (ORF) of Ma-TCRγ and Ma-TCRδ cDNAs contained 948 and 867 bp, encoding 316 and 288 amino acid residues, respectively. Read More

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November 2018

Peptides/Proteins Encoded by Non-coding RNA: A Novel Resource Bank for Drug Targets and Biomarkers.

Front Pharmacol 2018 13;9:1295. Epub 2018 Nov 13.

Biomedicine Research Center, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.

Non-coding RNAs (ncRNAs) are defined as RNA molecules that do not encode proteins, but recent evidence has proven that peptides/proteins encoded by ncRNAs do indeed exist and usually contain less than 100 amino acids. These peptides/proteins play an important role in regulating tumor energy metabolism, epithelial to mesenchymal transition of cancer cells, the stability of the c-Myc oncoprotein, and the ubiquitination and degradation of proliferating cell nuclear antigen (PCNA). These peptides/proteins represent promising drug targets for fighting against tumor growth or biomarkers for predicting the prognosis of cancer patients. Read More

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November 2018

Spatiotemporally controlled genetic perturbation for efficient large-scale studies of cell non-autonomous effects.

Elife 2018 Nov 27;7. Epub 2018 Nov 27.

Centre for Developmental Neurobiology, King's College London, London, United Kingdom.

Studies in genetic model organisms have revealed much about the development and pathology of complex tissues. Most have focused on cell-intrinsic gene functions and mechanisms. Much less is known about how transformed, or otherwise functionally disrupted, cells interact with healthy ones towards a favorable or pathological outcome. Read More

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November 2018
4 Reads

Fine mapping and molecular marker development of the Sm gene conferring resistance to gray leaf spot (Stemphylium spp.) in tomato.

Theor Appl Genet 2018 Nov 26. Epub 2018 Nov 26.

Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12, Zhongguancun Nandajie, Haidian District, Beijing, 100081, China.

Key Message: The tomato gray leaf spot resistance gene Sm was fine-mapped in a 185-kb region through a map-based cloning strategy and genome-wide association study; a candidate gene was proved to be involved in Sm-mediated resistance through transient gene silencing. Gray leaf spot, caused by Stemphylium spp., is a warm weather foliar disease in tomato (Solanum lycopersicum L). Read More

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November 2018

Association of an IRF3 putative functional uORF variant with resistance to Brucella infection: A candidate gene based analysis of InDel polymorphisms in goats.

Cytokine 2018 Nov 23. Epub 2018 Nov 23.

Instituto Nacional de Tecnología Agropecuaria, CICVyA, Instituto de Patobiología, Nicolás Repetto y de Los Reseros s/n, Hurlingham, Buenos Aires B1686, Argentina. Electronic address:

Brucellosis is an important zoonotic disease caused by infection with Brucella spp. It generates major economic losses in livestock production worldwide. Goats are the principal hosts of B. Read More

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November 2018

Brain size predicts behavioural plasticity in guppies (Poecilia reticulata): an experiment.

J Evol Biol 2018 Nov 26. Epub 2018 Nov 26.

Department of Ethology, Stockholm University, Svante Arrhenius väg 18B, Stockholm, 10691, Sweden.

Understanding how animal personality (consistent between-individual behavioural differences) arises has become a central topic in behavioural sciences. This endeavour is complicated by the fact that not only the mean behaviour of individuals (behavioural type), but also the strength of their reaction to environmental change (behavioural plasticity) varies consistently. Personality and cognitive abilities are linked and we suggest that behavioural plasticity could also be explained by differences in brain size (a proxy for cognitive abilities), since accurate decisions are likely essential to make behavioural plasticity beneficial. Read More

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November 2018
3 Reads

Molecular characterization of bovine ephemeral fever virus in Thailand between 2013 and 2017.

Vet Microbiol 2018 Dec 15;227:1-7. Epub 2018 Oct 15.

Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, 50th Ngamwongwan Rd., Chatuchak, Bangkok, 10900, Thailand; Center for Advanced Studies in Agriculture and Food (CASAF), KU Institute of Advances Studies, Kasetsart University, 10900, Thailand. Electronic address:

Bovine ephemeral fever (BEF) is an arthropod-borne disease caused by bovine ephemeral fever virus (BEFV), a negative sense, single-stranded RNA virus. BEFV is endemic in tropical and sub-tropical regions including Thailand, a country in mainland Southeast Asia. However, there are few studies on BEFV and no available information regarding molecular characteristics of BEFV in Thailand. Read More

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December 2018

Megaplasmid - A promising tool for higher protein production.

Biochem Biophys Res Commun 2018 Nov 21. Epub 2018 Nov 21.

Centre for Cellular and Molecular Platforms, NCBS-TIFR, GKVK Campus, Bellary Road, Bangalore, Karnataka, 560065, India. Electronic address:

Recombinant proteins have an increasing demand due to their application spanning across different fields. Hence, investigating strategies to increase the yield of recombinant proteins are highly significant. To achieve high yield, optimization of various parameters such as temperature, pH, aeration, inducer concentration, etc. Read More

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November 2018
3 Reads

Multiple calmodulin genes of the Pacific abalone, (Mollusca: Vetigastropoda: Haliotidae).

Anim Cells Syst (Seoul) 2018 19;22(5):341-351. Epub 2018 Sep 19.

Department of Marine and Fisheries Resources, Mokpo National University, Korea.

In this study, we identified four canonical calmodulin genes in the Pacific abalone, . Their full-length cDNAs were variable in the 5' and 3' untranslated regions, but highly similar (91-97%) in the coding region. Each of the genes encoded 149 amino acids, with 93-97% similarity among themselves and 94-98% similarity with human CAM I. Read More

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September 2018
3 Reads

Localization of the kinase Ataxia Telangiectasia Mutated to Adenovirus E4 mutant DNA replication centers is important for its inhibitory effect on viral DNA accumulation.

Virology 2018 Nov 16;527:47-56. Epub 2018 Nov 16.

Department of Microbiology, Pearson Hall, Miami University, 700 E. High Street, Oxford, OH 45056, United States; Cell Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, United States. Electronic address:

Adenovirus (Ad) type 5 (Ad5) E4 deletion mutants including H5dl1007 (E4-) induce a DNA damage response (DDR) that activates the kinase ataxia-telangiectasia mutated (ATM), which can interfere with efficient viral DNA replication. We find that localization of active phosphorylated ATM (pATM) to E4- viral replication centers (VRCs) is important for its inhibitory effect. ATM is necessary for localization of RNF8 and 53BP1 to E4 mutant VRCs, while recruitment of DDR factors Mre11, Mdc1 and γH2AX is ATM-independent, raising the possibility that ATM may affect viral chromatin at VRCs. Read More

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November 2018
1 Read

Identification of thioredoxin domain-containing protein 17 from big-belly seahorse Hippocampus abdominalis: Molecular insights, immune responses, and functional characterization.

Fish Shellfish Immunol 2018 Nov 16;86:301-310. Epub 2018 Nov 16.

Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea. Electronic address:

Thioredoxin domain-containing protein 17 (TXNDC17) is a small protein (∼14 kDa) involved in maintaining cellular redox homeostasis via a thiol-disulfide reductase activity. In this study, TXNDC17 was identified and characterized from Hippocampus abdominalis. The open reading frame (ORF) consisted of 369 bp and 123 amino acids. Read More

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November 2018
3 Reads

Variants of hepatitis B virus surface antigen observed during therapy with nucleic acid polymer REP 2139-Ca have no influence on treatment outcome and its detection by diagnostic assays.

J Viral Hepat 2018 Nov 19. Epub 2018 Nov 19.

Institute of Virology, Technische Universität München, Munich, Germany.

The treatment of patients suffering from HBeAg positive chronic hepatitis B with REP 2139-Ca resulted in potent reductions in HBsAg and HBV DNA, seroconversion to anti-HBs and the establishment of functional control of infection. In this cohort of 12 patients, we investigated whether differences between HBsAg sequences might explain lack of response to REP 2139-Ca observed in 3 of 12 patients. We also assessed if the reduction or complete loss of HBsAg in serum observed during therapy were caused by mutations in the "a" determinant preventing the detection of HBsAg by standard diagnostic assays. Read More

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November 2018
4 Reads

Mapping Cellular Reprogramming via Pooled Overexpression Screens with Paired Fitness and Single-Cell RNA-Sequencing Readout.

Cell Syst 2018 Nov 14;7(5):548-555.e8. Epub 2018 Nov 14.

Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. Electronic address:

Understanding the effects of genetic perturbations on the cellular state has been challenging using traditional pooled screens, which typically rely on the delivery of a single perturbation per cell and unidimensional phenotypic readouts. Here, we use barcoded open reading frame overexpression libraries coupled with single-cell RNA sequencing to assay cell state and fitness, a technique we call SEUSS (scalable functional screening by sequencing). Using SEUSS, we perturbed hPSCs with a library of developmentally critical transcription factors (TFs) and assayed the impact of TF overexpression on fitness and transcriptomic states. Read More

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November 2018
7 Reads

Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses.

Virus Evol 2018 Jul 12;4(2):vey026. Epub 2018 Nov 12.

MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, UK.

Amdoparvoviruses (family genus ) infect carnivores, and are a major cause of morbidity and mortality in farmed animals. In this study, we systematically screened animal genomes to identify endogenous parvoviral elements (EPVs) disclosing a high degree of similarity to amdoparvoviruses, and investigated their genomic, phylogenetic and protein structural features. We report the first examples of full-length, amdoparvovirus-derived EPVs in the genome of the Transcaucasian mole vole (). Read More

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Characterization of gene expression profiles and functional analysis of peptidoglycan recognition protein 2 from rock bream (Oplegnathus fasciatus).

Fish Shellfish Immunol 2018 Nov 12;84:1068-1074. Epub 2018 Nov 12.

Institute of Marine Industry, College of Marine Science, Gyeongsang National University, 455, Tongyeong, 650-160, Republic of Korea. Electronic address:

Peptidoglycan recognition protein 2 (PGRP2) is a Zn-dependent peptidase that plays important roles in binding to microbial components of the cell membrane, inducing phagocytosis and antimicrobial activity. Rock bream (Oplegnathus fasciatus) PGRP2 (RbPGRP2) was identified in the intestine by next generation sequencing (NGS) analysis. The open reading frame (ORF) the RbPGRP2 cDNA (470 amino acid residues) contains a peptidoglycan recognition protein domain (residues 300 to 446). Read More

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November 2018
1 Read

Detection of a Conspecific Mycovirus in Two Closely Related Native and Introduced Fungal Hosts and Evidence for Interspecific Virus Transmission.

Viruses 2018 Nov 13;10(11). Epub 2018 Nov 13.

Swiss Federal Institute for Forest, Snow and Landscape Research, WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland.

is a native fungus in Europe where it behaves as a harmless decomposer of leaves of common ash. Its close relative was introduced into Europe from Asia and currently threatens ash ( sp.) stands all across the continent causing ash dieback. Read More

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November 2018
2 Reads

Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce.

BMC Genomics 2018 Nov 13;19(1):815. Epub 2018 Nov 13.

Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland.

Background: The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative transcriptomic analysis of P. carnosa following growth on wood powder from one softwood (spruce; Picea glauca) and one hardwood (aspen; Populus tremuloides). Read More

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November 2018
2 Reads
3.990 Impact Factor

Insights into Streptococcus agalactiae PI-2b pilus biosynthesis and role in adherence to host cells.

Microbes Infect 2018 Nov 10. Epub 2018 Nov 10.

Institut Pasteur, Biology of Gram-positive Pathogens Unit, 75015, Paris, France; Centre National de la Recherche Scientifique (CNRS) ERL6002, France. Electronic address:

The core PI-2b pilus present in "hypervirulent" ST-17 Streptococcus agalactiae strains consists of three pilin subunits (Spb1, Ap1 and Ap2) assembled by sortase SrtC1 and cell-wall anchored by Srt2. Spb1 was shown to be the major pilin and Ap2 the anchor pilin. Ap1 is a putative adhesin. Read More

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November 2018
3 Reads

IRES-dependent ribosome repositioning directs translation of a +1 overlapping ORF that enhances viral infection.

Nucleic Acids Res 2018 Nov 10. Epub 2018 Nov 10.

Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.

RNA structures can interact with the ribosome to alter translational reading frame maintenance and promote recoding that result in alternative protein products. Here, we show that the internal ribosome entry site (IRES) from the dicistrovirus Cricket paralysis virus drives translation of the 0-frame viral polyprotein and an overlapping +1 open reading frame, called ORFx, via a novel mechanism whereby a subset of ribosomes recruited to the IRES bypasses 37 nucleotides downstream to resume translation at the +1-frame 13th non-AUG codon. A mutant of CrPV containing a stop codon in the +1 frame ORFx sequence, yet synonymous in the 0-frame, is attenuated compared to wild-type virus in a Drosophila infection model, indicating the importance of +1 ORFx expression in promoting viral pathogenesis. Read More

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November 2018

The transcriptome of the marine calanoid copepod Temora longicornis under heat stress and recovery.

Mar Environ Res 2018 Nov 1. Epub 2018 Nov 1.

Ghent University, Laboratory of Environmental Toxicology and Aquatic Ecology, Faculty of Bioscience Engineering, 9000, Ghent, Belgium.

Understanding the impacts of global change in zooplankton communities is crucial, as alterations in the zooplankton communities can affect entire marine ecosystems. Despite the economic and ecological importance of the calanoid copepod Temora longicornis in the Belgian part of the North Sea, molecular data is still very limited for this species. Using HiSeq Illumina sequencing, we sequenced the whole transcriptome of T. Read More

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November 2018

Complete genome sequence of a putative novel potyvirus isolated from Platycodon grandiflorum.

Arch Virol 2018 Nov 8. Epub 2018 Nov 8.

Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.

The complete 9,556-nt genomic sequence of a putative new potyvirus, tentatively named "platycodon mild mottle virus" (PlaMMV), infecting Platycodon grandiflorum was determined (GenBank accession no. MH779625). A single large open reading frame (ORF; nt 121-9360, 3079 aa) encoding a polyprotein that was predicted to be cleaved into 10 mature proteins was detected. Read More

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November 2018
3 Reads

FusionGDB: fusion gene annotation DataBase.

Nucleic Acids Res 2018 Nov 8. Epub 2018 Nov 8.

Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

Gene fusion is one of the hallmarks of cancer genome via chromosomal rearrangement initiated by DNA double-strand breakage. To date, many fusion genes (FGs) have been established as important biomarkers and therapeutic targets in multiple cancer types. To better understand the function of FGs in cancer types and to promote the discovery of clinically relevant FGs, we built FusionGDB (Fusion Gene annotation DataBase) available at https://ccsm. Read More

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November 2018
7 Reads

Reactivation of Simian Varicella Virus (SVV) in Rhesus Macaques After CD4 T Cell Depletion.

J Virol 2018 Nov 7. Epub 2018 Nov 7.

Department of Neurology, University of Colorado School of Medicine, Aurora, Colorado, USA

Rhesus macaques intrabronchially inoculated with simian varicella virus (SVV), the counterpart of human varicella zoster virus (VZV), developed primary infection with viremia and rash, which resolved upon clearance of viremia followed by establishment of latency. To assess the role of CD4 T cell immunity in reactivation, monkeys were treated with a single 50 mg/kg dose of a humanized monoclonal anti-CD4 antibody; within 1 week, circulating CD4 T cells were reduced from 40-60% to 5-30% of the total T cell population and remained low for 2 months. Very low viremia was seen only in some of the treated monkeys. Read More

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November 2018
1 Read

Heterologous expression of a Glyoxalase I gene from sugarcane confers tolerance to several environmental stresses in bacteria.

PeerJ 2018 31;6:e5873. Epub 2018 Oct 31.

Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China.

Glyoxalase I belongs to the glyoxalase system that detoxifies methylglyoxal (MG), a cytotoxic by-product produced mainly from triose phosphates. The concentration of MG increases rapidly under stress conditions. In this study, a novel glyoxalase I gene, designated as was identified from sugarcane. Read More

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October 2018
7 Reads

cDNA cloning, characterization, and expression analysis of the Rac1 and Rac2 genes from Cynoglossus semilaevis.

Fish Shellfish Immunol 2018 Nov 3;84:998-1006. Epub 2018 Nov 3.

Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology Yellow Sea Fisheries Research Institute, CAFS, Qingdao, 266071, China; Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China. Electronic address:

Rac1 and Rac2, belonging to the small Rho GTPase family, play an important role during the immune responses. In this study, a Rac1 homolog (CsRac1) and a Rac2 homolog (CsRac2) were cloned from the Cynoglossus semilaevis. The full-length of CsRac1 and CsRac2 cDNA was 1219 bp and 1047 bp, respectively. Read More

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November 2018
5 Reads

Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing.

PeerJ 2018 30;6:e5818. Epub 2018 Oct 30.

National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.

Background: Sugarcane is an important global food crop and energy resource. To facilitate the sugarcane improvement program, genome and gene information are important for studying traits at the molecular level. Most currently available transcriptome data for sugarcane were generated using second-generation sequencing platforms, which provide short reads. Read More

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October 2018
2 Reads

A combination CDK4/6 and IGF1R inhibitor strategy for Ewing sarcoma.

Clin Cancer Res 2018 Nov 5. Epub 2018 Nov 5.

Department of Pediatric Oncology, Dana-Farber Cancer Institute

Introduction: Novel targeted therapeutics have transformed the care of subsets of patients with cancer. In pediatric malignancies, however, with simple tumor genomes and infrequent targetable mutations, there have been few new FDA-approved targeted drugs. The cyclin-dependent kinase (CDK)4/6 pathway recently emerged as a dependency in Ewing sarcoma, an aggressive pediatric malignancy. Read More

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November 2018
17 Reads
8.720 Impact Factor

De novo assembly of wheat root transcriptomes and transcriptional signature of longitudinal differentiation.

PLoS One 2018 5;13(11):e0205582. Epub 2018 Nov 5.

Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States of America.

Hidden underground, root systems constitute an important part of the plant for its development, nourishment and sensing the soil environment around it, but we know very little about its genetic regulation in crop plants like wheat. In the present study, we de novo assembled the root transcriptomes in reference cultivar Chinese Spring from RNA-seq reads generated by the 454-GS-FLX and HiSeq platforms. The FLX reads were assembled into 24,986 transcripts with completeness of 54. Read More

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November 2018
2 Reads

Filling a niche in "ligand space" with bulky, electron-poor phosphorus (III) alkoxides.

Chemistry 2018 Nov 5. Epub 2018 Nov 5.

University of York, Department of Chemistry, Heslington, YO10 5DD, York, UNITED KINGDOM.

The chemistry of phosphorus(III) ligands, which are of key importance in coordination chemistry, organometallic chemistry and catalysis, is dominated by relatively electron-rich species. Many of the electron-poor P(III) ligands that are readily available have relatively small steric profiles. As such, there is a significant gap in "ligand space" where more sterically bulky, electron-poor P(III) ligands are needed. Read More

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November 2018
5 Reads