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The emerging role and significance of circular RNAs in viral infections and antiviral immune responses: possible implication as theranostic agents.

RNA Biol 2020 Jul 2. Epub 2020 Jul 2.

Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore (UOL) , Lahore, Pakistan.

Circular RNAs (circRNAs) are ubiquitously expressed, covalently closed rings, produced by pre-mRNA splicing in a reversed order during post-transcriptional processing. Circularity endows 3'-5'-linked circRNAs with stability and resistance to exonucleolytic degradation which raises the question whether circRNAs may be relevant as potential therapeutic targets or agents. High stability in biological systems is the most remarkable property and a major criterion for why circRNAs could be exploited for a range of RNA-centered medical applications. Read More

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http://dx.doi.org/10.1080/15476286.2020.1790198DOI Listing

Using AnABlast for intergenic sORF prediction in the C. elegans genome.

Bioinformatics 2020 Jul 2. Epub 2020 Jul 2.

Centro Andaluz de Biología del Desarrollo (CABD, UPO-CSIC). Universidad Pablo de Olavide, Ctra. de Utrera, km.1, Sevilla, Spain.

Motivation: Short bioactive peptides encoded by small open reading frames (sORFs) play important roles in eukaryotes. Bioinformatics prediction of ORFs is an early step in a genome sequence analysis, but sORFs encoding short peptides, often using non-AUG initiation codons, are not easily discriminated from false ORFs occurring by chance.

Results: AnABlast is a computational tool designed to highlight putative protein-coding regions in genomic DNA sequences. Read More

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http://dx.doi.org/10.1093/bioinformatics/btaa608DOI Listing

[Junk DNA is out of fashion].

Authors:
Bertrand Jordan

Med Sci (Paris) 2020 Jun-Jul;36(6-7):675-677. Epub 2020 Jul 2.

UMR 7268 ADÉS, Aix-Marseille, Université /EFS/CNRS ; CoReBio PACA, case 901, Parc scientifique de Luminy, 13288 Marseille Cedex 09, France.

A systematic search for non-conventional open reading frames in human DNA reveals a large number of small ORFs encoding peptides generally smaller than 100 amino-acids. These ORFs are transcribed and translated into small proteins, which are demonstrated to have functional significance by bulk CRISPR inactivation. Evidence is also found for bicistronic mRNAs including such a small ORF upstream of a canonical coding sequence. Read More

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http://dx.doi.org/10.1051/medsci/2020108DOI Listing

Heterobimetallic Transition-Metal Carbonyl Clusters: Changing the Charges.

Chemistry 2020 Jul 2. Epub 2020 Jul 2.

Albert-Ludwigs-Universitat Freiburg, Institut für Anorganische und Analytische Chemie, GERMANY.

The homoleptic group 5 carbonylates [M(CO)6]- (M = Nb, Ta) serve as ligands in carbonyl terminated heterobimetallic AgmMn-clusters containing 3 to 11 metal atoms. Based on our serendipitous [Ag6{Nb(CO)6}4]2+ (4a2+) precedent, we established access to such AgmMn-clusters of the composition [Agm{M(CO)6}n]x (M = Nb, Ta; m = 1, 2, 6; n = 2, 3, 4, 5; x = 1-, 1+, 2+). Salts of those molecular cluster ions were synthesized by the reaction of [NEt4][M(CO)6] and Ag[Al(ORF)4] (RF = C(CF3)3) in the correct stoichiometry in 1,2,3,4-tetrafluorobenzene at -35 °C. Read More

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http://dx.doi.org/10.1002/chem.202002339DOI Listing

Expression of Separate Heterologous Proteins from the Rotavirus NSP3 Genome Segment Using a Translational 2A Stop-Restart Element.

J Virol 2020 Jul 1. Epub 2020 Jul 1.

Department of Biology, Indiana University, Bloomington, Indiana, USA.

The segmented 18.5-kbp dsRNA genome of rotavirus expresses 6 structural and 6 nonstructural proteins. We investigated the possibility of using the recently-developed plasmid-based rotavirus reverse genetics (RG) system to generate recombinant viruses that express a separate heterologous protein, in addition to the 12 viral proteins. Read More

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http://dx.doi.org/10.1128/JVI.00959-20DOI Listing

Biological characterisation, expression and functional analysis of non-specific cytotoxic cell receptor protein 1 in Nile tilapia (Oreochromis niloticus).

Fish Shellfish Immunol 2020 Jun 28;104:579-586. Epub 2020 Jun 28.

Fisheries College of Guangdong Ocean University, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals & Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China. Electronic address:

Non-specific cytotoxic cell receptor protein 1 (NCCRP-1) plays a role in recognition of target cell and activation of non-specific cytotoxic cell (NCC). In this study, the full length of Nile tilapia NCCRP-1 (On-NCCRP-1) was cloned. cDNA is composed of 1045 bp with a 90 bp of 5'-Untranslated Regions (UTR), 702 bp open reading frame (ORF) and 253 bp 3'-UTR, encoding 233 amino acids (GenBank accession no: MF162296). Read More

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http://dx.doi.org/10.1016/j.fsi.2020.05.048DOI Listing

Multiplexed Profiling and Data Processing Methods to Identify Temperature-Regulated Primary Metabolites Using Gas Chromatography Coupled to Mass Spectrometry.

Methods Mol Biol 2020 ;2156:203-239

Applied Metabolome Analysis Research Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.

This book chapter describes the analytical procedures required for the profiling of a metabolite fraction enriched for primary metabolites. The profiling is based on routine gas chromatography coupled to mass spectrometry (GC-MS). The generic profiling method is adapted to plant material, specifically to the analysis of plant material that was exposed to temperature stress. Read More

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http://dx.doi.org/10.1007/978-1-0716-0660-5_15DOI Listing
January 2020

Quantification of translation uncovers the functions of the alternative transcriptome.

Nat Struct Mol Biol 2020 Jun 29. Epub 2020 Jun 29.

Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.

Translation has a fundamental function in defining the fate of the transcribed genome. RNA-sequencing (RNA-seq) data enable the quantification of complex transcript mixtures, often detecting several transcript isoforms of unknown functions for one gene. Here, we describe ORFquant, a method to annotate and quantify translation at the level of single open reading frames (ORFs), using information from Ribo-seq data. Read More

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http://dx.doi.org/10.1038/s41594-020-0450-4DOI Listing

Mixed infection by a partitivirus and a negative-sense RNA virus related to mymonaviruses in the polypore fungus Bondarzewia berkeleyi.

Virus Res 2020 Jun 26:198079. Epub 2020 Jun 26.

Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland.

Virus communities of forest fungi remain poorly characterized. In this study, we detected two new viruses co-infecting an isolate of the polypore fungus Bondarzewia berkeleyi using high-throughput sequencing. One of them was a putative new partitivirus designated as Bondarzewia berkeleyi partitivirus 1 (BbPV1), with two linear dsRNA genome segments of 1928 and 1863 bp encoding a putative RNA-dependent RNA polymerase (RdRP) of 591 aa and a putative capsid protein of 538 aa. Read More

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http://dx.doi.org/10.1016/j.virusres.2020.198079DOI Listing

Identification, characterization, and immunological analysis of complement component 4 from grass carp (Ctenopharyngodon idella).

Fish Shellfish Immunol 2020 Jun 26. Epub 2020 Jun 26.

Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China. Electronic address:

Complement component 4 (C4) has critical immunological functions in vertebrates. In the current study, a C4 homolog (gcC4) was identified in grass carp (Ctenopharyngodon idella). The full-length 5458 bp gcC4 cDNA contained a 5148 bp open reading frame (ORF) encoding a protein of 1715 amino acids with a signal peptide and eight conservative domains. Read More

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http://dx.doi.org/10.1016/j.fsi.2020.06.043DOI Listing

Lower nasopharyngeal viral load during the latest phase of COVID-19 pandemic in a Northern Italy University Hospital.

Clin Chem Lab Med 2020 Jun 29. Epub 2020 Jun 29.

Laboratory of Medical Microbiology and Virology, University "Vita-Salute" San Raffaele, Via Olgettina 58, 20132 Milan, Italy.

Objectives A milder clinical course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been anecdotally reported over the latest phase of COVID-19 pandemic in Italy. Several factors may contribute to this observation, including the effect of lockdown, social distancing, lower humidity, lower air pollution, and potential changes in the intrinsic pathogenicity of the virus. In this regard, the clinical severity of COVID-19 could be attenuated by mutations in SARS-CoV-2 genome that decrease its virulence, as well as by lower virus inocula. Read More

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http://dx.doi.org/10.1515/cclm-2020-0815DOI Listing
June 2020
2.955 Impact Factor

Complete genome sequence of a potential foot-and-mouth disease virus serotype O vaccine strain from Bangladesh.

Arch Virol 2020 Jun 26. Epub 2020 Jun 26.

Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.

One of the six sublineages of the dominant O/ME-SA/Ind2001 lineage of foot-and-mouth disease virus (FMDV), Ind2001BD1 has already spread throughout 14 countries, including Bangladesh. Here, we report the complete genome sequence of the potential serotype O vaccine strain BAN/TA/Dh-301/2016, which has been shown to provide protection against all the circulating serotype O viruses in Bangladesh. The viral genome is 8,211 nucleotide (nt) long with an open reading frame (ORF) of 6999 nt. Read More

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http://dx.doi.org/10.1007/s00705-020-04711-6DOI Listing

Only a single taxonomically restricted gene family in the Drosophila melanogaster subgroup can be identified with high confidence.

Genome Biol Evol 2020 Jun 26. Epub 2020 Jun 26.

University of Arizona, Department of Ecology and Evolutionary Biology, Tucson, AZ, USA.

Taxonomically restricted genes (TRGs) are genes that are present only in one clade. Protein-coding TRGs may evolve de novo from previously non-coding sequences: functional ncRNA, introns or alternative reading frames of older protein-coding genes, or intergenic sequences. A major challenge in studying de novo genes is the need to avoid both false positives (non-functional open reading frames and/or functional genes that did not arise de novo) and false negatives. Read More

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http://dx.doi.org/10.1093/gbe/evaa127DOI Listing

Isolation and characterization of a novel cripavirus, the first Dicistroviridae family member infecting the cotton mealybug Phenacoccus solenopsis.

Arch Virol 2020 Jun 25. Epub 2020 Jun 25.

Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion, 7505101, Israel.

A new virus belonging to the family Dicistroviridae was identified in the hibiscus-infesting cotton mealybug Phenacoccus solenopsis. Using high-throughput sequencing (HTS) on an Illumina HiSeq platform, a single contig of the complete genome sequence was assembled. The authenticity of the sequence obtained by HTS was validated by RT-PCR and Sanger sequencing of the amplicons, which was also employed for the 3' untranslated region (UTR). Read More

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http://dx.doi.org/10.1007/s00705-020-04702-7DOI Listing

Changes Introduced in the Open Reading Frame of Bovine Viral Diarrhea Virus During Serial Infection of Pregnant Swine.

Front Microbiol 2020 10;11:1138. Epub 2020 Jun 10.

Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States.

Bovine viral diarrhea virus (BVDV) is one of the most economically important viruses of cattle, but this pathogen is also able to infect pigs, camelids, and a wide range of domestic and wild ruminants. BVDV isolates circulating in animal populations are genetically and antigenically highly diverse. Acute BVDV infections in cattle cause the introduction of many substitutions in the viral genome. Read More

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http://dx.doi.org/10.3389/fmicb.2020.01138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7298064PMC

The C962R ORF of African Swine Fever Strain Georgia Is Non-Essential and Not Required for Virulence in Swine.

Viruses 2020 Jun 23;12(6). Epub 2020 Jun 23.

Plum Island Animal Disease Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Greenport, NY 11944, USA.

African swine fever virus (ASFV) is the causative agent of the African swine fever (ASF) epizootic currently affecting pigs throughout Eurasia, causing significant economic losses in the swine industry. The virus genome encodes for more than 160 genes, of which only a few have been studied in detail. Here we describe the previously uncharacterized ASFV open reading frame (ORF) , a gene encoding for a putative NTPase. Read More

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http://dx.doi.org/10.3390/v12060676DOI Listing
June 2020
3.279 Impact Factor

The roles of grouper TANK in innate immune defense against iridovirus and nodavirus infections.

Fish Shellfish Immunol 2020 Jun 22;104:506-516. Epub 2020 Jun 22.

Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, PR China. Electronic address:

The TRAF family member-associated nuclear factor (NF)-κB activator (TANK) was first identified as a TRAF-binding protein with both stimulatory and inhibitory properties in host innate immune activation. To elucidate the roles of TANK in teleosts, we cloned and characterized the TANK homologue of orange-spotted grouper (Epinephelus coioides). The open reading frame (ORF) of EcTANK consists of 1026 nucleotides encoding a 342 amino acid protein with a predicted molecular mass of 38. Read More

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http://dx.doi.org/10.1016/j.fsi.2020.06.017DOI Listing

Molecular characterization, inducible expression and functional analysis of an IKKβ from the tropical sea cucumber Holothuria leucospilota.

Fish Shellfish Immunol 2020 Jun 22. Epub 2020 Jun 22.

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, 510301, PR China; Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, PR China. Electronic address:

The inhibitory kappa B kinase (IKK) is a critical regulator for the nuclear factor-κB (NF-κB) pathway. In this study, an IKKβ named as HLIKKβ was identified from the sea cucumber Holothuria leucospilota. The full-length cDNA of HLIKKβ is 4246 bp in size, containing a 132 bp 5'-untranslated region (UTR), a 1783 bp 3'-UTR and a 2331 bp open reading frame (ORF) encoding a protein of 776 amino acids with a deduced molecular weight of 89. Read More

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http://dx.doi.org/10.1016/j.fsi.2020.06.024DOI Listing

Identification of a strong quorum sensing- and thermo-regulated promoter for the biosynthesis of a new metabolite pesticide phenazine-1-carboxamide in Pseudomonas strain PA1201.

ACS Synth Biol 2020 Jun 25. Epub 2020 Jun 25.

Phenazine-1-carboxamide (PCN) produced by multifarious Pseudomonas strains represents a promising candidate as a new metabolite pesticide due to its broad-spectrum antifungal activity and capacity to induce systemic resistance in plants. The rice rhizosphere Pseudomonas strain PA1201 contains two reiterated gene clusters, phz1 and phz2, for phenazine-1-carboxylic acid (PCA) biosynthesis; PCA is further converted into PCN by this strain using a functional phzH-encoding glutamine aminotransferase. However, PCN levels in PA1201 constitute approximately one-fifth of PCA levels and the optimal temperature for PCN synthesis is 28C. Read More

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http://dx.doi.org/10.1021/acssynbio.0c00161DOI Listing

Identification of the cDNA Encoding the Growth Hormone Receptor () and the Regulation of and Gene Expression by Nutritional Status in Reeves' Turtle ().

Front Genet 2020 9;11:587. Epub 2020 Jun 9.

College of Marine Sciences, South China Agricultural University, Guangzhou, China.

(Reeves' turtle) is a slow-growing reptile that is distributed widely across China. Prior to this study, the cDNA sequence of the growth hormone receptor () in the Reeve's turtle, or how periods of starvation might influence the gene expression of and insulin-like growth factor I () in this species, were unknown. Here, we identified the full-length sequence of the cDNA encoding GHR in Reeves' turtle by using RT-PCR and RACE. Read More

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http://dx.doi.org/10.3389/fgene.2020.00587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7296147PMC

Cloning, Expression, and Structural Elucidation of a Biotechnologically Potential Alkaline Serine Protease From a Newly Isolated Haloalkaliphilic JO-26.

Front Microbiol 2020 3;11:941. Epub 2020 Jun 3.

UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, India.

An alkaline protease gene of JO-26 from saline desert, Little Rann of Kutch, was cloned and expressed in BL21 (DE3). A 1,014-bp ORF encoded 337 amino acids. The recombinant protease (APrBL) with Asp 97, His 127, and Ser 280 forming catalytic triad belongs to the subtilase S8 protease family. Read More

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http://dx.doi.org/10.3389/fmicb.2020.00941DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7283590PMC

The Locus of Epstein-Barr Virus Contributes to Viral Latency and B-Cell Immortalization.

J Virol 2020 Jun 24. Epub 2020 Jun 24.

Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, and the Penn State Hershey Cancer Institute, Hershey, Pennsylvania, U.S.A.

The Epstein-Barr virus (EBV) gene encodes an abundant linear and several circular RNAs believed to perform non-coding functions during virus replication, though an open reading frame is retained among an unknown percentage of EBV isolates. Evidence suggests that is also transcribed during latent infection, which prompted us to investigate the contribution of this locus to latency. Analysis of transcripts transiting revealed its transcription is widespread among B-cell lines supporting the latency I or III program of EBV protein expression, and to be more complex than originally presumed. Read More

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http://dx.doi.org/10.1128/JVI.01215-20DOI Listing

An alternative for proteinase K-heat-sensitive protease from fungus Onygena corvina for biotechnology: cloning, engineering, expression, characterization and special application for protein sequencing.

Microb Cell Fact 2020 Jun 24;19(1):135. Epub 2020 Jun 24.

Institute for Molecular Bio Science, University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.

Background: A neutral, heat-sensitive serine protease (NHSSP) originating from the feather-degrading fungus Onygena corvina (O. corvina) was described and defined as an alkaline serine protease of the subtilisin type S8 family, exhibiting an enzymatic activity at neutral pH. Generally, broad specificity proteases, such as proteinase K or trypsin, have found numerous applications in research and biotechnology. Read More

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http://dx.doi.org/10.1186/s12934-020-01392-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7313183PMC

Sarbecovirus comparative genomics elucidates gene content of SARS-CoV-2 and functional impact of COVID-19 pandemic mutations.

bioRxiv 2020 Jun 3. Epub 2020 Jun 3.

MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA.

Despite its overwhelming clinical importance for understanding and mitigating the COVID-19 pandemic, the protein-coding gene content of the SARS-CoV-2 genome remains unresolved, with the function and even protein-coding status of many hypothetical proteins unknown and often conflicting among different annotations, thus hindering efforts for systematic dissection of its biology and the impact of recent mutations. Comparative genomics is a powerful approach for distinguishing protein-coding versus non-coding functional elements, based on their characteristic patterns of change, which we previously used to annotate protein-coding genes in human, fly, and other species. Here, we use comparative genomics to provide a high-confidence set of SARS-CoV-2 protein-coding genes, to characterize their protein-level and nucleotide-level evolutionary constraint, and to interpret the functional implications for SARS-CoV-2 mutations acquired during the current pandemic. Read More

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http://dx.doi.org/10.1101/2020.06.02.130955DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7302193PMC

Effects of high stocking density on the galectin gene expression in noble scallop Chalmys nobilis under bacterial infection.

Fish Shellfish Immunol 2020 Jun 19. Epub 2020 Jun 19.

Key Laboratory of Marine Biotechnology of Guangdong Province, Institute of Marine Science, Shantou University, Shantou, 515063, China; Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong, Province, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China. Electronic address:

High stocking densities have been shown to have adverse effects on the physiology of bivalves. The noble scallop Chlamys nobilis is one of the most important cultured shellfish in Southern China. However, the effects of scallop stocking density on its immunity is not well understood. Read More

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http://dx.doi.org/10.1016/j.fsi.2020.06.030DOI Listing

Expression of HSP70 family mRNAs in albino northern snakehead, Channa argus: Response to extreme temperature stress and bacterial infection.

Fish Shellfish Immunol 2020 Jun 18;104:457-469. Epub 2020 Jun 18.

Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China. Electronic address:

The wild albino northern snakehead, Channa argus, has only been found in Jialing Rivers System of China so far. It is easy to be affected by the environmental factors such as temperature changes and bacterial infection, thus causing a huge economic loss. Therefore, this study cloned a 2,213 bp cDNA that encodes a protein of heat shock protein 70 (CaHSP70), which has an open reading frame (ORF) that encodes 639 amino acids and the corresponding polypeptides of 70. Read More

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http://dx.doi.org/10.1016/j.fsi.2020.05.033DOI Listing

Characterization and functional analysis of liver-expressed antimicrobial peptide-2 (LEAP-2) from golden pompano Trachinotus ovatus (Linnaeus 1758).

Fish Shellfish Immunol 2020 Jun 17;104:419-430. Epub 2020 Jun 17.

Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China. Electronic address:

The liver-expressed antimicrobial peptide-2 (LEAP-2) is an important component of the innate immune defense system and plays an important role in resisting the invasion of pathogenic microorganisms. In this study, LEAP-2 from golden pompano (Trachinotus ovatus) was characterized and its expression in response to Photobacterium damselae was investigated. The full-length LEAP-2 cDNA was 1758 bp, which comprised a 5'-UTR of 250 bp, an ORF of 321 bp, and a 3'-UTR of 1187 bp, encoding 106 amino acids. Read More

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http://dx.doi.org/10.1016/j.fsi.2020.06.029DOI Listing

Multiple information carried by RNAs: total eclipse or a light at the end of the tunnel?

RNA Biol 2020 Jun 26:1-14. Epub 2020 Jun 26.

Université De Paris, Epigenetics and Cell Fate, CNRS , Paris, France.

The findings that an RNA is not necessarily either coding or non-coding, or that a precursor RNA can produce different types of mature RNAs, whether coding or non-coding, long or short, have challenged the dichotomous view of the RNA world almost 15 years ago. Since then, and despite an increasing number of studies, the diversity of information that can be conveyed by RNAs is rarely searched for, and when it is known, it remains largely overlooked in further functional studies. Here, we provide an update with prominent examples of multiple functions that are carried by the same RNA or are produced by the same precursor RNA, to emphasize their biological relevance in most living organisms. Read More

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http://dx.doi.org/10.1080/15476286.2020.1783868DOI Listing

Protective functions of alternative splicing transcripts (- and -) of from bermudagrass under multiple abiotic stresses.

Gene X 2020 Dec 22;5:100033. Epub 2020 Apr 22.

School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.

Dehydrins (DHNs) play critical roles in plant adaptation to abiotic stresses. The objective of this study was to characterize DHNs in bermudagrass ( spp.). Read More

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http://dx.doi.org/10.1016/j.gene.2020.100033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285969PMC
December 2020

Expression and functional analysis of the Akt gene from Daphnia pulex.

Comp Biochem Physiol B Biochem Mol Biol 2020 Jun 13;248-249:110462. Epub 2020 Jun 13.

School of Life Science, East China Normal University, Shanghai 200062, China. Electronic address:

Daphnia pulex is a nutrient-rich freshwater crustacean with two different reproduction methods. Akt is a serine/threonine protein kinase that plays an important role in cell growth, survival, and lifespan regulation. To explore the function of Akt in the growth and aging process of Daphnia pulex, we cloned the cDNA sequence of the open reading frame (ORF) of the akt gene based on the bioinformatic analysis of the transcriptome data of D. Read More

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http://dx.doi.org/10.1016/j.cbpb.2020.110462DOI Listing

-Based Vaccine Vector D1701-V Induces Strong CD8+ T Cell Response against the Transgene but Not against ORFV-Derived Epitopes.

Vaccines (Basel) 2020 Jun 10;8(2). Epub 2020 Jun 10.

Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany.

The potency of viral vector-based vaccines depends on their ability to induce strong transgene-specific immune response without triggering anti-vector immunity. Previously, (ORFV, ) strain D1701-V was reported as a novel vector mediating protection against viral infections. The short-lived ORFV-specific immune response and the absence of virus neutralizing antibodies enables repeated immunizations and enhancement of humoral immune responses against the inserted antigens. Read More

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http://dx.doi.org/10.3390/vaccines8020295DOI Listing

RNAseq Analysis of Rhizomania-Infected Sugar Beet Provides the First Genome Sequence of Beet Necrotic Yellow Vein Virus from the USA and Identifies a Novel Alphanecrovirus and Putative Satellite Viruses.

Viruses 2020 Jun 10;12(6). Epub 2020 Jun 10.

United States Department of Agriculture, Agricultural Research Service, Northern Crop Science Laboratory, Fargo, ND 58102, USA.

"Rhizomania" of sugar beet is a soilborne disease complex comprised of beet necrotic yellow vein virus (BNYVV) and its plasmodiophorid vector, . Although BNYVV is considered the causal agent of rhizomania, additional viruses frequently accompany BNYVV in diseased roots. In an effort to better understand the virus cohort present in sugar beet roots exhibiting rhizomania disease symptoms, five independent RNA samples prepared from diseased beet seedlings reared in a greenhouse or from field-grown adult sugar beet plants and enriched for virus particles were subjected to RNAseq. Read More

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http://dx.doi.org/10.3390/v12060626DOI Listing

Identification of Foxl2 in freshwater mussel Hyriopsis cumingii and its involvement in sex differentiation.

Gene 2020 Jun 9;754:144853. Epub 2020 Jun 9.

Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China. Electronic address:

The freshwater mussel Hyriopsis cumingii, is the most important species for pearl culture in China. At present, the mechanisms underlying sex differentiation and determination remain unclear in this species. Herein the open reading frame (ORF) of Foxl2 from H. Read More

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http://dx.doi.org/10.1016/j.gene.2020.144853DOI Listing

A microfibril-associated glycoprotein 4 (MFAP4) from Nile tilapia (Oreochromis niloticus) possesses agglutination and opsonization ability to bacterial pathogens.

Fish Shellfish Immunol 2020 Jun 9;104:182-191. Epub 2020 Jun 9.

Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, 510631, PR China. Electronic address:

Microfibril-associated glycoprotein 4 (MFAP4), a pattern recognition-like molecule with a fibrinogen-like domain (FBG), has the ability to combine and agglutinate pathogens, playing an essential role in the first line of innate immune defense. In this study, the sequence of Nile tilapia (Oreochromis niloticus) microfibril-associated glycoprotein 4 (OnMFAP4) open reading frame (ORF) was amplified and identified. The ORF of OnMFAP4 is 720 bp of nucleotides and codes for 239 amino acids. Read More

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http://dx.doi.org/10.1016/j.fsi.2020.06.009DOI Listing

Grouper interferon-induced transmembrane protein 3 (IFITM3) inhibits the infectivity of iridovirus and nodavirus by restricting viral entry.

Fish Shellfish Immunol 2020 Jun 10;104:172-181. Epub 2020 Jun 10.

Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China. Electronic address:

Interferon-induced transmembrane proteins (IFITMs) have been identified as important host restriction factors in mammals for the control of infection by multiple viruses. However, the antiviral functions of IFITMs against fish viruses remain largely uncertain. In this study, the IFITM3 homolog from orange spotted grouper (EcIFITM3) was cloned and its roles in grouper virus infection were investigated. Read More

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http://dx.doi.org/10.1016/j.fsi.2020.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7283088PMC

Novel genotype definition and genome characteristics of duck circovirus in central and Eastern China.

Transbound Emerg Dis 2020 Jun 12. Epub 2020 Jun 12.

College of Animal Science, South China Agricultural University, Guangzhou, PR China.

To explore genetic variations in duck circovirus (DuCV) and the molecular epidemiology of its infection, tissue samples were collected from 219 dead ducks from 20 farms in the central and eastern regions of China. All farms tested positive for DuCV, with duck-origin goose parvovirus, reovirus and Tembusu virus having co-infection rates of 100%, 0% and 0%, respectively. A total of 20 strains from the DuCV-positive flock were sequenced. Read More

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http://dx.doi.org/10.1111/tbed.13676DOI Listing

Role of the regulatory genes SEF1, VMA1 and SFU1 in riboflavin synthesis in the flavinogenic yeast Candida famata (Candida flareri).

Yeast 2020 Jun 11. Epub 2020 Jun 11.

Department of Molecular Biology and Biotechnology, Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, Ukraine.

Riboflavin or vitamin B is an essential dietary component for humans and animals that is the precursor of flavin coenzymes flavin mononucleotide and flavin adenine dinucleotide involved in numerous enzymatic reactions. The flavinogenic yeast Candida famata overproduces riboflavin under iron starvation; however, regulation of this process is poorly understood. Regulatory gene SEF1 encoding transcription activator has been identified. Read More

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http://dx.doi.org/10.1002/yea.3503DOI Listing

The UMAG_00031 gene from Ustilago maydis encodes a putative membrane protein involved in pH control and morphogenesis.

Arch Microbiol 2020 Jun 11. Epub 2020 Jun 11.

Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado Postal 629, 36500, Irapuato, Gto, Mexico.

We report the characterization of the gene UMAG_00031 from Ustilago maydis, previously identified as upregulated at alkaline pH. This gene is located on chromosome 1 and contains an ORF of 1539 bp that encodes a putative protein of 512 amino acids with an MW of 54.8 kDa. Read More

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http://dx.doi.org/10.1007/s00203-020-01936-6DOI Listing

Additional ORFs in Plant LTR-Retrotransposons.

Front Plant Sci 2020 26;11:555. Epub 2020 May 26.

Structure and Evolution of Plant Genomes Group, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Barcelona, Spain.

LTR-retrotransposons share a common genomic organization in which the 5' long terminal repeat (LTR) is followed by the and genes and terminates with the 3' LTR. Although GAG-POL-encoded proteins are considered sufficient to accomplish the LTR-retrotransposon transposition, a number of elements carrying additional open reading frames (aORF) have been described. In some cases, the presence of an aORF can be explained by a phenomenon similar to retrovirus gene transduction, but in these cases the aORFs are present in only one or a few copies. Read More

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http://dx.doi.org/10.3389/fpls.2020.00555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7264820PMC

N-terminal deletion of Swi3 created by the deletion of a dubious ORF YJL175W mitigates protein burden effect in S. cerevisiae.

Sci Rep 2020 Jun 11;10(1):9500. Epub 2020 Jun 11.

Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.

Extreme overproduction of gratuitous proteins can overload cellular protein production resources, leading to growth defects, a phenomenon known as the protein burden/cost effect. Genetic screening in the budding yeast Saccharomyces cerevisiae has isolated several dubious ORFs whose deletions mitigated the protein burden effect, but individual characterization thereof has yet to be delineated. We found that deletion of the YJL175W ORF yielded an N-terminal deletion of Swi3, a subunit of the SWI/SNF chromatin remodeling complex, and partial loss of function of Swi3. Read More

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http://dx.doi.org/10.1038/s41598-020-66307-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7289859PMC

Identification of a modori-inducing proteinase in the threadfin bream: Molecular cloning, tissue distribution and proteinase leakage from viscera during ice storage.

Food Chem 2020 Jun 4;330:127246. Epub 2020 Jun 4.

Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki 852-8521, Japan. Electronic address:

Previously we purified and characterized a sarcoplasmic serine proteinase (SSP) from the belly muscle of the threadfin bream as a modori-inducing proteinase. In our attempt to clarify the structure and physiological functions of SSP, we successfully cloned the full-length cDNA of SSP (ORF 726 bp). The deduced amino acid sequence of SSP (241 residues) was highly homologous to fish trypsinogen. Read More

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http://dx.doi.org/10.1016/j.foodchem.2020.127246DOI Listing

Revisiting the host adhesion determinants of Streptococcus thermophilus siphophages.

Microb Biotechnol 2020 Jun 11. Epub 2020 Jun 11.

School of Microbiology, University College Cork, Cork, Ireland.

Available 3D structures of bacteriophage modules combined with predictive bioinformatic algorithms enabled the identification of adhesion modules in 57 siphophages infecting Streptococcus thermophilus (St). We identified several carbohydrate-binding modules (CBMs) in so-called evolved distal tail (Dit) and tail-associated lysozyme (Tal) proteins of St phage baseplates. We examined the open reading frame (ORF) downstream of the Tal-encoding ORF and uncovered the presence of a putative p2-like receptor-binding protein (RBP). Read More

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http://dx.doi.org/10.1111/1751-7915.13593DOI Listing

Rv0341 Promotes Survival in In Vitro Hostile Environments and within Macrophages and Induces Cytokines Expression.

Pathogens 2020 Jun 8;9(6). Epub 2020 Jun 8.

State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Beibei, Chongqing 400715, China.

represents an ancient deadly human pathogen that can survive and multiply within macrophages. The effectors are key players for the successful pathogenesis of this bacterium. open reading frame (ORF) , a pathogenic mycobacteria-specific gene, was found to be upregulated in macrophages isolated from human tuberculosis granuloma and inside the macrophages during in vitro infection by . Read More

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http://dx.doi.org/10.3390/pathogens9060454DOI Listing

Orf virus infection after Eid al-Adha.

IDCases 2020 30;21:e00854. Epub 2020 May 30.

Section of Infectious Diseases, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA.

Human orf, also called ecthyma contagiosum, is a zoonotic infection that causes self-resolving skin lesions after contact with infected livestock. We present the case of a 45-year-old Moroccan-born man who developed multiple painful erythematous, violaceous plaques on his hands after butchering a sheep to celebrate the Muslim holiday Eid al-Adha. The diagnosis of orf virus infection was established based on exposure history, histopathology, and classic skin lesions. Read More

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http://dx.doi.org/10.1016/j.idcr.2020.e00854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7270598PMC

Thermal and Mechanical Properties of the Biocomposites of Biocarbon and Poly(3-ydroxybutyrate--3-ydroxyvalerate) (PHBV).

Polymers (Basel) 2020 Jun 6;12(6). Epub 2020 Jun 6.

Bioproducts Discovery and Development Centre, Department of Plant Agriculture, Crop Science Building, University of Guelph, Guelph, ON N1G 2W1, Canada.

biocarbon (MB), a renewable resource-based, carbon-rich material, was melt-processed with poly (3-hydroxybutyrate--3-hydroxyvalerate) (PHBV) to produce sustainable biocomposites. The addition of the biocarbon improved the Young's modulus of PHBV from 3.6 to 5. Read More

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http://dx.doi.org/10.3390/polym12061300DOI Listing

SARS-CoV-2 is sensitive to type I interferon pretreatment.

bioRxiv 2020 Apr 9. Epub 2020 Apr 9.

Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA.

SARS-CoV-2, a novel coronavirus (CoV), has recently emerged causing an ongoing outbreak of viral pneumonia around the world. While genetically distinct from the original SARS-CoV, both group 2B CoVs share similar genome organization and origins to coronaviruses harbored in bats. Importantly, initial guidance has used insights from SARS-CoV infection to inform treatment and public health strategies. Read More

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http://dx.doi.org/10.1101/2020.03.07.982264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239075PMC

Decoding SARS-CoV-2 Hijacking of Host Mitochondria in Pathogenesis of COVID-19.

Am J Physiol Cell Physiol 2020 Jun 8. Epub 2020 Jun 8.

Department of Biotechnology and BioinformaticsBirla Institute of Scientific Research Statue Circle, Jaipur, Rajasthan, 302001, India.

Due to ongoing pandemic around the world, the mechanisms underlying the SARS-CoV-2 induced COVID-19 are subject to intense investigation. Based on available data for the SARS-CoV-1 virus, we suggest how CoV-2 localization of RNA transcripts in mitochondria hijacks the host cell's mitochondrial function to viral advantage. Besides viral RNA transcripts, RNA also localizes to mitochondria. Read More

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http://dx.doi.org/10.1152/ajpcell.00224.2020DOI Listing

DNA tandem repeats contribute to the genetic diversity of Brevibacterium aurantiacum phages.

Environ Microbiol 2020 Jun 8. Epub 2020 Jun 8.

Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada.

This report presents the characterization of the first virulent phages infecting Brevibacterium aurantiacum, a bacterial species used during the manufacture of surface-ripened cheeses. These phages were also responsible for flavor and color defects in surface-ripened cheeses. Sixteen phages (out of sixty-two isolates) were selected for genome sequencing and comparative analyses. Read More

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http://dx.doi.org/10.1111/1462-2920.15113DOI Listing

COVID-19 target: A specific target for novel coronavirus detection.

Gene Rep 2020 Sep 30;20:100740. Epub 2020 May 30.

Antimicrobial Resistance Research Center, Medical School, Mashhad University of Medical Sciences, Mashhad, Iran.

An ongoing outbreak of pneumonia associated with a novel coronavirus has been reported worldwide and become a global health problem; hence, the diagnosis and differentiation of this virus from other types of coronavirus is essential to control of the disease. To this end, the analysis of genomics data plays a vital role in introducing a stronger target and consequently provides better results in laboratory examinations. The modified comparative genomics approach helps us to find novel specific targets by comparing two or more sequences on the nucleotide collection database. Read More

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http://dx.doi.org/10.1016/j.genrep.2020.100740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7261075PMC
September 2020

Complete genome sequence of begonia flower breaking virus, a novel member of the genus Potyvirus.

Arch Virol 2020 Jun 5. Epub 2020 Jun 5.

College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China.

We determined the complete genomic sequence of begonia flower breaking virus (BFBV), a novel putative member of the genus Potyvirus isolated from Begonia bowerae cv. 'Tiger' plants grown in Kunming. The genomic RNA comprises 9540 nucleotides (nt), excluding the 3'-terminal poly(A) tail, and contains a typical open reading frame (ORF) of potyviruses. Read More

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http://dx.doi.org/10.1007/s00705-020-04663-xDOI Listing