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Molecular characterization of a novel virga-like virus associated with wheat.

Arch Virol 2022 Jun 25. Epub 2022 Jun 25.

State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.

In this work, we report the detection of a novel single-strand RNA virus from wheat, tentatively named "Triticum aestivum-associated virga-like virus 1" (TaAVLV1). Further characterization revealed that the complete genome of TaAVLV1 is divided into two segments, RNA1 and RNA2, which are 3530 and 3466 nt in length, excluding their respective polyA tails, and each contains only one open reading frame (ORF). The ORF of RNA1 encodes an RNA-dependent RNA polymerase (RdRp), while the ORF of RNA2 encodes a putative protein with methyltransferase and helicase domains. Read More

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Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.

Nat Commun 2022 Jun 25;13(1):3645. Epub 2022 Jun 25.

New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.

Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, detection of recombination is only feasible when genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was infected with two distinct viral variants: Alpha (B. Read More

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Design of a US28 ORF Deletion Virus in a Temperature-Sensitive Cytomegalovirus Strain Fails to Promote Lytic Replication in Hematopoietic Cells.

Viruses 2022 Jun 12;14(6). Epub 2022 Jun 12.

Genomic Medicine, Infection Biology Program, Global Center for Pathogen & Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.

Human cytomegalovirus (CMV) is a ubiquitous pathogen that latently resides in hematopoietic cells. Latently infected individuals with dysfunctional immune systems often experience CMV reactivation, which can cause devastating disease and mortality. While factors dictating the balance between latency and reactivation are not completely understood, CMV US28 is required for maintaining latent infection, and viral mutants that alter US28 function result in a lytic-like, rather than latent, infection in hematopoietic cells. Read More

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Variable Gene Expression in Human Ganglia Latently Infected with Varicella-Zoster Virus.

Viruses 2022 Jun 9;14(6). Epub 2022 Jun 9.

Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK.

Varicella-Zoster virus (VZV) is a pathogenic human herpes virus that causes varicella ("chicken pox") as a primary infection, following which it becomes latent in neuronal cells in human peripheral ganglia. It may then reactivate to cause herpes zoster ("shingles"). Defining the pattern of VZV gene expression during latency is an important issue, and four highly expressed VZV genes were first identified by Randall Cohrs in 1996 using cDNA libraries. Read More

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Silencing of the Prophenoloxidase Gene Increased the Ability of Acquisition and Retention of Tomato chlorosis virus by .

Int J Mol Sci 2022 Jun 11;23(12). Epub 2022 Jun 11.

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

Tomato chlorosis virus (ToCV) has seriously impacted tomato production around the world. ToCV is semi-persistently transmitted by the whitefly, , which is a serious agricultural pest in the world. However, the interaction mechanism between ToCV and its whitefly vector is still poorly understood. Read More

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SARS-CoV-2: A Master of Immune Evasion.

Biomedicines 2022 Jun 7;10(6). Epub 2022 Jun 7.

Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.

Viruses and their hosts have coevolved for a long time. This coevolution places both the pathogen and the human immune system under selective pressure; on the one hand, the immune system has evolved to combat viruses and virally infected cells, while viruses have developed sophisticated mechanisms to escape recognition and destruction by the immune system. SARS-CoV-2, the pathogen that is causing the current COVID-19 pandemic, has shown a remarkable ability to escape antibody neutralization, putting vaccine efficacy at risk. Read More

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Characterization of peroxiredoxin from Neocaridina denticulata sinensis and its antioxidant and DNA protection activity analysis.

Fish Shellfish Immunol 2022 Jun 20;127:211-218. Epub 2022 Jun 20.

School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China. Electronic address:

Peroxiredoxin (Prx) is an antioxidant protein that widely exists in various organisms. To further investigate the role of Prx in the antioxidant and immune responses of Neocaridina denticulata sinensis, the full-length cDNA sequence of a Prx gene (Nd-Prx) from N. denticulata sinensis was obtained. Read More

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Molecular Characterization of Two Genes Encoding Novel Ca-Independent Phospholipase A2s from the Silkworm, .

Curr Issues Mol Biol 2022 Feb 4;44(2):777-790. Epub 2022 Feb 4.

State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400716, China.

Eicosanoids are crucial downstream signals in the insect immune responses. Phospholipase A2 (PLA2) catalyzes phospholipids, the initial step in eicosanoid biosynthesis. In mammals, the biological roles of have been extensively studied; however, only a few studies have attempted to explore functions in insects. Read More

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February 2022

Identification and antioxidant capacity of 4-hydroxyphenylpyruvate dioxygenase (HPPD), a new favored herbicide target, in Apis cerana cerana.

Pestic Biochem Physiol 2022 Jun 2;184:105110. Epub 2022 May 2.

State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China. Electronic address:

4-Hydroxyphenylpyruvate dioxygenase (HPPD), a nonheme oxygenase, catalyzes the second step of the tyrosine catabolic pathway, which is shared by almost all aerobic life forms. This demonstrates its importance in aerobic biology. We isolated an HPPD homolog from Apis cerana cerana and named it AccHPPD. Read More

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Knockdown of the chromatin remodeling ATPase gene Brahma impairs the reproductive potential of the brown planthopper, Nilaparvata lugens.

Pestic Biochem Physiol 2022 Jun 22;184:105106. Epub 2022 Apr 22.

State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China. Electronic address:

The brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the most destructive pests in rice-growing regions of Asia. Extensive studies have suggested that SWI/SNF chromatin remodeling ATPase Brahma (BRM) plays multiple roles in the insect model Drosophila. Yet much less is known about the physiological properties for NlBRM. Read More

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Molecular cloning and expression profiling of insulin-like growth factor 2 and IGF-binding protein 6 in (Hamilton 1822).

Anim Biotechnol 2022 Jun 17:1-12. Epub 2022 Jun 17.

Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, India.

Growth is an important trait in aquaculture and the major genes that regulate it are Insulin-like growth factors (IGFs) and IGF binding proteins (IGFBPs). In this study, the full-length coding sequences of IGF2 and IGFBP6 genes in the Indian catfish were cloned and characterized. The full-length cDNA sequences of IGF2 and IGFBP6 were 885 bp (ORF 642 bp) and 928 bp (ORF 600 bp), encoding 213 and 199 amino acids, respectively. Read More

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Culturing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) for Diagnosis and Genome Sequencing.

Lab Med 2022 Jun 17. Epub 2022 Jun 17.

State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.

Objective: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid detection "re-positive" phenomenon is encountered clinically. The accuracy of a viral nucleic acid test is crucial to prevent reintroduction of the virus into the community. This study evaluated the effect of virus culturing on increasing the sensitivity and specificity of real-time polymerase chain reaction (RT-PCR) detection and viral genomic sequencing. Read More

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A RAC-alpha serine/threonine-protein kinase (CgAKT1) involved in the synthesis of CgIFNLP in oyster Crassostrea gigas.

Fish Shellfish Immunol 2022 Jun 14;127:129-139. Epub 2022 Jun 14.

Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China. Electronic address:

The RAC-alpha serine/threonine-protein kinase (AKT) is one of the most important protein kinases involved in many biological processes in eukaryotes. In the present study, a novel AKT homologue named CgAKT1 was identified from the Pacific oyster Crassostrea gigas. The open reading frame (ORF) of CgAKT1 cDNA was of 1482 bp encoding a peptide with 493 amino acid residues. Read More

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Reference-aided full-length transcript assembly, cDNA cloning, and molecular characterization of coronatine-insensitive 1b (COI1b) gene in coconut (Cocos nucifera L.).

Mol Biol Rep 2022 Jun 16. Epub 2022 Jun 16.

Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, Laguna, Philippines.

Background: In the Philippines, 26% of the total agricultural land is devoted to coconut production making coconut one of the most valuable industrial crop in the country. However, the country's multimillion-dollar coconut industry is threatened by the outbreak of coconut scale insect (CSI) and other re-emerging insect pests promoting national research institutes to work jointly on developing new tolerant coconut varieties. Here, we report the cloning and characterization of coronatine-insensitive 1 (COI1) gene, one of the candidate insect defense genes, using 'Catigan Green Dwarf' (CATD) genome sequence assembly as reference. Read More

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ubiF is involved in acid stress tolerance and symbiotic competitiveness in Rhizobium favelukesii LPU83.

Braz J Microbiol 2022 Jun 15. Epub 2022 Jun 15.

Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 115 49 y 50 (1900), Buenos Aires, La Plata, Argentina.

The acidity of soils significantly reduces the productivity of legumes mainly because of the detrimental effects of hydrogen ions on the legume plants, leading to the establishment of an inefficient symbiosis and poor biological nitrogen fixation. We recently reported the analysis of the fully sequenced genome of Rhizobium favelukesii LPU83, an alfalfa-nodulating rhizobium with a remarkable ability to grow, nodulate and compete in acidic conditions. To gain more insight into the genetic mechanisms leading to acid tolerance in R. Read More

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Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames.

Brief Bioinform 2022 Jun 13. Epub 2022 Jun 13.

Chinese Academy of Agricultural Sciences, China.

Accurate prediction of open reading frames (ORFs) is important for studying and using genome sequences. Ribosomes move along mRNA strands with a step of three nucleotides and datasets carrying this information can be used to predict ORFs. The ribosome-protected footprints (RPFs) feature a significant 3-nt periodicity on mRNAs and are powerful in predicting translating ORFs, including small ORFs (sORFs), but the application of RPFs is limited because they are too short to be accurately mapped in complex genomes. Read More

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Genetic architecture of seed glycerolipids in Asian cultivated rice.

Plant Cell Environ 2022 Jun 13. Epub 2022 Jun 13.

Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.

Glycerolipids are essential for rice development and grain quality but its genetic regulation remains unknown. Here we report its genetic base using metabolite-based genome-wide association study and metabolite-based quantitative traits locus (QTL) analyses based on lipidomic profiles of seeds from 587 Asian cultivated rice accessions and 103 chromosomal segment substitution lines, respectively. We found that two genes encoding phosphatidylcholine (PC):diacylglycerol cholinephosphotransferase (OsLP1) and granule-bound starch synthase I (Waxy) contribute to variations in saturated triacylglycerol (TAG) and lyso-PC contents, respectively. Read More

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The MIP-T3 from shrimp Litopenaeus vannamei restricts white spot syndrome virus infection via regulating NF-κB activation.

Fish Shellfish Immunol 2022 Jun 11;127:56-64. Epub 2022 Jun 11.

State Key Laboratory of Biocontrol, School of Marine Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/ Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, PR China. Electronic address:

In vertebrate, MIP-T3 (microtubule-interacting protein associated with TRAF3) functions as a regulator of innate immune response that involves many cellular processes. However, the immune response regulated by shrimp (an arthropod) MIP-T3 remains unrevealed. In the present study, a MIP-T3 homolog from shrimp Litopenaeus vannamei (named as LvMIP-T3) was cloned and identified. Read More

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Kalanchoë blossfeldiana naturally transformed with Rhizobium rhizogenes exhibits superior root phenotype.

Plant Sci 2022 Aug 17;321:111323. Epub 2022 May 17.

Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, 2630 Tåstrup, Denmark.

Plant transformation with root oncogenic loci (rol) genes and open reading frames (ORFs) from Rhizobium rhizogenes have not yet targeted the underground root phenotype of these transformants. Hence, there is a need to develop plants with more efficient root system architecture (RSA). Here, RSA was assessed in naturally transformed (NT) and single rol/ORF Kalanchoë blossfeldiana 'Molly' lines in an aeroponic growth system combined with gene expression analysis. Read More

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RNA-seq transcriptome analysis and identification of the theromacin antimicrobial peptide of the copepod Apocyclops royi.

Dev Comp Immunol 2022 Jun 6;135:104464. Epub 2022 Jun 6.

Department of Food Technology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand. Electronic address:

Copepods, including Apocyclops royi, are small aquatic crustaceans and one of the important foods for fish and shellfish larvae. However, studies of the host-pathogen interactions and understanding of infectious disease in copepods are still very limited, yet they are likely to be a significant factor in the sustainable development of copepod aquaculture. In the present study, we performed de novo RNA sequence analysis of A. Read More

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Genome-edited ATP BINDING CASSETTE B1 transporter SD8 knockouts have optimized rice architecture without yield penalty.

Plant Commun 2022 Jun 10:100347. Epub 2022 Jun 10.

Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China. Electronic address:

Short Summary: In this work we identified that a putative rice ORF Semi-Dwarf in chr8 (SD8) that encodes a putative ortholog of the Arabidopsis thaliana ABCB1. Genome-edited SD8 could optimize rice architecture by reducing plant height and flag leaf angle without yield penalty. Moreover, SD8 knockouts may even have the potential for increased yield under high density planting in rice. Read More

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Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in asymptomatic and symptomatic populations.

PLoS One 2022 10;17(6):e0269798. Epub 2022 Jun 10.

Life Sciences Testing Center, Northeastern University, Burlington, MA, United States of America.

Clinical evidence for asymptomatic cases of coronavirus disease (COVID-19) has reinforced the significance of effective surveillance testing programs. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays are considered the 'gold standard' for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. However, the labor and resource requirements can be prohibitive with respect to large testing volumes associated with the pandemic. Read More

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A Novel Mutator-Like Transposable Elements With Unusual Structure and Recent Transpositions in Barley ().

Front Plant Sci 2022 23;13:904619. Epub 2022 May 23.

Wheat Health, Genetics, and Quality Research Unit, USDA-ARS, Pullman, WA, United States.

Mutator-like transposable elements (MULEs) represent a unique superfamily of DNA transposons as they can capture host genes and cause higher frequency of mutations in some eukaryotes. Despite their essential roles in plant evolution and functional genomics, MULEs are not fully understood yet in many important crops including barley (). In this study, we analyzed the barley genome and identified a new mutator transposon . Read More

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Varicella-Zoster virus ORF9 is an antagonist of the DNA sensor cGAS.

EMBO J 2022 Jun 7:e109217. Epub 2022 Jun 7.

MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.

Varicella-Zoster virus (VZV) causes chickenpox and shingles. Although the infection is associated with severe morbidity in some individuals, molecular mechanisms that determine innate immune responses remain poorly defined. We found that the cGAS/STING DNA sensing pathway was required for type I interferon (IFN) induction during VZV infection and that recognition of VZV by cGAS restricted its replication. Read More

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Detection and Stability of SARS-CoV-2 in Three Self-Collected Specimen Types: Flocked Midturbinate Swab (MTS) in Viral Transport Media, Foam MTS, and Saliva.

Microbiol Spectr 2022 Jun 6:e0103322. Epub 2022 Jun 6.

Integrated Research & Development Laboratory, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA.

Respiratory specimen collection materials shortages hampers severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. We compared specimen alternatives and evaluated SARS-CoV-2 RNA stability under simulated shipping conditions. We compared concordance of RT-PCR detection of SARS-CoV-2 from flocked midturbinate swabs (MTS) in viral transport media (VTM), foam MTS without VTM, and saliva. Read More

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Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Reveals Nematode Infection Activating Plant Defense Response.

Front Plant Sci 2022 18;13:866322. Epub 2022 May 18.

Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.

Full-length transcriptome sequencing with long reads is a powerful tool to analyze transcriptional and post-transcriptional events; however, it has not been applied on soybean (). Here, a comparative full-length transcriptome analysis was performed on soybean genotype 09-138 infected with soybean cyst nematode (SCN, ) race 4 (SCN4, incompatible reaction) and race 5 (SCN5, compatible reaction) using Oxford Nanopore Technology. Each of 9 full-length samples collected 8 days post inoculation with/without nematodes generated an average of 6. Read More

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A novel interleukin-1 receptor-associated kinase 4 from blunt snout bream (Megalobrama amblycephala) is involved in inflammatory response via MyD88-mediated NF-κB signal pathway.

Fish Shellfish Immunol 2022 Jun 1;127:23-34. Epub 2022 Jun 1.

Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China. Electronic address:

Interleukin-1 receptor-associated kinase 4 (IRAK4) plays a crucial role in the Toll-like receptor/IL-1R signal pathway, which mediates the downstream signal transduction involved in innate and adaptive immunity. In the present study, an IRAK4 homologue (named as MaIRAK4) from blunt snout bream (Megalobrama amblycephala) was cloned and characterized. The open reading frame (ORF) of MaIRAK4 contains 1422 nucleotides, encoding a putative protein of 473 amino acids. Read More

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Characterization of myogenic regulatory factors, myod and myf5 from Megalobrama amblycephala and the effect of lipopolysaccharide on satellite cells in skeletal muscle.

Gene 2022 Aug 31;834:146608. Epub 2022 May 31.

Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070 Wuhan, PR China. Electronic address:

Myod and Myf5 are muscle-specific basic helix-loop-helix (bHLH) transcription factors that play essential roles in regulating skeletal muscle development and growth. In order to investigate potential function of myod and myf5 of Megalobrama amblycephala, an economically important freshwater fish species, in the present study, we characterized the sequences and expression profiles of M. amblycephala myod and myf5. Read More

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Insertion-and-Deletion Mutations between the Genomes of SARS-CoV, SARS-CoV-2, and Bat Coronavirus RaTG13.

Tetsuya Akaishi

Microbiol Spectr 2022 Jun 6:e0071622. Epub 2022 Jun 6.

Division of General Medicine, Tohoku Universitygrid.69566.3a, Sendai, Japan.

The evolutional process of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) development remains inconclusive. This study compared the genome sequences of severe acute respiratory syndrome coronavirus (SARS-CoV), bat coronavirus RaTG13, and SARS-CoV-2. In total, the genomes of SARS-CoV-2 and RaTG13 were 77. Read More

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Exercise, Mitohormesis, and Mitochondrial ORF of the 12S rRNA Type-C (MOTS-c).

Diabetes Metab J 2022 05 25;46(3):402-413. Epub 2022 May 25.

Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.

Low levels of mitochondrial stress are beneficial for organismal health and survival through a process known as mitohormesis. Mitohormetic responses occur during or after exercise and may mediate some salutary effects of exercise on metabolism. Exercise-related mitohormesis involves reactive oxygen species production, mitochondrial unfolded protein response (UPRmt), and release of mitochondria-derived peptides (MDPs). Read More

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