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1. Metagenomic analysis suggests unique gut‐microbiota composition and GH family constitution of Macrotermes annandalei

Author:
Yongzhong Cui; Weiwei Wang; Qin Lu; Hai‐Xia Wu; Xiaofei Ling; Juan Liu; Jinwen Zhang; Hang Chen
Source:
Entomological research 2022 v.52 no.3 pp. 127-134
ISSN:
1738-2297
Subject:
open reading frames,   etc   ; Bacteroides; Firmicutes; Macrotermes; cellulose; clean energy; databases; energy; glycosides; humans; hydrolases; insects; intestines; metagenomics; renewable energy sources; research;     Show all 16 Subjects
Abstract:
... Energy supply is a major concern of human survival and development, and that concern demands new sources of renewable clean energy. Cellulose, as a renewable energy material is affected by low activity and high cost of cellulose. Studies of cellulose degrading bacterial microbiota in insect intestine have revealed that these potential microbes can be used as a rich resource of cellulose degrading ...
DOI:
10.1111/1748-5967.12572

2. Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution

Author:
Sk Sarif Hassan; Pallab Basu; Elrashdy M. Redwan; Kenneth Lundstrom; Pabitra Pal Choudhury; Ángel Serrano-Aroca; Gajendra Kumar Azad; Alaa A.A. Aljabali; Giorgio Palu; Tarek Mohamed Abd El-Aziz; Debmalya Barh; Bruce D. Uhal; Parise Adadi; Kazuo Takayama; Nicolas G. Bazan; Murtaza M. Tambuwala; Amos Lal; Gaurav Chauhan; Wagner Baetas-da-Cruz; Samendra P. Sherchan; Vladimir N. Uversky
Source:
Environmental research 2022 v.204 pp. 112092
ISSN:
0013-9351
Subject:
open reading frames,   etc   ; COVID-19 infection; Severe acute respiratory syndrome coronavirus 2; amino acids; asymmetry; evolution; pandemic; research; time series analysis; uncertainty; viruses; Brazil; India;     Show all 13 Subjects
Abstract:
... Various lineages of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have contributed to prolongation of the Coronavirus Disease 2019 (COVID-19) pandemic. Several non-synonymous mutations in SARS-CoV-2 proteins have generated multiple SARS-CoV-2 variants. In our previous report, we have shown that an evenly uneven distribution of unique protein variants of SARS-CoV-2 is geo-location or ...
DOI:
10.1016/j.envres.2021.112092

3. Genome-wide identification of insulin-like growth factor-binding protein family in Chinese tongue sole (Cynoglossus semilaevis) and their responses to sex steroids

Author:
Xihong Li; Qian Yang; Rui Shi; Xiwen Xu; Zhangfan Chen; Songlin Chen; Na Wang
Source:
Aquaculture 2022 v.557 pp. 738346
ISSN:
0044-8486
Subject:
open reading frames,   etc   ; Cynoglossus semilaevis; aquaculture; brain; females; genes; insulin-like growth factor binding proteins; liver; males; methylation; phylogeny; prediction; reproduction; sex reversal; sexual dimorphism; testosterone;     Show all 16 Subjects
Abstract:
... Chinese tongue sole (Cynoglossus semilaevis) is an economically important marine flatfish that shows typical female-biased Sexual Size Dimorphism (SSD) and sex reversal from female to pseudomale. Previous studies have shown that the insulin-like growth factor-binding protein (igfbp) genes are differentially expressed between sexes of C. semilaevis. The igfbp family is one of the important members ...
DOI:
10.1016/j.aquaculture.2022.738346

4. Characterization and function of mandarin fish c-Myc during viral infection process

Author:
Caimei Ye; Ningqiu Li; Yinjie Niu; Qiang Lin; Xia Luo; Hongru Liang; Lihui Liu; Xiaozhe Fu
Source:
Fish & shellfish immunology 2022 v.120 pp. 686-694
ISSN:
1050-4648
Subject:
open reading frames,   etc   ; Infectious spleen and kidney necrosis virus; Rhabdoviridae; Siniperca chuatsi; amino acid sequences; brain; fish; glutamine; immunology; kidneys; metabolism; protein content; shellfish; spleen; transcription factors; virus replication;     Show all 16 Subjects
Abstract:
... c-Myc is a transcription factor and master regulator of cellular metabolism, and plays a critical role in virus replication by regulating glutamine metabolism. In this study, the open-reading frame (ORF) of c-Myc, designated as Sc-c-Myc, was cloned and sequenced. Multiple alignment of the amino acid sequence showed that the conserved domain of Sc-c-Myc, including the helix–loop–helix-zipper (bHLHz ...
DOI:
10.1016/j.fsi.2021.12.045

5. Antigenic Characterization of ORF2 and ORF3 Proteins of Hepatitis E Virus (HEV)

Author:
Giulia Pezzoni; Lidia Stercoli; Eleonora Pegoiani; Emiliana Brocchi
Source:
Viruses 2021 v.13 no.7 pp. -
ISSN:
1999-4915
Subject:
open reading frames,   etc   ; Escherichia coli; Orthohepevirus A; epitopes; immunogenicity; swine;     Show all 6 Subjects
Abstract:
... To evaluate the antigenic properties of Hepatitis E Virus (HEV) Open Reading Frame 2 and 3 (ORF2 and ORF3) codified proteins, we expressed different portions of ORF2 and the entire ORF3 in E. coli, a truncated ORF2, was also expressed in baculovirus. A panel of 37 monoclonal antibodies (MAbs) was raised against ORF2 (1–660 amino acids) and MAbs were mapped and characterized using the ORF2 expresse ...
DOI:
10.3390/v13071385

6. Open Reading Frame 1 Protein of the Human Long Interspersed Nuclear Element 1 Retrotransposon Binds Multiple Equivalents of Lead

Author:
Tyler B. J. Pinter; Leela Ruckthong; Jeanne A. Stuckey; Aniruddha Deb; James E. Penner-Hahn; Vincent L. Pecoraro
Source:
Journal of the American Chemical Society 2021 v.143 no.37 pp. 15271-15278
ISSN:
1520-5126
Subject:
open reading frames,   etc   ; evolution; genetic engineering; heavy metals; humans; peptides; retrotransposons;     Show all 7 Subjects
Abstract:
... The human long interspersed nuclear element 1 (LINE1) has been implicated in numerous diseases and has been suggested to play a significant role in genetic evolution. Open reading frame 1 protein (ORF1p) is one of the two proteins encoded in this self-replicating mobile genetic element, both of which are essential for retrotransposition. The structure of the three-stranded coiled-coil domain of OR ...
DOI:
10.1021/jacs.1c06461

7. Genome sequence of a novel member of the order Picornavirales from the endoparasitoid wasp Diversinervus elegans

Author:
Chao-Yan Wu; You-Jie Zhao; Jia-Ying Zhu
Source:
Archives of virology 2021 v.166 no.1 pp. 295-297
ISSN:
0304-8608
Subject:
open reading frames,   etc   ; Dicistroviridae; endoparasitoids; genome; length; new species; nucleotides; phylogeny; polyproteins; tail; virology; viruses; wasps;     Show all 13 Subjects
Abstract:
... Here, we report a novel RNA virus from an encyrtid endoparasitoid wasp (Diversinervus elegans). This virus has a genome of 8845 nucleotides in length with a poly(A) tail. It contains one open reading frame (ORF) encoding a single polyprotein that shares the most significant similarity to the polyproteins of dicistroviruses. Phylogenetic analysis suggested that this virus belongs to the family Dici ...
DOI:
10.1007/s00705-020-04824-y

8. Translational enhancement conferred by the 3’ untranslated region of a transcript encoding a group 6 late embryogenesis abundant protein

Author:
Marina E. Battaglia; Ana Valeria Martínez-Silva; Yadira Olvera-Carrillo; Tzvetanka D. Dinkova; Alejandra A. Covarrubias
Source:
Environmental and experimental botany 2021 v.182 pp. 104310
ISSN:
0098-8472
Subject:
open reading frames,   etc   ; Arabidopsis; Phaseolus vulgaris; binding proteins; botany; genes; polyribosomes; protein synthesis; transcription (genetics); transgenic plants; water;     Show all 11 Subjects
Abstract:
... To assure an efficient protein production under stress conditions, some transcripts are modulated at the translational level. To better understand the control of protein production under stress, we analysed the enhancing effect of the 3′ untranslated region (UTR) of the water deficit responsive gene PvLEA6 from Phaseolus vulgaris on the regulation of its expression. GUS activity and transcript loa ...
DOI:
10.1016/j.envexpbot.2020.104310

9. Independent DSG4 frameshift variants in cats with hair shaft dystrophy

Author:
Sarah Kiener; Ana Rostaher; Silvia Rüfenacht; Vidhya Jagannathan; John P. Sundberg; Monika Welle; Tosso Leeb
Source:
Molecular genetics and genomics 2022 v.297 no.1 pp. 147-154
ISSN:
1617-4615
Subject:
open reading frames,   etc   ; adhesion; desmosomes; epithelium; genomics; glycoproteins; histopathology; homozygosity; keratin; loss-of-function mutation; phenotype; stop codon;     Show all 12 Subjects
Abstract:
... Investigations of hereditary phenotypes in spontaneous mutants may help to better understand the physiological functions of the altered genes. We investigated two unrelated domestic shorthair cats with bulbous swellings of the hair shafts. The clinical, histopathological, and ultrastructural features were similar to those in mice with lanceolate hair phenotype caused by loss-of-function variants i ...
DOI:
10.1007/s00438-021-01842-6

10. Multidimensional separation schemes enhance the identification and molecular characterization of low molecular weight proteomes and short open reading frame-encoded peptides in top-down proteomics

Author:
Liam Cassidy; Andreas O. Helbig; Philipp T. Kaulich; Kathrin Weidenbach; Ruth A. Schmitz; Andreas Tholey
Source:
Journal of proteomics 2021 v.230 pp. 103988
ISSN:
1874-3919
Subject:
open reading frames,   etc   ; Methanosarcina mazei; disulfide bonds; genome; molecular weight; peptides; post-translational modification; protein products; proteome; proteomics; solid phase extraction;     Show all 11 Subjects
Abstract:
... Short open reading frame-encoded peptides (SEP) represent a widely undiscovered part of the proteome. The detailed analysis of SEP has, despite inherent limitations such as incomplete sequence coverage, challenges encountered with protein inference, the identification of posttranslational modifications and the assignment of potential N- and C-terminal truncations, predominantly been assessed using ...
DOI:
10.1016/j.jprot.2020.103988

11. Disruption of the Interaction between ORF33 and the Conserved Carboxyl-Terminus of ORF45 Abolishes Progeny Virion Production of Kaposi Sarcoma-Associated Herpesvirus

Author:
Joseph Gillen; Fanxiu Zhu
Source:
Viruses 2021 v.13 no.9 pp. -
ISSN:
1999-4915
Subject:
open reading frames,   etc   ; Gammaherpesvirinae; peptides; progeny; virion; virus replication;     Show all 6 Subjects
Abstract:
... The Open Reading Frame 45 (ORF45) of Kaposi sarcoma-associated herpesvirus (KSHV) is a gammaherpesvirus-specific, immediate-early, tegument protein required for efficient viral replication and virion production. We have previously shown that ORF45 interacts with the conserved herpesviral protein ORF33 through the highly conserved C-terminal 19 amino acids (C19) of ORF45. Because the deletion of C1 ...
DOI:
10.3390/v13091828

12. Identification and analysis of small proteins and short open reading frame encoded peptides in Hep3B cell

Author:
Bing Wang; Junhui Hao; Ni Pan; Zhiwei Wang; Yinxuan Chen; Cuihong Wan
Source:
Journal of proteomics 2021 v.230 pp. 103965
ISSN:
1874-3919
Subject:
open reading frames,   etc   ; amino acids; cell lines; databases; genome; humans; molecular weight; neoplasms; non-coding RNA; peptides; peptidomics; proteins; proteome; solvents; tandem mass spectrometry;     Show all 15 Subjects
Abstract:
... The small proteins and short open reading frames encoded peptides (SEPs) are of fundamental importance because of their essential roles in biological processes. However, the annotation or identification of them is challenging, in part owing to the limitation of the traditional genome annotation pipeline and their inherent characteristics of low abundance and low molecular weight. To discover and c ...
DOI:
10.1016/j.jprot.2020.103965

13. Functional analysis of a chaetoglobosin A biosynthetic regulator in Chaetomium globosum

Author:
Ming Cheng; Shanshan Zhao; He Liu; Yutao Liu; Congyu Lin; Jinzhu Song; Chitti Thawai; Sittichai Charoensettasilp; Qian Yang
Source:
Fungal biology 2021 v.125 no.3 pp. 201-210
ISSN:
1878-6146
Subject:
open reading frames,   etc   ; Chaetomium globosum; antifungal properties; bioinformatics; biosynthesis; cytochalasins; fungi; gene targeting; light; morphogenesis; multigene family; mycology; polyketide synthases; secondary metabolites; spores; sporulation; transcription (genetics);     Show all 17 Subjects
Abstract:
... Cytochalasins are a group of fungal secondary metabolites with diverse structures and bioactivities, including chaetoglobosin A production. Chaetoglobosin A is produced by Chaetomium globosum and has potential antifungal activity. Bioinformatics analysis of the chaetoglobosin A gene cluster (che) showed it that consists of nine open reading frames, including those encoding polyketide synthases (PK ...
DOI:
10.1016/j.funbio.2020.10.010

14. SpTIA-1 suppresses WSSV infection by promoting apoptosis in mud crab (Scylla paramamosain)

Author:
Hang Hu; Xinshan Zhao; Yalei Cui; Shengkang Li; Yi Gong
Source:
Molecular immunology 2021 v.140 pp. 158-166
ISSN:
0161-5890
Subject:
open reading frames,   etc   ; RNA-binding proteins; Scylla paramamosain; T-lymphocytes; White spot syndrome virus; apoptosis; caspase-3; crabs; hemocytes; immune response; innate immunity; membrane potential; mitochondrial membrane;     Show all 13 Subjects
Abstract:
... TIA-1 (T cell restricted intracellular antigen-1) is a kind of RNA-binding protein which serves as the downstream of CED-9 (a BCL2 homolog) and induces apoptosis under stress conditions. So far, the function of apoptosis mediated by TIA-1 has been extensively studied in higher animals, and apoptosis happens to be related to biological immune defense. However, the involvement of TIA-1 in the study ...
DOI:
10.1016/j.molimm.2021.10.015

15. Characterization and expression analysis of ATG4 paralogs in response to the palmitic acid induced-ER stress in Ctenopharyngodon idellus kidney cells

Author:
Minghui Yang; Zhiguang Chang; Hong Ji
Source:
Comparative biochemistry and physiology 2021 v.252 pp. 110525
ISSN:
1096-4959
Subject:
open reading frames,   etc   ; Ctenopharyngodon idella; amino acids; autophagy; brain; endoplasmic reticulum stress; genes; heart; inflammation; kidney cells; kidneys; liver; messenger RNA; muscles; palmitic acid; proteinases; tissue distribution; tissues;     Show all 18 Subjects
Abstract:
... Autophagy is regulated by a variety of autophagy related genes (ATG), among them, ATG4 is a highly specific protease that is critical to autophagy. The purpose of this study was to investigate the role of the ATG4 response to Palmitic acid (PA) and their relationships with Endoplasmic reticulum (ER) stress in grass carp. In the present study, four ATG4 paralogs from grass carp were identified and ...
DOI:
10.1016/j.cbpb.2020.110525

16. Development of Brucella melitensis Rev.1 ΔOmp19 mutants with DIVA feature and comparison of their efficacy against three commercial vaccines in a mouse model

Author:
Ali Uslu; Osman Erganis
Source:
Molecular immunology 2021 v.133 pp. 44-52
ISSN:
0161-5890
Subject:
open reading frames,   etc   ; Brucella melitensis; Escherichia coli; ampicillin; antibodies; antigens; brucellosis; cattle; electroporation; gene transfer; heat stress; immunity; live vaccines; mice; mutants; outer membrane proteins; pathogens; plasmids; sheep; virulence;     Show all 20 Subjects
Abstract:
... Brucella is an intracellular zoonotic pathogen that can affect many hosts. Brucella melitensis Rev.1 is a live attenuated, is one of the most effective vaccine strain against brucellosis. It can be used safely in sheep, goats, and even cattle. Although many studies are available on this topic, there is no effective vaccine strain for sheep and goats that distinguishes the antibody titer produced b ...
DOI:
10.1016/j.molimm.2021.02.006

17. Genomic structure, expression and functional characterization of arginine kinase (EcAK) from Exopalaemon carinicauda

Author:
Zixuan Wu; Yujie Liu; Jiaqi Zheng; Yongzhao Zhou; Kefan Xing; Yuying Sun; Jiquan Zhang
Source:
Fish & shellfish immunology 2021 v.109 pp. 82-86
ISSN:
1050-4648
Subject:
open reading frames,   etc   ; Aeromonas hydrophila; Euphausia superba; Komagataella pastoris; Palaemonidae; Vibrio parahaemolyticus; arginine kinase; complementary DNA; exons; gene expression; genomics; introns; messenger RNA; muscles; recombinant proteins; shrimp; vibriosis; zymogens;     Show all 18 Subjects
Abstract:
... Arginine kinase (AK, EC 2.7.3.3) plays an important role in cells with high, fluctuating energy requirements. In invertebrates, AK is the major phosphagen kinase that modulates the energy metabolism. Here, the full-length cDNA sequence encoding arginine kinase (EcAK) was obtained from the Exopalaemon carinicauda. The complete nucleotide sequence of EcAK contained a 1068 bp open reading frame (ORF) ...
DOI:
10.1016/j.fsi.2020.12.009

18. Overexpression of Cerasus humilis ChAOX2 improves the tolerance of Arabidopsis to salt stress

Author:
Li Jiao Sun; Xiao Yu Zhao; Jing Ren; Shao Peng Yan; Xi Yang Zhao; Xing Shun Song
Source:
3 Biotech 2021 v.11 no.7 pp. 316
ISSN:
2190-572X
Subject:
open reading frames,   etc   ; Arabidopsis thaliana; Prunus yedoensis; amino acid sequences; mitochondria; mutants; nucleotides; peroxidase; plant growth; proline; reactive oxygen species; salt stress; salt tolerance; sequence homology; stress tolerance; superoxide dismutase;     Show all 16 Subjects
Abstract:
... Alternative oxidase (AOX) has a well-established involvement in plant growth and stress tolerance in many studies. In this study, we isolated and characterized the AOX2 from Cerasus humilis. The ChAOX2 Open Reading Frame (ORF) contains 1029 nucleotides and encodes 342 amino acid residues. The inferred amino acid sequence of ChAOX2 shared the highest sequence similarity with a homolog from Prunus y ...
DOI:
10.1007/s13205-021-02871-z

19. Characterization of vB_StuS_MMDA13, a Newly Discovered Bacteriophage Infecting the Agar-Degrading Species Sphingomonas turrisvirgatae

Author:
Pasquale Marmo; Maria Cristina Thaller; Gustavo Di Lallo; Lucia Henrici De Angelis; Noemi Poerio; Federica De Santis; Maurizio Fraziano; Luciana Migliore; Marco Maria D’Andrea
Source:
Viruses 2020 v.12 no.8 pp. -
ISSN:
1999-4915
Subject:
open reading frames,   etc   ; DNA; Siphoviridae; Sphingomonas; bacteriophages; bioremediation; biosynthesis; host range; multigene family; pH; temperature;     Show all 11 Subjects
Abstract:
... Members of Sphingomonas genus have gained a notable interest for their use in a wide range of biotechnological applications, ranging from bioremediation to the production of valuable compounds of industrial interest. To date, knowledge on phages targeting Sphingomonas spp. are still scarce. Here, we describe and characterize a lytic bacteriophage, named vB_StuS_MMDA13, able to infect the Sphingomo ...
DOI:
10.3390/v12080894

20. Citrus Tristeza Virus Isolates of the Same Genotype Differ in Stem Pitting Severity in Grapefruit

Author:
Glynnis Cook; Beatrix Coetzee; Rachelle Bester; Johannes H. J. Breytenbach; Chanel Steyn; Rochelle de Bruyn; Johan T. Burger; Hans J. Maree
Source:
Plant disease 2020 v.104 no.9 pp. 2362-2368
ISSN:
0191-2917
Subject:
open reading frames,   etc   ; Aphidoidea; Citrus; Citrus tristeza virus; genetic variation; genome; genotype; grapefruits; pathogenicity; proteinases;     Show all 10 Subjects
Abstract:
... Two isolates of the T68 genotype of citrus tristeza virus (CTV) were derived from a common source, GFMS12, by single aphid transmission. These isolates, named GFMS12-8 and GFMS12-1.3, induced stem pitting with differing severity in ‘Duncan’ grapefruit (Citrus × paradisi [Macfad.]). Full-genome sequencing of these isolates showed only minor nucleotide sequence differences totaling 45 polymorphisms. ...
DOI:
10.1094/PDIS-12-19-2586-RE