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

Author:
Wu, Chao-Yan; Zhao, You-Jie; Zhu, Jia-Ying
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

2. N-terminal truncated RHT-1 proteins generated by translational reinitiation cause semi-dwarfing of wheat Green Revolution alleles

Author:
Van De Velde, Karel; Thomas, Stephen G.; Heyse, Floor; Kaspar, Rim; Van Der Straeten, Dominique; Rohde, Antje
Source:
Molecular plant 2021 v.14 no.4 pp. 679-687
ISSN:
1674-2052
Subject:
open reading frames,   etc   ; alleles; degradation; dormancy; dwarfing; genetically modified organisms; gibberellins; plant height; proteins; stop codon; wheat; yields;     Show all 12 Subjects
Abstract:
... The unprecedented wheat yield increases during the Green Revolution were achieved through the introduction of the Reduced height (Rht)-B1b and Rht-D1b semi-dwarfing alleles. These Rht-1 alleles encode growth-repressing DELLA genes containing a stop codon within their open reading frame that confers gibberellin (GA)-insensitive semi-dwarfism. In this study, we successfully took the hurdle of detect ...
DOI:
10.1016/j.molp.2021.01.002

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

Author:
Battaglia, Marina E.; Martínez-Silva, Ana Valeria; Olvera-Carrillo, Yadira; Dinkova, Tzvetanka D.; Covarrubias, Alejandra A.
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

4. Overexpression of SARS-CoV-2 protein ORF6 dislocates RAE1 and NUP98 from the nuclear pore complex

Author:
Kato, Koki; Ikliptikawati, Dini Kurnia; Kobayashi, Akiko; Kondo, Hiroya; Lim, Keesiang; Hazawa, Masaharu; Wong, Richard W.
Source:
Biochemical and biophysical research communications 2021 v.536 pp. 59-66
ISSN:
0006-291X
Subject:
open reading frames,   etc   ; Severe acute respiratory syndrome coronavirus 2; cell growth; humans; nuclear pore; nucleoporins; pandemic; research;     Show all 8 Subjects
Abstract:
... The novel human betacoronavirus SARS-CoV-2 has caused an unprecedented pandemic in the 21st century. Several studies have revealed interactions between SARS-CoV-2 viral proteins and host nucleoporins, yet their functions are largely unknown. Here, we demonstrate that the open-reading frame 6 (ORF6) of SARS-CoV-2 can directly manipulate localization and functions of nucleoporins. We found that ORF6 ...
DOI:
10.1016/j.bbrc.2020.11.115

5. Complete nucleotide sequence of a novel partitivirus infecting the plant-pathogenic fungus Phomopsis vexans

Author:
Zhang, Chao Jun; Zhou, Xin Yu; Zhong, Jie; Guo, Jun; Yang, Xiao Ping; Zhu, Hong Jian
Source:
Archives of virology 2021 v.166 no.1 pp. 291-294
ISSN:
0304-8608
Subject:
open reading frames,   etc   ; Deltapartitivirus; Diaporthe; RNA-directed RNA polymerase; coat proteins; eggplants; phylogeny; plant pathogenic fungi; virology; viruses;     Show all 10 Subjects
Abstract:
... Here, we report the molecular characterization of a novel partitivirus from Phomopsis vexans strain PvHZ002, a plant-pathogenic fungus infecting eggplant. The virus was designated “Phomopsis vexans partitivirus 1” (PvPV1). PvPV1 contains two dsRNA segments, dsRNA1 and dsRNA2, which are 1,662 bp and 1,628 bp long, respectively. Each segment contains a single open reading frame, putatively encoding ...
DOI:
10.1007/s00705-020-04835-9

6. Characterization of the IS200/IS605 Insertion Sequence Family in Halanaerobium Hydrogeniformans

Author:
Sadler, Michael; R. Mormile, Melanie; L. Frank, Ronald
Source:
Genes 2020 v.11 no.5
ISSN:
2073-4425
Subject:
open reading frames,   etc   ; DNA; Halanaerobium; genome; genomics; loci; transposons;     Show all 7 Subjects
Abstract:
... Mobile DNA elements play a significant evolutionary role by promoting genome plasticity. Insertion sequences are the smallest prokaryotic transposable elements. They are highly diverse elements, and the ability to accurately identify, annotate, and infer the full genomic impact of insertion sequences is lacking. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium with an abnormally high ...
DOI:
10.3390/genes11050484

7. The ea22 gene of lambdoid phages: preserved prolysogenic function despite of high sequence diversity

Author:
Dydecka, Aleksandra; Bloch, Sylwia; Necel, Agnieszka; Topka, Gracja; Węgrzyn, Alicja; Tong, Jinge; Donaldson, Logan W.; Węgrzyn, Grzegorz; Nejman-Faleńczyk, Bożena
Source:
Virus genes 2020 v.56 no.2 pp. 266-277
ISSN:
0920-8569
Subject:
open reading frames,   etc   ; genes; integrases; phages; sequence diversity;     Show all 5 Subjects
Abstract:
... The exo-xis region of lambdoid phages contains open reading frames and genes that appear to be evolutionarily important. However, this region has received little attention up to now. In this study, we provided evidence that ea22, the largest gene of this region, favors the lysogenic pathway over the lytic pathway in contrast to other characterized exo-xis region genes including ea8.5, orf61, orf60 ...
DOI:
10.1007/s11262-020-01734-8
PubMed:
31970620
PubMed Central:
PMC7093339

8. TaHSP17.8 regulates TaJUB1D in the management of low cadmium accumulation in wheat

Author:
Wang, Hongcheng; Wei, Jialian; Li, Muzi; Liao, Sisi; Zhu, Bin; Yin, Huayan; Du, Xuye
Source:
Environmental and experimental botany 2021 v.184 pp. 104374
ISSN:
0098-8472
Subject:
open reading frames,   etc   ; administrative management; cadmium; chlorophyll; genetically modified organisms; heat shock proteins; proline; shoots; stress response; tissues; transcription factors; wheat;     Show all 12 Subjects
Abstract:
... In this work, the function of a wheat small heat shock protein TaHSP17.8 to respond to Cd stress was characterized. TaHSP17.8 is mainly expressed in root tissues and was found to be most highly expressed 4 h after Cd stress. The function of TaHSP17.8 in Cd stress response was investigated using transgenic wheat lines. Damage to both the root and shoot tissues of transgenic lines was reduced compar ...
DOI:
10.1016/j.envexpbot.2021.104374

9. Transcriptome analysis of the pheromone glands in Noorda blitealis reveals a novel AOX group of the superfamily Pyraloidea

Author:
Zhang, Zu-Bing; Yin, Ning-Na; Long, Ji-Ming; Zhang, Yong-Ke; Liu, Nai-Yong; Zhu, Jia-Ying
Source:
Journal of Asia-Pacific entomology 2021 v.24 no.1 pp. 110-119
ISSN:
1226-8615
Subject:
open reading frames,   etc   ; Crambidae; Moringa; aldehydes; bioinformatics; biosynthesis; degradation; entomology; enzymes; gene duplication; genomics; pests; pheromone glands; phylogeny; reproduction; sex pheromones; transcriptome; transcriptomics; trees; unigenes; yields;     Show all 21 Subjects
Abstract:
... Noorda blitealis (Lepidoptera: Pyraloidea: Crambidae) is a major defoliating pest of Moringa trees. Focusing on its mating and reproduction, here we sequenced and analyzed the transcriptome of its pheromone glands (PGs) with a combination of Illumina sequencing, bioinformatics and phylogenetics approaches, coupled with a genome-based analysis. Transcriptome sequencing led to the yields of approxim ...
DOI:
10.1016/j.aspen.2020.11.007

10. A new virus of the family Tombusviridae infecting sugarcane

Author:
Tahir, Muhammad N.; Bolus, Stephen; Grinstead, Samuel C.; McFarlane, Sharon A.; Mollov, Dimitre
Source:
Archives of virology 2021 v.166 no.3 pp. 961-965
ISSN:
0304-8608
Subject:
open reading frames,   etc   ; Saccharum officinarum; Tombusviridae; bioinformatics; high-throughput nucleotide sequencing; molecular cloning; new genus; phylogeny; plant viruses; sugarcane; viral diseases of plants; South Africa;     Show all 12 Subjects
Abstract:
... Many viral diseases of sugarcane negatively affect yield. A sugarcane accession originating from South Africa exhibiting mosaic symptoms was processed for high-throughput sequencing. Bioinformatic analysis revealed two known sugarcane viruses and a contig of around 2,800 nucleotides resembling umbra-like viruses of the family Tombusviridae. The sequence of the viral contig was confirmed by cloning ...
Handle:
10113/7280324
DOI:
10.1007/s00705-020-04908-9

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

Author:
Cheng, Ming; Zhao, Shanshan; Liu, He; Liu, Yutao; Lin, Congyu; Song, Jinzhu; Thawai, Chitti; Charoensettasilp, Sittichai; Yang, Qian
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

12. Regulation of Anthocyanin Accumulation by a Transcription Factor LcTT8 From Lonicera caerulea L.

Author:
Liu, Pei; Gang, Huixin; Liu, Huayu; Qin, Dong; Zhang, Yan; Huo, Junwei
Source:
Plant molecular biology reporter 2021 v.39 no.1 pp. 125-136
ISSN:
0735-9640
Subject:
open reading frames,   etc   ; Lonicera caerulea; Nicotiana tabacum; Paeonia suffruticosa; anthocyanins; enzymes; fruit color; fruits; genes; human health; molecular biology; phylogeny; tobacco; transcription factors;     Show all 14 Subjects
Abstract:
... The fruit of Lonicera caerulea L. is rich in anthocyanin, which has beneficial effects on human health. However, there is no research report on the regulation mechanism of anthocyanin synthesis in Lonicera caerulea L. TT8 gene-encoded protein belongs to bHLH transcription factor, and it has been reported to regulate anthocyanin synthesis. In the study, we cloned TT8 gene from Lonicera caerulea L. ...
DOI:
10.1007/s11105-020-01229-8

13. Tuberous sclerosis complex 1 (PvTSC1) participates in ammonia nitrogen induced oxidative stress in Penaeus vannamei by regulating autophagy

Author:
Wang, Feifei; Liang, Qingjian; Liu, Can; Dong, Wenna; Ou, Mufei; Li, Zhonghua; Liu, Yuan; Wang, Weina
Source:
Aquaculture 2021 v.533 pp. 736107
ISSN:
0044-8486
Subject:
open reading frames,   etc   ; Litopenaeus vannamei; amino acid sequences; amino acids; ammonium nitrogen; antioxidant enzymes; autophagy; cytoplasm; genes; hemocytes; hepatopancreas; messenger RNA; mortality; oxidative stress; polypeptides; sclerosis; shrimp; tissues;     Show all 18 Subjects
Abstract:
... The tuberous sclerosis complex 1 (TSC1) is a critical upstream regulator of autophagy. Nevertheless, the detailed molecular mechanism of TSC1 and its function in crustacean are still not well understood. In the present study, TSC1 was identified and characterized from Penaeus vannamei. Molecular feature analysis revealed that the open reading frame (ORF) of PvTSC1 was 3516 bp encoding a polypeptid ...
DOI:
10.1016/j.aquaculture.2020.736107

14. Characterization and functional analysis of SMAD2 regulation in hair follicle cycle in Angora rabbits

Author:
Bao, Zhiyuan; Zhao, Bohao; Hu, Shuaishuai; Yang, Naisu; Liu, Ming; Li, Jiali; Liang, Shuang; Zhou, Tong; Chen, Yang; Wu, Xinsheng
Source:
Gene 2021 v.770 pp. 145339
ISSN:
0378-1119
Subject:
open reading frames,   etc   ; Angora (rabbit breed); amino acids; bioinformatics; cell nucleus; genes; growth and development; hair follicles; hydrophilicity; length; signal transduction;     Show all 11 Subjects
Abstract:
... Hair follicle (HF) development is characterized by periodic growth cycles regulated by numerous factors. We previously showed that SMAD2 might be involved in the HF growth cycle in Angora rabbits. However, its extra role in the HF growth and development remains obscure. In this study, we cloned the complete coding sequence (CDS) of the Angora rabbit SMAD2 gene. Within SMAD2 CDS, we identified the ...
DOI:
10.1016/j.gene.2020.145339

15. Cloning and functional analysis of c/ebpα as negative regulator of dmrt1 in Chinese tongue sole (Cynoglossus semilaevis)

Author:
Wang, Qian; Wang, Rui; Feng, Bo; Li, Shuo; Mahboob, Shahid; Shao, Changwei
Source:
Gene 2021 v.768 pp. 145321
ISSN:
0378-1119
Subject:
open reading frames,   etc   ; Cynoglossus semilaevis; assays; cell growth; developmental stages; genes; information; leucine zipper; males; peptides; sex determination; testes; transcription factors;     Show all 13 Subjects
Abstract:
... c/ebpα is a member of the C/EBP family of transcription factors, which are involved in cell growth and differentiation and have a conserved basic leucine zipper (bZIP) domain. However, little is known about its function in sex determination and differentiation. In the present study, c/ebpα was cloned from the gonads of Chinese tongue sole (Cynoglossus semilaevis). The full-length cDNA of c/ebpα wa ...
DOI:
10.1016/j.gene.2020.145321

16. Next-generation sequencing reveals alternative L-DOPA decarboxylase (DDC) splice variants bearing novel exons, in human hepatocellular and lung cancer cells

Author:
Papatsirou, Maria; Adamopoulos, Panagiotis G.; Artemaki, Pinelopi I.; Georganti, Vasiliki P.; Scorilas, Andreas; Vassilacopoulou, Dido; Kontos, Christos K.
Source:
Gene 2021 v.768 pp. 145262
ISSN:
0378-1119
Subject:
open reading frames,   etc   ; L-dopa; algorithms; cell lines; enzymes; exons; high-throughput nucleotide sequencing; humans; lung neoplasms; neoplasm cells; physiology; protein isoforms; technology;     Show all 13 Subjects
Abstract:
... The human L-DOPA decarboxylase (DDC) is an enzyme that displays a pivotal role in metabolic processes. It is implicated in various human disorders, including hepatocellular and lung cancer. Several splice variants of DDC have previously been described, most of which encode for protein isoforms of this enzyme. In the present study, we used next-generation sequencing (NGS) technology along with nest ...
DOI:
10.1016/j.gene.2020.145262

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

Author:
Yang, Minghui; Chang, Zhiguang; Ji, Hong
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

18. Molecular characterization and expression of sirtuin 2, sirtuin 3, and sirtuin 5 in the Wuchang bream (Megalobrama amblycephala) in response to acute temperature and ammonia nitrogen stress

Author:
Qian, Linjie; Miao, Linghong; Abba, Butros Simon Ajak; Lin, Yan; Jiang, Wenqiang; Chen, Shiyou; Luo, Chenhao; Liu, Bo; Ge, Xianping
Source:
Comparative biochemistry and physiology 2021 v.252 pp. 110520
ISSN:
1096-4959
Subject:
open reading frames,   etc   ; Danio rerio; Megalobrama amblycephala; ammonium nitrogen; bioinformatics; complementary DNA; genes; gills; intestines; kidneys; liver; prediction; spleen; tissues; water temperature;     Show all 15 Subjects
Abstract:
... This study sought to characterize sirtuin 2 (sirt2), sirtuin 3 (sirt3), and sirtuin 5 (sirt5) in Megalobrama amblycephala (M. amblycephala) by cloning the open reading frame (ORF) of sirt2, sirt3, and sirt5. The full-lengths of the resulting M. amblycephala sirt2, sirt3, and sirt5 cDNA sequences were 1845, 1534, and 1920 bp, respectively, with 92%, 98%, and 91% similarities to Danio rerio sequence ...
DOI:
10.1016/j.cbpb.2020.110520

19. Interleukin-10 (IL-10) participates in host defense against bacterial pathogens and promotes IgM antibody production in Nile tilapia (Oreochromis niloticus)

Author:
Wu, Siwei; Duan, Chenxi; Kong, Linghe; Tu, Xiao; Wang, Lifei; Guo, Zheng; Ye, Jianmin
Source:
Aquaculture 2021 v.531 pp. 735829
ISSN:
0044-8486
Subject:
open reading frames,   etc   ; B-lymphocytes; Oreochromis niloticus; Streptococcus agalactiae; amino acids; antibody formation; complementary DNA; immunoglobulin M; interleukin-10; kidneys; messenger RNA; models; pathogens; recombinant proteins; spleen; tissues;     Show all 16 Subjects
Abstract:
... Interleukin 10 (IL-10) is a pleiotropic cytokine with important immune regulation function, not only participating in the differentiation of B cells, but also boosting B cell antibody production in mammals. In this study, OnIL-10 was successfully cloned and identified from Nile tilapia (Oreochromis niloticus). Its roles in response to bacterial challenge and promotion of IgM antibody production we ...
DOI:
10.1016/j.aquaculture.2020.735829

20. Nitroreductase Activites in Giardia lamblia: ORF 17150 Encodes a Quinone Reductase with Nitroreductase Activity

Author:
Müller, Joachim; Heller, Manfred; Uldry, Anne-Christine; Braga, Sophie; Müller, Norbert
Source:
Pathogens 2021 v.10 no.2
ISSN:
2076-0817
Subject:
open reading frames,   etc   ; Giardia lamblia; NAD(P)H dehydrogenase (quinone); enzyme activity; flavoproteins; gel chromatography; gene overexpression; mass spectrometry; metronidazole; nitroreductases; recombinant proteins;     Show all 11 Subjects
Abstract:
... The intestinal diplomonadid Giardia lamblia is a causative agent of persistent diarrhea. Current treatments are based on nitro drugs, especially metronidazole. Nitro compounds are activated by reduction, yielding toxic intermediates. The enzymatic systems responsible for this activation are not completely understood. By fractionating cell free crude extracts by size exclusion chromatography follow ...
DOI:
10.3390/pathogens10020129