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1. Genome Sequence Resource for Colletotrichum scovillei, the Cause of Anthracnose Disease of Chili

Author:
Huo, Jianfei; Wang, Yafei; Hao, Yongjuan; Yao, Yurong; Wang, Yong; Zhang, Kai; Tan, Xinqiu; Li, Zhiqiang; Wang, Wanli
Source:
Molecular plant-microbe interactions 2021 v.34 no.1 pp. 122-126
ISSN:
1943-7706
Subject:
nucleotide sequences,   etc   ; anthracnose; genome; spices;     Show all 4 Subjects
Abstract:
... Colletotrichum species cause anthracnose disease on the economically important spice crop chili. A total of 24 Colletotrichum species are known to infect chili and cause anthracnose. C. scovillei belongs to the C. acutatum species complex, and it shows greater aggressiveness than other species, particularly in the case of inoculation onto the nonwounded fruits of chili plants. The current work int ...
DOI:
10.1094/MPMI-03-20-0055-A

2. First report on Mermithidae (Mermithida) infection in Ligidium sp. (Isopoda, Ligiidae)

Author:
Yoshino, Hiroki; Waki, Tsukasa
Source:
Parasitology international 2021 v.82 pp. 102304
ISSN:
1383-5769
Subject:
nucleotide sequences,   etc   ; Isopoda; Japan; Mermithidae; parasitology;     Show all 5 Subjects
Abstract:
... Specimens of Ligidium sp. (Crustacea, Isopoda, Oniscidea) collected from Kanagawa Prefecture in Japan were found to be infected with parasitic nematodes. We have obtained two Mermithidae (Nematoda) by dissecting the fresh specimen and from the dead specimen of Ligidium, which marks the second known discovery of a mermithid infection in the order Isopoda. Herein, a report on the nuclear 28S rDNA an ...
DOI:
10.1016/j.parint.2021.102304

3. Molecular cloning of duck CD40 and its immune function research

Author:
Zhang, Rujuan; Wang, Mingshu; Cheng, Anchun; Yang, Qiao; Wu, Ying; Jia, Renyong; Chen, Shun; Zhu, Dekang; Liu, Mafeng; Zhao, Xinxin; Zhang, Shaqiu; Huang, Juan; Ou, Xumin; Mao, Sai; Gao, Qun; Yu, Yanling; Zhang, Ling; Liu, Yunya; Tian, Bin; Pan, Leichang
Source:
Poultry science 2021 v.100 no.6 pp. 101100
ISSN:
0032-5791
Subject:
nucleotide sequences,   etc   ; ducks; genes; immune response;     Show all 4 Subjects
Abstract:
... Cosignal molecules are cell surface molecules that transduce signals to other cells to modulate immune response positively (costimulate) or negatively (cosuppress). Costimulatory signals are key factors in determining whether T/B cells are capable of responding to specific antigens and ultimately mediating an appropriate immune response. In this study, the cDNA sequence containing the complete cod ...
DOI:
10.1016/j.psj.2021.101100

4. Optimization of Growth Conditions of Acinetobacter sp. Cr1 for Removal of Heavy Metal Cr Using Central Composite Design

Author:
Pang, Bingbing; Lv, Lijun; Pang, Caoping; Ye, Fengcai; Shang, Changhua
Source:
Current microbiology 2021 v.78 no.1 pp. 316-322
ISSN:
0343-8651
Subject:
nucleotide sequences,   etc   ; Acinetobacter; bioremediation; heavy metals; pH;     Show all 5 Subjects
Abstract:
... Growth conditions can significantly affect the removal efficiency of heavy metals by microorganisms. The goal of this study was enhancing the removal efficiency of Cr(VI) and improving the application of Acinetobacter sp. Cr1 (GenBank accession number of 16S rDNA sequence, MN900681). This study focused on pH, Cr(VI) concentration and culture time, which were the major influence factors for removal ...
DOI:
10.1007/s00284-020-02278-8

5. Challenges of functional expression of complex polyketide biosynthetic gene clusters

Author:
Gao, Yaojie; Zhao, Yuchun; He, Xinyi; Deng, Zixin; Jiang, Ming
Source:
Current opinion in biotechnology 2021 v.69 pp. 103-111
ISSN:
0958-1669
Subject:
nucleotide sequences,   etc   ; biosynthesis; biotechnology; databases; dietary supplements; drugs; polyketides;     Show all 7 Subjects
Abstract:
... Polyketide natural products are valuable sources of bioactive molecules such as nutraceuticals and pharmaceuticals. The tremendous development of the genome sequence database revealed that the majority of the biosynthetic gene clusters (BGCs) are cryptic. Activation of these cryptic BGCs and identification of the related products is essential for finding more lead compounds for pharmaceuticals. On ...
DOI:
10.1016/j.copbio.2020.12.007

6. Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools

Author:
Zallot, Remi; Oberg, Nils; Gerlt, John A
Source:
Current opinion in biotechnology 2021 v.69 pp. 77-90
ISSN:
0958-1669
Subject:
nucleotide sequences,   etc   ; biotechnology; databases; enzymology; genome; genomics; microbiology; sequence homology;     Show all 8 Subjects
Abstract:
... The continuing expansion of protein and genome sequence databases is an opportunity to identify novel enzymes with biotechnological applications. Whether applied to enzymology, chemical biology, systems biology, and microbiology, database mining must be ‘user-friendly’ so that experimentalists can devise focused strategies to discover the in vitro activities and in vivo functions of uncharacterize ...
DOI:
10.1016/j.copbio.2020.12.004

7. Marine bacteria associated with the green seaweed Ulva sp. for the production of polyhydroxyalkanoates

Author:
Gnaim, Rima; Polikovsky, Mark; Unis, Razan; Sheviryov, Julia; Gozin, Michael; Golberg, Alexander
Source:
Bioresource technology 2021 v.328 pp. 124815
ISSN:
0960-8524
Subject:
nucleotide sequences,   etc   ; Sulfitobacter; Ulva; hydrolysates; macroalgae; mannitol; phylogeny; polyhydroxyalkanoates;     Show all 8 Subjects
Abstract:
... This work aimed to isolate a series of bacterial strains associated with the green seaweed Ulva sp. and evaluate their capability to manufacture PHA. The effect of the type of supplemented sugars found to be in macroalgae, on the growth and PHA productivity of the strains was studied. Analysis of the 16S rRNA gene sequence of the isolated strains revealed that the PHA-producing bacteria were phylo ...
DOI:
10.1016/j.biortech.2021.124815

8. Complete genome sequence of a piezophilic bacterium Salinimonas sediminis N102T, isolated from deep-sea sediment of the New Britain Trench

Author:
Xue, Junyi; Fang, Jiasong; Zhang, Hongge; Wei, Yuli; Wang, Li; Liu, Rulong; Cao, Junwei
Source:
Marine genomics 2021 v.56 pp. 100807
ISSN:
1874-7787
Subject:
nucleotide sequences,   etc   ; genes; lifestyle; marine sediments; ribosomal RNA; transfer RNA;     Show all 6 Subjects
Abstract:
... Salinimonas sediminis N102ᵀ is a cold-adapted, slightly halophilic piezophile isolated from deep-sea sediment (4700 m) of the New Britain Trench. In this study, we report the complete genome sequence of S. sediminis N102ᵀ, which is comprised of 4,440,293 base pairs with a mean G + C content of 48.2 mol%. The complete genome harbors 3851 predicted protein-coding genes, 70 tRNA genes and 15 rRNA gen ...
DOI:
10.1016/j.margen.2020.100807

9. Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax

Author:
Yan, Ming-Hui; Li, Chun-Yang; Fritsch, Peter W.; Cai, Jie; Wang, Heng-Chang
Source:
Systematic botany 2021 v.46 no.1 pp. 162-174
ISSN:
0363-6445
Subject:
nucleotide sequences,   etc   ; Halesia; Pterostyrax; Styrax; data collection; monophyly; polyphyly;     Show all 7 Subjects
Abstract:
... The phylogenetic relationships among 11 out of the 12 genera of the angiosperm family Styracaceae have been largely resolved with DNA sequence data based on all protein-coding genes of the plastome. The only genus that has not been phylogenomically investigated in the family with molecular data is the monotypic genus Parastyrax, which is extremely rare in the wild and difficult to collect. To comp ...
DOI:
10.1600/036364421X16128061189576

10. Structures of Native-like Nucleosomes: One Step Closer toward Understanding the Structure and Function of Chromatin

Author:
Bai, Yawen; Zhou, Bing-Rui
Source:
Journal of molecular biology 2021 v.433 no.6 pp. 166648
ISSN:
0022-2836
Subject:
nucleotide sequences,   etc   ; DNA; antibodies; eukaryotic cells; histones; nucleosomes;     Show all 6 Subjects
Abstract:
... Genomic DNA in eukaryotes is organized into chromatin through association with core histone proteins to form nucleosomes. To understand the structure and function of chromatin, we must determine the structures of nucleosomes containing native DNA sequences. However, to date, our knowledge of nucleosome structures is mainly based on the crystallographic studies of the nucleosomes containing non-nat ...
DOI:
10.1016/j.jmb.2020.09.007

11. Urocleidus sayani n. sp. (Monogenea: Dactylogyridae) from Gills of Pirate Perch (Aphredoderus sayanus)

Author:
Leis, Eric M.; Easy, Russell H.; Scovil, Allie; Cone, David K.; Cloutman, Donald G.; McAllister, Chris T.; Robison, Henry W.
Source:
TheJournal of parasitology 2021 v.107 no.2 pp. 214-221
ISSN:
0022-3395
Subject:
nucleotide sequences,   etc   ; Aphredoderus sayanus; Dactylogyridae; parasitology; Mississippi River; Wisconsin;     Show all 6 Subjects
Abstract:
... Urocleidus sayani n. sp. is described from the gills of pirate perch (Aphredoderus sayanus) in the Wisconsin backwaters of the upper Mississippi River and was found in samples from the Southeastern United States. Urocleidus sayani n. sp. is the second monogenean described from the pirate perch and the first for this host within Dactylogyridae. The description includes a partial 18S rRNA gene seque ...
DOI:
10.1645/20-36

12. Transfer RNAs: diversity in form and function

Author:
Berg, Matthew D.; Brandl, Christopher J.
Source:
RNA biology 2021 v.18 no.3 pp. 316-339
ISSN:
1555-8584
Subject:
nucleotide sequences,   etc   ; biosynthesis; cell biology; protein synthesis; synthetic biology;     Show all 5 Subjects
Abstract:
... As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules ...
DOI:
10.1080/15476286.2020.1809197

13. Comparative analysis of the complete chloroplast genome of seven Nymphaea species

Author:
Sun, Chunqing; Chen, Fadi; Teng, Nianjun; Xu, Yingchun; Dai, Zhongliang
Source:
Aquatic botany 2021 v.170 pp. 103353
ISSN:
0304-3770
Subject:
nucleotide sequences,   etc   ; Nymphaea; botany; chloroplast genome; chloroplasts; genes; genomics; phylogeny;     Show all 8 Subjects
Abstract:
... Although there has been a long history of cultivation and research on Nymphaea, the taxonomic relationships and evolutionary relationships among Nymphaea species remain controversial. The chloroplast (cp) genome can provide a new method to determine species origin, evolution, and phylogenetic relationships of Nymphaea. The complete cp genomes of seven Nymphaea species were sequenced by high-throug ...
DOI:
10.1016/j.aquabot.2021.103353

14. Impact of Zero-Valent Iron on Freshwater Bacterioplankton Metabolism as Predicted from 16S rRNA Gene Sequence Libraries

Author:
Nguyen, Nhung H. A.; Špánek, Roman; Falagan-Lotsch, Priscila; Ševců, Alena
Source:
Current microbiology 2021 v.78 no.3 pp. 979-991
ISSN:
0343-8651
Subject:
nucleotide sequences,   etc   ; arsenates; bacterioplankton; biosynthesis; freshwater; microbiology; prediction;     Show all 7 Subjects
Abstract:
... The application of zero-valent iron particles (ZVI) for the treatment of heavily polluted environment and its biological effects have been studied for at least two decades. Still, information on the impact on bacterial metabolic pathways is lacking. This study describes the effect of microscale and nanoscale ZVI (mZVI and nZVI) on the abundance of different metabolic pathways in freshwater bacteri ...
DOI:
10.1007/s00284-021-02362-7

15. Phylogenetic Relationships of Flounders from the Family Pleuronectidae (Ostichties: Pleuronectiformes) Based on 16S rRNA Gene

Author:
Redin, A. D.; Kartavtsev, Yu. Ph.
Source:
Russian journal of genetics 2021 v.57 no.3 pp. 348-360
ISSN:
1022-7954
Subject:
nucleotide sequences,   etc   ; Lepidopsetta; genes; monophyly; statistical analysis; taxonomy; topology;     Show all 7 Subjects
Abstract:
... The systematics and phylogeny of flatfish is investigated on the basis of an incomplete nucleotide sequence of 16S rRNA and the complete Co-1 and Cyt-b sequences. In total 62 specimens of 14 species of our own collections were submitted to the GenBank/BOLD repositories and studied. Four types of gene trees were reconstructed: Bayesian (BA), maximum likelihood (ML), minimum evolution (ME), and neig ...
DOI:
10.1134/S102279542103011X

16. Complete genome sequence of Exiguobacterium mexicanum A-EM, isolated from seafloor hydrothermal vents in Atlantic Ocean

Author:
Lei, Jilin; Zheng, Minggang; Wang, Ling; Yin, Guobin; Lou, Yinghua; Shi, Lei
Source:
Marine genomics 2021 v.55 pp. 100801
ISSN:
1874-7787
Subject:
nucleotide sequences,   etc   ; Exiguobacterium; genes; genomics; pollution; toxins; Atlantic Ocean;     Show all 7 Subjects
Abstract:
... Exiguobacterium mexicanum A-EM was isolated from seafloor hydrothermal vents(Caifan field, 14.0S 14.4 W) and was shown to degrade toxins and contaminants. Here, we present the complete genome sequence of A-EM, consisting of 2,412,492 bp, with a GC content of 53.16%. A-EM sequence contains genes encoding enzymes that degrade toxins and contaminants. Complete genome sequence of the strain A-EM can f ...
DOI:
10.1016/j.margen.2020.100801

17. Genome Sequence Resources for the Maize Pathogen Fusarium temperatum Isolated in Poland

Author:
Wit, Marcin; Leng, Yueqiang; Du, Yang; Cegiełko, Małgorzata; Jabłońska, Emilia; Wakuliński, Wojciech; Zhong, Shaobin
Source:
Molecular plant-microbe interactions 2021 v.34 no.2 pp. 214-217
ISSN:
1943-7706
Subject:
nucleotide sequences,   etc   ; Fusarium fujikuroi; corn; fungi; genome; pathogenicity; pathogens; Poland;     Show all 8 Subjects
Abstract:
... Fusarium temperatum (Scaufl. & Munaut) is one of the most important fungal pathogens that cause ear and stalk rots in maize. In this study, we sequenced genomes of two F. temperatum isolates (KFI615 and KFI660) isolated from corn ears in Poland. A total of 110.3 and 116.3 million 100-nucleotide paired-end clean reads were obtained for KFI615 and KFI660, which were assembled into 20 and 18 scaffold ...
DOI:
10.1094/MPMI-09-20-0266-A

18. Reanalysis and Revision of the Complete Mitochondrial Genome of Artemia urmiana Günther, 1899 (Crustacea: Anostraca)

Author:
Asem, Alireza; Eimanifar, Amin; Li, Weidong; Shen, Chun-Yang; Shikhsarmast, Farnaz Mahmoudi; Dan, Ya-Ting; Lu, Hao; Zhou, Yang; Chen, You; Wang, Pei-Zheng; Wink, Michael
Source:
Diversity 2021 v.13 no.1
ISSN:
1424-2818
Subject:
nucleotide sequences,   etc   ; Artemia; lakes; mitochondrial genome; parthenogenesis; phylogeny;     Show all 6 Subjects
Abstract:
... In the previously published mitochondrial genome sequence of Artemia urmiana (NC_021382 [JQ975176]), the taxonomic status of the examined Artemia had not been determined, due to parthenogenetic populations coexisting with A. urmiana in Urmia Lake. Additionally, NC_021382 [JQ975176] has been obtained with pooled cysts of Artemia (0.25 g cysts consists of 20,000–25,000 cysts), not a single specimen. ...
DOI:
10.3390/d13010014

19. A method for estimating binding affinity from primary DEL selection data

Author:
Chen, Qiuxia; Hall, Justin; Foley, Timothy L.; Wan, Jinqiao; Li, You; Israel, David I.
Source:
Biochemical and biophysical research communications 2020 v.533 no.2 pp. 249-255
ISSN:
0006-291X
Subject:
nucleotide sequences,   etc   ; chemistry; ligands; research;     Show all 4 Subjects
Abstract:
... DEL selections are binding assays conducted with mixtures of chemically diverse DNA-tagged ligands and a screening target. DEL selections use DNA sequence counts to measure target binding, where ideally higher affinity ligands will have higher counts than weaker affinity ligands. However, there is not always a clear relationship between DNA sequence count (assay signal) and binding affinity. This ...
DOI:
10.1016/j.bbrc.2020.04.029

20. Predicting RNA SHAPE scores with deep learning

Author:
Bliss, Noah; Bindewald, Eckart; Shapiro, Bruce A.
Source:
RNA biology 2020 v.17 no.9 pp. 1324-1330
ISSN:
1555-8584
Subject:
nucleotide sequences,   etc   ; RNA; prediction; thermodynamics;     Show all 4 Subjects
Abstract:
... Secondary structure prediction approaches rely typically on models of equilibrium free energies that are themselves based on in vitro physical chemistry. Recent transcriptome-wide experiments of in vivo RNA structure based on SHAPE-MaP experiments provide important information that may make it possible to extend current in vitro-based RNA folding models in order to improve the accuracy of computat ...
DOI:
10.1080/15476286.2020.1760534