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1. Nucleic acid-cleaving catalytic DNA for sensing and therapeutics

Author:
Zimmermann, Alessandra C.; White, Ian M.; Kahn, Jason D.
Source:
Talanta 2020 v.211 pp. 120709
ISSN:
0039-9140
Subject:
nucleotide sequences,   etc   ; DNA; catalytic activity; therapeutics;     Show all 4 Subjects
Abstract:
... DNAzymes with nucleic acid-cleaving catalytic activity are increasing in versatility through concerted efforts to discover new sequences with unique functions, and they are generating excitement in the sensing community as cheap, stable, amplifiable detection elements. This review provides a comprehensive list and detailed descriptions of the DNAzymes identified to date, classified by their associ ...
DOI:
10.1016/j.talanta.2019.120709

2. Comparative genomics in infectious disease

Author:
Moustafa, Ahmed M; Lal, Arnav; Planet, Paul J
Source:
Current opinion in microbiology 2020 v.53 pp. 61-70
ISSN:
1369-5274
Subject:
nucleotide sequences,   etc   ; databases; genomics; infectious diseases; pathogenesis;     Show all 5 Subjects
Abstract:
... With more than one million bacterial genome sequences uploaded to public databases in the last 25 years, genomics has become a powerful tool for studying bacterial biology. Here, we review recent approaches that leverage large numbers of whole genome sequences to decipher the spread and pathogenesis of bacterial infectious diseases. ...
DOI:
10.1016/j.mib.2020.02.009

3. For common community phylogenetic analyses, go ahead and use synthesis phylogenies

Author:
Li, Daijiang; Trotta, Lauren; Marx, Hannah E.; Allen, Julie M.; Sun, Miao; Soltis, Douglas E.; Soltis, Pamela S.; Guralnick, Robert P.; Baiser, Benjamin
Source:
Ecology 2019 v.100 no.9 pp. e02788
ISSN:
0012-9658
Subject:
nucleotide sequences,   etc   ; phylogeny; trees;     Show all 3 Subjects
Abstract:
... Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose‐built phylogeny) requires more effort, expertise, and cost than subsetting an already available ...
DOI:
10.1002/ecy.2788
PubMed:
31225900
PubMed Central:
PMC7079099

4. RNA nanotechnology in synthetic biology

Author:
Kim, Jongmin; Franco, Elisa
Source:
Current opinion in biotechnology 2020 v.63 pp. 135-141
ISSN:
0958-1669
Subject:
nucleotide sequences,   etc   ; RNA; gene expression; nanotechnology; synthetic biology;     Show all 5 Subjects
Abstract:
... We review recent advances in the design and expression of synthetic RNA sequences inside cells, to regulate gene expression and to achieve spatial localization of components. We focus on approaches that exploit the programmability of the secondary and tertiary structure of RNA to build scalable and modular devices that fold spontaneously and have the capacity to respond to environmental inputs. ...
DOI:
10.1016/j.copbio.2019.12.016

5. Targeted DNA complementation on a 1,1′-carbonyldiimidazole-functionalized surface for identifying Mycobacterium tuberculosis

Author:
Xu, Shu; Xue, Yu; Guo, Fengyan; Xu, Miaomiao; Gopinath, Subash C. B.; Mao, Xiaohui
Source:
3 Biotech 2020 v.10 no.5 pp. 227
ISSN:
2190-572X
Subject:
nucleotide sequences,   etc   ; DNA; Mycobacterium tuberculosis; detection limit; electrodes; silica;     Show all 6 Subjects
Abstract:
... Herein, a rapid and sensitive current–volt measurement was developed for identifying the IS6110 DNA sequence to diagnose Mycobacterium tuberculosis (TB). An aminated capture probe was immobilized on a 1,1′-carbonyldiimidazole-functionalized interdigitated electrode (IDE) silica substrate, and the target sequence was detected by complementation. It was found that all tested concentrations displayed ...
DOI:
10.1007/s13205-020-02216-2
PubMed:
32373419
PubMed Central:
PMC7196115

6. Genetically encoded light-up RNA aptamers and their applications for imaging and biosensing

Author:
Swetha, Puchakayala; Fan, Ze; Wang, Fenglin; Jiang, Jian-Hui
Source:
Journal of materials chemistry B 2020 v.8 no.16 pp. 3382-3392
ISSN:
2050-7518
Subject:
nucleotide sequences,   etc   ; RNA; fluorescence; image analysis; ligands; nucleotide aptamers;     Show all 6 Subjects
Abstract:
... Intracellular small ligands and biomacromolecules are playing crucial roles not only as executors but also as regulators. It is essential to develop tools to investigate their dynamics to interrogate their functions and reflect the cellular status. Light-up RNA aptamers are RNA sequences that can bind with their cognate nonfluorescent fluorogens and greatly activate their fluorescence. The emergen ...
DOI:
10.1039/c9tb02668a

7. Deep learning for plant genomics and crop improvement

Author:
Wang, Hai; Cimen, Emre; Singh, Nisha; Buckler, Edward
Source:
Current opinion in plant biology 2020 v.54 pp. 34-41
ISSN:
1369-5266
Subject:
nucleotide sequences,   etc   ; DNA; genetic improvement; genomics; models; phenotype; synthetic biology;     Show all 7 Subjects
Abstract:
... Our era has witnessed tremendous advances in plant genomics, characterized by an explosion of high-throughput techniques to identify multi-dimensional genome-wide molecular phenotypes at low costs. More importantly, genomics is not merely acquiring molecular phenotypes, but also leveraging powerful data mining tools to predict and explain them. In recent years, deep learning has been found extreme ...
DOI:
10.1016/j.pbi.2019.12.010

8. Overcoming bottlenecks in plant gene editing

Author:
Atkins, Paul AP; Voytas, Daniel F
Source:
Current opinion in plant biology 2020 v.54 pp. 79-84
ISSN:
1369-5266
Subject:
nucleotide sequences,   etc   ; DNA; gene editing; genome; plant biology;     Show all 5 Subjects
Abstract:
... Agriculture has reached a technological inflection point. The development of novel gene editing tools and methods for their delivery to plant cells promises to increase genome malleability and transform plant biology. Whereas gene editing is capable of making a myriad of DNA sequence modifications, its widespread adoption has been hindered by a number of factors, particularly inefficiencies in cre ...
DOI:
10.1016/j.pbi.2020.01.002

9. Isolation and phylogenomic analysis of buffalopox virus from human and buffaloes in India

Author:
Yadav, Pragya D.; Mauldin, Matthew R.; Nyayanit, Dimpal A.; Albariño, César G.; Sarkale, Prasad; Shete, Anita; Guerrero, Lisa W.; Nakazawa, Yoshinori; Nichol, Stuart T.; Mourya, Devendra T.
Source:
Virus research 2020 v.277 pp. 197836
ISSN:
0168-1702
Subject:
nucleotide sequences,   etc   ; Vaccinia virus; buffaloes; humans; vaccines; viruses; India;     Show all 7 Subjects
Abstract:
... Three genome sequences of Buffalopox virus (BPVX) were retrieved from a human and two buffaloes scab samples. Phylogenomic analysis of the BPXV indicates that it shares a most recent common ancestor with Lister and closely related vaccine strains when compared to potential wild-type VACV strains (like Horsepox virus). ...
DOI:
10.1016/j.virusres.2019.197836

10. Rediscovering Halophila major (Zollinger) Miquel (1855) in Indonesia

Author:
Kurniawan, Fery; Imran, Zulhamsyah; Darus, Robba Fahrisy; Anggraeni, Fitriyah; Damar, Ario; Sunuddin, Adriani; Kamal, Mohammad Mukhlis; Murti Pratiwi, Niken Tunjung; Ayu, Inna Puspa; Iswantari, Aliati
Source:
Aquatic botany 2020 v.161 pp. 103171
ISSN:
0304-3770
Subject:
nucleotide sequences,   etc   ; DNA; Halophila; geographical distribution; seagrasses; sequence analysis; Indonesia;     Show all 7 Subjects
Abstract:
... Halophila major (Zollinger) Miquel (1855) has not been officially recorded as a species that exists in Indonesia until now. Evidence of this species for Indonesia was collected from four locations, including Sekotong Beach, Lombok, Tayando Island, Tual, Weduar Kei Besar Beach, Tual, and Malala Bay, Toli-toli, at a depth of 2–4 m. Morphological characteristics and DNA sequence analysis confirmed th ...
DOI:
10.1016/j.aquabot.2019.103171

11. Zero Intercalary Plates in Parvodinium (Peridiniopsidaceae, Peridiniales) and Phylogenetics of P. elpatiewskyi, comb. nov.

Author:
Kretschmann, Juliane; Žerdoner Čalasan, Anže; Meyer, Barbara; Gottschling, Marc
Source:
Protist 2020 v.171 no.1 pp. 125700
ISSN:
1434-4610
Subject:
nucleotide sequences,   etc   ; Peridiniales; new combination; phylogeny; ribosomal RNA; sutures; Germany;     Show all 7 Subjects
Abstract:
... Parvodinium elpatiewskyi, comb. nov., is a common freshwater dinophyte without intercalary plates and with various spines on hypothecal sutures. However, the taxonomy of the species has had a complex history, and its systematic placement remained unclear. The conserved type of P. elpatiewskyi, comb. nov., illustrated here for the first time using electron microscopy, is an environmental sample. Ba ...
DOI:
10.1016/j.protis.2019.125700

12. Erratum to: Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil

Author:
Kim, Jiyoun; Chhetri, Geeta; Kim, Inhyup; Kim, Hyungdong; Kim, Myung Kyum; Seo, Taegun
Source:
The journal of microbiology 2020 v.58 no.1 pp. 79
ISSN:
1225-8873
Subject:
nucleotide sequences,   etc   ; Methylobacterium; bacteria; genes; new species; ribosomal RNA; soil;     Show all 7 Subjects
Abstract:
... In the article by Kim et al. published in Journal of Microbiology 2019; 57, 959–966, The NBRC accession number NBRC 112879ᵀ on 33ᵗʰ line of 2ⁿᵈ paragraph in the section of ‘Description of Methylobacterium terrae sp. nov.’ on page 964 should be corrected in NBRC 112873ᵀ.The sentence in abstract should have read: The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and genome sequences of t ...
DOI:
10.1007/s12275-020-9722-2

13. Morphology, Morphogenesis, and Phylogeny of Urosoma caudata (Ehrenberg, 1833) Berger, 1999 (Ciliophora, Hypotrichia) based on a Chinese Population

Author:
Xu, Wenxin; Zhao, Yan; Pan, Bo; Liu, Yongqiang; Li, Yuan; Bourland, William A.; Luo, Xiaotian
Source:
Thejournal of eukaryotic microbiology 2020 v.67 no.1 pp. 76-85
ISSN:
1066-5234
Subject:
nucleotide sequences,   etc   ; Ciliophora; cortical granules; morphogenesis; ontogeny; phylogeny; ribosomal RNA;     Show all 7 Subjects
Abstract:
... We report the morphology and morphogenesis of Urosoma caudata (Ehrenberg, 1833) Berger, 1999 based on in vivo observation and protargol impregnation and provide an improved diagnosis of U. caudata based on previous and current work. Urosoma caudata differs from its congeners mainly by the combination of the following features: tail‐like posterior end, colorless cortical granules, and two macronucl ...
DOI:
10.1111/jeu.12756

14. Haplotype-aware diplotyping from noisy long reads

Author:
Ebler, Jana; Haukness, Marina; Pesout, Trevor; Marschall, Tobias; Paten, Benedict
Source:
Genome biology 2019 v.20 no.1 pp. 116
ISSN:
1474-760X
Subject:
nucleotide sequences,   etc   ; genome; genotyping; haplotypes;     Show all 4 Subjects
Abstract:
... Current genotyping approaches for single-nucleotide variations rely on short, accurate reads from second-generation sequencing devices. Presently, third-generation sequencing platforms are rapidly becoming more widespread, yet approaches for leveraging their long but error-prone reads for genotyping are lacking. Here, we introduce a novel statistical framework for the joint inference of haplotypes ...
DOI:
10.1186/s13059-019-1709-0
PubMed:
31159868
PubMed Central:
PMC6547545

15. Correction to: Complete genome sequence of a novel bacteriophage, PBKP05, infecting Klebsiella pneumoniae

Author:
Oh, Hyun Keun; Cha, Kyoungeun; Hwang, Yoon Jung; Cho, Jaehak; Jo, Yunyeol; Myung, Heejoon
Source:
Archives of virology 2019 v.164 no.9 pp. 2433
ISSN:
0304-8608
Subject:
nucleotide sequences,   etc   ; Klebsiella pneumoniae; bacteriophages;     Show all 3 Subjects
Abstract:
... Unfortunately, the original article was published with incorrect accession number and the correct version is updated here. ...
DOI:
10.1007/s00705-019-04326-6

16. MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis

Author:
Schwacke, Rainer; Ponce-Soto, Gabriel Y.; Krause, Kirsten; Bolger, Anthony M.; Arsova, Borjana; Hallab, Asis; Gruden, Kristina; Stitt, Mark; Bolger, Marie E.; Usadel, Björn
Source:
Molecular plant 2019 v.12 no.6 pp. 879-892
ISSN:
1674-2052
Subject:
nucleotide sequences,   etc   ; embryophytes; genes; proteins;     Show all 4 Subjects
Abstract:
... Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. ...
DOI:
10.1016/j.molp.2019.01.003

17. CRISPR-Cas Systems Reduced to a Minimum

Author:
Almendros, Cristóbal; Kieper, Sebastian N.; Brouns, Stan J.J.
Source:
Molecular cell 2019 v.73 no.4 pp. 641-642
ISSN:
1097-2765
Subject:
nucleotide sequences,   etc   ; endodeoxyribonucleases; gene editing;     Show all 3 Subjects
Abstract:
... In two recent studies in Molecular Cell, Wright et al. (2019) report complete spacer integration by a Cas1 mini-integrase and Edraki et al. (2019) describe accurate genome editing by a small Cas9 ortholog with less stringent PAM requirements. ...
DOI:
10.1016/j.molcel.2019.02.005

18. The Splicing Code Goes Deep

Author:
Bao, Suying; Moakley, Daniel F.; Zhang, Chaolin
Source:
Cell 2019 v.176 no.3 pp. 414-416
ISSN:
0092-8674
Subject:
nucleotide sequences,   etc   ; RNA splicing; transcriptome;     Show all 3 Subjects
Abstract:
... The importance of genomic sequence context in generating transcriptome diversity through RNA splicing is independently unmasked by two studies in this issue (Jaganathan et al., 2019; Baeza-Centurion et al., 2019). ...
DOI:
10.1016/j.cell.2019.01.013

19. Detection of quiescent fungi in harvested fruit using CMOS biosensor: A proof of concept study

Author:
Zamir, Dolev; Galsurker, Ortal; Alkan, Noam; Eltzov, Evgeni
Source:
Talanta 2020 v.217 pp. 120994
ISSN:
0039-9140
Subject:
nucleotide sequences,   etc   ; Glomerella cingulata; biosensors; fruits; fungi; gene expression regulation; messenger RNA; pathogenicity; pathogens; peroxidase;     Show all 10 Subjects
Abstract:
... Postharvest fruit decay is caused by fungal pathogens and leads to major losses. In this study, specific mRNA sequences that are upregulated in the fungus Colletotrichum gloeosporioides during its quiescent stage in fruits, were identified using a CMOS sensor. The identification process was based on sandwich approach, where strands complementary to the C. gloeosporioides mRNA sequences (quiescent ...
DOI:
10.1016/j.talanta.2020.120994

20. i4mC-ROSE, a bioinformatics tool for the identification of DNA N4-methylcytosine sites in the Rosaceae genome

Author:
Hasan, Md. Mehedi; Manavalan, Balachandran; Khatun, Mst. Shamima; Kurata, Hiroyuki
Source:
International journal of biological macromolecules 2020 v.157 pp. 752-758
ISSN:
0141-8130
Subject:
nucleotide sequences,   etc   ; DNA; DNA replication; Fragaria vesca; Rosa chinensis; bioinformatics; chromosomes; data collection; epigenetics; genome; prediction;     Show all 11 Subjects
Abstract:
... One of the most important epigenetic modifications is N4-methylcytosine, which regulates many biological processes including DNA replication and chromosome stability. Identification of N4-methylcytosine sites is pivotal to understand specific biological functions. Herein, we developed the first bioinformatics tool called i4mC-ROSE for identifying N4-methylcytosine sites in the genomes of Fragaria ...
DOI:
10.1016/j.ijbiomac.2019.12.009