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1. 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

2. 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

3. 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

4. Spectrum structures and biological functions of 8-mers in the human genome

Author:
Jia, Yun; Li, Hong; Wang, Jingfeng; Meng, Hu; Yang, Zhenhua
Source:
Genomics 2019 v.111 no.3 pp. 483-491
ISSN:
0888-7543
Subject:
nucleotide sequences,   etc   ; evolution; genomic islands; humans; nucleosomes;     Show all 5 Subjects
Abstract:
... The spectra of k-mer frequencies can reveal the structures and evolution of genome sequences. We confirmed that the trimodal spectrum of 8-mers in human genome sequences is distinguished only by CG2, CG1 and CG0 8-mer sets, containing 2,1 or 0 CpG, respectively. This phenomenon is called independent selection law. The three types of CG 8-mers were considered as different functional elements. We co ...
DOI:
10.1016/j.ygeno.2018.03.006

5. An improved plasmid size standard, 39R861+

Author:
Moran, Robert A.; Anantham, Sashindran; Hall, Ruth M.
Source:
Plasmid 2019 v.102 pp. 6-9
ISSN:
0147-619X
Subject:
nucleotide sequences,   etc   ; Escherichia coli; genetic conjugation; plasmids;     Show all 4 Subjects
Abstract:
... The four plasmids in E. coli 39R861 have been used as size standards for closed-circular plasmid DNA since the 1980s. However, their sizes had only been estimated. Here, the complete sequence of the 61.3 kb cryptic FII plasmid p39R861–3 is reported, and the sizes of p39R861–4, pSa and NTP168 were determined to be 155.8, 40.1 and 6.8 kb, respectively. An improved size standard, 39R861+, was created ...
DOI:
10.1016/j.plasmid.2019.01.002

6. Correction to: Loktanella aquimaris sp. nov., Isolated from Seawater

Author:
Kim, Kunho; Srinivasan, Sathiyaraj; Lee, Sang-Seob
Source:
Current microbiology 2019 v.76 no.1 pp. 130
ISSN:
0343-8651
Subject:
nucleotide sequences,   etc   ; bacteria; new species; seawater;     Show all 4 Subjects
Abstract:
... The original version of this article unfortunately contained a mistake in the species name description. Also the accession number was published incorrectly. ...
DOI:
10.1007/s00284-018-1590-1

7. Storage, visualization, and navigation of 3D genomics data

Author:
Waldispühl, Jérôme; Zhang, Eric; Butyaev, Alexander; Nazarova, Elena; Cyr, Yan
Source:
Methods 2018 v.142 pp. 74-80
ISSN:
1046-2023
Subject:
nucleotide sequences,   etc   ; genomics; technology;     Show all 3 Subjects
Abstract:
... The field of 3D genomics grew at increasing rates in the last decade. The volume and complexity of 2D and 3D data produced is progressively outpacing the capacities of the technology previously used for distributing genome sequences. The emergence of new technologies provides also novel opportunities for the development of innovative approaches. In this paper, we review the state-of-the-art comput ...
DOI:
10.1016/j.ymeth.2018.05.008

8. A comparative evaluation of hybrid error correction methods for error-prone long reads

Author:
Fu, Shuhua; Wang, Anqi; Au, Kin Fai
Source:
Genome biology 2019 v.20 no.1 pp. 26
ISSN:
1474-760X
Subject:
nucleotide sequences,   etc   ; data quality; genomics; guidelines; haplotypes; sequence analysis;     Show all 6 Subjects
Abstract:
... BACKGROUND: Third-generation sequencing technologies have advanced the progress of the biological research by generating reads that are substantially longer than second-generation sequencing technologies. However, their notorious high error rate impedes straightforward data analysis and limits their application. A handful of error correction methods for these error-prone long reads have been devel ...
DOI:
10.1186/s13059-018-1605-z

9. A k-mer grammar analysis to uncover maize regulatory architecture

Author:
Mejía-Guerra, María Katherine; Buckler, Edward S.
Source:
BMC plant biology 2019 v.19 no.1 pp. 103
ISSN:
1471-2229
Subject:
nucleotide sequences,   etc   ; chromatin; corn; gene expression regulation; intergenic DNA; models;     Show all 6 Subjects
Abstract:
... BACKGROUND: Only a small percentage of the genome sequence is involved in regulation of gene expression, but to biochemically identify this portion is expensive and laborious. In species like maize, with diverse intergenic regions and lots of repetitive elements, this is an especially challenging problem that limits the use of the data from one line to the other. While regulatory regions are rare, ...
DOI:
10.1186/s12870-019-1693-2

10. Complete genome of DENV2 isolated from mosquitoes in Mexico

Author:
Zárate, Selene; Hernández-Perez, Fabiola; Taboada, Blanca; Martínez, Norma E.; Alcaráz-Estrada, Sofía L.; del Moral, Oscar; Yocupicio-Monroy, Martha
Source:
Infection, genetics, and evolution 2019 v.71 pp. 98-107
ISSN:
1567-1348
Subject:
nucleotide sequences,   etc   ; Culicidae; Dengue virus; arboviruses; genome; humans; Mexico;     Show all 7 Subjects
Abstract:
... Dengue virus is the most prevalent arbovirus in Mexico, and although the diversity of this virus has been studied, the vast majority of sequences have been derived from viruses isolated from the human host. In this work, we aimed to sequence and to analyze DENVs derived from wild mosquitoes captured in Acapulco Guerrero, Mexico. We succeeded in determining three full genome sequences of such virus ...
DOI:
10.1016/j.meegid.2019.03.018

11. A review of microfabricated electrochemical biosensors for DNA detection

Author:
Blair, Ewen O.; Corrigan, Damion K.
Source:
Biosensors & bioelectronics 2019 v.134 pp. 57-67
ISSN:
0956-5663
Subject:
nucleotide sequences,   etc   ; DNA; biosensors; point-of-care systems;     Show all 4 Subjects
Abstract:
... This review article presents an overview of recent work on electrochemical biosensors developed using microfabrication processes, particularly sensors used to achieve sensitive and specific detection of DNA sequences. Such devices are important as they lend themselves to miniaturisation, reproducible mass-manufacture, and integration with other previously existing technologies and production metho ...
DOI:
10.1016/j.bios.2019.03.055

12. Authentication of nine snapper species by single-strand conformation polymorphism (SSCP) and forensically informative nucleotide sequencing (FINS) methods

Author:
Sivaraman, Balasubramanian; Jeyasekaran, Geevaretnam; Shakila, Robinson Jeya; Aanand, Samraj; Sukumar, Durairaj
Source:
Food control 2019 v.99 pp. 124-130
ISSN:
0956-7135
Subject:
nucleotide sequences,   etc   ; markets; mitochondria; polymerase chain reaction; snapper;     Show all 5 Subjects
Abstract:
... PCR-SSCP and PCR-FINS methods were developed to authenticate nine species of snapper. A highly variable mitochondrial D-loop region was chosen as a target region and three new primers viz., one forward (Fish-DL-F) and two reverse primers (Fish-DL-R and DLFR) were designed. PCR-SSCP was first targeted to amplify 515 bp D-loop fragment using Fish-DL-F/Fish-DL-R primers, but it could not differentiat ...
DOI:
10.1016/j.foodcont.2018.12.047

13. DNA Hybridization to Control Cellular Interactions

Author:
Furst, Ariel L.; Klass, Sarah H.; Francis, Matthew B.
Source:
Trends in biochemical sciences 2019 v.44 no.4 pp. 342-350
ISSN:
0968-0004
Subject:
nucleotide sequences,   etc   ; complementary DNA; nanoparticles; nucleic acid hybridization;     Show all 4 Subjects
Abstract:
... A key challenge in many biological studies is the inability to control the placement of cells in two and three dimensions. As our understanding of the importance of complexity in cellular communities increases, better tools are needed to control the spatial arrangements of cells. One universal method to govern these interactions is DNA hybridization, which relies on the inherent interaction betwee ...
DOI:
10.1016/j.tibs.2018.10.002

14. An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures

Author:
Jain, Swati; Saju, Sera; Petingi, Louis; Schlick, Tamar
Source:
Methods 2019
ISSN:
1046-2023
Subject:
nucleotide sequences,   etc   ; RNA; algorithms; databases; graphs; mathematical theory; topology; trees;     Show all 8 Subjects
Abstract:
... Exploring novel RNA topologies is imperative for understanding RNA structure and pursuing its design. Our RNA-As-Graphs (RAG) approach exploits graph theory tools and uses coarse-grained tree and dual graphs to represent RNA helices and loops by vertices and edges. Only dual graphs represent pseudoknotted RNAs fully. Here we develop a dual graph enumeration algorithm to generate an expanded librar ...
DOI:
10.1016/j.ymeth.2019.03.022

15. Distribution of Trichaleurina javanica (Rehm) M. Carbone, Agnello & P. Alvarado (Chorioactidaceae) in India

Author:
Patel, Ravi S.; Vasava, Ajit M.; Rajput, Kishore S.
Source:
Plant biosystems 2019 v.153 no.2 pp. 231-234
ISSN:
1724-5575
Subject:
nucleotide sequences,   etc   ; DNA barcoding; Pezizales; forests; fungi; India;     Show all 6 Subjects
Abstract:
... During the recent field visits to Saurashtra regions of Western India, one of the interesting fungi i.e. Trichaleurina javanica (Rehm) M. Carbone, Agnello & P. Alvarado (Chorioactidaceae, order Pezizales) was collected from Sarkhadiya Hanuman and Sasan (Gir Forest, India). Further confirmation of the identity was carried out by using molecular methods with its DNA barcoding. Review of literature s ...
DOI:
10.1080/11263504.2018.1461704

16. Are We Overestimating Protistan Diversity in Nature?

Author:
Caron, David A.; Hu, Sarah K.
Source:
Trends in microbiology 2019 v.27 no.3 pp. 197-205
ISSN:
0966-842X
Subject:
nucleotide sequences,   etc   ; DNA; morphospecies; protists; species richness; surveys;     Show all 6 Subjects
Abstract:
... Documenting the immense diversity of single-celled, eukaryotic organisms (protists) has been a formidable challenge for ecologists. These species were originally defined by morphological criteria, but shortcomings of the morphospecies concept, and a bewildering array of sizes and cellular attributes, has made constructing a taxonomy that is useful for ecologists nearly impossible. Consequently, ph ...
DOI:
10.1016/j.tim.2018.10.009

17. Systematic survey of non-retroviral virus-like elements in eukaryotic genomes

Author:
Kryukov, Kirill; Ueda, Mahoko Takahashi; Imanishi, Tadashi; Nakagawa, So
Source:
Virus research 2019 v.262 pp. 30-36
ISSN:
0168-1702
Subject:
nucleotide sequences,   etc   ; Retroviridae; databases; eukaryotic cells; genome; sequence homology; surveys;     Show all 7 Subjects
Abstract:
... Endogenous viral elements (EVEs) are viral sequences that are endogenized in the host cell. Recently, several eukaryotic genomes have been shown to contain EVEs. To improve the understanding of EVEs in eukaryotes, we have developed a system for detecting EVE-like sequences in eukaryotes and conducted a large-scale nucleotide sequence similarity search using all available eukaryotic and viral genom ...
DOI:
10.1016/j.virusres.2018.02.002

18. Genome Comparisons of Wild Isolates of Caulobacter crescentus Reveal Rates of Inversion and Horizontal Gene Transfer

Author:
Ely, Bert; Wilson, Kiesha; Ross, Keshawn; Ingram, Damyen; Lewter, Tajah; Herring, Jasmine; Duncan, David; Aikins, Anthea; Scott, Derrick
Source:
Current microbiology 2019 v.76 no.2 pp. 159-167
ISSN:
0343-8651
Subject:
nucleotide sequences,   etc   ; Caulobacter crescentus; genes; horizontal gene transfer; polymers;     Show all 5 Subjects
Abstract:
... Since previous interspecies comparisons of Caulobacter genomes have revealed extensive genome rearrangements, we decided to compare the nucleotide sequences of four C. crescentus genomes, NA1000, CB1, CB2, and CB13. To accomplish this goal, we used PacBio sequencing technology to determine the nucleotide sequence of the CB1, CB2, and CB13 genomes, and obtained each genome sequence as a single cont ...
DOI:
10.1007/s00284-018-1606-x

19. Naturally-occurring right terminal hairpin mutations in three genotypes of canine parvovirus (CPV-2a, CPV-2b and CPV-2c) have no effect on their growth characteristics

Author:
Yu, Yongle; Zhang, Jianlou; Wang, Jigui; Xi, Ji; Zhang, Xiaomei; Li, Peiran; Liu, Ying; Liu, Weiquan
Source:
Virus research 2019 v.261 pp. 31-36
ISSN:
0168-1702
Subject:
nucleotide sequences,   etc   ; Carnivore protoparvovirus 1; genotype; mutation; plasmids; China;     Show all 6 Subjects
Abstract:
... We have isolated 4 naturally-occurring strains of CPV in mainland China and have identified them as CPV-2, 2a, 2b and 2c genotypes according to their VP2 sequences which also revealed substitutions within their right terminal regions. To determine if these substitutions affected the growth characteristics of the 4 strains, we constructed plasmids based on their genomic sequences minus their right ...
DOI:
10.1016/j.virusres.2018.12.007

20. Charge Separation and Recombination Pathways in Diblock DNA Hairpins

Author:
Olshansky, Jacob H.; Young, Ryan M.; Wasielewski, Michael R.
Source:
TheJournal of physical chemistry 2019 v.123 no.7 pp. 1545-1553
ISSN:
1520-5207
Subject:
nucleotide sequences,   etc   ; DNA; adenines; kinetics; physical chemistry; spectroscopy;     Show all 6 Subjects
Abstract:
... Achieving high-yielding photoinduced charge separation through the π-stacked bases of DNA is a critical requirement for realizing numerous DNA-based technologies. In the current work, we combine two strategies for achieving high-yield charge separation. First, a chromophore with a high driving force for charge injection, naphthalenediimide (NDI), is used because it generates hot carriers that enha ...
DOI:
10.1021/acs.jpcb.8b11782