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1. 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

2. 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

3. Dialogue on the nomenclature and classification of prokaryotes

Author:
Rosselló-Móra, Ramon; Whitman, William B.
Source:
Systematic and applied microbiology 2019 v.42 no.1 pp. 5-14
ISSN:
0723-2020
Subject:
nucleotide sequences,   etc   ; ecology; high-throughput nucleotide sequencing; prokaryotic cells; taxonomy;     Show all 5 Subjects
Abstract:
... The application of next generation sequencing and molecular ecology to the systematics and taxonomy of prokaryotes offers enormous insights into prokaryotic biology. This discussion explores some major disagreements but also considers the opportunities associated with the nomenclature of the uncultured taxa, the use of genome sequences as type material, the plurality of the nomenclatural code, and ...
DOI:
10.1016/j.syapm.2018.07.002

4. Mitochondrial genome of Paruterina candelabraria (Cestoda: Paruterinidae), with implications for the relationships between the genera Cladotaenia and Paruterina

Author:
Guo, Aijiang; Wang, Li; Zhang, Shaohua; Zheng, Yadong; Georgiev, Boyko B.; Luo, Xuenong; Huang, Siyang; Cai, Xuepeng
Source:
Acta tropica 2019 v.189 pp. 1-5
ISSN:
0001-706X
Subject:
nucleotide sequences,   etc   ; Bayesian theory; Taeniidae; genes; mitochondria; mitochondrial genome; phylogeny;     Show all 7 Subjects
Abstract:
... The taxonomic concept for the family Paruterinidae is controversial, especially concerning the position of the genus Cladotaenia, since the latter genus has been placed sometimes in other families, i.e. in the Taeniidae or in the distinct family Cladotaeniidae; finding a solution based on morphological data is difficult and molecular data on paruterinids and related groups are scarce. In this stud ...
DOI:
10.1016/j.actatropica.2018.09.016

5. The importance of designating type material for uncultured taxa

Author:
Chuvochina, Maria; Rinke, Christian; Parks, Donovan H.; Rappé, Michael S.; Tyson, Gene W.; Yilmaz, Pelin; Whitman, William B.; Hugenholtz, Philip
Source:
Systematic and applied microbiology 2019 v.42 no.1 pp. 15-21
ISSN:
0723-2020
Subject:
nucleotide sequences,   etc   ; Archaea; bacteria; biological nomenclature; genome; prokaryotic cells;     Show all 6 Subjects
Abstract:
... Naming of uncultured Bacteria and Archaea is often inconsistent with the International Code of Nomenclature of Prokaryotes. The recent practice of proposing names for higher taxa without designation of lower ranks and nomenclature types is one of the most important inconsistencies that needs to be addressed to avoid nomenclatural instability. The Code requires names of higher taxa up to the rank o ...
DOI:
10.1016/j.syapm.2018.07.003

6. Tackling Hypotheticals in Helminth Genomes

Author:
Palevich, Nikola; Britton, Collette; Kamenetzky, Laura; Mitreva, Makedonka; de Moraes Mourão, Marina; Bennuru, Sasisekhar; Quack, Thomas; Scholte, Larissa Lopes Silva; Tyagi, Rahul; Slatko, Barton E.
Source:
Trends in parasitology 2018 v.34 pp. 179-183
ISSN:
1471-4922
Subject:
nucleotide sequences,   etc   ; databases; genome; helminths;     Show all 4 Subjects
Abstract:
... Advancements in genome sequencing have led to the rapid accumulation of uncharacterized ‘hypothetical proteins’ in the public databases. Here we provide a community perspective and some best-practice approaches for the accurate functional annotation of uncharacterized genomic sequences. ...
DOI:
10.1016/j.pt.2017.11.007

7. Nanoparticle based simple electrochemical biosensor platform for profiling of protein-nucleic acid interactions

Author:
Dai, Yifan; Chiu, Liang-Yuan; Sui, Yongkun; Dai, Quanbin; Penumutchu, Srinivasa; Jain, Niyati; Dai, Liming; Zorman, Christian A.; Tolbert, Blanton S.; Sankaran, R. Mohan; Liu, Chung Chiun
Source:
Talanta 2019 v.195 pp. 46-54
ISSN:
0039-9140
Subject:
nucleotide sequences,   etc   ; RNA; biophysics; biosensors; chemical bonding; nanoparticles; quantitative analysis; ribonucleoproteins;     Show all 8 Subjects
Abstract:
... The analysis of protein-nucleic acid interactions is essential for biophysics related research. However, simple, rapid, and accurate methods for quantitative analysis of biomolecular interactions are lacking. We herein establish an electrochemical biosensor approach for protein-nucleic acid binding analysis. Nanoparticle based sensors are fabricated by highly-controlled inkjet printing followed by ...
DOI:
10.1016/j.talanta.2018.11.021

8. Barcoding for diatoms in the Yangtze River from the morphological observation and 18S rDNA polymorphic analysis

Author:
Li, Zheng; Liu, Xiaorong; Yu, Yanfang; Huang, Huijie; Li, Xingling; Ji, Qiang; Li, Kai; Yu, Youjia; Li, Ding; Mao, Zhengsheng; Pu, Yan; Chen, Peng; Chen, Feng
Source:
Forensic science international 2019 v.297 pp. 81-89
ISSN:
0379-0738
Subject:
nucleotide sequences,   etc   ; Bacillariophyceae; DNA barcoding; death; expert opinion; forensic sciences; ribosomal DNA; Yangtze River;     Show all 8 Subjects
Abstract:
... In forensic science, the determination of diatoms bears several goals, for example to estimate the post mortem interval (PMI), to determine the cause of death of a corpse found in water as well as to further locate the suspected drowning site. However, to identify diatoms using morphological method beyond the genus level is difficult and requires expert knowledge. During the last decade, a new con ...
DOI:
10.1016/j.forsciint.2019.01.028

9. Lleida Bat Lyssavirus isolation in Miniopterus schreibersii in France

Author:
Picard‐Meyer, Evelyne; Beven, Veronique; Hirchaud, Edouard; Guillaume, Cédric; Larcher, Gérald; Robardet, Emmanuelle; Servat, Alexandre; Blanchard, Yannick; Cliquet, Florence
Source:
Zoonoses and public health 2019 v.66 no.2 pp. 254-258
ISSN:
1863-1959
Subject:
nucleotide sequences,   etc   ; Chiroptera; Lyssavirus; RNA; antigens; brain; high-throughput nucleotide sequencing; rabies; viruses; France;     Show all 10 Subjects
Abstract:
... Bat rabies cases are attributed in Europe to five different Lyssavirus species of 16 recognized Lyssavirus species causing rabies. One of the most genetically divergent Lyssavirus spp. has been detected in a dead Miniopterus schreibersii bat in France. Brain samples were found positive for the presence of antigen, infectious virus and viral RNA by classical virological methods and molecular method ...
DOI:
10.1111/zph.12535

10. Revising the taxonomy of the Acinetobacter lwoffii group: The description of Acinetobacter pseudolwoffii sp. nov. and emended description of Acinetobacter lwoffii

Author:
Nemec, Alexandr; Radolfová-Křížová, Lenka; Maixnerová, Martina; Nemec, Matěj; Clermont, Dominique; Bzdil, Jaroslav; Ježek, Petr; Španělová, Petra
Source:
Systematic and applied microbiology 2019 v.42 no.2 pp. 159-167
ISSN:
0723-2020
Subject:
nucleotide sequences,   etc   ; Acinetobacter lwoffii; genome; matrix-assisted laser desorption-ionization mass spectrometry; new species; phylogeny;     Show all 6 Subjects
Abstract:
... In 1986, Bouvet and Grimont delineated two related taxa of the genus Acinetobacter termed genospecies (GS) 8 and 9. They proposed the name Acinetobacter lwoffii for GS8, which included the supposed type strain (CIP 64.10). As the authenticity of CIP 64.10 was later questioned, this study aimed at reassessing the taxonomy of these genospecies. We investigated 52 strains of GS8 or GS9, including CIP ...
DOI:
10.1016/j.syapm.2018.10.004

11. Lateral flow test for meat authentication with visual detection

Author:
Magiati, Maria; Myridaki, Vasiliki M.; Christopoulos, Theodore K.; Kalogianni, Despina P.
Source:
Food chemistry 2019 v.274 pp. 803-807
ISSN:
0308-8146
Subject:
nucleotide sequences,   etc   ; DNA; beef; horses; immunoaffinity chromatography; nanogold; pork; raw meat; sheep;     Show all 9 Subjects
Abstract:
... A new lateral flow assay has been developed for meat authentication. The assay is based on gold nanoparticles and enables visual detection, by naked eye, of meat species-specific DNA sequences. The procedure includes DNA isolation from fresh meat samples, amplification of specific DNA sequences and detection by the lateral flow assay. The proposed assay is rapid and has been applied for the identi ...
DOI:
10.1016/j.foodchem.2018.09.063

12. A High-Quality Draft Genome Sequence of Colletotrichum gloeosporioides sensu stricto SMCG1#C, a Causal Agent of Anthracnose on Cunninghamia lanceolata in China

Author:
Huang, Lin; Kim, Ki-Tae; Yang, Ji-Yun; Song, Hyeunjeong; Choi, Gobong; Jeon, Jongbum; Cheong, Kyeongchae; Ko, Jaeho; Xu, Haibin; Lee, Yong-Hwan
Source:
Molecular plant-microbe interactions 2019 v.32 no.2 pp. 139-141
ISSN:
0894-0282
Subject:
nucleotide sequences,   etc   ; Colletotrichum; Cunninghamia lanceolata; Glomerella cingulata; anthracnose; crops; fungi; genome; genomics; host range; hosts; China;     Show all 12 Subjects
Abstract:
... Colletotrichum has a broad host range and causes major yield losses of crops. The fungus Colletotrichum gloeosporioides is associated with anthracnose on Chinese fir. In this study, we present a high-quality draft genome sequence of C. gloeosporioides sensu stricto SMCG1#C, providing a reference genomic data for further research on anthracnose of Chinese fir and other hosts. ...
DOI:
10.1094/MPMI-05-18-0144-A

13. Analytical epigenetics: single-molecule optical detection of DNA and histone modifications

Author:
Heck, Christian; Michaeli, Yael; Bald, Ilko; Ebenstein, Yuval
Source:
Current opinion in biotechnology 2019 v.55 pp. 151-158
ISSN:
0958-1669
Subject:
nucleotide sequences,   etc   ; DNA; RNA; diagnostic techniques; epigenetics; gene expression; genomics; genotype; histones; phenotype; physicochemical properties;     Show all 11 Subjects
Abstract:
... The field of epigenetics describes the relationship between genotype and phenotype, by regulating gene expression without changing the canonical base sequence of DNA. It deals with molecular genomic information that is encoded by a rich repertoire of chemical modifications and molecular interactions. This regulation involves DNA, RNA and proteins that are enzymatically tagged with small molecular ...
DOI:
10.1016/j.copbio.2018.09.006

14. A new species of Haliotrema (Monogenea: Ancyrocephalidae (sensu lato) Bychowsky & Nagibina, 1968) from holocentrids off Langkawi Island, Malaysia with notes on the phylogeny of related Haliotrema species

Author:
Soo, O.Y.M.
Source:
Parasitology international 2019 v.68 no.1 pp. 31-39
ISSN:
1383-5769
Subject:
nucleotide sequences,   etc   ; Ancyrocephalidae; Myripristis; gills; males; monophyly; new species; ribosomal DNA; statistical analysis; Malaysia;     Show all 10 Subjects
Abstract:
... Haliotrema susanae sp. nov. is described from the gills of the pinecone soldierfish, Myripristis murdjan off Langkawi Island, Malaysia. This species is differentiated from other Haliotrema species especially those from holocentrids in having a male copulatory organ with bract-like extensions at the initial of the copulatory tube, grooved dorsal anchors and ventral anchors with longer shafts. The m ...
DOI:
10.1016/j.parint.2018.09.003

15. Description of a new diatom genus Dorofeyukea gen. nov. with remarks on phylogeny of the family Stauroneidaceae

Author:
Kulikovskiy, Maxim; Maltsev, Yevhen; Andreeva, Svetlana; Glushchenko, Anton; Gusev, Evgeniy; Podunay, Yulia; Ludwig, Thelma Veiga; Tusset, Eduardo; Kociolek, John Patrick
Source:
Journal of phycology 2019 v.55 no.1 pp. 173-185
ISSN:
0022-3646
Subject:
nucleotide sequences,   etc   ; DNA; Navicula; Stauroneis; chloroplasts; fascia; loci; new combination; new genus; new species; phylogeny;     Show all 11 Subjects
Abstract:
... Type material of Navicula kotschyi was studied, and this species was transferred to Dorofeyukea gen. nov. as D. kotschyi comb. nov. Dorofeyukea was described on the basis of DNA sequence and morphological data. Additional species assigned to this genus that were previously included in Navicula include: D. ancisa comb. nov., D. grimmei comb. nov., D. ivatoensis comb. nov., D. orangiana comb. nov., ...
DOI:
10.1111/jpy.12810

16. Spontaneous epimutations in plants

Author:
Johannes, Frank; Schmitz, Robert J.
Source:
Thenew phytologist 2019 v.221 no.3 pp. 1253-1259
ISSN:
0028-646X
Subject:
nucleotide sequences,   etc   ; DNA; DNA methylation; byproducts; epigenetics; gene expression; genome; phenotype;     Show all 8 Subjects
Abstract:
... Contents Summary 1253 I. Introduction 1253 II. What is the rate and molecular spectrum of spontaneous epimutations? 1254 III. Do spontaneous epimutations have phenotypic consequences? 1257 IV. Conclusion and discussion 1258 Acknowledgements 1258 References 1258 SUMMARY: Heritable gains or losses of cytosine methylation can arise stochastically in plant genomes independently of DNA sequence changes ...
DOI:
10.1111/nph.15434

17. Self-Replication-Assisted Rapid Preparation of DNA Nanowires at Room Temperature and Its Biosensing Application

Author:
He, Hongfei; Dai, Jianyuan; Dong, Guixiu; Shi, Hongli; Wang, Fang; Qiu, Yunran; Liao, Ruoxing; Zhou, Cuisong; Guo, Yong; Xiao, Dan
Source:
Analytical chemistry 2019 v.91 no.4 pp. 3043-3047
ISSN:
1520-6882
Subject:
nucleotide sequences,   etc   ; DNA; DNA assembly; adenosine triphosphate; ambient temperature; catalytic activity; fuels; nanowires;     Show all 8 Subjects
Abstract:
... A rapid room-temperature DNA nanowires preparation strategy on the basis of self-replicating catalyzed hairpin assembly (SRCHA) was reported. In this system, three hairpin probes (P1, P2, and P3) were well-designed and partially hybridize to each other, and two split trigger DNA sequences were integrated into P1 and P3, respectively. When the SRCHA was initiated by the trigger DNA, a series of DNA ...
DOI:
10.1021/acs.analchem.8b05431

18. Detection of an animal-derived G4P[6] group A rotavirus strain in a symptomatic child, in Italy

Author:
Ianiro, Giovanni; Micolano, Roberto; Conte, Michela; Labianca, Michele; Vaccari, Gabriele; Monini, Marina
Source:
Virus research 2019 v.260 pp. 7-11
ISSN:
0168-1702
Subject:
nucleotide sequences,   etc   ; Rotavirus A; children; feces; gastroenteritis; genes; genomics; genotype; genotyping; humans; phylogeny; swine; Asia; Italy;     Show all 14 Subjects
Abstract:
... During 2017, a G4P[6] group A rotavirus strain was identified in the feces of an Italian child hospitalized for acute gastroenteritis in Southern Italy. Nucleotide sequencing of the 11 genomic segments, revealed the G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 genotype constellation. Phylogenetic analyses of the gene segments investigated revealed high nucleotide sequence identities with G4P[6] RVA strains ...
DOI:
10.1016/j.virusres.2018.11.003

19. Characterization of a lytic vibriophage VP06 of Vibrio parahaemolyticus

Author:
Wong, Hin-chung; Wang, Tzu-Yun; Yang, Chu-Wen; Tang, Chung-Tao; Ying, Chingwen; Wang, Chun-Hsiung; Chang, Wei-Hau
Source:
Research in microbiology 2019 v.170 no.1 pp. 13-23
ISSN:
0923-2508
Subject:
nucleotide sequences,   etc   ; Siphoviridae; Vibrio parahaemolyticus; bacteriophages; biological control agents; hosts; new genus; nucleotides; oysters; phylogeny;     Show all 10 Subjects
Abstract:
... Vibrio parahaemolyticus is a human enteropathogenic bacterium and is also pathogenic to shrimp and finfish. In a search for a biocontrol agent for V. parahaemolyticus and other pathogenic Vibrio species, a lytic phage VP06 was isolated from oyster using V. parahaemolyticus as the host. VP06 is a Siphoviridae phage with a polyhedral head and a long tail. The genome sequence of VP06 was 75,893 nucle ...
DOI:
10.1016/j.resmic.2018.07.003

20. Phylogeny and physiology of candidate phylum BRC1 inferred from the first complete metagenome-assembled genome obtained from deep subsurface aquifer

Author:
Kadnikov, Vitaly V.; Mardanov, Andrey V.; Beletsky, Alexey V.; Rakitin, Andrey L.; Frank, Yulia A.; Karnachuk, Olga V.; Ravin, Nikolai V.
Source:
Systematic and applied microbiology 2019 v.42 no.1 pp. 67-76
ISSN:
0723-2020
Subject:
nucleotide sequences,   etc   ; anaerobic conditions; aquifers; bacteria; carbohydrates; fermentation; genome; glycosidases; metagenomics; microbial communities; oxidation; phylogeny; Siberia;     Show all 13 Subjects
Abstract:
... Candidate bacterial phylum BRC1 has been identified in a broad range of mostly organic-rich oxic and anoxic environments through molecular analysis of microbial communities. None of the members of BRC1 have been cultivated and only a few draft genome sequences have been obtained from metagenomes or as a result of single-cell sequencing. We have reconstructed complete genome of BRC1 bacterium, BY40 ...
DOI:
10.1016/j.syapm.2018.08.013