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1. Keen on the tenure track job, are you? Know these things, you should

Author:
Voight, Benjamin F.
Source:
Genome biology 2019 v.20 no.1 pp. 6
ISSN:
1474-760X
Subject:
genome,   etc   ; geneticists; genomics; universities;     Show all 4 Subjects
Abstract:
... Success along the tenure track requires more than hard work and long hours. Here, the experiences of a recently tenured professor are distilled into a collection of tips to assist others along the path. ...
DOI:
10.1186/s13059-018-1617-8

2. De novo Assembly Vastly Expands the Known Microbial Universe

Author:
Minot, Samuel S.
Source:
Trends in microbiology 2019 v.27 no.5 pp. 385-386
ISSN:
0966-842X
Subject:
genome,   etc   ; databases; humans; microbiome;     Show all 4 Subjects
Abstract:
... The study of the human microbiome relies heavily on the genomes of bacterial isolates that can be grown in culture. A recent study (Pasolli et al. Cell 2019;176:649–662) of stool microbiome samples generated over 150 000 microbial genomes without any culture, vastly expanding our knowledge of the biases in existing reference databases. ...
DOI:
10.1016/j.tim.2019.02.007

3. Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning

Author:
Goodstadt, Mike N.; Marti-Renom, Marc A.
Source:
Journal of molecular biology 2019 v.431 no.6 pp. 1071-1087
ISSN:
0022-2836
Subject:
genome,   etc   ; learning; models;     Show all 3 Subjects
Abstract:
... Genome discoveries at the core of biology are made by visual description and exploration of the cell, from microscopic sketches and biochemical mapping to computational analysis and spatial modeling. We outline the experimental and visualization techniques that have been developed recently which capture the three-dimensional interactions regulating how genes are expressed. We detail the challenges ...
DOI:
10.1016/j.jmb.2018.11.008

4. The Strawberry Tales: Size Matters

Author:
Vergauwen, David; De Smet, Ive
Source:
Trends in plant science 2019 v.24 no.1 pp. 1-3
ISSN:
1360-1385
Subject:
genome,   etc   ; domestication; odors; strawberries;     Show all 4 Subjects
Abstract:
... The history of the strawberry is one of ambitious kings and cunning spies, overseas adventures, and religious symbolism. Here, we will tell these stories, illustrated by relevant paintings and drawings, to give insight into the domestication of the strawberry. Furthermore, we will briefly discuss the complex strawberry genomes and aroma. ...
DOI:
10.1016/j.tplants.2018.10.007

5. Non canonical genetic material

Author:
Eremeeva, Elena; Herdewijn, Piet
Source:
Current opinion in biotechnology 2019 v.57 pp. 25-33
ISSN:
0958-1669
Subject:
genome,   etc   ; DNA; RNA; oligonucleotides; xenobiotics;     Show all 5 Subjects
Abstract:
... To increase the scope of natural biosystem, nucleic acids have been intensively modified. One direction includes the development of a synthetic alternative to the native DNA and RNA, denoted Xenobiotic nucleic acids (XNAs) that are able to store and transfer genetic information either by base-modification or backbone-modification. Another line of research aims to develop alternative third base pai ...
DOI:
10.1016/j.copbio.2018.12.001

6. Epigenetic fates of gene silencing established by heterochromatin spreading in cell identity and genome stability

Author:
Greenstein, R. A.; Al-Sady, Bassem
Source:
Current genetics 2019 v.65 no.2 pp. 423-428
ISSN:
0172-8083
Subject:
genome,   etc   ; epigenetics; gene silencing; heterochromatin;     Show all 4 Subjects
Abstract:
... Heterochromatin spreading, the propagation of repressive chromatin along the chromosome, is a reaction critical to genome stability and defense, as well as maintenance of unique cell fates. Here, we discuss the intrinsic properties of the spreading reaction and circumstances under which its products, formed distal to DNA-encoded nucleation sites, can be epigenetically maintained. Finally, we specu ...
DOI:
10.1007/s00294-018-0901-1

7. Efficient clustering in collaborative filtering recommender system: Hybrid method based on genetic algorithm and gravitational emulation local search algorithm

Author:
Mohammadpour, Touraj; Bidgoli, Amir Massoud; Enayatifar, Rasul; Javadi, Hamid Haj Seyyed
Source:
Genomics 2019
ISSN:
0888-7543
Subject:
genome,   etc   ; algorithms; data collection; genomics;     Show all 4 Subjects
Abstract:
... The ultimate goal of the Recommender System (RS) is to offer a proposal that is very close to the user's real opinion. Data clustering can be effective in increasing the accuracy of production proposals by the RS. In this paper, single-objective hybrid evolutionary approach is proposed for clustering items in the offline collaborative filtering RS. This method, after generating a population of ran ...
DOI:
10.1016/j.ygeno.2019.01.001

8. bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes

Author:
DeMaere, Matthew Z.; Darling, Aaron E.
Source:
Genome biology 2019 v.20 no.1 pp. 46
ISSN:
1474-760X
Subject:
genome,   etc   ; algorithms; metagenomics; microorganisms; time series analysis;     Show all 5 Subjects
Abstract:
... Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of community complexity, target abundance, and sequencing depth. We describe an unsupervised ...
DOI:
10.1186/s13059-019-1643-1

9. Enhanced mammalian genome editing by new Cas12a orthologs with optimized crRNA scaffolds

Author:
Teng, Fei; Li, Jing; Cui, Tongtong; Xu, Kai; Guo, Lu; Gao, Qingqin; Feng, Guihai; Chen, Chuanyuan; Han, Dali; Zhou, Qi; Li, Wei
Source:
Genome biology 2019 v.20 no.1 pp. 15
ISSN:
1474-760X
Subject:
genome,   etc   ; RNA; enzymes; gene editing; humans; mice;     Show all 6 Subjects
Abstract:
... CRISPR-Cas12a/Cpf1, a single RNA-guided endonuclease system, provides a promising tool for genome engineering. However, only three Cas12a orthologs have been employed for mammalian genome editing, and the editing efficiency as well as targeting coverage still requires improvements. Here, we harness six novel Cas12a orthologs for genome editing in human and mouse cells, some of which utilize simple ...
DOI:
10.1186/s13059-019-1620-8

10. Bipedal DNA Walker Based Electrochemical Genosensing Strategy

Author:
Chai, Hua; Miao, Peng
Source:
Analytical chemistry 2019 v.91 no.8 pp. 4953-4957
ISSN:
1520-6882
Subject:
genome walking,   etc   ; DNA; electrochemistry; electrodes; magnetism; nanomaterials;     Show all 6 Subjects
Abstract:
... DNAs are one of the most fundamental molecules for life. Quantification of specific sequences is of great importance for biological research and clinical diagnosis. In order to determine extremely low abundant DNAs, we herein develop a novel electrochemical genosensor taking advantage of a smart bipedal DNA walking machine. Magnetic nanomaterials are first employed to enrich target DNA. Strand dis ...
DOI:
10.1021/acs.analchem.9b01118

11. The Genetic Basis of Metabolic Disease

Author:
Barroso, Inês; McCarthy, Mark I.
Source:
Cell 2019 v.177 no.1 pp. 146-161
ISSN:
0092-8674
Subject:
genome,   etc   ; genomics; loci; metabolic diseases; phenotype;     Show all 5 Subjects
Abstract:
... Recent developments in genetics and genomics are providing a detailed and systematic characterization of the genetic underpinnings of common metabolic diseases and traits, highlighting the inherent complexity within systems for homeostatic control and the many ways in which that control can fail. The genetic architecture underlying these common metabolic phenotypes is complex, with each trait infl ...
DOI:
10.1016/j.cell.2019.02.024

12. Optimization of DamID for use in primary cultures of mouse hepatocytes

Author:
Gatticchi, Leonardo; de las Heras, Jose I.; Roberti, Rita; Schirmer, Eric C.
Source:
Methods 2019 v.157 pp. 88-99
ISSN:
1046-2023
Subject:
genome,   etc   ; DNA; bioinformatics; hepatocytes; mice; tissue culture;     Show all 6 Subjects
Abstract:
... DamID, a method to identify DNA associating with a particular protein, was originally developed for use in immortalized tissue culture lines. The power of this technique has led to its adaptation for a number of additional systems. Here we report adaptations for its use in primary cells isolated from rodents with emphasis on the challenges this presents. Specifically, we present several modificati ...
DOI:
10.1016/j.ymeth.2018.11.005

13. Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny

Author:
Van Dam, Matthew H.; Trautwein, Michelle; Spicer, Greg S.; Esposito, Lauren
Source:
Molecular ecology resources 2019 v.19 no.2 pp. 465-475
ISSN:
1755-098X
Subject:
genome,   etc   ; Opiliones; Parasitiformes; genomics; loci; mites; paraphyly;     Show all 7 Subjects
Abstract:
... Mites (Acari) are one of the most diverse groups of life on Earth; yet, their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution, we design targeted ultraconserved genomic elements (UCEs) probes, intended for resol ...
DOI:
10.1111/1755-0998.12962

14. Hitting Undruggable Targets: Viewing Stabilized Peptide Development through the Lens of Quantitative Systems Pharmacology

Author:
Atangcho, Lydia; Navaratna, Tejas; Thurber, Greg M.
Source:
Trends in biochemical sciences 2019 v.44 no.3 pp. 241-257
ISSN:
0968-0004
Subject:
genome,   etc   ; drugs; peptides; pharmacokinetics; screening; therapeutics; toxicity;     Show all 7 Subjects
Abstract:
... Stabilized peptide therapeutics have the potential to hit currently undruggable targets, dramatically expanding the druggable genome. However, major obstacles to their development include poor intracellular delivery, rapid degradation, low target affinity, and membrane toxicity. With the emergence of multiple stabilization techniques and screening technologies, the high efficacy of various bioacti ...
DOI:
10.1016/j.tibs.2018.11.008

15. Replication Timing Becomes Intertwined with 3D Genome Organization

Author:
Ma, Jian; Duan, Zhijun
Source:
Cell 2019 v.176 no.4 pp. 681-684
ISSN:
0092-8674
Subject:
genome,   etc   ; DNA replication; regulatory sequences; transcription (genetics);     Show all 4 Subjects
Abstract:
... Through dissecting the link between spatial genome organization and DNA replication timing, Sima et al. (2018) discover early replicating control elements (ERCEs), a new type of cis-acting elements that regulate replication timing, transcription, and multiple layers of three-dimensional features of genome organization. The study has important implications for unraveling control elements of high-or ...
DOI:
10.1016/j.cell.2019.01.027

16. Chromatin mobility upon DNA damage: state of the art and remaining questions

Author:
Zimmer, Christophe; Fabre, Emmanuelle
Source:
Current genetics 2019 v.65 no.1 pp. 1-9
ISSN:
0172-8083
Subject:
genome,   etc   ; DNA; DNA damage; chromatin; metabolism; yeasts;     Show all 6 Subjects
Abstract:
... Chromosome organization and chromatin mobility are central to DNA metabolism. In particular, it has been recently shown by several labs that double strand breaks (DSBs) in yeast induce a change in chromatin mobility at the site of the damage. Intriguingly, DSB also induces a global mobility of the genome, at others, potentially undamaged positions. How mobility is regulated and what are the functi ...
DOI:
10.1007/s00294-018-0852-6

17. Nucleosome Orientation Map Finds Two New Chromatin Folding Motifs

Author:
Risca, Viviana I.
Source:
Cell 2019 v.176 no.3 pp. 412-413
ISSN:
0092-8674
Subject:
genome,   etc   ; Saccharomyces cerevisiae; molecular conformation; nucleosomes; yeasts;     Show all 5 Subjects
Abstract:
... A method for mapping nucleosome contacts and relative nucleosome orientations reveals new detail about the folding of the S. cerevisiae genome. Two new chromatin folding patterns emerge, with one enriched and the other depleted at transcription start and end sites. ...
DOI:
10.1016/j.cell.2019.01.011

18. Molecular phylogeny and morphology of Elatostema s.l. (Urticaceae): Implications for inter- and infrageneric classifications

Author:
Tseng, Yu-Hsin; Monro, Alex K.; Wei, Yi-Gang; Hu, Jer-Ming
Source:
Molecular phylogenetics and evolution 2019 v.132 pp. 251-264
ISSN:
1055-7903
Subject:
nuclear genome; plastid genome,   etc   ; DNA; Pellionia; herbs; internal transcribed spacers; synapomorphy; Africa; Asia; Australasian region;     Show all 10 Subjects
Abstract:
... Elatostema s.s. (Urticaceae) comprises approximately 500 species of herbs and subshrubs distributed in tropical and subtropical Asia, Australasia, and Africa. The delimitation of Elatostema s.s. and the closely related genera Elatostematoides, Pellionia, and Procris has long been problematic because of the large number of taxa and presumed homoplasy among diagnostic morphological characters. In th ...
DOI:
10.1016/j.ympev.2018.11.016

19. Natural products from anaerobes

Author:
Li, Jeffrey S.; Barber, Colin Charles; Zhang, Wenjun
Source:
Journal of industrial microbiology & biotechnology 2019 v.46 no.3-4 pp. 375-383
ISSN:
1367-5435
Subject:
genome; genome mining,   etc   ; aerobes; anaerobes; bioactive properties; biosynthesis; microorganisms; peptides; polyketides;     Show all 9 Subjects
Abstract:
... Natural product discovery in the microbial world has historically been biased toward aerobes. Recent in silico analysis demonstrates that genomes of anaerobes encode unexpected biosynthetic potential for natural products, however, chemical data on natural products from the anaerobic world are extremely limited. Here, we review the current body of work on natural products isolated from strictly ana ...
DOI:
10.1007/s10295-018-2086-5

20. A genome-wide view of mutations in respiration-deficient mutants of Saccharomyces cerevisiae selected following carbon ion beam irradiation

Author:
Guo, Xiaopeng; Zhang, Miaomiao; Gao, Yue; Cao, Guozhen; Yang, Yang; Lu, Dong; Li, Wenjian
Source:
Applied microbiology and biotechnology 2019 v.103 no.4 pp. 1851-1864
ISSN:
0175-7598
Subject:
mitochondrial genome; nuclear genome,   etc   ; Saccharomyces cerevisiae; breeding; carbon; chromosomes; genes; irradiation; mitochondria; mutants; screening; spontaneous mutation;     Show all 12 Subjects
Abstract:
... Mitochondrial dysfunction in Saccharomyces cerevisiae was selected as a marker of ion penetration following carbon ion beam (CIB) irradiation. Respiration-deficient mutants were screened. Following confirmation of negligible spontaneous mutation, eight genetically stable S. cerevisiae respiration-deficient mutant strains and a control strain were resequenced with ~ 200-fold read depth. Strategies ...
DOI:
10.1007/s00253-019-09626-0