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1. We aren’t good at picking candidate genes, and it’s slowing us down

Author:
Baxter, Ivan
Source:
Current opinion in plant biology 2020 v.54 pp. 57-60
ISSN:
1369-5266
Subject:
loci,   etc   ; alleles; humans; plants (botany);     Show all 4 Subjects
Abstract:
... In order to gain a molecular understanding of the genetic basis for plant traits, we need to be able to identify the underlying gene and the causal allele for genetic loci. This process usually involves a step where a researcher selects likely candidate genes from a list. The process of picking candidate genes is inherently prone to distortion due to human bias, and this is slowing down our resear ...
DOI:
10.1016/j.pbi.2020.01.006

2. Genomic Clustering Facilitates Nuclear Processing of Suboptimal Pri-miRNA Loci

Author:
Shang, Renfu; Baek, S. Chan; Kim, Kijun; Kim, Boseon; Kim, V. Narry; Lai, Eric C.
Source:
Molecular cell 2020 v.78 no.2 pp. 303-316.e4
ISSN:
1097-2765
Subject:
loci,   etc   ; biogenesis; genomics; microRNA; operon; ribonucleases;     Show all 6 Subjects
Abstract:
... Nuclear processing of most miRNAs is mediated by Microprocessor, comprised of RNase III enzyme Drosha and its cofactor DGCR8. Here, we uncover a hidden layer of Microprocessor regulation via studies of Dicer-independent mir-451, which is clustered with canonical mir-144. Although mir-451 is fully dependent on Drosha/DGCR8, its short stem and small terminal loop render it an intrinsically weak Micr ...
DOI:
10.1016/j.molcel.2020.02.009

3. Analysing the effects of power swing on wind farms using instantaneous impedances

Author:
Zeno, Aldrich; Orillaza, Jordan Rel; Kolhe, Mohan Lal
Source:
Renewable energy 2020 v.147 pp. 1432-1452
ISSN:
0960-1481
Subject:
loci,   etc   ; models; wind farms; wind power;     Show all 4 Subjects
Abstract:
... Most of the grid disturbances happen due to the presence of faults and power swing. This article focuses on power swing in view of the amount of penetration of renewable energy resources especially the wind farms. There are two sections. First section approached power swing by deriving a mathematical expression which would be able to track the locus of impedance in time domain and subsequently ana ...
DOI:
10.1016/j.renene.2019.09.017

4. Characterization the role of GacA-dependent small RNAs and RsmA family proteins on 2,4-diacetylphloroglucinol production in Pseudomonas fluorescens 2P24

Author:
Zhang, Yang; Zhang, Bo; Wu, Xiaogang; Zhang, Li-Qun
Source:
Microbiological research 2020 v.233 pp. 126391
ISSN:
0944-5013
Subject:
loci,   etc   ; Pseudomonas fluorescens; RNA; proteins; translation (genetics);     Show all 5 Subjects
Abstract:
... Pseudomonas fluorescens 2P24 is a plant-beneficial rhizobacteria that controls many root diseases caused by soil-borne pathogens, and the production of the antibiotic compound 2,4-diacetylphloroglucinol (2,4-DAPG) is essential for its biocontrol ability. In the present study, we investigated the regulatory mechanism acting on the production of 2,4-DAPG by the GacA-dependent small non-coding RNAs ( ...
DOI:
10.1016/j.micres.2019.126391

5. CRISPR-Based Directed Evolution for Crop Improvement

Author:
Butt, Haroon; Zaidi, Syed Shan-e-Ali; Hassan, Norhan; Mahfouz, Magdy
Source:
Trends in biotechnology 2020 v.38 no.3 pp. 236-240
ISSN:
0167-7799
Subject:
loci,   etc   ; directed evolution; gene editing; genes; genomics;     Show all 5 Subjects
Abstract:
... Directed evolution involves generating diverse sequence variants of a gene of interest to produce a desirable trait under selective pressure. CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9) systems can be programmed to target any genomic locus and perform targeted directed evolution. Here, we discuss the opportunities and challenges of this emerg ...
DOI:
10.1016/j.tibtech.2019.08.001

6. CAG Repeat Not Polyglutamine Length Determines Timing of Huntington’s Disease Onset

Author:
Lee, Jong-Min; Correia, Kevin; Loupe, Jacob; Kim, Kyung-Hee; Barker, Douglas; Hong, Eun Pyo; Chao, Michael J.; Long, Jeffrey D.; Lucente, Diane; Vonsattel, Jean Paul G.; Pinto, Ricardo Mouro; Abu Elneel, Kawther; Ramos, Eliana Marisa; Mysore, Jayalakshmi Srinidhi; Gillis, Tammy; Wheeler, Vanessa C.; MacDonald, Marcy E.; Gusella, James F.; McAllister, Branduff; Massey, Thomas; Medway, Christopher; Stone, Timothy C.; Hall, Lynsey; Jones, Lesley; Holmans, Peter; Kwak, Seung; Ehrhardt, Anka G.; Sampaio, Cristina; Ciosi, Marc; Maxwell, Alastair; Chatzi, Afroditi; Monckton, Darren G.; Orth, Michael; Landwehrmeyer, G. Bernhard; Paulsen, Jane S.; Dorsey, E. Ray; Shoulson, Ira; Myers, Richard H.
Source:
Cell 2019 v.178 no.4 pp. 887-900.e14
ISSN:
0092-8674
Subject:
loci,   etc   ; DNA; genes; pathogenesis;     Show all 4 Subjects
Abstract:
... Variable, glutamine-encoding, CAA interruptions indicate that a property of the uninterrupted HTT CAG repeat sequence, distinct from the length of huntingtin’s polyglutamine segment, dictates the rate at which Huntington’s disease (HD) develops. The timing of onset shows no significant association with HTT cis-eQTLs but is influenced, sometimes in a sex-specific manner, by polymorphic variation at ...
DOI:
10.1016/j.cell.2019.06.036
PubMed:
31398342
PubMed Central:
PMC6700281

7. Improving the efficiency of the CRISPR-Cas12a system with tRNA-crRNA arrays

Author:
Hu, Xixun; Meng, Xiangbing; Li, Jiayang; Wang, Kejian; Yu, Hong
Source:
The crop journal 2020 v.8 no.3 pp. 403-407
ISSN:
2214-5141
Subject:
loci,   etc   ; Oryza sativa; RNA; callus; gene editing; genomics; rice;     Show all 7 Subjects
Abstract:
... CRISPR-Cas12a offers a convenient tool for multiplex genome editing in rice. However, the CRISPR-Cas12a system displays variable editing efficiency across genomic loci, with marked influence by CRISPR RNAs (crRNAs). To improve the efficiency of the CRISPR-Cas12a system for multiplex genome editing, we identified various architectures and expression strategies for crRNAs. Transformation of binary v ...
DOI:
10.1016/j.cj.2019.06.007

8. Organization of the Escherichia coli Chromosome by a MukBEF Axial Core

Author:
Mäkelä, Jarno; Sherratt, David J.
Source:
Molecular cell 2020 v.78 no.2 pp. 250-260.e5
ISSN:
1097-2765
Subject:
loci,   etc   ; DNA; Escherichia coli; adenosine triphosphate; hydrolysis; mitosis; replication origin;     Show all 7 Subjects
Abstract:
... Structural maintenance of chromosomes (SMC) complexes organize chromosomes ubiquitously, thereby contributing to their faithful segregation. We demonstrate that under conditions of increased chromosome occupancy of the Escherichia coli SMC complex, MukBEF, the chromosome is organized as a series of loops around a thin (<130 nm) MukBEF axial core, whose length is ∼1,100 times shorter than the chrom ...
DOI:
10.1016/j.molcel.2020.02.003
PubMed:
32097603
PubMed Central:
PMC7163298

9. Multiplexed primer extension sequencing: A targeted RNA-seq method that enables high-precision quantitation of mRNA splicing isoforms and rare pre-mRNA splicing intermediates

Author:
Gildea, Michael A.; Dwyer, Zachary W.; Pleiss, Jeffrey A.
Source:
Methods 2020 v.176 pp. 34-45
ISSN:
1046-2023
Subject:
loci,   etc   ; alternative splicing; introns; messenger RNA; reverse transcription; sequence analysis;     Show all 6 Subjects
Abstract:
... The study of pre-mRNA splicing has been greatly aided by the advent of RNA sequencing (RNA-seq), which enables the genome-wide detection of discrete splice isoforms. Quantification of these splice isoforms requires analysis of splicing informative sequencing reads, those that unambiguously map to a single splice isoform, including exon-intron spanning alignments corresponding to retained introns, ...
DOI:
10.1016/j.ymeth.2019.05.013
PubMed:
31121301
PubMed Central:
PMC6868320

10. Genomic evidence suggests Mesapamea remmi is an imaginary species (Lepidoptera: Noctuidae)

Author:
Sihvonen, Pasi; Lee, Kyung Min; Lundsten, Karl‐Erik; Mutanen, Marko
Source:
Systematic entomology 2020 v.45 no.2 pp. 302-311
ISSN:
0307-6970
Subject:
loci,   etc   ; DNA; Noctuidae; females; genes; genomics; hybrids; males; moths;     Show all 9 Subjects
Abstract:
... Taxonomic status of the noctuid moth Mesapamea remmi Rezbanyai‐Reser (Lepidoptera) has remained controversial since its description in 1985. Based on morphology, it has been considered a valid species or a hybrid between Mesapamea secalis (Linnaeus) and Mesapamea didyma (Esper). We studied this case of uncertain identity by using traditional Sanger sequencing techniques (COI and seven nuclear gene ...
DOI:
10.1111/syen.12397

11. Systemic building blocks for creating and capturing value from circular economy

Author:
Hopkinson, Peter; De Angelis, Roberta; Zils, Marcus
Source:
Resources, conservation, and recycling 2020 v.155 pp. 104672
ISSN:
0921-3449
Subject:
loci,   etc   ; business enterprises; circular economy; education programs; issues and policy;     Show all 5 Subjects
Abstract:
... The idea of a circular economy has generated widespread academic, policy and business interest for its potential to address economic, ecological and societal concerns posed by current production and consumption systems. The growth in the number of academic publications reflects a period of critique, clarification and validation leading to research challenges, questions and a call for real world ev ...
DOI:
10.1016/j.resconrec.2019.104672

12. Single-molecule real-time (SMRT) sequencing facilitates Tachypleus tridentatus genome annotation

Author:
Lou, Fangrui; Song, Na; Han, Zhiqiang; Gao, Tianxiang
Source:
International journal of biological macromolecules 2020 v.147 pp. 89-97
ISSN:
0141-8130
Subject:
loci,   etc   ; Tachypleus tridentatus; databases; genes; secretion; sequence analysis; transcriptome;     Show all 7 Subjects
Abstract:
... Tachypleus tridentatus is a keystone species in marine ecosystems. Its hemolymph also provides the limulus amebocyte lysate (LAL) for detection of bacterial endotoxin in human medical service. Here we combined SMRT sequencing and Illumina RNA-seq to characterize the novel isoforms, novel genetic loci, fusion isoforms formation and transcriptome structure and further to unveil the transcriptome com ...
DOI:
10.1016/j.ijbiomac.2020.01.029

13. A Well-Mixed E. coli Genome: Widespread Contacts Revealed by Tracking Mu Transposition

Author:
Walker, David M.; Freddolino, Peter L.; Harshey, Rasika M.
Source:
Cell 2020 v.180 no.4 pp. 703-716.e18
ISSN:
0092-8674
Subject:
loci,   etc   ; Escherichia coli; genes; genomics; phages; protein subunits; transposition (genetics);     Show all 7 Subjects
Abstract:
... The three-dimensional structures of chromosomes are increasingly being recognized as playing a major role in cellular regulatory states. The efficiency and promiscuity of phage Mu transposition was exploited to directly measure in vivo interactions between genomic loci in E. coli. Two global organizing principles have emerged: first, the chromosome is well-mixed and uncompartmentalized, with trans ...
DOI:
10.1016/j.cell.2020.01.031

14. A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes

Author:
Faircloth, Brant C.; Alda, Fernando; Hoekzema, Kendra; Burns, Michael D.; Oliveira, Claudio; Albert, James S.; Melo, Bruno F.; Ochoa, Luz E.; Roxo, Fábio F.; Chakrabarty, Prosanta; Sidlauskas, Brian L.; Alfaro, Michael E.
Source:
Copeia 2020 v.108 no.1 pp. 47-60
ISSN:
0045-8511
Subject:
loci,   etc   ; Clupeiformes; computer simulation; data collection; fish; genome assembly; phylogeny;     Show all 7 Subjects
Abstract:
... Target enrichment of conserved nuclear loci has helped reconstruct evolutionary relationships among a wide variety of species. While there are preexisting bait sets to enrich a few hundred loci across all fishes or a thousand loci from acanthomorph fishes, no bait set exists to enrich large numbers (>1,000 loci) of ultraconserved nuclear loci from ostariophysans, the second largest actinopterygian ...
DOI:
10.1643/CG-18-139

15. A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary

Author:
Galupa, Rafael; Nora, Elphège Pierre; Worsley-Hunt, Rebecca; Picard, Christel; Gard, Chris; van Bemmel, Joke Gerarda; Servant, Nicolas; Zhan, Yinxiu; El Marjou, Fatima; Johanneau, Colin; Diabangouaya, Patricia; Le Saux, Agnès; Lameiras, Sonia; Pipoli da Fonseca, Juliana; Loos, Friedemann; Gribnau, Joost; Baulande, Sylvain; Ohler, Uwe; Giorgetti, Luca; Heard, Edith
Source:
Molecular cell 2020 v.77 no.2 pp. 352-367.e8
ISSN:
1097-2765
Subject:
loci,   etc   ; X chromosome; genome; mammals; non-coding RNA;     Show all 5 Subjects
Abstract:
... cis-Regulatory communication is crucial in mammalian development and is thought to be restricted by the spatial partitioning of the genome in topologically associating domains (TADs). Here, we discovered that the Xist locus is regulated by sequences in the neighboring TAD. In particular, the promoter of the noncoding RNA Linx (LinxP) acts as a long-range silencer and influences the choice of X chr ...
DOI:
10.1016/j.molcel.2019.10.030
PubMed:
31759823
PubMed Central:
PMC6964159

16. Hi-C detects novel structural variants in HL-60 and HL-60/S4 cell lines

Author:
Jacobson, Elsie C.; Grand, Ralph S.; Perry, Jo K.; Vickers, Mark H.; Olins, Ada L.; Olins, Donald E.; O'Sullivan, Justin M.
Source:
Genomics 2020 v.112 no.1 pp. 151-162
ISSN:
0888-7543
Subject:
loci,   etc   ; cell lines; karyotyping; myeloid leukemia; neoplasm cells; sequence analysis;     Show all 6 Subjects
Abstract:
... Cancer cell lines often have large structural variants (SVs) that evolve over time. There are many reported differences in large scale SVs between HL-60 and HL-60/S4, two cell lines derived from the same acute myeloid leukemia sample. However, the stability and variability of inter- and intra-chromosomal structural variants between different sources of the same cell line is unknown. Here, we used ...
DOI:
10.1016/j.ygeno.2019.05.009

17. Integrated Meta-QTL and Genome-Wide Association Study Analyses Reveal Candidate Genes for Maize Yield

Author:
Wang, Yijun; Wang, Yali; Wang, Xin; Deng, Dexiang
Source:
Journal of plant growth regulation 2020 v.39 no.1 pp. 229-238
ISSN:
0721-7595
Subject:
loci; quantitative trait loci,   etc   ; Zea mays; chromosome mapping; corn; corn ears; crop yield; domestication; genes; genome-wide association study; meristems;     Show all 11 Subjects
Abstract:
... Crop yield is of a quantitative nature. Two complementary approaches linkage mapping and genome-wide association study (GWAS) have been employed for the identification of loci influencing maize yield. In previous research, we meta-analyzed QTL for maize yield. Here, we tried to integrate meta-QTL and GWAS analyses to dissect candidate genes for maize yield. A total of seven candidate genes were de ...
DOI:
10.1007/s00344-019-09977-y

18. A Comparative Genomic Analysis of the Barley Pathogen Pyrenophora teres f. teres Identifies Subtelomeric Regions as Drivers of Virulence

Author:
Wyatt, Nathan A.; Richards, Jonathan K.; Brueggeman, Robert S.; Friesen, Timothy L.
Source:
Molecular plant-microbe interactions 2020 v.33 no.2 pp. 173-188
ISSN:
0894-0282
Subject:
loci; quantitative trait loci,   etc   ; Pyrenophora teres; barley; chromosome translocation; evolution; genes; genomics; net blotch; nucleotide sequences; pathogens; proteins; virulence;     Show all 13 Subjects
Abstract:
... Pyrenophora teres f. teres causes net form net blotch of barley and is an economically important pathogen throughout the world. However, P. teres f. teres is lacking in the genomic resources necessary to characterize the mechanisms of virulence. Recently a high-quality reference genome was generated for P. teres f. teres isolate 0-1. Here, we present the reference quality sequence and annotation o ...
DOI:
10.1094/MPMI-05-19-0128-R

19. Supergene validation: A model-based protocol for assessing the accuracy of non-model-based supergene methods

Author:
Adams, Richard H.; Castoe, Todd A.
Source:
MethodsX 2019 v.6 pp. 2181-2188
ISSN:
2215-0161
Subject:
loci,   etc   ; data collection; phylogeny; topology;     Show all 4 Subjects
Abstract:
... Genome-scale species tree inference is largely restricted to heuristic approaches that use estimated gene trees to reconstruct species-level relationships. Central to these heuristic species tree methods is the assumption that the gene trees are estimated without error. To increase the accuracy of input gene trees used to infer species trees, several techniques have recently been developed for con ...
DOI:
10.1016/j.mex.2019.09.025
PubMed:
31667118
PubMed Central:
PMC6812401

20. Analysis of early-flowering genes at barley chromosome 2H expands the repertoire of mutant alleles at the Mat-c locus

Author:
Matyszczak, Izabela; Tominska, Marta; Zakhrabekova, Shakhira; Dockter, Christoph; Hansson, Mats
Source:
Plant cell reports 2020 v.39 no.1 pp. 47-61
ISSN:
0721-7714
Subject:
loci; quantitative trait loci,   etc   ; Antirrhinum majus; Arabidopsis thaliana; X-radiation; alleles; barley; crop yield; early flowering; flowering time; introgression; mutants; mutation; prediction; reproductive success; temporal variation;     Show all 16 Subjects
Abstract:
... KEY MESSAGE: Analyses of barley mat-c loss of function mutants reveal deletions, splice-site mutations and nonsynonymous substitutions in a key gene regulating early flowering. Optimal timing of flowering is critical for reproductive success and crop yield improvement. Several major quantitative trait loci for flowering time variation have been identified in barley. In the present study, we analyz ...
DOI:
10.1007/s00299-019-02472-4
PubMed:
31541262
PubMed Central:
PMC6960220