Top 7 Biorxiv Papers Today in Genetics


0.0 Mikeys
#1. CRISPR/Cas with ribonucleoprotein complexes and transiently selected telomere vectors allows highly efficient marker-free and multiple genome editing in Botrytis cinerea
Matthias Hahn, Thomas Leisen, Fabian Bietz, Janina Werner, Alex Wegner, Ulrich Schaffrath, David Scheuring, Felix Willmund, Andreas Mosbach, Gabriel Scalliet
CRISPR/Cas has become the state-of-the-art technology for genetic manipulation in diverse organisms, enabling targeted genetic changes to be performed with unprecedented efficiency. Here we report on the first establishment of robust CRISPR/Cas editing in the important necrotrophic plant pathogen Botrytis cinerea based on the introduction of optimized Cas9-sgRNA ribonucleoprotein complexes (RNPs) into protoplasts. Editing yields were further improved by development of a novel strategy that combines RNP delivery with transiently stable telomeres containing vectors, which allowed temporary selection and convenient screening of marker-free editing. We demonstrate that this approach provides vastly superior editing rates compared to existing CRISPR/Cas-based methods in filamentous fungi, including the model plant pathogen Magnaporthe oryzae. The high performance of telomere vector-mediated coediting was demonstrated by random mutagenesis of codon 272ย of the sdhB gene, a major determinant of resistance to succinate dehydrogenase...
more | pdf
Figures
None.
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 10
Total Words: 0
Unqiue Words: 0

0.0 Mikeys
#2. Cultural variation impacts paternal and maternal genetic lineages of the 1 Hmong-Mien and Sino-Tibetan groups from Thailand
Wibhu Kutanan, Rasmi Shoocongdej, Metawee Srikummool, Alexander Huebner, Thanatip Suttipai, Suparat Srithawong, Jatupol Kampuansai, Mark Stoneking
The Hmong-Mien (HM) and Sino-Tibetan (ST) speaking groups are known as hill tribes in Thailand; they were the subject of the first studies to show an impact of patrilocality vs. matrilocality on patterns of mitochondrial (mt) DNA vs. male-specific portion of the Y chromosome (MSY) variation. However, HM and ST groups have not been studied in as much detail; here we report and analyze 234 partial MSY sequences (โˆผ2.3 mB) and 416 complete mtDNA sequences from 14 populations that, when combined with our previous published data, provides the largest dataset yet for the hill tribes. We find a striking difference between Hmong and IuMien (Mien-speaking) groups: the Hmong are genetically different from both the IuMien and all other Thai groups, whereas the IuMien are genetically more similar to other linguistic groups than to the Hmong. In general, we find less of an impact of patrilocality vs. matrilocality on patterns of mtDNA vs. MSY variation than previous studies. However, there is a dramatic difference in the frequency of MSY and...
more | pdf
Figures
None.
Tweets
biorxivpreprint: Cultural variation impacts paternal and maternal genetic lineages of the 1 Hmong-Mien and Sino-Tibetan groups from Thailand https://t.co/IApLVAV9fe #bioRxiv
biorxiv_genetic: Cultural variation impacts paternal and maternal genetic lineages of the 1 Hmong-Mien and Sino-Tibetan groups from Thailand https://t.co/zQoLCObgAi #biorxiv_genetic
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 8
Total Words: 0
Unqiue Words: 0

0.0 Mikeys
#3. Reduced function of the glutathione S-transferase S1 suppresses behavioral hyperexcitability in Drosophila expressing a mutant voltage-gated sodium channel
Hung-Lin Chen, Junko Kasuya, Patrick Lansdon, Garrett A Kaas, Hanxi Tang, Maggie Sodders, Toshihiro Kitamoto
Voltage-gated sodium (Nav) channels play a central role in the generation and propagation of action potentials in excitable cells such as neurons and muscles. To determine how the phenotypes of Nav-channel mutants are affected by other genes, we performed a forward genetic screen for dominant modifiers of the seizure-prone, gain-of-function Drosophila melanogaster Nav-channel mutant, paraShu. Our analyses using chromosome deficiencies, gene-specific RNA interference, and single-gene mutants revealed that a null allele of glutathione S-transferase S1 (GstS1) dominantly suppresses paraShu phenotypes. Reduced GstS1 function also suppressed phenotypes of other seizure-prone Nav-channel mutants, paraGEFS+ and parabss. Notably, paraShu mutants expressed 50% less GstS1 than wild-type flies, further supporting the notion that paraShu and GstS1 interact functionally. Introduction of a loss-of-function GstS1 mutation into a paraShu background led to up- and down-regulation of various genes, with those encoding cytochrome P450 (CYP) enzymes...
more | pdf
Figures
None.
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 7
Total Words: 0
Unqiue Words: 0

0.0 Mikeys
#4. Deciphering cattle temperament measures derived from a four-platform standing scale using genetic factor analytic modeling
Haipeng Yu, Gota Morota, Elfren F. Celestino, Carl R. Dahlen, Sarah A. Wagner, David G. Riley, Lauren L. Hulsman Hanna
Background: The animal's reaction to human handling, also known as temperament, is critical for work safety, productivity, and welfare. Subjective phenotyping methods, such as docility score, have been traditionally used in cattle production as a means for improving the safety, productivity, and welfare of animals. Even so, subjective scales rely on the evaluator's knowledge and interpretation of temperament, which may require substantial experience. With that being said, selection based on such subjective scores may not precisely impact temperament preferences in cattle. Results: We investigated the statistical relationships among subjective methods including docility score (DS), temperament score (TS), 12 qualitative behavior assessment (QBA) attributes along with a movement-based objective method (four-platform standing scale, FPSS) including the standard deviation of total weight on FPSS over time (SSD) and coefficient of variation of SSD (CVSSD) using 1,528 calves at weaning age. An exploratory factor analysis (EFA)...
more | pdf
Figures
None.
Tweets
biorxivpreprint: Deciphering cattle temperament measures derived from a four-platform standing scale using genetic factor analytic modeling https://t.co/uKi5DyMar4 #bioRxiv
biorxiv_genetic: Deciphering cattle temperament measures derived from a four-platform standing scale using genetic factor analytic modeling https://t.co/b3cYQziZgQ #biorxiv_genetic
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 7
Total Words: 0
Unqiue Words: 0

0.0 Mikeys
#5. A genome-wide association study finds genetic variants associated with neck or shoulder pain in UK Biobank
Weihua Meng, Brian W Chan, Cameron Harris, Maxim B Freidin, Harry L Herbert, Mark J Adams, Archie Campbell, Caroline Hayward, Hua Zheng, Xianwei Zhang, Lesley A Colvin, Tim G Hales, Colin NA Palmer, Frances MK Williams, Andrew M McIntosh, Blair H Smith
Background: Common types of musculoskeletal conditions include pain in the neck and shoulder areas. This study seeks to identify the genetic variants associated with neck or shoulder pain based on a genome-wide association approach using 203,309 subjects from the UK Biobank cohort and look for replication evidence from the Generation Scotland: Scottish Family Health Study (GS:SFHS) and TwinsUK. Methods: Cases in the UK Biobank were determined by a question which asked the participants if they had experienced pain in the neck or shoulder in the previous month influencing daily activities. Controls were the UK Biobank participants who reported no pain anywhere in the last month. A genome-wide association study was performed adjusting for age, sex, BMI and 9 population principal components. Significant and independent genetic variants were then sent to GS:SFHS and TwinsUK for replication. Results: We identified 3 genetic loci that were associated with neck or shoulder pain in the UK Biobank samples. The most significant locus was in...
more | pdf
Figures
None.
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 16
Total Words: 0
Unqiue Words: 0

0.0 Mikeys
#6. Application of Pedimap โ€” a pedigree visualization tool โ€” to facilitate the decisioning of rice breeding in Sri Lanka
PGRG Rathnayake, SM Sahibdeen, UAKS Udawela, CK Weebadde, WMW Weerakoon, SDSS Sooriyapathirana
The development of rice cultivars with desirable traits is essential. The decision-making is a crucial step in rice breeding programs. The breeders can make efficient and pragmatic decisions if an organized pedigree visualization platform is available for the material of the rice breeding germplasm. The staple food in Sri Lanka is rice, and there is a great demand for improved varieties with high yield and other promising traits. In the present study, the available data of all the rice varieties released by Rice Research and Development Institute, Sri Lanka, and the related landraces and genotypes were arranged in Pedimap, a pedigree visualization tool. Pedimap can showcase pedigree relationships, phenotypic, and molecular data. The Identity by Descent (IBD) probabilities were calculated using FlexQTL software and included in the Pedimap database. The parentage selection based on the variations of phenotypic traits, selection of marker alleles for molecular breeding, and detection of the founders of genetic effects can be swiftly...
more | pdf
Figures
Tweets
biorxivpreprint: Application of Pedimap -- a pedigree visualization tool -- to facilitate the decisioning of rice breeding in Sri Lanka https://t.co/9aiYAhaoma #bioRxiv
biorxiv_genetic: Application of Pedimap -- a pedigree visualization tool -- to facilitate the decisioning of rice breeding in Sri Lanka https://t.co/qC7tEYvtfE #biorxiv_genetic
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 6
Total Words: 7334
Unqiue Words: 2618

0.0 Mikeys
#7. Heritable endogenization of an RNA virus in a mammalian species
Atsuo Iida, Ronald Tarigan, Hiroshi Shimoda, Kanako Endo, Masaya Furuta, Hitoshi Takemae, Daisuke Hayasaka, Kenji Ichiyanagi, Ken Maeda, Eiichi Hondo
Viruses are considered one of the driving forces for genome rearrangements via infection and endogenization into the host genome (Kazazian, 2004; Maksakova et al., 2006). In 2010, Horie and colleagues demonstrated that a non-retroviral RNA virus, Borna disease virus (BDV), could integrate into the genome in cultured somatic cells (Horie et al., 2010). However, germline transmission of viral-derived sequences using animal models is yet to be experimentally demonstrated. In this study, we reported a case of heritable endogenization using the encephalomyocarditis virus (EMCV) and laboratory mice. The EMCV is a small non-enveloped single-strand RNA virus without its own reverse transcriptase activity (Carocci et al., 2012). Here, we demonstrated that the EMCV genomic RNA was reverse transcribed into DNA fragments in the murine testes. The DNA sequence originated from the RNA genome of EMCV was also detected in the liver and earlobes of the offspring generated from the EMCV-infected father. This suggests that the exogenous sequence...
more | pdf
Figures
None.
Tweets
biorxivpreprint: Heritable endogenization of an RNA virus in a mammalian species https://t.co/CBNRHER3og #bioRxiv
biorxiv_genetic: Heritable endogenization of an RNA virus in a mammalian species https://t.co/Op0i5Nd34g #biorxiv_genetic
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 10
Total Words: 0
Unqiue Words: 0

About

Assert is a website where the best academic papers on arXiv (computer science, math, physics), bioRxiv (biology), BITSS (reproducibility), EarthArXiv (earth science), engrXiv (engineering), LawArXiv (law), PsyArXiv (psychology), SocArXiv (social science), and SportRxiv (sport research) bubble to the top each day.

Papers are scored (in real-time) based on how verifiable they are (as determined by their Github repos) and how interesting they are (based on Twitter).

To see top papers, follow us on twitter @assertpub_ (arXiv), @assert_pub (bioRxiv), and @assertpub_dev (everything else).

To see beautiful figures extracted from papers, follow us on Instagram.

Tracking 257,111 papers.

Search
Sort results based on if they are interesting or reproducible.
Interesting
Reproducible
Feedback
Online
Stats
Tracking 257,111 papers.