journal
MENU ▼
Read by QxMD icon Read
search

Genetics

journal
https://www.readbyqxmd.com/read/28646043/an-efficient-flp-based-toolkit-for-spatiotemporal-control-of-gene-expression-in-caenorhabditis-elegans
#1
Celia María Muñoz-Jiménez, Cristina Ayuso, Agnieszka Dobrzynska, Antonio Torres, Patricia de la Cruz Ruiz, Peter Askjaer
Site-specific recombinases are potent tools to regulate gene expression. In particular, the Cre and FLP enzymes are widely used to either activate or inactivate genes in a precise spatiotemporal manner. Both recombinases work efficiently in the popular model organism Caenorhabditis elegans but their use in this nematode is still only sporadic. To increase the utility of the FLP system in C. elegans we have generated a series of single-copy transgenic strains that stably express an optimized version of FLP in specific tissues or by heat induction...
June 23, 2017: Genetics
https://www.readbyqxmd.com/read/28642272/networks-underpinning-symbiosis-revealed-through-cross-species-eqtl-mapping
#2
Yuelong Guo, Sylwia Fudali, Jacinta Gimeno, Peter DiGennaro, Stella Chang, Valerie M Williamson, David McK Bird, Dahlia M Nielsen
Organisms engage in extensive cross-species molecular dialogue, yet the underlying molecular actors are known for only a few interactions. Many techniques have been designed to uncover genes involved in signaling between organisms. Typically, these focus on only one of the partners. We developed an expression quantitative trait locus (eQTL) mapping-based approach to identify cause-and-effect relationships between genes from two partners engaged in an interspecific interaction. We demonstrated the approach by assaying expression of ninety-eight isogenic plants (Medicago truncatula), each inoculated with a genetically distinct line of the diploid parasitic nematode Meloidogyne hapla With this design, systematic differences in gene expression across host plants could be mapped to genetic polymorphisms of their infecting parasites...
June 22, 2017: Genetics
https://www.readbyqxmd.com/read/28642271/powerful-genetic-association-analysis-for-common-or-rare-variants-with-high-dimensional-structured-traits
#3
Xiang Zhan, Ni Zhao, Anna Plantinga, Timothy A Thornton, Karen N Conneely, Michael P Epstein, Michael C Wu
Many genetic association studies collect a wide range of complex traits. As these traits may be correlated and share a common genetic mechanism, joint analysis can be statistically more powerful and biologically more meaningful. However, most existing tests for multiple traits cannot be used for high-dimensional and possibly structured traits, such as network-structured transcriptomic pathway expressions. To overcome potential limitations, in this paper we propose the dual kernel-based association test (DKAT) for testing the association between multiple traits and multiple genetic variants, both common and rare...
June 22, 2017: Genetics
https://www.readbyqxmd.com/read/28642270/heritable-micro-environmental-variance-covaries-with-fitness-in-an-outbred-population-of-drosophila-serrata
#4
Jacqueline L Sztepanacz, Katrina McGuigan, Mark W Blows
The genetic basis of stochastic variation within a defined environment, and the consequences of such micro-environmental variance for fitness are poorly understood. Using a multigenerational breeding design in Drosophila serrata, we demonstrated that the micro-environmental variance in a set of morphological wing traits in a randomly mating population had significant additive genetic variance in most single wing traits. Although heritability was generally low (< 1%), coefficients of additive genetic variance were of a magnitude typical of other morphological traits, indicating that the micro-environmental variance is an evolvable trait...
June 22, 2017: Genetics
https://www.readbyqxmd.com/read/28637712/shrinking-daughters-rlm1-dependent-g1-s-checkpoint-maintains-saccharomyces-cerevisiae-daughter-cell-size-and-viability
#5
Sarah Piccirillo, Deepshikha Neog, David Spade, J David Van Horn, LeAnn M Tiede-Lewis, Sarah L Dallas, Tamas Kapros, Saul M Honigberg
The Rlm1 transcription factor is a target of the cell-wall integrity pathway. We report that an rlm1Δ; mutant grown on a non-fermentable carbon source at low osmolarity forms cell groups in which a mother cell is surrounded by smaller "satellite daughter" cells. Mother cells in these groups progressed through repeated rounds of cell division with normal rates of bud growth and genetic stability; however, these cells underwent precocious START relative to wild-type mothers. Thus, once activated, Rlm1 delays the transition from G1 to S, a mechanism we term the CW/START checkpoint...
June 21, 2017: Genetics
https://www.readbyqxmd.com/read/28637711/the-exon-junction-complex-and-srp54-contribute-to-drosophila-hedgehog-signaling-via-ci-rna-splicing
#6
Elisa Garcia Garcia, Jamie C Little, Daniel Kalderon
Hedgehog (Hh) regulates the Cubitus interruptus (Ci) transcription factor in Drosophila melanogaster by activating full-length Ci-155 and blocking processing to Ci-75 repressor. However, the interplay between regulation of Ci-155 levels and activity, as well as processing-independent mechanisms that affect Ci-155 levels have not been explored extensively. Here we identified Mago Nashi (Mago) and Y14 core Exon Junction Complex (EJC) proteins, as well as the Srp54 splicing factor as modifiers of Hh pathway activity under sensitized conditions...
June 21, 2017: Genetics
https://www.readbyqxmd.com/read/28637710/the-combined-action-of-duplicated-boron-transporters-is-required-for-maize-growth-in-boron-deficient-conditions
#7
Mithu Chatterjee, Qiujie Liu, Caitlin Menello, Mary Galli, Andrea Gallavotti
The micronutrient boron is essential in maintaining the structure of plant cell walls and is critical for high yields in crop species. Boron can move into plants by diffusion or by active and facilitated transport mechanisms. We recently showed that mutations in the maize boron efflux transporter ROTTEN EAR (RTE) cause severe developmental defects and sterility. RTE is part of a small gene family containing five additional members (RTE2-RTE6) that show tissue specific expression. The close paralogous gene RTE2 encodes a protein with 95% amino acid identity with RTE and is similarly expressed in shoot and root cells surrounding the vasculature...
June 21, 2017: Genetics
https://www.readbyqxmd.com/read/28637709/genome-wide-association-analyses-based-on-broadly-different-specifications-for-prior-distributions-genomic-windows-and-estimation-methods
#8
Chunyu Chen, Juan P Steibel, Robert J Tempelman
A currently popular strategy (EMMAX) for genome wide association (GWA) analysis infers association for the specific marker of interest by treating its effect as fixed while treating all other marker effects as classical Gaussian random effects. It may be more statistically coherent to specify all markers as sharing the same prior distribution, whether that distribution is Gaussian, heavy-tailed (BayesA), or has variable selection specifications based on a mixture of, say, two Gaussian distributions (SSVS). Furthermore, all such GWA inference should be formally based on posterior probabilities or test statistics as we present here, rather than merely being based on point estimates...
June 21, 2017: Genetics
https://www.readbyqxmd.com/read/28634160/high-throughput-characterization-of-cascade-type-i-e-crispr-guide-efficacy-reveals-unexpected-pam-diversity-and-target-sequence-preferences
#9
Becky Xu Hua Fu, Michael Wainberg, Anshul Kundaje, Andrew Z Fire
Interactions between Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs and CRISPR-associated (Cas) proteins form an RNA-guided adaptive immune system in prokaryotes. The adaptive immune system utilizes segments of the genetic material of invasive foreign elements in the CRISPR locus. The loci are transcribed and processed to produce small CRISPR RNAs (crRNAs), with degradation of invading genetic material directed by a combination of complementarity between RNA and DNA and in some cases recognition of adjacent motifs called PAMs (Protospacer Adjacent Motifs)...
June 20, 2017: Genetics
https://www.readbyqxmd.com/read/28634159/a-role-for-the-nonsense-mediated-mrna-decay-pathway-in-maintaining-genome-stability-in-caenorhabditis-elegans
#10
Víctor González-Huici, Bin Wang, Anton Gartner
Ionizing radiation (IR) is commonly used in cancer therapy and is a main source of DNA double-strand-breaks (DSBs), one of the most toxic forms of DNA damage. We have used Caenorhabditis elegans as an invertebrate model to identify novel factors required for repair of DNA damage inflicted by IR. We have performed an unbiased genetic screen, finding that smg-1 mutations confer strong hypersensitivity to IR. SMG-1 is a phosphoinositide-3 kinase (PI3K) kinase involved in mediating nonsense-mediated mRNA decay (NMD) of transcripts containing premature stop codons and related to the ATM and ATR kinases which are at the apex of DNA damage signalling pathways...
June 20, 2017: Genetics
https://www.readbyqxmd.com/read/28630115/discovering-complete-quasispecies-in-bacterial-genomes
#11
Frederic Bertels, Chaitanya S Gokhale, Arne Traulsen
Mobile genetic elements can be found in almost all genomes. Possibly the most common non-autonomous mobile genetic elements in bacteria are REPINs that can occur hundreds of times within a genome. The sum of all REPINs in a genome can be viewed as an evolving population because REPINs replicate and mutate. In contrast to most other biological populations, we know the exact composition of the REPIN population and the sequence of each member of the population. Here, we model the evolution of REPINs as quasispecies...
June 19, 2017: Genetics
https://www.readbyqxmd.com/read/28630114/towards-universal-forward-genetics-using-a-draft-genome-sequence-of-the-nematode-oscheius-tipulae-to-identify-mutations-affecting-vulva-development
#12
Fabrice Besnard, Georgios Koutsovoulos, Sana Dieudonné, Mark Blaxter, Marie-Anne Félix
Mapping-by-sequencing has become a standard method to map and identify phenotype-causing mutations in model species. Here, we show that a fragmented draft assembly is sufficient to perform mapping-by-sequencing in non-model species. We generated a draft assembly and annotation of the genome of the free-living nematode Oscheius tipulae, a distant relative of the model Caenorhabditis elegans We used this draft to identify the likely causative mutations at the O. tipulae cov-3 locus, which affect vulval development...
June 19, 2017: Genetics
https://www.readbyqxmd.com/read/28630113/complex-coding-and-regulatory-polymorphisms-in-a-restriction-factor-determine-the-susceptibility-of-drosophila-to-viral-infection
#13
Chuan Cao, Rodrigo Cogni, Vincent Barbier, Francis M Jiggins
It is common to find that major-effect genes are an important cause of variation in susceptibility to infection. Here we have characterised natural variation in a gene called pastrel that explains over half of the genetic variance in susceptibility to the virus DCV in populations of Drosophila melanogaster We found extensive allelic heterogeneity, with a sample of seven alleles of pastrel from around the world conferring four phenotypically distinct levels of resistance. By modifying candidate SNPs in transgenic flies, we show that the largest effect is caused by an amino acid polymorphism that arose when an ancestral threonine was mutated to alanine, greatly increasing resistance to DCV...
June 19, 2017: Genetics
https://www.readbyqxmd.com/read/28630112/rapid-evolution-of-ovarian-biased-genes-in-the-yellow-fever-mosquito-aedes-aegypti
#14
Carrie A Whittle, Cassandra G Extavour
Males and females exhibit highly dimorphic phenotypes, particularly in their gonads, which is believed to be driven largely by differential gene expression. Typically, the protein sequences of genes upregulated in males, or male-biased genes, evolve rapidly as compared to female-biased and unbiased genes. To date, the specific study of gonad-biased genes remains uncommon in metazoans. Here, we identified and studied a total of 2,927, 2,013 and 4,449 coding-sequences (CDS) with ovary-biased, testis-biased and unbiased expression respectively in the yellow-fever mosquito Aedes aegypti The results showed that ovary-biased and unbiased CDS had higher nonsynonymous to synonymous substitution rates (dN/dS) and lower optimal codon usage (those codons that promote efficient translation) than testis-biased genes...
June 19, 2017: Genetics
https://www.readbyqxmd.com/read/28630111/investigation-of-seizure-susceptibility-in-a-drosophila-model-of-human-epilepsy-with-optogenetic-stimulation
#15
Arunesh Saras, Veronica V Wu, Harlan J Brawer, Mark A Tanouye
We examined seizure-susceptibility in a Drosophila model of human epilepsy using optogenetic stimulation of ReaChR opsin. Photostimulation of the seizure-sensitive mutant para(bss1) causes behavioral paralysis that resembles paralysis caused by mechanical stimulation, in many aspects. Electrophysiology shows that photostimulation evokes abnormal seizure-like neuronal firing in para(bss1) followed by a quiescent period resembling synaptic failure and apparently responsible for paralysis. The pattern of neuronal activity concludes with seizure-like activity just prior to recovery (recovery)...
June 19, 2017: Genetics
https://www.readbyqxmd.com/read/28615283/cis-and-trans-regulatory-effects-on-gene-expression-in-a-natural-population-of-drosophila-melanogaster
#16
Naoki Osada, Ryutaro Miyagi, Aya Takahashi
Cis- and trans-regulatory mutations are important contributors to transcriptome evolution. Quantifying their relative contributions to intraspecific variation in gene expression is essential for understanding the population genetic processes that underlie evolutionary changes in gene expression. Here, we have examined this issue by quantifying genome-wide allele specific expression (ASE) variation using a crossing scheme that produces F1 hybrids between 18 different Drosophila melanogaster strains sampled from the Drosophila Genetic Reference Panel (DGRP) and a reference strain from another population...
June 14, 2017: Genetics
https://www.readbyqxmd.com/read/28615282/maternal-haploid-a-metalloprotease-enriched-at-the-largest-satellite-repeat-and-essential-for-genome-integrity-in-drosophila-embryos
#17
Xiaona Tang, Jingguo Cao, Liang Zhang, Yingzi Huang, Qianyi Zhang, Yikang S Rong
The incorporation of the paternal genome into the zygote during fertilization requires chromatin remodeling. The maternal haploid (mh) mutation in Drosophila affects this process and leads to the formation of haploid embryos without the paternal genome. mh encodes the Drosophila homolog of SPRTN, a conserved protease essential for resolving DNA-protein cross-linked products. Here we characterize the role of MH in genome maintenance. It is not understood how MH protects the paternal genome during fertilization particularly in lights of our finding that MH is present in both parental pro-nuclei during zygote formation...
June 14, 2017: Genetics
https://www.readbyqxmd.com/read/28607146/epigenetic-transcriptional-memory-of-gal-genes-depends-on-growth-in-glucose-and-the-tup1-transcription-factor-in-saccharomyces-cerevisiae
#18
Varun Sood, Ivelisse Cajigas, Agustina D'Urso, William H Light, Jason H Brickner
Previously expressed inducible genes can remain poised for faster reactivation for multiple cell divisions, a conserved phenomenon called epigenetic transcriptional memory. The GAL genes in Saccharomyces cerevisiae show faster reactivation for up to seven generations after being repressed. During memory, previously produced Gal1 protein enhances the rate of reactivation of GAL1, GAL10, GAL2 and GAL7 These genes also interact with the nuclear pore complex (NPC) and localize to the nuclear periphery both when active and during memory...
June 12, 2017: Genetics
https://www.readbyqxmd.com/read/28600327/the-oxidative-stress-response-in-caenorhabditis-elegans-requires-the-gata-transcription-factor-elt-3-and-skn-1-nrf2
#19
Queenie Hu, Dayana R D'Amora, Lesley T MacNeil, Albertha J M Walhout, Terrance J Kubiseski
Cellular damage caused by reactive oxygen species (ROS) is believed to be a major contributor to age-associated diseases. Previously, we characterized the C. elegans Brap2 ortholog (BRAP-2) and found that it is required to prevent larval arrest in response to elevated levels of oxidative stress. Here, we report that C. elegans brap-2 mutants display increased expression of SKN-1-dependent phase II detoxification enzymes that is dependent on PMK-1 (a p38 MAP kinase C. elegans ortholog). An RNAi screen was conducted using a transcription factor library to identify genes required for increased expression of the SKN-1 target gst-4 in brap-2 mutants...
June 9, 2017: Genetics
https://www.readbyqxmd.com/read/28600326/up-frameshift-protein-upf1-regulates-neurospora-crassa-circadian-and-diurnal-growth-rhythms
#20
Yilan Wu, Yin Zhang, Yunpeng Sun, Jiali Yu, Peiliang Wang, Huan Ma, Shijunyin Chen, Lizhen Ma, Dongyang Zhang, Qun He, Jinhu Guo
Nonsense-mediated RNA decay (NMD) is a crucial post-transcriptional regulatory mechanism that recognizes and eliminates aberrantly processed transcripts, and mediates the expression of normal gene transcripts. In this study, we report that in the filamentous fungus Neurospora crassa, the NMD factors play a conserved role in regulating the surveillance of NMD targets including PTC-containing transcripts and normal transcripts. The circadian rhythms in all of the upf1-3 knockout strains, which are principle NMD factors, were aberrant...
June 9, 2017: Genetics
journal
journal
23713
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"