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https://www.readbyqxmd.com/read/28449263/multi-dice-r-package-for-comparative-population-genomic-inference-under-hierarchical-co-demographic-models-of-independent-single-population-size-changes
#1
Alexander T Xue, Michael J Hickerson
Population genetic data from multiple taxa can address comparative phylogeographic questions about community-scale response to environmental shifts, and a useful strategy to this end is to employ hierarchical co-demographic models that directly test multi-taxa hypotheses within a single, unified analysis while benefiting in statistical power from aggregating datasets. This approach has been applied to classical phylogeographic datasets such as mitochondrial barcodes as well as reduced-genome polymorphism datasets that can yield 10,000s of SNPs, produced by emergent technologies such as RAD-seq and GBS...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28446918/microrna-and-transcription-factor-key-players-in-plant-regulatory-network
#2
REVIEW
Abdul F A Samad, Muhammad Sajad, Nazaruddin Nazaruddin, Izzat A Fauzi, Abdul M A Murad, Zamri Zainal, Ismanizan Ismail
Recent achievements in plant microRNA (miRNA), a large class of small and non-coding RNAs, are very exciting. A wide array of techniques involving forward genetic, molecular cloning, bioinformatic analysis, and the latest technology, deep sequencing have greatly advanced miRNA discovery. A tiny miRNA sequence has the ability to target single/multiple mRNA targets. Most of the miRNA targets are transcription factors (TFs) which have paramount importance in regulating the plant growth and development. Various families of TFs, which have regulated a range of regulatory networks, may assist plants to grow under normal and stress environmental conditions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28446605/crispr-cas9-mediated-gene-knockout-screens-and-target-identification-via-whole-genome-sequencing-uncover-host-genes-required-for-picornavirus-infection
#3
Heon Seok Kim, Kyungjin Lee, Sangsu Bae, Jeongbin Park, Chong-Kyo Lee, Meehyein Kim, Eunji Kim, Minju Kim, Seokjoong Kim, Chonsaeng Kim, Jin-Soo Kim
Several groups have used genome-wide libraries of lentiviruses encoding small-guide RNAs (sgRNAs) for genetic screens. In most cases, sgRNA expression cassettes are integrated into cells by using lentiviruses, and target genes are statistically estimated by the readout of sgRNA sequences after targeted sequencing. We present a new virus-free method for human gene-knockout screens using a genome-wide library of CRISPR/Cas9 sgRNAs based on plasmids, and target gene identification via whole-genome sequencing (WGS) confirming authentic mutations rather than statistical estimating through targeted amplicon sequencing...
April 26, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28445399/advances-in-psychiatric-diagnosis-past-present-and-future
#4
EDITORIAL
Carol S North, Alina M Surís
This editorial examines controversies identified by the articles in this special issue, which explore psychopathology in the broad history of the classification of selected psychiatric disorders and syndromes over time through current American criteria. Psychiatric diagnosis has a long history of scientific investigation and application, with periods of rapid change, instability, and heated controversy associated with it. The articles in this issue examine the history of psychiatric nomenclature and explore current and future directions in psychiatric diagnosis through the various versions of accepted diagnostic criteria and accompanying research literature addressing the criteria...
April 26, 2017: Behavioral Sciences
https://www.readbyqxmd.com/read/28444624/targeting-ntrk-fusion-in-non-small-cell-lung-cancer-rationale-and-clinical-evidence
#5
REVIEW
Biagio Ricciuti, Marta Brambilla, Giulio Metro, Sara Baglivo, Roberta Matocci, Matteo Pirro, Rita Chiari
In the era of personalized medicine, the identification of targetable genetic alterations represented a major step forward in anticancer therapy. NTRK rearrangements represent the molecular driver of a subset of solid tumors, including 3% of non-small-cell lung cancers (NSCLCs). Preliminary data indicate that molecularly selected NSCLC patients harboring NTRK fusions derive an unprecedented clinical benefit from Trk-directed targeted therapies. The aim of this review is to describe the molecular biology of NTRK signaling pathway and to summarize the preclinical data on novel Trk inhibitors, touching upon the clinical development of these inhibitors for the treatment of advanced NSCLC, which have already shown encouraging anticancer activity and acceptable safety profile in early phase I clinical trials...
June 2017: Medical Oncology
https://www.readbyqxmd.com/read/28439863/large-scale-phenotyping-of-root-traits-in-the-model-legume-lotus-japonicus
#6
Marco Giovannetti, Anna Małolepszy, Christian Göschl, Wolfgang Busch
Plants are sessile organisms that can tune their body architecture to the environment. This is very pronounced in their root system. In particular, nutrient availability strongly influences the architecture of the root system; depending on the abundance of specific nutrients, root growth rates and lateral root number are modulated. The extent of these effects is important for plant adaptation and has a major impact on plant fitness. However, the assessment of quantitative effects on a scale large enough for identifying genes and variants using quantitative genetics is difficult, and well-developed methods have been largely restricted to the model species Arabidopsis thaliana...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439275/arabidopsis-ala1-and-ala2-mediate-rnai-based-antiviral-immunity
#7
Biyun Zhu, Hua Gao, Gang Xu, Dewei Wu, Susheng Song, Hongshan Jiang, Shuifang Zhu, Tiancong Qi, Daoxin Xie
RNA intereferencing (RNAi) pathway regulates antiviral immunity and mediates plant growth and development. Despite considerable research efforts, a few components in RNAi pathway have been revealed, including ARGONAUTEs (AGOs), DICER-LIKEs (DCLs), RNA-dependent RNA polymerase 1 and 6 (RDR1/6), and ALTERED MERISTEM PROGRAM 1 (AMP1). In this study, we performed a forward genetic screening for enhancers of rdr6 via inoculation of CMV2aTΔ2b, a 2b-deficient Cucumber Mosaic Virus that is unable to suppress RNAi-mediated antiviral immunity...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28436089/a-novel-dense-granule-protein-gra41-regulates-timing-of-egress-and-calcium-sensitivity-in-toxoplasma-gondii
#8
Kaice A LaFavers, Karla M Márquez-Nogueras, Isabelle Coppens, Silvia N J Moreno, Gustavo Arrizabalaga
Toxoplasma gondii is an obligate intracellular apicomplexan parasite with high seroprevalence in humans. Repeated lytic cycles of invasion, replication and egress drive both the propagation and the virulence of this parasite. Key steps in this cycle, including invasion and egress, depend on tightly regulated calcium fluxes and, while many of the calcium-dependent effectors have been identified, the factors that detect and regulate the calcium fluxes are mostly unknown. To address this knowledge gap, we used a forward genetic approach to isolate mutants resistant to extracellular exposure to the calcium ionophore A23187...
April 24, 2017: Cellular Microbiology
https://www.readbyqxmd.com/read/28436004/engineering-of-an-h2-o2-auto-scavenging-in-vivo-cascade-for-pinoresinol-production
#9
Yongkun Lv, Xiaozhong Cheng, Guocheng Du, Jingwen Zhou, Jian Chen
Pinoresinol is a natural lignan with a high market value that has potential pharmacological and food supplement applications. Pinoresinol is currently isolated from plants, which suffers from low efficiency and yield. To produce pinoresinol from inexpensive and industrially available eugenol, an in vivo enzymatic cascade composed of vanillyl alcohol oxidase and peroxidase was designed, which scavenges H2 O2 automatically and eliminates protein purification and cofactor addition. Two peroxidases were screened and identified from Escherichia coli BL21 (DE3), and tested in the enzymatic cascade...
April 24, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28434859/tissue-specific-emission-of-e-%C3%AE-bergamotene-helps-resolve-the-dilemma-when-pollinators-are-also-herbivores
#10
Wenwu Zhou, Anke Kügler, Erica McGale, Alexander Haverkamp, Markus Knaden, Han Guo, Franziska Beran, Felipe Yon, Ran Li, Nathalie Lackus, Tobias G Köllner, Julia Bing, Meredith C Schuman, Bill S Hansson, Danny Kessler, Ian T Baldwin, Shuqing Xu
More than 87% of flowering plant species are animal-pollinated [1] and produce floral scents and other signals to attract pollinators. These floral cues may however also attract antagonistic visitors, including herbivores [2]. The dilemma is exacerbated when adult insects pollinate the same plant that their larvae consume. It remains largely unclear how plants maximize their fitness under these circumstances. Here we show that in the night-flowering wild tobacco Nicotiana attenuata, the emission of a sesquiterpene, (E)-α-bergamotene, in flowers increases adult Manduca sexta moth-mediated pollination success, while the same compound in leaves is known to mediate indirect defense against M...
April 13, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28432353/severe-hearing-loss-and-outer-hair-cell-death-in-homozygous-foxo3-knockout-mice-after-moderate-noise-exposure
#11
Felicia Gilels, Stephen T Paquette, Holly J Beaulac, Anwen Bullen, Patricia M White
Noise induced hearing loss (NIHL) is a disease that affects millions of Americans. Identifying genetic pathways that influence recovery from noise exposure is an important step forward in understanding NIHL. The transcription factor Foxo3 integrates the cellular response to oxidative stress and plays a role in extending lifespan in many organisms, including humans. Here we show that Foxo3 is required for auditory function after noise exposure in a mouse model system, measured by ABR. Absent Foxo3, outer hair cells are lost throughout the middle and higher frequencies...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28428935/genetic-analysis-of-mosquito-detection-of-humans
#12
Joshua I Raji, Matthew DeGennaro
Mosquitoes detect the presence of humans by integrating chemosensory, thermal, and visual cues. Among these, odors are crucial for mosquito host detection. Insects have evolved a diverse repertoire of receptors to detect their plant and animal hosts. Genetic analysis of these receptors in Drosophila has set the stage for similar studies in mosquitoes. The diversity of the cues involved in mosquito host-seeking has made designing behavioral control strategies a challenge. The sensory receptors that are most important for mosquito detection of humans can now be determined using genome editing...
April 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28428341/ctf4-related-protein-recruits-lhp1-prc2-to-maintain-h3k27me3-levels-in-dividing-cells-in-arabidopsis-thaliana
#13
Yue Zhou, Emmanuel Tergemina, Haitao Cui, Alexander Förderer, Benjamin Hartwig, Geo Velikkakam James, Korbinian Schneeberger, Franziska Turck
Polycomb Repressive Complex (PRC) 2 catalyzes the H3K27me3 modification that warrants inheritance of a repressive chromatin structure during cell division, thereby assuring stable target gene repression in differentiated cells. It is still under investigation how H3K27me3 is passed on from maternal to filial strands during DNA replication; however, cell division can reinforce H3K27me3 coverage at target regions. To identify novel factors involved in the Polycomb pathway in plants, we performed a forward genetic screen for enhancers of the like heterochromatin protein 1 (lhp1) mutant, which shows relatively mild phenotypic alterations compared with other plant PRC mutants...
April 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28421098/fine-mapping-the-branching-habit-trait-in-cultivated-peanut-by-combining-bulked-segregant-analysis-and-high-throughput-sequencing
#14
Galya Kayam, Yael Brand, Adi Faigenboim-Doron, Abhinandan Patil, Ilan Hedvat, Ran Hovav
The growth habit of lateral shoots (also termed "branching habit") is an important descriptive and agronomic character of peanut. Yet, both the inheritance of branching habit and the genetic mechanism that controls it in this crop remain unclear. In addition, the low degree of polymorphism among cultivated peanut varieties hinders fine-mapping of this and other traits in non-homozygous genetic structures. Here, we combined high-throughput sequencing with a well-defined genetic system to study these issues in peanut...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28421090/comparative-genomics-and-phylogenomics-of-east-asian-tulips-amana-liliaceae
#15
Pan Li, Rui-Sen Lu, Wu-Qin Xu, Tetsuo Ohi-Toma, Min-Qi Cai, Ying-Xiong Qiu, Kenneth M Cameron, Cheng-Xin Fu
The genus Amana Honda (Liliaceae), when it is treated as separate from Tulipa, comprises six perennial herbaceous species that are restricted to China, Japan and the Korean Peninsula. Although all six Amana species have important medicinal and horticultural uses, studies focused on species identification and molecular phylogenetics are few. Here we report the nucleotide sequences of six complete Amana chloroplast (cp) genomes. The cp genomes of Amana range from 150,613 bp to 151,136 bp in length, all including a pair of inverted repeats (25,629-25,859 bp) separated by the large single-copy (81,482-82,218 bp) and small single-copy (17,366-17,465 bp) regions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28416205/the-link-between-schizophrenia-and-substance-use-disorder-a-unifying-hypothesis
#16
REVIEW
Jibran Y Khokhar, Lucas L Dwiel, Angela M Henricks, Wilder T Doucette, Alan I Green
Substance use disorders occur commonly in patients with schizophrenia and dramatically worsen their overall clinical course. While the exact mechanisms contributing to substance use in schizophrenia are not known, a number of theories have been put forward to explain the basis of the co-occurrence of these disorders. We propose here a unifying hypothesis that combines recent evidence from epidemiological and genetic association studies with brain imaging and pre-clinical studies to provide an updated formulation regarding the basis of substance use in patients with schizophrenia...
April 14, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28416203/the-s4-s5-linker-gearbox-of-trp-channel-gating
#17
REVIEW
Laura Hofmann, Hongmei Wang, Wang Zheng, Stephan E Philipp, Patricia Hidalgo, Adolfo Cavalié, Xing-Zhen Chen, Andreas Beck, Veit Flockerzi
Transient receptor potential (TRP) channels are cation channels which participate in a wide variety of physiological processes in organisms ranging from fungi to humans. They fulfill roles in body homeostasis, are sensors for noxious chemicals and temperature in the mammalian somatosensory system and are activated by light stimulated phospholipase C activity in Drosophila or by hypertonicity in yeast. The transmembrane topology of TRP channels is similar to that of voltage-gated cation channels. TRP proteins assemble as tetramers with each subunit containing six transmembrane helices (S1-S6) and intracellular N- and C-termini...
April 4, 2017: Cell Calcium
https://www.readbyqxmd.com/read/28411893/genomic-approaches-to-hypertension
#18
REVIEW
Sheriff N Dodoo, Ivor J Benjamin
Genomic insights and analyses of Mendelian hypertension (HTN) syndromes and Genome-Wide Association study (GWAS) on essential hypertension have contributed to the depth of understanding of the genetics origins of hypertension. Mendelian syndromes are important for the field, since such knowledge leads to specific insights about disease pathogenesis and the potential for precision medicine. The clinical impact of findings of on essential hypertension is continuously evolving, and the insights accrued will refine efforts to combat the societal impact of hypertension...
May 2017: Cardiology Clinics
https://www.readbyqxmd.com/read/28411389/the-comet-assay-in-folsomia-candida-a-suitable-approach-to-assess-genotoxicity-in-collembolans
#19
Diogo N Cardoso, Ana Rita R Silva, Andreia Cruz, Joana Lourenço, Joana Neves, Catarina Malheiro, Sónia Mendo, Amadeu M V M Soares, Susana Loureiro
The present study shows the comet assay technique being successfully applied for the first time to one of the most widely used soil organisms in standardized ecotoxicological tests, Folsomia candida, providing a step forward in assessing the genotoxicity induced by xenobiotics. Because collembolans have a high content of chitin, a new methodology was developed in which the heads of the collembolans were separated from the rest of the body, allowing the hemolymph to leak out. This procedure allows the cells to be released, and after lysis the genetic material is available for the comet assay...
March 16, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28411216/construction-of-a-dcas9-based-gene-knockdown-system-in-staphylococcus-aureus
#20
Changlong Zhao, Xueqin Shu, Baolin Sun
There has been constant absence of an efficient gene knockdown method in the important human pathogen Staphylococcus aureus like RNA interference in eukaryotes. The early developed antisense RNA technology is mainly applied for forward genetic screen, but is rather limiting in specific gene knockdown for the lack of rational antisense RNA design strategies. Here we report an efficient and specific gene knockdown system in S. aureus based on type II clustered regularly interspaced short palindromic repeats (CRISPR) system from Streptococcus pyogenes...
April 14, 2017: Applied and Environmental Microbiology
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