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https://www.readbyqxmd.com/read/30297676/comparative-rna-seq-analysis-of-high-and-low-oil-yellow-horn-during-embryonic-development
#1
Li Wang, Chengjiang Ruan, Lingyue Liu, Wei Du, Aomin Bao
Yellow horn ( Xanthoceras sorbifolium Bunge) is an endemic oil-rich shrub that has been widely cultivated in northern China for bioactive oil production. However, little is known regarding the molecular mechanisms that contribute to oil content in yellow horn. Herein, we measured the oil contents of high- and low-oil yellow horn embryo tissues at four developmental stages and investigated the global gene expression profiles through RNA-seq. The results found that at 40, 54, 68, and 81 days after anthesis, a total of 762, 664, 599, and 124 genes, respectively, were significantly differentially expressed between the high- and low-oil lines...
October 8, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/30082020/-meta-analysis-on-association-between-genetic-polymorphisms-of-cytochrome-p450-2e1-and-susceptibility-to-chinese-gastric-cancer
#2
Yuqian Mi, Xiaofeng Liang, Jing Wu
OBJECTIVE: To conduct a comprehensive quantitative analysis about the association between genetic polymorphisms of CYP 2E1 and susceptibility to Chinese gastric cancer in order to offer evidence-based evidence for the etiology of gastric cancer. METHODS: Using the keywords and entry terms of cytochrom P450 2E1, cytochrome P450, CYP 2E1, stomach neoplasms, individual susceptibility, gene polymorphism, risk factors in English and Chinese, we searched medical literature databases, such as Pub Med, Embase, CBM, VIP, CNKI, China Info, published from January 1 th, 1997 to December 31 th, 2016, the Chines population was selected as the research object...
May 2018: Wei Sheng Yan Jiu, Journal of Hygiene Research
https://www.readbyqxmd.com/read/30076867/detecting-pathogens-with-zinc-finger-tale-and-crispr-based-programmable-nucleic-acid-binding-proteins
#3
REVIEW
Angelo C Batista, Luis G C Pacheco
The recent availability of highly adaptable engineered nucleic acid binding proteins has brought about a revolution in the genome-editing field. Now, several studies have harnessed these Zinc-Finger-based, Transcription Activator-like Effector (TALE)-based, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based programmable DNA and RNA-binding proteins to develop very specific diagnostic platforms to detect pathogen's nucleic acids, with sensitivities that go down to single molecule resolution...
September 2018: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/30072760/transcriptome-analysis-highlights-key-differentially-expressed-genes-involved-in-cellulose-and-lignin-biosynthesis-of-sugarcane-genotypes-varying-in-fiber-content
#4
Lakshmi Kasirajan, Nam V Hoang, Agnelo Furtado, Frederik C Botha, Robert J Henry
Sugarcane (Saccharum spp. hybrids) is a potential lignocellulosic feedstock for biofuel production due to its exceptional biomass accumulation ability, high convertible carbohydrate content and a favorable energy input/output ratio. Genetic modification of biofuel traits to improve biomass conversion requires an understanding of the regulation of carbohydrate and lignin biosynthesis. RNA-Seq was used to investigate the transcripts differentially expressed between the immature and mature tissues of the sugarcane genotypes varying in fiber content...
August 2, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29973943/crabs-claw-acts-as-a-bifunctional-transcription-factor-in-flower-development
#5
Thomas Gross, Suvi Broholm, Annette Becker
One of the crucial steps in the life cycle of angiosperms is the development of carpels. They are the most complex plant organs, harbor the seeds, and, after fertilization, develop into fruits and are thus an important ecological and economic trait. CRABS CLAW (CRC), a YABBY protein and putative transcription factor, is one of the major carpel developmental regulators in A. thaliana that includes a C2C2 zinc finger and a domain with similarities to an HMG box. CRC is involved in the regulation of processes such as carpel fusion and growth, floral meristem termination, and nectary formation...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29968258/oxidative-stress-index-is-increased-in-children-exposed-to-industrial-discharges-and-is-inversely-correlated-with-metabolite-excretion-of-voc
#6
Rocío López-Vargas, Alejandra Méndez-Serrano, Arnulfo Albores-Medina, Fernando Oropeza-Hernández, Leticia Hernández-Cadena, Franciso Mercado-Calderón, Esmeralda Alvarado-Toledo, Selene Herrera-Morales, Omar Arellano-Aguilar, Guadalupe García-Vargas, Regina Montero-Montoya
Although the Atoyac River has been classified as highly polluted by environmental authorities, several communities are settled on its banks, affecting around 1.5 million persons, as well as farmland, due to an environmental distribution of toxics in the area. Our aim was to demonstrate that this environment affects important physiological processes that have an impact in health, so we conducted a study of schoolchildren from small communities on the banks of the river and in another similar town located far from it...
August 2018: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/29940185/molecular-mechanisms-of-rna-targeting-by-cas13-containing-type-vi-crispr-cas-systems
#7
REVIEW
Mitchell R O'Connell
Prokaryotic adaptive immune systems use Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and CRISPR-associated (Cas) proteins for RNA-guided cleavage of foreign genetic elements. The focus of this review, Type VI CRISPR-Cas systems, contain a single protein, Cas13 (formerly C2c2) that when assembled with a CRISPR RNA (crRNA) forms a crRNA-guided RNA-targeting effector complex. Type VI CRISPR-Cas systems can be divided into four subtypes (A-D) based on Cas13 phylogeny. All Cas13 proteins studied to date possess two enzymatically distinct ribonuclease activities that are required for optimal interference...
June 22, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29915237/genome-editing-by-natural-and-engineered-crispr-associated-nucleases
#8
REVIEW
Wen Y Wu, Joyce H G Lebbink, Roland Kanaar, Niels Geijsen, John van der Oost
Over the last decade, research on distinct types of CRISPR systems has revealed many structural and functional variations. Recently, several novel types of single-polypeptide CRISPR-associated systems have been discovered including Cas12a/Cpf1 and Cas13a/C2c2. Despite distant similarities to Cas9, these additional systems have unique structural and functional features, providing new opportunities for genome editing applications. Here, relevant fundamental features of natural and engineered CRISPR-Cas variants are compared...
July 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29710373/transforming-plant-biology-and-breeding-with-crispr-cas9-cas12-and-cas13
#9
REVIEW
Patrick Schindele, Felix Wolter, Holger Puchta
Currently, biology is revolutionized by ever growing applications of the CRISPR/Cas system. As discussed in this Review, new avenues have opened up for plant research and breeding by the use of the sequence-specific DNases Cas9 and Cas12 (formerly named Cpf1) and, more recently, the RNase Cas13 (formerly named C2c2). Although double strand break-induced gene editing based on error-prone nonhomologous end joining has been applied to obtain new traits, such as powdery mildew resistance in wheat or improved pathogen resistance and increased yield in tomato, improved technologies based on CRISPR/Cas for programmed change in plant genomes via homologous recombination have recently been developed...
June 2018: FEBS Letters
https://www.readbyqxmd.com/read/29644554/curcumin-ameliorates-palmitate-induced-inflammation-in-skeletal-muscle-cells-by-regulating-jnk-nf-kb-pathway-and-ros-production
#10
Asie Sadeghi, Atefeh Rostamirad, Shadisadat Seyyedebrahimi, Reza Meshkani
Curcumin, a natural polyphenol compound, has the beneficial effects on several diseases such as metabolic syndrome, cancer, and diabetes. The anti-inflammatory property of curcumin has been demonstrated in different cells; however, its role in prevention of palmitate-induced inflammation in skeletal muscle C2C12 cells is not known. In this study, we examined the effect of curcumin on the inflammatory responses stimulated by palmitate in C2C2 cells. The results showed that palmitate upregulated the mRNA expression and protein release of IL-6 and TNF-α cytokines in C2C12 cells, while pretreatment with curcumin was able to attenuate the effect of palmitate on inflammatory cytokines...
October 2018: Inflammopharmacology
https://www.readbyqxmd.com/read/29619129/sickle-cell-anemia-patients-in-use-of-hydroxyurea-association-between-polymorphisms-in-genes-encoding-metabolizing-drug-enzymes-and-laboratory-parameters
#11
Sètondji Cocou Modeste Alexandre Yahouédéhou, Magda Oliveira Seixas Carvalho, Rodrigo Mota Oliveira, Rayra Pereira Santiago, Caroline Conceição da Guarda, Suellen Pinheiro Carvalho, Júnia Raquel Dutra Ferreira, Milena Magalhães Aleluia, Elisângela Vitória Adorno, Marilda de Souza Gonçalves
This study investigated associations between SNPs in genes encoding metabolizing drug enzymes and laboratory parameters in sickle cell anemia patients under hydroxyurea (SCA-HU+ ). We evaluated hematologic and biochemical parameters by electronic methods and SNPs by PCR-RFLP and multiplex PCR in 35 SCA-HU+ patients and 67 SCA-HU- patients. The HbS, total cholesterol, lactate dehydrogenase, aspartate aminotransferase, total bilirubin and fractions levels, and leukocyte, eosinophil, monocyte, and erythroblast counts were reduced in SCA-HU+ patients ( p < 0...
2018: Disease Markers
https://www.readbyqxmd.com/read/29575326/the-crispr-cas-revolution-reaches-the-rna-world-cas13-a-new-swiss-army-knife-for-plant-biologists
#12
REVIEW
Felix Wolter, Holger Puchta
Application of the bacterial CRISPR/Cas systems to eukaryotes is revolutionizing biology. Cas9 and Cas12 (previously called Cpf1) are widely used as DNA nucleases for inducing site-specific DNA breaks for different kinds of genome engineering applications, and in their mutated forms as DNA-binding proteins to modify gene expression. Moreover, histone modifications, as well as cytosine methylation or base editing, were achieved with these systems in plants. Recently, with the discovery of the nuclease Cas13a (previously called C2c2), molecular biologists have obtained a system that enables sequence-specific cleavage of single-stranded RNA molecules...
June 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29387191/maternal-natural-killer-cell-immunoglobulin-receptor-genes-and-human-leukocyte-antigen-c-ligands-influence-recurrent-spontaneous-abortion-in-the-han-chinese-population
#13
Ning Su, Hongdan Wang, Bowei Zhang, Yiqing Kang, Qiannan Guo, Hai Xiao, Hecai Yang, Shixiu Liao
The underlying mechanism of recurrent spontaneous abortion (RSA) has remained elusive for many years. Several previous studies have suggested that the killer cell immunoglobulin receptor (KIR) gene family is associated with RSA, however, it is not clear exactly how. The present study detected KIR and human leukocyte antigen-C (HLA-C) genes in 110 Han Chinese women with unexplained RSA and 105 Han Chinese healthy females. The aim of the present study was to determine if certain genotypes were more susceptible to the occurrence of miscarriage...
January 2018: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29301551/rna-virus-interference-via-crispr-cas13a-system-in-plants
#14
Rashid Aman, Zahir Ali, Haroon Butt, Ahmed Mahas, Fatimah Aljedaani, Muhammad Zuhaib Khan, Shouwei Ding, Magdy Mahfouz
BACKGROUND: CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleaving single-stranded RNA (ssRNA) molecules of the phage genome. Here, we employ CRISPR/Cas13a to engineer interference with an RNA virus, Turnip Mosaic Virus (TuMV), in plants. RESULTS: CRISPR/Cas13a produces interference against green fluorescent protein (GFP)-expressing TuMV in transient assays and stable overexpression lines of Nicotiana benthamiana...
January 4, 2018: Genome Biology
https://www.readbyqxmd.com/read/29166879/a-compendium-of-transcription-factor-and-transcriptionally-active-protein-coding-gene-families-in-cowpea-vigna-unguiculata-l
#15
Vikram A Misra, Yu Wang, Michael P Timko
BACKGROUND: Cowpea (Vigna unguiculata (L.) Walp.) is the most important food and forage legume in the semi-arid tropics of sub-Saharan Africa where approximately 80% of worldwide production takes place primarily on low-input, subsistence farm sites. Among the major goals of cowpea breeding and improvement programs are the rapid manipulation of agronomic traits for seed size and quality and improved resistance to abiotic and biotic stresses to enhance productivity. Knowing the suite of transcription factors (TFs) and transcriptionally active proteins (TAPs) that control various critical plant cellular processes would contribute tremendously to these improvement aims...
November 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29156840/association-between-cyp2e1-genetic-polymorphisms-and-urinary-cancer-risk-a-meta-analysis
#16
Zhiqing Fang, Yun Wu, Ning Zhang
Objective: Studies investigating the contribution of Cytochrome P4502E1 (CYP2E1) polymorphisms to the etiology of urinary cancer draw inconsistent conclusions. Thus, we performed a meta-analysis to evaluate the association between CYP2E1 Rsa I/Pst I and Dra I polymorphisms and urinary cancer susceptibility. Materials and Methods: Meta-analysis based on the eligible case-control studies that assess the association of CYP2E1 Rsa I/Pst I and Dra I polymorphisms with urinary cancer was conducted...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28976959/rna-targeting-with-crispr-cas13
#17
Omar O Abudayyeh, Jonathan S Gootenberg, Patrick Essletzbichler, Shuo Han, Julia Joung, Joseph J Belanto, Vanessa Verdine, David B T Cox, Max J Kellner, Aviv Regev, Eric S Lander, Daniel F Voytas, Alice Y Ting, Feng Zhang
RNA has important and diverse roles in biology, but molecular tools to manipulate and measure it are limited. For example, RNA interference can efficiently knockdown RNAs, but it is prone to off-target effects, and visualizing RNAs typically relies on the introduction of exogenous tags. Here we demonstrate that the class 2 type VI RNA-guided RNA-targeting CRISPR-Cas effector Cas13a (previously known as C2c2) can be engineered for mammalian cell RNA knockdown and binding. After initial screening of 15 orthologues, we identified Cas13a from Leptotrichia wadei (LwaCas13a) as the most effective in an interference assay in Escherichia coli...
October 12, 2017: Nature
https://www.readbyqxmd.com/read/28968770/crispr-rt-a-web-application-for-designing-crispr-c2c2-crrna-with-improved-target-specificity
#18
Houxiang Zhu, Emily Richmond, Chun Liang
Summary: CRISPR-Cas systems have been successfully applied in genome editing. Recently, the CRISPR-C2c2 system has been reported as a tool for RNA editing. Here we describe CRISPR-RT (CRISPR RNA-Targeting), the first web application to help biologists design crRNAs with improved target specificity for the CRISPR-C2c2 system. CRISPR-RT allows users to set up a wide range of parameters, making it highly flexible for current and future research in CRISPR-based RNA editing. CRISPR-RT covers major model organisms and can be easily extended to cover other species...
January 1, 2018: Bioinformatics
https://www.readbyqxmd.com/read/28955602/genome-wide-analysis-of-phaseolus-vulgaris-c2c2-yabby-transcription-factors-under-salt-stress-conditions
#19
Behcet İnal, İlker Büyük, Emre İlhan, Sümer Aras
The aim of this study was to identify and characterize the C2C2 - YABBY family of genes by a genome-wide scale in common bean. Various in silico approaches were used for the study and the results were confirmed through common molecular biology techniques. Quantitative real-time PCR (qPCR) analysis was performed for identified putative PvulYABBY genes in leaf and root tissues of two common bean cultivars, namely Yakutiye and Zulbiye under salt stress condition. Eight candidate PvulYABBY proteins were discovered and the length of these proteins ranged from 173 to 256 amino acids...
October 2017: 3 Biotech
https://www.readbyqxmd.com/read/28866235/genome-wide-analysis-of-the-yabby-family-in-soybean-and-functional-identification-of-gmyabby10-involvement-in-high-salt-and-drought-stresses
#20
Shu-Ping Zhao, Dan Lu, Tai-Fei Yu, Yu-Jie Ji, Wei-Jun Zheng, Shuang-Xi Zhang, Shou-Cheng Chai, Zhan-Yu Chen, Xi-Yan Cui
YABBY family is a plant specific transcription factor family, with the typical N-terminal C2C2 type zinc finger domain and the C-terminal YABBY conservative structure domain, which plays important biological roles in plant growth, development and morphogenesis. In this study, a total of 17 YABBY genes were identified in the soybean genome. The results of this research showed that 17 soybean YABBY genes were located on 11 chromosomes. Analysis of putative cis-acting elements showed that soybean YABBY genes contained lots of MYB and MYC elements...
October 2017: Plant Physiology and Biochemistry: PPB
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