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https://www.readbyqxmd.com/read/29911924/comprehensive-search-for-accessory-proteins-encoded-with-archaeal-and-bacterial-type-iii-crispr-cas-gene-cassettes-reveals-39-new-cas-gene-families
#1
Shiraz A Shah, Omer S Alkhnbashi, Juliane Behler, Wenyuan Han, Qunxin She, Wolfgang R Hess, Roger A Garrett, Rolf Backofen
A study was undertaken to identify conserved proteins that are encoded adjacent to cas gene cassettes of Type III CRISPR-Cas (Clusters of Regularly IntersSpaced Palindromic Repeats - CRISPR associated) interference modules. Type III modules have been shown to target and degrade dsDNA, ssDNA and ssRNA and are frequently intertwined with cofunctional accessory genes, including genes encoding CRISPR-associated Rossman Fold (CARF) domains. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families...
June 18, 2018: RNA Biology
https://www.readbyqxmd.com/read/29900693/genome-wide-screening-of-potential-rnase-y-processed-mrnas-in-the-m49-serotype-streptococcus-pyogenes-nz131
#2
Zhiyun Chen, Rahul Raghavan, Fengxia Qi, Justin Merritt, Jens Kreth
RNase Y is a major endoribonuclease in Group A streptococcus (GAS) and other Gram-positive bacteria. Our previous study showed that RNase Y was involved in mRNA degradation and processing in GAS. We hypothesized that mRNA processing regulated the expression of important GAS virulence factors via altering their mRNA stabilities and that RNase Y mediated at least some of the mRNA-processing events. The aims of this study were to (1) identify mRNAs that were processed by RNase Y and (2) confirm the mRNA-processing events...
June 13, 2018: MicrobiologyOpen
https://www.readbyqxmd.com/read/29891760/small-rna-ngs-revealed-the-presence-of-cherry-virus-a-and-little-cherry-virus-1-on-apricots-in-hungary
#3
Dániel Baráth, Nikoletta Jaksa-Czotter, János Molnár, Tünde Varga, Júlia Balássy, Luca Krisztina Szabó, Zoltán Kirilla, Gábor E Tusnády, Éva Preininger, Éva Várallyay
Fruit trees, such as apricot trees, are constantly exposed to the attack of viruses. As they are propagated in a vegetative way, this risk is present not only in the field, where they remain for decades, but also during their propagation. Metagenomic diagnostic methods, based on next generation sequencing (NGS), offer unique possibilities to reveal all the present pathogens in the investigated sample. Using NGS of small RNAs, a special field of these techniques, we tested leaf samples of different varieties of apricot originating from an isolator house or open field stock nursery...
June 11, 2018: Viruses
https://www.readbyqxmd.com/read/29876974/the-chimeric-mitochondrial-gene-orf182-causes-non-pollen-type-abortion-in-dongxiang-cytoplasmic-male-sterile-rice
#4
Hongwei Xie, Xiaojue Peng, Mingjuan Qian, Yicong Cai, Xia Ding, Qiusheng Chen, Qiying Cai, Youlin Zhu, Longan Yan, Yaohui Cai
D1-cytoplasmic male sterility (CMS) rice is a sporophytic cytoplasmic male-sterile rice developed from Dongxiang wild rice that exhibits a no-pollen-grain phenotype. A mitochondrial chimeric gene (orf182) was detected by mitochondrial genome sequencing and a comparative analysis. Orf182 is composed of three recombinant fragments, the largest of which is homologous to Sorghum bicolor mitochondrial sequences. In addition, orf182 was found only in wild rice species collected from China. Northern blot analysis showed that orf182 transcripts were affected by Rf genes in the isocytoplasmic restorer line DR7...
June 7, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29867881/identification-and-characterization-of-a-cis-antisense-rna-of-the-rpoh-gene-of-salmonella-enterica-serovar-typhi
#5
Changyan Xiong, Xuejiao Li, Juanli Liu, Xin Zhao, Shungao Xu, Xinxiang Huang
Antisense RNAs from complementary strands of protein coding genes regulate the expression of genes involved in many cellular processes. Using deep sequencing analysis of the Salmonella enterica serovar Typhi ( S. Typhi) transcriptome, a novel antisense RNA encoded on the strand complementary to the rpoH gene was revealed. In this study, the molecular features of this antisense RNA were assessed using northern blotting and rapid amplification of cDNA ends. The 3,508 nt sequence of RNA was identified as the antisense RNA of the rpoH gene and was named ArpH...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29858069/tyrosinase-based-reporter-gene-for-photoacoustic-imaging-of-microrna-9-regulated-by-dna-methylation-in-living-subjects
#6
Haifeng Zheng, Lin Zhou, Yaru Shi, Jie Tian, Fu Wang
MicroRNAs (miRNAs) are a class of negative regulators of gene expression and play critical roles in various biological processes. Conventional approaches for detecting miRNAs, such as northern blotting, microarray, and real-time PCR, usually require the lysis of cell samples and could not provide the in vivo information about miRNAs in living organisms. Here, we designed a tyrosinase (TYR)-based reporter to monitor miR-9 expression that is regulated by DNA methylation in living cells and animals. During DNA methylation of A549 cells treated by 5-aza-2'-deoxycytidine (5-Aza-dC), the CMV/TYR-3xTS reporter-transfected cells demonstrated a gradual decrease in melanin content, TYR activity, and photoacoustic signal because of the gradual activation of miR-9 expression...
June 1, 2018: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/29843993/a-case-control-study-on-hdl-associated-pon1-enzyme-level-in-northern-indian-type-2-diabetes-mellitus-patients
#7
Mohd Wamique, Wahid Ali, D Himanshu Reddy, Preeti Vishwakarma, Mohd Waseem
AIM: To evaluate the serum paraoxonase 1 activity and determine its association with duration in type 2 Diabetes mellitus patients. METHODS: A total of 80 cases from type 2 diabetes mellitus and healthy controls were enrolled in the present case control study. Human serum PON1 concentration was measured by ELISA and western blotting and it activity was determined spectrophotometrically using 4-nitrophenyle acetate. Diagnostic accuracy of serum PON1 to identify type 2 Diabetes mellitus was calculated with ROC analysis...
March 22, 2018: Diabetes & Metabolic Syndrome
https://www.readbyqxmd.com/read/29785587/a-study-on-the-use-of-strain-specific-and-homologous-promoters-for-heterologous-expression-in-industrial-saccharomyces-cerevisiae-strains
#8
Daniel Pereira de Paiva, Tiago Benoliel Rocha, Marciano Regis Rubini, André Moraes Nicola, Viviane Castelo Branco Reis, Fernando Araripe Gonçalves Torres, Lidia Maria Pepe de Moraes
Polymorphism is well known in Saccharomyces cerevisiae strains used for different industrial applications, however little is known about its effects on promoter efficiency. In order to test this, five different promoters derived from an industrial and a laboratory (S288c) strain were used to drive the expression of eGFP reporter gene in both cells. The ADH1 promoter (P ADH1 ) in particular, which showed more polymorphism among the promoters analyzed, also exhibited the highest differences in intracellular fluorescence production...
May 21, 2018: AMB Express
https://www.readbyqxmd.com/read/29726968/characterization-and-alternative-splicing-profiles-of-lipoxygenase-gene-family-in-tea-plant-camellia-sinensis
#9
Junyan Zhu, Xuewen Wang, Lingxiao Guo, Qingshan Xu, Shiqi Zhao, Fangdong Li, Xiaomei Yan, Shengrui Liu, Chaoling Wei
Oxylipins, including jasmonic acid (JA) and volatiles, are important for signaling in plants, and these are formed by the Lipoxygenases (LOX) enzyme family. There is a large gap in understanding of the underlying molecular basis of their roles in tea plants. Here, we identified eleven CsLOX genes from tea plant (Camellia sinensis), and characterized their phylogeny, gene structure and protein features into three subclasses. We then examined their enzymatic activities, LOX expression and alternative splicing of transcripts during development and in response to abiotic or biotic stresses in tea plants...
May 2, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29721083/targeting-cpt1a-mediated-fatty-acid-oxidation-sensitizes-nasopharyngeal-carcinoma-to-radiation-therapy
#10
Zheqiong Tan, Lanbo Xiao, Min Tang, Fang Bai, Jiangjiang Li, Liling Li, Feng Shi, Namei Li, Yueshuo Li, Qianqian Du, Jingchen Lu, Xinxian Weng, Wei Yi, Hanwen Zhang, Jia Fan, Jian Zhou, Qiang Gao, José N Onuchic, Ann M Bode, Xiangjian Luo, Ya Cao
Nasopharyngeal carcinoma (NPC) has a particularly high prevalence in southern China, southeastern Asia and northern Africa. Radiation resistance remains a serious obstacle to successful treatment in NPC. This study aimed to explore the metabolic feature of radiation-resistant NPC cells and identify new molecular-targeted agents to improve the therapeutic effects of radiotherapy in NPC. Methods : Radiation-responsive and radiation-resistant NPC cells were used as the model system in vitro and in vivo . Metabolomics approach was used to illustrate the global metabolic changes...
2018: Theranostics
https://www.readbyqxmd.com/read/29704454/accumulation-of-24-nucleotide-transgene-derived-sirnas-is-associated-with-crinivirus-immunity-in-transgenic-plants
#11
Wenjie Qiao, Aleksandra Zarzyńska-Nowak, Luca Nerva, Yen-Wen Kuo, Bryce W Falk
RNA silencing is a conserved antiviral defense mechanism that has been used to develop robust resistance against plant virus infections. Previous efforts have been made to develop RNA silencing-mediated resistance to criniviruses, yet none have given immunity. In this study, transgenic Nicotiana benthamiana plants harboring a hairpin construct of the Lettuce infectious yellows virus (LIYV) RdRp sequence exhibited immunity to systemic LIYV infection. Deep-sequencing analysis was performed to characterize virus-derived siRNAs (vsiRNAs) generated upon systemic LIYV infection in non-transgenic N...
April 28, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29698715/molecular-cloning-and-expression-profiles-of-igfbp-1a-in-common-carp-cyprinus-carpio-and-its-expression-regulation-by-growth-hormone-in-hepatocytes
#12
Wenbo Chen, Haoran Lin, Wensheng Li
In this study, we cloned and determined IGFBP-1a cDNA from common carp (Cyprinus carpio) liver. The 1655 bp full-length cDNA consisted of a 96 bp 5-untranslated region (UTR), a 789 bp open reading frame encoding 262 amino acid residues and a 770 bp 3-UTR containing seven mRNA instability motifs. Northern blot revealed a 1.8 kb IGFBP-1a transcript. IGFBP-1a mRNA was widely distributed in all tissues examined and predominantly expressed in the liver. During embryogenesis, IGFBP-1a mRNA was firstly observed in blastula stage, and significant increases were observed in body segment stage, lens formation stage and blood cycling stage...
July 2018: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/29694026/directed-evolution-of-heterologous-trnas-leads-to-reduced-dependence-on-post-transcriptional-modifications
#13
Kevin C Baldridge, Manasses Jora, Andre C Maranhao, Matthew M Quick, Balasubrahmanyam Addepalli, Jennifer S Brodbelt, Andrew D Ellington, Patrick A Limbach, Lydia M Contreras
Heterologous tRNA:aminoacyl tRNA synthetase pairs are often employed for noncanonical amino acid incorporation in the quest for an expanded genetic code. In this work, we investigated one possible mechanism by which directed evolution can improve orthogonal behavior for a suite of Methanocaldococcus jannaschii ( Mj) tRNATyr -derived amber suppressor tRNAs. Northern blotting demonstrated that reduced expression of heterologous tRNA variants correlated with improved orthogonality. We suspected that reduced expression likely minimized nonorthogonal interactions with host cell machinery...
May 18, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29687222/trans-splicing-of-plastid-rps12-transcripts-mediated-by-atppr4-is-essential-for-embryo-patterning-in-arabidopsis-thaliana
#14
Luca Tadini, Roberto Ferrari, Marie-Kristin Lehniger, Chiara Mizzotti, Fabio Moratti, Francesca Resentini, Monica Colombo, Alex Costa, Simona Masiero, Paolo Pesaresi
AtPPR4-mediated trans-splicing of plastid rps12 transcripts is essential for key embryo morphogenetic events such as development of cotyledons, determination of provascular tissue, and organization of the shoot apical meristem (SAM), but not for the formation of the protodermal layer. Members of the pentatricopeptide repeat (PPR) containing protein family have emerged as key regulators of the organelle post-transcriptional processing and to be essential for proper plant embryo development. In this study, we report the functional characterization of the AtPPR4 (At5g04810) gene encoding a plastid nucleoid PPR protein...
July 2018: Planta
https://www.readbyqxmd.com/read/29680705/over-expression-of-3-hydroxy-3-methylglutaryl-coenzyme-a-reductase-1-hmgr1-gene-under-super-promoter-for-enhanced-latex-biosynthesis-in-rubber-tree-hevea-brasiliensis-muell-arg
#15
R Jayashree, P A Nazeem, K Rekha, S Sreelatha, A Thulaseedharan, R Krishnakumar, R G Kala, M Vineetha, P Leda, U Jinu, P Venkatachalam
Natural rubber (cis-1, 4-polyisoprene) is being produced from bark laticifer cells of Hevea brasiliensis and the popular high latex yielding Indian rubber clones are easily prone to onset of tapping panel dryness syndrome (TPD) which is considered as a physiological syndrome affecting latex production either partially or completely. This report describes an efficient protocol for development of transgenic rubber plants by over-expression of 3-hydroxy 3-methylglutaryl Co-enzyme A reductase 1 (hmgr1) gene which is considered as rate limiting factor for latex biosynthesis via Agrobacterium-mediated transformation...
June 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29668464/effects-of-%C3%AE-prazosin-and-yohimbine-and-%C3%AE-receptors-activity-on-camp-generation-and-ucp1-gene-expression-in-brown-adipocytes
#16
Hirendra M Biswas
BACKGROUND: Brown adipose tissue (BAT) contains both α- and β-adrenergic receptors. In the literature, the activity of α-adrenoreceptors is less documented, and their functions still remain puzzling. The present investigation has been undertaken to understand α-adrenoreceptors' activity and their relation between uncoupling protein 1 (UCP1) mRNA expression and cyclic AMP (cAMP) generation in BAT. METHODS: BAT precursor cells from young mice were grown in culture...
April 18, 2018: Journal of Basic and Clinical Physiology and Pharmacology
https://www.readbyqxmd.com/read/29644261/detection-and-analysis-of-circular-rnas-by-rt-pcr
#17
Amaresh C Panda, Myriam Gorospe
Gene expression in eukaryotic cells is tightly regulated at the transcriptional and posttranscriptional levels. Posttranscriptional processes, including pre-mRNA splicing, mRNA export, mRNA turnover, and mRNA translation, are controlled by RNA-binding proteins (RBPs) and noncoding (nc)RNAs. The vast family of ncRNAs comprises diverse regulatory RNAs, such as microRNAs and long noncoding (lnc)RNAs, but also the poorly explored class of circular (circ)RNAs. Although first discovered more than three decades ago by electron microscopy, only the advent of high-throughput RNA-sequencing (RNA-seq) and the development of innovative bioinformatic pipelines have begun to allow the systematic identification of circRNAs (Szabo and Salzman, 2016; Panda et al ...
March 20, 2018: Bio-protocol
https://www.readbyqxmd.com/read/29593895/cross-sectional-serological-survey-of-human-fascioliasis-in-canutama-municipality-in-western-amazon-brazil
#18
Marcel Gonçalves Maciel, Walter Dos Santos Lima, Francisco Lazaro Moreira de Almeida, Leila Inês Aguiar Raposo Câmara Coelho, Guilherme Alfredo Novelino Araújo, Mariana Gomes Lima, Luiz Henrique Gonçalves Maciel, Cíntia Aparecida de Jesus Pereira, Thaís Costa da Silva Maciel, Jorge Augusto de Oliveira Guerra, Rosa Amélia Gonçalves Santana, Maria das Graças Vale Barbosa Guerra
Background: Fascioliasis is an important parasitic disease. In the northern region of Brazil, a human parasite infection has been reported through a coprological survey. Eggs of Fasciola hepatica were found in fecal samples of 11 individuals. Knowledge of the infection in animals or the presence of snails is necessary to address the possibility of the parasite cycle occurrence in that region. The aim of this study was to describe the transmission of human fascioliasis in Canutama, Amazonas, in Western Amazonia, Brazil...
2018: Journal of Parasitology Research
https://www.readbyqxmd.com/read/29588481/comparative-genome-wide-analysis-of-extracellular-small-rnas-from-the-mucormycosis-pathogen-rhizopus-delemar
#19
Muxing Liu, Gillian O Bruni, Christopher M Taylor, Zhengguang Zhang, Ping Wang
Rhizopus delemar is an emerging fungal pathogen causing devastating mucormycosis in immunocompromised individuals. The organism remains understudied and there are urgent needs for new methods of rapid disease diagnosis for timely therapy. Extracellular vesicles with encapsulated RNAs have recently been discovered to have great potential applications for disease diagnoses and treatments. To explore the utilization of ex-RNA in studies of mucormycosis, we have performed RNA-Seq of ex-sRNAs from two clinical strains of R...
March 27, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29574975/lncrna-flvcr1-as1-acts-as-mir-513c-sponge-to-modulate-cancer-cell-proliferation-migration-and-invasion-in-hepatocellular-carcinoma
#20
Kunsong Zhang, Zhenxian Zhao, Junfeng Yu, Wei Chen, Qiongcong Xu, Liuhua Chen
In the present study, we aimed to search for dysregulated lnRNAs in Hepatocellular carcinoma (HCC) tissues, and analyze the relationship of its expression level with the clinicopathological feature and patient prognosis. The biological function of FLVCR1-AS1, the identified lncRNA, in the process of HCC development, and progression was investigated in vitro and in vivo. The underlying molecular mechanism was further explored. We determined FLVCR1-AS1 expression in HCC tissues and peri-tumor tissues by bioinformatic analysis, qRT-PCR, Northern blot and in situ hybridization...
March 25, 2018: Journal of Cellular Biochemistry
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