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https://www.readbyqxmd.com/read/28441782/deep-sequencing-analysis-of-rnas-from-citrus-plants-grown-in-a-citrus-sudden-death-affected-area-reveals-diverse-known-and-putative-novel-viruses
#1
Emilyn E Matsumura, Helvecio D Coletta-Filho, Shahideh Nouri, Bryce W Falk, Luca Nerva, Tiago S Oliveira, Silvia O Dorta, Marcos A Machado
Citrus sudden death (CSD) has caused the death of approximately four million orange trees in a very important citrus region in Brazil. Although its etiology is still not completely clear, symptoms and distribution of affected plants indicate a viral disease. In a search for viruses associated with CSD, we have performed a comparative high-throughput sequencing analysis of the transcriptome and small RNAs from CSD-symptomatic and -asymptomatic plants using the Illumina platform. The data revealed mixed infections that included Citrus tristeza virus (CTV) as the most predominant virus, followed by the Citrus sudden death-associated virus (CSDaV), Citrus endogenous pararetrovirus (CitPRV) and two putative novel viruses tentatively named Citrus jingmen-like virus (CJLV), and Citrus virga-like virus (CVLV)...
April 24, 2017: Viruses
https://www.readbyqxmd.com/read/28441432/dysbiosis-of-intestinal-microbiota-and-decrease-in-paneth-cell-antimicrobial-peptide-level-during-acute-necrotizing-pancreatitis-in-rats
#2
Jing Chen, Chunlan Huang, Jingjing Wang, Hui Zhou, Yingying Lu, Lihong Lou, Junyuan Zheng, Ling Tian, Xingpeng Wang, Zhongwei Cao, Yue Zeng
OBJECTIVES: Intestinal barrier dysfunction plays an important role in acute necrotizing pancreatitis (ANP) and intestinal microbiota dysbiosis was involved in intestinal barrier failure. Paneth cells protect intestinal barrier and are associated with intestinal microbiota. Here, we investigated changes in intestinal microbiota and antimicrobial peptides of Paneth cells in ileum during ANP. METHODS: Rats with ANP were established by retrograde injection of 3.5% sodium taurocholate into biliopancreatic duct and sacrificed at 24h and 48h, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28441150/long-non-coding-rnas-in-leukemia-biology-and-clinical-impact
#3
Tim Lammens, Kaat Durinck, Annelynn Wallaert, Frank Speleman, Pieter Van Vlierberghe
PURPOSE OF REVIEW: Over the last years, long non-coding RNAs (lncRNAs) have emerged as putative regulators of malignant hematopoietic development. Here, we review recent literature on the involvement of lncRNAs in leukemia, including their role in driving or sustaining disease and their potential impact on diagnosis, classification, and prognosis. RECENT FINDINGS: Leukemogenesis is a complex process resulting from the accumulation of multiple genetic alterations...
April 22, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28439855/enabling-reverse-genetics-in-medicago-truncatula-using-high-throughput-sequencing-for-tnt1-flanking-sequence-recovery
#4
Xiaofei Cheng, Nick Krom, Shulan Zhang, Kirankumar S Mysore, Michael Udvardi, Jiangqi Wen
The genome sequence of Medicago truncatula was published and released in 2011. A Tnt1 insertional mutant population with 21,700 independently regenerated lines was completed in 2012 at The Samuel Roberts Noble Foundation. With an estimated 25 insertions per line, the Tnt1 mutant population harbors more than 500,000 insertions in the M. truncatula genome. Based on the genome size, average gene length, and random insertion of Tnt1into the genome, the mutant population affects about 90% of genes in the M. truncatula genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439835/the-uea-small-rna-workbench-a-suite-of-computational-tools-for-small-rna-analysis
#5
Irina Mohorianu, Matthew Benedict Stocks, Christopher Steven Applegate, Leighton Folkes, Vincent Moulton
RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439833/srnatoolboxvm-small-rna-analysis-in-a-virtual-machine
#6
Cristina Gómez-Martín, Ricardo Lebrón, Antonio Rueda, José L Oliver, Michael Hackenberg
High-throughput sequencing (HTS) data for small RNAs (noncoding RNA molecules that are 20-250 nucleotides in length) can now be routinely generated by minimally equipped wet laboratories; however, the bottleneck in HTS-based research has shifted now to the analysis of such huge amount of data. One of the reasons is that many analysis types require a Linux environment but computers, system administrators, and bioinformaticians suppose additional costs that often cannot be afforded by small to mid-sized groups or laboratories...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439823/high-throughput-rt-qpcr-for-the-analysis-of-circulating-micrornas
#7
Geok Wee Tan, Lu Ping Tan
Reverse transcription followed by real-time or quantitative polymerase chain reaction (RT-qPCR) is the gold standard for validation of results from transcriptomic profiling studies such as microarray and RNA sequencing. The current need for most studies, especially biomarker studies, is to evaluate the expression levels or fold changes of many transcripts in a large number of samples. With conventional low to medium throughput qPCR platforms, many qPCR plates would have to be run and a significant amount of RNA input per sample will be required to complete the experiments...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439397/transcriptomic-analysis-of-maternally-provisioned-cues-for-phenotypic-plasticity-in-the-annual-killifish-austrofundulus-limnaeus
#8
Amie L Romney, Jason E Podrabsky
BACKGROUND: Genotype and environment can interact during development to produce novel adaptive traits that support life in extreme conditions. The development of the annual killifish Austrofundulus limnaeus is unique among vertebrates because the embryos have distinct cell movements that separate epiboly from axis formation during early development, can enter into a state of metabolic dormancy known as diapause and can survive extreme environmental conditions. The ability to enter into diapause can be maternally programmed, with young females producing embryos that do not enter into diapause...
2017: EvoDevo
https://www.readbyqxmd.com/read/28439265/bacterial-and-fungal-community-structures-in-loess-plateau-grasslands-with-different-grazing-intensities
#9
Huhe, Xianjiang Chen, Fujiang Hou, Yanpei Wu, Yunxiang Cheng
The Loess Plateau of China is one of the most fragile ecosystems worldwide; thus, human production activities need to be conducted very cautiously. In this study, MiSeq high-throughput sequencing was applied to assess the relationship between bacterial and fungal community structures and changes in vegetation and soil physical and chemical properties induced by grazing, in four grasslands with different levels of grazing intensity (0, 2.67, 5.33, and 8.67 sheep/ha) in the semiarid region of the Loess Plateau...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28439121/bioinformatic-approaches-including-predictive-metagenomic-profiling-reveal-characteristics-of-bacterial-response-to-petroleum-hydrocarbon-contamination-in-diverse-environments
#10
Arghya Mukherjee, Bobby Chettri, James S Langpoklakpam, Pijush Basak, Aravind Prasad, Ashis K Mukherjee, Maitree Bhattacharyya, Arvind K Singh, Dhrubajyoti Chattopadhyay
Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28438359/impact-of-selectively-enriched-microbial-communities-on-long-term-fermentative-biohydrogen-production
#11
R Kanniah Goud, Kotakonda Arunasri, Dileep Kumar Yeruva, K Vamshi Krishna, Shikha Dahiya, S Venkata Mohan
The effect of selectively enriched inoculum for biohydrogen production and shifts in microbial communities was observed using anaerobic sequencing batch reactor (AnSBR). Significantly, combined pretreatment using acid and iodopropane resulted 3 fold increase in H2 production (8.65mol/kgCODR) over untreated control (2.63mol/kgCODR). Pretreatment showed significant shifts in the microbial communities which are thus accounted for enhanced H2 production. The high-throughput pyrosequence analysis depicted shifts in phylum Firmicutes and Proteobacteria...
March 27, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28438207/large-scale-validation-of-an-efficient-crispr-cas-based-multi-gene-editing-protocol-in-escherichia-coli
#12
Francesca Zerbini, Ilaria Zanella, Davide Fraccascia, Enrico König, Carmela Irene, Luca F Frattini, Michele Tomasi, Laura Fantappiè, Luisa Ganfini, Elena Caproni, Matteo Parri, Alberto Grandi, Guido Grandi
BACKGROUND: The exploitation of the CRISPR/Cas9 machinery coupled to lambda (λ) recombinase-mediated homologous recombination (recombineering) is becoming the method of choice for genome editing in E. coli. First proposed by Jiang and co-workers, the strategy has been subsequently fine-tuned by several authors who demonstrated, by using few selected loci, that the efficiency of mutagenesis (number of mutant colonies over total number of colonies analyzed) can be extremely high (up to 100%)...
April 24, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28438193/pathos-a-decision-support-system-for-reporting-high-throughput-sequencing-of-cancers-in-clinical-diagnostic-laboratories
#13
Kenneth D Doig, Andrew Fellowes, Anthony H Bell, Andrei Seleznev, David Ma, Jason Ellul, Jason Li, Maria A Doyle, Ella R Thompson, Amit Kumar, Luis Lara, Ravikiran Vedururu, Gareth Reid, Thomas Conway, Anthony T Papenfuss, Stephen B Fox
BACKGROUND: The increasing affordability of DNA sequencing has allowed it to be widely deployed in pathology laboratories. However, this has exposed many issues with the analysis and reporting of variants for clinical diagnostic use. Implementing a high-throughput sequencing (NGS) clinical reporting system requires a diverse combination of capabilities, statistical methods to identify variants, global variant databases, a validated bioinformatics pipeline, an auditable laboratory workflow, reproducible clinical assays and quality control monitoring throughout...
April 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28438123/small-rna-sequencing-reveals-a-role-for-sugarcane-mirnas-and-their-targets-in-response-to-sporisorium-scitamineum-infection
#14
Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo, Youxiong Que
BACKGROUND: Sugarcane smut caused by Sporisorium scitamineum leads to a significant reduction in cane yield and sucrose content. MicroRNAs (miRNAs) play an important role in regulating plant responses to biotic stress. The present study was the first to use two sugarcane genotypes, YA05-179 (smut-resistant) and ROC22 (smut-susceptible), to identify differentially expressed miRNAs in sugarcane challenged with S. scitamineum by using high-throughput sequencing. RESULTS: The predicted target gene number corresponding to known differentially expressed miRNAs in YA05-179 was less than that in ROC22, however most of them were in common...
April 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28438116/the-predictive-nature-of-transcript-expression-levels-on-protein-expression-in-adult-human-brain
#15
Amy L Bauernfeind, Courtney C Babbitt
BACKGROUND: Next generation sequencing methods are the gold standard for evaluating expression of the transcriptome. When determining the biological implications of such studies, the assumption is often made that transcript expression levels correspond to protein levels in a meaningful way. However, the strength of the overall correlation between transcript and protein expression is inconsistent, particularly in brain samples. RESULTS: Following high-throughput transcriptomic (RNA-Seq) and proteomic (liquid chromatography coupled with tandem mass spectrometry) analyses of adult human brain samples, we compared the correlation in the expression of transcripts and proteins that support various biological processes, molecular functions, and that are located in different areas of the cell...
April 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28436466/genome-wide-profiling-of-heritable-and-de-novo-str-variations
#16
Thomas Willems, Dina Zielinski, Jie Yuan, Assaf Gordon, Melissa Gymrek, Yaniv Erlich
Short tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic casework. However, it has proven problematic to genotype STRs from high-throughput sequencing data. Here, we describe HipSTR, a novel haplotype-based method for robustly genotyping and phasing STRs from Illumina sequencing data, and we report a genome-wide analysis and validation of de novo STR mutations. HipSTR is freely available at https://hipstr-tool...
April 24, 2017: Nature Methods
https://www.readbyqxmd.com/read/28435132/phylogenetic-position-of-the-rainbow-sardine-dussumieria-dussumieriidae-and-its-bearing-on-the-early-evolution-of-the-clupeoidei
#17
Sébastien Lavoué, Joris A M Bertrand, Wei-Jen Chen, Hsuan-Ching Hans Ho, Hiroyuki Motomura, Tetsuya Sado, Masaki Miya
The fish family Dussumieriidae (suborder Clupeoidei), commonly called round herrings, is traditionally considered to be a key taxon for understanding the evolution of the Clupeoidei because some of its morphological characteristics have been interpreted as being either derived or primitive, such as the nearly complete absence of abdominal scutes. Recent molecule-based studies showed that the Dussumieriidae is likely not a monophyletic group. None of those studies, however, included the genus Dussumieria (rainbow sardines) which is the type genus of the family Dussumieriidae...
April 20, 2017: Gene
https://www.readbyqxmd.com/read/28434189/changes-in-rumen-protozoal-community-by-condensed-tannin-fractions-of-different-molecular-weights-from-a-leucaena-leucocephala-hybrid-in-vitro
#18
Saminathan Mookiah, Han Ming Gan, Norhani Abdullah, Clemente Michael Vui Ling Wong, Suriya Kumari Ramiah, Hui Yin Tan, Chin Chin Sieo, Yin Wan Ho
AIMS: To evaluate the effects of condensed tannins (CTs) fractions of differing molecular weights (MWs) from a Leucaena leucocephala hybrid-Rendang (LLR) on the rumen protozoal community in vitro. METHODS AND RESULTS: The effects of unfractionated CTs (F0) and CT fractions of different MWs (F1 > F2 > F3 > F4 > F5) on protozoal population and community were evaluated in vitro using rumen microbes and ground guinea grass as the substrate. Higher-MW CT fractions F1 and F2 significantly (P < 0...
April 23, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28433919/identification-of-differentially-expressed-mirnas-through-high-throughput-sequencing-in-the-chicken-lung-in-response-to-mycoplasma-gallisepticum-hs
#19
Yabo Zhao, Yue Hou, Kang Zhang, Bo Yuan, Xiuli Peng
Mycoplasma gallisepticum (MG) infects chickens, causes chronic respiratory diseases (CRD) and severely damages the poultry industry. It has been suggested that micro-ribonucleic acids (miRNAs) are involved in microbial pathogenesis. Here, we identified miRNAs that are associated with MG infection in chicken lungs at 3 and 10days post-infection by deep sequencing. Thirty-six down-regulated and 9 up-regulated miRNAs belonging to 31 miRNA families were detected at 3days post-infection, whereas 50 down-regulated and 18 up-regulated miRNAs belonging to 41 miRNA families were found at 10days post-infection...
April 12, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28433722/high-precision-genome-sequencing-of-engineered-g-oxydans-621h-by-combining-long-nanopore-and-short-accurate-illumina-reads
#20
Angela Kranz, Alexander Vogel, Ursula Degner, Ines Kiefler, Michael Bott, Björn Usadel, Tino Polen
State of the art and novel high-throughput DNA sequencing technologies enable fascinating opportunities and applications in the life sciences including microbial genomics. Short high-quality read data already enable not only microbial genome sequencing, yet can be inadequately to solve problems in genome assemblies and for the analysis of structural variants, especially in engineered microbial cell factories. Single-molecule real-time sequencing technologies generating long reads promise to solve such assembly problems...
April 19, 2017: Journal of Biotechnology
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