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https://www.readbyqxmd.com/read/28531310/nascent-rna-sequencing-reveals-mechanisms-of-gene-regulation-in-the-human-malaria-parasite-plasmodium-falciparum
#1
Xueqing Maggie Lu, Gayani Batugedara, Michael Lee, Jacques Prudhomme, Evelien M Bunnik, Karine G Le Roch
Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P...
May 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28531277/genome-wide-discovery-of-viral-micrornas-based-on-phylogenetic-analysis-and-structural-evolution-of-various-human-papillomavirus-subtypes
#2
Shun-Long Weng, Kai-Yao Huang, Julia Tzu-Ya Weng, Fang-Yu Hung, Tzu-Hao Chang, Tzong-Yi Lee
In mammals, microRNAs (miRNAs) play key roles in controlling posttranscriptional regulation through binding to the mRNAs of target genes. Recently, it was discovered that viral miRNAs may be involved in human cancers and diseases. It is likely that viral miRNAs help viruses enter the latent phase of their life cycle and become undetected by the host's immune system, while increasing the host's risk for cancer development. Cervical cancer is typically related to the infection of human papillomavirus (HPV) through sexual transmission...
May 20, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28530238/micrornas-146a-b-5-and-425-3p-and-24-3p-are-markers-of-antidepressant-response-and-regulate-mapk-wnt-system-genes
#3
Juan Pablo Lopez, Laura M Fiori, Cristiana Cruceanu, Rixing Lin, Benoit Labonte, Hannah M Cates, Elizabeth A Heller, Vincent Vialou, Stacy M Ku, Christophe Gerald, Ming-Hu Han, Jane Foster, Benicio N Frey, Claudio N Soares, Daniel J Müller, Faranak Farzan, Francesco Leri, Glenda M MacQueen, Harriet Feilotter, Kathrin Tyryshkin, Kenneth R Evans, Peter Giacobbe, Pierre Blier, Raymond W Lam, Roumen Milev, Sagar V Parikh, Susan Rotzinger, Steven C Strother, Cathryn M Lewis, Katherine J Aitchison, Gayle M Wittenberg, Naguib Mechawar, Eric J Nestler, Rudolf Uher, Sidney H Kennedy, Gustavo Turecki
Antidepressants (ADs) are the most common treatment for major depressive disorder (MDD). However, only ∼30% of patients experience adequate response after a single AD trial, and this variability remains poorly understood. Here, we investigated microRNAs (miRNAs) as biomarkers of AD response using small RNA-sequencing in paired samples from MDD patients enrolled in a large, randomized placebo-controlled trial of duloxetine collected before and 8 weeks after treatment. Our results revealed differential expression of miR-146a-5p, miR-146b-5p, miR-425-3p and miR-24-3p according to treatment response...
May 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28528706/long-noncoding-rnas-in-the-pathogenesis-of-barrett-s-esophagus-and-esophageal-carcinoma
#4
REVIEW
John M Abraham, Stephen J Meltzer
For many years, only a small fraction of the human genome was believed to regulate cell function and development. This protein-coding portion composed only 1% to 2% of 3 billion human DNA base pairs-the remaining sequence was classified as junk DNA. Subsequent research has revealed that most of the genome is transcribed into a broad array of noncoding RNAs, ranging in size from microRNA (20-23 nucleotides) to long noncoding RNA (lncRNA, more than 200 nucleotides). These noncoding RNA classes have been shown to use diverse molecular mechanisms to control gene expression and organ system development...
May 18, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28525966/gene-expression-of-vibrio-parahaemolyticus-growing-in-laboratory-isolation-conditions-compared-to-those-common-in-its-natural-ocean-environment
#5
Katherine García, Cristian Yáñez, Nicolás Plaza, Francisca Peña, Pedro Sepúlveda, Diliana Pérez-Reytor, Romilio T Espejo
BACKGROUND: Vibrio parahaemolyticus is an autochthonous marine bacterial species comprising strains able to grow in broth containing bile salts at 37 °C, a condition seldom found in the ocean. However, this condition is used for isolation in the laboratory because it is considered a necessary property for pathogenesis. In this context, revealing how gene expression enables V. parahaemolyticus to adapt to this particular condition -common to almost all V. parahaemolyticus isolates- will improve our understanding of the biology of this important pathogen...
May 19, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28525645/molecular-characterization-of-prototheca-strains-isolated-in-china-revealed-the-first-cases-of-protothecosis-associated-with-prototheca-zopfii-genotype-1
#6
Noriyuki Hirose, Zhensheng Hua, Yuichi Kato, Qiangqiang Zhang, Ruoyu Li, Kazuko Nishimura, Michiaki Masuda
In this study, six strains of Prototheca isolated in China from human patients diagnosed as protothecosis and cows with mastitis were characterized by polymerase chain reaction (PCR) and nucleotide sequencing of the ribosomal RNA gene (rDNA) and by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). The results indicated that three strains isolated from the human patients were P. zopfii genotype 1, revealing the first cases of human protothecosis associated with P. zopfii genotype 1...
May 19, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/28524354/an-aggregating-amphiphilic-squaraine-a-light-up-probe-that-discriminates-parallel-g-quadruplexes
#7
Vincenzo Grande, Filippo Doria, Mauro Freccero, Frank Würthner
G-quadruplexes (G4s) are peculiar DNA or RNA tertiary structures that are involved in the regulation of many biological events within mammalian cells, bacteria, and viruses. Although their role as versatile therapeutic targets has been emphasized for 35 years, G4 selectivity over ubiquitous double-stranded DNA/RNA, as well as G4 differentiation by small molecules, still remains challenging. Here, a new amphiphilic dicyanovinyl-substituted squaraine, SQgl, is reported to act as an NIR fluorescent light-up probe discriminating an extensive panel of parallel G4s while it is non-fluorescent in the aggregated state...
May 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28523997/differences-in-relative-levels-of-88-micrornas-in-various-regions-of-the-normal-adult-human-brain
#8
Elena Vladislavovna Filatova, Anelya Khanlarovna Alieva, Maria Igorevna Shadrina, Petr Andreevich Slominsky
AIM OF STUDY: Since the discovery of microRNAs (miRNAs) in the 1990s, our knowledge about their biology has grown considerably. The increasing number of studies addressing the role of miRNAs in development and in various diseases emphasizes the need for a comprehensive catalogue of accurate sequence, expression and conservation information regarding the large number of miRNAs proposed recently in all organs and tissues. The objective of this study was to provide data on the levels of miRNA expression in 15 tissues of the normal human brain...
May 19, 2017: MicroRNA
https://www.readbyqxmd.com/read/28522719/genome-sequence-of-a-novel-positive-sense-single-stranded-rna-virus-isolated-from-western-corn-rootworm-diabrotica-virgifera%C3%A2-virgifera-leconte
#9
Sijun Liu, Yuting Chen, Thomas W Sappington, Bryony C Bonning
The genome sequence of a novel small RNA virus was assembled from the transcriptome of the western corn rootworm, Diabrotica virgifera virgifera The assembled genome has 13,182 nucleotides with a 3' polyadenylated tail. Two open reading frames are predicted to encode polyproteins of 2,838 and 1,073 amino acids.
May 18, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28522718/genome-sequence-of-diabrotica-virgifera-virgifera-virus2-a-novel-small-rna-virus-of-the-western-corn-rootworm-diabrotica-virgifera-virgifera-leconte
#10
Sijun Liu, Yuting Chen, Thomas W Sappington, Bryony C Bonning
The genome of a novel small RNA virus, tentatively named Diabrotica virgifera virgifera virus 2 (DvvV2), was identified in the western corn rootworm, Diabrotica virgifera virgifera LeConte, through transcriptome sequencing and confirmed by reverse transcription-PCR. Here, we report the near-complete nucleotide sequence and the genome organization of DvvV2.
May 18, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28522256/sporadic-early-onset-diffuse-gastric-cancers-have-high-frequency-of-somatic-cdh1-alterations-but-low-frequency-of-somatic-rhoa-mutations-compared-with-late-onset-cancers
#11
Soo Young Cho, Jun Won Park, Yang Liu, Young Soo Park, Ju Hee Kim, Hanna Yang, Hyejin Um, Woo Ri Ko, Byung Il Lee, Sun Young Kwon, Seung Wan Ryu, Chae Hwa Kwon, Do Youn Park, Jae-Hyuk Lee, Sang Il Lee, Kyu Sang Song, Hoon Hur, Sang-Uk Han, Heekyung Chang, Su-Jin Kim, Byung-Sik Kim, Jeong-Hwan Yook, Moon-Won Yoo, Beom-Su Kim, In-Seob Lee, Myeong-Cherl Kook, Nina Thiessen, An He, Chip Stewart, Andrew Dunford, Jaegil Kim, Juliann Shih, Gordon Saksena, Andrew D Cherniack, Steven Schumacher, Amaro-Taylor Weiner, Mara Rosenberg, Gad Getz, Eun Gyeong Yang, Min Hee Ryu, Adam J Bass, Hark Kyun Kim
BACKGROUND & AIMS: Early-onset gastric cancer, which develops in younger patients than most gastric cancers, is usually detected at advanced stages, has diffuse histologic features, and occurs more frequently in women. We investigated somatic genomic alterations associated with the unique characteristics of sporadic diffuse gastric cancers (DGCs) from younger patients. METHODS: We conducted whole exome and RNA sequence analyses of 80 resected DGC samples from patients 45 years old or younger in Korea...
May 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28522157/antiviral-goes-viral-harnessing-crispr-cas9-to-combat-viruses-in-humans
#12
REVIEW
Jasper Adriaan Soppe, Robert Jan Lebbink
The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems are RNA-guided sequence-specific prokaryotic antiviral immune systems. In prokaryotes, small RNA molecules guide Cas effector endonucleases to invading foreign genetic elements in a sequence-dependent manner, resulting in DNA cleavage by the endonuclease upon target binding. A rewired CRISPR/Cas9 system can be used for targeted and precise genome editing in eukaryotic cells. CRISPR/Cas has also been harnessed to target human pathogenic viruses as a potential new antiviral strategy...
May 15, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28521398/effect-of-satb1-silencing-on-the-proliferation-invasion-and-apoptosis-of-te-1-esophageal-cancer-cells
#13
Bo Huang, Fei Xiong, Siwang Wang, Xianping Lang, Xiaodong Wang, Hongli Zhou
The aim of the present study was to investigate the effect of special AT-rich sequence-binding protein-1 (SATB1)-targeted small interfering RNA (siRNA) on the proliferation, invasion and apoptosis of TE-1 human esophageal cancer cells. SATB1 has been correlated with the metastasis and poor prognosis of colon and breast cancer, but the role of SATB1 in esophageal cancer remains unknown. Therefore, the present study constructed and transfected SATB1-siRNA into TE-1 cells in order to knockdown the expression of the SATB1 gene...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28520720/identification-of-human-short-introns
#14
Emmanuel L Abebrese, Syed H Ali, Zachary R Arnold, Victoria M Andrews, Katharine Armstrong, Lindsay Burns, Hannah R Crowder, R Thomas Day, Daniel G Hsu, Katherine Jarrell, Grace Lee, Yi Luo, Daphine Mugayo, Zain Raza, Kyle Friend
Canonical pre-mRNA splicing requires snRNPs and associated splicing factors to excise conserved intronic sequences, with a minimum intron length required for efficient splicing. Non-canonical splicing-intron excision without the spliceosome-has been documented; most notably, some tRNAs and the XBP1 mRNA contain short introns that are not removed by the spliceosome. There have been some efforts to identify additional short introns, but little is known about how many short introns are processed from mRNAs. Here, we report an approach to identify RNA short introns from RNA-Seq data, discriminating against small genomic deletions...
2017: PloS One
https://www.readbyqxmd.com/read/28515299/a-diverse-range-of-novel-rna-viruses-in-geographically-distinct-honey-bee-populations
#15
Emily J Remnant, Mang Shi, Gabriele Buchmann, Tjeerd Blacquière, Edward C Holmes, Madeleine Beekman, Alyson Ashe
Understanding the diversity and consequences of viruses present in honey bees is critical to maintain pollinator health and manage the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as Deformed wing virus. Previous genomic studies have focused on colonies suffering from Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity...
May 17, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28515293/virus-like-vesicles-of-kaposi-s-sarcoma-associated-herpesvirus-activate-lytic-replication-through-triggering-differentiation-signaling
#16
Danyang Gong, Xinghong Dai, Yuchen Xiao, Yushen Du, Travis J Chapa, Jeffrey R Johnson, Xinmin Li, Nevan J Krogan, Hongyu Deng, Ting-Ting Wu, Ren Sun
Virus-like vesicles (VLVs) are membrane enclosed vesicles that resemble native enveloped viruses in organization, but lack viral capsid and genome. During the productive infection of tumor associated gamma-herpesviruses, both virions and VLVs are produced and released into the extracellular space. However, studies of gamma-herpesvirus associated VLVs have been largely restricted by the technical difficulty of separating VLVs from mature virions. Here, we report a strategy of using a Kaposi's sarcoma-associated herpesvirus (KSHV) mutant defective in small capsid protein, unable to produce mature virions, to selectively isolate VLVs...
May 17, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28515146/transcriptome-of-wheat-inflorescence-development-from-spikelet-initiation-to-floral-patterning
#17
Nan Feng, Gaoyuan Song, Jiantao Guan, Kai Chen, Meiling Jia, Dehua Huang, Jiajie Wu, Lichao Zhang, Xiuying Kong, Shuaifeng Geng, Jun Liu, Aili Li, Long Mao
Early reproductive development in cereals is crucial for final grain number per spike, and hence the yield potential of the crop. To date, however, no systematic analyses of gene expression profiles during this important process have been conducted for common wheat (Triticum aestivum). Here, we studied the transcriptome profiles at four stages of early wheat reproductive development, from spikelet initiation to floral organ differentiation. K-means clustering and stage-specific transcript identification detected dynamically expressed homoeologs of important transcription regulators in spikelet and floral meristems that may be involved in spikelet initiation, floret meristem specification, and floral organ patterning, as inferred from their homologs in model plants...
May 17, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28514744/characterization-of-mouse-serum-exosomal-small-rna-content-the-origins-and-their-roles-in-modulating-inflammatory-response
#18
Xin Zhou, Zinan Jiao, Juling Ji, Shuyuan Li, Xiaodi Huang, Xiaoshuang Lu, Heng Zhao, Jingwen Peng, Xinya Chen, Qiuhong Ji, Yuhua Ji
In the last decade, although studies on exosomal microRNAs (miRNAs) derived from serum and other body fluids have increased dramatically; the contents and biological significance of serum exosomes under normal conditions remain unclear. In the present study, we profiled the small RNA content of mouse serum exosomes (mSEs) using small RNAseq and found that fragments of transfer RNAs (tRNAs) and miRNAs were the two predominant exosomal RNA species, accounting for approximately 60% and 10% of mapped reads, respectively...
April 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28513534/unraveling-prion-protein-interactions-with-aptamers-and-other-prp-binding-nucleic-acids
#19
REVIEW
Bruno Macedo, Yraima Cordeiro
Transmissible spongiform encephalopathies (TSEs) are a group of neurodegenerative disorders that affect humans and other mammals. The etiologic agents common to these diseases are misfolded conformations of the prion protein (PrP). The molecular mechanisms that trigger the structural conversion of the normal cellular PrP (PrP(C)) into the pathogenic conformer (PrP(Sc)) are still poorly understood. It is proposed that a molecular cofactor would act as a catalyst, lowering the activation energy of the conversion process, therefore favoring the transition of PrP(C) to PrP(Sc)...
May 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28512457/the-25-26-nt-small-rnas-in-phytophthora-parasitica-are-associated-with-efficient-silencing-of-homologous-endogenous-genes
#20
Jinbu Jia, Wenqin Lu, Chengcheng Zhong, Ran Zhou, Junjie Xu, Wei Liu, Xiuhong Gou, Qinhu Wang, Junliang Yin, Cheng Xu, Weixing Shan
Small RNAs (sRNAs) are important non-coding RNA regulators, playing key roles in developmental regulation, transposon suppression, environmental response, host-pathogen interaction and other diverse biological processes. However, their roles in oomycetes are poorly understood. Here, we performed sRNA sequencing and RNA sequencing of Phytophthora parasitica at stages of vegetative growth and infection of Arabidopsis roots to examine diversity and function of sRNAs in P. parasitica, a model hemibiotrophic oomycete plant pathogen...
2017: Frontiers in Microbiology
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