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https://www.readbyqxmd.com/read/29156628/-differentially-expressed-trna-derived-small-rnas-co-sediment-primarily-with-non-polysomal-fractions-in-drosophila
#1
Çağdaş Göktaş, Hatice Yiğit, Mehmet İlyas Coşacak, Bünyamin Akgül
Recent studies point to the existence of poorly characterized small regulatory RNAs generated from mRNAs, rRNAs and tRNAs. To explore the subcellular location of tRNA-derived small RNAs, 0-1 and 7-8 h Drosophila embryos were fractionated on sucrose density gradients. Analysis of 12,553,921 deep-sequencing reads from unfractionated and fractionated Drosophila embryos has revealed that tRFs, which are detected mainly from the 5'ends of tRNAs, co-sediment with the non-polysomal fractions. Interestingly, the expression levels of a subset of tRFs change temporally following the maternal-to-zygotic transition in embryos...
November 20, 2017: Genes
https://www.readbyqxmd.com/read/29156625/gene-based-pathogen-detection-can-we-use-qpcr-to-predict-the-outcome-of-diagnostic-metagenomics
#2
Sandra Christine Andersen, Mette Sofie Rousing Fachmann, Kristoffer Kiil, Eva Møller Nielsen, Jeffrey Hoorfar
In microbial food safety, molecular methods such as quantitative PCR (qPCR) and next-generation sequencing (NGS) of bacterial isolates can potentially be replaced by diagnostic shotgun metagenomics. However, the methods for pre-analytical sample preparation are often optimized for qPCR, and do not necessarily perform equally well for qPCR and sequencing. The present study investigates, through screening of methods, whether qPCR can be used as an indicator for the optimization of sample preparation for NGS-based shotgun metagenomics with a diagnostic focus...
November 20, 2017: Genes
https://www.readbyqxmd.com/read/29149093/evolutionarily-distant-streptophyta-respond-differently-to-genotoxic-stress
#3
Radka Vágnerová, Alena Lukešová, Martin Lukeš, Petra Rožnovská, Marcela Holá, Jana Fulnečková, Jiří Fajkus, Karel J Angelis
Research in algae usually focuses on the description and characterization of morpho-and phenotype as a result of adaptation to a particular habitat and its conditions. To better understand the evolution of lineages we characterized responses of filamentous streptophyte green algae of the genera Klebsormidium and Zygnema, and of a land plant-the moss Physcomitrellapatens-to genotoxic stress that might be relevant to their environment. We studied the induction and repair of DNA double strand breaks (DSBs) elicited by the radiomimetic drug bleomycin, DNA single strand breaks (SSB) as consequence of base modification by the alkylation agent methyl methanesulfonate (MMS) and of ultra violet (UV)-induced photo-dimers, because the mode of action of these three genotoxic agents is well understood...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29149087/taxonomic-classification-for-living-organisms-using-convolutional-neural-networks
#4
Saed Khawaldeh, Usama Pervaiz, Mohammed Elsharnoby, Alaa Eddin Alchalabi, Nayel Al-Zubi
Taxonomic classification has a wide-range of applications such as finding out more about evolutionary history. Compared to the estimated number of organisms that nature harbors, humanity does not have a thorough comprehension of to which specific classes they belong. The classification of living organisms can be done in many machine learning techniques. However, in this study, this is performed using convolutional neural networks. Moreover, a DNA encoding technique is incorporated in the algorithm to increase performance and avoid misclassifications...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29149052/flanking-variation-influences-rates-of-stutter-in-simple-repeats
#5
August E Woerner, Jonathan L King, Bruce Budowle
It has been posited that the longest uninterrupted stretch (LUS) of tandem repeats, as defined by the number of exactly matching repeating motif units, is a better predictor of rates of stutter than the parental allele length (PAL). While there are cases where this hypothesis is likely correct, such as the 9.3 allele in the TH01 locus, there can be situations where it may not apply as well. For example, the PAL may capture flanking indel variations while remaining insensitive to polymorphisms in the repeat, and these haplotypic changes may impact the stutter rate...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29149047/new-insights-into-phasmatodea-chromosomes
#6
Thomas Liehr, Olesya Buleu, Tatyana Karamysheva, Alexander Bugrov, Nikolai Rubtsov
Currently, approximately 3000 species of stick insects are known; however, chromosome numbers, which range between 21 and 88, are known for only a few of these insects. Also, centromere banding staining (C-banding) patterns were described for fewer than 10 species, and fluorescence in situ hybridization (FISH) was applied exclusively in two Leptynia species. Interestingly, 10-25% of stick insects (Phasmatodea) are obligatory or facultative parthenogenetic. As clonal and/or bisexual reproduction can affect chromosomal evolution, stick insect karyotypes need to be studied more intensely...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29149041/the-hmga1-pseudogene-7-induces-mir-483-and-mir-675-upregulation-by-activating-egr1-through-a-cerna-mechanism
#7
Marco De Martino, Giuseppe Palma, Amalia Azzariti, Claudio Arra, Alfredo Fusco, Francesco Esposito
Several studies have established that pseudogene mRNAs can work as competing endogenous RNAs and, when deregulated, play a key role in the onset of human neoplasias. Recently, we have isolated two HMGA1 pseudogenes, HMGA1P6 and HMGA1P7. These pseudogenes have a critical role in cancer progression, acting as micro RNA (miRNA) sponges for HMGA1 and other cancer-related genes. HMGA1 pseudogenes were found overexpressed in several human carcinomas, and their expression levels positively correlate with an advanced cancer stage and a poor prognosis...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29149037/development-of-novel-polymorphic-est-ssr-markers-in-bailinggu-pleurotus-tuoliensis-for-crossbreeding
#8
Yueting Dai, Wenying Su, Chentao Yang, Bing Song, Yu Li, Yongping Fu
Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu). However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR) markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29149036/identification-of-the-caprine-keratin-associated-protein-20-2-kap20-2-gene-and-its-effect-on-cashmere-traits
#9
Jiqing Wang, Longjie Che, Jon G H Hickford, Huitong Zhou, Zhiyun Hao, Yuzhu Luo, Jiang Hu, Xiu Liu, Shaobin Li
The gene encoding the high glycine/tyrosine keratin-associated protein 20-2 (KAP20-2) gene has been described in humans, but has not been identified in any livestock species. A search for similar sequences in the caprine genome using the human KAP20-2 gene (KRTAP20-2) revealed a homologous sequence on chromosome 1. Three different banding patterns representing distinct sequences (A-C) in Longdong cashmere goats were identified using polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) analysis...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29144427/the-chloroplast-genome-of-symplocarpus-renifolius-a-comparison-of-chloroplast-genome-structure-in-araceae
#10
Kyoung Su Choi, Kyu Tae Park, SeonJoo Park
Symplocarpus renifolius is a member of Araceae family that is extraordinarily diverse in appearance. Previous studies on chloroplast genomes in Araceae were focused on duckweeds (Lemnoideae) and root crops (Colocasia, commonly known as taro). Here, we determined the chloroplast genome of Symplocarpus renifolius and compared the factors, such as genes and inverted repeat (IR) junctions and performed phylogenetic analysis using other Araceae species. The chloroplast genome of S. renifolius is 158,521 bp and includes 113 genes...
November 16, 2017: Genes
https://www.readbyqxmd.com/read/29137177/comprehensive-profiling-of-lincrnas-in-lung-adenocarcinoma-of-never-smokers-reveals-their-roles-in-cancer-development-and-prognosis
#11
Ying Li, Zheng Wang, Asha Nair, Wei Song, Ping Yang, Xiaoju Zhang, Zhifu Sun
Long intergenic non-coding RNA (lincRNA) is a family of gene transcripts, the functions of which are largely unknown. Although cigarette smoking is the main cause for lung cancer, lung cancer in non-smokers is a separate entity and its underlying cause is little known. Growing evidence suggests lincRNAs play a significant role in cancer development and progression; however, such data is lacking for lung cancer in non-smokers, or those who have never smoked. This study conducted comprehensive profiling of lincRNAs from RNA sequencing (RNA-seq) data of non-smoker patients with lung adenocarcinoma...
November 13, 2017: Genes
https://www.readbyqxmd.com/read/29137168/origin-and-evolution-of-the-neo-sex-chromosomes-in-pamphagidae-grasshoppers-through-chromosome-fusion-and-following-heteromorphization
#12
Ilyas Yerkinovich Jetybayev, Alexander Gennadievich Bugrov, Olesya Georgievna Buleu, Anton Gennadievich Bogomolov, Nikolay Borisovich Rubtsov
In most phylogenetic lineages, the evolution of sex chromosomes is accompanied by their heteromorphization and degradation of one of them. The neo-sex chromosomes are useful model for studying early stages of these processes. Recently two lineages of the neo-sex chromosomes on different stages of heteromorphization was discovered in Pamphagidae family. The neo-sex chromosome heteromorphization was analyzed by generation of DNA probes derived from the neo-Xs and neo-Ys followed with chromosome painting in nineteen species of Pamphagidae family...
November 13, 2017: Genes
https://www.readbyqxmd.com/read/29137167/transmission-dynamics-of-hiv-1-drug-resistance-among-treatment-na%C3%A3-ve-individuals-in-greece-the-added-value-of-molecular-epidemiology-to-public-health
#13
Dimitrios Paraskevis, Evangelia Kostaki, Panagiotis Gargalianos, Georgios Xylomenos, Marios Lazanas, Maria Chini, Athanasios Skoutelis, Vasileios Papastamopoulos, Dimitra Paraskeva, Anastasia Antoniadou, Antonios Papadopoulos, Mina Psichogiou, Georgios L Daikos, Georgios Chrysos, Vasileios Paparizos, Sofia Kourkounti, Helen Sambatakou, Nikolaos V Sipsas, Malvina Lada, Periklis Panagopoulos, Efstratios Maltezos, Stylianos Drimis, Angelos Hatzakis
The presence of human immunodeficiency virus type 1 (HIV-1) drug resistance among drug-naïve patients remains stable, although the proportion of patients with virological failure to therapy is decreasing. The dynamics of transmitted resistance among drug-naïve patients remains largely unknown. The prevalence of non-nucleoside reverse transcriptase inhibitors (NNRTI) resistance was 16.9% among treatment-naïve individuals in Greece. We aimed to investigate the transmission dynamics and the effective reproductive number (Re) of the locally transmitted NNRTI resistance...
November 13, 2017: Genes
https://www.readbyqxmd.com/read/29125590/novel-insights-into-antiviral-gene-regulation-of-red-swamp-crayfish-procambarus-clarkii-infected-with-white-spot-syndrome-virus
#14
Shaokui Yi, Yanhe Li, Linlin Shi, Long Zhang
White spot syndrome virus (WSSV), one of the major pathogens of Procambarus clarkii, has caused severe disruption to the aquaculture industry of P. clarkii in China. To reveal the gene regulatory mechanisms underlying WSSV infection, a comparative transcriptome analysis was performed among WSSV-infected susceptible individuals (GS), viral resistant individuals (GR), and a non-infected control group (GC). A total of 61,349 unigenes were assembled from nine libraries. Subsequently, 515 and 1033 unigenes exhibited significant differential expression in sensitive and resistant crayfish individuals compared to the control group (GC)...
November 10, 2017: Genes
https://www.readbyqxmd.com/read/29125589/human-organ-tissue-identification-by-targeted-rna-deep-sequencing-to-aid-the-investigation-of-traumatic-injury
#15
Erin Hanson, Jack Ballantyne
Molecular analysis of the RNA transcriptome from a putative tissue fragment should permit the assignment of its source to a specific organ, since each will exhibit a unique pattern of gene expression. Determination of the organ source of tissues from crime scenes may aid in shootings and other investigations. We have developed a prototype massively parallel sequencing (MPS) mRNA profiling assay for organ tissue identification that is designed to definitively identify 10 organ/tissue types using a targeted panel of 46 mRNA biomarkers...
November 10, 2017: Genes
https://www.readbyqxmd.com/read/29125582/next-generation-sequencing-of-chromosome-specific-libraries-sheds-light-on-genome-evolution-in-paleotetraploid-sterlet-acipenser-ruthenus
#16
Daria A Andreyushkova, Alexey I Makunin, Violetta R Beklemisheva, Svetlana A Romanenko, Anna S Druzhkova, Larisa B Biltueva, Natalya A Serdyukova, Alexander S Graphodatsky, Vladimir A Trifonov
Several whole genome duplication (WGD) events followed by rediploidization took place in the evolutionary history of vertebrates. Acipenserids represent a convenient model group for investigation of the consequences of WGD as their representatives underwent additional WGD events in different lineages resulting in ploidy level variation between species, and these processes are still ongoing. Earlier, we obtained a set of sterlet (Acipenser ruthenus) chromosome-specific libraries by microdissection and revealed that they painted two or four pairs of whole sterlet chromosomes, as well as additional chromosomal regions, depending on rediploidization status and chromosomal rearrangements after genome duplication...
November 10, 2017: Genes
https://www.readbyqxmd.com/read/29125533/sequencing-and-de-novo-assembly-of-the-toxicodendron-radicans-poison-ivy-transcriptome
#17
Alexandra J Weisberg, Gunjune Kim, James H Westwood, John G Jelesko
Contact with poison ivy plants is widely dreaded because they produce a natural product called urushiol that is responsible for allergenic contact delayed-dermatitis symptoms lasting for weeks. For this reason, the catchphrase most associated with poison ivy is "leaves of three, let it be", which serves the purpose of both identification and an appeal for avoidance. Ironically, despite this notoriety, there is a dearth of specific knowledge about nearly all other aspects of poison ivy physiology and ecology...
November 10, 2017: Genes
https://www.readbyqxmd.com/read/29120399/a-microbiomic-analysis-in-african-americans-with-colonic-lesions-reveals-streptococcus-sp-vt162-as-a-marker-of-neoplastic-transformation
#18
Hassan Brim, Shibu Yooseph, Edward Lee, Zaki Sherif, Muneer Abbas, Adeyinka O Laiyemo, Sudhir Varma, Manolito Torralba, Scot E Dowd, Karen E Nelson, Wimal Pathmasiri, Susan Sumner, Willem de Vos, Qiaoyi Liang, Jun Yu, Erwin Zoetendal, Hassan Ashktorab
Increasing evidence suggests a role of the gut microbiota in colorectal carcinogenesis (CRC). To detect bacterial markers of colorectal cancer in African Americans a metabolomic analysis was performed on fecal water extracts. DNA from stool samples of adenoma and healthy subjects and from colon cancer and matched normal tissues was analyzed to determine the microbiota composition (using 16S rDNA) and genomic content (metagenomics). Metagenomic functions with discriminative power between healthy and neoplastic specimens were established...
November 9, 2017: Genes
https://www.readbyqxmd.com/read/29120392/impact-of-lateral-transfers-on-the-genomes-of-lepidoptera
#19
REVIEW
Jean-Michel Drezen, Thibaut Josse, Annie Bézier, Jérémy Gauthier, Elisabeth Huguet, Elisabeth Anne Herniou
Transfer of DNA sequences between species regardless of their evolutionary distance is very common in bacteria, but evidence that horizontal gene transfer (HGT) also occurs in multicellular organisms has been accumulating in the past few years. The actual extent of this phenomenon is underestimated due to frequent sequence filtering of "alien" DNA before genome assembly. However, recent studies based on genome sequencing have revealed, and experimentally verified, the presence of foreign DNA sequences in the genetic material of several species of Lepidoptera...
November 9, 2017: Genes
https://www.readbyqxmd.com/read/29120386/high-quality-unigenes-and-microsatellite-markers-from-tissue-specific-transcriptome-and-development-of-a-database-in-clusterbean-cyamopsis-tetragonoloba-l-taub
#20
Hukam C Rawal, Shrawan Kumar, Amitha Mithra S V, Amolkumar U Solanke, Deepti Nigam, Swati Saxena, Anshika Tyagi, Sureshkumar V, Neelam R Yadav, Pritam Kalia, Narendra Pratap Singh, Nagendra Kumar Singh, Tilak Raj Sharma, Kishor Gaikwad
Clusterbean (Cyamopsis tetragonoloba L. Taub), is an important industrial, vegetable and forage crop. This crop owes its commercial importance to the presence of guar gum (galactomannans) in its endosperm which is used as a lubricant in a range of industries. Despite its relevance to agriculture and industry, genomic resources available in this crop are limited. Therefore, the present study was undertaken to generate RNA-Seq based transcriptome from leaf, shoot, and flower tissues. A total of 145 million high quality Illumina reads were assembled using Trinity into 127,706 transcripts and 48,007 non-redundant high quality (HQ) unigenes...
November 9, 2017: Genes
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