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Reyna Cristina Colli-Dula, Xiefan Fang, David Moraga-Amador, Nacira Albornoz-Abud, Roberto Zamora-Bustillos, Ana Conesa, Omar Zapata-Perez, Diego Moreno, Emanuel Hernandez-Nuñez
Despite a wide number of toxicological studies that describe benzo[a]pyrene (BaP) effects, the metabolic mechanisms that underlie these effects in fish are largely unknown. Of great concern is the presence of BaP in aquatic systems, especially those in close proximity to human activity leading to consumption of potentially contaminated foods. BaP is a known carcinogen and it has been reported to have adverse effects on the survival, development and reproduction of fish. The purpose of this study was to investigate if a low dose of BaP can alter genes and key metabolic pathways in the liver and testis in male adult tilapia, and whether these could be associated with biological endpoints disruption...
June 8, 2018: Aquatic Toxicology
Sapna Badhan, Pravas Kole, Andrew Ball, Nitin Mantri
Chickpea (Cicer arietinum L.) is the second most important winter crop which is consumed globally due to its high nutritional value. Chickpea as one of the leguminous crop is important in crop rotation with cereal crops like wheat and barley. The main constraints for chickpea production are abiotic stresses such as drought, salinity, and heat. Among these, drought is a major cause of the decline in chickpea production in worldwide. Studies conducted so far have provided a limited insight into different genetic pathways associated with drought tolerance/response...
June 13, 2018: Plant Physiology and Biochemistry: PPB
Andrew J Fisher, Peter A Beal
All messenger RNAs in eukaryotes are modified co-transcriptionally and post-transcriptionally. They are all capped at the 5'-end and polyadenylated at the 3'-end. However, many mRNAs are also found to be chemically modified internally for regulation of mRNA processing, translation, stability, and to recode the message. This review will briefly summarize the structural basis for formation of the two most common modifications found at internal sites in mRNAs; methylation and deamination. The structures of the enzymes that catalyze these modifications show structural similarity to other family members within each modifying enzyme class...
June 15, 2018: Current Opinion in Structural Biology
Georg Mohr, Sean Yoon-Seo Kang, Seung Kuk Park, Yidan Qin, Jacob Grohman, Jun Yao, Jennifer L Stamos, Alan M Lambowitz
The thermostable Geobacillus stearothermophilus GsI-IIC intron is among the few bacterial group II introns found to proliferate to high copy number in its host genome. Here, we developed a bacterial genetic assay for retrohoming and biochemical assays for protein-dependent and self-splicing of GsI-IIC. We found that GsI-IIC, like other group IIC introns, retrohomes into sites having a 5'-exon DNA hairpin, typically from a bacterial transcription terminator, followed by short intron-binding sequences (IBSs) recognized by base pairing of exon-binding sequences (EBSs) in the intron RNA...
June 15, 2018: Journal of Molecular Biology
Romuald Loutre, Anne-Marie Heckel, Damien Jeandard, Ivan Tarassov, Nina Entelis
Mutations in mitochondrial DNA are an important source of severe and incurable human diseases. The vast majority of these mutations are heteroplasmic, meaning that mutant and wild-type genomes are present simultaneously in the same cell. Only a very high proportion of mutant mitochondrial DNA (heteroplasmy level) leads to pathological consequences. We previously demonstrated that mitochondrial targeting of small RNAs designed to anneal with mutant mtDNA can decrease the heteroplasmy level by specific inhibition of mutant mtDNA replication, thus representing a potential therapy...
2018: PloS One
Constanza P Silva, William J Horton, Michael J Caruso, Aswathy Sebastian, Laura C Klein, Istvan Albert, Helen M Kamens
Nicotine and alcohol are often co-abused. Adolescence is a vulnerable period for the initiation of both nicotine and alcohol use, which can lead to subsequent neurodevelopmental and behavioral alterations. It is possible that during this vulnerable period, use of one drug leads to neurobiological alterations that affect subsequent consumption of the other drug. The aim of the present study was to determine the effect of nicotine exposure during adolescence on ethanol intake, and the effect of these substances on brain gene expression...
2018: PloS One
Lilian Motta Cantanhêde, Flavia Gonçalves Fernandes, Gabriel Eduardo Melim Ferreira, Renato Porrozzi, Ricardo de Godoi Mattos Ferreira, Elisa Cupolillo
Cutaneous leishmaniasis is a neglected parasitic disease that manifests in infected individuals under different phenotypes, with a range of factors contributing to its broad clinical spectrum. One factor, Leishmania RNA Virus 1 (LRV1), has been described as an endosymbiont present in different species of Leishmania. LRV1 significantly worsens the lesion, exacerbating the immune response in both experimentally infected animals and infected individuals. Little is known about the composition and genetic diversity of these viruses...
2018: PloS One
Brendan C Dickson, Cristina R Antonescu, Prokopios P Argyris, Elizabeth A Bilodeau, Martin J Bullock, Paul D Freedman, Douglas R Gnepp, Richard C Jordan, Ioannis G Koutlas, Cheng-Han Lee, Iona Leong, Mihai Merzianu, Bibianna M Purgina, Lester D R Thompson, Bret Wehrli, John M Wright, David Swanson, Lei Zhang, Justin A Bishop
Ectomesenchymal chondromyxoid tumor is a rare and benign neoplasm with a predilection for the anterior dorsal tongue. Despite morphologic heterogeneity, most cases are characterized by a proliferation of bland spindle cells with a distinctive reticular growth pattern and myxoid stroma. The immunophenotype of these neoplasms is likewise variable; most cases express glial fibrillary acid protein and S100 protein, with inconsistent reports of keratin and myoid marker expression. The molecular pathogenesis is poorly understood; however, a subset of cases has been reported to harbor EWSR1 gene rearrangement...
June 15, 2018: American Journal of Surgical Pathology
Ana Saksida, Nina Jakopin, Mateja Jelovšek, Nataša Knap, Luka Fajs, Lara Lusa, Stanka Lotrič-Furlan, Petra Bogovič, Maja Arnež, Franc Strle, Tatjana Avšič-Županc
We determined levels of tick-borne encephalitis (TBE) virus (TBEV) RNA in serum samples obtained from 80 patients during the initial phase of TBE in Slovenia. For most samples, levels were within the range of 3-6 log10 copies RNA/mL. Levels were higher in female patients than in male patients, but we found no association between virus load and several laboratory and clinical parameters, including severity of TBE. However, a weak humoral immune response was associated with a more severe disease course, suggesting that inefficient clearance of virus results in a more serious illness...
July 2018: Emerging Infectious Diseases
Charlotte Capitanchik, Charles Dixon, Selene K Swanson, Laurence Florens, Alastair R W Kerr, Eric C Schirmer
Nuclear envelopathies/laminopathies yield tissue-specific pathologies, yet arise from mutation of ubiquitously-expressed genes. One possible explanation of this tissue specificity is that tissue-specific partners become disrupted from larger complexes, but a little investigated alternate hypothesis is that the mutated proteins themselves have tissue-specific splice variants. Here, we analyze RNA-Seq datasets to identify muscle-specific splice variants of nuclear envelope genes that could be relevant to the study of laminopathies, particularly muscular dystrophies, that are not currently annotated in sequence databases...
June 18, 2018: Nucleus
Cuiling Lu, Hongbin Chi, Yapeng Wang, Xue Feng, Lina Wang, Shuo Huang, Liying Yan, Shengli Lin, Ping Liu, Jie Qiao
In an attempt to explore the early developmental arrest in embryos from polycystic ovarian syndrome (PCOS) patients, we sequenced the transcriptome profiles of PCOS arrested 2-cell embryos, non-PCOS arrested 2-cell embryos and non-arrested 2-cell embryos using single-cell RNA-Seq technique. Differential expression analysis was performed using the DEGSeq R package. Gene Ontology (GO) enrichment was analyzed using the GOseq R package. Data revealed 62 differentially expressed genes between non-PCOS arrested and PCOS arrested embryos and 2217 differentially expressed genes between PCOS arrested and non-arrested 2-cell embryos...
June 18, 2018: Cell Cycle
Antti Häkkinen, Amjad Alkodsi, Chiara Facciotto, Kaiyang Zhang, Katja Kaipio, Sirpa Leppä, Olli Carpén, Seija Grénman, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Motivation: DNA methylation aberrations are common in many cancer types. A major challenge hindering comparison of patient-derived samples is that they comprise of heterogeneous collection of cancer and microenvironment cells. We present a computational method that allows comparing cancer methylomes in two or more heterogeneous tumor samples featuring differing, unknown fraction of cancer cells. The method is unique in that it allows comparison also in the absence of normal cell control samples and without prior tumor purity estimates, as these are often unavailable or unreliable in clinical samples...
April 18, 2018: Bioinformatics
Joana Pereira, Andrei N Lupas
Motivation: The direct ancestor of the DNA-protein world of today is considered to have been an RNA-peptide world, in which peptides were co-factors of RNA-mediated catalysis and replication. Evidence for these ancestral peptides, from which folded proteins evolved, can be derived even today from regions of local sequence similarity within globally dissimilar folds. One of these is the 45-residue motif common to both folds of the hnRNP K homology (KH) domain. Results: In a survey of KH domains, we found a third fold that contains the KH motif at its core...
June 15, 2018: Bioinformatics
Dilip A Durai, Marcel H Schulz
Motivation: De Bruijn graphs are a common assembly data structure for sequencing datasets. But with the advances in sequencing technologies, assembling high coverage datasets has become a computational challenge. Read normalization, which removes redundancy in datasets, is widely applied to reduce resource requirements. Current normalization algorithms, though efficient, provide no guarantee to preserve important k-mers that form connections between regions in the graph. Results: Here, normalization is phrased as a set multi-cover problem on reads and a heuristic algorithm, ORNA, is proposed...
April 18, 2018: Bioinformatics
Caitlin E Moss, Andrew Robson, Erol Fikrig, Sukanya Narasimhan
Infectious diseases transmitted by arthropod vectors continue to pose a significant threat to human health worldwide. The pathogens causing these diseases, do not exist in isolation when they colonize the vector; rather, they likely engage in interactions with resident microorganisms in the gut lumen. The vector microbiota has been demonstrated to play an important role in pathogen transmission for several vector-borne diseases. Whether resident bacteria in the gut of the Ixodes scapularis tick, the vector of several human pathogens including Borrelia burgdorferi, influence tick transmission of pathogens is not determined...
June 1, 2018: Journal of Visualized Experiments: JoVE
D Brenda Salantes, Yu Zheng, Felicity Mampe, Tuhina Srivastava, Subul Beg, Jun Lai, Jonathan Z Li, Randall L Tressler, Richard A Koup, James Hoxie, Mohamed Abdel-Mohsen, Scott Sherrill-Mix, Kevin McCormick, E Turner Overton, Frederic D Bushman, Gerald H Learn, Robert F Siliciano, Janet M Siliciano, Pablo Tebas, Katharine J Bar
BACKGROUND: The effect of a brief analytical treatment interruption (ATI) on the HIV-1 latent reservoir of individuals who initiate antiretroviral therapy (ART) during chronic infection is unknown. METHODS: We evaluated the impact of transient viremia on the latent reservoir in participants who underwent an ATI and at least 6 months of subsequent viral suppression in a clinical trial testing the effect of passive infusion of the broadly neutralizing Ab VRC01 during ATI...
June 18, 2018: Journal of Clinical Investigation
Aminallah Tahmasebi, Alireza Afsharifar, Ahmad Heydari, Mohammad Mehrabadi
The cysteine-rich 8K protein of Potato mop-top virus (PMTV) suppresses host RNA silencing. In this study, evolutionary analysis of 8K sequences of PMTV isolates was studied on the basis of nucleotide and amino acid sequences. Twenty-one positively selected sites were identified in 8K coding regions. Recombination events were found in the 8K of PMTV isolates with a rate of 1.8. Totally 30 haplotypes were detected with haplotype diversity ranging from 0.8 to 1.0 and nucleotide diversity from 7.58 to 13.62. The positions 33 and 30 indicated the highly positive and negative selection (with the highest and the lowest dN-dS values), respectively...
March 2018: Molecular Biology Research Communications
Robert Edgar
Sequencing of the 16S ribosomal RNA (rRNA) gene is widely used to survey microbial communities. Specialized 16S rRNA databases have been developed to support this approach including Greengenes, RDP and SILVA. Most taxonomy annotations in these databases are predictions from sequence rather than authoritative assignments based on studies of type strains or isolates. In this work, I investigated the taxonomy annotations and guide trees provided by these databases. Using a blinded test, I estimated that the annotation error rate of the RDP database is ∼10%...
2018: PeerJ
Ge-Min Fang, Jasmine Chamiolo, Svenja Kankowski, Felix Hövelmann, Dhana Friedrich, Alexander Löwer, Jochen C Meier, Oliver Seitz
Oligonucleotide probes that show enhanced fluorescence upon nucleic acid hybridization enable the detection and visualization of specific mRNA molecules, in vitro and in cellulo . A challenging problem is the analysis of single nucleotide alterations that occur, for example, when cellular mRNA is subject to C → U editing. Given the length required for uniqueness of the targeted segment, the commonly used probes do not provide the level of sequence specificity needed to discriminate single base mismatched hybridization...
June 7, 2018: Chemical Science
Arjan P Palstra, Jeroen Kals, Ainhoa Blanco Garcia, Ron P Dirks, Marnix Poelman
Seaweeds may represent immuno-stimulants that could be used as health-promoting fish feed components. This study was performed to gain insights into the immunomodulatory effects of dietary seaweeds in Atlantic salmon. Specifically tested were 10% inclusion levels of Laminaria digitata (SW1) and a commercial blend of seaweeds (Oceanfeed® ) (SW2) against a fishmeal based control diet (FMC). Differences between groups were assessed in growth, feed conversion ratio and blood parameters hematocrit and hemoglobin...
2018: Frontiers in Physiology
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