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Juan Manuel Vazquez, Michael Sulak, Sravanthi Chigurupati, Vincent J Lynch
Large-bodied organisms have more cells that can potentially turn cancerous than small-bodied organisms, imposing an increased risk of developing cancer. This expectation predicts a positive correlation between body size and cancer risk; however, there is no correlation between body size and cancer risk across species ("Peto's paradox"). Here, we show that elephants and their extinct relatives (proboscideans) may have resolved Peto's paradox in part through refunctionalizing a leukemia inhibitory factor pseudogene (LIF6) with pro-apoptotic functions...
August 14, 2018: Cell Reports
Anastasia M Sorokina, Michael Saul, Tassia M Goncalves, Joseph V Gogola, Petra Majdak, Sandra L Rodriguez-Zas, Justin S Rhodes
Despite the prevalence and high heritability of Attention-Deficit/Hyperactivity Disorder (ADHD), genetic etiology remains elusive. Clinical evidence points in part to reduced function of the striatum, but which specific genes are differentially expressed and how they sculpt striatal physiology to predispose ADHD are not well understood. As an exploratory tool, a polygenic mouse model of ADHD was recently developed through selective breeding for high home cage activity. Relative to the Control line, the High-Active line displays hyperactivity and motor impulsivity which are ameliorated with amphetamine...
2018: PloS One
Jelle Slager, Rieza Aprianto, Jan-Willem Veening
A precise understanding of the genomic organization into transcriptional units and their regulation is essential for our comprehension of opportunistic human pathogens and how they cause disease. Using single-molecule real-time (PacBio) sequencing we unambiguously determined the genome sequence of Streptococcus pneumoniae strain D39 and revealed several inversions previously undetected by short-read sequencing. Significantly, a chromosomal inversion results in antigenic variation of PhtD, an important surface-exposed virulence factor...
August 13, 2018: Nucleic Acids Research
Alexey I Makunin, Svetlana A Romanenko, Violetta R Beklemisheva, Polina L Perelman, Anna S Druzhkova, Kristina O Petrova, Dmitry Yu Prokopov, Ekaterina N Chernyaeva, Jennifer L Johnson, Anna V Kukekova, Fengtang Yang, Malcolm A Ferguson-Smith, Alexander S Graphodatsky, Vladimir A Trifonov
B chromosomes (Bs) represent a variable addition to the main karyotype in some lineages of animals and plants. Bs accumulate through non-Mendelian inheritance and become widespread in populations. Despite the presence of multiple genes, most Bs lack specific phenotypic effects, although their influence on host genome epigenetic status and gene expression are recorded. Previously, using sequencing of isolated Bs of ruminants and rodents, we demonstrated that Bs originate as segmental duplications of specific genomic regions, and subsequently experience pseudogenization and repeat accumulation...
August 10, 2018: Genes
Xiaoyan Zhao, Qian Zhou, Liangqi Cai, Zijun Zhao, Linglin Zhang, Peiru Wang, Guolong Zhang
OBJECTIVE: To detect mutations of the NF1 gene in two sporadic cases with neurofibromatosis type 1 (NF1) and explore their molecular mechanisms. METHODS: Clinical data of the two patients was collected. Genomic DNA was extracted from peripheral blood samples. Specific primers were designed to exclude pseudogenes. PCR was performed to amplify all coding exons of the NF1 gene. PCR products were directly sequenced. RESULTS: Two novel mutations of the NF1 gene (c...
August 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Dagmara McGuinness, Suhaib Mohammed, Laura Monaghan, Paul A Wilson, David B Kingsmore, Oliver Shapter, Karen S Stevenson, Shana M Coley, Luke Devey, Robert B Kirkpatrick, Paul G Shiels
Chronic kidney disease and associated comorbidities (diabetes, cardiovascular diseases) manifest with an accelerated ageing phenotype, leading ultimately to organ failure and renal replacement therapy. This process can be modulated by epigenetic and environmental factors which promote loss of physiological function and resilience to stress earlier, linking biological age with adverse outcomes post-transplantation including delayed graft function (DGF). The molecular features underpinning this have yet to be fully elucidated...
August 9, 2018: Aging Cell
Gregory D Sloop, Gheorghe Pop, Joseph J Weidman, John A St Cyr
Apolipoprotein(a) [apo(a)] is an apolipoprotein unique to lipoprotein(a) [Lp(a)]. Although it has no known function, Lp(a) is a risk factor for accelerated atherothrombosis. We hypothesize that LPA, the gene which encodes apo(a), is a heretofore unrecognized unprocessed pseudogene created by duplication of PLG, the gene which encodes plasminogen. Unprocessed pseudogenes are genes which were created by duplication of functional genes and subsequently lost function after acquiring various mutations. This hypothesis explains many of the unusual features of Lp(a) and apo(a)...
May 31, 2018: Curēus
Yanxia Sun, Michael J Moore, Jacob B Landis, Nan Lin, Li Chen, Tao Deng, Jianwen Zhang, Aiping Meng, Shoujun Zhang, Omiljon Sh Tojibaev, Hang Sun, Hengchang Wang
The relationships among the genera of the early-diverging eudicot family Berberidaceae have long been controversial. To resolve these relationships and to better understand plastome evolution within the family, we sequenced the complete plastome sequences of ten Berberidaceae genera, combined these with six existing plastomes for the family, and conducted a series of phylogenomic analyses on the resulting data set. Five of the newly sequenced plastomes were found to possess the typical angiosperm plastome complement of 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes...
August 1, 2018: Molecular Phylogenetics and Evolution
Xinling Hu, Liu Yang, Yin-Yuan Mo
Functional genomics has provided evidence that the human genome transcribes a large number of non-coding genes in addition to protein-coding genes, including microRNAs and long non-coding RNAs (lncRNAs). Among the group of lncRNAs are pseudogenes that have not been paid attention in the past, compared to other members of lncRNAs. However, increasing evidence points the important role of pseudogenes in diverse cellular functions, and dysregulation of pseudogenes are often associated with various human diseases including cancer...
August 1, 2018: Cancers
Liang Feng, Hui Liu, Dandan Cheng, Xumei Mao, Yan Wang, Zhen Wu, Qiong Wu
A bacterium capable of utilizing dimethyl phthalate (DMP), diethyl phthalate (DEP), di- n -butyl phthalate (DBP), and diisobuthyl phthalate (DIBP) as the sole carbon and energy source was isolated from shallow aquifer sediments. The strain was identified as Sphingobium yanoikuyae SHJ based on morphological characteristics, 16S rDNA gene phylogeny, and whole genome average nucleotide identity (ANI). The degradation half-life of DBP with substrate concentration of 8.5 and 50.0 mg/L by strain SHJ was 99.7 and 101...
2018: BioMed Research International
Brian Li, Sonal Kaushik, Pola Kalinowski, BaRun Kim, Cynthia Gershome, Joyce Ching, Damon Poburko
Absolute quantification of mitochondrial DNA copy number (mCN) provides important insights in many fields of research including cancer, cardiovascular and reproductive health. Droplet digital PCR (ddPCR) natively reports absolute copy number, and we have developed a single-dye, multiplex assay to measure rat mCN that is accurate, precise and affordable. We demonstrate simple methods to optimize this assay and to determine nuclear reference pseudogene copy number to extend the range of mCN that can be measured with this assay...
July 30, 2018: Scientific Reports
Kelly Kries, Marília A S Barros, Gwen Duytschaever, Joseph D Orkin, Mareike C Janiak, Daniel M A Pessoa, Amanda D Melin
Bats are a diverse radiation of mammals of enduring interest for understanding the evolution of sensory specialization. Colour vision variation among species has previously been linked to roosting preferences and echolocation form in the suborder Yinpterochiroptera, yet questions remain about the roles of diet and habitat in shaping bat visual ecology. We sequenced OPN1SW and OPN1LW opsin genes for 20 species of leaf-nosed bats (family Phyllostomidae; suborder Yangochiroptera) with diverse roosting and dietary ecologies, along with one vespertilionid species (Myotis lavali)...
July 30, 2018: Molecular Ecology
Min Yang, Xiaoyu Kong, Wei Shi, Li Gong, Hairong Luo, Baosheng Wu
Highly conserved 18S rDNA sequences encode ribosomal RNA and evolve in a concerted manner. In this study, 178 sequences of 18S rDNA from the ridge-eyed flounder, Pleuronichthys cornutus, were analyzed. The total sequences yielded five distinguishable types of 18S rDNA-A, B, R, S, and L-that were defined based on sequence alignments, clone clustering, and recombination detection. The length of 176 clones ranged from 1838 bp to 1846 bp, with one particularly short clone reaching only 1466 bp and one long clone reaching up to1869 bp...
July 25, 2018: Gene
Alessandra Allione, Barbara Pardini, Clara Viberti, Giuliana Giribaldi, Stefano Turini, Cornelia Di Gaetano, Simonetta Guarrera, Francesca Cordero, Marco Oderda, Marco Allasia, Paolo Gontero, Carlotta Sacerdote, Paolo Vineis, Giuseppe Matullo
Urothelial bladder cancer (UBC) represents a public health problem because of its high incidence/relapse rates. At present, there are no suitable biomarkers for early diagnosis or relapse/progression prognosis. To improve diagnostic accuracy and overcome the disadvantages of current diagnostic strategies, the detection of UBC biomarkers in easily accessible biofluids, such as urine, represents a promising approach compared to painful biopsies.We investigated the levels of MMP23 genes (microarray and qPCR) and protein (Western Blot and ELISA) in a set of samples (blood, plasma and urine) from UBC patients and controls as biomarkers for this cancer...
July 20, 2018: Carcinogenesis
Marin M Jukic, Volker M Lauschke, Takahiro Saito, Masahiro Hiratsuka, Magnus Ingelman-Sundberg
The ultrarapid CYP2D6 metabolizer (UM) phenotype is caused by CYP2D6 gene duplications in some, but not all, UM individuals. CYP2D6 and the adjacent pseudogene CYP2D7 are highly homologous; however, CYP2D7 harbors a premature stop codon, which is absent in carriers of the rare CYP2D7 variant rs530303678. We addressed whether rs530303678 could generate a functionally active protein, causing the UM phenotype. However, unlike CYP2D6 variants, two CYP2D7 rs530303678 variant isoforms, previously described in liver, showed neither significant protein expression nor catalytic activity toward the CYP2D6 substrates bufuralol or dextromethorphan...
August 1, 2018: Pharmacogenomics
Xinlian Chen, Jianguo Zhou, Yingxian Cui, Yu Wang, Baozhong Duan, Hui Yao
More than 30 Ligularia Cass. (Asteraceae) species have long been used in folk medicine in China. Morphological features and common DNA regions are both not ideal to identify Ligularia species. As some Ligularia species contain pyrrolizidine alkaloids, which are hazardous to human and animal health and are involved in metabolic toxification in the liver, it is important to find a better way to distinguish these species. Here, we report complete chloroplast (CP) genomes of six Ligularia species, L. intermedia , L...
2018: Frontiers in Pharmacology
Rebecca Johnson, Elli Mylona, Gad Frankel
Although nontyphoidal Salmonella (NTS; including Salmonella Typhimurium) mainly cause gastroenteritis, typhoidal serovars (Salmonella Typhi and Salmonella Paratyphi A) cause typhoid fever, the treatment of which is threatened by increasing drug resistance. Our understanding of S. Typhi infection in human remains poorly understood, likely due to the host restriction of typhoidal strains and the subsequent popularity of the S. Typhimurium mouse typhoid model. However, translating findings with S. Typhimurium across to S...
July 21, 2018: Cellular Microbiology
Diego Felipe Alves Batista, Oliveiro Caetano de Freitas Neto, Adriana Maria de Almeida, Grazieli Maboni, Tatiane Furtado de Carvalho, Thaynara Parente de Carvalho, Paul Andrew Barrow, Angelo Berchieri
The diseases caused by Salmonella Gallinarum and S. Pullorum in chickens known as fowl typhoid and pullorum disease, respectively, pose a great threat to the poultry industry mainly in developing countries, since they have already been controlled in the developed ones. These bacteria are very similar at the genomic level but develop distinct host-pathogen relationships with chickens. Therefore, a deep understanding of the molecular mechanisms whereby S. Gallinarum and S. Pullorum interact with the host could lead to the development of new approaches to control and, perhaps, eradicate both diseases from the chicken flocks worldwide...
2018: PloS One
Ming Gao, Changying Li, Ming Xu, Yun Liu, Min Cong, Sijin Liu
Although cadmium (Cd)-induced hepatoxicity is well established, pronounced knowledge gaps remain existed regarding the inherent cellular signaling that dictates Cd toxicity. Specifically, the molecular basis for determining the equilibrium between prosurvival and proapoptotic signaling remains poorly understood. Thus, it is recently revealed that long non-coding RNA (lncRNA) MT1DP, a pseudogene in the metallothionein (MT) family, promoted Cd-induced cell death through activating the RhoC-CCN1/2-AKT pathway and modulating MT1H induction...
July 2018: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
Soňa Vyskočilová, Wee Tek Tay, Sharon van Brunschot, Susan Seal, John Colvin
Bemisia tabaci is a cryptic whitefly-species complex that includes some of the most damaging pests and plant-virus vectors of a diverse range of food and fibre crops worldwide. We combine experimental evidence of: (i) differences in reproductive compatibility, (ii) hybrid verification using a specific nuclear DNA marker and hybrid fertility confirmation and (iii) high-throughput sequencing-derived mitogenomes, to show that the "Mediterranean" (MED) B. tabaci comprises at least two distinct biological species; the globally invasive MED from the Mediterranean Basin and the "African silver-leafing" (ASL) from sub-Saharan Africa, which has no associated invasion records...
July 18, 2018: Scientific Reports
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