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Benjamin L S Furman, Utkarsh J Dang, Ben J Evans, G Brian Golding
Whole genome duplication (WGD), the doubling of the nuclear DNA of a species, contributes to biological innovation by creating ge-netic redundancy. One mode of WGD is allopolyploidization, wherein each genome from two ancestral species becomes a 'subgenome' of a polyploid descendant species. The evolutionary trajectory of a dupli-cated gene that arises from WGD is influenced both by natural selec-tion, that may favour redundant, new, or partitioned functions, and by gene silencing (pseudogenization). Here, we explored how these two phenomena varied over time and within allopolyploid genomes in several allotetraploid clawed frog species (Xenopus)...
October 20, 2018: Journal of Evolutionary Biology
Binghai Chen, Chengyue Wang, Jin Zhang, Yang Zhou, Wei Hu, Tao Guo
Background: Increasing evidence suggests a critical role for long noncoding RNAs (LncRNAs) and pseudogenes in cancer. Renal cell carcinoma (RCC), the most common primary renal neoplasm, is highly aggressive and difficult to treat because of its resistance to chemotherapy and radiotherapy. Despite many identified LncRNAs and pseudogenes, few have been clearly elucidated. Methods: This study provides new insights into LncRNAs and pseudogenes in the prognosis of RCC...
2018: Cancer Cell International
Chuang Tian, Yong Jin, Songshan Shi
Long non-coding RNAs (lncRNAs) have been suggested to serve important roles in the development of a number of human cancer types. An increasing amount of data has indicated that the lncRNA small ubiquitin-like modifier 1 (SUMO1) pseudogene 3 (SUMO1P3) has been involved in various types of human cancer. However, the function SUMO1P3 in the development of pancreatic cancer remains unclear. Firstly, reverse transcription-quantitative polymerase chain reaction was performed to determine the expression of SUMO1P3 in pancreatic cancer tissues and cell lines...
November 2018: Oncology Letters
Scott A Hinger, Diana J Cha, Jeffrey L Franklin, James N Higginbotham, Yongchao Dou, Jie Ping, Lihua Shu, Nripesh Prasad, Shawn Levy, Bing Zhang, Qi Liu, Alissa M Weaver, Robert J Coffey, James G Patton
The regulation and functional roles of secreted coding and long noncoding RNAs (lncRNAs; >200 nt) are largely unknown. We previously showed that mutant KRAS colorectal cancer (CRC) cells release extracellular vesicles (EVs) containing distinct proteomes, microRNAs (miRNAs), and circular RNAs. Here, we comprehensively identify diverse classes of CRC extracellular long RNAs secreted in EVs and demonstrate differential export of specific RNAs. Distinct noncoding RNAs, including antisense transcripts and transcripts derived from pseudogenes, are enriched in EVs compared to cellular profiles...
October 16, 2018: Cell Reports
Daniel Soukup, Alma Kuechler, Joachim Roesler, Leopold Pichlmaier, Maximillian Eckerland, Margarete Olivier, Florian Stehling
We report the case of a 19-years-old patient who presented with a perplexing variety of symptoms which included remarkable facial features, intellectual disability, granulomatous upper lip swelling (previously diagnosed as Melkersson-Rosenthal syndrome), Crohn's-like disease, non-productive cough, and a granulomatous mass localized in the left lung. Chronic granulomatous disease (CGD) was diagnosed using dihydrorhodamine 123 assay that showed low levels of phagocytic NADPH-oxidase. DNA sequencing revealed a heterozygous mutation in the NCF-1 gene on chromosome 7...
2018: Frontiers in Genetics
Diego Santos-Garcia, Ksenia Juravel, Shiri Freilich, Einat Zchori-Fein, Amparo Latorre, Andrés Moya, Shai Morin, Francisco J Silva
Insect lineages feeding on nutritionally restricted diets such as phloem sap, xylem sap, or blood, were able to diversify by acquiring bacterial species that complement lacking nutrients. These bacteria, considered obligate/primary endosymbionts, share a long evolutionary history with their hosts. In some cases, however, these endosymbionts are not able to fulfill all of their host's nutritional requirements, driving the acquisition of additional symbiotic species. Phloem-feeding members of the insect family Aleyrodidae (whiteflies) established an obligate relationship with Candidatus Portiera aleyrodidarum, which provides its hots with essential amino acids and carotenoids...
2018: Frontiers in Microbiology
Fanglin Ma, Xiaomin Du, Yudong Wei, Zhe Zhou, Daguia Zambe John Clotaire, Na Li, Sha Peng, Guangpeng Li, Jinlian Hua
LIN28A serves as a crucial marker of dairy goat male germline stem cells (GmGSCs). In our previous study, we demonstrated that LIN28A promotes proliferation, self-renewal, and maintains the stemness of GmGSCs. Here, we found that LIN28A could activate the transcription of NANOG in a let-7g independent manner. We cloned the 5' upstream of two NANOG genes which were located on chromosome 15 ( NANOG-ch15) and chromosome 5 ( NANOG-ch5), respectively, and then examined their promoter activities and promoter methylation levels...
October 14, 2018: Journal of Cellular Physiology
Tao Huang, Xiao Wang, Xiaokun Yang, Jianlei Ji, Qinghai Wang, Xuan Yue, Zheng Dong
BACKGROUND Renal cell carcinoma (RCC) is one of the common malignant tumors in the urinary system, which endangers human health for a long time. The past decade, the molecular biology of renal cell carcinoma has made considerable progress, so that we have a more profound understanding of renal cell carcinoma. Molecular biological mechanism of renal cell carcinoma remains to be explored. Evidence indicates that long non-coding RNAs (lncRNAs) may be important players in human cancer progression, including RCC...
October 14, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Hugh M Robertson
The evolutionary origins of the three major families of chemoreceptors in arthropods-the odorant receptor (OR), gustatory receptor (GR), and ionotropic receptor (IR) families-occurred at the base of the Insecta, Animalia, and Protostomia, respectively. Comparison of receptor family sizes across arthropods reveals a generally positive correlation with their widely disparate complexity of chemical ecology. Closely related species reveal the ongoing processes of gene family evolution, including gene duplication, divergence, pseudogenization, and loss, that mediate these larger patterns...
October 12, 2018: Annual Review of Entomology
Muhammad Azman Zakaria, Mohd Zulkhairi Mohd Yusoff, Mohd Rafein Zakaria, Mohd Ali Hassan, Thomas K Wood, Toshinari Maeda
Pseudogenes in the Escherichia coli genome are assumed to be non-functional. In this study, Keio collection BW25113∆ yqiG and YqiG-producing strain (BW25113/pCA24N-YqiG) were used to evaluate the importance of pseudogene yqiG in hydrogen metabolism. Our results show pseudogene protein YqiG was identified as an essential protein in the production of biohydrogen from glucose. The mutant yqiG decreased biohydrogen production from 37 µmol mg-1 protein to 6 µmol mg-1 protein compared to the wild-type strain, and glucose consumption was reduced by 80%...
October 2018: 3 Biotech
Tõnu Reintamm, Nele Aas-Valleriani, Merike Kelve
Deoxynucleoside 5-monophosphate N-glycosidase, DNPH1 is a member of the nucleoside 2-deoxyribosyltransferase (NDT) family. This enzyme catalyzes the hydrolysis of deoxynucleoside monophosphates into free nucleobase moieties and 2-deoxyribose 5-phosphates. The DNPH1 enzymatic activity was first demonstrated in rats and then in humans. Subsequently the DNPH1 gene was identified in a variety of organisms, mainly in Metazoa. Herein, we demonstrate that despite DNPH1 genes being distributed in almost all metazoans, the occurrence of DNPH1genes is mosaic...
October 6, 2018: Gene
Vladimir Shiriagin, Sigrun I Korsching
A sensory deficit both at the individual and the species level can be compensated by increased acuity in other senses. The loss of vision in blind cavefish, Astyanaxmexicanus appears to be partially counterbalanced by enhanced chemosensory perception. Whether such improvement also involves adaptive changes in chemosensory receptor repertoires was unknown. The typical bitter taste receptor repertoire of teleost fishes is reported as three to five genes, much smaller than that of many terrestrial species. Interestingly, several fish species, e...
October 5, 2018: Chemical Senses
Pragyan Acharya, Rintu Kutum, Rajesh Pandey, Asha Mishra, Rohini Saha, Akshay Munjal, Vineet Ahuja, Mitali Mukerji, Govind K Makharia
INTRODUCTION: Celiac disease (CeD) is an autoimmune enteropathy which affects approximately 0.7% of the global population. While first-degree relatives (FDR) of patients with CeD have a 7.5% risk of developing enteropathy, many remain protected. Therefore, intestinal mucosa of FDR might have protective compensatory mechanisms against immunological injury. We have explored the protective mechanisms that may be active in intestinal mucosa of FDR. METHODS: Intestinal mucosal biopsies (4-5 pieces) from treatment naïve patients with CeD (n = 12), FDR (n = 12) (anti-tTG negative) and controls (n = 12) (anti-tTG negative) were obtained from each individual and subjected to microarray analysis using HT-12-v4 Human Expression BeadChips (Illumina)...
October 8, 2018: Clinical and Translational Gastroenterology
Philippe Silar, Jean-Marc Dauget, Valérie Gautier, Pierre Grognet, Michelle Chablat, Sylvie Hermann-Le Denmat, Arnaud Couloux, Patrick Wincker, Robert Debuchy
Mechanisms involved in fine adaptation of fungi to their environment include differential gene regulation associated with single nucleotide polymorphisms and indels (including transposons), horizontal gene transfer, gene copy amplification, as well as pseudogenization and gene loss. The two Podospora genome sequences examined here emphasize the role of pseudogenization and gene loss, which have rarely been documented in fungi. Podospora comata is a species closely related to Podospora anserina, a fungus used as model in several laboratories...
October 4, 2018: Molecular Genetics and Genomics: MGG
Subbroto Kumar Saha, Yeojin Jeong, Sungha Cho, Ssang-Goo Cho
OCT4 is a master transcription factor that regulates the pluripotency of pluripotent stem cells and cancer stem cells along with other factors, including SOX2, KLF4, and C-MYC. Three different transcripts, OCT4A, OCT4B, and OCT4B1, are known to be generated by alternative splicing and eight OCT4 pseudogenes have been found in the human genome. Among them, we examined OCT4 and three pseudogenes (POU5F1P1, POU5F1P3, and POU5F1P4) because of their high expression possibility in cancer. In addition, previous studies indicated that OCT4 expression is augmented in cervical cancer and associated with poor prognosis, whereas OCT4 is down-regulated and correlated with good clinical outcomes in breast cancer...
October 4, 2018: Scientific Reports
Shankari Prasad Datta, Kuladip Jana, Avisek Mondal, Sandipan Ganguly, Srimonti Sarkar
BACKGROUND: The differently-diverged parasitic protist Giardia lamblia is known to have minimal machinery for vesicular transport. Yet, it has three paralogues of SNAP, a crucial component that together with NSF brings about disassembly of the cis-SNARE complex formed following vesicle fusion to target membranes. Given that most opisthokont hosts of this gut parasite express only one α-SNAP, this study was undertaken to determine whether these giardial SNAP proteins have undergone functional divergence...
October 4, 2018: Parasites & Vectors
Christopher T Esapa, Sian E Piret, M Andrew Nesbit, Gethin P Thomas, Leslie A Coulton, Orla M Gallagher, Michelle M Simon, Saumya Kumar, Ann-Marie Mallon, Ilaria Bellantuono, Matthew A Brown, Peter I Croucher, Paul K Potter, Steve Dm Brown, Roger D Cox, Rajesh V Thakker
Kyphosis and scoliosis are common spinal disorders that occur as part of complex syndromes or as nonsyndromic, idiopathic diseases. Familial and twin studies implicate genetic involvement, although the causative genes for idiopathic kyphoscoliosis remain to be identified. To facilitate these studies, we investigated progeny of mice treated with the chemical mutagen N -ethyl- N -nitrosourea (ENU) and assessed them for morphological and radiographic abnormalities. This identified a mouse with kyphoscoliosis due to fused lumbar vertebrae, which was inherited as an autosomal dominant trait; the phenotype was designated as hereditary vertebral fusion (HVF) and the locus as Hvf ...
May 2018: JBMR Plus
Andrej Benjak, Charlotte Avanzi, Yvonne Benito, Franck Breysse, Christophe Chartier, Maria-Laura Boschiroli, Christine Fourichon, Lorraine Michelet, Didier Pin, Jean-Pierre Flandrois, Pierre Bruyere, Oana Dumitrescu, Stewart T Cole, Gerard Lina
Nodular thelitis is a chronic enzootic infection affecting dairy cows and goats. The causative agent was recently shown to be related to the leprosy-causing bacilli Mycobacterium leprae and Mycobacterium lepromatosis In this study, the genome of this pathogen was sequenced and analyzed. Phylogenomic analyses confirmed that the pathogen present in nodular thelitis and tuberculoid scrotitis is a distinct species related to the leprosy bacilli and Mycobacterium haemophilum Because the pathogen was originally isolated from a bovine udder, it was named " Mycobacterium uberis " The genome of " M...
October 3, 2018: MSphere
Sang Kyun Ahn, Vanessa Tran, Andrea Leung, Mark Ng, Ming Li, Jun Liu
The live tuberculosis vaccine Mycobacterium bovis BCG (Bacille Calmette-Guérin) comprises a number of genetically distinct substrains. In BCG-Prague, phoP of the PhoP-PhoR two-component system is a pseudogene due to a single insertion mutation. We hypothesized that this mutation partially accounts for the low immunogenicity of BCG-Prague observed in the 1970s. In this study, we showed that complementation with the M. bovis allele of phoP restored BCG-Prague's immunogenicity. Furthermore, we showed that overexpression of the M...
September 1, 2018: Molecular Therapy: the Journal of the American Society of Gene Therapy
Peter van den Hurk, Harald M I Kerkkamp
While it has been known for a while that some snake species are extremely sensitive to acetaminophen, the underlying mechanism for this toxicity has not been reported. To investigate if essential detoxification enzymes are missing in snake species that are responsible for biotransformation of acetaminophen in other vertebrate species, livers were collected from a variety of snake species, together with samples from alligator, snapping turtle, cat, rat, and cattle. Subcellular fractions were analyzed for enzymatic activities of phenol-type sulfotransferase and UDP‑glucuronosyltransferase, total glutathione S‑transferase, and N‑acetyltransferase...
September 27, 2018: Comparative Biochemistry and Physiology. Toxicology & Pharmacology: CBP
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