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Mónica Lopes-Marques, André M Machado, Luís Q Alves, Miguel M Fonseca, Susana Barbosa, Mikkel-Holger S Sinding, Marianne Helene Rasmussen, Maria Refsgaard Iversen, Mads Frost Bertelsen, Paula F Campos, Rute da Fonseca, Raquel Ruivo, L Filipe C Castro
Genomes are dynamic biological units, with processes of gene duplication and loss triggering evolutionary novelty. The mammalian skin provides a remarkable case study on the occurrence of adaptive morphological innovations. Skin sebaceous glands, for instance, emerged in the ancestor of mammals serving pivotal roles, such as lubrication, waterproofing, immunity and thermoregulation, through the secretion of sebum, a complex mixture of various neutral lipids such as triacylglycerol, free fatty acids, wax esters, cholesterol and squalene...
March 20, 2019: Molecular Biology and Evolution
Tony Gamble
Corneous proteins are an important component of the tetrapod integument. Duplication and diversification of keratins and associated proteins are linked with the origin of most novel integumentary structures like mammalian hair, avian feathers, and scutes covering turtle shells. Accordingly, the loss of integumentary structures often coincides with the loss of genes encoding keratin and associated proteins. For example, many hair keratins in dolphins and whales have become pseudogenes. The adhesive setae of geckos and anoles are composed of both intermediate filament keratins (IF-keratins, formerly known as alpha-keratins) and corneous beta-proteins (CBPs, formerly known as beta-keratins) and recent whole genome assemblies of two gecko species and an anole uncovered duplications in seta-specific CBPs in each of these lineages...
March 21, 2019: Integrative and Comparative Biology
Greg L Stewart, Katey S S Enfield, Adam P Sage, Victor D Martinez, Brenda C Minatel, Michelle E Pewarchuk, Erin A Marshall, Wan L Lam
Transcriptome sequencing has led to the widespread identification of long non-coding RNAs (lncRNAs). Subsequently, these genes have been shown to hold functional importance in human cellular biology, which can be exploited by tumors to drive the hallmarks of cancer. Due to the complex tertiary structure and unknown binding motifs of lncRNAs, there is a growing disparity between the number of lncRNAs identified and those that have been functionally characterized. As such, lncRNAs deregulated in cancer may represent critical components of cancer pathways that could serve as novel therapeutic intervention points...
2019: Frontiers in Genetics
Ticao Zhang, Qin Qiao, Polina Yu Novikova, Qia Wang, Jipei Yue, Yanlong Guan, Shengping Ming, Tianmeng Liu, Ji De, Yixuan Liu, Ihsan A Al-Shehbaz, Hang Sun, Marc Van Montagu, Jinling Huang, Yves Van de Peer, La Qiong
Crucihimalaya himalaica , a close relative of Arabidopsis and Capsella , grows on the Qinghai-Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8...
March 20, 2019: Proceedings of the National Academy of Sciences of the United States of America
Daniel Gebert, Hans Zischler, David Rosenkranz
PIWI proteins and their guiding Piwi-interacting (pi-) RNAs direct the silencing of target nucleic acids in the animal germline and soma. While in mammal testes fetal piRNAs are involved in extensive silencing of transposons, pachytene piRNAs have additionally been shown to act in post-transcriptional gene regulation. The bulk of pachytene piRNAs is produced from large genomic loci, named piRNA clusters. Recently, the presence of reversed pseudogenes within piRNA clusters prompted the idea that piRNAs derived from such sequences might direct regulation of their parent genes...
March 19, 2019: Genome Biology and Evolution
Xu Zhao, Shuai Hao, Minqing Wang, Deguang Xing, Chengwei Wang
A large number of pseudogenes as well as long non-coding RNAs (lncRNAs) have been identified as important regulators in human tumors. However, the clinical role and potential functional effects of the double homeobox A pseudogene 8 (DUXAP8) in glioma remains unknown. In the present study, it was revealed that pseudogene DUXAP8 is significantly upregulated in glioma tissues, compared with adjacent normal tissues. Patients with increased DUXAP8 expression were associated with higher Karnofsky Performance Status, advanced World Health Organization grade, poor disease-free survival and overall survival rates of patients with glioma...
March 2019: Oncology Letters
Yi Shao, Chunyan Chen, Hao Shen, Bin Z He, Daqi Yu, Shuai Jiang, Shilei Zhao, Zhiqiang Gao, Zhenglin Zhu, Xi Chen, Yan Fu, Hua Chen, Ge Gao, Manyuan Long, Yong E Zhang
The origination of new genes contributes to phenotypic evolution in humans. Two major challenges in the study of new genes are the inference of gene ages and annotation of their protein-coding potential. To tackle these challenges, we created GenTree, an integrated online database that compiles age inferences from three major methods together with functional genomic data for new genes. Genome-wide comparison of the age inference methods revealed that the synteny-based pipeline (SBP) is most suited for recently duplicated genes, whereas the protein-family-based methods are useful for ancient genes...
March 12, 2019: Genome Research
Dominik Wrona, Ulrich Siler, Janine Reichenbach
Chronic granulomatous disease (CGD) is a primary immunodeficiency caused by mutations of the phagocytic nicotinamide adenine dinucleotide phosphate (NADPH) oxidase. Autosomal recessive p47 phox -deficient CGD (p47 phox CGD) is the second most frequent form of the disease in western countries, and more than 94% of patients have a disease-causing dinucleotide deletion (ΔGT) in the neutrophil cytosolic factor 1 ( NCF1 ) gene. The ΔGT mutation is most likely transferred onto the NCF1 from one of its two pseudogenes co-localized on the same chromosome...
June 14, 2019: Molecular Therapy. Methods & Clinical Development
Hamad Ali, Fahd Al-Mulla, Naser Hussain, Medhat Naim, Akram M Asbeutah, Ali AlSahow, Mohamed Abu-Farha, Jehad Abubaker, Ashraf Al Madhoun, Sajjad Ahmad, Peter C Harris
Autosomal dominant polycystic kidney disease (ADPKD) is an inherited monogenic renal disease characterised by the accumulation of clusters of fluid-filled cysts in the kidneys and is caused by mutations in PKD1 or PKD2 genes. ADPKD genetic diagnosis is complicated by PKD1 pseudogenes located proximal to the original gene with a high degree of homology. The next generation sequencing (NGS) technology including whole exome sequencing (WES) and whole genome sequencing (WGS), is becoming more affordable and its use in the detection of ADPKD mutations for diagnostic and research purposes more widespread...
March 11, 2019: Scientific Reports
Xiang-Cui Guo, Li Li, Zhi-Hui Gao, Hong-Wei Zhou, Jun Li, Qian-Qing Wang
The outgrowth and metastasis of cervical cancer (CC) contribute to its malignancy. Pituitary Tumor Transforming Gene 1 (PTTG1) is upregulated in many types of cancer, and enhances tumor cell growth and metastasis. However, the activation and regulation of PTTG1 in CC, especially by its pseudogene PTTG3P, have not been shown. Here, we detected significantly higher levels of PTTG1 and PTTG3P in the resected CC tissue, compared to the paired adjacent normal cervical tissue. Interestingly, the PTTG3P levels positively correlated with the PTTG1 levels...
March 10, 2019: Aging
Youwei Zhang, Yang Li, Liang Han, Peiying Zhang, Sanyuan Sun
Long non-coding RNA small ubiquitin-like modifier 1 pseudogene 3 (SUMO1P3) is located on chromosome 1q23.2, and has been suggested to serve as oncogenic lncRNA in many kinds of human malignancy. The role of SUMO1P3 in non-small cell lung cancer (NSCLC) was still unknown. In our study, we analyzed The Cancer Genome Atlas (TCGA) database, and observed SUMO1P3 expression was increased in both lung squamous cell carcinoma and lung adenocarcinoma. Then, we confirmed that SUMO1P3 expression was significantly increased in NSCLC cancer tissues and cell lines...
March 6, 2019: Biomedicine & Pharmacotherapy
M C F Silva-Malta, C C S Santos, P C Gonçalves, L C Schmidt, M L Martins
OBJECTIVES: In this study, we aimed to present a strategy for the detection of the RHD pseudogene (RHDψ) based on a real-time polymerase chain reaction (PCR) assay. BACKGROUND: The D-negative phenotype is associated with many genetic alterations. In populations with African ancestry, this phenotype commonly results from the silent variant RHDψ. The evaluation of RHDψ is essential for correct inference of the RhD phenotype in order to avoid false-positive results...
March 7, 2019: Transfusion Medicine
Dinusha C Maheepala, Christopher A Emerling, Alex Rajewski, Jenna Macon, Maya Strahl, Natalia Pabón-Mora, Amy Litt
Ecologically and economically important fleshy edible fruits have evolved from dry fruit numerous times during angiosperm diversification. However, the molecular mechanisms that underlie these shifts are unknown. In the Solanaceae there has been a major shift to fleshy fruits in the subfamily Solanoideae. Evidence suggests that an ortholog of FRUITFULL ( FUL ), a transcription factor that regulates cell proliferation and limits the dehiscence zone in the silique of Arabidopsis , plays a similar role in dry-fruited Solanaceae...
2019: Frontiers in Plant Science
Roderick M Card, Tom La, Eric R Burrough, Richard J Ellis, Javier Nunez-Garcia, Jill R Thomson, Maxime Mahu, Nyree D Phillips, David J Hampson, Judith Rohde, Alexander W Tucker
Brachyspira (B.) hyodysenteriae is widespread globally, and can cause mucohaemorrhagic colitis (swine dysentery, SD) with severe economic impact in infected herds. Typical strains of B. hyodysenteriae are strongly haemolytic on blood agar, and the haemolytic activity is believed to contribute to virulence in vivo. However, recently there have been reports of atypical weakly haemolytic isolates of B. hyodysenteriae (whBh). In this study, 34 European whBh and 82 strongly haemolytic isolates were subjected to comparative genomic analysis...
March 7, 2019: Veterinary Research
Li-Yuan Lv, Xu-Fang Liang, Shan He
Olfaction, which is mediated by olfactory receptor (OR) genes, is essential in the daily life of fish, especially in foraging. However, Chinese perch ( Siniperca chuatsi ) is believed to prey with reliance on vision and lateral sensation, but not on olfaction. Therefore, understanding the evolutionary dynamics of the Chinese perch OR repertoire could provide insights into genetic evidence for adapting to a decreasing reliance on olfaction. Here, we reported a whole-genome analysis of the Chinese perch OR repertoire...
February 25, 2019: Genes
Baoling Liu, Guanhong Huang, Hongming Zhu, Zhaoming Ma, Xiaokang Tian, Li Yin, Xingya Gao, Xia He
In patients with head and neck cancer (HNC), lymph node (N) metastases are associated with cancer aggressiveness and poor prognosis. Identifying meaningful gene modules and representative biomarkers relevant to the N stage helps predict prognosis and reveal mechanisms underlying tumor progression. The present study used a step‑wise approach for weighted gene co‑expression network analysis (WGCNA). Dataset GSE65858 was subjected to WGCNA. RNA sequencing data of HNC downloaded from the Cancer Genome Atlas (TCGA) and dataset GSE39366 were utilized to validate the results...
February 18, 2019: Oncology Reports
Jessada Thutkawkorapin, Annika Lindblom, Emma Tham
BACKGROUND: Colorectal cancer (CRC) cases with an age of onset <40 years suggests a germline genetic cause. In total, 51 simplex cases were included to test the hypothesis of CRC as a mendelian trait caused by either heterozygous autosomal dominant or bi-allelic autosomal recessive pathogenic variants. METHODS: The cohort was whole exome sequenced (WES) at 100× coverage. Both a dominant- and recessive model were used for searching predisposing genetic factors...
February 27, 2019: Molecular Genetics & Genomic Medicine
Zhang-Hai Li, Xiao Ma, De-Yi Wang, Yun-Xia Li, Cheng-Wang Wang, Xiao-Hua Jin
BACKGROUND: The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of plastome evolution at the infrageneric or intraspecific level remain elusive. Holcoglossum is a small genus of Orchidaceae, consisting of approximately 20 species of recent radiation...
February 26, 2019: BMC Evolutionary Biology
Tilak Saha, Vivek K Ranjan, Sriradha Ganguli, Subarna Thakur, Biswanath Chakraborty, Partha Barman, Wriddhiman Ghosh, Ranadhir Chakraborty
A Gram-stain-positive, spore-forming bacterium, EAG3T , capable of growing on 3-nitropropionic acid as the sole source of carbon, nitrogen and energy, was isolated from the anterior gut of an earthworm (Eisenia fetida) reared at the Centre of Floriculture and Agribusiness Management of the University of North Bengal at Siliguri (26.7072° N, 88.3558° E), West Bengal, India. The DNA G+C content of strain EAG3T was 42.5 mol%. Strain EAG3T contained MK-7 and MK-8 as predominant menaquinones. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine...
February 25, 2019: International Journal of Systematic and Evolutionary Microbiology
Maria Eugenia Nuñez-Valdez, Anne Lanois, Sylvie Pagès, Bernard Duvic, Sophie Gaudriault
We evaluated the impact of bacterial rhabduscin synthesis on bacterial virulence and phenoloxidase inhibition in a Spodoptera model. We first showed that the rhabduscin cluster of the entomopathogenic bacterium Xenorhabdus nematophila was not necessary for virulence in the larvae of Spodoptera littoralis and Spodoptera frugiperda. Bacteria with mutations affecting the rhabduscin synthesis cluster (ΔisnAB and ΔGT mutants) were as virulent as the wild-type strain. We then developed an assay for measuring phenoloxidase activity in S...
2019: PloS One
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