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https://www.readbyqxmd.com/read/28748501/a-step-by-step-microrna-guide-to-cancer-development-and-metastasis
#1
REVIEW
Georgios S Markopoulos, Eugenia Roupakia, Maria Tokamani, Evangelia Chavdoula, Maria Hatziapostolou, Christos Polytarchou, Kenneth B Marcu, Athanasios G Papavassiliou, Raphael Sandaltzopoulos, Evangelos Kolettas
BACKGROUND: Cancer is one of the leading causes of mortality. The neoplastic transformation of normal cells to cancer cells is caused by a progressive accumulation of genetic and epigenetic alterations in oncogenes, tumor suppressor genes and epigenetic regulators, providing cells with new properties, collectively known as the hallmarks of cancer. During the process of neoplastic transformation cells progressively acquire novel characteristics such as unlimited growth potential, increased motility and the ability to migrate and invade adjacent tissues, the ability to spread from the tumor of origin to distant sites, and increased resistance to various types of stresses, mostly attributed to the activation of genetic stress-response programs...
July 26, 2017: Cellular Oncology (Dordrecht)
https://www.readbyqxmd.com/read/28748222/an-improved-plasmodium-cynomolgi-genome-assembly-reveals-an-unexpected-methyltransferase-gene-expansion
#2
Erica M Pasini, Ulrike Böhme, Gavin G Rutledge, Annemarie Voorberg-Van der Wel, Mandy Sanders, Matt Berriman, Clemens Hm Kocken, Thomas Dan Otto
BACKGROUND: Plasmodium cynomolgi, a non-human primate malaria parasite species, has been an important model parasite since its discovery in 1907. Similarities in the biology of P. cynomolgi to the closely related, but less tractable, human malaria parasite P. vivax make it the model parasite of choice for liver biology and vaccine studies pertinent to P. vivax malaria. Molecular and genome-scale studies of P. cynomolgi have relied on the current reference genome sequence, which remains highly fragmented with 1,649 unassigned scaffolds and little representation of the subtelomeres...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28747496/parainfluenza-virus-5-piv5-expressing-wild-type-or-pre-fusion-respiratory-syncytial-virus-rsv-fusion-protein-protect-mice-and-cotton-rats-from-rsv-challenge
#3
Shannon I Phan, James R Zengel, Huiling Wei, Zhuo Li, Dai Wang, Biao He
Human respiratory syncytial virus (RSV) is the leading cause of pediatric bronchiolitis and hospitalizations. RSV can also cause severe complications in elderly and immunocompromised individuals. There is no licensed vaccine. We previously generated a PIV5-vectored vaccine candidate expressing the RSV fusion protein (F) that was immunogenic and protective in mice. In this work, our goal was to improve the original vaccine candidate by modifying the PIV5 vector or by modifying the RSV-F antigen. We previously demonstrated that inserting a foreign gene at the PIV5 SH-HN junction or deleting PIV5 SH increased vaccine efficacy...
July 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28743015/plant-domestication-wild-date-palms-illuminate-a%C3%A2-crop-s-sticky-origins
#4
Nathan Wales, Benjamin K Blackman
In a new study, previously unknown populations of wild date palm have been identified in remote areas of Oman. Genomic analyses indicate date palm domestication occurred in the eastern portion of the Arabian Peninsula and reveal substantial subsequent gene flow with African palm populations.
July 24, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28742865/a-novel-mitochondrial-genome-of-arborophila-and-new-insight-into-arborophila-evolutionary-history
#5
Chaochao Yan, Biqin Mou, Yang Meng, Feiyun Tu, Zhenxin Fan, Megan Price, Bisong Yue, Xiuyue Zhang
The lineage of the Bar-backed Partridge (Arborophila brunneopectus) was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant...
2017: PloS One
https://www.readbyqxmd.com/read/28742823/genome-wide-identification-and-analysis-of-the-mads-box-gene-family-in-bread-wheat-triticum-aestivum-l
#6
Jian Ma, Yujie Yang, Wei Luo, Congcong Yang, Puyang Ding, Yaxi Liu, Linyi Qiao, Zhijian Chang, Hongwei Geng, Penghao Wang, Qiantao Jiang, Jirui Wang, Guoyue Chen, Yuming Wei, Youliang Zheng, Xiujin Lan
The MADS-box genes encode transcription factors with key roles in plant growth and development. A comprehensive analysis of the MADS-box gene family in bread wheat (Triticum aestivum) has not yet been conducted, and our understanding of their roles in stress is rather limited. Here, we report the identification and characterization of the MADS-box gene family in wheat. A total of 180 MADS-box genes classified as 32 Mα, 5 Mγ, 5 Mδ, and 138 MIKC types were identified. Evolutionary analysis of the orthologs among T...
2017: PloS One
https://www.readbyqxmd.com/read/28742812/broad-range-lytic-bacteriophages-that-kill-staphylococcus-aureus-local-field-strains
#7
Virginia Abatángelo, Natalia Peressutti Bacci, Carina A Boncompain, Ariel A Amadio, Soledad Carrasco, Cristian A Suárez, Héctor R Morbidoni
Staphylococcus aureus is a very successful opportunistic pathogen capable of causing a variety of diseases ranging from mild skin infections to life-threatening sepsis, meningitis and pneumonia. Its ability to display numerous virulence mechanisms matches its skill to display resistance to several antibiotics, including β-lactams, underscoring the fact that new anti-S. aureus drugs are urgently required. In this scenario, the utilization of lytic bacteriophages that kill bacteria in a genus -or even species- specific way, has become an attractive field of study...
2017: PloS One
https://www.readbyqxmd.com/read/28738084/the-dkk3-gene-encodes-a-vital-intracellular-regulator-of-cell-proliferation
#8
Jack L Leonard, Deborah M Leonard, Scot A Wolfe, Jilin Liu, Jaime Rivera, Michelle Yang, Ryan T Leonard, Jacob P S Johnson, Prashant Kumar, Kate L Liebmann, Amanda A Tutto, Zhongming Mou, Karl J Simin
Members of the Dickkopf (Dkk) family of Wnt antagonists interrupt Wnt-induced receptor assembly and participate in axial patterning and cell fate determination. One family member, DKK3, does not block Wnt receptor activation. Loss of Dkk3 expression in cancer is associated with hyperproliferation and dysregulated ß-catenin signaling, and ectopic expression of Dkk3 halts cancer growth. The molecular events mediating the DKK3-dependent arrest of ß-catenin-driven cell proliferation in cancer cells are unknown...
2017: PloS One
https://www.readbyqxmd.com/read/28736815/a-widespread-cyanobacterium-supported-by-polyphasic-approach-proposition-of-koinonema-pervagatum-gen-sp-nov-oscillatoriales
#9
Bruna Buch, Mariéllen Dornelles Martins, Luis Henrique Z Branco
Several new genera originally classified as the genus Phormidium, a polyphyletic and taxonomically complex genus within the Oscillatoriales, were recently described. The simple morphology of Phormidium does not reflect its genetic diversity and the delimitation of a natural group is not possible with traditional classification systems based on morphology alone. Therefore, this study used morphological, ecological and molecular approaches to evaluate four populations morphologically similar to Ammassolinea, Kamptonema and Ancylothrix (simple, curved and gradually attenuated at the ends trichome), found in subtropical and tropical Brazilian regions...
July 24, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28736296/a-new-targeted-cftr-mutation-panel-based-on-next-generation-sequencing-technology
#10
Marco Lucarelli, Luigi Porcaro, Alice Biffignandi, Lucy Costantino, Valentina Giannone, Luisella Alberti, Sabina Maria Bruno, Carlo Corbetta, Erminio Torresani, Carla Colombo, Manuela Seia
Searching for mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) is a key step in the diagnosis of and neonatal and carrier screening for cystic fibrosis (CF), and it has implications for prognosis and personalized therapy. The large number of mutations and genetic and phenotypic variability make this search a complex task. Herein, we tested the clinical and laboratory validity of an extended search for mutations in CFTR using a next-generation sequencing-based method, with a panel of 188 CFTR mutations customized for the Italian population...
July 19, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28733989/detecting-ancient-co-dispersals-and-host-shifts-by-double-dating-of-host-and-parasite-phylogenies-application-in-proctophyllodid-feather-mites-associated-with-passerine-birds
#11
Pavel B Klimov, Sergey V Mironov, Barry M OConnor
Inferring co-phylogeographic events requires matching the timing of these events on both host and symbiont (e.g., parasites) phylogenies because divergences of hosts and their symbionts may not temporally coincide, and host switches may occur. We investigate a large radiation of birds (Passeriformes) and their permanent symbionts, the proctophyllodid feather mites (117 species from 116 bird species; 6 genes, 11,468 nt aligned) using two time-calibration strategies for mites: fossils only and host phylogeography only...
July 22, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28727805/turgor-responsive-starch-phosphorylation-in-oryza-sativa-stems-a-primary-event-of-starch-degradation-associated-with-grain-filling-ability
#12
Hiroshi Wada, Chisato Masumoto-Kubo, Koichi Tsutsumi, Hiroshi Nonami, Fukuyo Tanaka, Haruka Okada, Rosa Erra-Balsells, Kenzo Hiraoka, Taiken Nakashima, Makoto Hakata, Satoshi Morita
Grain filling ability is mainly affected by the translocation of carbohydrates generated from temporarily stored stem starch in most field crops including rice (Oryza sativa L.). The partitioning of non-structural stem carbohydrates has been recognized as an important trait for raising the yield ceiling, yet we still do not fully understand how carbohydrate partitioning occurs in the stems. In this study, two rice subspecies that exhibit different patterns of non-structural stem carbohydrates partitioning, a japonica-dominant cultivar, Momiroman, and an indica-dominant cultivar, Hokuriku 193, were used as the model system to study the relationship between turgor pressure and metabolic regulation of non-structural stem carbohydrates, by combining the water status measurement with gene expression analysis and a dynamic prefixed 13C tracer analysis using a mass spectrometer...
2017: PloS One
https://www.readbyqxmd.com/read/28726632/dynamics-of-genomic-innovation-in-the-unicellular-ancestry-of-animals
#13
Xavier Grau-Bové, Guifré Torruella, Stuart Donachie, Hiroshi Suga, Guy Leonard, Thomas A Richards, Iñaki Ruiz-Trillo
Which genomic innovations underpinned the origin of multicellular animals is still an open debate. Here, we investigate this question by reconstructing the genome architecture and gene family diversity of ancestral premetazoans, aiming to date the emergence of animal-like traits. Our comparative analysis involves genomes from animals and their closest unicellular relatives (the Holozoa), including four new genomes: three Ichthyosporea and Corallochytrium limacisporum. Here we show that the earliest animals were shaped by dynamic changes in genome architecture before the emergence of multicellularity: an early burst of gene diversity in the ancestor of Holozoa, enriched in transcription factors and cell adhesion machinery, was followed by multiple and differently-timed episodes of synteny disruption, intron gain and genome expansions...
July 20, 2017: ELife
https://www.readbyqxmd.com/read/28725230/genetics-and-genomics-of-cotton-leaf-curl-disease-its-viral-causal-agents-and-whitefly-vector-a-way-forward-to-sustain-cotton-fiber-security
#14
REVIEW
Mehboob-Ur- Rahman, Ali Q Khan, Zainab Rahmat, Muhammad A Iqbal, Yusuf Zafar
Cotton leaf curl disease (CLCuD) after its first epidemic in 1912 in Nigeria, has spread to different cotton growing countries including United States, Pakistan, India, and China. The disease is of viral origin-transmitted by the whitefly Bemisia tabaci, which is difficult to control because of the prevalence of multiple virulent viral strains or related species. The problem is further complicated as the CLCuD causing virus complex has a higher recombination rate. The availability of alternate host crops like tomato, okra, etc...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28724393/methicillin-resistant-staphylococcus-aureus-emerged-long-before-the-introduction-of-methicillin-into-clinical-practice
#15
Catriona P Harkins, Bruno Pichon, Michel Doumith, Julian Parkhill, Henrik Westh, Alexander Tomasz, Herminia de Lencastre, Stephen D Bentley, Angela M Kearns, Matthew T G Holden
BACKGROUND: The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use of antibiotics has generated selective pressures that have driven the emergence of resistant strains. Methicillin-resistant Staphylococcus aureus (MRSA) was first observed in 1960, less than one year after the introduction of this second generation beta-lactam antibiotic into clinical practice. Epidemiological evidence has always suggested that resistance arose around this period, when the mecA gene encoding methicillin resistance carried on an SCCmec element, was horizontally transferred to an intrinsically sensitive strain of S...
July 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/28720801/mapping-and-characterization-of-g-quadruplexes-in-mycobacterium-tuberculosis-gene-promoter-regions
#16
Rosalba Perrone, Enrico Lavezzo, Erika Riello, Riccardo Manganelli, Giorgio Palù, Stefano Toppo, Roberta Provvedi, Sara N Richter
Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), one of the top 10 causes of death worldwide in 2015. The recent emergence of strains resistant to all current drugs urges the development of compounds with new mechanisms of action. G-quadruplexes are nucleic acids secondary structures that may form in G-rich regions to epigenetically regulate cellular functions. Here we implemented a computational tool to scan the presence of putative G-quadruplex forming sequences in the genome of Mycobacterium tuberculosis and analyse their association to transcription start sites...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720143/mhc-class-ii-expression-and-potential-antigen-presenting-cells-in-the-retina-during-experimental-autoimmune-uveitis
#17
Deborah A Lipski, Rémi Dewispelaere, Vincent Foucart, Laure E Caspers, Matthieu Defrance, Catherine Bruyns, François Willermain
BACKGROUND: Controversy exists regarding which cell types are responsible for autoantigen presentation in the retina during experimental autoimmune uveitis (EAU) development. In this study, we aimed to identify and characterize the retinal resident and infiltrating cells susceptible to express major histocompatibility complex (MHC) class II during EAU. METHODS: EAU was induced in C57BL/6 mice by adoptive transfer of autoreactive lymphocytes from IRBP1-20-immunized animals...
July 18, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28719033/identification-of-driver-copy-number-alterations-in-diverse-cancer-types-and-application-in-drug-repositioning
#18
Wenbin Zhou, Zhangxiang Zhao, Ruiping Wang, Yue Han, Chengyu Wang, Fan Yang, Ya Han, Haihai Liang, Lishuang Qi, Chenguang Wang, Zheng Guo, Yunyan Gu
Results from numerous studies suggest an important role for somatic copy number alterations (SCNAs) in cancer progression. Our work aimed to identify the drivers (oncogenes or tumor suppressor genes) that reside in recurrently aberrant genomic regions, including a large number of genes or non-coding genes, which remain a challenge for decoding the SCNAs involved in carcinogenesis. Here, we propose a new approach to comprehensively identify drivers, using 8740 cancer samples involving 18 cancer types from The Cancer Genome Atlas (TCGA)...
July 18, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28717144/radseq-provides-evidence-for-parallel-ecotypic-divergence-in-the-autotetraploid-cochlearia-officinalis-in-northern-norway
#19
Marie K Brandrud, Ovidiu Paun, Maria T Lorenzo, Inger Nordal, Anne K Brysting
Speciation encompasses a continuum over time from freely interbreeding populations to reproductively isolated species. Along this process, ecotypes - the result of local adaptation - may be on the road to new species. We investigated whether three autotetraploid Cochlearia officinalis ecotypes, adapted to different habitats (beach, estuary, spring), are genetically differentiated and result from parallel ecotypic divergence in two distinct geographical regions. We obtained genetic data from thousands of single nucleotide polymorphisms (SNPs) from restriction-site associated DNA sequencing (RADseq) and from six microsatellite markers for 12 populations to assess genetic divergence at ecotypic, geographic and population level...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717021/genetic-and-metabolic-engineering-in-diatoms
#20
REVIEW
Weichao Huang, Fayza Daboussi
Diatoms have attracted considerable attention due to their success in diverse environmental conditions, which probably is a consequence of their complex origins. Studies of their metabolism will provide insight into their adaptation capacity and are a prerequisite for metabolic engineering. Several years of investigation have led to the development of the genome engineering tools required for such studies, and a profusion of appropriate tools is now available for exploring and exploiting the metabolism of these organisms...
September 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
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