keyword
MENU ▼
Read by QxMD icon Read
search

genomic evolution

keyword
https://www.readbyqxmd.com/read/29351238/telomeres-implications-for-cancer-development
#1
REVIEW
Aina Bernal, Laura Tusell
Telomeres facilitate the protection of natural ends of chromosomes from constitutive exposure to the DNA damage response (DDR). This is most likely achieved by a lariat structure that hides the linear telomeric DNA through protein-protein and protein-DNA interactions. The telomere shortening associated with DNA replication in the absence of a compensatory mechanism culminates in unmasked telomeres. Then, the subsequent activation of the DDR will define the fate of cells according to the functionality of cell cycle checkpoints...
January 19, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29350130/ecology-and-evolution-of-chromosomal-gene-transfer-between-environmental-microorganisms-and-pathogens
#2
José Luis Martínez
Inspection of the genomes of bacterial pathogens indicates that their pathogenic potential relies, at least in part, on the activity of different elements that have been acquired by horizontal gene transfer from other (usually unknown) microorganisms. Similarly, in the case of resistance to antibiotics, besides mutation-driven resistance, the incorporation of novel resistance genes is a widespread evolutionary procedure for the acquisition of this phenotype. Current information in the field supports the idea that most (if not all) genes acquired by horizontal gene transfer by bacterial pathogens and contributing to their virulence potential or to antibiotic resistance originate in environmental, not human-pathogenic, microorganisms...
January 2018: Microbiology Spectrum
https://www.readbyqxmd.com/read/29349607/molecular-characterization-of-fagaceae-species-using-inter-primer-binding-site-ipbs-markers
#3
João Paulo Coutinho, Ana Carvalho, Antonio Martín, José Lima-Brito
Retrotransposons (RTNs) contribute for genome evolution, influencing its size and structure. We investigated the utility of the RTN-based markers inter-primer binding site (iPBS) for the molecular characterization of 25 Fagaceae species from genera Castanea, Fagus and Quercus. The assessment of genetic diversity, relationships and structure, as well as taxonomic classification of Fagaceae based on molecular data is important for definition of conservation, forestry management strategies and discrimination among natural hybrids and their parents since natural hybridization may increase with the climate changes...
January 18, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29349599/evolution-of-eukaryal-and-archaeal-pseudouridine-synthase-pus10
#4
Elisabeth Fitzek, Archi Joardar, Ramesh Gupta, Matt Geisler
In archaea, pseudouridine (Ψ) synthase Pus10 modifies uridine (U) to Ψ at positions 54 and 55 of tRNA. In contrast, Pus10 is not found in bacteria, where modifications at those two positions are carried out by TrmA (U54 to m5U54) and TruB (U55 to Ψ55). Many eukaryotes have an apparent redundancy; their genomes contain orthologs of archaeal Pus10 and bacterial TrmA and TruB. Although eukaryal Pus10 genes share a conserved catalytic domain with archaeal Pus10 genes, their biological roles are not clear for the two reasons...
January 18, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29348864/the-macro-evolutionary-events-in-esophageal-squamous-cell-carcinoma
#5
Bin Yang, Ting Yan, Heyang Cui, Enwei Xu, Yanchun Ma, Caixia Cheng, Ling Zhang, Pengzhou Kong, Fang Wang, Yu Qian, Jian Yang, Yaoping Li, Hongyi Li, Yanghui Bi, Xiaoling Hu, Juan Wang, Bin Song, Jie Yang, Wei Gao, Jing Liu, Binbin Zou, Ruyi Shi, Yanyan Zhang, Haiyan Liu, Yiqian Liu, Yuanfang Zhai, Lu Chang, Yi Wang, Yingchun Zhang, Zhiwu Jia, Xing Chen, Yanfeng Xi, Guodong Li, Jianfang Liang, Jiansheng Guo, Shiping Guo, Rongsheng Zhang, Xiaolong Cheng, Yongping Cui
Understanding the evolutionary processes operative in cancer genome may provide insights into clinical outcome and drug-resistance. However, studies focus on genomic signatures, especially for macro-evolutionary events, in esophageal squamous cell carcinoma (ESCC) are limited. Here, we integrated published genomic sequencing data to investigate underlying evolutionary characteristics in ESCC. We found most of ESCC genomes were polyploidy with high genomic instability. Whole genome doubling that acts as one of mechanisms for polyploidy was predicted as a late event in the majority of ESCC genome...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348602/the-ten-year-evolutionary-trajectory-of-a-highly-recurrent-paediatric-high-grade-neuroepithelial-tumour-with-mn1-bend2-fusion
#6
Anna Burford, Alan Mackay, Sergey Popov, Maria Vinci, Diana Carvalho, Matthew Clarke, Elisa Izquierdo, Aimee Avery, Thomas S Jacques, Wendy J Ingram, Andrew S Moore, Kieran Frawley, Timothy E Hassall, Thomas Robertson, Chris Jones
Astroblastomas are rare brain tumours which predominate in children and young adults, and have a controversial claim as a distinct entity, with no established WHO grade. Reports suggest a better outcome than high grade gliomas, though they frequently recur. Recently, they have been described to overlap with a newly-discovered group of tumours described as'high grade neuroepithelial tumour with MN1 alteration' (CNS HGNET-MN1), defined by global methylation patterns and strongly associated with gene fusions targeting MN1...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348510/genome-and-secretome-analysis-of-pochonia-chlamydosporia-provide-new-insight-into-egg-parasitic-mechanisms
#7
Runmao Lin, Feifei Qin, Baoming Shen, Qianqian Shi, Chichuan Liu, Xi Zhang, Yang Jiao, Jun Lu, Yaoyao Gao, Marta Suarez-Fernandez, Federico Lopez-Moya, Luis Vicente Lopez-Llorca, Gang Wang, Zhenchuan Mao, Jian Ling, Yuhong Yang, Xinyue Cheng, Bingyan Xie
Pochonia chlamydosporia infects eggs and females of economically important plant-parasitic nematodes. The fungal isolates parasitizing different nematodes are genetically distinct. To understand their intraspecific genetic differentiation, parasitic mechanisms, and adaptive evolution, we assembled seven putative chromosomes of P. chlamydosporia strain 170 isolated from root-knot nematode eggs (~44 Mb, including 7.19% of transposable elements) and compared them with the genome of the strain 123 (~41 Mb) isolated from cereal cyst nematode...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348143/detecting-polygenic-adaptation-in-admixture-graphs
#8
Fernando Racimo, Jeremy J Berg, Joseph K Pickrell
An open question in human evolution is the importance of polygenic adaptation: adaptive changes in the mean of a multifactorial trait due to shifts in allele frequencies across many loci. In recent years, several methods have been developed to detect polygenic adaptation using loci identified in genome-wide association studies (GWAS). Though powerful, these methods suffer from limited interpretability: they can detect which sets of populations have evidence for polygenic adaptation, but are unable to reveal where in the history of multiple populations these processes occurred...
January 18, 2018: Genetics
https://www.readbyqxmd.com/read/29346682/receptor-usage-of-a-novel-bat-lineage-c-betacoronavirus-reveals-evolution-of-mers-related-coronavirus-spike-proteins-for-human-dpp4-binding
#9
Susanna K P Lau, Libiao Zhang, Hayes K H Luk, Lifeng Xiong, Xingwen Peng, Kenneth S M Li, Xiangyang He, Pyrear Su-Hui Zhao, Rachel Y Y Fan, Antonio C P Wong, Syed Shakeel Ahmed, Jian-Piao Cai, Jasper F W Chan, Yinyan Sun, Dongyan Jin, Honglin Chen, Terrence C K Lau, Raven K H Kok, Wenhui Li, Kwok-Yung Yuen, Patrick C Y Woo
Although bats are known to harbor MERS-CoV-related viruses, the role of bats in the evolutionary origin and pathway remains obscure. We identified a novel MERS-CoV-related betacoronavirus, Hp-BatCoV HKU25, from Chinese pipistrelle bats. While being closely related to MERS-CoV in most genome regions, its spike protein occupies a phylogenetic position between that of Ty-BatCoV HKU4 and Pi-BatCoV HKU5. Since Ty-BatCoV HKU4 but not Pi-BatCoV HKU5 can utilize MERS-CoV receptor, hDPP4, for cell entry, we tested the ability of Hp-BatCoV HKU25 to bind and utilize hDPP4...
January 16, 2018: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29346651/bipartite-network-analysis-of-gene-sharings-in-the-microbial-world
#10
Eduardo Corel, Raphaël Méheust, Andrew K Watson, James O McInerney, Philippe Lopez, Eric Bapteste
Extensive microbial gene flows affect how we understand virology, microbiology, medical sciences, genetic modification and evolutionary biology. Phylogenies only provide a narrow view of these gene flows: plasmids and viruses, lacking core genes, cannot be attached to cellular life on phylogenetic trees. Yet viruses and plasmids have a major impact on cellular evolution, affecting both the gene content and the dynamics of microbial communities. Using bipartite graphs that connect up to 149,000 clusters of homologous genes with 8217 related and unrelated genomes, we can in particular show patterns of gene sharing that do not map neatly with the organismal phylogeny...
January 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29346271/-bacterial-toxins-section-in-the-journal-toxins-a-fantastic-multidisciplinary-interplay-between-bacterial-pathogenicity-mechanisms-physiological-processes-genomic-evolution-and-subsequent-development-of-identification-methods-efficient-treatment-and-prevention
#11
EDITORIAL
Michel R Popoff
Toxins are powerful pathogenicity factors produced by certain bacteria, fungi, animals, and plants which mediate drastic interactions of these pathogens on the organism host[...].
January 18, 2018: Toxins
https://www.readbyqxmd.com/read/29344954/mixed-ductal-lobular-carcinomas-evidence-for-progression-from-ductal-to-lobular-morphology
#12
Amy E McCart Reed, Jamie R Kutasovic, Katia Nones, Jodi M Saunus, Leonard Da Silva, Felicity Newell, Stephen Kazakoff, Lewis Melville, Janani Jayanthan, Ana Cristina Vargas, Lynne E Reid, Jonathan Beesley, Xiao Qing Chen, Anne Marie Patch, D David Clouston, Alan Porter, Elizabeth Evans, John V Pearson, Georgia Chenevix-Trench, Margaret C Cummings, Nic Waddell, Sunil R Lakhani, Peter T Simpson
Mixed ductal-lobular carcinomas (MDL) display both ductal and lobular morphology, and are an archetypal example of intra-tumour morphological heterogeneity. The mechanisms underlying coexistence of these different morphologic entities are poorly understood, although theories include that these components either represent 'collision' of independent tumours or evolve from a common ancestor. We performed comprehensive clinico-pathological analysis of a cohort of 82 MDLs and found: i) MDLs more frequently co-exist with ductal carcinoma in situ (DCIS) than lobular carcinoma in situ (LCIS); ii) the E-cadherin-catenin complex was normal in the ductal component in 77...
January 18, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29344951/the-rise-of-a-novel-classification-system-for-endometrial-carcinoma-integration-of-molecular-subclasses
#13
REVIEW
Jessica McAlpine, Alicia Leon-Castillo, Tjalling Bosse
Endometrial cancer is a clinically heterogeneous disease and it is becoming increasingly clear that this heterogeneity may be a function of the diversity of the underlying molecular alterations. Recent large scale genomic studies have revealed that endometrial cancer can be divided into at least four distinct molecular subtypes, with well described underlying genomic aberrations. These subtypes can be reliably delineated and carry significant prognostic as well as predictive information; embracing and incorporating them into clinical practice is thus attractive...
January 17, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29344884/analyzing-dna-methylation-patterns-during-tumor-evolution
#14
Heng Pan, Olivier Elemento
Epigenetic modifications play a key role in cellular development and tumorigenesis. Recent large-scale genomic studies have shown that mutations in players of the epigenetic machinery and concomitant perturbation of epigenomic patterning are frequent events in tumors. Among epigenetic marks, DNA methylation is one of the best studied. Hyper- and hypo-methylation events of specific regulatory elements (such as promoters and enhancers) are sometimes thought to be correlated with expression of nearby genes. High-throughput bisulfite converted sequencing is currently the technology of choice for studying DNA methylation in base-pair resolution and on whole-genome scale...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344851/the-evolution-of-crispr-cas9-and-their-cousins-hope-or-hype
#15
REVIEW
Kulbhushan Chaudhary, Anirudha Chattopadhyay, Dharmendra Pratap
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system allows biologists to edit genomic DNA of any cell in precise and specific way, entailing great potential for crop improvement, drug development and gene therapy. The system involves a nuclease (Cas9) and a designed guide RNA that are involved in wide range of applications such as genome modification, transcriptional modulation, genomic loci marking and RNA tracking. The limitation of the technique, in view of resistance of thymidine-rich genome to Cas9 cleavage, has now been overcome by the use of Cpf1 nuclease...
January 17, 2018: Biotechnology Letters
https://www.readbyqxmd.com/read/29344811/metabolic-evolution-and-a-comparative-omics-analysis-of-corynebacterium-glutamicum-for-putrescine-production
#16
Zhen Li, Yu-Ping Shen, Xuan-Long Jiang, Li-Shen Feng, Jian-Zhong Liu
Putrescine is widely used in the industrial production of bioplastics, pharmaceuticals, agrochemicals, and surfactants. Because the highest titer of putrescine is much lower than that of its precursor L-ornithine reported in microorganisms to date, further work is needed to increase putrescine production in Corynebacterium glutamicum. We first compared 7 ornithine decarboxylase genes and found that the Enterobacter cloacae ornithine decarboxylase gene speC1 was most suitable for putrescine production in C. glutamicum...
January 17, 2018: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29344267/break-breast-cancer-addiction-by-crispr-cas9-genome-editing
#17
REVIEW
Haitao Yang, MariaLynn Jaeger, Averi Walker, Daniel Wei, Katie Leiker, Tao Weitao
Breast cancer is the leading diagnosed cancer for women globally. Evolution of breast cancer in tumorigenesis, metastasis and treatment resistance appears to be driven by the aberrant gene expression and protein degradation encoded by the cancer genomes. The uncontrolled cancer growth relies on these cellular events, thus constituting the cancerous programs and rendering the addiction towards them. These programs are likely the potential anticancer biomarkers for Personalized Medicine of breast cancer. This review intends to delineate the impact of the CRSPR/Cas-mediated genome editing in identification and validation of these anticancer biomarkers...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/29343788/multiple-losses-of-photosynthesis-and-convergent-reductive-genome-evolution-in-the-colourless-green-algae-prototheca
#18
Shigekatsu Suzuki, Rikiya Endoh, Ri-Ichiroh Manabe, Moriya Ohkuma, Yoshihisa Hirakawa
Autotrophic eukaryotes have evolved by the endosymbiotic uptake of photosynthetic organisms. Interestingly, many algae and plants have secondarily lost the photosynthetic activity despite its great advantages. Prototheca and Helicosporidium are non-photosynthetic green algae possessing colourless plastids. The plastid genomes of Prototheca wickerhamii and Helicosporidium sp. are highly reduced owing to the elimination of genes related to photosynthesis. To gain further insight into the reductive genome evolution during the shift from a photosynthetic to a heterotrophic lifestyle, we sequenced the plastid and nuclear genomes of two Prototheca species, P...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343598/coadaptation-of-mitochondrial-and-nuclear-genes-and-the-cost-of-mother-s-curse
#19
Tim Connallon, M Florencia Camus, Edward H Morrow, Damian K Dowling
Strict maternal inheritance renders the mitochondrial genome susceptible to accumulating mutations that harm males, but are otherwise benign or beneficial for females. This 'mother's curse' effect can degrade male survival and fertility if unopposed by counteracting evolutionary processes. Coadaptation between nuclear and mitochondrial genomes-with nuclear genes evolving to compensate for male-harming mitochondrial substitutions-may ultimately resolve mother's curse. However, males are still expected to incur a transient fitness cost during mito-nuclear coevolution, and it remains unclear how severe such costs should be...
January 31, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29343217/ceratocystis-cacaofunesta-genome-analysis-reveals-a-large-expansion-of-extracellular-phosphatidylinositol-specific-phospholipase-c-genes-pi-plc
#20
Eddy Patricia Lopez Molano, Odalys García Cabrera, Juliana Jose, Leandro Costa do Nascimento, Marcelo Falsarella Carazzolle, Paulo José Pereira Lima Teixeira, Javier Correa Alvarez, Ricardo Augusto Tiburcio, Paulo Massanari Tokimatu Filho, Gustavo Machado Alvares de Lima, Rafael Victório Carvalho Guido, Thamy Lívia Ribeiro Corrêa, Adriana Franco Paes Leme, Piotr Mieczkowski, Gonçalo Amarante Guimarães Pereira
BACKGROUND: The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus...
January 17, 2018: BMC Genomics
keyword
keyword
53798
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"