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https://www.readbyqxmd.com/read/29149047/new-insights-into-phasmatodea-chromosomes
#1
Thomas Liehr, Olesya Buleu, Tatyana Karamysheva, Alexander Bugrov, Nikolai Rubtsov
Currently, approximately 3000 species of stick insects are known; however, chromosome numbers, which range between 21 and 88, are known for only a few of these insects. Also, centromere banding staining (C-banding) patterns were described for fewer than 10 species, and fluorescence in situ hybridization (FISH) was applied exclusively in two Leptynia species. Interestingly, 10-25% of stick insects (Phasmatodea) are obligatory or facultative parthenogenetic. As clonal and/or bisexual reproduction can affect chromosomal evolution, stick insect karyotypes need to be studied more intensely...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29145855/generation-of-a-platform-strain-for-ionic-liquid-tolerance-using-adaptive-laboratory-evolution
#2
Elsayed T Mohamed, Shizeng Wang, Rebecca M Lennen, Markus J Herrgård, Blake A Simmons, Steven W Singer, Adam M Feist
BACKGROUND: There is a need to replace petroleum-derived with sustainable feedstocks for chemical production. Certain biomass feedstocks can meet this need as abundant, diverse, and renewable resources. Specific ionic liquids (ILs) can play a role in this process as promising candidates for chemical pretreatment and deconstruction of plant-based biomass feedstocks as they efficiently release carbohydrates which can be fermented. However, the most efficient pretreatment ILs are highly toxic to biological systems, such as microbial fermentations, and hinder subsequent bioprocessing of fermentative sugars obtained from IL-treated biomass...
November 16, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29144072/relapse-and-cytogenetic-evolution-in-myeloid-neoplasms
#3
Natalie Ertz-Archambault, Katalin Kelemen
Based on the current WHO Classification of Myeloid Neoplasms, cytogenetic findings play a central role in the diagnostic classification of the myeloid malignancies. Cytogenetic abnormalities detected at primary diagnosis may change over time. Karyotype changes can be characterized as cytogenetic evolution, cytogenetic regression or a combination of both. While the exact mechanism of cytogenetic evolution is not completely understood, the process of cytogenetic evolution is not random, but follows different, and often disease-specific patterns during progression and relapse of myeloid neoplasms...
December 2017: Panminerva Medica
https://www.readbyqxmd.com/read/29138301/genomic-variation-and-evolution-of-vibrio-parahaemolyticus-st36-over-the-course-of-a-transcontinental-epidemic-expansion
#4
Jaime Martinez-Urtaza, Ronny van Aerle, Michel Abanto, Julie Haendiges, Robert A Myers, Joaquin Trinanes, Craig Baker-Austin, Narjol Gonzalez-Escalona
Vibrio parahaemolyticus is the leading cause of seafood-related infections with illnesses undergoing a geographic expansion. In this process of expansion, the most fundamental change has been the transition from infections caused by local strains to the surge of pandemic clonal types. Pandemic clone sequence type 3 (ST3) was the only example of transcontinental spreading until 2012, when ST36 was detected outside the region where it is endemic in the U.S. Pacific Northwest causing infections along the U.S. northeast coast and Spain...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29134647/serial-profiling-of-circulating-tumor-dna-for-optimization-of-anti-vegf-chemotherapy-in-metastatic-colorectal-cancer-patients
#5
Masami Yamauchi, Yuji Urabe, Atsushi Ono, Daiki Miki, Hidenori Ochi, Kazuaki Chayama
Understanding the molecular changes in tumors in response to anti-VEGF chemotherapy is crucial for optimization of the treatment strategy for metastatic colorectal cancer. We prospectively investigated changes in the amount and constitution of circulating tumor DNA (ctDNA) in serial peripheral blood samples during chemotherapy. Sixty-one plasma samples taken at different time points (baseline, remission, and post-progression) and pre-treatment tumor samples were collected from 21 patients who received bevacizumab-containing first-line chemotherapy...
November 14, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29132167/smoldering-development-of-acute-megakaryoblastic-leukemia-with-clonal-evolution-in-an-infant-without-down-syndrome
#6
Eva Schmidt, Ute Fischer, Wolfgang Biskup, Claudia Haferlach, Roland Meisel, Michaela Kuhlen, Arndt Borkhardt
No abstract text is available yet for this article.
November 2017: Klinische Pädiatrie
https://www.readbyqxmd.com/read/29117356/spatio-temporal-genomic-heterogeneity-phylogeny-and-metastatic-evolution-in-salivary-adenoid-cystic-carcinoma
#7
Bin Liu, Yoshitsugu Mitani, Xiayu Rao, Mark Zafereo, Jianjun Zhang, Jianhua Zhang, P Andrew Futreal, Guillermina Lozano, Adel K El-Naggar
Background: Adenoid cystic carcinoma (ACC), an uncommon and indolent salivary gland malignancy, is characterized by varied morphologic and clinical manifestations. Molecular genetic studies of ACC identified certain structural and mutational alterations that may play a driver role in tumor development. The evolution and regional consistency of these events in ACC development progression are uncertain. Methods: To investigate the spatial and temporal clonal landscape of ACC, whole-genome sequencing and variant analyses were performed on 34 regionally sampled primary tumors and their concurrent and metachronous metastatic deposits from eight patients...
October 1, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29117127/amphibian-and-avian-karyotype-evolution-insights-from-lampbrush-chromosome-studies
#8
REVIEW
Anna Zlotina, Dmitry Dedukh, Alla Krasikova
Amphibian and bird karyotypes typically have a complex organization, which makes them difficult for standard cytogenetic analysis. That is, amphibian chromosomes are generally large, enriched with repetitive elements, and characterized by the absence of informative banding patterns. The majority of avian karyotypes comprise a small number of relatively large macrochromosomes and numerous tiny morphologically undistinguishable microchromosomes. A good progress in investigation of amphibian and avian chromosome evolution became possible with the usage of giant lampbrush chromosomes typical for growing oocytes...
November 8, 2017: Genes
https://www.readbyqxmd.com/read/29116628/the-biology-and-epidemiology-of-mycobacterium-canettii
#9
Philip Supply, Roland Brosch
Genome-based insights into the evolution of Mycobacterium tuberculosis and other tuberculosis-causing mycobacteria are constantly increasing. In particular, the recent genomic and functional characterization of several Myocbacterium canettii strains, which are thought to resemble in many aspects the putative common ancestor of the members of the M. tuberculosis complex (MTBC), has consolidated a plausible scenario of the early evolution of tuberculosis-causing mycobacteria, in which the clonal MTBC, comprising numerous key pathogens of mammalian hosts, has evolved from a generalist mycobacterium living in the environment...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29116627/the-nature-and-evolution-of-genomic-diversity-in-the-mycobacterium-tuberculosis-complex
#10
Daniela Brites, Sebastien Gagneux
The Mycobacterium tuberculosis Complex (MTBC) consists of a clonal group of several mycobacterial lineages pathogenic to a range of different mammalian hosts. In this chapter, we discuss the origins and the evolutionary forces shaping the genomic diversity of the human-adapted MTBC. Advances in whole-genome sequencing have brought invaluable insights into the macro-evolution of the MTBC, and the biogeographical distribution of the different MTBC lineages, the phylogenetic relationships between these lineages...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29112206/intratumoral-heterogeneity-and-clonal-evolution-in-blood-malignancies-and-solid-tumors
#11
Ignacio Varela, Pablo Menendez, Alejandra Sanjuan-Pla
This meeting held at the University of Barcelona in March 2017, brought together scientists and clinicians worldwide to discuss current and future clinico-biological implications of intratumoral heterogeneity (ITH) and subclonal evolution in cancer diagnosis, patient stratification, and treatment resistance in diagnosis, treatment and follow-up. There was consensus that both longitudinal and tumor multi-region studies in matched samples are needed to better understand the dynamics of ITH. The contribution of the epigenome and microenvironment to ITH and subclone evolution remains understudied...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29106464/application-of-single-cell-sequencing-in-human-cancer
#12
Mattias Rantalainen
Precision medicine is emerging as a cornerstone of future cancer care with the objective of providing targeted therapies based on the molecular phenotype of each individual patient. Traditional bulk-level molecular phenotyping of tumours leads to significant information loss, as the molecular profile represents an average phenotype over large numbers of cells, while cancer is a disease with inherent intra-tumour heterogeneity at the cellular level caused by several factors, including clonal evolution, tissue hierarchies, rare cells and dynamic cell states...
November 2, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29104505/effect-of-population-size-and-mutation-rate-on-the-evolution-of-rna-sequences-on-an-adaptive-landscape-determined-by-rna-folding
#13
Ali R Vahdati, Kathleen Sprouffske, Andreas Wagner
The dynamics of populations evolving on an adaptive landscape depends on multiple factors, including the structure of the landscape, the rate of mutations, and effective population size. Existing theoretical work often makes ad hoc and simplifying assumptions about landscape structure, whereas experimental work can vary important parameters only to a limited extent. We here overcome some of these limitations by simulating the adaptive evolution of RNA molecules, whose fitness is determined by the thermodynamics of RNA secondary structure folding...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29103700/mlva-16-typing-of-brucella-suis-biovar-2-strains-circulating-in-europe
#14
A C Ferreira, M I Corrêa de Sá, R Dias, R Tenreiro
Swine brucellosis due to Brucella suis biovar 2 is an emerging disease in Europe, associated with increase of extensive swine farms and high density of infected wild boars. Since knowledge of predominant circulating strains is a prerequisite for any epidemiological study, accurate molecular typing procedures were applied to a collection of 176 B. suis isolates. By using suis-ladder multiplex PCR and PCR-RFLP analysis of omp2a, omp2b and omp31 genes, five haplotypes were identified among 160 biovar 2 isolates, with haplotypes 2d and 2e restricted to Portugal and Spain and haplotypes 2a, 2b and 2c widespread in Europe (except Portugal)...
October 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/29101368/mutational-signatures-reveal-the-dynamic-interplay-of-risk-factors-and-cellular-processes-during-liver-tumorigenesis
#15
Eric Letouzé, Jayendra Shinde, Victor Renault, Gabrielle Couchy, Jean-Frédéric Blanc, Emmanuel Tubacher, Quentin Bayard, Delphine Bacq, Vincent Meyer, Jérémy Semhoun, Paulette Bioulac-Sage, Sophie Prévôt, Daniel Azoulay, Valérie Paradis, Sandrine Imbeaud, Jean-François Deleuze, Jessica Zucman-Rossi
Genomic alterations driving tumorigenesis result from the interaction of environmental exposures and endogenous cellular processes. With a diversity of risk factors, liver cancer is an ideal model to study these interactions. Here, we analyze the whole genomes of 44 new and 264 published liver cancers and we identify 10 mutational and 6 structural rearrangement signatures showing distinct relationships with environmental exposures, replication, transcription, and driver genes. The liver cancer-specific signature 16, associated with alcohol, displays a unique feature of transcription-coupled damage and is the main source of CTNNB1 mutations...
November 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/29096703/regulatory-and-evolutionary-signatures-of-sex-biased-genes-on-both-the-x-chromosome-and-the-autosomes
#16
Jiangshan J Shen, Ting-You Wang, Wanling Yang
BACKGROUND: Sex is an important but understudied factor in the genetics of human diseases. Analyses using a combination of gene expression data, ENCODE data, and evolutionary data of sex-biased gene expression in human tissues can give insight into the regulatory and evolutionary forces acting on sex-biased genes. METHODS: In this study, we analyzed the differentially expressed genes between males and females. On the X chromosome, we used a novel method and investigated the status of genes that escape X-chromosome inactivation (escape genes), taking into account the clonality of lymphoblastoid cell lines (LCLs)...
November 2, 2017: Biology of Sex Differences
https://www.readbyqxmd.com/read/29090344/the-role-of-mutant-idh1-and-idh2-inhibitors-in-the-treatment-of-acute-myeloid-leukemia
#17
REVIEW
Samah Nassereddine, Coen J Lap, Faysal Haroun, Imad Tabbara
For decades, researchers have looked into the pathophysiology of acute myeloid leukemia (AML). With the advances in molecular techniques, the two-hit hypothesis was replaced by a multi-hit model, which also emphasizes the importance of aberrant epigenetic regulation in the pathogenesis of AML. IDH1 and IDH2 are two isoforms of isocitrate dehydrogenase that perform crucial roles in cellular metabolism. Somatic mutations in either of these two genes impart a neomorphic enzymatic activity upon the encoded enzymes resulting in the ability to convert α-ketoglutarate (αKG) into the oncometabolite R2-hydroxyglutarate (R2-HG), which can competitively inhibit multiple αKG-dependent dioxygenases...
October 31, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/29079134/impact-of-chromosome-alterations-genetic-mutations-and-clonal-hematopoiesis-of-indeterminate-potential-chip-on-the-classification-and-risk-stratification-of-mds
#18
REVIEW
Bani Bandana Ganguly, Debasis Banerjee, Mohan B Agarwal
The advent of technological development has undoubtedly advanced biological and molecular inputs for better understanding the heterogeneous hematopoietic pre-malignant disorder of the stem cells known as myelodysplastic syndromes (MDS). Chromosomal rearrangements, including del(3q/5q/7q/11q/12p/20q), loss of 5/7/Y, trisomy 8/19, i(17q), etc. frequently detected in MDS with variable frequencies and combinations, are the integral components of the 5-tier risk-stratification and WHO-2016 classification. Observations on mutations in genes involved in RNA-splicing, DNA methylation, chromatin modification, transcription factor, signal transduction/kinases, RAS pathway, cohesin complex, DNA repair and other pathways have given insights in independent effects and biological interaction of co-occurrence on disease-phenotype and treatment outcome...
October 16, 2017: Blood Cells, Molecules & Diseases
https://www.readbyqxmd.com/read/29076131/minimal-residual-disease-in-non-hodgkin-lymphoma-current-applications-and-future-directions
#19
REVIEW
Matthew L Chase, Philippe Armand
Non-Hodgkin Lymphomas (NHLs) are a heterogeneous group of tumours with distinct treatment paradigms, but in all cases the goal of treatment is to maximize quality and duration of remission while minimizing therapy-related toxicity. Identification of persistent disease or relapse is most often the trigger to intensify or re-initiate anti-neoplastic therapy, respectively. In the current era of NHL treatment, this determination is mostly based on imaging and clinical evaluations, tools with imperfect sensitivity and specificity...
October 26, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/29075131/diversity-and-evolution-of-drug-resistance-mechanisms-in-mycobacterium-tuberculosis
#20
REVIEW
Mashael Al-Saeedi, Sahal Al-Hajoj
Despite the efficacy of antibiotics to protect humankind against many deadly pathogens, such as Mycobacterium tuberculosis, nothing can prevent the emergence of drug-resistant strains. Several mechanisms facilitate drug resistance in M. tuberculosis including compensatory evolution, epistasis, clonal interference, cell wall integrity, efflux pumps, and target mimicry. In this study, we present recent findings relevant to these mechanisms, which can enable the discovery of new drug targets and subsequent development of novel drugs for treatment of drug-resistant M...
2017: Infection and Drug Resistance
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