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https://www.readbyqxmd.com/read/28926571/whole-genome-sequencing-illuminates-the-evolution-and-spread-of-multidrug-resistant-tuberculosis-in-southwest-nigeria
#1
Madikay Senghore, Jacob Otu, Adam Witney, Florian Gehre, Emma L Doughty, Gemma L Kay, Phillip Butcher, Kayode Salako, Aderemi Kehinde, Nneka Onyejepu, Emmanuel Idigbe, Tumani Corrah, Bouke de Jong, Mark J Pallen, Martin Antonio
Nigeria has an emerging problem with multidrug-resistant tuberculosis (MDR-TB). Whole-genome sequencing was used to understand the epidemiology of tuberculosis and genetics of multi-drug resistance among patients from two tertiary referral centers in Southwest Nigeria. In line with previous molecular epidemiology studies, most isolates of Mycobacterium tuberculosis from this dataset belonged to the Cameroon clade within the Euro-American lineage. Phylogenetic analysis showed this clade was undergoing clonal expansion in this region, and suggests that it was involved in community transmission of sensitive and multidrug-resistant tuberculosis...
2017: PloS One
https://www.readbyqxmd.com/read/28926153/comparative-and-population-genomics-landscape-of-phellinus-noxius-a-hypervariable-fungus-causing-root-rot-in-trees
#2
Chia-Lin Chung, Tracy J Lee, Mitsuteru Akiba, Hsin-Han Lee, Tzu-Hao Kuo, Dang Liu, Huei-Mien Ke, Toshiro Yokoi, Marylette B Roa, Meiyeh J Lu, Ya-Yun Chang, Pao-Jen Ann, Jyh-Nong Tsai, Chien-Yu Chen, Shean-Shong Tzean, Yuko Ota, Tsutomu Hattori, Norio Sahashi, Ruey-Fen Liou, Taisei Kikuchi, Isheng J Tsai
The order Hymenochaetales of white rot fungi contain some of the most aggressive wood decayers causing tree deaths around the world. Despite their ecological importance and the impact of diseases they cause, little is known about the evolution and transmission patterns of these pathogens. Here, we sequenced and undertook comparative genomics analyses of Hymenochaetales genomes using brown root rot fungus Phellinus noxius, wood-decomposing fungus Phellinus lamaensis, laminated root rot fungus Phellinus sulphurascens, and trunk pathogen Porodaedalea pini...
September 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28925932/chloroplast-genome-sequence-of-clusterbean-cyamopsis-tetragonoloba-l-genome-structure-and-comparative-analysis
#3
Tanvi Kaila, Pavan K Chaduvla, Hukam C Rawal, Swati Saxena, Anshika Tyagi, S V Amitha Mithra, Amolkumar U Solanke, Pritam Kalia, T R Sharma, N K Singh, Kishor Gaikwad
Clusterbean (Cyamopsis tetragonoloba L.), also known as guar, belongs to the family Leguminosae, and is an annual herbaceous legume. Guar is the main source of galactomannan for gas mining industries. In the present study, the draft chloroplast genome of clusterbean was generated and compared to some of the previously reported legume chloroplast genomes. The chloroplast genome of clusterbean is 152,530 bp in length, with a quadripartite structure consisting of large single copy (LSC) and small single copy (SSC) of 83,025 bp and 17,879 bp in size, respectively, and a pair of inverted repeats (IRs) of 25,790 bp in size...
September 19, 2017: Genes
https://www.readbyqxmd.com/read/28924377/current-progresses-of-single-cell-dna-sequencing-in-breast-cancer-research
#4
REVIEW
Jianlin Liu, Ragini Adhav, Xiaoling Xu
Breast cancers display striking genetic and phenotypic diversities. To date, several hypotheses are raised to explain and understand the heterogeneity, including theories for cancer stem cell (CSC) and clonal evolution. According to the CSC theory, the most tumorigenic cells, while maintaining themselves through symmetric division, divide asymmetrically to generate non-CSCs with less tumorigenic and metastatic potential, although they can also dedifferentiate back to CSCs. Clonal evolution theory recapitulates that a tumor initially arises from a single cell, which then undergoes clonal expansion to a population of cancer cells...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/28924040/a-b-z-junction-induced-by-an-a-a-mismatch-in-gac-repeats-in-the-gene-for-cartilage-oligomeric-matrix-protein-promotes-binding-with-the-hz%C3%AE-adar1-protein
#5
Narendar Kolimi, Yogeeshwar Ajjugal, Thenmalarchelvi Rathinavelan
GAC repeat expansion from five to seven in the exonic region of the gene for cartilage oligomeric matrix protein (COMP) leads to pseudoachondroplasia, a skeletal abnormality. However, the molecular mechanism by which GAC expansions in the COMP gene lead to skeletal dysplasias is poorly understood. Here, we used MD simulations which indicate that an A...A mismatch in a d(GAC)6.d(GAC)6 duplex induces negative supercoiling, leading to a local B-to-Z DNA transition. This transition facilitates the binding of d(GAC)7...
September 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28923642/pancreas-transplantation-is-feasible-in-donors-with-shprintzen-goldberg-syndrome
#6
A Zanetti-Yabur, T Butler, J P Rocca, J A Graham
Shprintzen-Goldberg syndrome (SGS) is an autosomal dominant connective tissue disorder. To date, this report is the first account of a successful pancreas transplantation from an SGS donor. The similarity of the outcomes from previous year-on-year pancreas transplantations at the same center demonstrates promising results. Increasing awareness of the utilization of donors with SGS may promote expansion of center-specific criteria for organ acceptance. Therefore, every consideration should be given for use of organs from donors with this genetic abnormality because there is no evidence to suggest poorer allograft viability...
October 2017: Transplantation Proceedings
https://www.readbyqxmd.com/read/28923105/genetic-engineering-of-human-nk-cells-to-express-cxcr2-improves-migration-to-renal-cell-carcinoma
#7
Veronika Kremer, Maarten Ligtenberg, Rosa Zendehdel, Christina Seitz, Annet Duivenvoorden, Erik Wennerberg, Eugenia Colón, Ann-Helén Scherman-Plogell, Andreas Lundqvist
BACKGROUND: Adoptive natural killer (NK) cell transfer is being increasingly used as cancer treatment. However, clinical responses have so far been limited to patients with hematological malignancies. A potential limiting factor in patients with solid tumors is defective homing of the infused NK cells to the tumor site. Chemokines regulate the migration of leukocytes expressing corresponding chemokine receptors. Various solid tumors, including renal cell carcinoma (RCC), readily secrete ligands for the chemokine receptor CXCR2...
September 19, 2017: Journal for Immunotherapy of Cancer
https://www.readbyqxmd.com/read/28923025/intrafamilial-phenotypic-heterogeneity-in-a-taiwanese-family-with-a-mapt-p-r5h-mutation-a-case-report-and-literature-review
#8
Hui-Chi Lin, Chin-Hsien Lin, Pei-Lung Chen, Shih-Jung Cheng, Pei-Hao Chen
BACKGROUND: Frontotemporal degeneration (FTD) is a clinically and genetically heterogeneous neurodegenerative disorder characterized by deficits in executive function that frequently overlaps with parkinsonism and motor neuron disorders. Several genes have been identified to cause autosomal dominant forms of FTD, including the gene coding for the protein associated with microtubule tau (MAPT). While most reported pathogenic mutations in MAPT occur in exons 9-13, few families have been reported with mutations outside of this region...
September 18, 2017: BMC Neurology
https://www.readbyqxmd.com/read/28920889/therapies-targeting-dna-and-rna-in-huntington-s-disease
#9
REVIEW
Edward J Wild, Sarah J Tabrizi
No disease-slowing treatment exists for Huntington's disease, but its monogenic inheritance makes it an appealing candidate for the development of therapies targeting processes close to its genetic cause. Huntington's disease is caused by CAG repeat expansions in the HTT gene, which encodes the huntingtin protein; development of therapies to target HTT transcription and the translation of its mRNA is therefore an area of intense investigation. Huntingtin-lowering strategies include antisense oligonucleotides and RNA interference targeting mRNA, and zinc finger transcriptional repressors and CRISPR-Cas9 methods aiming to reduce transcription by targeting DNA...
October 2017: Lancet Neurology
https://www.readbyqxmd.com/read/28919995/mammary-tumor-derived-ccl2-enhances-pro-metastatic-systemic-inflammation-through-upregulation-of-il1%C3%AE-in-tumor-associated-macrophages
#10
Kelly Kersten, Seth B Coffelt, Marlous Hoogstraat, Niels J M Verstegen, Kim Vrijland, Metamia Ciampricotti, Chris W Doornebal, Cheei-Sing Hau, Max D Wellenstein, Camilla Salvagno, Parul Doshi, Esther H Lips, Lodewyk F A Wessels, Karin E de Visser
Patients with primary solid malignancies frequently exhibit signs of systemic inflammation. Notably, elevated levels of neutrophils and their associated soluble mediators are regularly observed in cancer patients, and correlate with reduced survival and increased metastasis formation. Recently, we demonstrated a mechanistic link between mammary tumor-induced IL17-producing γδ T cells, systemic expansion of immunosuppressive neutrophils and metastasis formation in a genetically engineered mouse model for invasive breast cancer...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28917518/genome-stability-of-programmed-stem-cell-products
#11
REVIEW
Ulrich Martin
Inherited and acquired genomic abnormalities are known to cause genetic diseases and contribute to cancer formation. Recent studies demonstrated a substantial mutational load in mouse and human embryonic and induced pluripotent stem cells (ESCs and iPSCs). Single nucleotide variants, copy number variations, and larger chromosomal abnormalities may influence the differentiation capacity of pluripotent stem cells and the functionality of their derivatives in disease modelling and drug screening, and are considered a serious risk for cellular therapies based on ESC or iPSC derivatives...
September 13, 2017: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/28916733/clonal-expansion-and-epigenetic-reprogramming-following-deletion-or-amplification-of-mutant-idh1
#12
Tali Mazor, Charles Chesnelong, Aleksandr Pankov, Llewellyn E Jalbert, Chibo Hong, Josie Hayes, Ivan V Smirnov, Roxanne Marshall, Camila F Souza, Yaoqing Shen, Pavithra Viswanath, Houtan Noushmehr, Sabrina M Ronen, Steven J M Jones, Marco A Marra, J Gregory Cairncross, Arie Perry, Sarah J Nelson, Susan M Chang, Andrew W Bollen, Annette M Molinaro, Henrik Bengtsson, Adam B Olshen, Samuel Weiss, Joanna J Phillips, H Artee Luchman, Joseph F Costello
IDH1 mutation is the earliest genetic alteration in low-grade gliomas (LGGs), but its role in tumor recurrence is unclear. Mutant IDH1 drives overproduction of the oncometabolite d-2-hydroxyglutarate (2HG) and a CpG island (CGI) hypermethylation phenotype (G-CIMP). To investigate the role of mutant IDH1 at recurrence, we performed a longitudinal analysis of 50 IDH1 mutant LGGs. We discovered six cases with copy number alterations (CNAs) at the IDH1 locus at recurrence. Deletion or amplification of IDH1 was followed by clonal expansion and recurrence at a higher grade...
September 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28916614/dysregulated-molecular-pathways-in-amyotrophic-lateral-sclerosis-frontotemporal-dementia-spectrum-disorder
#13
REVIEW
Fen-Biao Gao, Sandra Almeida, Rodrigo Lopez-Gonzalez
Frontotemporal dementia (FTD), the second most common form of dementia in people under 65 years of age, is characterized by progressive atrophy of the frontal and/or temporal lobes. FTD overlaps extensively with the motor neuron disease amyotrophic lateral sclerosis (ALS), especially at the genetic level. Both FTD and ALS can be caused by many mutations in the same set of genes; the most prevalent of these mutations is a GGGGCC repeat expansion in the first intron of C9ORF72 As shown by recent intensive studies, some key cellular pathways are dysregulated in the ALS-FTD spectrum disorder, including autophagy, nucleocytoplasmic transport, DNA damage repair, pre-mRNA splicing, stress granule dynamics, and others...
September 15, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28916533/sex-differences-in-the-prevalence-of-genetic-mutations-in-ftd-and-als-a-meta-analysis
#14
REVIEW
Ashley F Curtis, Mario Masellis, Ging-Yuek Robin Hsiung, Rahim Moineddin, Kathy Zhang, Bonnie Au, Geneva Millett, Ian Mackenzie, Ekaterina Rogaeva, Mary C Tierney
OBJECTIVE: To conduct a meta-analysis that investigates sex differences in the prevalence of mutations in the 3 most common genes that cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD)-chromosome 9 open reading frame 72 (C9orf72), progranulin (GRN), or microtubule-associated protein tau (MAPT)-in patients clinically diagnosed with these conditions. METHODS: MEDLINE, EMBASE, and PsycINFO databases were searched (inception to June 30, 2016)...
September 15, 2017: Neurology
https://www.readbyqxmd.com/read/28916451/switches-in-a-genetic-regulatory-system-under-multiplicative-non-gaussian-noise
#15
Xi Chen, Yan-Mei Kang, Yu-Xuan Fu
The non-Gaussian noise is multiplicatively introduced to model the universal fluctuation in the gene regulation of the bacteriophage λ. To investigate the key effect of non-Gaussian noise on the genetic on/off switch dynamics from the viewpoint of quantitative analysis, we employ the high-order perturbation expansion to deduce the stationary probability density of repressor concentration and the mean first passage time from low concentration to high concentration and vice versa. The occupation probability of different concentration states can be estimated from the height and shape of the peaks of the stationary probability density, which could be used to determine the overall expression level...
September 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28916151/dna-aptamer-generation-by-exselex-using-genetic-alphabet-expansion-with-a-mini-hairpin-dna-stabilization-method
#16
REVIEW
Ichiro Hirao, Michiko Kimoto, Kyung Hyun Lee
A novel aptamer generation method to greatly augment the affinity and stability of DNA aptamers was developed by genetic alphabet expansion combined with mini-hairpin DNA technology. The genetic alphabet expansion increases the physicochemical and structural diversities of DNA aptamers by introducing extra components, unnatural bases, as a fifth base, allowing for the enhancement of DNA aptamer affinities. Furthermore, the mini-hairpin DNA technology stabilizes DNA aptamers against nuclease digestion and thermal denaturation, by introducing an extraordinarily stable mini-hairpin DNA containing a GCGAAGC sequence...
September 12, 2017: Biochimie
https://www.readbyqxmd.com/read/28914569/mutations-in-myeloproliferative-neoplasms-their-significance-and-clinical-use
#17
Fiorella Schischlik, Robert Kralovics
Clonal hematologic diseases of the blood such as polycythemia vera, essential thrombocythemia and primary myelofibrosis belong to the BCR-ABL negative Myeloproliferative Neoplasms (MPN). These diseases are characterized by clonal expansion of hematopoietic precursor cells followed by increased production of differentiated cells of the myeloid lineage. Initiation of clonal hematopoiesis, formation of a clinical phenotype as well as disease progression form part of MPN disease evolution. The disease is driven by acquired somatic mutations in critical pathways such as cytokine signaling, epigenetic regulation, RNA splicing, and transcription factor signaling...
September 15, 2017: Expert Review of Hematology
https://www.readbyqxmd.com/read/28912245/a-neolithic-expansion-but-strong-genetic-structure-in-the-independent-history-of-new-guinea
#18
Anders Bergström, Stephen J Oppenheimer, Alexander J Mentzer, Kathryn Auckland, Kathryn Robson, Robert Attenborough, Michael P Alpers, George Koki, William Pomat, Peter Siba, Yali Xue, Manjinder S Sandhu, Chris Tyler-Smith
New Guinea shows human occupation since ~50 thousand years ago (ka), independent adoption of plant cultivation ~10 ka, and great cultural and linguistic diversity today. We performed genome-wide single-nucleotide polymorphism genotyping on 381 individuals from 85 language groups in Papua New Guinea and find a sharp divide originating 10 to 20 ka between lowland and highland groups and a lack of non-New Guinean admixture in the latter. All highlanders share ancestry within the last 10 thousand years, with major population growth in the same period, suggesting population structure was reshaped following the Neolithic lifestyle transition...
September 15, 2017: Science
https://www.readbyqxmd.com/read/28912174/senescence-is-a-spi1-pu-1-induced-anti-proliferative-mechanism-in-primary-hematopoietic-cells
#19
Laure Delestré, Cui Hengxiang, Michela Esposito, Cyril Quiveron, Elena Mylonas, Virginie Penard-Lacronique, Oliver Bischof, Christel Guillouf
Transcriptional deregulation caused by epigenetic or genetic alterations is a major cause of leukemic transformation. The Spi1/PU.1 transcription factor is a key regulator of many steps of hematopoiesis, and limits self-renewal of hematopoietic stem cells. The deregulation of its expression or activity contributes to leukemia, in which Spi1 can be either an oncogene or a tumor suppressor. Here, we explored whether cellular senescence, an anti-tumoral pathway that restrains cell proliferation, is a mechanism by which Spi1 limits hematopoietic cells expansion, and thus prevents the development of leukemia...
September 14, 2017: Haematologica
https://www.readbyqxmd.com/read/28906289/update-on-the-therapeutic-efficacy-of-tregs-in-ibd-thumbs-up-or-thumbs-down
#20
Massimo C Fantini, Giovanni Monteleone
Crohn's disease and ulcerative colitis, the 2 major forms of inflammatory bowel disease (IBD) in humans, arise in genetically predisposed individuals because of an abnormal immune response direct against constituents of the gut flora. Defects in counter-regulatory mechanisms are supposed to amplify and maintain the IBD-associated mucosal inflammation. Therefore, restoring the balance between inflammatory and anti-inflammatory pathways in the gut could contribute to halt the IBD-associated tissue-damaging immune response...
October 2017: Inflammatory Bowel Diseases
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