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https://www.readbyqxmd.com/read/29346589/urban-evolutionary-ecology-and-the-potential-benefits-of-implementing-genomics
#1
Christopher J Schell
Urban habitats are quickly becoming exceptional models to address adaptation under rapid environmental change, given the expansive temporal and spatial scales with which anthropogenic landscape conversion occurs. Urban ecologists in the last 10-15 years have done an extraordinary job of highlighting phenotypic patterns that correspond with urban living, as well as delineating urban population structure using traditional genetic markers. The underpinning genetic mechanisms that govern those phenotypic patterns, however, are less well established...
January 13, 2018: Journal of Heredity
https://www.readbyqxmd.com/read/29343630/emergence-and-dynamics-of-self-producing-information-niches-as-a-step-towards-pre-evolutionary-organization
#2
Richard J Carter, Karoline Wiesner, Stephen Mann
As a step towards understanding pre-evolutionary organization in non-genetic systems, we develop a model to investigate the emergence and dynamics of proto-autopoietic networks in an interacting population of simple information processing entities (automata). Our simulations indicate that dynamically stable strongly connected networks of mutually producing communication channels emerge under specific environmental conditions. We refer to these distinct organizational steady states as information niches In each case, we measure the information content by the Shannon entropy, and determine the fitness landscape, robustness and transition pathways for information niches subjected to intermittent environmental perturbations under non-evolutionary conditions...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29343286/diagnosis-and-management-of-transthyretin-familial-amyloid-polyneuropathy-in-japan-red-flag-symptom-clusters-and-treatment-algorithm
#3
REVIEW
Yoshiki Sekijima, Mitsuharu Ueda, Haruki Koike, Sonoko Misawa, Tomonori Ishii, Yukio Ando
Hereditary ATTR (ATTRm) amyloidosis (also called transthyretin-type familial amyloid polyneuropathy [ATTR-FAP]) is an autosomal-dominant, adult-onset, rare systemic disorder predominantly characterized by irreversible, progressive, and persistent peripheral nerve damage. TTR gene mutations (e.g. replacement of valine with methionine at position 30 [Val30Met (p.Val50Met)]) lead to destabilization and dissociation of TTR tetramers into variant TTR monomers, which form amyloid fibrils that deposit in peripheral nerves and various organs, giving rise to peripheral and autonomic neuropathy and several non-disease specific symptoms...
January 17, 2018: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/29340399/landscape-of-gene-networks-for-random-parameter-perturbation
#4
Chunhe Li
Landscape approaches have been exploited to study the stochastic dynamics of gene networks. However, how to calculate the landscape with a wide range of parameter variations and how to investigate the influence of the network topology on the global properties of gene networks remain to be elucidated. Here, I developed an approach for the landscape of random parameter perturbation (LRPP) to address this issue. Based on a self-consistent approximation approach, by making perturbations to parameters in a given range, I obtained the landscape for gene network systems...
January 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29338715/landscape-genomics-natural-selection-drives-the-evolution-of-mitogenome-in-penguins
#5
Barbara Ramos, Daniel González-Acuña, David E Loyola, Warren E Johnson, Patricia G Parker, Melanie Massaro, Gisele P M Dantas, Marcelo D Miranda, Juliana A Vianna
BACKGROUND: Mitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation can generate more efficient coupling of energy production. However, selection over mitochondrial DNA (mtDNA) genes has usually been evaluated at the population level. We sequenced by NGS 12 mitogenomes and with four published genomes, assessed genetic variation in ten penguin species distributed from the equator to Antarctica...
January 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29335433/conformational-landscape-of-the-prkaca-dnajb1-chimeric-kinase-the-driver-for-fibrolamellar-hepatocellular-carcinoma
#6
Michael D Tomasini, Yingjie Wang, Adak Karamafrooz, Geoffrey Li, Thijs Beuming, Jiali Gao, Susan S Taylor, Gianluigi Veglia, Sanford M Simon
In fibrolamellar hepatocellular carcinoma a single genetic deletion results in the fusion of the first exon of the heat shock protein 40, DNAJB1, which encodes the J domain, with exons 2-10 of the catalytic subunit of protein kinase A, PRKACA. This produces an enzymatically active chimeric protein J-PKAcα. We used molecular dynamics simulations and NMR to analyze the conformational landscape of native and chimeric kinase, and found an ensemble of conformations. These ranged from having the J-domain tucked under the large lobe of the kinase, similar to what was reported in the crystal structure, to others where the J-domain was dislodged from the core of the kinase and swinging free in solution...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29334896/global-analysis-of-prokaryotic-trna-derived-cyclodipeptide-biosynthesis
#7
Michael A Skinnider, Chad W Johnston, Nishanth J Merwin, Chris A Dejong, Nathan A Magarvey
BACKGROUND: Among naturally occurring small molecules, tRNA-derived cyclodipeptides are a class that have attracted attention for their diverse and desirable biological activities. However, no tools are available to link cyclodipeptide synthases identified within prokaryotic genome sequences to their chemical products. Consequently, it is unclear how many genetically encoded cyclodipeptides represent novel products, and which producing organisms should be targeted for discovery. RESULTS: We developed a pipeline for identification and classification of cyclodipeptide biosynthetic gene clusters and prediction of aminoacyl-tRNA substrates and complete chemical structures...
January 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29334187/surveying-the-landscape-of-optogenetic-methods-for-detection-of-protein-protein-interactions
#8
REVIEW
Matthew D Wiens, Robert E Campbell
Mapping the protein-protein interaction (PPi) landscape is of critical importance to furthering our understanding how cells and organisms function. Optogenetic methods, that is, approaches that utilize genetically encoded fluorophores or fluorogenic enzyme reactions, uniquely enable the visualization of biochemical phenomena in live cells with high spatial and temporal accuracy. Applying optogenetic methods to the detection of PPis requires the engineering of protein-based systems in which an optical signal undergoes a substantial change when the two proteins of interest interact...
January 15, 2018: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29332359/novel-molecular-and-metabolic-aspects-in-osteosarcoma
#9
Evangelos Tsiambas, Panagiotis P Fotiades, Chrissa Sioka, Dimitrios Kotrotsios, Evangelia Gkika, Andreas Fotopoulos, Stylianos N Mastronikolis, Ilianna E Armata, Evangelos Giotakis, Vasileios Ragos
Osteosarcoma (OS) is the most frequent bone-forming malignancy in children and adolescents. Concerning its molecular landscape, there is no a direct relationship with a specific gene, but a combination of genetic events. A broad spectrum of activated oncogenes and downregulated suppressor genes has been already explored and considered crucial for its progressive pathogenesis. Mechanisms of gene deregulation include amplifications, point mutations, allelic losses and also epigenetic abnormalities such as aberrant promoter methylation...
November 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/29330750/immunologic-and-gene-expression-profiles-of-spontaneous-canine-oligodendrogliomas
#10
Anna Filley, Mario Henriquez, Tanmoy Bhowmik, Brij Nath Tewari, Xi Rao, Jun Wan, Margaret A Miller, Yunlong Liu, R Timothy Bentley, Mahua Dey
Malignant glioma (MG), the most common primary brain tumor in adults, is extremely aggressive and uniformly fatal. Several treatment strategies have shown significant preclinical promise in murine models of glioma; however, none have produced meaningful clinical responses in human patients. We hypothesize that introduction of an additional preclinical animal model better approximating the complexity of human MG, particularly in interactions with host immune responses, will bridge the existing gap between these two stages of testing...
January 12, 2018: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29330292/microenvironmental-derived-regulation-of-hif-signaling-drives-transcriptional-heterogeneity-in-glioblastoma-multiforme
#11
Dieter Henrik Heiland, Annette Gaebelein, Melanie Boerries, Jakob Woerner, Nils Pompe, Pamela Franco, Sabrina Heynckes, Mark D Bartholomä, Darren Ó hAilín, Maria Stella Carro, Marco Prinz, Stefan Weber, Irina Mader, Daniel Delev, Oliver Schnell
The evolving and highly heterogeneous nature of malignant brain tumors underlies their limited response to therapy and poor prognosis. In addition to genetic alterations, highly dynamic processes such as transcriptional and metabolic reprogramming play an important role in the development of tumor heterogeneity. The present study reports an adaptive mechanism in which the metabolic environment of malignant glioma drives transcriptional reprogramming. Multi-regional analysis of a glioblastoma patient biopsy revealed a metabolic landscape marked by varying stages of hypoxia and creatine enrichment...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29325622/the-emerging-genetic-landscape-of-cerebral-palsy
#12
C L van Eyk, M A Corbett, A H Maclennan
Cerebral palsy (CP) is a broad clinical descriptor that encompasses a heterogeneous group of nonprogressive neurodevelopmental disabilities affecting movement and posture. While linked by the presence of damage to the developing brain, the etiology of CP is likely varied and the clinical outcomes are diverse. There is now a large body of evidence supporting a significant role for genetics in causation of CP. An increasing number of studies have identified likely causative genetic variants in families with CP, as well as in individual sporadic cases...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29324850/generalization-of-the-ewens-sampling-formula-to-arbitrary-fitness-landscapes
#13
Pavel Khromov, Constantin D Malliaris, Alexandre V Morozov
In considering evolution of transcribed regions, regulatory sequences, and other genomic loci, we are often faced with a situation in which the number of allelic states greatly exceeds the size of the population. In this limit, the population eventually adopts a steady state characterized by mutation-selection-drift balance. Although new alleles continue to be explored through mutation, the statistics of the population, and in particular the probabilities of seeing specific allelic configurations in samples taken from the population, do not change with time...
2018: PloS One
https://www.readbyqxmd.com/read/29321891/population-genetic-structure-of-the-endemic-rosewoods-dalbergia-cochinchinensis-and-d-%C3%A2-oliveri-at-a-regional-scale-reflects-the-indochinese-landscape-and-life-history-traits
#14
Ida Hartvig, Thea So, Suchitra Changtragoon, Hoa Thi Tran, Somsanith Bouamanivong, Ida Theilade, Erik Dahl Kjær, Lene Rostgaard Nielsen
Indochina is a biodiversity hot spot and harbors a high number of endemic species, most of which are poorly studied. This study explores the genetic structure and reproductive system of the threatened endemic timber species Dalbergia cochinchinensis and Dalbergia oliveri using microsatellite data from populations across Indochina and relates it to landscape characteristics and life-history traits. We found that the major water bodies in the region, Mekong and Tonle Sap, represented barriers to gene flow and that higher levels of genetic diversity were found in populations in the center of the distribution area, particularly in Cambodia...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29321190/genomic-landscape-of-pancreatic-neuroendocrine-tumours-the-international-cancer-genome-consortium
#15
Andrea Mafficini, Aldo Scarpa
Neuroendocrine tumours (NETs) may arise throughout the body and are a highly heterogeneous, relatively rare class of neoplasms difficult to study also for the lack of disease models. Despite this, knowledge on their molecular alterations has expanded in the latest years, also building from genetic syndromes causing their onset. Pancreatic NETs (PanNETs) have been among the most studied, and research so far has outlined a series of recurring features, as inactivation of MEN1, VHL, TSC1/2 genes, and hyperactivation of the PI3K/mTOR pathway...
January 10, 2018: Journal of Endocrinology
https://www.readbyqxmd.com/read/29317621/integrated-omics-dissection-of-proteome-dynamics-during-cardiac-remodeling
#16
Edward Lau, Quan Cao, Maggie P Y Lam, Jie Wang, Dominic C M Ng, Brian J Bleakley, Jessica M Lee, David A Liem, Ding Wang, Henning Hermjakob, Peipei Ping
Transcript abundance and protein abundance show modest correlation in many biological models, but how this impacts disease signature discovery in omics experiments is rarely explored. Here we report an integrated omics approach, incorporating measurements of transcript abundance, protein abundance, and protein turnover to map the landscape of proteome remodeling in a mouse model of pathological cardiac hypertrophy. Analyzing the hypertrophy signatures that are reproducibly discovered from each omics data type across six genetic strains of mice, we find that the integration of transcript abundance, protein abundance, and protein turnover data leads to 75% gain in discovered disease gene candidates...
January 9, 2018: Nature Communications
https://www.readbyqxmd.com/read/29317610/enrichment-of-schizophrenia-heritability-in-both-neuronal-and-glia-cell-regulatory-elements
#17
Katherine E Tansey, Matthew J Hill
Genome-wide association studies have identified over 100 robust risk loci for schizophrenia with thousands of variants mediating genetic heritability, the majority of which reside in non-coding regions. Analytical approaches have shown this heritability is strongly enriched at variants within regulatory elements identified from human post-mortem brain tissue. However, bulk post-mortem brain tissue has a heterogeneous cell composition, making biological interpretations difficult. We sought to refine the cell types mediating schizophrenia heritability by separating neuronal and glial signals using data from: (1) NeuN-sorted post-mortem brain and (2) cell culture systems...
January 10, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29316426/clinical-sequencing-defines-the-genomic-landscape-of-metastatic-colorectal-cancer
#18
Rona Yaeger, Walid K Chatila, Marla D Lipsyc, Jaclyn F Hechtman, Andrea Cercek, Francisco Sanchez-Vega, Gowtham Jayakumaran, Sumit Middha, Ahmet Zehir, Mark T A Donoghue, Daoqi You, Agnes Viale, Nancy Kemeny, Neil H Segal, Zsofia K Stadler, Anna M Varghese, Ritika Kundra, Jianjiong Gao, Aijazuddin Syed, David M Hyman, Efsevia Vakiani, Neal Rosen, Barry S Taylor, Marc Ladanyi, Michael F Berger, David B Solit, Jinru Shia, Leonard Saltz, Nikolaus Schultz
Metastatic colorectal cancers (mCRCs) are clinically heterogeneous, but the genomic basis of this variability remains poorly understood. We performed prospective targeted sequencing of 1,134 CRCs. We identified splice alterations in intronic regions of APC and large in-frame deletions in CTNNB1, increasing oncogenic WNT pathway alterations to 96% of CRCs. Right-sided primary site in microsatellite stable mCRC was associated with shorter survival, older age at diagnosis, increased mutations, and enrichment of oncogenic alterations in KRAS, BRAF, PIK3CA, AKT1, RNF43, and SMAD4 compared with left-sided primaries...
January 8, 2018: Cancer Cell
https://www.readbyqxmd.com/read/29316027/somatic-mutations-activating-wiskott-aldrich-syndrome-protein-concomitant-with-ras-pathway-mutations-in-juvenile-myelomonocytic-leukemia-patients
#19
A Coppe, L Nogara, M S Pizzuto, A Cani, S Cesaro, R Masetti, F Locatelli, G Te Kronnie, G Basso, S Bortoluzzi, S Bresolin
The WAS gene product is expressed exclusively in the cytoplasm of hematopoietic cells and constitutional genetic abrogation of WASP leads to Wiskott-Aldrich syndrome (WAS). Moreover, mutational activation of WASP has been associated with X-linked neutropenia (XLN). Although studies reported that patients with constitutional WAS mutations affecting functional WASP expression may present Juvenile MyeloMonocytic Lukemia (JMML)-like features, confounding differential diagnosis above all in the co-presence of mutated RAS, an activating somatic mutation of WASP has not been previously described in JMML patients...
January 7, 2018: Human Mutation
https://www.readbyqxmd.com/read/29315108/review-of-molecular-classification-and-treatment-implications-of-pediatric-brain-tumors
#20
Ana S Guerreiro Stucklin, Vijay Ramaswamy, Craig Daniels, Michael D Taylor
PURPOSE OF REVIEW: Brain tumors are the most common solid tumors and leading cause of cancer-related death in children. The advent of large-scale genomics has resulted in a plethora of profiling studies that have mapped the genetic and epigenetic landscapes of pediatric brain tumors, ringing in a new era of precision diagnostics and targeted therapies. In this review, we highlight the most recent findings, focusing on studies published after 2015, and discuss how new evidence is changing the care of children with brain tumors...
February 2018: Current Opinion in Pediatrics
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