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landscape genetics

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https://www.readbyqxmd.com/read/29792700/the-energy-landscapes-of-mini-dumbbell-dna-octanucleotides
#1
James S Klimavicz, Konstantin Röder, David J Wales
Single-stranded DNA structures play a significant role in biological systems, in particular during replication, translation and DNA repair. Tracts of simple repetitive DNA (srDNA) are associated with slipped-strand mispairing (SSMs), that can lead to genetic diseases. Recent NMR studies of TTTA and CCTG repeats have shown that these sequences form mini-dumbbells (MDBs), leading to frameshift mutations. Here we explore the energy landscapes of (CCTG)2 and (TTTA)2 , which are currently the smallest known molecules to form MDBs...
May 24, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29785967/eighty-routes-to-a-ribonucleotide-world-dispersion-and-stringency-in-the-decisive-selection
#2
Michael Yarus
We examine the initial emergence of genetics; that is, of an inherited chemical capability. The crucial actors are ribonucleotides, occasionally meeting in a prebiotic landscape. Previous work identified six influential variables during such random ribonucleotide pooling. Geochemical pools can be in periodic danger (e.g., from tides) or constant danger (e.g., from unfavorable weather). Such pools receive Gaussian nucleotide amounts sporadically, at random times, or get varying substrates simultaneously. Pools use cross-templated RNA synthesis (5'-5' product from 5'-3' template) or para-templated (5'-5' product from 5'-5' template) synthesis...
May 21, 2018: RNA
https://www.readbyqxmd.com/read/29785028/the-reference-epigenome-and-regulatory-chromatin-landscape-of-chronic-lymphocytic-leukemia
#3
Renée Beekman, Vicente Chapaprieta, Núria Russiñol, Roser Vilarrasa-Blasi, Núria Verdaguer-Dot, Joost H A Martens, Martí Duran-Ferrer, Marta Kulis, François Serra, Biola M Javierre, Steven W Wingett, Guillem Clot, Ana C Queirós, Giancarlo Castellano, Julie Blanc, Marta Gut, Angelika Merkel, Simon Heath, Anna Vlasova, Sebastian Ullrich, Emilio Palumbo, Anna Enjuanes, David Martín-García, Sílvia Beà, Magda Pinyol, Marta Aymerich, Romina Royo, Montserrat Puiggros, David Torrents, Avik Datta, Ernesto Lowy, Myrto Kostadima, Maša Roller, Laura Clarke, Paul Flicek, Xabier Agirre, Felipe Prosper, Tycho Baumann, Julio Delgado, Armando López-Guillermo, Peter Fraser, Marie-Laure Yaspo, Roderic Guigó, Reiner Siebert, Marc A Martí-Renom, Xose S Puente, Carlos López-Otín, Ivo Gut, Hendrik G Stunnenberg, Elias Campo, Jose I Martin-Subero
Chronic lymphocytic leukemia (CLL) is a frequent hematological neoplasm in which underlying epigenetic alterations are only partially understood. Here, we analyze the reference epigenome of seven primary CLLs and the regulatory chromatin landscape of 107 primary cases in the context of normal B cell differentiation. We identify that the CLL chromatin landscape is largely influenced by distinct dynamics during normal B cell maturation. Beyond this, we define extensive catalogues of regulatory elements de novo reprogrammed in CLL as a whole and in its major clinico-biological subtypes classified by IGHV somatic hypermutation levels...
May 21, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29781169/effects-of-urbanization-on-the-population-structure-of-freshwater-turtles-across-the-united-states
#4
David R Bowne, Bradley J Cosentino, Laurel J Anderson, Christopher P Bloch, Sandra Cooke, Patrick W Crumrine, Jason Dallas, Alexandra Doran, Jerald J Dosch, Daniel L Druckenbrod, Richard D Durtsche, Danielle Garneau, Kristen S Genet, Todd S Fredericksen, Peter A Kish, Mary Beth Kolozsvary, Frank T Kuserk, Erin S Lindquist, Carol Mankiewicz, James G March, Timothy J Muir, K Greg Murray, Madeline N Santulli, Frank J Sicignano, Peter D Smallwood, Rebecca A Urban, Kathy Winnett-Murray, Craig R Zimmermann
Landscape-scale alterations that accompany urbanization may negatively affect the population structure of wildlife species such as freshwater turtles. Changes to nesting sites and higher mortality rates due to vehicular collisions and increased predator populations may particularly affect immature turtles and mature female turtles. We hypothesized that the proportions of adult female and immature turtles in a population will negatively correlate with landscape urbanization. As a collaborative effort of the Ecological Research as Education Network (EREN), we sampled freshwater turtle populations in 11 states across the central and eastern United States...
May 20, 2018: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/29779206/old-new-and-emerging-immunohistochemical-markers-in-pheochromocytoma-and-paraganglioma
#5
REVIEW
Veronica K Y Cheung, Anthony J Gill, Angela Chou
The evolution of genetic research over the past two decades has greatly improved the understanding of pheochromocytomas and paragangliomas. It is now accepted that more than one third of pheochromocytoma and paragangliomas arise in the context of syndromic disease, usually hereditary. The genetic profile of these tumors also has important prognostic implications which may help guide treatment. Accompanying the changing molecular landscape is the development of new immunohistochemical markers. Initially used in assisting with diagnosis, immunohistochemical markers have now become an important adjunct to screening programs for inherited conditions and subsequently as prognostic markers...
May 19, 2018: Endocrine Pathology
https://www.readbyqxmd.com/read/29778791/evolutionary-transitions-in-controls-reconcile-adaptation-with-continuity-of-evolution
#6
REVIEW
Alexander V Badyaev
Evolution proceeds by accumulating functional solutions, necessarily forming an uninterrupted lineage from past solutions of ancestors to the current design of extant forms. At the population level, this process requires an organismal architecture in which the maintenance of local adaptation does not preclude the ability to innovate in the same traits and their continuous evolution. Representing complex traits as networks enables us to visualize a fundamental principle that resolves tension between adaptation and continuous evolution: phenotypic states encompassing adaptations traverse the continuous multi-layered landscape of past physical, developmental and functional associations among traits...
May 17, 2018: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29775654/targeting-cancer-s-metabolic-co-dependencies-a-landscape-shaped-by-genotype-and-tissue-context
#7
REVIEW
Junfeng Bi, Sihan Wu, Wenjing Zhang, Paul S Mischel
Tumors cells reprogram their metabolism to fuel rapid growth. The ability to trace nutrient fluxes in the context of specific alterations has provided new mechanistic insight into the process of oncogenic transformation. A broad array of complementary genetic, epigenetic, transcriptional and translational mechanisms has been identified, revealing a metabolic landscape of cancer. However, cancer metabolism is not a static or uniform process, including within a single tumor. Tumor cells adapt to changing environmental conditions, profoundly shaping the enzymatic dependencies of individual cells...
May 15, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29775073/diffuse-gliomas-for-nonneuropathologists-the-new-integrated-molecular-diagnostics
#8
Sunhee C Lee
Diffuse gliomas comprise the bulk of "brain cancer" in adults. The recent update to the 4th edition of the World Health Organization's classification of tumors of the central nervous system reflects an unprecedented change in the landscape of the diagnosis and management of diffuse gliomas that will affect all those involved in the management and care of patients. Of the recently discovered gene alterations, mutations in the Krebs cycle enzymes isocitrate dehydrogenases (IDHs) 1 and 2 have fundamentally changed the way the gliomas are understood and classified...
May 18, 2018: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/29773754/a-critical-neurodevelopmental-role-for-l-type-voltage-gated-calcium-channels-in-neurite-extension-and-radial-migration
#9
Satoshi Kamijo, Yuichiro Ishii, Shin-Ichiro Horigane, Kanzo Suzuki, Masamichi Ohkura, Junichi Nakai, Hajime Fujii, Sayaka Takemoto-Kimura, Haruhiko Bito
In spite of many association studies linking gene polymorphisms and mutations of L-type Voltage-Gated Ca2+ Channels (VGCC) in neurodevelopmental disorders, such as autism and schizophrenia, specific L-type VGCC roles during brain development remain unclear. Yet, calcium signaling has been shown to be essential for neurodevelopmental processes such as sculpting of neurites, functional wiring and fine tuning of growing networks. To bridge this gap, we performed submembraneous calcium imaging using a membrane-tethered genetically-encoded calcium indicator (GECI) Lck-G-CaMP7...
May 17, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29772684/the-changing-landscape-in-the-genetic-etiology-of-human-tooth-agenesis
#10
REVIEW
Meredith A Williams, Ariadne Letra
Despite much progress in understanding the genetics of syndromic tooth agenesis (TA), the causes of the most common, isolated TA remain elusive. Recent studies have identified novel genes and variants contributing to the etiology of TA, and revealed new pathways in which tooth development genes belong. Further, the use of new research approaches including next-generation sequencing has provided increased evidence supporting an oligogenic inheritance model for TA, and may explain the phenotypic variability of the condition...
May 16, 2018: Genes
https://www.readbyqxmd.com/read/29771000/molecular-testing-in-holoprosencephaly
#11
Paul Kruszka, Ariel F Martinez, Maximilian Muenke
Holoprosencephaly (HPE) is a structural brain anomaly characterized by failure of the forebrain to separate during early embryogenesis. Both genetic and environmental etiologies of HPE have been discovered over the last three decades. Traditionally, the genetic workup for HPE has been a karyotype, chromosomal microarray, and/or Sanger sequencing of select genes. The recent increased availability of next-generation sequencing has changed the molecular diagnostic landscape for HPE, associating new genes with this disorder such as FGFR1...
May 17, 2018: American Journal of Medical Genetics. Part C, Seminars in Medical Genetics
https://www.readbyqxmd.com/read/29764516/somatic-mutation-landscape-of-a-meningioma-and-its-pulmonary-metastasis
#12
Yaran Du, Ting Lu, Song Huang, Fangfang Ren, Gang Cui, Jian Chen
BACKGROUND: Extracranial metastasis (ENM) of meningiomas is extremely rare, and typically occurs several years after a primary tumor is diagnosed. However, the genetic changes underlying ENM events have not yet been investigated. CASE PRESENTATION: A 58-year-old male patient was sent to the emergency room of our hospital because of a sudden fall. Magnetic resonance imaging detected a mass at the right frontal sagittal sinus. He underwent tumor resection and recovered well, but post-operative computed tomography revealed three lumps on the right side of his chest...
May 4, 2018: Cancer communications
https://www.readbyqxmd.com/read/29763720/bap1-loss-is-unusual-in-well-differentiated-papillary-mesothelioma-and-may-predict-development-of-malignant-mesothelioma
#13
Hee Eun Lee, Julian R Molina, William R Sukov, Anja C Roden, Eunhee S Yi
Literature on BRCA1-associated protein 1 (BAP1) expression status in well-differentiated papillary mesothelioma (WDPM) is limited. In the present study, we examined the prevalence of BAP1 loss in WDPM by immunohistochemistry with clinical correlation, along with CDKN2A deletion status by fluorescence in situ hybridization (FISH). Eight patients diagnosed as WDPM were identified from the surgical pathology file. Adenomatoid tumors (n=8) and malignant mesothelioma (MM) (n=39) were included for comparison. BAP1 immunohistochemistry was performed on representative block(s) from each case...
May 12, 2018: Human Pathology
https://www.readbyqxmd.com/read/29762714/field-populations-of-wild-apis-cerana-honey-bees-exhibit-increased-genetic-diversity-under-pesticide-stress-along-an-agricultural-intensification-gradient-in-eastern-india
#14
Priyadarshini Chakrabarti, Sagartirtha Sarkar, Parthiba Basu
Pesticides have been reported to be one of the major drivers in the global pollinator losses. The large-scale decline in honey bees, an important pollinator group, has resulted in comprehensive studies on honey bee colonies. Lack of information on native wild pollinators has paved the way for this study, which highlights the underlying evolutionary changes occurring in the wild honey bee populations exposed to pesticides along an agricultural intensification landscape. The study reports an increased genetic diversity in native Apis cerana Fabricius (Hymenoptera: Apidae) populations continually exposed to pesticide stress...
May 1, 2018: Journal of Insect Science
https://www.readbyqxmd.com/read/29755524/a-clinical-roadmap-to-investigate-the-genetic-basis-of-pediatric-pheochromocytoma-which-genes-should-physicians-think-about
#15
REVIEW
Bernardo Dias Pereira, Tiago Nunes da Silva, Ana Teresa Bernardo, Rui César, Henrique Vara Luiz, Karel Pacak, Luísa Mota-Vieira
Pheochromocytoma is very rare at a pediatric age, and when it is present, the probability of a causative genetic mutation is high. Due to high costs of genetic surveys and an increasing number of genes associated with pheochromocytoma, a sequential genetic analysis driven by clinical and biochemical phenotypes is advised. The published literature regarding the genetic landscape of pediatric pheochromocytoma is scarce, which may hinder the establishment of genotype-phenotype correlations and the selection of appropriate genetic testing at this population...
2018: International Journal of Endocrinology
https://www.readbyqxmd.com/read/29755111/genomic-landscape-and-prognostic-analysis-of-mantle-cell-lymphoma
#16
Ping Yang, Weilong Zhang, Jing Wang, Yuanyuan Liu, Ran An, Hongmei Jing
To gain insight into the molecular pathogenesis of patients with mantle cell lymphoma (MCL), next-generation whole-exome sequencing of 16 MCL patients was performed. We identified recurrent mutations in genes that are well known to be functionally relevant in MCL, including ATM (37.5%), TP53 (31.3%), WHSC1 (31.3%), CCND1 (18.8%), NOTCH2 (6.3%), and CDKN2A (6.3%). We also identified somatic mutations in genes for which a functional role in MCL has not been previously suspected. These genes included CCDC15, APC, CDH1, S1PR1, ATRX, BRCA2, CASP8, and NOTCH3...
May 14, 2018: Cancer Gene Therapy
https://www.readbyqxmd.com/read/29754753/a-genetically-encoded-biosensor-reveals-location-bias-of-opioid-drug-action
#17
Miriam Stoeber, Damien Jullié, Braden T Lobingier, Toon Laeremans, Jan Steyaert, Peter W Schiller, Aashish Manglik, Mark von Zastrow
Opioid receptors (ORs) precisely modulate behavior when activated by native peptide ligands but distort behaviors to produce pathology when activated by non-peptide drugs. A fundamental question is how drugs differ from peptides in their actions on target neurons. Here, we show that drugs differ in the subcellular location at which they activate ORs. We develop a genetically encoded biosensor that directly detects ligand-induced activation of ORs and uncover a real-time map of the spatiotemporal organization of OR activation in living neurons...
May 5, 2018: Neuron
https://www.readbyqxmd.com/read/29749693/modeling-the-complex-etiology-of-holoprosencephaly-in-mice
#18
Mingi Hong, Robert S Krauss
Holoprosencephaly (HPE) is a common developmental defect caused by failure to define the midline of the forebrain and/or midface. HPE is associated with heterozygous mutations in Nodal and Sonic hedgehog (SHH) pathway components, but clinical presentation is highly variable, and many mutation carriers are unaffected. It is therefore thought that such mutations interact with more common modifiers, genetic and/or environmental, to produce severe patterning defects. Modifiers are difficult to identify, as their effects are context-dependent and occur within the complex genetic and environmental landscapes that characterize human populations...
May 11, 2018: American Journal of Medical Genetics. Part C, Seminars in Medical Genetics
https://www.readbyqxmd.com/read/29749054/dehydration-responsive-nuclear-proteome-landscape-of-chickpea-cicer-arietinum-l-reveals-phosphorylation-mediated-regulation-of-stress-response
#19
Pragya Barua, Nilesh Vikram Lande, Pratigya Subba, Dipak Gayen, Sneha Pinto, T S Keshav Prasad, Subhra Chakraborty, Niranjan Chakraborty
Non-availability of water or dehydration remains recurring climatic disorder affecting yield of major food crops, legumes in particular. Nuclear proteins (NP) and phosphoproteins (NPPs) execute crucial cellular functions that form the regulatory hub for coordinated stress response. Phosphoproteins hold enormous influence over cellular signalling. Four-week-old seedlings of a grain legume, chickpea, were subjected to gradual dehydration and nuclear proteins were extracted from unstressed control as well as from 72 and 144 h stressed tissues...
May 10, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29748182/a-pdx-organoid-biobank-of-advanced-prostate-cancers-captures-genomic-and-phenotypic-heterogeneity-for-disease-modeling-and-therapeutic-screening
#20
Michael L Beshiri, Caitlin M Tice, Crystal Tran, Holly M Nguyen, Adam G Sowalsky, Supreet Agarwal, Keith H Jansson, Qi Yang, Kerry A McGowen, Juan Juan Yin, Aian Neil Alilin, Fatima H Karzai, William Dahut, Eva Corey, Kathleen Kelly
PURPOSE: Prostate cancer translational research has been hampered by the lack of comprehensive and tractable models   that represent the genomic landscape of clinical disease. Metastatic castrate-resistant prostate cancer (mCRPC) patient-derived xenografts (PDXs) recapitulate the genetic and phenotypic diversity of the disease. We sought to establish a representative, preclinical platform of PDX-derived organoids that is experimentally facile for high throughput and mechanistic analysis...
May 10, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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