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https://www.readbyqxmd.com/read/28218921/visualizing-excitations-at-buried-heterojunctions-in-organic-semiconductor-blends
#1
Andreas C Jakowetz, Marcus L Böhm, Aditya Sadhanala, Sven Huettner, Akshay Rao, Richard H Friend
Interfaces play a crucial role in semiconductor devices, but in many device architectures they are nanostructured, disordered and buried away from the surface of the sample. Conventional optical, X-ray and photoelectron probes often fail to provide interface-specific information in such systems. Here we develop an all-optical time-resolved method to probe the local energetic landscape and electronic dynamics at such interfaces, based on the Stark effect caused by electron-hole pairs photo-generated across the interface...
February 20, 2017: Nature Materials
https://www.readbyqxmd.com/read/28211582/what-can-genome-wide-association-studies-tell-us-about-the-evolutionary-forces-maintaining-genetic-variation-for-quantitative-traits
#2
REVIEW
Emily B Josephs, John R Stinchcombe, Stephen I Wright
I. II. III. IV. V. References SUMMARY: Understanding the evolutionary forces that shape genetic variation within species has long been a goal of evolutionary biology. Integrating data for the genetic architecture of traits from genome-wide association mapping studies (GWAS) along with the development of new population genetic methods for identifying selection in sequence data may allow us to evaluate the roles of mutation-selection balance and balancing selection in shaping genetic variation at various scales...
February 17, 2017: New Phytologist
https://www.readbyqxmd.com/read/28196481/nuctools-analysis-of-chromatin-feature-occupancy-profiles-from-high-throughput-sequencing-data
#3
Yevhen Vainshtein, Karsten Rippe, Vladimir B Teif
BACKGROUND: Biomedical applications of high-throughput sequencing methods generate a vast amount of data in which numerous chromatin features are mapped along the genome. The results are frequently analysed by creating binary data sets that link the presence/absence of a given feature to specific genomic loci. However, the nucleosome occupancy or chromatin accessibility landscape is essentially continuous. It is currently a challenge in the field to cope with continuous distributions of deep sequencing chromatin readouts and to integrate the different types of discrete chromatin features to reveal linkages between them...
February 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28193203/first-insight-into-the-somatic-mutation-burden-of-neurofibromatosis-type-2-associated-grade-i-and-grade-ii-meningiomas-a-case-report-comprehensive-genomic-study-of-two-cranial-meningiomas-with-vastly-different-clinical-presentation
#4
Ramita Dewan, Alexander Pemov, Amalia S Dutra, Evgenia D Pak, Nancy A Edwards, Abhik Ray-Chaudhury, Nancy F Hansen, Settara C Chandrasekharappa, James C Mullikin, Ashok R Asthagiri, John D Heiss, Douglas R Stewart, Anand V Germanwala
BACKGROUND: Neurofibromatosis type 2 (NF2) is a rare autosomal dominant nervous system tumor predisposition disorder caused by constitutive inactivation of one of the two copies of NF2. Meningiomas affect about one half of NF2 patients, and are associated with a higher disease burden. Currently, the somatic mutation landscape in NF2-associated meningiomas remains largely unexamined. CASE PRESENTATION: Here, we present an in-depth genomic study of benign and atypical meningiomas, both from a single NF2 patient...
February 13, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28188333/use-of-modern-tomato-breeding-germplasm-for-deciphering-the-genetic-control-of-agronomical-traits-by-genome-wide-association-study
#5
Guillaume Bauchet, Stéphane Grenier, Nicolas Samson, Julien Bonnet, Laurent Grivet, Mathilde Causse
A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato...
February 10, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28173793/the-landscape-of-sex-differential-transcriptome-and-its-consequent-selection-in-human-adults
#6
Moran Gershoni, Shmuel Pietrokovski
BACKGROUND: The prevalence of several human morbid phenotypes is sometimes much higher than intuitively expected. This can directly arise from the presence of two sexes, male and female, in one species. Men and women have almost identical genomes but are distinctly dimorphic, with dissimilar disease susceptibilities. Sexually dimorphic traits mainly result from differential expression of genes present in both sexes. Such genes can be subject to different, and even opposing, selection constraints in the two sexes...
February 7, 2017: BMC Biology
https://www.readbyqxmd.com/read/28167752/cross-cultural-regularities-in-the-cognitive-architecture-of-pride
#7
Daniel Sznycer, Laith Al-Shawaf, Yoella Bereby-Meyer, Oliver Scott Curry, Delphine De Smet, Elsa Ermer, Sangin Kim, Sunhwa Kim, Norman P Li, Maria Florencia Lopez Seal, Jennifer McClung, Jiaqing O, Yohsuke Ohtsubo, Tadeg Quillien, Max Schaub, Aaron Sell, Florian van Leeuwen, Leda Cosmides, John Tooby
Pride occurs in every known culture, appears early in development, is reliably triggered by achievements and formidability, and causes a characteristic display that is recognized everywhere. Here, we evaluate the theory that pride evolved to guide decisions relevant to pursuing actions that enhance valuation and respect for a person in the minds of others. By hypothesis, pride is a neurocomputational program tailored by selection to orchestrate cognition and behavior in the service of: (i) motivating the cost-effective pursuit of courses of action that would increase others' valuations and respect of the individual, (ii) motivating the advertisement of acts or characteristics whose recognition by others would lead them to enhance their evaluations of the individual, and (iii) mobilizing the individual to take advantage of the resulting enhanced social landscape...
February 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28152414/coexisting-and-cooperating-mutations-in-npm1-mutated-acute-myeloid-leukemia
#8
Jay L Patel, Jonathan A Schumacher, Kimberly Frizzell, Shelly Sorrells, Wei Shen, Adam Clayton, Rakhi Jattani, Todd W Kelley
NPM1 insertion mutations represent a common recurrent genetic abnormality in acute myeloid leukemia (AML) patients. The frequency of these mutations varies from approximately 30% overall up to 50% in patients with a normal karyotype. Several recent studies have exploited advances in massively parallel sequencing technology to shed light on the complex genomic landscape of AML. We hypothesize that variant allele fraction (VAF) data derived from massively parallel sequencing studies may provide further insights into the clonal architecture and pathogenesis of NPM1-driven leukemogenesis...
January 23, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28120152/copy-number-variations-in-amyotrophic-lateral-sclerosis-piecing-the-mosaic-tiles-together-through-a-systems-biology-approach
#9
REVIEW
Giovanna Morello, Maria Guarnaccia, Antonio Gianmaria Spampinato, Valentina La Cognata, Velia D'Agata, Sebastiano Cavallaro
Amyotrophic lateral sclerosis (ALS) is a devastating and still untreatable motor neuron disease. Despite the molecular mechanisms underlying ALS pathogenesis that are still far from being understood, several studies have suggested the importance of a genetic contribution in both familial and sporadic forms of the disease. In addition to single-nucleotide polymorphisms (SNPs), which account for only a limited number of ALS cases, a consistent number of common and rare copy number variations (CNVs) have been associated to ALS...
January 24, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28089515/navigation-through-the-plasma-membrane-molecular-landscape-shapes-random-organelle-movement
#10
Alison R Dun, Gabriel J Lord, Rhodri S Wilson, Deirdre M Kavanagh, Katarzyna I Cialowicz, Shuzo Sugita, Seungmee Park, Lei Yang, Annya M Smyth, Andreas Papadopulos, Colin Rickman, Rory R Duncan
Eukaryotic plasma membrane organization theory has long been controversial, in part due to a dearth of suitably high-resolution techniques to probe molecular architecture in situ and integrate information from diverse data streams [1]. Notably, clustered patterning of membrane proteins is a commonly conserved feature across diverse protein families (reviewed in [2]), including the SNAREs [3], SM proteins [4, 5], ion channels [6, 7], and receptors (e.g., [8]). Much effort has gone into analyzing the behavior of secretory organelles [9-13], and understanding the relationship between the membrane and proximal organelles [4, 5, 12, 14] is an essential goal for cell biology as broad concepts or rules may be established...
February 6, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28089252/practical-approaches-for-whole-genome-sequence-analysis-of-heart-and-blood-related-traits
#11
Alanna C Morrison, Zhuoyi Huang, Bing Yu, Ginger Metcalf, Xiaoming Liu, Christie Ballantyne, Josef Coresh, Fuli Yu, Donna Muzny, Elena Feofanova, Navin Rustagi, Richard Gibbs, Eric Boerwinkle
Whole-genome sequencing (WGS) allows for a comprehensive view of the sequence of the human genome. We present and apply integrated methodologic steps for interrogating WGS data to characterize the genetic architecture of 10 heart- and blood-related traits in a sample of 1,860 African Americans. In order to evaluate the contribution of regulatory and non-protein coding regions of the genome, we conducted aggregate tests of rare variation across the entire genomic landscape using a sliding window, complemented by an annotation-based assessment of the genome using predefined regulatory elements and within the first intron of all genes...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28087070/can-evolution-supply-what-ecology-demands
#12
REVIEW
Hanna Kokko, Anurag Chaturvedi, Daniel Croll, Martin C Fischer, Frédéric Guillaume, Sophie Karrenberg, Ben Kerr, Gregor Rolshausen, Jessica Stapley
A simplistic view of the adaptive process pictures a hillside along which a population can climb: when ecological 'demands' change, evolution 'supplies' the variation needed for the population to climb to a new peak. Evolutionary ecologists point out that this simplistic view can be incomplete because the fitness landscape changes dynamically as the population evolves. Geneticists meanwhile have identified complexities relating to the nature of genetic variation and its architecture, and the importance of epigenetic variation is under debate...
January 11, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/28065669/the-role-of-chromatin-structure-in-gene-regulation-of-the-human-malaria-parasite
#13
REVIEW
Gayani Batugedara, Xueqing M Lu, Evelien M Bunnik, Karine G Le Roch
The human malaria parasite, Plasmodium falciparum, depends on a coordinated regulation of gene expression for development and propagation within the human host. Recent developments suggest that gene regulation in the parasite is largely controlled by epigenetic mechanisms. Here, we discuss recent advancements contributing to our understanding of the mechanisms controlling gene regulation in the parasite, including nucleosome landscape, histone modifications, and nuclear architecture. In addition, various processes involved in regulation of parasite-specific genes and gene families are examined...
January 5, 2017: Trends in Parasitology
https://www.readbyqxmd.com/read/28041874/economic-and-social-activities-on-ancient-cypriot-terraced-landscapes
#14
Elizabeth Ridder, Christopher S Galletti, Patricia L Fall, Steven E Falconer
We investigate ancient agricultural terraces and their associated social and economic activities across the site complex consisting of the village at Politiko-Troullia and its more extensive associated taskscape. Surface artifact distributions mapped over 12 ha are integrated with evidence excavated from this Bronze Age settlement in central Cyprus. Contrary to expectations, artifact densities do not diminish with distance from the village architecture. In particular, concentrations of Prehistoric Bronze Age ceramics and ground stone artifacts are most pronounced on nearby terraced hillsides...
December 29, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/28030373/what-are-the-most-promising-new-agents-in-acute-myeloid-leukemia
#15
David A Sallman, Jeffrey E Lancet
PURPOSE OF REVIEW: Although the treatment paradigm for acute myeloid leukemia (AML) had been largely unchanged for many years, in-depth molecular characterization has revolutionized our understanding of mutations that drive the disease, subsequently serving to guide current clinical investigation. Furthermore, recent advances in the field have highlighted the importance of optimizing known efficacious agents by improving drug delivery or bypassing resistance mechanisms. The current status of novel agents which are shaping the clinical management of AML patients are summarized in this review...
March 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28001295/gradients-in-cytoarchitectural-landscapes-of-the-isocortex-diprotodont-marsupials-in-comparison-to-eutherian-mammals
#16
Christine J Charvet, Cheryl D Stimpson, Young Do Kim, Mary Ann Raghanti, Albert H Lewandowski, Patrick R Hof, Aida Gómez-Robles, Fenna M Krienen, Chet C Sherwood
Although it has been claimed that marsupials possess a lower density of isocortical neurons compared with other mammals, little is known about cross-cortical variation in neuron distributions in this diverse taxonomic group. We quantified upper layer (layers II-IV) and lower layer (layers V-VI) neuron numbers per unit of cortical surface area in three diprotodont marsupial species (two macropodiformes, the red kangaroo and the parma wallaby, and a vombatiform, the koala) and compared these results to eutherian mammals (e...
December 21, 2016: Journal of Comparative Neurology
https://www.readbyqxmd.com/read/27999899/control-of-signaling-molecule-range-during-developmental-patterning
#17
REVIEW
Scott G Wilcockson, Catherine Sutcliffe, Hilary L Ashe
Tissue patterning, through the concerted activity of a small number of signaling pathways, is critical to embryonic development. While patterning can involve signaling between neighbouring cells, in other contexts signals act over greater distances by traversing complex cellular landscapes to instruct the fate of distant cells. In this review, we explore different strategies adopted by cells to modulate signaling molecule range to allow correct patterning. We describe mechanisms for restricting signaling range and highlight how such short-range signaling can be exploited to not only control the fate of adjacent cells, but also to generate graded signaling within a field of cells...
December 20, 2016: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/27999094/the-epigenetic-landscape-of-alu-repeats-delineates-the-structural-and-functional-genomic-architecture-of-colon-cancer-cells
#18
Mireia Jordà, Anna Díez-Villanueva, Izaskun Mallona, Berta Martín, Sergi Lois, Víctor Barrera, Manel Esteller, Tanya Vavouri, Miguel A Peinado
Cancer cells exhibit multiple epigenetic changes with prominent local DNA hypermethylation and widespread hypomethylation affecting large chromosomal domains. Epigenome studies often disregard the study of repeat elements owing to technical complexity and their undefined role in genome regulation. We have developed NSUMA (Next-generation Sequencing of UnMethylated Alu), a cost-effective approach allowing the unambiguous interrogation of DNA methylation in more than 130,000 individual Alu elements, the most abundant retrotransposon in the human genome...
January 2017: Genome Research
https://www.readbyqxmd.com/read/27993639/the-impact-of-detergents-on-the-tissue-decellularization-process-a-tof-sims-study
#19
Lisa J White, Adam J Taylor, Denver M Faulk, Timothy J Keane, Lindsey T Saldin, Janet E Reing, Ilea T Swinehart, Neill J Turner, Buddy D Ratner, Stephen F Badylak
: Biologic scaffolds are derived from mammalian tissues, which must be decellularized to remove cellular antigens that would otherwise incite an adverse immune response. Although widely used clinically, the optimum balance between cell removal and the disruption of matrix architecture and surface ligand landscape remains a considerable challenge. Here we describe the use of time of flight secondary ion mass spectroscopy (ToF-SIMS) to provide sensitive, molecular specific, localized analysis of detergent decellularized biologic scaffolds...
December 16, 2016: Acta Biomaterialia
https://www.readbyqxmd.com/read/27992089/the-genetics-of-adaptation-to-discrete-heterogeneous-environments-frequent-mutation-or-large-effect-alleles-can-allow-range-expansion
#20
Kimberly J Gilbert, Michael C Whitlock
Range expansions are complex evolutionary and ecological processes. From an evolutionary standpoint, a populations' adaptive capacity can determine the success or failure of expansion. Using individual-based simulations we model range expansion over a two-dimensional, approximately continuous landscape. We investigate the ability of populations to adapt across patchy environmental gradients and examine how the effect sizes of mutations influence the ability to adapt to novel environments during range expansion...
December 19, 2016: Journal of Evolutionary Biology
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