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https://www.readbyqxmd.com/read/28087070/can-evolution-supply-what-ecology-demands
#1
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 10, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/28065669/the-role-of-chromatin-structure-in-gene-regulation-of-the-human-malaria-parasite
#2
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
#3
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
#4
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...
December 26, 2016: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28001295/gradients-in-cytoarchitectural-landscapes-of-the-isocortex-diprotodont-marsupials-in-comparison-to-eutherian-mammals
#5
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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/27991561/genome-wide-analysis-of-wd40-protein-family-in-human
#10
Xu-Dong Zou, Xue-Jia Hu, Jing Ma, Tuan Li, Zhi-Qiang Ye, Yun-Dong Wu
The WD40 proteins, often acting as scaffolds to form functional complexes in fundamental cellular processes, are one of the largest families encoded by the eukaryotic genomes. Systematic studies of this family on genome scale are highly required for understanding their detailed functions, but are currently lacking in the animal lineage. Here we present a comprehensive in silico study of the human WD40 family. We have identified 262 non-redundant WD40 proteins, and grouped them into 21 classes according to their domain architectures...
December 19, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27989779/tracking-thoughts-exploring-the-neural-architecture-of-mental-time-travel-during-mind-wandering
#11
Theodoros Karapanagiotidis, Boris C Bernhardt, Elizabeth Jefferies, Jonathan Smallwood
The capacity to imagine situations that have already happened or fictitious events that may take place in the future is known as mental time travel (MTT). Studies have shown that MTT is an important aspect of spontaneous thought, yet we lack a clear understanding of how the neurocognitive architecture of the brain constrains this element of human cognition. Previous functional magnetic resonance imaging (MRI) studies have shown that MTT involves the coordination between multiple regions that include mesiotemporal structures such as the hippocampus, as well as prefrontal and parietal regions commonly associated with the default mode network (DMN)...
December 15, 2016: NeuroImage
https://www.readbyqxmd.com/read/27956125/open-mhealth-architecture-a-primer-for-tomorrow-s-orthopedic-surgeon-and-introduction-to-its-use-in-lower-extremity-arthroplasty
#12
REVIEW
Prem N Ramkumar, George F Muschler, Kurt P Spindler, Joshua D Harris, Patrick C McCulloch, Michael A Mont
BACKGROUND: The recent private-public partnership to unlock and utilize all available health data has large-scale implications for public health and personalized medicine, especially within orthopedics. Today, consumer based technologies such as smartphones and "wearables" store tremendous amounts of personal health data (known as "mHealth") that, when processed and contextualized, have the potential to open new windows of insight for the orthopedic surgeon about their patients. METHODS: In the present report, the landscape, role, and future technical considerations of mHealth and open architecture are defined with particular examples in lower extremity arthroplasty...
November 17, 2016: Journal of Arthroplasty
https://www.readbyqxmd.com/read/27939217/phb-associates-with-the-hira-complex-to-control-an-epigenetic-metabolic-circuit-in-human-escs
#13
Zhexin Zhu, Chunliang Li, Yanwu Zeng, Jianyi Ding, Zepeng Qu, Junjie Gu, Laixiang Ge, Fan Tang, Xin Huang, Chenlin Zhou, Ping Wang, Deyou Zheng, Ying Jin
The chromatin landscape and cellular metabolism both contribute to cell fate determination, but their interplay remains poorly understood. Using genome-wide siRNA screening, we have identified prohibitin (PHB) as an essential factor in self-renewal of human embryonic stem cells (hESCs). Mechanistically, PHB forms protein complexes with HIRA, a histone H3.3 chaperone, and stabilizes the protein levels of HIRA complex components. Like PHB, HIRA is required for hESC self-renewal. PHB and HIRA act together to control global deposition of histone H3...
November 17, 2016: Cell Stem Cell
https://www.readbyqxmd.com/read/27923844/characterization-of-hundreds-of-regulatory-landscapes-in-developing-limbs-reveals-two-regimes-of-chromatin-folding
#14
Guillaume Andrey, Robert Schöpflin, Ivana Jerković, Verena Heinrich, Daniel Murad Ibrahim, Christina Paliou, Myriam Hochradel, Bernd Timmermann, Stefan Haas, Martin Vingron, Stefan Mundlos
Complex regulatory landscapes control the pleiotropic transcriptional activities of developmental genes. For most genes, the number, location and dynamic of their associated regulatory elements are unknown. In this work we characterized the three-dimensional chromatin micro-architecture and regulatory landscape of 446 limb-associated gene loci in mouse using Capture-C, ChIP-seq and RNA-seq in forelimb, hindlimb at three developmental stages and midbrain. The fine mapping of chromatin interactions revealed a strong preference for functional genomic regions such as repressed or active domains...
December 6, 2016: Genome Research
https://www.readbyqxmd.com/read/27919246/adjacent-sequences-disclose-potential-for-intra-genomic-dispersal-of-satellite-dna-repeats-and-suggest-a-complex-network-with-transposable-elements
#15
Eva Satović, Tanja Vojvoda Zeljko, Andrea Luchetti, Barbara Mantovani, Miroslav Plohl
BACKGROUND: Satellite DNA (satDNA) sequences are typically arranged as arrays of tandemly repeated monomers. Due to the similarity among monomers, their organizational pattern and abundance, satDNAs are hardly accessible to structural and functional studies and still represent the most obscure genome component. Although many satDNA arrays of diverse length and even single monomers exist in the genome, surprisingly little is known about transition from satDNAs to other sequences. Studying satDNA monomers at junctions and identifying DNA sequences adjacent to them can help to understand the processes that (re)distribute satDNAs and significance that evolution of these sequence elements might have in creating the genomic landscape...
December 6, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27911722/dawn-of-the-in-vivo-rna-structurome-and-interactome
#16
REVIEW
Chun Kit Kwok
RNA is one of the most fascinating biomolecules in living systems given its structural versatility to fold into elaborate architectures for important biological functions such as gene regulation, catalysis, and information storage. Knowledge of RNA structures and interactions can provide deep insights into their functional roles in vivo For decades, RNA structural studies have been conducted on a transcript-by-transcript basis. The advent of next-generation sequencing (NGS) has enabled the development of transcriptome-wide structural probing methods to profile the global landscape of RNA structures and interactions, also known as the RNA structurome and interactome, which transformed our understanding of the RNA structure-function relationship on a transcriptomic scale...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27889101/highly-heterogeneous-genomic-landscape-of-uterine-leiomyomas-by%C3%A2-whole-exome-sequencing-and-genome-wide-arrays
#17
Svetlana A Yatsenko, Priya Mittal, Michelle A Wood-Trageser, Mirka W Jones, Urvashi Surti, Robert P Edwards, Anil K Sood, Aleksandar Rajkovic
OBJECTIVE: To determine the genomic signatures of human uterine leiomyomas and prevalence of MED12 mutations in human uterine leiomyosarcomas. DESIGN: Retrospective cohort study. SETTING: Not applicable. PATIENT(S): This study included a set of 16 fresh frozen leiomyoma and corresponding unaffected myometrium specimens as well as 153 leiomyosarcomas collected from women diagnosed with uterine leiomyomas or leiomyosarcomas who underwent clinically indicated abdominal hysterectomy...
November 23, 2016: Fertility and Sterility
https://www.readbyqxmd.com/read/27881085/the-ebola-outbreak-catalyzing-a-shift-in-global-health-governance
#18
Tim K Mackey
BACKGROUND: As the 2014 Ebola virus disease outbreak (EVD) transitions to its post-endemic phase, its impact on the future of global public health, particularly the World Health Organization (WHO), is the subject of continued debate. Criticism of WHO's performance grew louder in the outbreak's wake, placing this international health UN-specialized agency in the difficult position of navigating a complex series of reform recommendations put forth by different stakeholders. Decisions on WHO governance reform and the broader role of the United Nations could very well shape the future landscape of 21st century global health and how the international community responds to health emergencies...
November 24, 2016: BMC Infectious Diseases
https://www.readbyqxmd.com/read/27873369/the-genetic-architecture-of-novel-trophic-specialists-larger-effect-sizes-are-associated-with-exceptional-oral-jaw-diversification-in-a-pupfish-adaptive-radiation
#19
Christopher H Martin, Priscilla A Erickson, Craig T Miller
The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here, we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining the origins of ecological novelty: a sympatric radiation of pupfishes endemic to San Salvador Island, Bahamas, containing a large-jawed scale-eater and a short-jawed molluscivore with a skeletal nasal protrusion...
November 22, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27863252/the-allelic-landscape-of-human-blood-cell-trait-variation-and-links-to-common-complex-disease
#20
William J Astle, Heather Elding, Tao Jiang, Dave Allen, Dace Ruklisa, Alice L Mann, Daniel Mead, Heleen Bouman, Fernando Riveros-Mckay, Myrto A Kostadima, John J Lambourne, Suthesh Sivapalaratnam, Kate Downes, Kousik Kundu, Lorenzo Bomba, Kim Berentsen, John R Bradley, Louise C Daugherty, Olivier Delaneau, Kathleen Freson, Stephen F Garner, Luigi Grassi, Jose Guerrero, Matthias Haimel, Eva M Janssen-Megens, Anita Kaan, Mihir Kamat, Bowon Kim, Amit Mandoli, Jonathan Marchini, Joost H A Martens, Stuart Meacham, Karyn Megy, Jared O'Connell, Romina Petersen, Nilofar Sharifi, Simon M Sheard, James R Staley, Salih Tuna, Martijn van der Ent, Klaudia Walter, Shuang-Yin Wang, Eleanor Wheeler, Steven P Wilder, Valentina Iotchkova, Carmel Moore, Jennifer Sambrook, Hendrik G Stunnenberg, Emanuele Di Angelantonio, Stephen Kaptoge, Taco W Kuijpers, Enrique Carrillo-de-Santa-Pau, David Juan, Daniel Rico, Alfonso Valencia, Lu Chen, Bing Ge, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Ying Yang, Roderic Guigo, Stephan Beck, Dirk S Paul, Tomi Pastinen, David Bujold, Guillaume Bourque, Mattia Frontini, John Danesh, David J Roberts, Willem H Ouwehand, Adam S Butterworth, Nicole Soranzo
Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (<5%) and rare (<1%) variants with a strong impact on blood cell phenotypes. Our data highlight general properties of the allelic architecture of complex traits, including the proportion of the heritable component of each blood trait explained by the polygenic signal across different genome regulatory domains...
November 17, 2016: Cell
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