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Functional mapping

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https://www.readbyqxmd.com/read/29356296/beyond-pathways-genetic-dissection-of-tocopherol-content-in-maize-kernels-by-combining-linkage-and-association-analyses
#1
Hong Wang, Shutu Xu, Yaming Fan, Nannan Liu, Wei Zhan, Haijun Liu, Yingjie Xiao, Kun Li, Qingchun Pan, Wenqiang Li, Min Deng, Jie Liu, Min Jin, Xiaohong Yang, Jiansheng Li, Qing Li, Jianbing Yan
Although tocopherols play an important role in plants and animals, the genetic architecture of tocopherol content in maize kernels has remained largely unknown. In this study, linkage and association analyses were conducted to examine the genetic architecture of tocopherol content in maize kernels. Forty-one unique quantitative trait loci (QTLs) were identified by linkage mapping in six populations of recombinant inbred lines (RILs). In addition, 32 significant loci were detected via genome-wide association study (GWAS), 18 of which co-localized with the QTLs identified by linkage mapping...
January 21, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29355798/awake-surgery-for-gliomas-within-the-right-inferior-parietal-lobule-new-insights-into-the-functional-connectivity-gained-from-stimulation-mapping-and-surgical-implications
#2
Alice Rolland, Guillaume Herbet, Hugues Duffau
OBJECTIVE: Little is known about the functional role of the white matter connections running within and around the right inferior parietal lobule (IPL). We used direct electrostimulation during awake surgery to investigate this connectivity and to avoid permanent deficit following resection for right IPL gliomas. METHODS: We reviewed patients who underwent awake mapping for a glioma involving the right IPL. Resection was achieved up to functional cortico-subcortical boundaries detected by electrostimulation...
January 16, 2018: World Neurosurgery
https://www.readbyqxmd.com/read/29355763/transcriptomic-analysis-of-exosomal-shuttle-mrna-in-pacific-oyster-crassostrea-gigas-during-bacterial-stimulation
#3
Mengqiang Wang, Mei Liu, Baojie Wang, Keyong Jiang, Zhihao Jia, Lingling Wang, Lei Wang
As marine invertebrates, oysters lack adaptive immunity and employ innate immunity as the front line and almost the solo defense mechanism to protect them against invaders. Accumulating research achievements demonstrated that exosomes could act as innate immune effectors that contribute to host defense mechanism. To better understand the immune functions of exosomes in Crassostrea gigas against bacterial stimulation, RNA-Seq was applied to explore the global expression changes of exosomes in oyster after Staphylococcus aureus and Vibrio splendidus stimulation...
January 17, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29355703/genetic-influence-on-splenic-natural-killer-cell-frequencies-and-maturation-among-aged-mice
#4
S A Bumgardner, Y Zhou, Z Jiang, E J Coe, C L Yakaitis, Y Xiao, R Pazdro
Natural killer (NK) cells are cytotoxic innate lymphocytes that are integral to host defenses against viruses and neoplastic cells. Aging causes phenotypic and functional impairment of NK cells, which diminishes innate immune surveillance, yet the factors that determine the aged NK cell phenotype have not been completely defined. For instance, the genetic basis of the aged NK cell phenotype has not been established, but if determined, could highlight important genetic regulators of NK cells later in life. In this study, we estimated the heritability of splenic NK cell frequencies in aged mice from 15 classical and four wild-derived inbred strains...
January 17, 2018: Experimental Gerontology
https://www.readbyqxmd.com/read/29355597/elucidating-the-gene-regulatory-networks-modulating-cancer-stem-cells-and-non-stem-cancer-cells-in-high-grade-serous-ovarian-cancer
#5
Sibun Parida, Sohini Chakraborty, Ranjan Kumar Maji, Zhumur Ghosh
The origin and pathogenesis of epithelial ovarian cancer have perplexed investigators for decades. The most prevalent type of it is the high-grade serous ovarian carcinoma (HGSOv) which is a highly aggressive disease with high relapse rates and insurgence of chemo-resistance at later stages of treatment. These are driven by a rare population of stem cell like cancer cells called cancer stem cells (CSCs). We have taken up a systems approach to find out the common gene interaction paths between non-stem cancer cells and CSCs in HGSOv...
January 17, 2018: Genomics
https://www.readbyqxmd.com/read/29355077/the-cop9-signalosome-inhibits-cullin-ring-e3-ubiquitin-ligases-independently-of-its-deneddylase-activity
#6
Annabelle Suisse, Miklós Békés, Tony T Huang, Jessica E Treisman
The COP9 signalosome inhibits the activity of Cullin-RING E3 ubiquitin ligases by removing Nedd8 modifications from their Cullin subunits. Neddylation renders these complexes catalytically active, but deneddylation is also necessary for them to exchange adaptor subunits and avoid auto-ubiquitination. Although deneddylation is thought to be the primary function of the COP9 signalosome, additional activities have been ascribed to some of its subunits. We recently showed that COP9 subunits protect the transcriptional repressor and tumor suppressor Capicua from two distinct modes of degradation...
January 22, 2018: Fly
https://www.readbyqxmd.com/read/29355033/the-impact-of-operating-room-layout-on-circulating-nurse-s-work-patterns-and-flow-disruptions-a-behavioral-mapping-study
#7
Sara Bayramzadeh, Anjali Joseph, Dee San, Amin Khoshkenar, Kevin Taaffe, Roxana Jafarifiroozabadi, David M Neyens
AIM: To assess how the adjacencies of functionally different areas within operating rooms (ORs) can influence the circulating nurse's (CN) workflow patterns and disruptions. BACKGROUND: The CN plays a significant role in promoting patient safety during surgical procedures by observing, monitoring, and managing potential threats at and around the surgical field. Their work requires constant movement to different parts of the OR to support team members. The layout of the OR and crowded and cluttered environment might impact the CN's workflow and cause disruptions during the surgery...
January 1, 2018: HERD
https://www.readbyqxmd.com/read/29354284/mapping-the-operational-landscape-of-micrornas-in-synthetic-gene-circuits
#8
Tyler Quarton, Kristina Ehrhardt, James Lee, Srijaa Kannan, Yi Li, Lan Ma, Leonidas Bleris
MicroRNAs are a class of short, noncoding RNAs that are ubiquitous modulators of gene expression, with roles in development, homeostasis, and disease. Engineered microRNAs are now frequently used as regulatory modules in synthetic biology. Moreover, synthetic gene circuits equipped with engineered microRNA targets with perfect complementarity to endogenous microRNAs establish an interface with the endogenous milieu at the single-cell level. The function of engineered microRNAs and sensor systems is typically optimized through extensive trial-and-error...
2018: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/29354257/drought-effects-on-the-tissue-and-cell-specific-cytokinin-activity-in-poplar
#9
Shanty Paul, Henning Wildhagen, Dennis Janz, Andrea Polle
Climate change with increasing periods of drought is expected to reduce the yield of biomass crops such as poplars. To combat yield loss, it is important to better understand the molecular mechanisms that control growth under drought. Here, the goal was to resolve the drought-induced changes of active cytokinins, a main growth hormone in plants, at the tissue level in different cell types and organs of poplars (Populus × canescens) in comparison with growth, biomass, leaf shedding, photosynthesis and water potential...
February 2018: AoB Plants
https://www.readbyqxmd.com/read/29352808/frontal-dysconnectivity-in-22q11-2-deletion-syndrome-an-atlas-based-functional-connectivity-analysis
#10
Leah M Mattiaccio, Ioana L Coman, Carlie A Thompson, Wanda P Fremont, Kevin M Antshel, Wendy R Kates
BACKGROUND: 22q11.2 deletion syndrome (22q11DS) is a neurodevelopmental syndrome associated with deficits in cognitive and emotional processing. This syndrome represents one of the highest risk factors for the development of schizophrenia. Previous studies of functional connectivity (FC) in 22q11DS report aberrant connectivity patterns in large-scale networks that are associated with the development of psychotic symptoms. METHODS: In this study, we performed a functional connectivity analysis using the CONN toolbox to test for differential connectivity patterns between 54 individuals with 22q11DS and 30 healthy controls, between the ages of 17-25 years old...
January 20, 2018: Behavioral and Brain Functions: BBF
https://www.readbyqxmd.com/read/29352778/continuum-percolation-of-polydisperse-rods-in-quadrupole-fields-theory-and-simulations
#11
Shari P Finner, Mihail I Kotsev, Mark A Miller, Paul van der Schoot
We investigate percolation in mixtures of nanorods in the presence of external fields that align or disalign the particles with the field axis. Such conditions are found in the formulation and processing of nanocomposites, where the field may be electric, magnetic, or due to elongational flow. Our focus is on the effect of length polydispersity, which-in the absence of a field-is known to produce a percolation threshold that scales with the inverse weight average of the particle length. Using a model of non-interacting spherocylinders in conjunction with connectedness percolation theory, we show that a quadrupolar field always increases the percolation threshold and that the universal scaling with the inverse weight average no longer holds if the field couples to the particle length...
January 21, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29352123/tumor-tissue-detection-using-blood-oxygen-level-dependent-functional-mri-based-on-independent-component-analysis
#12
Huiyuan Huang, Junfeng Lu, Jinsong Wu, Zhongxiang Ding, Shuda Chen, Lisha Duan, Jianling Cui, Fuyong Chen, Dezhi Kang, Le Qi, Wusi Qiu, Seong-Whan Lee, ShiJun Qiu, Dinggang Shen, Yu-Feng Zang, Han Zhang
Accurate delineation of gliomas from the surrounding normal brain areas helps maximize tumor resection and improves outcome. Blood-oxygen-level-dependent (BOLD) functional MRI (fMRI) has been routinely adopted for presurgical mapping of the surrounding functional areas. For completely utilizing such imaging data, here we show the feasibility of using presurgical fMRI for tumor delineation. In particular, we introduce a novel method dedicated to tumor detection based on independent component analysis (ICA) of resting-state fMRI (rs-fMRI) with automatic tumor component identification...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352103/dynamic-cycling-of-t-snare-acylation-regulates-platelet-exocytosis
#13
Jinchao Zhang, Yunjie Huang, Jing Chen, Haining Zhu, Sidney W Whiteheart
Platelets regulate vascular integrity by secreting a host of molecules that promote hemostasis and its sequelae. Given the importance of platelet exocytosis, it is critical to understand how it is controlled. The t-SNAREs, SNAP-23 and syntaxin-11, lack classical transmembrane domains (TMDs), yet both are associated with platelet membranes and redistributed into cholesterol-dependent, lipid rafts when platelets were activated. Using metabolic labeling and hydroxylamine/HCl (HA) treatment, we showed that both contain thioester-linked acyl groups...
January 19, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29352046/local-corticotropin-releasing-factor-signaling-in-the-hypothalamic-paraventricular-nucleus
#14
Zhiying Jiang, Shivakumar Rajamanickam, Nicholas J Justice
Corticotropin-releasing factor (CRF) neurons in the Paraventricular Nucleus of the Hypothalamus (PVN) initiate Hypothalamic-Pituitary-Adrenal (HPA) axis activity through release of CRF into the portal system as part of a coordinated neuroendocrine, autonomic, and behavioral response to stress. Recent discovery of neurons expressing CRF receptor type 1 (CRFR1), the primary receptor for CRF, adjacent to CRF neurons within the PVN, suggest that CRF also signals within the hypothalamus to coordinate aspects of the stress response...
January 19, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29352038/microenvironment-induced-cd44v6-promotes-early-disease-progression-in-chronic-lymphocytic-leukemia
#15
Julia C Gutjahr, Eva Szenes, Lisa Tschech, Daniela Asslaber, Michaela Schlederer, Simone Roos, Xiaobing Yu, Tamara Girbl, Christina Sternberg, Alexander Egle, Fritz Aberger, Ronen Alon, Lukas Kenner, Richard Greil, Veronique Orian-Rousseau, Tanja N Hartmann
Chronic lymphocytic leukemia (CLL) outgrowth depends on signals from the microenvironment. We have previously found that in vitro reconstitution of this microenvironment induces specific variant isoforms of the adhesion molecule CD44, which confer human CLL with high affinity to hyaluronan (HA). Here, we determined the in vivo contribution of standard CD44 and its variants to leukemic B-cell homing and proliferation in Tcl1 transgenic mice with a B-cell-specific CD44 deficiency. In these mice, leukemia onset was delayed and leukemic infiltration of spleen, liver, and lungs, but not of bone marrow was decreased...
January 19, 2018: Blood
https://www.readbyqxmd.com/read/29352030/the-daunting-polygenicity-of-mental-illness-making-a-new-map
#16
REVIEW
Steven E Hyman
An epochal opportunity to elucidate the pathogenic mechanisms of psychiatric disorders has emerged from advances in genomic technology, new computational tools and the growth of international consortia committed to data sharing. The resulting large-scale, unbiased genetic studies have begun to yield new biological insights and with them the hope that a half century of stasis in psychiatric therapeutics will come to an end. Yet a sobering picture is coming into view; it reveals daunting genetic and phenotypic complexity portending enormous challenges for neurobiology...
March 19, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29351928/mapping-and-quantification-of-over-2-000-o-linked-glycopeptides-in-activated-human-t-cells-with-isotope-targeted-glycoproteomics-isotag
#17
Christina M Woo, Peder J Lund, Andrew C Huang, Mark M Davis, Carolyn R Bertozzi, Sharon Pitteri
Post-translational modifications (PTMs) on proteins often function to regulate signaling cascades, with the activation of T cells during an adaptive immune response being a classic example.  Mounting evidence indicates that the modification of proteins by O-linked N-acetylglucosamine (O-GlcNAc), the only mammalian glycan found on nuclear and cytoplasmic proteins, helps regulate T cell activation.  Yet, a mechanistic understanding of how O-GlcNAc functions in T cell activation remains elusive, partly because of the difficulties in mapping and quantifying O-GlcNAc sites...
January 19, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29351914/high-resolution-transcription-maps-reveal-the-widespread-impact-of-roadblock-termination-in-yeast
#18
Tito Candelli, Drice Challal, Jean-Baptiste Briand, Jocelyne Boulay, Odil Porrua, Jessie Colin, Domenico Libri
Transcription termination delimits transcription units but also plays important roles in limiting pervasive transcription. We have previously shown that transcription termination occurs when elongating RNA polymerase II (RNAPII) collides with the DNA-bound general transcription factor Reb1. We demonstrate here that many different DNA-binding proteins can induce termination by a similar roadblock (RB) mechanism. We generated high-resolution transcription maps by the direct detection of RNAPII upon nuclear depletion of two essential RB factors or when the canonical termination pathways for coding and non-coding RNAs are defective...
January 19, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29351890/evolutionary-mechanisms-studied-through-protein-fitness-landscapes
#19
REVIEW
Aneth S Canale, Pamela A Cote-Hammarlof, Julia M Flynn, Daniel Na Bolon
Biology has, and continues to be, shaped by evolutionary mechanisms. Within the past decade, local fitness landscapes have become experimentally tractable and are providing new perspectives on evolutionary mechanisms. Powered by next-generation sequencing, the impacts of all individual amino acid substitutions on function have been quantified for dozens of proteins. These fitness maps have been utilized to investigate the biophysical underpinnings of existing protein function as well as the appearance and enhancement of new protein functions...
January 16, 2018: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29351872/low-cortical-iron-and-high-entorhinal-cortex-volume-promote-cognitive-functioning-in-the-oldest-old
#20
Jiri M G van Bergen, Xu Li, Frances C Quevenco, Anton F Gietl, Valerie Treyer, Sandra E Leh, Rafael Meyer, Alfred Buck, Philipp A Kaufmann, Roger M Nitsch, Peter C M van Zijl, Christoph Hock, Paul G Unschuld
The aging brain is characterized by an increased presence of neurodegenerative and vascular pathologies. However, there is substantial variation regarding the relationship between an individual's pathological burden and resulting cognitive impairment. To identify correlates of preserved cognitive functioning at highest age, the relationship between β-amyloid plaque load, presence of small vessel cerebrovascular disease (SVCD), iron-burden, and brain atrophy was investigated. Eighty cognitively unimpaired participants (44 oldest-old, aged 85-96 years; 36 younger-old, aged 55-80 years) were scanned by integrated positron emission tomography-magnetic resonance imaging for assessing beta regional amyloid plaque load (18F-flutemetamol), white matter hyperintensities as an indicator of SVCD (fluid-attenuated inversion recovery-magnetic resonance imaging), and iron load (quantitative susceptibility mapping)...
December 20, 2017: Neurobiology of Aging
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