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Functional mapping

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https://www.readbyqxmd.com/read/28938400/il-1%C3%AE-inhibits-connexin-43-and-disrupts-decidualization-of-human-endometrial-stromal-cells-through-erk1-2-and-p38-map-kinase
#1
Jie Yu, Sarah L Berga, Wei Zou, D Grace Yook, Joshua C Pan, Aurora Arroyo Andrade, Lijuan Zhao, Neil Sidell, Indrani C Bagchi, Milan K Bagchi, Robert N Taylor
Inflammation can interfere with endometrial receptivity. We examined how IL-1β affects expression of the uterine gap junction protein, Cx43, which is known to be critical for embryonic implantation. We used an in vitro model of human endometrial stromal cells (ESC), Western blotting and a combination of validated, selective kinase inhibitors to evaluate five canonical IL-1β signaling pathways. Cx43 and two other markers of ESC differentiation (prolactin and VEGF) were inhibited predominantly via IL-1β-activated ERK1/2 and p38 MAP kinase cascades...
September 11, 2017: Endocrinology
https://www.readbyqxmd.com/read/28938276/anesthesia-with-dexmedetomidine-and-low-dose-isoflurane-increases-solute-transport-via-the-glymphatic-pathway-in-rat-brain-when-compared-with-high-dose-isoflurane
#2
Helene Benveniste, Hedok Lee, Fengfei Ding, Qian Sun, Ehab Al-Bizri, Rany Makaryus, Stephen Probst, Maiken Nedergaard, Elliot A Stein, Hanbing Lu
BACKGROUND: The glymphatic pathway transports cerebrospinal fluid through the brain, thereby facilitating waste removal. A unique aspect of this pathway is that its function depends on the state of consciousness of the brain and is associated with norepinephrine activity. A current view is that all anesthetics will increase glymphatic transport by inducing unconsciousness. This view implies that the effect of anesthetics on glymphatic transport should be independent of their mechanism of action, as long as they induce unconsciousness...
September 22, 2017: Anesthesiology
https://www.readbyqxmd.com/read/28938219/age-dependent-effects-of-acute-methylphenidate-on-amygdala-reactivity-in-stimulant-treatment-naive-patients-with-attention-deficit-hyperactivity-disorder
#3
Marco A Bottelier, Anouk Schrantee, Bart Ferguson, Hyke G H Tamminga, Cheima Bouziane, J J Sandra Kooij, Michiel B de Ruiter, Liesbeth Reneman
In the present study, we investigate whether methylphenidate (MPH) affects emotional processing and whether this effect is modulated by age. We measured amygdala reactivity with functional Magnetic Resonance Imaging (fMRI) during processing of angry and fearful facial expressions in male stimulant treatment-naive patients with ADHD (N = 35 boys; N = 46 men) and 23 healthy control subjects (N = 11 boys; N = 12 men). In ADHD patients, we also measured amygdala reactivity 90min after an acute oral challenge with MPH (0...
September 12, 2017: Psychiatry Research
https://www.readbyqxmd.com/read/28938018/genome-wide-identification-of-bacterial-plant-colonization-genes
#4
Benjamin J Cole, Meghan E Feltcher, Robert J Waters, Kelly M Wetmore, Tatiana S Mucyn, Elizabeth M Ryan, Gaoyan Wang, Sabah Ul-Hasan, Meredith McDonald, Yasuo Yoshikuni, Rex R Malmstrom, Adam M Deutschbauer, Jeffery L Dangl, Axel Visel
Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizing bacterium, to establish a genome-wide map of bacterial genes required for colonization of the Arabidopsis thaliana root system. We identified 115 genes (2% of all P. simiae genes) with functions that are required for maximal competitive colonization of the root system...
September 22, 2017: PLoS Biology
https://www.readbyqxmd.com/read/28937943/multiomics-analysis-of-tumor-microenvironment-reveals-gata2-and-mirna-124-3p-as-potential-novel-biomarkers-in-ovarian-cancer
#5
Esra Gov, Medi Kori, Kazim Yalcin Arga
Ovarian cancer is a common and, yet, one of the most deadly human cancers due to its insidious onset and the current lack of robust early diagnostic tests. Tumors are complex tissues comprised of not only malignant cells but also genetically stable stromal cells. Understanding the molecular mechanisms behind epithelial-stromal crosstalk in ovarian cancer is a great challenge in particular. In the present study, we performed comparative analyses of transcriptome data from laser microdissected epithelial, stromal, and ovarian tumor tissues, and identified common and tissue-specific reporter biomolecules-genes, receptors, membrane proteins, transcription factors (TFs), microRNAs (miRNAs), and metabolites-by integration of transcriptome data with genome-scale biomolecular networks...
September 22, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28937230/vagal-immune-interactions-involved-in-cholinergic-anti-inflammatory-pathway
#6
I Zila, D Mokra, J Kopincova, M Kolomaznik, M Javorka, A Calkovska
Inflammation and other immune responses are involved in the variety of diseases and disorders. The acute response to endotoxemia includes activation of innate immune mechanisms as well as changes in autonomic nervous activity. The autonomic nervous system and the inflammatory response are intimately linked and sympathetic and vagal nerves are thought to have anti-inflammation functions. The basic functional circuit between vagus nerve and inflammatory response was identified and the neuroimmunomodulation loop was called cholinergic anti-inflammatory pathway...
September 22, 2017: Physiological Research
https://www.readbyqxmd.com/read/28936896/fat-fraction-mapping-using-magnetic-resonance-imaging-insight-into-pathophysiology
#7
Timothy J P Bray, Manil D Chouhan, Shonit Punwani, Alan Bainbridge, Margaret A Hall-Craggs
Adipose cells have traditionally been viewed as a simple, passive energy storage depot for triglycerides. However, in recent years it has become clear that adipose cells are highly physiologically active and have a multitude of endocrine, metabolic, haematological and immune functions. Changes in the number or size of adipose cells may be directly implicated in disease (for example, in the metabolic syndrome), but may also be linked to other pathological processes such as inflammation, malignant infiltration or infarction...
September 22, 2017: British Journal of Radiology
https://www.readbyqxmd.com/read/28936641/empathy-and-the-aesthetic-why-does-art-still-move-us
#8
Despina Stamatopoulou
In this article I will argue for the affective-motivation (background affective attitude or orientation) hypothesis that incubates the aesthetic experience and sets the deep frame of our engagement with art. For this, I look at these microgenetic-early passages of (a) affective perception as mapped into the early emergence of tertiary qualities that underlie a sensorimotor synchronization-a coupling of action, emotion and perception via mirroring that result in dynamic embodied anticipatory control and a feeling of proximity/connectedness and (b) developmental passages that are characterized by spatiotemporal coordination and proximity of the self-other/interactive object and thus structure intentionality, shape experience, in an engaging world of action potentialities forming a background affective attitude...
September 21, 2017: Cognitive Processing
https://www.readbyqxmd.com/read/28935966/silent-sentence-completion-shows-superiority-localizing-wernicke-s-area-and-activation-patterns-of-distinct-language-paradigms-correlate-with-genomics-prospective-study
#9
Kamel El Salek, Islam S Hassan, Aikaterini Kotrotsou, Srishti Abrol, Scott H Faro, Feroze B Mohamed, Pascal O Zinn, Wei Wei, Nan Li, Ashok J Kumar, Jeffrey S Weinberg, Jeffrey S Wefel, Shelli R Kesler, Ho-Ling Anthony Liu, Ping Hou, R Jason Stafford, Sujit Prabhu, Raymond Sawaya, Rivka R Colen
Preoperative mapping of language areas using fMRI greatly depends on the paradigms used, as different tasks harness distinct capabilities to activate speech processing areas. In this study, we compared the ability of 3 covert speech paradigms: Silent Sentence Completion (SSC), category naming (CAT) and verbal fluency (FAS), in localizing the Wernicke's area and studied the association between genomic markers and functional activation. Fifteen right-handed healthy volunteers and 35 mixed-handed patients were included...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935893/trap-diversity-and-character-evolution-in-carnivorous-bladderworts-utricularia-lentibulariaceae
#10
Anna Sofia Westermeier, Andreas Fleischmann, Kai Müller, Bastian Schäferhoff, Carmen Rubach, Thomas Speck, Simon Poppinga
Bladderworts (Utricularia, Lentibulariaceae, Lamiales) constitute the largest genus of carnivorous plants but only aquatic species (about one fifth of the genus) have so far been thoroughly studied as to their suction trap functioning. In this study, we comparatively investigated trap biomechanics in 19 Utricularia species to examine correlations between life-forms, trapping mechanisms, and functional-morphological traits. Our investigations show the existence of two functional trap principles (passive trap in U...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935754/pervasive-genome-wide-transcription-in-the-organelle-genomes-of-diverse-plastid-bearing-protists
#11
Matheus Sanitá Lima, David Roy Smith
Organelle genomes are among the most sequenced kinds of chromosome. This is largely because they are small and widely used in molecular studies, but also because next-generation sequencing (NGS) technologies made sequencing easier, faster, and cheaper. However, studies of organelle RNA have not kept pace with those of DNA, despite huge amounts of freely available eukaryotic RNA-sequencing (RNA-seq) data. Little is known about organelle transcription in non-model species, and most of the available eukaryotic RNA-seq data have not been mined for organelle transcripts...
September 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28935753/mechanisms-of-transmission-ratio-distortion-at-hybrid-sterility-loci-within-and-between-mimulus-species
#12
Rachel E Kerwin, Andrea L Sweigart
Hybrid incompatibilities are a common correlate of genomic divergence and a potentially important contributor to reproductive isolation. However, we do not yet have a detailed understanding of how hybrid incompatibility loci function and evolve within their native species, or why they are dysfunctional in hybrids. Here, we explore these issues for a well-studied, two-locus hybrid incompatibility between hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2) in the closely related yellow monkeyflower species Mimulus guttatus and M...
September 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28935460/myocardial-fibrosis-detected-by-magnetic-resonance-in-systemic-sclerosis-patients-relationship-with-biochemical-and-echocardiography-parameters
#13
Milan Hromádka, Jitka Seidlerová, David Suchý, Daniel Rajdl, Jan Lhotský, Jaroslav Ludvík, Richard Rokyta, Jan Baxa
OBJECTIVES: Systemic scleroderma (SSc) is a rare connective tissue disease presenting with fibrosis affecting skin and internal organs. Cardiovascular magnetic resonance (CMR) with quantification of extracellular volume (ECV) and T1 mapping might help to detect heart involvement. We aimed to evaluate whether myocardial involvement correlates with functional and laboratory parameters. METHODS: Thirty-three asymptomatic SSc patients (29 women, aged 56.6±12.2years) and 20 controls (10 women, 53...
September 18, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/28935260/insights-of-lr28-mediated-wheat-leaf-rust-resistance-transcriptomic-approach
#14
Dharmendra Singh, Dhananjay Kumar, Lopamudra Satapathy, Jyoti Pathak, Saket Chandra, Adnan Riaz, Govindraj Bhaganagre, Raman Dhariwal, Manish Kumar, Kumble Vinod Prabhu, Harindra Singh Balyan, Pushpendra Kumar Gupta, Kunal Mukhopadhyay
Leaf rust is a fungal disease that causes severe yield losses in wheat. Resistant varieties with major and quantitative resistance genes are the most effective method to control the disease. However, the main problem is inadequate information for understanding resistance mechanism and its usefulness. This paper presents Lr28 mediated genome-wide response of known and unknown genes during wheat-Puccinia triticina interaction. In this study, we prepared Serial Analysis of Gene Expression (SAGE) libraries using seedling wheat mRNA for infected and mock conditions...
September 18, 2017: Gene
https://www.readbyqxmd.com/read/28935195/the-dimensionalities-of-lesion-deficit-mapping
#15
Tianbo Xu, Ashwani Jha, Parashkev Nachev
Lesion-deficit mapping remains the most powerful method for localising function in the human brain. As the highest court of appeal where competing theories of cerebral function conflict, it ought to be held to the most stringent inferential standards. Though at first sight elegantly transferable, the mass-univariate statistical framework popularized by functional imaging is demonstrably ill-suited to the task, both theoretically and empirically. The critical difficulty lies with the handling of the data's intrinsically high dimensionality...
September 18, 2017: Neuropsychologia
https://www.readbyqxmd.com/read/28935183/identification-of-novel-pde%C3%AE-interacting-proteins
#16
Philipp Küchler, Gunther Zimmermann, Michael Winzker, Petra Janning, Herbert Waldmann, Slava Ziegler
Prenylation is a post-translational modification that increases the affinity of proteins for membranes and mediates protein-protein interactions. The retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (PDEδ) is a prenyl binding protein that is essential for the shuttling of small GTPases between different membrane compartments and, thus, for their proper functioning. Although the prenylome comprises up to 2% of the mammalian proteome, only few prenylated proteins are known to interact with PDEδ...
August 31, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28934506/clip-seq-analysis-of-multi-mapped-reads-discovers-novel-functional-rna-regulatory-sites-in-the-human-transcriptome
#17
Zijun Zhang, Yi Xing
Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934477/a-structural-map-of-oncomir-1-at-single-nucleotide-resolution
#18
Saikat Chakraborty, Yamuna Krishnan
The miR-17-92a cluster, also known as 'oncomiR-1', is an RNA transcript that plays a pivotal regulatory role in cellular processes, including the cell cycle, proliferation and apoptosis. Its dysregulation underlies the development of several cancers. Oncomir-1 comprises six constituent miRNAs, each processed with different efficiencies as a function of both developmental time and tissue type. The structural mechanisms that regulate such differential processing are unknown, and this has impeded our understanding of the dysregulation of oncomiR-1 in pathophysiology...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934317/photosynthetic-epibionts-and-endobionts-of-pacific-oyster-shells-from-oyster-reefs-in-rocky-versus-mudflat-shores
#19
Laurent Barillé, Anthony Le Bris, Vona Méléder, Patrick Launeau, Marc Robin, Ioanna Louvrou, Lourenço Ribeiro
The Pacific oyster, Crassostrea gigas (Thunberg), is the main bivalve species cultivated in the world. With global warming enabling its reproduction and larval survival at higher latitudes, this species is now recognized as invasive and creates wild oyster reefs globally. In this study, the spatial distribution of photosynthetic assemblages colonizing the shells of wild C. gigas was investigated on both a large scale (two contrasting types of reefs found in mudflats and rocky areas) and a small scale (within individual shells) using a hyperspectral imager...
2017: PloS One
https://www.readbyqxmd.com/read/28934298/transcriptome-analysis-of-callery-pear-pyrus-calleryana-reveals-a-comprehensive-signalling-network-in-response-to-alternaria-alternata
#20
Jialiang Kan, Tingli Liu, Na Ma, Hui Li, Xiaogang Li, Jinyan Wang, Baolong Zhang, Youhong Chang, Jing Lin
The pear is an important temperate fruit worldwide that is produced by a group of species in the genus Pyrus. Callery pear (Pyrus calleryana Decne) is characterized by high resistance to multiple diseases, good adaptability, and high ornamental value, and is therefore widely planted in pear orchards for edible fruit production or as stock. Plant pathogens are a major threat to pear yield. Black spot disease, caused by the filamentous fungus Alternaria alternata, is one of the most serious diseases in pear. Elucidation of resistant genes to black spot disease is extremely important for understanding the underlying mechanisms as well as for the development of resistant cultivars...
2017: PloS One
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