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https://www.readbyqxmd.com/read/28446202/analyzing-the-genes-related-to-alzheimer-s-disease-via-a-network-and-pathway-based-approach
#1
Yan-Shi Hu, Juncai Xin, Ying Hu, Lei Zhang, Ju Wang
BACKGROUND: Our understanding of the molecular mechanisms underlying Alzheimer's disease (AD) remains incomplete. Previous studies have revealed that genetic factors provide a significant contribution to the pathogenesis and development of AD. In the past years, numerous genes implicated in this disease have been identified via genetic association studies on candidate genes or at the genome-wide level. However, in many cases, the roles of these genes and their interactions in AD are still unclear...
April 27, 2017: Alzheimer's Research & Therapy
https://www.readbyqxmd.com/read/28446158/parameter-inference-for-stochastic-single-cell-dynamics-from-lineage-tree-data
#2
Irena Kuzmanovska, Andreas Milias-Argeitis, Jan Mikelson, Christoph Zechner, Mustafa Khammash
BACKGROUND: With the advance of experimental techniques such as time-lapse fluorescence microscopy, the availability of single-cell trajectory data has vastly increased, and so has the demand for computational methods suitable for parameter inference with this type of data. Most of currently available methods treat single-cell trajectories independently, ignoring the mother-daughter relationships and the information provided by the population structure. However, this information is essential if a process of interest happens at cell division, or if it evolves slowly compared to the duration of the cell cycle...
April 26, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28445522/revealing-phenotype-associated-functional-differences-by-genome-wide-scan-of-ancient-haplotype-blocks
#3
Ritsuko Onuki, Rui Yamaguchi, Tetsuo Shibuya, Minoru Kanehisa, Susumu Goto
Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP) data...
2017: PloS One
https://www.readbyqxmd.com/read/28443631/a-peripheral-epigenetic-signature-of-immune-system-genes-is-linked-to-neocortical-thickness-and-memory
#4
Virginie Freytag, Tania Carrillo-Roa, Annette Milnik, Philipp G Sämann, Vanja Vukojevic, David Coynel, Philippe Demougin, Tobias Egli, Leo Gschwind, Frank Jessen, Eva Loos, Wolfgang Maier, Steffi G Riedel-Heller, Martin Scherer, Christian Vogler, Michael Wagner, Elisabeth B Binder, Dominique J-F de Quervain, Andreas Papassotiropoulos
Increasing age is tightly linked to decreased thickness of the human neocortex. The biological mechanisms that mediate this effect are hitherto unknown. The DNA methylome, as part of the epigenome, contributes significantly to age-related phenotypic changes. Here, we identify an epigenetic signature that is associated with cortical thickness (P=3.86 × 10(-8)) and memory performance in 533 healthy young adults. The epigenetic effect on cortical thickness was replicated in a sample comprising 596 participants with major depressive disorder and healthy controls...
April 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28442471/development-of-organoids-from-mouse-and-human-endometrium-showing-endometrial-epithelium-physiology-and-long-term-expandability
#5
Matteo Boretto, Benoit Cox, Manuel Noben, Nikolai Hendriks, Amelie Fassbender, Heleen Roose, Frédéric Amant, Dirk Timmerman, Carla Tomassetti, Arne Vanhie, Christel Meuleman, Marc Ferrante, Hugo Vankelecom
The endometrium, which is of crucial importance for reproduction, undergoes dynamic cyclic tissue remodeling. Knowledge of its molecular and cellular regulation is poor, primarily owing to a lack of study models. Here, we have established a novel and promising organoid model from both mouse and human endometrium. Dissociated endometrial tissue, embedded in Matrigel under WNT-activating conditions, swiftly formed organoid structures that showed long-term expansion capacity, and reproduced the molecular and histological phenotype of the tissue's epithelium...
April 25, 2017: Development
https://www.readbyqxmd.com/read/28441401/ancient-genes-establish-stress-induced-mutation-as-a-hallmark-of-cancer
#6
Luis Cisneros, Kimberly J Bussey, Adam J Orr, Milica Miočević, Charles H Lineweaver, Paul Davies
Cancer is sometimes depicted as a reversion to single cell behavior in cells adapted to live in a multicellular assembly. If this is the case, one would expect that mutation in cancer disrupts functional mechanisms that suppress cell-level traits detrimental to multicellularity. Such mechanisms should have evolved with or after the emergence of multicellularity. This leads to two related, but distinct hypotheses: 1) Somatic mutations in cancer will occur in genes that are younger than the emergence of multicellularity (1000 million years [MY]); and 2) genes that are frequently mutated in cancer and whose mutations are functionally important for the emergence of the cancer phenotype evolved within the past 1000 million years, and thus would exhibit an age distribution that is skewed to younger genes...
2017: PloS One
https://www.readbyqxmd.com/read/28440735/nuclear-factor-e2-related-factor-2-knockdown-enhances-glucose-uptake-and-alters-glucose-metabolism-in-aml12-hepatocytes
#7
Xiaoyang Yuan, Huijing Huang, Yi Huang, Jinli Wang, Jinhua Yan, Ling Ding, Cuntai Zhang, Le Zhang
Nuclear factor E2-related factor 2 (Nrf2) is a transcription factor known to induce the expression of a variety of antioxidant and detoxification genes. Recently, increasing evidence has revealed roles for Nrf2 in glucose, lipid, and energy metabolism; however, the exact functions of Nrf2 in hepatocyte biology are largely unclear. In the current study, the transient knockdown of Nrf2 via siRNA transfection enhanced the glucose uptake of fasting AML12 hepatocytes to 325.3 ± 11.1% ( P < 0.05) of that of untransfected control cells...
May 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28439722/dna-methylation-age-acceleration-is-associated-with-disease-duration-and-age-at-onset-in-c9orf72-patients
#8
Ming Zhang, Maria Carmela Tartaglia, Danielle Moreno, Christine Sato, Paul McKeever, Anna Weichert, Julia Keith, Janice Robertson, Lorne Zinman, Ekaterina Rogaeva
The repeat expansion in C9orf72 is the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia. C9orf72 patients present with a wide range in disease duration and age of onset. The strongest risk factor for both syndromes is aging, which was linked to DNA methylation (DNAm) age based on the cumulative assessment of the methylation levels of 353 CpGs included on the genome-wide 450k BeadChip. DNAm age may reflect biological age better than chronological age. We conducted a genome-wide blood DNA methylation study of 46 unrelated C9orf72 patients...
April 24, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28439288/systemic-mastocytosis-with-kit-v560g-mutation-presenting-as-recurrent-episodes-of-vascular-collapse-response-to-disodium-cromoglycate-and-disease-outcome
#9
Iolanda Conde-Fernandes, Rita Sampaio, Filipa Moreno, José Palla-Garcia, Maria Dos Anjos Teixeira, Inês Freitas, Esmeralda Neves, Maria Jara-Acevedo, Luis Escribano, Margarida Lima
BACKGROUND: Mastocytosis are rare diseases characterized by an accumulation of clonal mast cells (MCs) in one or multiple organs or tissues. Patients with systemic mastocytosis (SM), whose MCs frequently arbor the activating D816V KIT mutation, may have indolent to aggressive diseases, and they may experience MC mediator related symptoms. Indolent SM with recurrent anaphylaxis or vascular collapse in the absence of skin lesions, ISMs(-), is a specific subtype indolent SM (ISM), and this clonal MC activation disorder represents a significant fraction of all MC activation syndromes...
2017: Allergy, Asthma, and Clinical Immunology
https://www.readbyqxmd.com/read/28439038/pseudomonas-aeruginosa-derived-rhamnolipids-and-other-detergents-modulate-colony-morphotype-and-motility-in-the-burkholderia-cepacia-complex
#10
Steve P Bernier, Courtney Hum, Xiang Li, George A O'Toole, Nathan Magarvey, Michael G Surette
Competitive interactions mediated by released chemicals (e.g. toxins) are prominent in multispecies communities, but their effect at subinhibitory concentrations on susceptible bacteria is poorly understood. Although Pseudomonas aeruginosa and species of the Burkholderia cepacia complex (Bcc) can exist together as a co-infection in cystic fibrosis airways, P. aeruginosa toxins can kill Bcc species in vitro Consequently, these bacteria become an ideal in vitro model system to study the impact of sublethal levels of toxins on the biology of typical susceptible bacteria such as the Bcc when exposed to P...
April 24, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28438397/endothelial-to-mesenchymal-transition-a-novel-therapeutic-target-for-cardiovascular-diseases
#11
REVIEW
Ampadu O Jackson, Jingjing Zhang, Zhisheng Jiang, Kai Yin
Endothelial-to-mesenchymal transition (EndMT) is a complex biological process in which endothelial cells lose their specific markers and acquire a mesenchymal or myofibroblastic phenotype. Similar to epithelial-to-mesenchymal transition (EMT), EndMT can be induced by multiple stimulants such as cytokines and metabolic factors that play crucial roles in the development of the cardiovascular system. Recent studies have demonstrated that EndMT may play a significant role in the pathogenesis of cardiovascular diseases (CVDs), and may represent a novel therapeutic target for cardiovascular remodeling and fibrotic disorders...
March 16, 2017: Trends in Cardiovascular Medicine
https://www.readbyqxmd.com/read/28436551/genomics-and-metabolomics-of-post-weaning-return-to-estrus
#12
REVIEW
Lea A Rempel, Gary A Rohrer, Danny J Nonneman
The weaning-to-estrus interval is a multifaceted trait that has the potential to substantially improve production efficiency in today's global swine industry, if variation in this measure can be reduced. Systems-biology approaches should help close the knowledge gap and increase selection tools and management strategies - such as gilt development programs, farrowing, and lactation feeding programs - to decrease the weaning-to-estrus interval. Metabolomics, the study of small compounds within biofluids and tissues, provides links between genotype and phenotype...
April 24, 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/28435157/the-systemic-nature-of-ckd
#13
REVIEW
Carmine Zoccali, Raymond Vanholder, Ziad A Massy, Alberto Ortiz, Pantelis Sarafidis, Friedo W Dekker, Danilo Fliser, Denis Fouque, Gunnar H Heine, Kitty J Jager, Mehmet Kanbay, Francesca Mallamaci, Gianfranco Parati, Patrick Rossignol, Andrzej Wiecek, Gerard London
The accurate definition and staging of chronic kidney disease (CKD) is one of the major achievements of modern nephrology. Intensive research is now being undertaken to unravel the risk factors and pathophysiologic underpinnings of this disease. In particular, the relationships between the kidney and other organs have been comprehensively investigated in experimental and clinical studies in the last two decades. Owing to technological and analytical limitations, these links have been studied with a reductionist approach focusing on two organs at a time, such as the heart and the kidney or the bone and the kidney...
April 24, 2017: Nature Reviews. Nephrology
https://www.readbyqxmd.com/read/28434869/worms-on-the-spectrum-c-elegans-models-in-autism-research
#14
REVIEW
Kathrin Schmeisser, J Alex Parker
The small non-parasitic nematode Caenorhabditis elegans is widely used in neuroscience thanks to its well-understood development and lineage of the nervous system. Furthermore, C. elegans has been used to model many human developmental and neurological conditions to better understand disease mechanisms and identify potential therapeutic strategies. Autism spectrum disorder (ASD) is the most prevalent of all neurodevelopmental disorders, and the C. elegans system may provide opportunities to learn more about this complex disorder...
April 20, 2017: Experimental Neurology
https://www.readbyqxmd.com/read/28434692/immune-hyperreactivity-of-a%C3%AE-plaque-associated-microglia-in-alzheimer-s-disease
#15
Zhuoran Yin, Divya Raj, Nasrin Saiepour, Debby Van Dam, Nieske Brouwer, Inge R Holtman, Bart J L Eggen, Thomas Möller, Joseph A Tamm, Aicha Abdourahman, Elly M Hol, Willem Kamphuis, Thomas A Bayer, Peter P De Deyn, Erik Boddeke
Alzheimer's disease (AD) is strongly associated with microglia-induced neuroinflammation. Particularly, Aβ plaque-associated microglia take on an "activated" morphology. However, the function and phenotype of these Aβ plaque-associated microglia are not well understood. We show hyperreactivity of Aβ plaque-associated microglia upon systemic inflammation in transgenic AD mouse models (i.e., 5XFAD and APP23). Gene expression profiling of Aβ plaque-associated microglia (major histocompatibility complex II(+) microglia) isolated from 5XFAD mice revealed a proinflammatory phenotype...
March 27, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28428983/rapid-inducible-protein-displacement-in-plasmodiumin-vivo-and-in-vitro-using-knocksideways-technology
#16
Katie R Hughes, Andy P Waters
A deeper understanding of the biology of the Plasmodium parasite is essential in order to identify targets for interventions, with the ultimate aim of eliminating malaria. Determining the function(s) of essential proteins in Plasmodium has, until recently, been hampered by the lack of efficient conditional systems to abrogate proteins. We report the adaptation of a conditional technology, knocksideways (KS), for use in Plasmodium berghei, which can potentially rapidly inactivate proteins of interest through relocalisation...
March 14, 2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28428821/genome-wide-search-for-candidate-genes-for-yeast-robustness-improvement-against-formic-acid-reveals-novel-susceptibility-trk1-and-positive-regulators-and-resistance-haa1-regulon-determinants
#17
Sílvia F Henriques, Nuno P Mira, Isabel Sá-Correia
BACKGROUND: Formic acid is an inhibitory compound present in lignocellulosic hydrolysates. Understanding the complex molecular mechanisms underlying Saccharomyces cerevisiae tolerance to this weak acid at the system level is instrumental to guide synthetic pathway engineering for robustness improvement of industrial strains envisaging their use in lignocellulosic biorefineries. RESULTS: This study was performed to identify, at a genome-wide scale, genes whose expression confers protection or susceptibility to formic acid, based on the screening of a haploid deletion mutant collection to search for these phenotypes in the presence of 60, 70 and 80 mM of this acid, at pH 4...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28422570/an-induced-adipocyte-sheet-reduces-inflammatory-reactions-during-remodeling-of-xenogeneic-scaffolds-in-vivo
#18
Tong Yi, Qiang Wang, Fan Fan, Gouhui Fan
Surgical therapy of cardiovascular diseases frequently requires replacement of diseased tissues with prosthetic devices or grafts. Calcification is the main reason for the degeneration of implanted grafts. However, some factors reduce stenosis and attenuate calcification of implanted grafts. In this study, we used an autologous induced adipocyte cell-sheet (IACS) as a drug delivery system to determine whether its secretion ability has a beneficial effect on the remodeling process of grafts in a rat subcutaneous model...
April 19, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28417974/the-e-coli-molecular-phenotype-under-different-growth-conditions
#19
Mehmet U Caglar, John R Houser, Craig S Barnhart, Daniel R Boutz, Sean M Carroll, Aurko Dasgupta, Walter F Lenoir, Bartram L Smith, Viswanadham Sridhara, Dariya K Sydykova, Drew Vander Wood, Christopher J Marx, Edward M Marcotte, Jeffrey E Barrick, Claus O Wilke
Modern systems biology requires extensive, carefully curated measurements of cellular components in response to different environmental conditions. While high-throughput methods have made transcriptomics and proteomics datasets widely accessible and relatively economical to generate, systematic measurements of both mRNA and protein abundances under a wide range of different conditions are still relatively rare. Here we present a detailed, genome-wide transcriptomics and proteomics dataset of E. coli grown under 34 different conditions...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28416607/human-milk-oligosaccharides-inhibit-growth-of-group-b-streptococcus
#20
Ann E Lin, Chloe A Autran, Alexandra Szyszka, Tamara Escajadillo, Mia Huang, Kamil Godula, Anthony R Prudden, Geert-Jan Boons, Amanda L Lewis, Kelly S Doran, Victor Nizet, Lars Bode
Streptococcus agalactiae (group B Streptococcus; GBS) is a leading cause of invasive bacterial infections in newborns, typically acquired vertically during childbirth secondary to maternal vaginal colonization. Human milk oligosaccharides (HMOs) have important nutritional and biological activities that guide development of the infant's immune system and shape the composition of normal gut microbiota. In this manner, HMOs help protect against pathogen colonization and reduce risk of infection. In the course of our studies of HMO-microbial interactions, we unexpectedly uncovered a novel HMO property to directly inhibit the growth of GBS, independent of host immunity...
April 17, 2017: Journal of Biological Chemistry
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