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https://www.readbyqxmd.com/read/28528256/evaluation-of-artificial-time-series-microarray-data-for-dynamic-gene-regulatory-network-inference
#1
P Xenitidis, I Seimenis, S Kakolyris, A Adamopoulos
High-throughput technology like microarrays is widely used in the inference of gene regulatory networks (GRNs). We focused on time series data since we are interested in the dynamics of GRNs and the identification of dynamic networks. We evaluated the amount of information that exists in artificial time series microarray data and the ability of an inference process to produce accurate models based on them. We used dynamic artificial gene regulatory networks in order to create artificial microarray data. Key features that characterize microarray data such as the time separation of directly triggered genes, the percentage of directly triggered genes and the triggering function type were altered in order to reveal the limits that are imposed by the nature of microarray data on the inference process...
May 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28527949/microproteome-of-dentoalveolar-tissues
#2
Cristiane R Salmon, Ana Paula O Giorgetti, Adriana F Paes Leme, Romênia R Domingues, Tamara N Kolli, Brian L Foster, Francisco H Nociti
Proteomic analysis of extracellular matrices (ECM) of dentoalveolar tissues can provide insights into developmental, pathological, and reparative processes. However, targeted dissection of mineralized tissues, dental cementum (DC), alveolar bone (AB), and dentin (DE), presents technical difficulties. We demonstrate an approach combining EDTA decalcification and laser capture microdissection (LCM), followed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), to analyze proteome profiles of these tissues...
May 17, 2017: Bone
https://www.readbyqxmd.com/read/28527793/prevalence-of-non-aureus-staphylococcus-species-causing-intramammary-infections-in-canadian-dairy-herds
#3
Larissa A Z Condas, Jeroen De Buck, Diego B Nobrega, Domonique A Carson, Sohail Naushad, Sarne De Vliegher, Ruth N Zadoks, John R Middleton, Simon Dufour, John P Kastelic, Herman W Barkema
Non-aureus staphylococci (NAS), the microorganisms most frequently isolated from bovine milk worldwide, are a heterogeneous group of numerous species. To establish their importance as a group, the distribution of individual species needs to be determined. In the present study, NAS intramammary infection (IMI) was defined as a milk sample containing ≥1,000 cfu/mL in pure or mixed culture that was obtained from a cohort of cows assembled by the Canadian Bovine Mastitis Research Network. Overall, 6,213 (6.3%) of 98,233 quarter-milk samples from 5,149 cows and 20,305 udder quarters were associated with an NAS IMI...
May 17, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28526529/adding-biological-meaning-to-human-protein-protein-interactions-identified-by-yeast-two-hybrid-screenings-a-guide-through-bioinformatics-tools
#4
Juliana Felgueiras, Joana Vieira Silva, Margarida Fardilha
"A man is known by the company he keeps" is a popular expression that perfectly fits proteins. A common approach to characterize the function of a target protein is to identify its interacting partners and thus infer its roles based on the known functions of the interactors. Protein-protein interaction networks (PPINs) have been created for several organisms, including humans, primarily as results of high-throughput screenings, such as yeast two-hybrid (Y2H). Their unequivocal use to understand events underlying human pathophysiology is promising in identifying genes and proteins associated with diseases...
May 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28525726/characterization-of-an-ionic-liquid-tolerant-%C3%AE-xylosidase-from-a-marine-derived-fungal-endophyte
#5
Anindita Sengupta, Angela Zabala, Si Yu Tan, Arthur Broadstock, T S Suryanarayanan, Venkat Gopalan
Ionic liquids (ILs) are used in lignocellulosic biomass (LCB) pretreatment due to their ability to disrupt the extensive hydrogen-bonding network in cellulose and hemicellulose, and thereby decrease LCB recalcitrance to subsequent enzymatic degradation. However, this approach necessitates development of a cellulases and hemicellulases that can tolerate ~20% (w/v) IL, an amount that either co-precipitates with the sugar polymers after the initial pretreatment or is typically used in single-pot biomass deconstructions...
May 19, 2017: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/28523286/synthetic-lethality-screens-using-rnai-in-combination-with-crispr-based-knockout-in-drosophila-cells
#6
Benjamin E Housden, Hilary E Nicholson, Norbert Perrimon
A synthetic lethal interaction is a type of genetic interaction where the disruption of either of two genes individually has little effect but their combined disruption is lethal. Knowledge of synthetic lethal interactions can allow for elucidation of network structure and identification of candidate drug targets for human diseases such as cancer. In Drosophila, combinatorial gene disruption has been achieved previously by combining multiple RNAi reagents. Here we describe a protocol for high-throughput combinatorial gene disruption by combining CRISPR and RNAi...
February 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28522639/definition-of-a-rack1-interaction-network-in-drosophila-melanogaster-using-swath-ms
#7
Lauriane Kuhn, Karim Majzoub, Evelyne Einhorn, Johana Chicher, Pompon Julien, Jean-Luc Imler, Philippe Hammann, Carine Meignin
Receptor for Activated C kinase 1 (RACK1) is a scaffold protein that has been found in association with several signaling complexes, and with the 40S subunit of the ribosome. Using the model organism Drosophila melanogaster, we recently showed that RACK1 is required at the ribosome for IRES-mediated translation of viruses. Here, we report a proteomic characterization of the interactome of RACK1 in Drosophila S2 cells. We carried out Label-Free quantitation using both Data-Dependent and Data-Independent Acquisition and observed a significant advantage for the Sequential Window Acquisition of all THeoretical fragment-ion spectra (SWATH) method both in terms of identification of interactants and quantification of low abundance proteins...
May 18, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28521377/-checklist-for-the-development-and-assessment-of-cost-of-illness-studies
#8
Dirk Müller, Stephanie Stock, Charalabos-Markos Dintsios, Nadja Chernyak, Andreas Gerber-Grote, Tristan Daniel Gloede, Benita Hermann, Eduard Huppertz, Fabian Jülich, Sarah Mostardt, Juliane Köberlein-Neu, Anne Prenzler, Hans-Joachim Salize, Sara Santos, Benjamin Scheckel, Astrid Seidl, Katharina Wahlers, Andrea Icks
Background Cost-of-illness (CoI) studies are important instruments for estimating the socioeconomic burden of specified diseases. CoI studies provide important information about the cost structure of a disease, the resulting research need, approaches to improve aspects of care and, monetary consequences from different perspectives. This information can be useful for healthcare research and health policy. Due to heterogeneity of available Cost-of-Illness studies, the working group 'Health Economics' of the German Network for Healthcare Research (DNVF) in accordance with the German Society for Health Economics (DGGÖ) developed an instrument for the planning, conduct and assessment of CoI studies...
May 18, 2017: Das Gesundheitswesen
https://www.readbyqxmd.com/read/28521136/dopamine-depletion-impairs-bilateral-sensory-processing-in-the-striatum-in-a-pathway-dependent-manner
#9
M Ketzef, G Spigolon, Y Johansson, A Bonito-Oliva, G Fisone, G Silberberg
Parkinson's disease (PD) is a movement disorder caused by the loss of dopaminergic innervation, particularly to the striatum. PD patients often exhibit sensory impairments, yet the underlying network mechanisms are unknown. Here we examined how dopamine (DA) depletion affects sensory processing in the mouse striatum. We used the optopatcher for online identification of direct and indirect pathway projection neurons (MSNs) during in vivo whole-cell recordings. In control mice, MSNs encoded the laterality of sensory inputs with larger and earlier responses to contralateral than ipsilateral whisker deflection...
May 17, 2017: Neuron
https://www.readbyqxmd.com/read/28520805/identification-of-key-contributors-in-complex-population-structures
#10
Markus Neuditschko, Herman W Raadsma, Mehar S Khatkar, Elisabeth Jonas, Eike J Steinig, Christine Flury, Heidi Signer-Hasler, Mirjam Frischknecht, Ruedi von Niederhäusern, Tosso Leeb, Stefan Rieder
Evaluating the genetic contribution of individuals to population structure is essential to select informative individuals for genome sequencing, genotype imputation and to ascertain complex population structures. Existing methods for the selection of informative individuals for genomic imputation solely focus on the identification of key ancestors, which can lead to a loss of phasing accuracy of the reference population. Currently many methods are independently applied to investigate complex population structures...
2017: PloS One
https://www.readbyqxmd.com/read/28520598/imaging-plus-x-multimodal-models-of-neurodegenerative-disease
#11
Neil P Oxtoby, Daniel C Alexander
PURPOSE OF REVIEW: This article argues that the time is approaching for data-driven disease modelling to take centre stage in the study and management of neurodegenerative disease. The snowstorm of data now available to the clinician defies qualitative evaluation; the heterogeneity of data types complicates integration through traditional statistical methods; and the large datasets becoming available remain far from the big-data sizes necessary for fully data-driven machine-learning approaches...
May 16, 2017: Current Opinion in Neurology
https://www.readbyqxmd.com/read/28515993/triage-amalgamated-dermoscopic-algorithm-tada-for-skin-cancer-screening
#12
Tova Rogers, Maria Marino, Stephen W Dusza, Shirin Bajaj, Michael A Marchetti, Ashfaq Marghoob
IMPORTANCE: Dermoscopic triage algorithms have been shown to improve beginners' abilities for identifying pigmented skin lesions requiring biopsy. OBJECTIVE: To estimate the diagnostic accuracy of the Triage Amalgamated Dermoscopic Algorithm (TADA) for pigmented and nonpigmented skin cancers. Secondarily, to compare TADAs performance to those of existing triage algorithms for the identification of pigmented skin cancers. DESIGN: Cross-sectional, observational, reader study that took place at a beginner and intermediate level dermoscopy course...
April 2017: Dermatology Practical & Conceptual
https://www.readbyqxmd.com/read/28515146/transcriptome-of-wheat-inflorescence-development-from-spikelet-initiation-to-floral-patterning
#13
Nan Feng, Gaoyuan Song, Jiantao Guan, Kai Chen, Meiling Jia, Dehua Huang, Jiajie Wu, Lichao Zhang, Xiuying Kong, Shuaifeng Geng, Jun Liu, Aili Li, Long Mao
Early reproductive development in cereals is crucial for final grain number per spike, and hence the yield potential of the crop. To date, however, no systematic analyses of gene expression profiles during this important process have been conducted for common wheat (Triticum aestivum). Here, we studied the transcriptome profiles at four stages of early wheat reproductive development, from spikelet initiation to floral organ differentiation. K-means clustering and stage-specific transcript identification detected dynamically expressed homoeologs of important transcription regulators in spikelet and floral meristems that may be involved in spikelet initiation, floret meristem specification, and floral organ patterning, as inferred from their homologs in model plants...
May 17, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28514875/identification-of-novel-nicotinamide-phosphoribosyltransferase-nampt-inhibitors-using-computational-approaches
#14
Manish Kesherwani, Sriram Raghavan, Krishnasamy Gunasekaran, Devadasan Velmurugan
Nicotinamide Phosphoribosyltransferase (NAMPT) is a rate-limiting enzyme in the biosynthesis of NAD. Cancer cells have elevated poly [ADP-Ribose] polymerase 1 (PARP) activity as well as the immense necessity of ATP: thereby consuming NAD at a higher rate than normal tissues. The perturbation of these intracellular processes is more sensitive and highly dependent on NAMPT to maintain the required NAD levels. Functional inhibition of NAMPT is, therefore, a promising drug target in therapeutic oncology. In this study, the importance of intermolecular contacts was realized based on contact occupancy and favorable energetic from molecular dynamic simulation to discern non-critical contacts of four different classes of potential NAMPT inhibitor bound complexes...
May 17, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28514737/integration-of-phytochemicals-and-phytotherapy-into-cancer-precision-medicine
#15
REVIEW
Thomas Efferth, Mohamed E M Saeed, Elhaj Mirghani, Awadh Alim, Zahir Yassin, Elfatih Saeed, Hassan E Khalid, Salah Daak
Concepts of individualized therapy in the 1970s and 1980s attempted to develop predictive in vitro tests for individual drug responsiveness without reaching clinical routine. Precision medicine attempts to device novel individual cancer therapy strategies. Using bioinformatics, relevant knowledge is extracted from huge data amounts. However, tumor heterogeneity challenges chemotherapy due to genetically and phenotypically different cell subpopulations, which may lead to refractory tumors. Natural products always served as vital resources for cancer therapy (e...
April 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28511097/the-relationship-between-social-desirability-bias-and-self-reports-of-health-substance-use-and-social-network-factors-among-urban-substance-users-in-baltimore-maryland
#16
Carl A Latkin, Catie Edwards, Melissa A Davey-Rothwell, Karin E Tobin
BACKGROUND: Social desirability response bias may lead to inaccurate self-reports and erroneous study conclusions. The present study examined the relationship between social desirability response bias and self-reports of mental health, substance use, and social network factors among a community sample of inner-city substance users. METHODS: The study was conducted in a sample of 591 opiate and cocaine users in Baltimore, Maryland from 2009 to 2013. Modified items from the Marlowe-Crowne Social Desirability Scale were included in the survey, which was conducted face-to-face and using Audio Computer Self Administering Interview (ACASI) methods...
May 9, 2017: Addictive Behaviors
https://www.readbyqxmd.com/read/28510528/identification-of-octopaminergic-neurons-that-modulate-sleep-suppression-by-male-sex-drive
#17
Daniel R Machado, Dinis Js Afonso, Alexandra R Kenny, Arzu Öztu Rk-Çolak, Emilia H Moscato, Benjamin Mainwaring, Matthew Kayser, Kyunghee Koh
Molecular and circuit mechanisms for balancing competing drives are not well understood. While circadian and homeostatic mechanisms generally ensure sufficient sleep at night, other pressing needs can overcome sleep drive. Here, we demonstrate that the balance between sleep and sex drives determines whether male flies sleep or court, and identify a subset of octopaminergic neurons (MS1) that regulate sleep specifically in males. When MS1 neurons are activated, isolated males sleep less, and when MS1 neurons are silenced, the normal male sleep suppression in female presence is attenuated and mating behavior is impaired...
May 16, 2017: ELife
https://www.readbyqxmd.com/read/28510271/application-of-combination-high-throughput-phenotypic-screening-and-target-identification-methods-for-the-discovery-of-natural-product-based-combination-drugs
#18
REVIEW
Monica Isgut, Mukkavilli Rao, Chunhua Yang, Vangala Subrahmanyam, Padmashree C G Rida, Ritu Aneja
Modern drug discovery efforts have had mediocre success rates with increasing developmental costs, and this has encouraged pharmaceutical scientists to seek innovative approaches. Recently with the rise of the fields of systems biology and metabolomics, network pharmacology (NP) has begun to emerge as a new paradigm in drug discovery, with a focus on multiple targets and drug combinations for treating disease. Studies on the benefits of drug combinations lay the groundwork for a renewed focus on natural products in drug discovery...
May 16, 2017: Medicinal Research Reviews
https://www.readbyqxmd.com/read/28508373/an-advanced-omic-approach-to-identify-co-regulated-clusters-and-transcription-regulation-network-with-agct-and-shoe-methods
#19
Natalia Polouliakh, Richard Nock
To obtain the global picture of genetic machinery for massive high-throughput gene expression data, novel data-driven unsupervised learning approaches are becoming essentially important. For this purpose, basic analytic workflow has been established and should include two steps: first, unsupervised clustering to identify genes with similar behavior upon exposure to a signal, and second, identification of transcription factors regulating those genes. In this chapter, we will describe an advanced tool that can be used for analyzing and characterizing large-scale time-series gene expression composed of a two-step approach...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28507724/deep-learning-and-3d-desi-imaging-reveal-the-hidden-metabolic-heterogeneity-of-cancer
#20
Paolo Inglese, James S McKenzie, Anna Mroz, James Kinross, Kirill Veselkov, Elaine Holmes, Zoltan Takats, Jeremy K Nicholson, Robert C Glen
Visual inspection of tumour tissues does not reveal the complex metabolic changes that differentiate cancer and its sub-types from healthy tissues. Mass spectrometry imaging, which quantifies the underlying chemistry, represents a powerful tool for the molecular exploration of tumour tissues. A 3-dimensional topological description of the chemical properties of the tumour permits the formulation of hypotheses about the biological composition and interactions and the possible causes of its heterogeneous structure...
May 1, 2017: Chemical Science
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