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https://www.readbyqxmd.com/read/27932294/large-scale-structure-based-prediction-and-identification-of-novel-protease-substrates-using-computational-protein-design
#1
Manasi A Pethe, Aliza B Rubenstein, Sagar D Khare
Characterizing the substrate specificity of protease enzymes is critical for illuminating the molecular basis of their diverse and complex roles in a wide array of biological processes. Rapid and accurate prediction of their extended substrate specificity would also aid in the design of custom proteases capable of selectively and controllably cleaving biotechnologically or therapeutically relevant targets. However, current in silico approaches for protease specificity prediction, rely on, and are therefore limited by, machine learning of sequence patterns in known experimental data...
December 5, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27924481/machine-learning-approaches-toward-building-predictive-models-for-small-molecule-modulators-of-mirna-and-its-utility-in-virtual-screening-of-molecular-databases
#2
Vinita Periwal, Vinod Scaria
The ubiquitous role of microRNAs (miRNAs) in a number of pathological processes has suggested that they could act as potential drug targets. RNA-binding small molecules offer an attractive means for modulating miRNA function. The availability of bioassay data sets for a variety of biological assays and molecules in public domain provides a new opportunity toward utilizing them to create models and further utilize them for in silico virtual screening approaches to prioritize or assign potential functions for small molecules...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924046/new-data-and-features-for-advanced-data-mining-in-manteia
#3
Olivier Tassy
Manteia is an integrative database available online at http://manteia.igbmc.fr which provides a large array of OMICs data related to the development of the mouse, chicken, zebrafish and human. The system is designed to use different types of data together in order to perform advanced datamining, test hypotheses or provide candidate genes involved in biological processes or responsible for human diseases. In this new version of the database, Manteia has been enhanced with new expression data originating from microarray and next generation sequencing experiments...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923476/establishment-of-quantitative-retention-activity-model-by-optimized-microemulsion-liquid-chromatography
#4
Liyuan Xu, Haoshi Gao, Liangxing Li, Yinnong Li, Liuyun Wang, Chongkai Gao, Ning Li
The effective permeability coefficient is of theoretical and practical importance in evaluation of the bioavailability of drug candidates. However, most methods currently used to measure this coefficient are expensive and time-consuming. In this paper, we addressed these problems by proposing a new measurement method which is based on the microemulsion liquid chromatography. First, the parallel artificial membrane permeability assays model was used to determine the effective permeability of drug so that quantitative retention-activity relationships could be established, which were used to optimize the microemulsion liquid chromatography...
November 4, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/27922074/resistance-gene-identification-from-larimichthys-crocea-with-machine-learning-techniques
#5
Yinyin Cai, Zhijun Liao, Ying Ju, Juan Liu, Yong Mao, Xiangrong Liu
The research on resistance genes (R-gene) plays a vital role in bioinformatics as it has the capability of coping with adverse changes in the external environment, which can form the corresponding resistance protein by transcription and translation. It is meaningful to identify and predict R-gene of Larimichthys crocea (L.Crocea). It is friendly for breeding and the marine environment as well. Large amounts of L.Crocea's immune mechanisms have been explored by biological methods. However, much about them is still unclear...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920762/artificial-intelligence-vs-statistical-modeling-and-optimization-of-continuous-bead-milling-process-for-bacterial-cell-lysis
#6
Shafiul Haque, Saif Khan, Mohd Wahid, Sajad A Dar, Nipunjot Soni, Raju K Mandal, Vineeta Singh, Dileep Tiwari, Mohtashim Lohani, Mohammed Y Areeshi, Thavendran Govender, Hendrik G Kruger, Arshad Jawed
For a commercially viable recombinant intracellular protein production process, efficient cell lysis and protein release is a major bottleneck. The recovery of recombinant protein, cholesterol oxidase (COD) was studied in a continuous bead milling process. A full factorial response surface methodology (RSM) design was employed and compared to artificial neural networks coupled with genetic algorithm (ANN-GA). Significant process variables, cell slurry feed rate (A), bead load (B), cell load (C), and run time (D), were investigated and optimized for maximizing COD recovery...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27919211/development-of-mlr-and-svm-aided-qsar-models-to-identify-common-sar-of-gaba-uptake-herbal-inhibitors-used-in-the-treatment-of-schizophrenia
#7
Sahila Mohammed Marunnan, Babitha Pallikkara Pulikka, V K Gopalakrishnan, Srinivas Bandaru, Mukesh Yadav, Anuraj Nayarisseri, Victor Arokia Doss
Deficits in GABAnergic system is implicated in the pathophysiology of schizophrenia. Available antipsychotics that target GABA receptor form a desirable therapeutic strategy in the treatment regimen of schizophrenia but, unfortunately, suffers serious setback due to their prolonged side effects. The present investigation focuses on developing QSAR models from the biological activity of herbal compounds and their derivatives that promise to be alternative candidates to GABA uptake inhibitors. Three sets of compounds were undertaken in the study to develop the QSAR models...
December 5, 2016: Current Neuropharmacology
https://www.readbyqxmd.com/read/27912165/biomarker-analysis-of-american-toad-anaxyrus-americanus-and-grey-tree-frog-hyla-versicolor-tadpoles-following-exposure-to-atrazine
#8
Marcía N Snyder, W Matthew Henderson, Donna A Glinski, S Thomas Purucker
The objective of the current study was to use a biomarker-based approach to investigate the influence of atrazine exposure on American toad (Anaxyrus americanus) and grey tree frog (Hyla versicolor) tadpoles. Atrazine is one of the most frequently detected herbicides in environmental matrices throughout the United States. In surface waters, it has been found at concentrations from 0.04-2859μg/L and thus presents a likely exposure scenario for non-target species such as amphibians. Studies have examined the effect of atrazine on the metamorphic parameters of amphibians, however, the data are often contradictory...
November 21, 2016: Aquatic Toxicology
https://www.readbyqxmd.com/read/27912064/modular-assembly-of-the-bacterial-large-ribosomal-subunit
#9
Joseph H Davis, Yong Zi Tan, Bridget Carragher, Clinton S Potter, Dmitry Lyumkis, James R Williamson
The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of ribosome assembly in vivo is difficult, as few intermediates have been isolated and thoroughly characterized. Herein, we deploy a genetic system to starve cells of an essential ribosomal protein, which results in the accumulation of assembly intermediates that are competent for maturation. Quantitative mass spectrometry and single-particle cryo-electron microscopy reveal 13 distinct intermediates, which were each resolved to ∼4-5 Å resolution and could be placed in an assembly pathway...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27909020/the-design-and-transformation-of-biofundamentals-a-nonsurvey-introductory-evolutionary-and-molecular-biology-course
#10
Michael W Klymkowsky, Jeremy D Rentsch, Emina Begovic, Melanie M Cooper
Many introductory biology courses amount to superficial surveys of disconnected topics. Often, foundational observations and the concepts derived from them and students' ability to use these ideas appropriately are overlooked, leading to unrealistic expectations and unrecognized learning obstacles. The result can be a focus on memorization at the expense of the development of a meaningful framework within which to consider biological phenomena. About a decade ago, we began a reconsideration of what an introductory course should present to students and the skills they need to master...
2016: CBE Life Sciences Education
https://www.readbyqxmd.com/read/27905893/computational-prediction-of-multidisciplinary-team-decision-making-for-adjuvant-breast-cancer-drug-therapies-a-machine-learning-approach
#11
Frank P Y Lin, Adrian Pokorny, Christina Teng, Rachel Dear, Richard J Epstein
BACKGROUND: Multidisciplinary team (MDT) meetings are used to optimise expert decision-making about treatment options, but such expertise is not digitally transferable between centres. To help standardise medical decision-making, we developed a machine learning model designed to predict MDT decisions about adjuvant breast cancer treatments. METHODS: We analysed MDT decisions regarding adjuvant systemic therapy for 1065 breast cancer cases over eight years. Machine learning classifiers with and without bootstrap aggregation were correlated with MDT decisions (recommended, not recommended, or discussable) regarding adjuvant cytotoxic, endocrine and biologic/targeted therapies, then tested for predictability using stratified ten-fold cross-validations...
December 1, 2016: BMC Cancer
https://www.readbyqxmd.com/read/27905059/exposure-to-secondhand-smoke-impairs-fracture-healing-in-rats
#12
Hildemberg A R Santiago, Ariane Zamarioli, Manoel D Sousa Neto, Jose B Volpon
BACKGROUND: Nonsmokers may be affected by environmental tobacco smoke (secondhand smoke), but the effects of such exposure on fracture healing have not been well studied. QUESTIONS/PURPOSES: To explore the possible effects of passive inhalation of tobacco smoke on the healing of a diaphyseal fracture in femurs of rats. We hypothesized that secondhand exposure to tobacco smoke adversely affects fracture healing. METHODS: A mid-diaphyseal fracture was created in the femur of 41 female Wistar rats and fixed with an intramedullary metallic pin; 14 rats were excluded (nine for inadequate fractures and five for K wire extrusion)...
November 30, 2016: Clinical Orthopaedics and related Research
https://www.readbyqxmd.com/read/27903825/synthetic-biology-routes-to-bio-artificial-intelligence
#13
REVIEW
Darren N Nesbeth, Alexey Zaikin, Yasushi Saka, M Carmen Romano, Claudiu V Giuraniuc, Oleg Kanakov, Tetyana Laptyeva
The design of synthetic gene networks (SGNs) has advanced to the extent that novel genetic circuits are now being tested for their ability to recapitulate archetypal learning behaviours first defined in the fields of machine and animal learning. Here, we discuss the biological implementation of a perceptron algorithm for linear classification of input data. An expansion of this biological design that encompasses cellular 'teachers' and 'students' is also examined. We also discuss implementation of Pavlovian associative learning using SGNs and present an example of such a scheme and in silico simulation of its performance...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903639/automated-classification-of-pain-perception-using-high-density-electroencephalography-data
#14
Gaurav Misra, Wei-En Wang, Derek B Archer, Arnab Roy, Stephen A Coombes
Translating brief millisecond-long pain-eliciting stimuli to the subjective perception of pain is associated with changes in theta, alpha, beta, and gamma oscillations over sensorimotor cortex. However, when a pain-eliciting stimulus continues for minutes, regions beyond the sensorimotor cortex such as the prefrontal cortex are also engaged. Abnormalities in prefrontal cortex have been associated with chronic pain states, but conventional millisecond-long EEG paradigms do not engage prefrontal regions. In the current study we collected high-density EEG data during an experimental paradigm in which subjects experienced a 4 second low or high intensity pain-eliciting stimulus...
November 30, 2016: Journal of Neurophysiology
https://www.readbyqxmd.com/read/27900448/the-archaeal-signal-recognition-particle-present-understanding-and-future-perspective
#15
REVIEW
Sayandeep Gupta, Mousam Roy, Abhrajyoti Ghosh
The signal recognition particle (SRP) and its receptor constitute universally conserved and essential cellular machinery that controls the proper membrane localization of nascent polypeptides with the transmembrane domain. In the past decade, there has been an immense advancement in our understanding of this targeting machine in all three domains of life. A significant portion of such progress came from the structural analysis of archaeal SRP components. Despite the availability of structural insights from different archaeal SRP components, little is known about protein translocation in this domain of life compared to either bacteria or eukaryotes...
November 29, 2016: Current Microbiology
https://www.readbyqxmd.com/read/27900404/erasing-borders-a-brief-chronicle-of-early-synthetic-biology
#16
REVIEW
Juli Peretó
Synthetic Biology is currently presented as an emergent field involving the application of engineering principles to living matter. However, the scientific pursuit of making life in a laboratory is not new and has been the ultimate, if somewhat distant, aim of the origin-of-life research program for many years. Actually, over a century ago, the idea that the synthesis of life was indispensable to fully understand its nature already appealed to material scientists and evolutionists alike. Jacques Loeb proposed a research program from an engineering standpoint, following a synthetic method (experimental abiogenesis) and based on his mechanist vision of living beings, which he considered true chemical machines...
December 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27896760/opportunities-and-challenges-of-multiplex-assays-a-machine-learning-perspective
#17
Junfang Chen, Emanuel Schwarz
Multiplex assays that allow the simultaneous measurement of multiple analytes in small sample quantities have developed into a widely used technology. Their implementation spans across multiple assay systems and can provide readouts of similar quality as the respective single-plex measures, albeit at far higher throughput. Multiplex assay systems are therefore an important element for biomarker discovery and development strategies but analysis of the derived data can face substantial challenges that may limit the possibility of identifying meaningful biological markers...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896759/identification-and-clinical-translation-of-biomarker-signatures-statistical-considerations
#18
Emanuel Schwarz
Powerful machine learning tools exist to extract biological patterns for diagnosis or prediction from high-dimensional datasets. Simultaneous advances in high-throughput profiling technologies have led to a rapid acceleration of biomarker discovery investigations across all areas of medicine. However, the translation of biomarker signatures into clinically useful tools has thus far been difficult. In this chapter, several important considerations are discussed that influence such translation in the context of classifier design...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896599/inflammatory-cell-response-to-ultra-thin-amorphous-and-crystalline-hydroxyapatite-surfaces
#19
Louise Rydén, Omar Omar, Anna Johansson, Ryo Jimbo, Anders Palmquist, Peter Thomsen
It has been suggested that surface modification with a thin hydroxyapatite (HA) coating enhances the osseointegration of titanium implants. However, there is insufficient information about the biological processes involved in the HA-induced response. This study aimed to investigate the inflammatory cell response to titanium implants with either amorphous or crystalline thin HA. Human mononuclear cells were cultured on titanium discs with a machined surface or with a thin, 0.1 μm, amorphous or crystalline HA coating...
January 2017: Journal of Materials Science. Materials in Medicine
https://www.readbyqxmd.com/read/27895194/systematic-characterization-and-prediction-of-human-hypertension-genes
#20
Yan-Hui Li, Gai-Gai Zhang, Nanping Wang
Hypertension is a major cardiovascular risk factor and accounts for a large part of cardiovascular mortality. In this work, we analyzed the properties of hypertension genes and found that when compared with genes not yet known to be involved in hypertension regulation, known hypertension genes display distinguishing features: (1) hypertension genes tend to be located at network center; (2) hypertension genes tend to interact with each other; and (3) hypertension genes tend to enrich in certain biological processes and show certain phenotypes...
November 28, 2016: Hypertension
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