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https://www.readbyqxmd.com/read/28330294/immuno-hybrid-algorithm-a-novel-hybrid-approach-for-grn-reconstruction
#1
A S Jereesh, V K Govindan
Bio-inspired algorithms are widely used to optimize the model parameters of GRN. In this paper, focus is given to develop improvised versions of bio-inspired algorithm for the specific problem of reconstruction of gene regulatory network. The approach is applied to the data set that was developed by the DNA microarray technology through biological experiments in the lab. This paper introduced a novel hybrid method, which combines the clonal selection algorithm and BFGS Quasi-Newton algorithm. The proposed approach implemented for real world E...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330277/classical-and-bayesian-predictions-applied-to-bacillus-toxin-production
#2
Karim Ennouri, Rayda Ben Ayed, Maura Mazzarello, Ennio Ottaviani, Fathi Hertelli, Hichem Azzouz
Bacillus thuringiensis is a bacterium with unusual properties that make it useful for pest control in ecoagriculture. It can form a parasporal crystal containing polypeptides (also called delta-endotoxins). These entomopathogenic toxins are made during the stationary phase of the bacterial growth cycle and were initially characterized as an insect pathogen. Nowadays, the use of saturated two-level designs is very popular. This method is especially used in industrial applications where the cost of experiments is expensive...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330230/isolation-and-biological-evaluation-of-n-4-aminocyclooctyl-3-5-dinitrobenzamide-a-new-semisynthetic-derivative-from-the-mangrove-associated-actinomycete-pseudonocardia-endophytica-vuk-10
#3
Usha Kiranmayi Mangamuri, Muvva Vijayalakshmi, Sudhakar Poda, Bramanandam Manavathi, Bhujangarao Chitturi, Venkateswarlu Yenamandra
The present study was aimed to isolate novel bioactive compounds from actinomycetes species isolated from mangrove habitats. With this connection, Pseudonocardia endophytica (VUK-10) was isolated using dilution plate technique and was examined for its secondary metabolite profiling. After successive purification and spectroscopic characterization viz., FTIR, mass, NMR, DEPT, HMQC, HMBC, and COSY spectroscopy, two compounds were identified including a semi synthetic derivative N-(4-aminocyclooctyl)-3, 5-dinitrobenzamide (1), obtained from the precursor of novel natural product cyclooctane-1,4-diamine (3), along with a known compound 3-((1H-indol-6-yl) methyl) hexahydropyrrolo [1, 2-a] pyrazine-1, 4-dione (2)...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330205/dna-record-of-some-traditional-small-millet-landraces-in-india-and-nepal
#4
Subramanyam Ragupathy, Shanmughanandhan Dhivya, Kirit Patel, Abiran Sritharan, Kathirvelu Sambandan, Hom Gartaula, Ramalingam Sathishkumar, Kamal Khadka, Balasubramanian C Nirmala, A Nirmala Kumari, Steven G Newmaster
Despite the extensive use of small millet landraces as an important source of nutrition for people living in semi-arid regions, they are presently marginalized and their diversity and distribution are threatened at a global scale. Local farmers have developed ancient breeding programs entrenched in traditional knowledge (TK) that has sustained rural cultures for thousands of years. The convention on biological diversity seeks fair and equitable sharing of genetic resources arising from local knowledge and requires signatory nations to provide appropriate policy and legal framework to farmers' rights over plant genetic resources and associated TK...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330111/effect-of-stat3-inhibitor-in-chronic-myeloid-leukemia-associated-signaling-pathway-a-mathematical-modeling-simulation-and-systems-biology-study
#5
Himansu Kumar, Swapnil Tichkule, Utkarsh Raj, Saurabh Gupta, Swati Srivastava, Pritish Kumar Varadwaj
Chronic myeloid leukemia (CML) is a hematopoietic stem-cell disorder which proliferates due to abnormal growth of basophil cells. Several proangiogenic molecules have been reported to be associated in CML progression, including the hepatocyte growth factor (HGF). However, detail mechanism about the cellular distribution and function of HGF in CML is yet to be revealed. The proliferation of hematopoietic cells are regulated by some of the growth factors like interleukin 3 (IL-3), IL-6, erythropoietin, thrombopoietin, etc...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329838/neighborhood-disadvantage-and-biological-aging-using-marginal-structural-models-to-assess-the-link-between-neighborhood-census-variables-and-epigenetic-aging
#6
Man-Kit Lei, Ronald L Simons, Steven R H Beach, Robert A Philibert
Objectives: Past research has reported an association between neighborhood disadvantage and healthy aging, but most of these studies utilize self-report measures of health or physical functioning and do not properly account for neighborhood selection effects, creating concerns regarding inflated associations. To overcome these limitations and provide a more stringent estimate of effects, the current study investigated the effect of neighborhood disadvantage on aging using newly developed epigenetic methods to assess rate of biological aging and marginal structural modeling (MSM) to account for potential confounds due to neighborhood selection...
March 3, 2017: Journals of Gerontology. Series B, Psychological Sciences and Social Sciences
https://www.readbyqxmd.com/read/28329724/accurate-predictions-of-postmortem-interval-using-linear-regression-analyses-of-gene-meter-expression-data
#7
M Colby Hunter, Alex E Pozhitkov, Peter A Noble
In criminal and civil investigations, postmortem interval is used as evidence to help sort out circumstances at the time of human death. Many biological, chemical, and physical indicators can be used to determine the postmortem interval - but most are not accurate. Here, we sought to validate an experimental design to accurately predict the time of death by analyzing the expression of hundreds of upregulated genes in two model organisms, the zebrafish and mouse. In a previous study, the death of healthy adults was conducted under strictly controlled conditions to minimize the effects of confounding factors such as lifestyle and temperature...
March 4, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28329685/critical-role-for-gab2-in-neuroblastoma-pathogenesis-through-the-promotion-of-shp2-mycn-cooperation
#8
Xiaoling Zhang, Zhiwei Dong, Cheng Zhang, Choong Yong Ung, Shuning He, Ting Tao, Andre M Oliveira, Alexander Meves, Baoan Ji, A Thomas Look, Hu Li, Benjamin G Neel, Shizhen Zhu
Growing evidence suggests a major role for Src-homology-2-domain-containing phosphatase 2 (SHP2/PTPN11) in MYCN-driven high-risk neuroblastoma, although biologic confirmation and a plausible mechanism for this contribution are lacking. Using a zebrafish model of MYCN-overexpressing neuroblastoma, we demonstrate that mutant ptpn11 expression in the adrenal gland analog of MYCN transgenic fish promotes the proliferation of hyperplastic neuroblasts, accelerates neuroblastomagenesis, and increases tumor penetrance...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28329682/the-swi-snf-protein-pbrm1-restrains-vhl-loss-driven-clear-cell-renal-cell-carcinoma
#9
Amrita M Nargund, Can G Pham, Yiyu Dong, Patricia I Wang, Hatice U Osmangeyoglu, Yuchen Xie, Omer Aras, Song Han, Toshinao Oyama, Shugaku Takeda, Chelsea E Ray, Zhenghong Dong, Mathieu Berge, A Ari Hakimi, Sebastien Monette, Carl L Lekaye, Jason A Koutcher, Christina S Leslie, Chad J Creighton, Nils Weinhold, William Lee, Satish K Tickoo, Zhong Wang, Emily H Cheng, James J Hsieh
PBRM1 is the second most commonly mutated gene after VHL in clear cell renal cell carcinoma (ccRCC). However, the biological consequences of PBRM1 mutations for kidney tumorigenesis are unknown. Here, we find that kidney-specific deletion of Vhl and Pbrm1, but not either gene alone, results in bilateral, multifocal, transplantable clear cell kidney cancers. PBRM1 loss amplified the transcriptional outputs of HIF1 and STAT3 incurred by Vhl deficiency. Analysis of mouse and human ccRCC revealed convergence on mTOR activation, representing the third driver event after genetic inactivation of VHL and PBRM1...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28329081/a-new-preclinical-paradigm-for-testing-anti-aging-therapeutics
#10
Warren Ladiges, Jessica M Snyder, Erby Wilkinson, Denise M Imai, Tim Snider, Xuan Ge, Marcia Ciol, Christina Pettan-Brewer, Smitha P S Pillai, John Morton, Ellen Quarles, Peter Rabinovitch, Laura Niedernhofer, Denny Liggitt
Testing drugs for anti-aging effects has historically been conducted in mouse life-span studies, but are costly and time consuming, and more importantly, difficult to recapitulate in humans. In addition, life-span studies in mice are not well suited to testing drug combinations that target multiple factors involved in aging. Additional paradigms for testing therapeutics aimed at slowing aging are needed. A new paradigm, designated as the Geropathology Grading Platform (GGP), is based on a standardized set of guidelines developed to detect the presence or absence of low-impact histopathological lesions and to determine the level of severity of high-impact lesions in organs from aged mice...
February 22, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28328998/combinatorial-selection-for-replicable-rna-by-q%C3%AE-replicase-while-maintaining-encoded-gene-function
#11
Mio Yumura, Natsuko Yamamoto, Katsushi Yokoyama, Hirotada Mori, Tetsuya Yomo, Norikazu Ichihashi
Construction of a complex artificial self-replication system is challenging in the field of in vitro synthetic biology. Recently, we developed a translation-coupled RNA replication system, wherein an artificial genomic RNA replicates with the Qβ RNA replicase gene encoded on itself. The challenge is to introduce additional genes into the RNA to develop a complex system that mimics natural living systems. However, most RNA sequence encoding genes are not replicable by the Qβ replicase owing to its requirement for strong secondary structures throughout the RNA sequence that are absent in most genes...
2017: PloS One
https://www.readbyqxmd.com/read/28328943/structurally-detailed-coarse-grained-model-for-sec-facilitated-co-translational-protein-translocation-and-membrane-integration
#12
Michiel J M Niesen, Connie Y Wang, Reid C Van Lehn, Thomas F Miller
We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations...
March 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28328880/swine-models-genomic-tools-and-services-to-enhance-our-understanding-of-human-health-and-diseases
#13
Eric M Walters, Kevin D Wells, Elizabeth C Bryda, Susan Schommer, Randall S Prather
The pig is becoming increasingly important as a biomedical model. Given the similarities between pigs and humans, a greater understanding of the underlying biology of human health and diseases may come from the pig rather than from classical rodent models. With an increasing need for swine models, it is essential that the genomic tools, models and services be readily available to the scientific community. Many of these are available through the National Swine Resource and Research Center (NSRRC), a facility funded by the US National Institutes of Health at the University of Missouri...
March 22, 2017: Lab Animal
https://www.readbyqxmd.com/read/28328509/multitask-protein-function-prediction-through-task-dissimilarity
#14
Marco Frasca, Nicolo Cesa-Bianchi
Automated protein function prediction is a challenging problem with distinctive features, such as the hierarchical organization of protein functions and the scarcity of annotated proteins for most biological functions. We propose a multitask learning algorithm addressing both issues. Unlike standard multitask algorithms, which use task (protein functions) similarity information as a bias to speed up learning, we show that dissimilarity information enforces separation of rare class labels from frequent class labels, and for this reason is better suited for solving unbalanced protein function prediction problems...
March 17, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28328501/monte-carlo-simulations-of-diffusion-weighted-mri-in-myocardium-validation-and-sensitivity-analysis
#15
Joanne Bates, Darryl McClymont, Irvin Teh, Peter Kohl, Jurgen Schneider, Vicente Grau
A model of cardiac microstructure and diffusion MRI is presented, and compared with experimental data from ex vivo rat hearts. The model includes a simplified representation of individual cells, with physiologically correct cell size and orientation, as well as intra- to extracellular volume ratio. Diffusion MRI is simulated using a Monte Carlo model and realistic MRI sequences. The results show good correspondence between the simulated and experimental MRI signals. Similar patterns are observed in the eigenvalues of the diffusion tensor, the mean diffusivity (MD) and the fractional anisotropy (FA)...
March 10, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28328372/psychiatric-genomics-and-mental-health-treatment-setting-the-ethical-agenda
#16
Camillia Kong, Michael Dunn, Michael Parker
Realizing the benefits of translating psychiatric genomics research into mental health care is not straightforward. The translation process gives rise to ethical challenges that are distinctive from challenges posed within psychiatric genomics research itself, or that form part of the delivery of clinical psychiatric genetics services. This article outlines and considers three distinct ethical concerns posed by the process of translating genomic research into frontline psychiatric practice and policy making...
April 2017: American Journal of Bioethics: AJOB
https://www.readbyqxmd.com/read/28328227/ultrafast-relaxation-dynamics-of-photoexcited-heme-model-compounds-observation-of-multiple-electronic-spin-states-and-vibrational-cooling
#17
Chinju Govind, Venugopal Karunakaran
Hemin is a unique model compound of heme proteins carrying out variable biological functions. Here the excited state relaxation dynamics of heme model compounds in the ferric form are systematically investigated by changing the axial ligand (Cl/Br), the peripheral substituent (Vinyl/Ethylmeso) and the solvent (Methanol/DMSO) using femtosecond pump-probe spectroscopy upon excitation at 380 nm. The relaxation time constants of these model compounds are obtained by global analysis. Excited state deactivation pathway of the model compounds comprising the decay of the porphyrin excited state (S*) to Ligand to Metal Charge Transfer state (LMCT, t1), back electron transfer from Metal to Ligand (MLCT, t2) and relaxation to the ground state through different electronic spin states of iron (t3 and t4), is proposed along with the vibrational cooling processes...
March 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28328075/role-of-amino-acids-in-rheumatoid-arthritis-studied-by-metabolomics
#18
Min He, Amy C Harms, Eduard van Wijk, Mei Wang, Ruud Berger, Slavik Koval, Thomas Hankemeier, Jan van der Greef
BACKGROUND: Rheumatoid arthritis (RA) is a complex, chronic autoimmune disease characterized by various inflammatory symptoms, including joint swelling, joint pain, and both structural and functional joint damage. The most commonly used animal model for studying RA is mice with collagen-induced arthritis (CIA); the wide use of this model is due primarily to many similarities with RA in human patients. Metabolomics is used increasingly in biological studies for diagnosing disease and for predicting and evaluating drug interventions, as a large number of disease-associated metabolites can be analyzed and interpreted from a biological perspective...
March 22, 2017: International Journal of Rheumatic Diseases
https://www.readbyqxmd.com/read/28328067/diminishing-returns-limit-energetic-costs-of-climate-change
#19
Ofir Levy, Jason D Borchert, Travis W Rusch, Lauren B Buckley, Michael J Angilletta
Changes in the time available for organisms to maintain physiologically preferred temperatures (thermal opportunity) is a primary mechanism by which climate change impacts the fitness and population dynamics of organisms. Yet, it is unclear whether losses or gains in thermal opportunity result in proportional changes in rates of energy procurement and use. We experimentally quantified lizard food consumption and energy assimilation at different durations of thermal opportunity. We incorporated these data in an individual-based model of foraging and digestion in lizards to explore the implications of nonlinear responses to shifts in thermal opportunity across a wide geographic range...
March 22, 2017: Ecology
https://www.readbyqxmd.com/read/28327669/pollen-mediated-gene-flow-from-glyphosate-resistant-common-waterhemp-amaranthus-rudis-sauer-consequences-for-the-dispersal-of-resistance-genes
#20
Debalin Sarangi, Andrew J Tyre, Eric L Patterson, Todd A Gaines, Suat Irmak, Stevan Z Knezevic, John L Lindquist, Amit J Jhala
Gene flow is an important component in evolutionary biology; however, the role of gene flow in dispersal of herbicide-resistant alleles among weed populations is poorly understood. Field experiments were conducted at the University of Nebraska-Lincoln to quantify pollen-mediated gene flow (PMGF) from glyphosate-resistant (GR) to -susceptible (GS) common waterhemp using a concentric donor-receptor design. More than 130,000 common waterhemp plants were screened and 26,199 plants were confirmed resistant to glyphosate...
March 22, 2017: Scientific Reports
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