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https://www.readbyqxmd.com/read/27914045/achievements-and-challenges-in-computational-protein-design
#1
Ilan Samish
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914027/the-role-of-guided-growth-as-it-relates-to-limb-lengthening
#2
REVIEW
Peter M Stevens
For decades, the classic indication for limb lengthening has been reserved for anisomelia that was expected to reach or exceed 5 cm at maturity. Epiphysiodesis was reserved for discrepancies in the 2-5 cm range. With the increasing sophistication of fixators, including rail, hexapod, and hybrid, complex deformities may be corrected simultaneously while moderate to extreme lengthening is achieved. More recently, iterations of telescoping intramedullary rods have further strengthened our armamentarium. Meanwhile, permanent epiphysiodesis techniques, both open and percutaneous, have yielded to more versatile and reversible tethering of one (angle) or both (length) sides of a physis...
December 2, 2016: Journal of Children's Orthopaedics
https://www.readbyqxmd.com/read/27913892/early-harvest-effects-on-hydrophilic-phenolic-components-of-extra-virgin-olive-oils-cvs-ayval%C3%A4-k-memecik-and-topaka%C3%A5-%C3%A4
#3
Fatma Yıldırım, Adnan Nurhan Yıldırım, Gülcan Özkan, Bekir Şan, Mehmet Polat, Hatice Aşık, Yaşar Karakurt, Sezai Ercişli
The study was conducted to determine the effects of cultivar, harvest period, and their interaction on the hydrophilic phenolic components extra virgin olive oils of the cultivars 'Ayvalık,' 'Memecik,' and 'Topakaşı.' Olives were collected at three different harvesting periods: (1) early harvest period-1 (Beginning of spotting), (2) early harvest period-2 (End of spotting), and (3) optimum harvest period. Oils were extracted using the Abencor system. HPLC (High-performance liquid chromatograph) technique was used to quantify the phenolic compounds including tyrosol (p-HPEA), hydroxytyrosol (3,4-DHPEA), luteolin, rutin, quercetin, catechin, sinapinic acid, p-coumaric acid, cinnamic acid, vanillin, vanillic acid, ferulic acid, and gallic acid...
December 2, 2016: Biochemical Genetics
https://www.readbyqxmd.com/read/27913890/performance-improvement-of-raw-water-pretreatment-process-with-pre-inoculation-biofilm-feasibility-and-limiting-factors
#4
Guang-Feng Yang, Li-Juan Feng, Cai-Rong Guo, Tian Xia, Xiang-Yang Xu, Liang Zhu
The initial formation of biofilm and the removal performance of pollutants in biological pretreatment process for polluted raw water were limited due to the oligotrophic niche in raw water. In this study, the feasibility of using pre-inoculation biofilm formed under nutrients enhanced condition for polluted raw water treatment was analyzed in nine batch reactors. Results showed that the pollutants removal performance of biofilm was improved under nutrients enhanced conditions. Ammonia oxidation rate (AOR) was exponentially increased with the increasing in NH4(+)-N levels, and organic matter removal rate (ORR) was positively related to the initial total organic carbon (TOC) concentration...
December 2, 2016: Biodegradation
https://www.readbyqxmd.com/read/27913778/effect-of-deslorelin-acetate-treatment-in-oocyte-recovery-and-in-vitro-embryo-production-in-domestic-cats
#5
Camila Louise Ackermann, Eduardo Trevisol, Leticia Ferrari Crocomo, Tatiana da Silva Rascado, Rodrigo Volpato, Carlos Renato de Freitas Guaitolini, Carlize Lopes, Talita de Almeida Costa, Maria Denise Lopes
OBJECTIVES: The present study investigated the effect of contraceptive treatment with deslorelin acetate on in vitro embryo production and oocyte recovery in domestic queens. METHODS: Twenty-one mature domestic cats were used. Eleven queens (treated group) and one tom were kept in an experimental cattery, and 10 queens were privately owned (control group). When in interestrus or diestrus (day 0) a deslorelin acetate implant (Suprelorin, 4.7 mg/animal) was inserted into the subcutaneous tissue of the interscapular region in all queens in the treated group...
December 2, 2016: Journal of Feline Medicine and Surgery
https://www.readbyqxmd.com/read/27913766/myocardial-cytochrome-oxidase-activity-increases-with-age-and-hypoxemia-in-patients-with-congenital-heart-disease
#6
Michael Onwugbufor, Richard J Levy, David Zurakowski, Richard A Jonas, Pranava Sinha
BACKGROUND: Myocardial tolerance to ischemia is influenced by age and preoperative cyanosis through unknown mechanisms and significantly affects postoperative outcomes. Cytochrome c oxidase (CcOx), the terminal enzyme of the mitochondrial electron transport chain, may play a role in the susceptibility to ischemic-reperfusion (IR) injury. Our study aimed at investigating changes in human myocardial CcOx activity based on age and preoperative oxygen saturation to understand its role in transition from neonatal to mature myocardium and hypoxic conditions...
December 1, 2016: Perfusion
https://www.readbyqxmd.com/read/27913676/translational-control-by-mtor-independent-routes-how-eif6-organizes-metabolism
#7
REVIEW
Annarita Miluzio, Sara Ricciardi, Nicola Manfrini, Roberta Alfieri, Stefania Oliveto, Daniela Brina, Stefano Biffo
Over the past few years, there has been a growing interest in the interconnection between translation and metabolism. Important oncogenic pathways, like those elicited by c-Myc transcription factor and mTOR kinase, couple the activation of the translational machinery with glycolysis and fatty acid synthesis. Eukaryotic initiation factor 6 (eIF6) is a factor necessary for 60S ribosome maturation. eIF6 acts also as a cytoplasmic translation initiation factor, downstream of growth factor stimulation. eIF6 is up-regulated in several tumor types...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913641/translation-repression-by-maternal-rna-binding-protein-zar1-is-essential-for-early-oogenesis-in-zebrafish
#8
Liyun Miao, Yue Yuan, Feng Cheng, Junshun Fang, Fang Zhou, Weirui Ma, Yan Jiang, Xiahe Huang, Yingchun Wang, Lingjuan Shan, Dahua Chen, Jian Zhang
Large numbers of maternal RNAs are deposited in oocytes and are reserved for later development. Control of maternal RNA translation during oocyte maturation has been extensively investigated and its regulatory mechanisms are well documented. However, translational regulation of maternal RNAs in early oogenesis is largely unexplored. In this study, we generated zebrafish zar1 mutants which result in early oocyte apoptosis and fully penetrant male development. Loss of p53 suppresses the apoptosis in zar1 mutants and restores oocyte development...
December 2, 2016: Development
https://www.readbyqxmd.com/read/27913638/ms23-a-master-basic-helix-loop-helix-factor-regulates-the-specification-and-development-of-tapetum-in-maize
#9
Guo-Ling Nan, Jixian Zhai, Siwaret Arikit, Darren Morrow, John Fernandes, Lan Mai, Nhi Nguyen, Blake C Meyers, Virginia Walbot
Successful male gametogenesis involves orchestration of sequential gene regulation for somatic differentiation in pre-meiotic anthers. We report here the cloning of Male Sterile23 (Ms23), encoding an anther-specific predicted basic helix-loop-helix (bHLH) transcription factor required for tapetal differentiation; transcripts localize initially to the precursor secondary parietal cells then predominantly to daughter tapetal cells. In knockout ms23-ref mutant anthers, five instead of the normal four wall layers are observed...
December 2, 2016: Development
https://www.readbyqxmd.com/read/27913620/pb1-f2-derived-from-avian-influenza-a-virus-h7n9-induces-inflammation-via-activation-of-the-nlrp3-inflammasome
#10
Anita Pinar, Jennifer K Dowling, Natalie J Bitto, Avril B Robertson, Eicke Latz, Cameron R Stewart, Grant R Drummond, Matthew A Cooper, Julie L McAuley, Michelle D Tate, Ashley Mansell
The emergence of avian H7N9 influenza A virus (IAV) in humans with associated high mortality, has highlighted the threat of a potential pandemic. Fatal H7N9 infections are characterised by hyperinflammation and increased cellular infiltrates in the lung. Currently there are limited therapies to address the pathologies associated with H7N9 infection and what virulence factors may contribute to these pathologies. We have found that PB1-F2 derived from H7N9 activates the NLRP3 inflammasome and induces lung inflammation and cellular recruitment that is NLRP3 dependent...
December 2, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27913589/integrin-linked-kinase-ilk-deletion-disrupts-oligodendrocyte-development-by-altering-cell-cycle
#11
Rashad Hussain, Wendy B Macklin
: During development, oligodendrocytes are initially specified, after which oligodendrocyte precursor cells (OPCs) migrate and proliferate before differentiating into myelinating cells. Lineage specific programming of oligodendrocytes results from sensing environmental cues through membrane-bound receptors and related intracellular signaling molecules. Integrin linked kinase (ILK) is an important protein expressed at the inner margins of the plasma membrane, which can mediate some of these signals...
December 2, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27913431/pro-brain-derived-neurotrophic-factor-probdnf-mediated-p75ntr-activation-promotes-depolarizing-actions-of-gaba-and-increases-susceptibility-to-epileptic-seizures
#12
Baptiste Riffault, Nazim Kourdougli, Camille Dumon, Nadine Ferrand, Emmanuelle Buhler, Fabienne Schaller, Caroline Chambon, Claudio Rivera, Jean-Luc Gaiarsa, Christophe Porcher
The brain-derived neurotrophic factor (BDNF) is synthesized as a precursor, namely proBDNF, which can be processed into mature BDNF (mBDNF). Evidences suggest that proBDNF signaling through p75(NTR) may account for the emergence of neurological disorders. These findings support the view that the relative availability of mBDNF and proBDNF forms is an important mechanism underlying brain circuit formation and cognitive functions. Here we describe novel insights into the proBDNF/p75(NTR) mechanisms and function in vivo in modulating neuronal circuit and synaptic plasticity during the first postnatal weeks in rats...
December 1, 2016: Cerebral Cortex
https://www.readbyqxmd.com/read/27913428/migration-pathways-of-thalamic-neurons-and-development-of-thalamocortical-connections-in-humans-revealed-by-diffusion-mr-tractography
#13
Molly Wilkinson, Tara Kane, Rongpin Wang, Emi Takahashi
The thalamus plays an important role in signal relays in the brain, with thalamocortical (TC) neuronal pathways linked to various sensory/cognitive functions. In this study, we aimed to see fetal and postnatal development of the thalamus including neuronal migration to the thalamus and the emergence/maturation of the TC pathways. Pathways from/to the thalami of human postmortem fetuses and in vivo subjects ranging from newborns to adults with no neurological histories were studied using high angular resolution diffusion MR imaging (HARDI) tractography...
December 2, 2016: Cerebral Cortex
https://www.readbyqxmd.com/read/27913249/comparison-of-the-transcriptomic-profile-of-hepatic-human-induced-pluripotent-stem-like-cells-cultured-in-plates-and-in-a-3d-microscale-dynamic-environment
#14
Eric Leclerc, Keiichi Kimura, Marie Shinohara, Mathieu Danoy, Morgane Le Gall, Taketomo Kido, Atsushi Miyajima, Teruo Fujii, Yasuyuki Sakai
We have compared the transcriptomic profiles of human induced pluripotent stem cells after their differentiation in hepatocytes like cells in plates and microfluidic biochips. The biochips provided a 3D and dynamic support during the cell differentiation when compared to the 2D static cultures in plates. The microarray have demonstrated the up regulation of important pathway related to liver development and maturation during the culture in biochips. Furthermore, the results of the transcriptomic profile, coupled with immunostaining, and RTqPCR analysis have shown typical biomarkers illustrating the presence of responders of biliary like cells, hepatocytes like cells, and endothelial like cells...
November 29, 2016: Genomics
https://www.readbyqxmd.com/read/27913207/overexpression-of-stim1-in-neurons-in-mouse-brain-improves-contextual-learning-and-impairs-long-term-depression
#15
Łukasz Majewski, Filip Maciąg, Paweł M Boguszewski, Iga Wasilewska, Grzegorz Wiera, Tomasz Wójtowicz, Jerzy Mozrzymas, Jacek Kuznicki
STIM1 is an endoplasmic reticulum calcium sensor that is involved in several processes in neurons, including store-operated calcium entry. STIM1 also inhibits voltage-gated calcium channels, such as Cav1.2 and Cav3.1, and is thus considered a multifunctional protein. The aim of this work was to investigate the ways in which transgenic neuronal overexpression of STIM1 in FVB/NJ mice affects animal behavior and the electrophysiological properties of neurons in acute hippocampal slices. We overexpressed STIM1 from the Thy1...
November 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27913170/effects-of-the-feeding-ratio-of-food-waste-on-fed-batch-aerobic-composting-and-its-microbial-community
#16
Xiaojun Wang, Songqing Pan, Zhaoji Zhang, Xiangyu Lin, Yuzhen Zhang, Shaohua Chen
To determine the suitable feeding ratio for fed-batch aerobic composting, four fermenters were operated by adding 0%, 5%, 10% or 15% of food waste every day. The results showed that the 5% and 10% treatments were able to maintain continuous thermophilic conditions, while the 15% treatment performed badly in regard to composting temperature, which was probably due to the negative effects of excessive moisture on microbial activity. As composting proceeded, both the 5% and the 10% treatments reached maturity and achieved weight losses of approximately 65%...
November 22, 2016: Bioresource Technology
https://www.readbyqxmd.com/read/27913103/ontogeny-aging-and-gender-related-changes-in-hepatic-multidrug-resistant-protein-genes-in-rats
#17
Qiong-Ni Zhu, Wei-Yu Hou, Shang-Fu Xu, Yuan-Fu Lu, Jie Liu
: Multidrug resistance proteins (Mrps) are efflux transporters playing important roles in endogenous substances and xenobiotics transport out of the liver. Children, elderly, gender and physio-pathological conditions could influence their expression and result in changes in drug disposition. AIM: This study was aimed to examine the development-, ageing-, and sex-dependent changes in Mrp1-4 and ATP-binding cassette sub-family G member 2 (Abcg2) gene expressions in livers of rats...
November 29, 2016: Life Sciences
https://www.readbyqxmd.com/read/27913095/soft-hard-tissues-and-pharyngeal-airway-volume-changes-following-maxillomandibular-transverse-osteodistraction-computed-tomography-and-three-dimensional-laser-scanner-evaluation
#18
Francesca Antonella Bianchi, Giovanni Gerbino, Marina Corsico, Eleonora Schellino, Niccolò Barla, Laura Verzè, Guglielmo Ramieri
INTRODUCTION: Maxillomandibular transverse osteodistraction (MMTOD) is an alternative approach to the traditional treatment for transverse maxillary and mandibular deficiencies and crowding. The aim was to report soft and hard-tissues changes and airway volume variation. METHODS: In this study, skeletally mature, non-syndromic patients with transverse maxillary and mandibular hypoplasia, who underwent a MMTOD between 2010 and 2012, were included. Surgical changes were analysed using clinical evaluation, three-dimensional facial surface data and computed tomography analysis before (T0) and after the completion of post-op orthodontic treatment (T1)...
October 18, 2016: Journal of Cranio-maxillo-facial Surgery
https://www.readbyqxmd.com/read/27912876/in-vitro-and-ex-vivo-activity-of-an-azadirachta-indica-a-juss-seed-kernel-extract-on-early-sporogonic-development-of-plasmodium-in-comparison-with-azadirachtin-a-its-most-abundant-constituent
#19
Nisha Dahiya, Giuseppina Chianese, Solomon Mequanente Abay, Orazio Taglialatela-Scafati, Fulvio Esposito, Giulio Lupidi, Massimo Bramucci, Luana Quassinti, George Christophides, Annette Habluetzel, Leonardo Lucantoni
BACKGROUND: NeemAzal(®) (NA) is a quantified extract from seed kernels of neem, Azadirachta indica A.Juss. (Meliaceae), with a wide spectrum of biological properties, classically ascribed to its limonoid content. NA contains several azadirachtins (A to L), azadirachtin A (AzaA) being its main constituent. AzaA has been shown to inhibit microgamete formation of the rodent malaria parasite Plasmodium berghei, and NA was found to completely inhibit the transmission of Plasmodium berghei to Anopheles stephensi mosquitoes when administered to gametocytemic mice at a corresponding AzaA dose of 50mg/kg before exposure to mosquitoes...
December 15, 2016: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
https://www.readbyqxmd.com/read/27912819/endodontic-treatment-outcomes
#20
REVIEW
Nadia Chugal, Sanjay M Mallya, Bill Kahler, Louis M Lin
The primary goal of conventional endodontic treatment is prevention and/or elimination of apical periodontitis for both mature permanent teeth and immature teeth with an open apex. Besides these goals, the objectives of endodontic treatment of immature teeth include preservation of pulp vitality and often further root maturation. Robust criteria for outcome assessment are an essential determinant for any measure of treatment success for both mature and immature teeth.
January 2017: Dental Clinics of North America
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