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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/27908585/innovative-pretreatment-strategies-for-biogas-production
#2
REVIEW
Regina J Patinvoh, Osagie A Osadolor, Konstantinos Chandolias, Ilona Sárvári Horváth, Mohammad J Taherzadeh
Biogas or biomethane is traditionally produced via anaerobic digestion, or recently by thermochemical or a combination of thermochemical and biological processes via syngas (CO and H2) fermentation. However, many of the feedstocks have recalcitrant structure and are difficult to digest (e.g., lignocelluloses or keratins), or they have toxic compounds (such as fruit flavors or high ammonia content), or not digestible at all (e.g., plastics). To overcome these challenges, innovative strategies for enhanced and economically favorable biogas production were proposed in this review...
November 22, 2016: Bioresource Technology
https://www.readbyqxmd.com/read/27889432/decrease-of-high-voltage-ca-2-currents-in-the-dentate-gyrus-granule-cells-by-entorhinal-amyloidopathy-is-reversed-by-calcium-channel-blockade
#3
Hamid Gholami Pourbadie, Nima Naderi, Hadi Mirzapour Delavar, Mahshid Hosseinzadeh, Nasrin Mehranfard, Fariba Khodagholi, Mahyar Janahmadi, Fereshteh Motamedi
In the Alzheimer's disease (AD), entorhinal-hippocampal circuit is one of the earliest affected networks. There are some evidences indicating abnormal neuronal excitability and impaired synaptic plasticity in the dentate gyrus (DG) of AD animal model. However, the underlying mechanism leading to DG dysfunction particularly in the early phase of AD is not known. Since calcium dyshomeostasis has a critical role in the etiology of AD, it is possible that this phenomenon precedes electrophysiological alteration in the DG...
November 24, 2016: European Journal of Pharmacology
https://www.readbyqxmd.com/read/27889215/benzotriazole-type-ultraviolet-stabilizers-and-antioxidants-in-plastic-marine-debris-and-their-new-products
#4
Manviri Rani, Won Joon Shim, Gi Myung Han, Mi Jang, Young Kyoung Song, Sang Hee Hong
Ultraviolet stabilizers (UVSs) and antioxidants are the most widely used additives in plastics to enhance the lifetime of polymeric materials. There is growing interest in the roles of plastic marine debris and microplastics as source or vector of toxic substances to marine environment and organisms. However, there is limited information available on plastic associated chemicals, particularly additive chemicals. Therefore, to evaluate their extent of exposure from plastics to the marine environment, we determined UVSs and antioxidants in plastic debris (n=29) collected from beaches along with their corresponding new plastic products in markets (n=27) belonging to food, fisheries, and general use...
November 23, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27883090/sphingosine-1-phosphate-lyase-ablation-disrupts-presynaptic-architecture-and-function-via-an-ubiquitin-proteasome-mediated-mechanism
#5
Daniel N Mitroi, André U Deutschmann, Maren Raucamp, Indulekha Karunakaran, Konstantine Glebov, Michael Hans, Jochen Walter, Julie Saba, Markus Gräler, Dan Ehninger, Elena Sopova, Oleg Shupliakov, Dieter Swandulla, Gerhild van Echten-Deckert
The bioactive lipid sphingosine 1-phosphate (S1P) is a degradation product of sphingolipids that are particularly abundant in neurons. We have shown previously that neuronal S1P accumulation is toxic leading to ER-stress and an increase in intracellular calcium. To clarify the neuronal function of S1P, we generated brain-specific knockout mouse models in which S1P-lyase (SPL), the enzyme responsible for irreversible S1P cleavage was inactivated. Constitutive ablation of SPL in the brain (SPL(fl/fl/Nes)) but not postnatal neuronal forebrain-restricted SPL deletion (SPL(fl/fl/CaMK)) caused marked accumulation of S1P...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27879349/ncam1-polysialylation-the-prion-protein-s-elusive-reason-for-being
#6
REVIEW
Mohadeseh Mehrabian, Herbert Hildebrandt, Gerold Schmitt-Ulms
Much confusion surrounds the physiological function of the cellular prion protein (PrP(C)). It is, however, anticipated that knowledge of its function will shed light on its contribution to neurodegenerative diseases and suggest ways to interfere with the cellular toxicity central to them. Consequently, efforts to elucidate its function have been all but exhaustive. Building on earlier work that uncovered the evolutionary descent of the prion founder gene from an ancestral ZIP zinc transporter, we recently investigated a possible role of PrP(C) in a morphogenetic program referred to as epithelial-to-mesenchymal transition (EMT)...
December 2016: ASN Neuro
https://www.readbyqxmd.com/read/27878210/t-regulatory-cell-mediated-immunotherapy-for-solid-organ-transplantation-a-clinical-perspective
#7
Mohammad Afzal Khan
T regulatory cells (Tregs) play a vital role in suppressing heightened immune responses, and thereby promote a state of immunological tolerance. Tregs modulate both innate and adaptive immunity, which make them a potential candidate for cell-based immunotherapy to suppress uncontrolled activation of graft specific inflammatory cells and their toxic mediators. These grafts specific inflammatory cells (T effector cells) and other inflammatory mediators (Immunoglobulins, active complement mediators) are mainly responsible for graft vascular deterioration followed by acute/chronic rejection...
November 22, 2016: Molecular Medicine
https://www.readbyqxmd.com/read/27876410/clinical-outcome-of-high-dose-rate-interstitial-brachytherapy-in-vulvar-cancer-a-single-institutional-experience
#8
Umesh Mahantshetty, Pushpa Naga, Reena Engineer, Supriya Sastri, Yogesh Ghadi, Udita Upreti, Vijaya Somesan, Sudarshan Kadam, Satish Kohle, Deepak Deshpande, Shyam Kishore Shrivastava
PURPOSE: With an aim to evaluate and report high dose date interstitial brachytherapy (HDR-ISBT) in vulvar cancers, we undertook this retrospective analysis. METHODS AND MATERIALS: Histologically proven vulvar cancers treated with HDR-ISBT between 2001 and 2016 were analyzed. Radiotherapy details, clinical outcome in terms of local control rates, survivals, and toxicities were evaluated. RESULTS: A total of 38 patients received HDR-ISBT, with definitive radiation in 29 (76...
November 19, 2016: Brachytherapy
https://www.readbyqxmd.com/read/27876228/toxic-effects-of-microplastic-on-marine-microalgae-skeletonema-costatum-interactions-between-microplastic-and-algae
#9
Cai Zhang, Xiaohua Chen, Jiangtao Wang, Liju Tan
To investigate toxic effects of microplastic on marine microalgae Skeletonema costatum, both algal growth inhibition test and non-contact shading test were carried out, and algal photosynthesis parameters were also determined. The SEM images were used to observe interactions between microplastic and algae. It was found that microplastic (mPVC, average diameter 1 μm) had obvious inhibition on growth of microalgae and the maximum growth inhibition ratio (IR) reached up to 39.7% after 96 h exposure. However, plastic debris (bPVC, average diameter 1 mm) had no effects on growth of microalgae...
January 2017: Environmental Pollution
https://www.readbyqxmd.com/read/27866379/effects-of-oral-exposure-to-the-phthalate-substitute-acetyl-tributyl-citrate-on-female-reproduction-in-mice
#10
Lindsay M Rasmussen, Nivedita Sen, Xiaosong Liu, Zelieann R Craig
Acetyl tributyl citrate (ATBC), is a phthalate substitute used in food and medical plastics, cosmetics and toys. Although systemically safe up to 1000 mg kg(-1)  day(-1) , its ability to cause reproductive toxicity in females at levels below 50 mg kg(-1)  day(-1) has not been examined. This study evaluated the effects of lower ATBC exposures on female reproduction using mice. Adult CD-1 females (n = 7-8 per treatment) were dosed orally with tocopherol-stripped corn oil (vehicle), 5 or 10 mg kg(-1)  day(-1) ATBC daily for 15 days, and then bred with a proven breeder male...
November 20, 2016: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/27859543/chemical-activity-based-environmental-risk-analysis-of-the-plasticizer-di-ethylhexyl-phthalate-and-its-main-metabolite-mono-ethylhexyl-phthalate
#11
Frank A P C Gobas, S Victoria Otton, Laura F Tupper-Ring, Meara A Crawford, Kathryn E Clark, Michael G Ikonomou
This study applies a chemical activity-based approach to (i) evaluate environmental concentrations of di-ethylhexyl phthalate (DEHP) (n = 23,651) and its metabolite mono-ethylhexyl phthalate (MEHP) (n = 1,232) in 16 environmental media from 1,174 studies in the United States, Canada, Europe and Asia, and in-vivo toxicity data from 934 studies in 20 species as well as in-vitro biological activity data from USEPA's Toxicity Forecaster (ToxCast) and other sources; and (ii) conduct a comprehensive environmental risk analysis...
November 17, 2016: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/27827528/in-vitro-responses-of-t-lymphocytes-to-poly-butylene-succinate-based-biomaterials
#12
Montree Toso, Somying Patntirapong, Wanida Janvikul, Weerachai Singhatanadgit
BACKGROUND: Poly(butylene succinate) (PBSu) and PBSu/β-tricalcium phosphate (TCP) composites are biocompatible and good candidates as bone graft materials. However, little is known about the responses of T lymphocytes to these biomaterials, which play an important role in the success of bone grafting. METHODS: Activated T lymphocytes were seeded onto 32 mm diameter films (PBSu, PBSu/TCP8020 and PBSu/TCP6040) that have previously placed in 6-well culture plates for 8 h, 24 h and 72 h...
November 9, 2016: Minerva Stomatologica
https://www.readbyqxmd.com/read/27825933/comparative-toxicity-oxidative-stress-and-endocrine-disruption-potential-of-plasticizers-in-jeg-3-human-placental-cells
#13
Elisabet Pérez-Albaladejo, Denise Fernandes, Silvia Lacorte, Cinta Porte
Plasticizers are suspected to be toxic and/or to modulate or disrupt the endocrine system of humans and to cross the placental barrier, being embryonic and fetal development a particularly vulnerable period. This work investigates the comparative toxicity and ability to interfere with the synthesis of steroids and to generate reactive oxygen species (ROS) of a selected number of plasticizers, including bisphenol A (BPA), nonyl- (NP) and octylphenol (OP), benzyl butyl phthalate (BBP), dibutyl phthalate (DBP), di(2-ethylhexyl)phthalate (DEHP) and dimethyl phthalate (DMP), in the human placenta JEG-3 cells...
November 4, 2016: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/27823782/enantiomeric-fraction-of-styrene-glycol-as-a-biomarker-of-occupational-risk-exposure-to-styrene
#14
J J Lima, A Aguilar, F G Sánchez, A N Díaz
This work reports a new analytical approach for monitoring the enantiomeric ratios of styrene glycol (SG), encountered during the manufacture of plastics, by chiral liquid chromatography and the application as a biomarker for exposure to styrene. The isomers were separated using an AGP column running in the reverse phase and isocratic mode with a mobile phase consisting of 20 mM phosphate buffer saline (pH 4.15) and methanol at a flow rate of 0.8 mL/min. Photometric, polarimetric, and circular dichroism detectors were employed...
November 4, 2016: Chemosphere
https://www.readbyqxmd.com/read/27814532/effects-of-nanoplastics-and-microplastics-on-toxicity-bioaccumulation-and-environmental-fate-of-phenanthrene-in-fresh-water
#15
Yini Ma, Anna Huang, Siqi Cao, Feifei Sun, Lianhong Wang, Hongyan Guo, Rong Ji
Contamination of fine plastic particles (FPs), including micrometer to millimeter plastics (MPs) and nanometer plastics (NPs), in the environment has caught great concerns. FPs are strong adsorbents for hydrophobic toxic pollutants and may affect their fate and toxicity in the environment; however, such information is still rare. We studied joint toxicity of FPs with phenanthrene to Daphnia magna and effects of FPs on the environmental fate and bioaccumulation of (14)C-phenanthrene in fresh water. Within the five sizes particles we tested (from 50 nm to 10 μm), 50-nm NPs showed significant toxicity and physical damage to D...
October 27, 2016: Environmental Pollution
https://www.readbyqxmd.com/read/27805450/elution-of-platinum-from-carboplatin-impregnated-calcium-sulfate-hemihydrate-beads-in-vitro
#16
Rachel J Tulipan, Heidi Phillips, Laura D Garrett, Levent Dirikolu, Mark A Mitchell
OBJECTIVE To characterize the elution of platinum from carboplatin-impregnated calcium sulfate hemihydrate (CSH) beads in vitro. SAMPLE 60 carboplatin-impregnated CSH beads and 9 CSH beads without added carboplatin (controls). PROCEDURES Carboplatin-impregnated CSH beads (each containing 4.6 mg of carboplatin [2.4 mg of platinum]) were placed into separate 10-mL plastic tubes containing 5 mL of PBSS in groups of 1, 3, 6, or 10; 3 control beads were placed into a single tube of PBSS at the same volume. Experiments were conducted in triplicate at 37°C and a pH of 7...
November 2016: American Journal of Veterinary Research
https://www.readbyqxmd.com/read/27800447/bisphenol-a-in-edible-part-of-seafood
#17
REVIEW
Adele Repossi, Federica Farabegoli, Teresa Gazzotti, Elisa Zironi, Giampiero Pagliuca
Bisphenol A (BPA) is a man-made compound, mainly used as a monomer to produce polycarbonate (PC), epoxy resins, non-polymer additives to other plastics, which have many food related applications, such as food storage containers, tableware and internal coating of cans, as well as non-food applications such as electronic equipment, construction materials and medical devices. BPA exposure can occur when the residual monomer migrates into packaged food and beverages. Moreover, due to the ubiquitous presence of this compound, the general population can be exposed to environmental sources such as water, air and soil...
April 19, 2016: Italian Journal of Food Safety
https://www.readbyqxmd.com/read/27791136/probing-the-free-energy-landscapes-of-als-disease-mutants-of-sod1-by-nmr-spectroscopy
#18
Ashok Sekhar, Jessica A O Rumfeldt, Helen R Broom, Colleen M Doyle, Ryan E Sobering, Elizabeth M Meiering, Lewis E Kay
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that, in some cases, has been linked with mutations to the antioxidant metalloenzyme superoxide dismutase (SOD1). Although the mature form of this enzyme is highly stable and resistant to aggregation, the most immature form, lacking metal and a stabilizing intrasubunit disulfide bond, apoSOD1(2SH), is dynamic and hypothesized to be a major cause of toxicity in vivo. Previous solution NMR studies of wild-type apoSOD1(2SH) have shown that the ground state interconverts with a series of sparsely populated and transiently formed conformers, some of which have aberrant nonnative structures...
October 24, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27790286/sol-gel-encapsulation-of-au-nanoparticles-in-hybrid-silica-improves-gold-oxidation-catalysis
#19
Rosaria Ciriminna, Valerica Pandarus, Riccardo Delisi, Antonino Scurria, Maria Pia Casaletto, Francesco Giordano, François Béland, Mario Pagliaro
BACKGROUND: The introduction of an heterogeneously catalyzed gold-based alcohol oxidation process of broad applicability using a clean primary oxidant would be highly desirable. Gold is non toxic and carbonyl and carboxyl compounds are widely used to produce medicines, plastics, colorants, paints, detergents, fragrances, flavors, and other valued functional products. RESULTS: The sol-gel entrapment of gold nanoparticles in hybrid silica improves gold-based oxidation catalysis applied to the selective oxidation of alcohols with aqueous hydrogen peroxide as eco-friendly primary oxidant...
2016: Chemistry Central Journal
https://www.readbyqxmd.com/read/27788207/small-open-reading-frames-non-coding-rnas-and-repetitive-elements-in-bradyrhizobium-japonicum-usda-110
#20
Julia Hahn, Olga V Tsoy, Sebastian Thalmann, Jelena Čuklina, Mikhail S Gelfand, Elena Evguenieva-Hackenberg
Small open reading frames (sORFs) and genes for non-coding RNAs are poorly investigated components of most genomes. Our analysis of 1391 ORFs recently annotated in the soybean symbiont Bradyrhizobium japonicum USDA 110 revealed that 78% of them contain less than 80 codons. Twenty-one of these sORFs are conserved in or outside Alphaproteobacteria and most of them are similar to genes found in transposable elements, in line with their broad distribution. Stabilizing selection was demonstrated for sORFs with proteomic evidence and bll1319_ISGA which is conserved at the nucleotide level in 16 alphaproteobacterial species, 79 species from other taxa and 49 other Proteobacteria...
2016: PloS One
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