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https://www.readbyqxmd.com/read/29045882/untangling-the-hairball-fitness-based-asymptotic-reduction-of-biological-networks
#1
Félix Proulx-Giraldeau, Thomas J Rademaker, Paul François
Complex mathematical models of interaction networks are routinely used for prediction in systems biology. However, it is difficult to reconcile network complexities with a formal understanding of their behavior. Here, we propose a simple procedure (called ϕ¯) to reduce biological models to functional submodules, using statistical mechanics of complex systems combined with a fitness-based approach inspired by in silico evolution. The ϕ¯ algorithm works by putting parameters or combination of parameters to some asymptotic limit, while keeping (or slightly improving) the model performance, and requires parameter symmetry breaking for more complex models...
October 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29045746/identification-of-natural-products-as-inhibitors-of-human-organic-anion-transporters-oat1-and-oat3-and-their-protective-effect-on-mercury-induced-toxicity
#2
Xue Wang, Lifeng Han, Gentao Li, Wei Peng, Xiumei Gao, Curtis D Klaassen, Guanwei Fan, Youcai Zhang
Mercury accumulates in kidneys and produces acute kidney injury. Semen cassiae (SC), a widely consumed tea and herbal medicine in Eastern Asia, has been reported to have protective effects on kidneys. In this study, SC extract was shown to almost abolish the histological alterations induced by mercuric chloride (HgCl2) in rat kidneys. A total of 22 compounds were isolated from SC, and 1,7,8-methoxyl-2-hydroxyl-3-methyl-anthraquinone was detected in SC for the first time. Among the 8 compounds identified in the blood of rats after SC treatment, 6 were strong inhibitors of human organic anion transporter 1 and 3 (OAT1 and OAT3)...
October 13, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29044771/alkaloids-of-amaryllidaceae-as-inhibitors-of-cholinesterases-aches-and-bches-an-integrated-bioguided-study
#3
Natalie Cortes, Karina Sierra, Fernando Alzate, Edison H Osorio, Edison Osorio
INTRODUCTION: Enzymatic inhibition of acetylcholinesterase (AChE) is an essential therapeutic target for the treatment of Alzheimer's disease (AD) and AChE inhibitors are the first-line drugs for it treatment. However, butyrylcholinesterase (BChE), contributes critically to cholinergic dysfunction associated with AD. Thus, the development of novel therapeutics may involve the inhibition of both cholinesterase enzymes. OBJECTIVE: To evaluate, in an integrated bioguided study, cholinesterases alkaloidal inhibitors of Amaryllidaceae species...
October 17, 2017: Phytochemical Analysis: PCA
https://www.readbyqxmd.com/read/29044436/preterm-infant-associated-clostridium-tertium-clostridium-cadaveris-and-clostridium-paraputrificum-strains-genomic-and-evolutionary-insights
#4
Raymond Kiu, Shabhonam Caim, Cristina Alcon-Giner, Gusztav Belteki, Paul Clarke, Derek Pickard, Gordon Dougan, Lindsay J Hall
Clostridium species (particularly Clostridium difficile, Clostridium botulinum, Clostridium tetani and Clostridium perfringens) are associated with a range of human and animal diseases. Several other species including Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum have also been linked with sporadic human infections, however there is very limited, or in some cases, no genomic information publicly available. Thus, we isolated one C. tertium strain, one C. cadaveris strain and three C...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29043886/assessing-the-risk-of-alcohol-induced-dose-dumping-from-sustained-release-oral-dosage-forms-in-vitro-in-silico-approach
#5
Sandra Cvijić, Ivana Aleksić, Svetlana Ibrić, Jelena Parojčić
Consumption of alcoholic beverages with sustained-release oral dosage forms may pose a risk to patients due to potential alcohol-induced dose dumping (ADD). Regulatory guidances recommend in vitro dissolution testing to identify the risk of ADD, but the question remains whether currently proposed test conditions can be considered biopredictive. The purpose of this study was to evaluate different dissolution setups to assess ADD, and the potential of combined in vitro-in silico approach to predict drug absorption after concomitant alcohol intake for hydrophilic and lipophilic sustained-release tablets containing ibuprofen or diclofenac sodium...
October 18, 2017: Pharmaceutical Development and Technology
https://www.readbyqxmd.com/read/29043794/dynamic-transition-from-%C3%AE-helices-to-%C3%AE-sheets-in-polypeptide-coiled-coil-motifs
#6
Kirill A Minin, Artem Zhmurov, Kenneth A Marx, Prashant K Purohit, Valeri Barsegov
We carried out dynamic force manipulations in silico on a variety of coiled-coil protein fragments from myosin, chemotaxis receptor, vimentin, fibrin, and phenylalanine zippers that vary in size and topology of their α-helical packing. When stretched along the superhelical axis, all superhelices show elastic, plastic, and inelastic elongation regimes, and undergo a dynamic transition from the α-helices to the β-sheets, which marks the onset of plastic deformation. Using Abeyaratne-Knowles formulation of phase transitions, we developed a new theoretical methodology to model mechanical and kinetic properties of protein coiled-coils under mechanical non-equilibrium conditions and to map out their energy landscapes...
October 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29043394/in-silico-analyses-reveal-the-relationship-between-six1-eya1-mutations-and-conotruncal-heart-defects
#7
Bojian Li, Lijuan Xu, Nanchao Hong, Sun Chen, Rang Xu
Conotruncal heart defects (CTDs) represent a group of severe and complicated congenital cardiovascular malformations and require opportune clinical interventions once diagnosed. Occurrence of CTD is related to the functional abnormality of the second heart field (SHF), and variants of genes which regulate the development of the second heart field have been recognized as the main genetic factors leading to CTDs. Previous studies indicated that transcriptional complex SIX1/EYA1 may contribute to SHF development, and SIX1/EYA1 knockout mice exhibited a series of conotruncal malformations...
October 17, 2017: Pediatric Cardiology
https://www.readbyqxmd.com/read/29042257/in-vivo-pharmacokinetic-interaction-by-ethanolic-extract-of-gymnema-sylvestre-with-cyp2c9-tolbutamide-cyp3a4-amlodipine-and-cyp1a2-phenacetin-in-rats
#8
Madhuri Vaghela, Niteshkumar Sahu, Prashant Kharkar, Nancy Pandita
Gymnema sylvestre (GS) is a medicinal herb used for diabetes mellitus (DM). Herbs are gaining popularity as medicines in DM for its safety purpose. The aim of the present study was to evaluate in vivo pharmacokinetic (PK) interaction between allopathic drugs tolbutamide (TOLBU), amlodipine (AMLO), and phenacetin (PHENA) at low (L) and high (H) doses with ethanolic extract (EL) from GS. EL was extracted and subjected to TLC, total triterpenoid content (19.76 ± 0.02 W/W) and sterol content (0.1837 ± 0...
October 14, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/29041842/identifying-novel-small-molecule-antagonists-for-mlst8-protein-using-computational-approaches
#9
Tuleshwori Devi Sapam, Anbumani Velmurugan Ilavarasi, Bhagath Kumar Palaka, Elakkiya Elumalai, Nirmala Devi Kanika, Dinakara Rao Ampasala
Mammalian lethal with SEC13 protein 8 (mLST8), is an indispensable protein subunit of mammalian target of rapamycin (mTOR) signaling pathway that interacts with the kinase domain of mTOR protein, thereby stabilizing its active site. Experimental studies reported the over expression of mLST8 in human colon and prostate cancers by activation of both mTORC1/2 complexes and subsequent downstream substrates leading to tumor progression. Considering its role, targeting mLST8 protein would be a therapeutic approach against tumor progression in colon and prostate cancers...
October 17, 2017: Journal of Receptor and Signal Transduction Research
https://www.readbyqxmd.com/read/29041840/identification-of-novel-scaffolds-to-inhibit-human-mitotic-kinesin-eg5-targeting-the-second-allosteric-binding-site-using-in-silico-methods
#10
Himesh Makala, Venkatasubramanian Ulaganathan
Human mitotic kinesins are potential anticancer drug targets because of their essential role in mitotic cell division. The kinesin Eg5 (Kinesin-5, kif11) has gained much attention in this regard and has many inhibitors in different phases of clinical trials. All drug candidates considered for Eg5 so far binds to the binding site (Site 1) formed by the loop L5, helices α2 and α3 and are uncompetitive to ATP/ADP. Recently, it has been reported that Eg5 also has a second binding site (Site 2) formed by helices α4 and α6...
October 17, 2017: Journal of Receptor and Signal Transduction Research
https://www.readbyqxmd.com/read/29040583/taste-receptor-polymorphisms-and-male-infertility
#11
M Gentiluomo, L Crifasi, A Luddi, D Locci, R Barale, P Piomboni, D Campa
STUDY QUESTION: Are polymorphisms of taste receptor genes associated with male infertility? SUMMARY ANSWER: This study has showed the associations between three single nucleotide polymorphisms (SNPs) in taste receptors genes (TASR) and male infertility. WHAT IS KNOWN ALREADY: Recent studies showed the expression of taste receptors in the testis and in spermatozoa, suggesting their possible role in infertility. The vast genetic variability in taste genes results in a large degree of diversity in various human phenotypes...
October 12, 2017: Human Reproduction
https://www.readbyqxmd.com/read/29039611/altered-expression-of-different-galnac%C3%A2-transferases-is-associated-with-disease-progression-and-poor-prognosis-in-women-with-high-grade-serous-ovarian-cancer
#12
Razan Sheta, Magdalena Bachvarova, Marie Plante, Jean Gregoire, Marie-Claude Renaud, Alexandra Sebastianelli, Ion Popa, Dimcho Bachvarov
Protein glycosylation perturbations are implicated in a variety of diseases, including cancer. Aberrant glycosylation in cancer is frequently attributed to altered expression of polypeptide GalNAc transferases (GalNAc‑Ts) - enzymes initiating mucin-type O-glycosylation. A previous study from our group demonstrated that one member of this family (GALNT3) is overexpressed in epithelial ovarian cancer (EOC), and GALNT3 expression correlated with shorter progression-free survival (PFS) in EOC patients with advanced disease...
October 9, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/29039308/actibacterium-pelagium-sp-nov-a-novel-alphaproteobacterium-and-emended-description-of-the-genus-actibacterium
#13
Li-Li Guo, Yue-Hong Wu, Xiao-Wu Xu, Chao-Jie Huang, Yun-Yun Xu, Hong Cheng, Chun-Sheng Wang, Min Wu, Xue-Wei Xu
A Gram-stain-negative, non-motile, rod-shaped bacterium, designated JN33(T), was isolated from seawater collected from the western Pacific Ocean. Strain JN33(T) was positive for hydrolysis of aesculin and gelatin. On the basis of 16S rRNA gene sequence analysis, strain JN33(T) showed high 16S rRNA gene sequence similarity to Actibacterium atlanticum 22II-S11-z10(T) (97.3 %), A. mucosum KCTC 23349(T) (96.6 %) and A. ureilyticum LS-811(T) (95.7 %) and exhibited less than 97.0 % 16S rRNA gene sequence similarity with respect to the other type strains within the family Rhodobacteraceae...
October 17, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29039247/high-throughput-in-silico-identification-and-characterization-of-plasmodium-falciparum-prl-phosphatase-inhibitors
#14
Rajan Pandey, Rakesh Kumar, Priya Gupta, Asif Mohmmed, Rita Tewari, Pawan Malhotra, Dinesh Gupta
Kinases and phosphatases are involved in many essential processes in Plasmodium life cycle. Among the identified 67 Plasmodium falciparum phosphatases, Phosphatase of Regenerating Liver (PRL) family protein homolog, PfPRL is an essential parasite tyrosine phosphatase. PfPRL is shown to be prenylated, secreted and involved in the host invasion process. In the present study, a structure based high throughput in-silico screening of PfPRL binders, using ChEMBL-NTD compounds lead to the identification of nine compounds based on binding energy, Lipinski rule of five and QED score...
October 17, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29039242/computational-elucidation-mutational-and-hot-spot-based-designing-of-potential-inhibitors-against-human-acid-sensing-ion-channels-hasic-1a-to-treatment-of-various-physiological-conditions
#15
Anurag Singh Chauhan, Md Yousuf Ansari, Rani Mansuri, Manas Ranjan Dikhit, Vahab Ali, Ganesh Chandra Sahoo, Pradeep Das
Acid-sensing ion channels (ASICs) are ligand/proton-gated ion channels belonging to the family of the degenerin/epithelial Na(+) channel (DEG/ENaC). They function as a sodium-selective pore for Ca(2+) entry into neuronal cells during pathological conditions. The blocking of this channel has therapeutic importance, because at basal physiological pH (7.2), it is in a closed state and under a more acidic condition, and the ASIC1a ion channel is activated. To investigate the different states of the hASIC1a channel based on mutational analysis, structure based virtual screening and molecular dynamics simulation studies...
October 17, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29039067/in-silico-system-pharmacology-for-the-potential-bioactive-ingredients-contained-in-xingnaojing-injection-and-its-material-basis-for-sepsis-treatment
#16
Shi-Tang Ma, Cheng-Tao Feng, You-Xi Xiong, Xiao-Lin Zhang, Cheng-Gui Miao, Hao Yu
OBJECTIVE: To elucidate the action mechanism of Xingnaojing Injection (, XNJI) for sepsis, and to target screen the potential bioactive ingredients. METHODS: An integrated protocol that combines in silico target screen (molecular docking) and database mapping was employed to find the potential inhibitors from XNJI for the sepsis-related targets and to establish the compound-target (C-T) interaction network. The XNJI's bioactive components database was investigated and the sepsis-associated targets were comprehensively constructed; the 3D structure of adenosine receptor A2a and 5-lipoxygenase proteins were established and evaluated with homology modeling method; system network pharmacology for sepsis treatment was studied between the bioactive ingredients and the sepsis targets using computational biology methods to distinguish inhibitors from non inhibitors for the selected sepsis-related targets and C-T network construction...
October 17, 2017: Chinese Journal of Integrative Medicine
https://www.readbyqxmd.com/read/29039021/fifty-hertz-magnetic-field-affects-the-epigenetic-modulation-of-the-mir-34b-c-in-neuronal-cells
#17
Claudia Consales, Claudia Cirotti, Giuseppe Filomeni, Martina Panatta, Alessio Butera, Caterina Merla, Vanni Lopresto, Rosanna Pinto, Carmela Marino, Barbara Benassi
The exposure to extremely low-frequency magnetic fields (ELF-MFs) has been associated to increased risk of neurodegenerative diseases, although the underlying molecular mechanisms are still undefined. Since epigenetic modulation has been recently encountered among the key events leading to neuronal degeneration, we here aimed at assessing if the control of gene expression mediated by miRNAs, namely miRs-34, has any roles in driving neuronal cell response to 50-Hz (1 mT) magnetic field in vitro. We demonstrate that ELF-MFs drive an early reduction of the expression level of miR-34b and miR-34c in SH-SY5Y human neuroblastoma cells, as well as in mouse primary cortical neurons, by affecting the transcription of the common pri-miR-34...
October 16, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/29038887/mutations-in-inf2-may-be-associated-with-renal-histology-other-than-focal-segmental-glomerulosclerosis
#18
Anja K Büscher, Nora Celebi, Peter F Hoyer, Hanns-Georg Klein, Stefanie Weber, Julia Hoefele
BACKGROUND: In 2010, INF2 mutations were associated with autosomal-dominant focal segmental glomerulosclerosis (FSGS), clinically presenting with moderate proteinuria in adolescence. However, in the meantime, cases with more severe clinical courses have been described, including progression to end-stage renal disease (ESRD) during childhood. INF2 mutations in patients with isolated FSGS are clustered in exons 2 to 4, encoding the diaphanous inhibitory domain, involved in the regulation of the podocyte actin cytoskeleton...
October 6, 2017: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
https://www.readbyqxmd.com/read/29038815/distinct-oligomerization-and-fibrillization-dynamics-of-amyloid-core-sequences-of-amyloid-beta-and-islet-amyloid-polypeptide
#19
Yunxiang Sun, Bo Wang, Xinwei Ge, Feng Ding
A direct observation of amyloid aggregation from isolated peptides to cross-β fibrils is crucial for understanding the nucleation-dependence process, but the corresponding macroscopic timescales impose a major computational challenge. Using rapid all-atom discrete molecular dynamics simulations, we capture the oligomerization and fibrillization dynamics of the amyloid core sequences of amyloid-β (Aβ) in Alzheimer's disease and islet amyloid polypeptide (IAPP) in type-2 diabetes, namely Aβ16-22 and IAPP22-28...
October 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29038659/in-silico-prediction-analysis-of-idiotope-driven-t-b-cell-collaboration-in-multiple-sclerosis
#20
Rune A Høglund, Andreas Lossius, Jorunn N Johansen, Jane Homan, Jūratė Šaltytė Benth, Harlan Robins, Bjarne Bogen, Robert D Bremel, Trygve Holmøy
Memory B cells acting as antigen-presenting cells are believed to be important in multiple sclerosis (MS), but the antigen they present remains unknown. We hypothesized that B cells may activate CD4(+) T cells in the central nervous system of MS patients by presenting idiotopes from their own immunoglobulin variable regions on human leukocyte antigen (HLA) class II molecules. Here, we use bioinformatics prediction analysis of B cell immunoglobulin variable regions from 11 MS patients and 6 controls with other inflammatory neurological disorders (OINDs), to assess whether the prerequisites for such idiotope-driven T-B cell collaboration are present...
2017: Frontiers in Immunology
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