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In silico

Luria Leslie Founou, Raspail Carrel Founou, Arshad Ismail, Mushal Allam, Sabiha Yusuf Essack
OBJECTIVES: The draft genome sequences of two Enterobacter aerogenes HN503E2II and PN108E5IIB isolated from two Cameroonian abattoirs, are reported here. METHODS: Genomic DNA of these isolates was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using the Qiagen CLC Genomics Workbench. The assembled contigs were annotated and antibiotic resistance genes, virulence factors and plasmids were identified. RESULTS: The whole genome sequencing revealed that both strains are similar with genomes of 4,878,638 and 4,794,257bp and encoded several resistance genes associated with resistance to β-lactams, fluoroquinolones, aminoglycosides, fosfomycin, phenicols, sulphonamides, trimethoprim, macrolide and tetracycline...
June 20, 2018: Journal of Global Antimicrobial Resistance
Tayyebeh Zamani-Badi, Mohammad Karimian, Abolfazl Azami Tameh, Hossein Nikzad
BACHGROUND: IL-1α produced by Sertoli cells is considered to act as a growth factor for spermatogonia. In this study, we investigated the association of the C376A polymorphism in IL-1α with male infertility in men referring to the Kashan IVF Center. MATERIALS AND METHODS: In this case-control study, 2 ml of blood was collected from 230 fertile and 230 infertile men. After DNA extraction, the C376A variant was genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)...
June 2018: International Journal of Fertility & Sterility
Simeen Ber Rahman, Asif Mir, Nafees Ahmad, Syed Husnain Haider, Salman Akbar Malik, Muhammad Nasir
Non-bullous congenital ichthyosiform erythroderma (NCIE) is characterized by skin scaling with erythema. In this study, two Pakistani families with NCIE are genetically characterized through Whole Exome and Sanger sequencing to identify molecular basis of the disease. We identified a nonsense homozygous c.2026C>T mutation of ALOXE3, causing premature termination of the eLOX3 protein (p.Q676X). In silico studies predicted impaired enzymatic activity of the premature truncated eLOX3, leading to abnormal synthesis of specific hepoxilin derivatives, essential for epidermal barrier formation...
June 23, 2018: Congenital Anomalies
Ronan Bureau
The assessment of acute toxicity of chemicals by in silico methods is actually done by two methodologies, read-across and QSAR. The two approaches are strongly based on the similarity between the chemical for which a risk assessment is required and the reference chemical(s) for which the experimental data are known. Here, we describe the two methodologies with some main publications as illustrations and the in silico data associated with acute toxicity endpoints (ECHA, REACH) accessible via eChemPortal.
2018: Methods in Molecular Biology
Oriol López-Massaguer, Manuel Pastor, Ferran Sanz, Pablo Carbonell
The present method describes a systems biology approach for the in silico predictive modeling of drug toxicity. The data from LINCS were used to determine the type and number of pathways disturbed by each compound and to estimate the extent of disturbance (network perturbation elasticity). Moreover, the most frequently disturbed metabolic pathways and reactions were determined across the studied toxicants. The process was exemplified by successful predictions on various statins. In conclusion, an entirely new approach linking gene expression alterations to the prediction of complex organ toxicity was developed...
2018: Methods in Molecular Biology
Supratik Kar, Kunal Roy, Jerzy Leszczynski
An extensive use of pharmaceuticals and the widespread practices of their erroneous disposal measures have made these products contaminants of emerging concern (CEC). Especially, active pharmaceutical ingredients (APIs) are ubiquitously detected in surface water and soil, mainly in the aquatic compartment, where they do affect the living systems. Unfortunately, there is a huge gap in the availability of ecotoxicological data on pharmaceuticals' environmental behavior and ecotoxicity which force EMEA (European Medicines Agency) to release guidelines for their risk assessment...
2018: Methods in Molecular Biology
Antonio Lopalco, Nunzio Denora
This chapter presents an outline of the recent available information regarding safety, toxicity, and efficacy of nano drug delivery systems. Of particular importance is the evaluation of several key factors to design nontoxic and effective nanoformulations. Among them, we focus on nanostructure materials and synthesis methods, mechanisms of interactions with biological systems, treatment of nanoparticles, manufacture impurities, and nanostability. Emphasis is given to in silico, in vitro, and in vivo models used to assess and predict the toxicity of these new formulations...
2018: Methods in Molecular Biology
Paola Imbrici, Orazio Nicolotti, Francesco Leonetti, Diana Conte, Antonella Liantonio
Ion channels are membrane proteins involved in almost all physiological processes, including neurotransmission, muscle contraction, pace-making activity, secretion, electrolyte and water balance, immune response, and cell proliferation. Due to their broad distribution in human body and physiological roles, ion channels are attractive targets for drug discovery and safety pharmacology. Over the years ion channels have been associated to many genetic diseases ("channelopathies"). For most of these diseases the therapy is mainly empirical and symptomatic, often limited by lack of efficacy and tolerability for a number of patients...
2018: Methods in Molecular Biology
Anna Lombardo, Giuseppa Raitano, Domenico Gadaleta, Emilio Benfenati
Nontesting methods (NTM) proved to be a valuable resource for risk assessment of chemical substances. Indeed, they can be particularly useful when the information provided by different sources was integrated to increase the confidence in the final result. This integration can be sometimes difficult because different methods can lead to conflicting results, and because a clear guideline for integrating information from different sources was not available in the recent past. In this chapter, we present and discuss the recently published guideline from EFSA for integrating and weighting evidence for scientific assessment...
2018: Methods in Molecular Biology
Daniela Trisciuzzi, Domenico Alberga, Francesco Leonetti, Ettore Novellino, Orazio Nicolotti, Giuseppe F Mangiatordi
Molecular docking is an in silico method widely applied in drug discovery programs to predict the binding mode of a given molecule interacting with a specific biological target. This computational technique is today emerging also in the field of predictive toxicology for regulatory purposes, being for instance successfully applied to develop classification models for the prediction of the endocrine disruptor potential of chemicals. Herein, we describe the protocol for adapting molecular docking to the purposes of predictive toxicology...
2018: Methods in Molecular Biology
Muhammad Ismail Khan, Soyeon Choi, Muhammad Zahid, Habib Ahmad, Roshan Ali, Musharraf Jelani, Changsoo Kang
Palmoplantar keratoderma (PPK) is a rare group of excessive skin disorder characterized by thickness over the palms and soles. The striate palmoplantar keratoderma (PPKS) is a form in which hyperkeratotic lesions are restricted to the pressure regions extending longitudinally in the length of each finger to the palm. Dominantly inherited mutations in genes including desmoglein 1, desmoplakin and keratin 1 have been suggested as genetic causes of PPKS. In this study, we investigated a three-generation Pakistani family segregating PPKS phenotype in autosomal dominant fashion to identify genetic cause in this family...
July 2018: Genes & Genomics
Simone Di Micco, Luana Pulvirenti, Ines Bruno, Stefania Terracciano, Alessandra Russo, Maria C Vaccaro, Dafne Ruggiero, Vera Muccilli, Nunzio Cardullo, Corrado Tringali, Raffaele Riccio, Giuseppe Bifulco
The natural product magnolol (1) and a selection of its bioinspired derivatives 2-5, were investigated by Inverse Virtual Screening in order to identify putative biological targets from a panel of 308 proteins involved in cancer processes. By this in silico analysis we selected tankyrase-2 (TNKS2), casein kinase 2 (CK2) and bromodomain 9 (Brd9) as potential targets for experimental evaluations. The Surface Plasmon Resonance assay revealed that 3-5 present a good affinity for tankyrase-2, and, in particular, 3 showed an antiproliferative activity on A549 cells higher than the well-known tankyrase-2 inhibitor XAV939 used as reference compound...
June 20, 2018: Bioorganic & Medicinal Chemistry
Ting-Ting Tong, Er-Hu Zhao, Hai-Long Gao, Yong-Hui Xu, Yong-Ju Zhao, Gang Fu, Hong-Juan Cui
The 1-DNJ named 1-deoxynojirimycinis (2R,3R,4R,5S)-2-(hydroxymethyl) piperidine-3,4,5-triol, which is the nature active components existingin mulberryresources including leaves, stems, roots and silkworm larva, silkworm chrysalis, etc.The 1-deoxynojirimycin is a polyhydroxylated piperidine alkaloid, which was first found in Streptomyces as an antibiotic. Then the Japanese researchers isolated it from the mulberry root. 1-DNJ can inhibit postprandial hyperglycemia by suppressing intestinal alpha glucosidase...
May 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Ilaria Passarini, Sharon Rossiter, John Malkinson, Mire Zloh
Cationic peptides with antimicrobial properties are ubiquitous in nature and have been studied for many years in an attempt to design novel antibiotics. However, very few molecules are used in the clinic so far, sometimes due to their complexity but, mostly, as a consequence of the unfavorable pharmacokinetic profile associated with peptides. The aim of this work is to investigate cationic peptides in order to identify common structural features which could be useful for the design of small peptides or peptido-mimetics with improved drug-like properties and activity against Gram negative bacteria...
June 21, 2018: Pharmaceutics
Luria Leslie Founou, Raspail Carrel Founou, Mushal Allam, Arshad Ismail, Sabiha Yusuf Essack
OBJECTIVES: We report here the draft genome sequence of E. coli strain HN503E1II isolated from a nasal sample of an abattoir worker in Cameroon. METHODS: Genomic DNA of E. coli was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using the Qiagen CLC Genomics Workbench. The assembled contigs were annotated and antibiotic resistance genes, virulence factors, plasmids and sequence types were identified. RESULTS: The genome comprised a circular chromosome of 4,674,201bp, with a 50...
June 19, 2018: Journal of Global Antimicrobial Resistance
Santiago Coelho, Jose M Pozo, Marina Costantini, J Robin Highley, Meghdoot Mozumder, Julie E Simpson, Paul G Ince, Alejandro F Frangi
This study aims to statistically describe histologically stained white matter brain sections to subsequently inform and validate diffusion MRI techniques. For the first time, we characterise volume fraction distributions of three of the main structures in deep subcortical white matter (axons, astrocytes, and myelinated axons) in a representative cohort of an ageing population for which well-characterized neuropathology data is available. We analysed a set of samples from 90 subjects of the Cognitive Function and Ageing Study (CFAS), stratified into three groups of 30 subjects each, in relation to the presence of age-associated deep subcortical lesions...
June 19, 2018: NeuroImage
Andras Gabor Miklosi, Giorgia Del Favero, Doris Marko, Tibor Harkany, Gert Lubec
For more than a century, the precision at which any protein (or RNA) could be localized in living cells depended on the spatial resolution of microscopy. Light microscopy, even recently benchmarked laser-scanning microscopy, is inherently liable to the diffraction limit of visible light. Electron microscopy that had existed as the only alternative for decades is, in turn, of low through-put and sensitive to processing artefacts. Therefore, researchers have looked for alternative technologies particularly with ever-growing interest in resolving structural underpinnings of cellular heterogeneity in the human body...
June 22, 2018: Proteomics
Alexandra La Mura, David R Arahal, María J Pujalte
The genomes of the type strains of Roseivivax atlanticusand Roseivivax marinus(Rhodobacteraceae, Alphaproteobacteria), were analysed to determine their respective Average Nucleotide Identity (ANI) and in silico DNA-DNA hybridization (DDH) values. These species were proposed and effectively published relatively closely in time (February and August 2014, respectively) and so not taking account of the other. The intergenomic relatedness between both type strains, 97.0-97.4 % ANI and 82.8 % in silico DDH, confirm that they represent members of the same genomic species...
June 22, 2018: International Journal of Systematic and Evolutionary Microbiology
Peter Kämpfer, Stefanie P Glaeser, Gabriele Packroff, Katja Behringer, Martin Exner, Trinad Chakraborty, Ricarda M Schmithausen, Swapnil Doijad
Five beige-pigmented, oxidase-negative bacterial isolates, 6331-17T , 6332-17, 6333-17, 6334-17 and 9827-07, isolated either from a drinking water storage reservoir or drinking water in 2006 and 2017 in Germany, were examined in detail applying by a polyphasic taxonomic approach. Cells of the isolates were rod-shaped and Gram-stain-negative. Comparison of the 16S rRNA gene sequences of these five isolates showed highest sequence similarities to Lelliottia amnigena (99.98 %) and Lelliottia nimipressuralis (99...
June 22, 2018: International Journal of Systematic and Evolutionary Microbiology
Christopher N Miller, Lyne Jossé, Anastasios D Tsaousis
Cryptosporidium is a protozoan, apicomplexan, parasite that poses significant risk to humans and animals, as a common cause of potentially fatal diarrhea in immunodeficient hosts. The parasites have evolved a number of unique biological features that allow them to thrive in a highly specialized parasitic lifestyle. For example, the genome of Cryptosporidium parvum is highly reduced, encoding only 3,805 proteins, which is also reflected in its reduced cellular and organellar content and functions. As such, its remnant mitochondrion, dubbed a mitosome, is one of the smallest mitochondria yet found...
June 22, 2018: Journal of Eukaryotic Microbiology
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