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Systems biology

Jérôme Casas, Claudio Lazzari, Teresita Insausti, Pascal Launois, Florence Fouque
Major emergency efforts are being mounted for each vector-borne disease epidemiological crisis anew, while knowledge about the biology of arthropods vectors is dwindling slowly but continuously, as is the number of field entomologists. The discrepancy between the rates of production of knowledge and its use and need for solving crises is widening, in particular due to the highly differing time spans of the two concurrent processes. A worldwide web based search using multiple key words and search engines of onsite and online courses in English, Spanish, Portuguese, French, Italian and German concerned with the biology of vectors identified over 140 courses...
October 13, 2016: Memórias do Instituto Oswaldo Cruz
D Caballero, J Katuri, J Samitier, S Sánchez
The ubiquitous random motion of mesoscopic active particles, such as cells, can be "rectified" or directed by embedding the particles in systems containing local and periodic asymmetric cues. Incorporated on lab-on-a-chip devices, these microratchet-like structures can be used to self-propel fluids, transport particles, and direct cell motion in the absence of external power sources. In this Focus article we discuss recent advances in the use of ratchet-like geometries in microfluidics which could open new avenues in biomedicine for applications in diagnosis, cancer biology, and bioengineering...
October 19, 2016: Lab on a Chip
Heewon Park, Atsushi Niida, Seiya Imoto, Satoru Miyano
Driver gene selection is crucial to understand the heterogeneous system of cancer. To identity cancer driver genes, various statistical strategies have been proposed, especially the L1-type regularization methods have drawn a large amount of attention. However, the statistical approaches have been developed purely from algorithmic and statistical point, and the existing studies have applied the statistical approaches to genomic data analysis without consideration of biological knowledge. We consider a statistical strategy incorporating biological knowledge to identify cancer driver gene...
October 19, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Grace Yim, Wenliang Wang, Maulik N Thaker, Stephanie Tan, Gerard D Wright
Modification of natural product backbones is a proven strategy for the development of clinically useful antibiotics. Such modifications have traditionally been achieved through medicinal chemistry strategies or via in vitro enzymatic activities. In an orthogonal approach, engineering of biosynthetic pathways using synthetic biology techniques can generate chemical diversity. Here we report the use of a minimal teicoplanin class glycopeptide antibiotic (GPA) scaffold expressed in a production-optimized Streptomyces coelicolor strain to expand GPA chemical diversity...
September 9, 2016: ACS Infectious Diseases
Justin A Lemkul, Alexander D MacKerell
Mg2+ ions are important in biological systems, particularly in stabilizing compact RNA folds. Mg2+ is strongly polarizing, and representing its interactions in heterogeneous environments is a challenge for empirical force field development. To date, the most commonly used force fields in molecular dynamics simulations utilize a pairwise-additive approximation for electrostatic interactions, which cannot account for the significant polarization response in systems containing Mg2+. In the present work, we refine the interactions of Mg2+ with water, Cl- ions, and nucleic acid moieties using a polarizable force field based on the classical Drude oscillator model...
October 19, 2016: Journal of Physical Chemistry. B
Oleksandr Zagorodko, Juan José Arroyo-Crespo, Vicent J Nebot, María J Vicent
Synthetic polypeptides or polyamino acids have become a useful and multifunctional platform in advanced drug delivery studies. Nonetheless, the full potential of these systems has yet to be achieved. The final structure of polypeptide conjugates and their in vivo behavior are dependent on an extraordinarily complex pattern of interconnected physico-chemical and structural parameters, making sophisticated directional design of such systems difficult and often unachievable. In this review, the authors aim to discuss the role of these parameters in the successful design of different drug delivery architectures and to delineate some basic correlations between structure, properties, and the biological behavior of polypeptide-based conjugates...
October 18, 2016: Macromolecular Bioscience
Lucia Mastrototaro, Gerhard Sponder, Behnam Saremi, Jörg R Aschenbach
Methionine (Met) is a neutral, sulfur-containing, essential amino acid with biological functions in the initiation and prolongation step of protein synthesis, transmethylation reactions, the synthesis of cysteine and cystine, and as a component of antioxidant systems. Its key importance is reflected by the fact that it is usually absorbed from the diet with highest efficiency among all proteinogenic amino acids but may yet not optimally support metabolism and health. As such, crystalline Met supplements are partly used in man and heavily used in production of animal species (poultry, fish, shrimps, pigs and cattle) to provide improved health and performance...
October 17, 2016: IUBMB Life
Huiting Su, Ning Na, Xiaodong Zhang, Yong Zhao
CD74 (MHC class II invariant chain, Ii) is a non-polymorphic type II transmembrane glycoprotein. It is clear that, in addition to be an MHC class II chaperone, CD74 has a diversity of biological functions in physiological and pathological situations. CD74 also participates in other non-MHC II protein trafficking, such as angiotensin II type I receptor. In addition, CD74 is a cell membrane high-affinity receptor for macrophage migration inhibitory factor (MIF), D-dopachrome tautomerase (D-DT/MIF-2) and bacterial proteins...
October 17, 2016: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
Jeganathan Manivannan, Manjunath Prashanth, Venkatesan Saravana Kumar, Manickaraj Shairam, Jayachandran Subburaj
Since there is no precise therapy for treating vascular calcification by directly targeting the vascular wall, we aim to unveil novel drug targets through mining the molecular effect of a high phosphate environment on vascular cells through computational methods. Here, we hypothesize that manipulation of the vascular pathogenic network by small molecule therapeutics predicted from prior knowledge might offer great promise. With this, we intend to understand the publicly available transcriptomic data of vascular smooth muscle cells and endothelial cells exposed to the high phosphate induced vascular calcification milieu and to re-examine the above published experiments for reasons different from those examined in the previous studies through multilevel systems biological understanding...
October 18, 2016: Molecular BioSystems
Sun-Hyung Kim, Yeun-Sun Ji, Eui-Seok Lee, Soon-Taek Hong
Curcumin is a flavonoid found in the rhizome of the turmeric plant (Curcuma longa L.) and has recently attracted interest because it has numerous biological functions and therapeutic properties. In the present study, we attempted to incorporate curcumin into medium-chain triglyceride (MCT) nanoemulsions (0.15 wt% curcumin, 10 wt% MCT oil, and 10 wt% emulsifiers) with various emulsifiers [polyoxyethylene (20) sorbitan monolaurate (Tween-20), sorbitan monooleate (SM), and soy lecithin (SL)]. The physicochemical properties of the nanoemulsions including the Ostwald ripening stability were investigated...
September 2016: Preventive Nutrition and Food Science
Su Jin Kang, Ji Yeon Seo, Kye Man Cho, Chang Kwon Lee, Jeong Hwan Kim, Jong-Sang Kim
A new type of doenjang was manufactured by mixing soaked soybean, koji (Rhizopus oryzae), cheonggukjang (Bacillus amyloliquefaciens MJ1-4 and B. amyloliquefaciens EMD17), and Pichia farinosa SY80 as a yeast, salt, and water, followed by fermentation with koji that was made by fermenting whole wheat with R. oryzae. The mixed culture doenjang was designed to have a more palatable flavor and stronger biological activities than the conventional product. The extract of mixed culture doenjang showed higher antioxidant activity than the commercial doenjang as evaluated by the ferric reducing antioxidant power assay although it was not significantly different from the commercial product in 2,2-diphenyl-1-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) radical scavenging activities...
September 2016: Preventive Nutrition and Food Science
Filipa Oliveira-Ramos, Mónica Eusébio, Fernando M Martins, Ana Filipa Mourão, Carolina Furtado, Raquel Campanilho-Marques, Inês Cordeiro, Joana Ferreira, Marcos Cerqueira, Ricardo Figueira, Iva Brito, Helena Canhão, Maria José Santos, José A Melo-Gomes, João Eurico Fonseca
OBJECTIVES: To determine how adult juvenile idiopathic arthritis (JIA) patients fulfil classification criteria for adult rheumatic diseases, evaluate their outcomes and determine clinical predictors of inactive disease, functional status and damage. METHODS: Patients with JIA registered on the Rheumatic Diseases Portuguese Register ( older than 18 years and with more than 5 years of disease duration were included. Data regarding sociodemographic features, fulfilment of adult classification criteria, Health Assessment Questionnaire, Juvenile Arthritis Damage Index-articular (JADI-A) and Juvenile Arthritis Damage Index-extra-articular (JADI-E) damage index and disease activity were analysed...
2016: RMD Open
Matthew L Paff, Scott L Nuismer, Andrew D Ellington, Ian J Molineux, Ryan H May, James J Bull
BACKGROUND: We propose, model, and implement a novel system of population-level intervention against a virus. One context is a treatment against a chronic infection such as HIV. The underlying principle is a form of virus 'wars' in which a benign, transmissible agent is engineered to protect against infection by and spread of a lethal virus. In our specific case, the protective agent consists of two entities, a benign virus and a gene therapy vector mobilized by the benign virus. RESULTS: Numerical analysis of a mathematical model identified parameter ranges in which adequate, population-wide protection is achieved...
2016: Journal of Biological Engineering
Salma Malik, Kapil Suchal, Jagriti Bhatia, Sana I Khan, Swati Vasisth, Ameesha Tomar, Sameer Goyal, Rajeev Kumar, Dharamvir S Arya, Shreesh K Ojha
Emblica officinalis Gaertn. belonging to family Euphorbiaceae is commonly known as Indian gooseberry or "Amla" in India. It is used as a 'rejuvenating herb' in traditional system of Indian medicine. It has been shown to possess antioxidant, anti-inflammatory and anti-apoptotic effects. Thus, on the basis of its biological effects, the present study was undertaken to evaluate the protective effect of the dried fruit extract of the E. Officinalis (EO) in cisplatin-induced nephrotoxicity in rats and also to evaluate the mechanism of its nephroprotection...
2016: Frontiers in Pharmacology
Athanassios D Velentzas, Panagiotis D Velentzas, Niki E Sagioglou, Eumorphia G Konstantakou, Athanasios K Anagnostopoulos, Maria M Tsioka, Vassiliki E Mpakou, Zoe Kollia, Christos Consoulas, Lukas H Margaritis, Issidora S Papassideri, George Th Tsangaris, Evangelia Sarantopoulou, Alkiviadis-Constantinos Cefalas, Dimitrios J Stravopodis
Drosophila chorion represents a model biological system for the in vivo study of gene activity, epithelial development, extracellular-matrix assembly and morphogenetic-patterning control. It is produced during the late stages of oogenesis by epithelial follicle cells and develops into a highly organized multi-layered structure that exhibits regional specialization and radial complexity. Among the six major proteins involved in chorion's formation, the s36 and s38 ones are synthesized first and regulated in a cell type-specific and developmental stage-dependent manner...
October 18, 2016: Scientific Reports
Michael V Lombardo, Meng-Chuan Lai, Bonnie Auyeung, Rosemary J Holt, Carrie Allison, Paula Smith, Bhismadev Chakrabarti, Amber N V Ruigrok, John Suckling, Edward T Bullmore, Christine Ecker, Michael C Craig, Declan G M Murphy, Francesca Happé, Simon Baron-Cohen
Individuals affected by autism spectrum conditions (ASC) are considerably heterogeneous. Novel approaches are needed to parse this heterogeneity to enhance precision in clinical and translational research. Applying a clustering approach taken from genomics and systems biology on two large independent cognitive datasets of adults with and without ASC (n = 694; n = 249), we find replicable evidence for 5 discrete ASC subgroups that are highly differentiated in item-level performance on an explicit mentalizing task tapping ability to read complex emotion and mental states from the eye region of the face (Reading the Mind in the Eyes Test; RMET)...
October 18, 2016: Scientific Reports
Gavin D Merrifield, James Mullin, Lindsay Gallagher, Carl Tucker, Maurits A Jansen, Martin Denvir, William M Holmes
Increasing scientific interest in the zebrafish as a model organism across a range of biomedical and biological research areas raises the need for the development of in vivo imaging tools appropriate to this subject. Development of the embryonic and early stage forms of the subject can currently be assessed using optical based techniques due to the transparent nature of the species at these early stages. However this is not an option during the juvenile and adult stages when the subjects become opaque. Magnetic Resonance Imaging (MRI) techniques would allow for the longitudinal and non-invasive assessment of development and health in these later life stages...
October 14, 2016: Magnetic Resonance Imaging
Mamatha Bhat, Peter Ghali, Benoît Dupont, Roy Hilzenrat, Mahmood Tazari, André Roy, Prosanto Chaudhury, Fernando Alvarez, Michel Carrier, Marc Bilodeau
BACKGROUND & AIMS: Patients listed with exception points for Hepatocellular carcinoma (HCC) have been more likely to be transplanted than those listed for chronic liver failure (LF) based on the Model for End-Stage Liver Disease (MELD) score. The aim of this study was to determine outcomes in the 5-year experience of a scoring system designed to reflect heterogeneity of tumor load of patients listed for HCC. METHODS: A novel MELD exception point system based on size and number of HCC was implemented in July 2009...
October 14, 2016: Journal of Hepatology
Juan Bai, Ying Zhu, Ying Dong
ETHNOPHARMACOLOGICAL RELEVANCE: Bitter melon (Momordica charantia L.) is rich in a variety of biologically active ingredients, and has been widely used in traditional Chinese medicine (TCM) to treat various diseases, including type 2 diabetes and obesity. AIM OF THE STUDY: We aimed to investigate how bitter melon powder (BMP) could affect obesity-associated inflammatory responses to ameliorate high-fat diet (HFD)-induced insulin resistance, and investigated whether its anti-inflammatory properties were effected by modulating the gut microbiota...
October 14, 2016: Journal of Ethnopharmacology
A Fagan-Murphy, L Hachoumi, M S Yeoman, B A Patel
Reactive oxygen and nitrogen species (ROS/RNS) have been widely implicated in the ageing process and various approaches exist for monitoring these species in biological tissues. These approaches at present are limited to monitoring either a single pro-oxidant species or total pro-oxidant levels and therefore provide limited insight into the range of pro-oxidant species and their relative proportions in the ageing process. We have utilised a sensor that allows us to simultaneously monitor hydrogen peroxide, peroxynitrite, nitric oxide and nitrite...
October 14, 2016: Mechanisms of Ageing and Development
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