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Complex system in biology

Somayeh Bakhteh, Alireza Ghaffari-Hadigheh, Nader Chaparzadeh
Identification of master regulatory genes is one of the primary challenges in systems biology. The minimum dominating set problem is a powerful paradigm in analyzing such complex networks. In these models, genes stand as nodes and their interactions are assumed as edges. Here, members of a minimal dominating set could be regarded as master genes. As finitely many minimum dominating sets may exist in a network, it is difficult to identify which one represents the most appropriate set of master genes. In this paper, we develop a weighted gene regulatory network problem with two objectives as a version of the dominating set problem...
October 12, 2018: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Melissa L D Rayner, Simão Laranjeira, Rachael E Evans, Rebecca J Shipley, Jess Healy, James B Phillips
Peripheral nerve injuries (PNI) have a high prevalence and can be debilitating, resulting in life-long loss or disturbance in end-organ function, which compromises quality of life for patients. Current therapies use microsurgical approaches but there is the potential for enhancing recovery through other therapeutic modalities such as; cell-based conduits, gene therapy and small molecules. A number of molecular targets and drugs which have the potential to improve nerve regeneration have been identified, however, there are challenges associated with moving therapies toward clinical translation...
October 17, 2018: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
Matthew E R Butchbach
Systems biology uses a combination of experimental and mathematical approaches to investigate the complex and dynamic interactions with a given system or biological process. Systems biology integrates genetics, signal transduction, biochemistry and cell biology with mathematical modeling. It can be used to identify novel pathways implicated in diseases as well as to understand the mechanisms by which a specific gene is regulated. This review describes the development of mathematical models for the regulation of an endogenous modifier gene, SMN2, in spinal muscular atrophy-an early-onset motor neuron disease that is a leading genetic cause of infant mortality worldwide-by cAMP signaling...
2018: Advances in Neurobiology
Kai Gao, Yujia Zhang, Ling Zhang, Weijing Kong, Han Xie, Jingmin Wang, Ye Wu, Xiru Wu, Xiaoyan Liu, Yuehua Zhang, Feng Zhang, Albert Cheung-Hoi Yu, Yuwu Jiang
Epilepsy is one of the most common complex neurological diseases. It is frequently associated with intellectual and developmental disabilities (ID/DD). In recent years, copy number variation (CNV), especially microdeletion, was proven to be a potential key factor of genetic epilepsy. In this paper, the authors tested the hypothesis that the large de novo rare CNV is an important cause of epilepsy with ID/DD. We performed a custom array comparative genomic hybridization (aCGH) to detect the CNVs of 96 Chinese epileptic patients with ID/DD...
2018: Advances in Neurobiology
Emil Lou, Edward Zhai, Akshat Sarkari, Snider Desir, Phillip Wong, Yoshie Iizuka, Jianbo Yang, Subbaya Subramanian, James McCarthy, Martina Bazzaro, Clifford J Steer
Intercellular communication is vital to the ecosystem of cancer cell organization and invasion. Identification of key cellular cargo and their varied modes of transport are important considerations in understanding the basic mechanisms of cancer cell growth. Gap junctions, exosomes, and apoptotic bodies play key roles as physical modalities in mediating intercellular transport. Tunneling nanotubes (TNTs)-narrow actin-based cytoplasmic extensions-are unique structures that facilitate direct, long distance cell-to-cell transport of cargo, including microRNAs, mitochondria, and a variety of other sub cellular components...
2018: Frontiers in Cell and Developmental Biology
Patricia Vázquez-Villegas, Edith Espitia-Saloma, Mario A Torres-Acosta, Federico Ruiz-Ruiz, Marco Rito-Palomares, Oscar Aguilar
Aqueous two-phase systems (ATPS) have been reported as an attractive biocompatible extraction system for recovery and purification of biological products. In this work, the implementation, characterization, and optimization (operational and economic) of invertase extraction from spent brewery yeast in a semi-automatized pilot plant using ATPS is reported. Gentian violet was used as tracer for the selection of phase composition through phase entrainment minimization. Yeast suspension was chosen as a complex cell matrix model for the recovery of the industrial relevant enzyme invertase...
2018: Frontiers in Chemistry
Gary P T Choi, L Mahadevan
Inspired by the question of quantifying wing shape, we propose a computational approach for analysing planar shapes. We first establish a correspondence between the boundaries of two planar shapes with boundary landmarks using geometric functional data analysis and then compute a landmark-matching curvature-guided Teichmüller mapping with uniform quasi-conformal distortion in the bulk. This allows us to analyse the pair-wise difference between the planar shapes and construct a similarity matrix on which we deploy methods from network analysis to cluster shapes...
September 2018: Proceedings. Mathematical, Physical, and Engineering Sciences
Yueqi Wang, Abbas Khan, Aman Chandra Kaushik, Muhammad Junaid, Xuehong Zhang, Dong-Qing Wei
Phenazine compounds have good activity against Mycobacterium tuberculosis. Based on the reported activities that were obtained in Mycobacterium tuberculosis H37Rv, a three-dimensional quantitative structure-activity relationship (3D-QSAR) model was built to design novel compounds against MTB. A 5-fold cross-validation method and external validation were used to analyze the accuracy of forecasting. The model has a cross-validation coefficient q2 =0.7 and a non-cross-validation coefficient r2 =0.903, indicating that the model has good predictive possibility...
October 17, 2018: Journal of Biomolecular Structure & Dynamics
Matteo Biolatti, Valentina Dell'Oste, Sara Scutera, Francesca Gugliesi, Gloria Griffante, Marco De Andrea, Tiziana Musso, Santo Landolfo
Interleukin-1β (IL-1β) is a key effector of the inflammasome complex in response to pathogens and danger signals. Although it is well known that assembly of the inflammasome triggers proteolytic cleavage of the biologically inactive precursor pro-IL-1β into its mature secreted form, the mechanism by which human cytomegalovirus (HCMV) regulates IL-1β production via the inflammasome is still poorly understood. Here, we show that the infection of human foreskin fibroblasts (HFFs) with a mutant HCMV lacking the tegument protein pp65 (v65Stop) results in higher expression levels of mature IL-1β compared to its wild-type counterpart, suggesting that pp65 mediates HCMV immune evasion through downmodulation of IL-1β...
October 16, 2018: Viruses
Amar Deep, Prabhakar Tiwari, Sakshi Agarwal, Soni Kaundal, Saqib Kidwai, Ramandeep Singh, Krishan G Thakur
Toxin-antitoxin (TA) systems are involved in diverse physiological processes in prokaryotes, but their exact role in Mycobacterium tuberculosis (Mtb) virulence and in vivo stress adaptation has not been extensively studied. Here, we demonstrate that the VapBC11 TA module is essential for Mtb to establish infection in guinea pigs. RNA-sequencing revealed that overexpression of VapC11 toxin results in metabolic slowdown, suggesting that modulation of the growth rate is an essential strategy for in vivo survival...
October 17, 2018: Nucleic Acids Research
Ameneh Asgari-Targhi, Elizabeth B Klerman
Circadian rhythms are endogenous ~24-hr oscillations usually entrained to daily environmental cycles of light/dark. Many biological processes and physiological functions including mammalian body temperature, the cell cycle, sleep/wake cycles, neurobehavioral performance, and a wide range of diseases including metabolic, cardiovascular, and psychiatric disorders are impacted by these rhythms. Circadian clocks are present within individual cells and at tissue and organismal levels as emergent properties from the interaction of cellular oscillators...
October 17, 2018: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
Bin Yang, Yuehui Chen, Wei Zhang, Jiaguo Lv, Wenzheng Bao, De-Shuang Huang
Gene regulatory network (GRN) inference can understand the growth and development of animals and plants, and reveal the mystery of biology. Many computational approaches have been proposed to infer GRN. However, these inference approaches have hardly met the need of modeling, and the reducing redundancy methods based on individual information theory method have bad universality and stability. To overcome the limitations and shortcomings, this thesis proposes a novel algorithm, named HSCVFNT, to infer gene regulatory network with time-delayed regulations by utilizing a hybrid scoring method and complex-valued flexible neural network (CVFNT)...
October 15, 2018: International Journal of Molecular Sciences
Xiaojuan Han, Zhentao Man, Shenghao Xu, Lin Cong, Yongxiang Wang, Xiang Wang, Yifeng Du, Qinghua Zhang, Shi Tang, Zengfa Liu, Wei Li
Alzheimer's disease (AD) is a common neurodegenerative disorder in elderly people, and is associated with a heavy financial burden on our society. The use of serologic biomarkers is an attractive method to diagnose AD. Although the determination of blood-based biomarkers for AD has been explored in many studies, few practical diagnosis methods have been used in the clinic. In this work, we constructed a "chemical tongue" sensor array that is easy to use and based on four kinds of fluorescent gold nanoclusters (Au NCs) for discriminating between multiple proteins at nanomolar concentrations...
October 10, 2018: Colloids and Surfaces. B, Biointerfaces
Malte Lehmann, Elisabeth Knust, Sarita Hebbar
Retinitis pigmentosa (RP) is a complex inherited disease. It is associated with mutations in a wide variety of genes with many different functions. These mutations impact the integrity of rod photoreceptors and ultimately result in the progressive degeneration of rods and cone photoreceptors in the retina, leading to complete blindness. A hallmark of this disease is the variable degree to which symptoms are manifest in patients. This is indicative of the influence of the environment, and/or of the distinct genetic makeup of the individual...
2019: Methods in Molecular Biology
Yupeng Shi, Flavien Guenneau, Xiaolin Wang, Christophe Hélary, Thibaud Coradin
Multifunctional nanomaterials combining diagnosis and therapeutic properties have attracted a considerable attention in cancer research. Yet some important challenges are still to be faced, including an optimal coupling between these two types of properties that would be effective within complex biological tissues. To address these points, we have prepared novel nanoplatforms associating controlled drug delivery of doxorubicin and Magnetic Resonance Imaging (MRI) contrast-enhancement that exhibit high specificity towards cancer cells compared to normal cells and evaluated them both in 2D cultures and within 3D tissue-like biomimetic matrices...
2018: Nanotheranostics
Hisham F Bahmad, Tarek H Mouhieddine, Reda M Chalhoub, Sahar Assi, Tarek Araji, Farah Chamaa, Muhieddine M Itani, Amaly Nokkari, Firas Kobeissy, Georges Daoud, Wassim Abou-Kheir
Nervous system tumors represent some of the highly aggressive cancers in both children and adults, particularly neuroblastoma and glioblastoma. Many studies focused on the pathogenic role of the Akt pathway and the mechanistic target of Rapamycin (mTOR) complex in mediating the progression of various types of cancer, which designates the Akt/mTOR signaling pathway as a master regulator for cancer. Current studies are also elucidating the mechanisms of cancer stem cells (CSCs) in replenishing tumors and explicating the strong correlation between the Akt/mTOR pathway and CSC biology...
September 11, 2018: Oncotarget
Peng-Fei Chen, Fan Wang, Jia-Yan Nie, Jue-Rong Feng, Jing Liu, Rui Zhou, Hong-Ling Wang, Qiu Zhao
Background and aims: Gastric cancer (GC) is one of the most common cancers worldwide, and its pathogenesis is related to a complex network of gene interactions. The aims of our study were to find hub genes associated with the progression and prognosis of GC and illustrate the underlying mechanisms. Methods: Weighted gene co-expression network analysis (WGCNA) was conducted using the microarray dataset and clinical data of GC patients from Gene Expression Omnibus (GEO) database to identify significant gene modules and hub genes associated with TNM stage in GC...
2018: OncoTargets and Therapy
Satyavani Kaliamurthi, Gurudeeban Selvaraj, Aman Chandra Kaushik, Ke-Ren Gu, Dong-Qing Wei
Background and aim: Human papillomavirus (HPV) is an oncogenic agent that causes over 90% of cases of cervical cancer in the world. Currently available prophylactic vaccines are type specific and have less therapeutic efficiency. Therefore, we aimed to predict the potential species-specific and therapeutic epitopes from the protein sequences of HPV45 by using different immunoinformatics tools. Methods: Initially, we determined the antigenic potential of late (L1 and L2) and early (E1, E2, E4, E5, E6, and E7) proteins...
2018: Biologics: Targets & Therapy
Jackson A Buss, Vadim Baidin, Michael A Welsh, Josué Flores-Kim, Hongbaek Cho, B McKay Wood, Tsuyoshi Uehara, Suzanne Walker, Daniel Kahne, Thomas G Bernhardt
New antibiotics are needed to combat the growing problem of resistant bacterial infections. An attractive avenue towards the discovery of such next generation therapies is to identify novel inhibitors of clinically validated targets like cell wall biogenesis. We have therefore developed a pathway-directed, whole-cell screen for small molecules that block the activity of the Rod system of Escherichia coli This conserved multi-protein complex is required for cell elongation and the morphogenesis of rod-shaped bacteria...
October 15, 2018: Antimicrobial Agents and Chemotherapy
Yingfeng Qin, Suqi Liao, Yufeng Huang, Jingjin Zhao, Shulin Zhao
A simple and homogenous label-free fluorescent method based on target-triggered and enzymatic-assisted isothermal cascade signal amplification was established for nucleic acid detection. This amplification method consists of two circuits that depend on polymerase and nicking endonuclease. In the presence of a target, a hairpin probe was opened to initiate the polymerization and nicking reaction, producing target analogues and G-rich sequences, and releasing the original target DNA. The released target and produced target analogues then trigger a new amplification cycle...
December 18, 2018: Analytica Chimica Acta
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