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https://www.readbyqxmd.com/read/28437683/pink1-and-parkin-emerging-themes-in-mitochondrial-homeostasis
#1
REVIEW
Thomas G McWilliams, Miratul Mk Muqit
The Parkinson's disease (PD)-associated protein kinase, PTEN-induced putative kinase1 (PINK1), and ubiquitin E3 ligase, Parkin function in a common signalling pathway known to regulate mitochondrial network homeostasis and quality control, including mitophagy. The multistep activation of this pathway, as well as an unexpected convergence between the post-translational modifications of ubiquitylation and phosphorylation, has added breadth to our understanding of cellular damage responses during human disease...
April 21, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28437616/neural-network-and-nearest-neighbour-algorithms-for-enhancing-sampling-of-molecular-dynamics
#2
Raimondas Galvelis, Yuji Sugita
The free energy calculations of complex chemical and biological systems with molecular dynamics (MD) are inefficient due to multiple local minima separated by high-energy barriers. The minima can be escaped using an enhanced sampling method such as metadynamics, which apply bias (i.e. importance sampling) along a set of collective variables (CV), but the maximum number of CVs (or dimensions) is severely limited. We propose a high-dimensional bias potential method (NN2B) based on two machine learning algorithms: the nearest neighbour density estimator (NNDE) and the artificial neural network (ANN) for the bias potential approximation...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28437614/engineering-highly-interconnected-neuronal-networks-on-nanowire-scaffolds
#3
Vini Gautam, Shagufta Naureen, Naeem Shahid, Qian Gao, Yi Wang, David R Nisbet, Chennupati Jagadish, Vincent R Daria
Identifying the specific role of physical guidance cues in the growth of neurons is crucial for understanding the fundamental biology of brain development and for designing scaffolds for tissue engineering. Here, we investigate the structural significance of nanoscale topographies as physical cues for neurite outgrowth and circuit formation by growing neurons on semiconductor nanowires. We monitored neurite growth using optical and scanning electron microscopy, and evaluated the spontaneous neuronal network activity using functional calcium imaging...
April 24, 2017: Nano Letters
https://www.readbyqxmd.com/read/28437094/rational-design-of-an-ultrasensitive-quorum-sensing-switch
#4
Weiqian Zeng, Pei Du, Qiuli Lou, Lili Wu, Haoqian M Zhang, Chunbo Lou, Hongli Wang, Qi Ouyang
One of the purposes of synthetic biology is to develop rational methods that accelerate the design of genetic circuits, saving time and effort spent on experiments and providing reliably predictable circuit performance. We applied a reverse engineering approach to design an ultrasensitive transcriptional quorum-sensing switch. We want to explore how systems biology can guide synthetic biology in the choice of specific DNA sequences and their regulatory relations to achieve a targeted function. The workflow comprises network enumeration that achieves the target function robustly, experimental restriction of the obtained candidate networks, global parameter optimization via mathematical analysis, selection and engineering of parts based on these calculations, and finally, circuit construction based on the principles of standardization and modularization...
April 24, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28436883/a-bipartite-network-and-resource-transfer-based-approach-to-infer-lncrna-environmental-factor-associations
#5
Jie Zhou, Yuan-Yuan Shi
Phenotypes and diseases are often determined by the complex interactions between genetic factors and environmental factors (EFs). However, compared with protein-coding genes and microRNAs, there is a paucity of computational methods for understanding the associations between long non-coding RNAs (lncRNAs) and EFs. In this study, we focused on the associations between lncRNA and EFs. By using the common miRNA partners of any pair of lncRNA and EF, based on the competing endogenous RNA (ceRNA) hypothesis and the technique of resources transfer within the experimentally-supported lncRNA-miRNA and miRNA-EF association bipartite networks, we propose an algorithm for predicting new lncRNA-EF associations...
April 18, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28436874/track-everything-limiting-prior-knowledge-in-online-multi-object-recognition
#6
Sebastien C Wong, Victor Stamatescu, Adam Gatt, David Kearney, Ivan Lee, Mark D McDonnell
This paper addresses the problem of online tracking and classification of multiple objects in an image sequence. Our proposed solution is to first track all objects in the scene without relying on object-specific prior knowledge, which in other systems can take the form of hand-crafted features or user-based track initialization. We then classify the tracked objects with a fastlearning image classifier that is based on a shallow convolutional neural network architecture and demonstrate that object recognition improves when this is combined with object state information from the tracking algorithm...
April 24, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28436848/challenging-the-time-complexity-of-exact-subgraph-isomorphism-for-huge-and-dense-graphs-with-vf3
#7
Vincenzo Carletti, Pasquale Foggia, Alessia Saggese, Mario Vento
Graph matching is essential in several fields that use structured information, such as biology, chemistry, social networks, knowledge management, document analysis and others. Except for special classes of graphs, graph matching has in the worst-case an exponential complexity; however, there are algorithms that show an acceptable execution time, as long as the graphs are not too large and not too dense. In this paper we introduce a novel subgraph isomorphism algorithm, VF3, particularly efficient in the challenging case of graphs with thousands of nodes and a high edge density...
April 24, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28436483/itraq-based-proteomic-analysis-reveals-key-proteins-affecting-muscle-growth-and-lipid-deposition-in-pigs
#8
Zhixiu Wang, Peng Shang, Qinggang Li, Liyuan Wang, Yangzom Chamba, Bo Zhang, Hao Zhang, Changxin Wu
Growth rate and meat quality, two economically important traits in pigs, are controlled by multiple genes and biological pathways. In the present study, we performed a proteomic analysis of longissimus dorsi muscle from six-month-old pigs from two Chinese native mini-type breeds (TP and DSP) and two introduced western breeds (YY and LL) using isobaric tag for relative and absolute quantification (iTRAQ). In total, 4,815 peptides corresponding to 969 proteins were detected. Comparison of expression patterns between TP-DSP and YY-LL revealed 288 differentially expressed proteins (DEPs), of which 169 were up-regulated and 119 were down-regulated...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28436127/tip110-deletion-impaired-embryonic-and-stem-cell-development-involving-down-regulation-of-stem-cell-factors-nanog-oct4-and-sox2
#9
Amanda Whitmill, Ying Liu, Khalid Amine Timani, Yinghua Niu, Johnny J He
HIV-1 Tat-interacting protein of 110 kDa, Tip110, plays important roles in multiple biological processes. In this study, we aimed to characterize the function of Tip110 in embryonic development. Transgenic mice lacking expression of a functional Tip110 gene (Tip110(-/-) ) died post-implantation, and Tip110(-/-) embryos exhibited developmental arrest between 8.5 and 9.5 days post coitum. However, in vitro cultures of Tip110(-/-) embryos showed that Tip110 loss did not impair embryo growth from the zygote to the blastocyst...
April 24, 2017: Stem Cells
https://www.readbyqxmd.com/read/28435988/the-key-genes-of-chronic-pancreatitis-which-bridge-chronic-pancreatitis-and-pancreatic-cancer-can-be-therapeutic-targets
#10
Shuang Li, Rui Li, Heping Wang, Lisha Li, Huiyu Li, Yulin Li
An important question in systems biology is what role the underlying molecular mechanisms play in disease progression. The relationship between chronic pancreatitis and pancreatic cancer needs further exploration in a system view. We constructed the disease network based on gene expression data and protein-protein interaction. We proposed an approach to discover the underlying core network and molecular factors in the progression of pancreatic diseases, which contain stages of chronic pancreatitis and pancreatic cancer...
April 24, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/28435812/scientometrics-on-public-health-research-in-iran-increase-of-area-studies-despite-embargoes-a-review-article
#11
REVIEW
Brice Poreau
BACKGROUND: Due to embargoes and sanctions from 1979 until 2015, impact on scientific research in Iran may be critical. Public health is the main example of this burning point. In this paper, the aim was to map the scientific research in public health in Iran until 2014 with area studies as well as networks of countries involved. METHODS: We used bibliographic analyses using VOS viewer software for network analysis during the period 1975-2014. Two databases were used: Web of Science and PubMed...
March 2017: Iranian Journal of Public Health
https://www.readbyqxmd.com/read/28435518/sparc-overexpression-alters-microrna-expression-profiles-involved-in-tumor-progression
#12
Bhavesh K Ahir, Nasya M Elias, Sajani S Lakka
Medulloblastoma is the most common malignant brain tumor in children. SPARC (secreted protein acidic and rich in cysteine), a multicellular non-structural glycoprotein is known to be involved in multiple processes in various cancers. Previously, we reported that SPARC expression significantly impairs medulloblastoma tumor growth in vitro and in vivo and also alters chemo sensitivity. MicroRNAs are a class of post-transcriptional gene regulators with critical functions in tumor progression. In addition, microRNA (miRNA) expression changes are also involved in chemo-resistance...
January 2017: Genes & Cancer
https://www.readbyqxmd.com/read/28435296/spotlight-on-bevacizumab-and-its-potential-in-the-treatment-of-malignant-pleural-mesothelioma-the-evidence-to-date
#13
REVIEW
Pavel A Levin, Jonathan E Dowell
Malignant pleural mesothelioma (MPM) is a rare, but aggressive cancer. Surgery and radiation offer limited benefit, and systemic chemotherapy remains the primary treatment modality for the majority of patients. Vascular endothelial growth factor (VEGF) and its receptor have been recognized as important players in the biology of this disease. Bevacizumab is a monoclonal antibody that binds VEGF and blocks its interaction with the VEGF receptor. Recent studies have shown benefit with the addition of bevacizumab to the combination of cisplatin and pemetrexed in MPM...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28435053/in-depth-analysis-of-the-synaptic-plasma-membrane-proteome-of-small-hippocampal-slices-using-an-integrated-approach
#14
Rui Qiao, Shuiming Li, Mi Zhou, Penghui Chen, Zhao Liu, Min Tang, Jian Zhou
Comprehensive knowledge of the synaptic plasma membrane (SPM) proteome of a distinct brain region in a defined pathological state would greatly advance the understanding of the underlying biology of synaptic plasticity. The development of innovative approaches for studying the SPM proteome of small brain tissues is highly desired. This study presents a suitable protocol that integrates biotinylation-based affinity capture of cell surface-exposed proteins, isolation of synaptosomes, and biochemical extraction of SPM proteins from biotinylated hippocampal slices...
April 20, 2017: Neuroscience
https://www.readbyqxmd.com/read/28434999/smfret-experiments-of-the-rna-polymerase-ii-transcription-initiation-complex
#15
REVIEW
Nicole Malkusch, Thilo Dörfler, Julia Nagy, Tobias Eilert, Jens Michaelis
Single-molecule fluorescence and in particular single-molecule Förster Resonance Energy Transfer (smFRET(1)) is a powerful tool to provide real-time information on the dynamic architecture of large macromolecular structures such as eukaryotic transcription initiation complexes. In contrast to other structural biology methods, not only structural details, but dynamics transitions are revealed thus closing in on the underlying molecular mechanisms. Here, we describe a comprehensive quantitative biophysical toolbox which can be used for rigorous analysis of dynamic protein-nucleic acid complexes and is applied to the study of eukaryotic transcription initiation...
April 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28434948/international-and-multidisciplinary-expert-recommendations-for-the-use-of-biologics-in-systemic-lupus-erythematosus
#16
REVIEW
Jean-François Kleinmann, Florence Tubach, Véronique Le Guern, Alexis Mathian, Christophe Richez, David Saadoun, Karim Sacre, Jérémie Sellam, Raphaèle Seror, Zahir Amoura, Emmanuel Andres, Sylvain Audia, Brigitte Bader-Meunier, Gilles Blaison, Bernard Bonnotte, Patrice Cacoub, Sophie Caillard, Laurent Chiche, Olivier Chosidow, Nathalie Costedoat-Chalumeau, Claire Daien, Eric Daugas, Nairouz Derdèche, Andrea Doria, Olivier Fain, Fadi Fakhouri, Dominique Farge, Cem Gabay, Sylvie Guillo, Eric Hachulla, Najia Hajjaj-Hassouni, Mohamed Hamidou, Frédéric A Houssiau, Noémie Jourde-Chiche, Isabelle Koné-Paut, Aïcha Ladjouz-Rezig, Olivier Lambotte, Dan Lipsker, Xavier Mariette, Nicolas Martin-Silva, Thierry Martin, François Maurier, Roderich Meckenstock, Arsène Mékinian, Olivier Meyer, Shirine Mohamed, Jacques Morel, Bruno Moulin, Denis Mulleman, Thomas Papo, Vincent Poindron, Xavier Puéchal, Leonardo Punzi, Pierre Quartier, Laurent Sailler, Amar Smail, Martin Soubrier, Agnès Sparsa, Zoubida Tazi-Mezalek, Leith Zakraoui, Stéphane Zuily, Jean Sibilia, Jacques-Eric Gottenberg
BACKGROUND/PURPOSE: Despite conventional immunosuppressants, active and steroid-dependent systemic lupus erythematosus (SLE) represents a therapeutic challenge. Only one biologic, belimumab, has been approved, but other biologics are sometimes used off-label. Given the lack of evidence-based data in some clinical situations encountered in real life, we developed expert recommendations for the use of biologics for SLE. METHODS: The recommendations were developed by a formal consensus method...
April 18, 2017: Autoimmunity Reviews
https://www.readbyqxmd.com/read/28433874/systematically-characterize-the-absorbed-effective-substances-of-wutou-decoction-and-their-metabolic-pathways-in-rat-plasma-using-uhplc-q-tof-ms-combined-with-a-target-network-pharmacological-analysis
#17
Tengfei Xu, Shizhe Li, Yufei Sun, Zifeng Pi, Shu Liu, Fengrui Song, Zhiqiang Liu
Wu-tou Decoction (WTD) is a famous traditional Chinese medicine (TCM) formula which is applied to treat arthritis and pain of joints. In this study, a sensitive and rapid method was developed for the separation and identification of the absorbed constituents and metabolites of WTD in the rats plasma by ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS). A total of 22 absorbed prototype constituents and 49 metabolites were identified or tentatively characterized in dosed plasma...
April 13, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28433760/elucidation-of-the-dynamic-nature-of-interactome-networks-a-practical-tutorial
#18
Sandra I Anjo, Tania Martins-Marques, Paulo Pereira, Henrique Girão, Bruno Manadas
Considering that proteins are usually engaged in complex and dynamic networks of interactions to exert their activity, a way to understand proteins' functions and the molecular mechanisms in which those proteins are involved, is by studying their interactome. In this sense, this tutorial presents a simple pipeline for the analysis of the network of interactions of a protein in order to reach a biological interpretation of the mechanisms modulated by those interactions, and understand how these interactions are affected by the experimental conditions...
April 19, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28433629/a-novel-strategy-to-dissect-endogenous-gene-transcriptional-regulation-in-live-cells
#19
Wenqing Yang, Siliang Zhang, Yi Zhang, Xin Huang
Gene transcription is a central tenet of biology, traditionally measured by RT-PCR, microarray, or more recently, RNA sequencing. However, these measurements only provide a snapshot of the state of gene transcription and only represent an overall readout of complex transcriptional networks that regulate gene expression. In this report, we describe a novel strategy to dissect endogenous gene transcription regulation in live cells by knocking in a reporter gene, EGFP, under the control of the endogenous gene promoter, using the ARID1A gene as an example...
April 19, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28433052/metabolomics-strategies-to-define-the-role-of-metabolism-in-virus-infection-and-pathogenesis
#20
Marianne Manchester, Anisha Anand
Metabolomics is an analytical profiling technique for measuring and comparing large numbers of metabolites present in biological samples. Combining high-throughput analytical chemistry and multivariate data analysis, metabolomics offers a window on metabolic mechanisms. Because they intimately utilize and often rewire host metabolism, viruses are an excellent choice to study by metabolomics techniques. Studies of the effects of viruses on metabolism during replication in vitro and infection in animal models or human subjects have provided novel insights into these networks and provided new targets for therapy and biomarker development...
2017: Advances in Virus Research
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