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Computational biology

Zhijie Zhu, Shuang-Zhuang Guo, Tessa Hirdler, Cindy Eide, Xiaoxiao Fan, Jakub Tolar, Michael C McAlpine
Conventional 3D printing technologies typically rely on open-loop, calibrate-then-print operation procedures. An alternative approach is adaptive 3D printing, which is a closed-loop method that combines real-time feedback control and direct ink writing of functional materials in order to fabricate devices on moving freeform surfaces. Here, it is demonstrated that the changes of states in the 3D printing workspace in terms of the geometries and motions of target surfaces can be perceived by an integrated robotic system aided by computer vision...
April 25, 2018: Advanced Materials
D Cheshmedzhieva, N Toshev, M Gerova, O Petrov, T Dudev
Hydroxamic acids are regarded as potent inhibitors of histone deacetylases (HDAC), and can therefore be used to reduce malignancy growth and size in affected organisms. Although there is a substantial body of information on the structures, syntheses, and biological activities of HDAC inhibitors, several important questions regarding their physicochemical properties and metal affinities/selectivities remain answered. First, how do the conformation and ionization of the hydroxamic group depend on its chemical composition and the dielectric properties of the medium? Second, how do these factors affect the affinities and selectivities of HDAC inhibitors for essential biogenic metal cations? Third, what is the preferred deprotonation site of the hydroxamic moiety and its mode of binding to the metal cation? The present work addressed these questions by performing density functional calculations combined with polarizable continuum model computations...
April 24, 2018: Journal of Molecular Modeling
Frederick Kofi Korley, John K Yue, David Wilson, Kevin Hrusovsky, Ramon Diaz-Arrasta, Adam R Ferguson, Esther Lim Yuh, Pratik Mukherjee, Kevin K W Wang, Alex Valadka, Ava Puccio, David O Okonkwo, Geoffrey Manley
Traumatic brain injury (TBI) results in heterogeneous pathology affecting multiple cells and tissue types in the brain. It is likely that assessment of such complexity will require simultaneous measurement of multiple molecular biomarkers in a single sample of biological fluid. We measured glial fibrillary acidic protein (GFAP), ubiquitin c-terminal hydrolase L1 (UCH-L1), neurofilament light chain (NF-L) and total tau in plasma samples obtained from 107 subjects enrolled in the Transforming Research and Clinical Knowledge in Traumatic Brain Injury Pilot (TRACK-TBI Pilot) Study using the Quanterix Simoa 4-Plex assay...
April 25, 2018: Journal of Neurotrauma
Maria Kondratova, Nicolas Sompairac, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein
Generation and usage of high-quality molecular signalling network maps can be augmented by standardizing notations, establishing curation workflows and application of computational biology methods to exploit the knowledge contained in the maps. In this manuscript, we summarize the major aims and challenges of assembling information in the form of comprehensive maps of molecular interactions. Mainly, we share our experience gained while creating the Atlas of Cancer Signalling Network. In the step-by-step procedure, we describe the map construction process and suggest solutions for map complexity management by introducing a hierarchical modular map structure...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Tammy C Tobin, Ashley Shade
Microbiology increasingly relies upon bioinformatics to understand complex microbial interactions. Nevertheless, biology undergraduates often lack the basic quantitative and computer-based skills required for bioinformatics analyses. To address these issues, the course module 'A Town on Fire! 16S rRNA Gene Amplicon Analysis of Microbial Communities Overlying the Centralia, PA Mine Fire' was developed for an undergraduate microbiology lecture course. In this module, microbiology students used Quantitative Insights into Microbial Ecology (QIIME) to perform taxonomic, phylogenetic and statistical analyses on bacterial communities from three hot mine fire-impacted surface soils using 16S rRNA gene amplicon sequences...
April 23, 2018: FEMS Microbiology Letters
Mehmet Emin Bakir, Savas Konur, Marian Gheorghe, Natalio Krasnogor, Mike Stannett
Motivation: Formal verification is a computational approach that checks system correctness (in relation to a desired functionality). It has been widely used in engineering applications to verify that systems work correctly. Model checking, an algorithmic approach to verification, looks at whether a system model satisfies its requirements specification. This approach has been applied to a large number of models in systems and synthetic biology as well as in systems medicine. Model checking is, however, computationally very expensive, and is not scalable to large models and systems...
April 24, 2018: Bioinformatics
Pearl Chang, Moloya Gohain, Ming-Ren Yen, Pao-Yang Chen
The hierarchical organization of chromatin is known to associate with diverse cellular functions; however, the precise mechanisms and the 3D structure remain to be determined. With recent advances in high-throughput next generation sequencing (NGS) techniques, genome-wide profiling of chromatin structures is made possible. Here, we provide a comprehensive overview of NGS-based methods for profiling "higher-order" and "primary-order" chromatin structures from both experimental and computational aspects...
2018: Computational and Structural Biotechnology Journal
Ievgen Kurylo, Guillaume Gines, Yannick Rondelez, Yannick Coffinier, Alexis Vlandas
In recent years, DNA computing frameworks have been developed to create dynamical systems which can be used for information processing. These emerging synthetic biochemistry tools can be leveraged to gain a better understanding of fundamental biology but can also be implemented in biosensors and unconventional computing. Most of the efforts so far have focused on changing the topologies of DNA molecular networks or scaling them up. Several issues have thus received little attention and remain to be solved to turn them into real life technologies...
April 23, 2018: Scientific Reports
Ben E Clifton, Joe A Kaczmarski, Paul D Carr, Monica L Gerth, Nobuhiko Tokuriki, Colin J Jackson
The emergence of enzymes through the neofunctionalization of noncatalytic proteins is ultimately responsible for the extraordinary range of biological catalysts observed in nature. Although the evolution of some enzymes from binding proteins can be inferred by homology, we have a limited understanding of the nature of the biochemical and biophysical adaptations along these evolutionary trajectories and the sequence in which they occurred. Here we reconstructed and characterized evolutionary intermediate states linking an ancestral solute-binding protein to the extant enzyme cyclohexadienyl dehydratase...
April 23, 2018: Nature Chemical Biology
Shu Jia, Boran Han, J Nathan Kutz
Capturing biological dynamics with high spatiotemporal resolution demands the advancement in imaging technologies. Super-resolution fluorescence microscopy offers spatial resolution surpassing the diffraction limit to resolve near-molecular-level details. While various strategies have been reported to improve the temporal resolution of super-resolution imaging, all super-resolution techniques are still fundamentally limited by the trade-off associated with the longer image acquisition time that is needed to achieve higher spatial information...
April 23, 2018: Scientific Reports
Jeet Sukumaran, L Lacey Knowles
The development of process-based probabilistic models for historical biogeography has transformed the field by grounding it in modern statistical hypothesis testing. However, most of these models abstract away biological differences, reducing species to interchangeable lineages. We present here the case for reintegration of biology into probabilistic historical biogeographical models, allowing a broader range of questions about biogeographical processes beyond ancestral range estimation or simple correlation between a trait and a distribution pattern, as well as allowing us to assess how inferences about ancestral ranges themselves might be impacted by differential biological traits...
April 20, 2018: Trends in Ecology & Evolution
Durba Sengupta, Xavier Prasanna, Madhura Mohole, Amitabha Chattopadhyay
G protein-coupled receptors (GPCRs) are seven transmembrane receptors that mediate a large number of cellular responses and are important drug targets. One of the current challenges in GPCR biology is to analyze the molecular signatures of receptor-lipid interactions, and their subsequent effects on GPCR structure, organization and function. Molecular dynamics simulation studies have been successful in predicting molecular determinants of receptor-lipid interactions. In particular, predicted cholesterol interaction sites appear to correspond well with experimentally determined binding sites and estimated time scales of association...
April 23, 2018: Journal of Physical Chemistry. B
Jiayan Wu, Junchao Xie, Yanxin Zhao, Li Gong, Xueyuan Liu, Wangmi Liu
BACKGROUND/AIMS: Acute ischemic stroke is caused by stenosis of artery supplying to brain. We aimed to detect some metabolites in the serum that would be related to the degree of artery stenosis and to analyze potential mechanisms. METHODS: Patients diagnosed with acute ischemic stroke were divided into two groups according to their degree of artery stenosis (which was determined by computed tomographic angiography): a mild group (stenosis ≤ 30%) and a severe group (stenosis > 30%)...
2018: Cellular Physiology and Biochemistry
Michael F Bonner, Russell A Epstein
Biologically inspired deep convolutional neural networks (CNNs), trained for computer vision tasks, have been found to predict cortical responses with remarkable accuracy. However, the internal operations of these models remain poorly understood, and the factors that account for their success are unknown. Here we develop a set of techniques for using CNNs to gain insights into the computational mechanisms underlying cortical responses. We focused on responses in the occipital place area (OPA), a scene-selective region of dorsal occipitoparietal cortex...
April 23, 2018: PLoS Computational Biology
Chonnipa Nantavithya, Daniel R Gomez, Xiong Wei, Ritsuko Komaki, Zhongxing Liao, Steven H Lin, Melenda Jeter, Quynh-Nhu Nguyen, Heng Li, Xiaodong Zhang, Falk Poenisch, X Ronald Zhu, Peter A Balter, Lei Feng, Noah C Choi, Radhe Mohan, Joe Y Chang
PURPOSE: To report the feasibility of conducting a randomized study to compare the toxicity and efficacy of stereotactic body radiation therapy (SBRT) versus stereotactic body proton therapy (SBPT) for high-risk, medically inoperable, early-stage non-small cell lung cancer (NSCLC). PATIENTS AND METHODS: Patients with medically inoperable NSCLC with high-risk features (centrally located or <5 cm T3 tumor or isolated lung parenchymal recurrences) were randomly assigned to SBRT or SBPT...
March 2, 2018: International Journal of Radiation Oncology, Biology, Physics
Azam Hamidinekoo, Erika Denton, Andrik Rampun, Kate Honnor, Reyer Zwiggelaar
Recent improvements in biomedical image analysis using deep learning based neural networks could be exploited to enhance the performance of Computer Aided Diagnosis (CAD) systems. Considering the importance of breast cancer worldwide and the promising results reported by deep learning based methods in breast imaging, an overview of the recent state-of-the-art deep learning based CAD systems developed for mammography and breast histopathology images is presented. In this study, the relationship between mammography and histopathology phenotypes is described, which takes biological aspects into account...
March 26, 2018: Medical Image Analysis
Tien Yew Chern, Allan Kwok, Soni Putnis
BACKGROUND: Traumatic diaphragmatic injuries from blunt or penetrating trauma are difficult to detect in the acute setting and, if missed, can result in significant morbidity and mortality in the future. We present a case demonstrating the natural progression of this resulting in faecopneumothorax, which is a rare but serious presentation. CASE PRESENTATION: A 22-year-old young man presented with left upper quadrant and chest pain, nausea, vomiting, and intermittent obstipation with a background of previous lower chest wall stabbings...
April 20, 2018: Surgical Case Reports
Cangzhi Jia, Qing Yang, Quan Zou
The nucleosome is the basic structure of chromatin in eukaryotic cells, with essential roles in the regulation of many biological processes, such as DNA transcription, replication and repair, and RNA splicing. Because of the importance of nucleosomes, the factors that determine their positioning within genomes should be investigated. High-resolution nucleosome-positioning maps are now available for organisms including Saccharomyces cerevisiae, Drosophila melanogaster and Caenorhabditis elegans, enabling the identification of nucleosome positioning by application of computational tools...
April 17, 2018: Journal of Theoretical Biology
Krittima Anekthanakul, Apiradee Hongsthong, Jittisak Senachak, Marasri Ruengjitchatchawalya
BACKGROUND: Bioactive peptides, including biological sources-derived peptides with different biological activities, are protein fragments that influence the functions or conditions of organisms, in particular humans and animals. Conventional methods of identifying bioactive peptides are time-consuming and costly. To quicken the processes, several bioinformatics tools are recently used to facilitate screening of the potential peptides prior their activity assessment in vitro and/or in vivo...
April 20, 2018: BMC Bioinformatics
Lena Smirnova, Nicole Kleinstreuer, Raffaella Corvi, Andre Levchenko, Suzanne C Fitzpatrick, Thomas Hartung
A biological system is more than the sum of its parts - it accomplishes many functions via synergy. Deconstructing the system down to the molecular mechanism level necessitates the complement of reconstructing functions on all levels, i.e., in our conceptualization of biology and its perturbations, our experimental models and computer modelling. Toxicology contains the somewhat arbitrary subclass "systemic toxicities"; however, there is no relevant toxic insult or general disease that is not systemic...
2018: ALTEX
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