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Computational Biology
Hydrophilicities of amylose and natural cellulose are regulated by the linkage between sugar rings
Feb 24, 2017   Nanoscale
Bao Y, Xu D, Qian L, Zhao L, Lu ZY, Cui S
Hydrophilicities of amylose and natural cellulose are regulated by the linkage between sugar rings
Feb 24, 2017
Nanoscale
Comparative studies of single molecule force spectroscopy and molecular dynamics simulations indicate that natural cellulose is more hydrophobic than amylose at the single-chain level, implying that the hydrophobicities of these polymeric isomers are regulated by only one parameter in the chains, the linkage between the sugar rings.
3-D phononic crystals with ultra-wide band gaps
Feb 24, 2017   Scientific Reports
Lu Y, Yang Y, Guest JK, Srivastava A
3-D phononic crystals with ultra-wide band gaps
Feb 24, 2017
Scientific Reports
In this paper gradient based topology optimization (TO) is used to discover 3-D phononic structures that exhibit ultra-wide normalized all-angle all-mode band gaps. The challenging computational task of repeated 3-D phononic band-structure evaluations is accomplished by a combination of a fast mixed variational eigenvalue solver and distributed Graphic Processing Unit (GPU) parallel computations. The TO algorithm utilizes the material distribution-based approach and a gradient-based optimizer. The design sensitivity for the mixed variational eigenvalue problem is derived using the adjoint method and is implemented through highly efficient vectorization techniques. We present optimized results for two-material simple cubic (SC), body centered cubic (BCC), and face centered cubic (FCC) crystal structures and show that in each of these cases different initial designs converge to single inclusion network topologies within their corresponding primitive cells. The optimized results show that large phononic stop bands for bulk wave propagation can be achieved at lower than close packed spherical configurations leading to lighter unit cells. For tungsten carbide - epoxy crystals we identify all angle all mode normalized stop bands exceeding 100%, which is larger than what is possible with only spherical inclusions.
High-bandwidth nanopore data analysis by using a modified hidden Markov model
Feb 24, 2017   Nanoscale
Zhang J, Liu X, Ying YL, Gu Z, Meng FN, Long YT
High-bandwidth nanopore data analysis by using a modified hidden Markov model
Feb 24, 2017
Nanoscale
Nanopore-based sensing is an emerging analytical technique with a number of important applications, including single-molecule detection and DNA sequencing. In this paper, we developed a Modified Hidden Markov Model (MHMM) to analyze directly the raw (unfiltered) nanopore current blockade data, which significantly reduced the filtering-induced distortion of the nanopore events. Traditionally, prior to further analysis, the measured nanopore data need to be pre-filtered to supress the strong noises. Nonetheless, this would result in the distortion of the shape of the blockade current especially for rapid translocations and bumping blockades. The HMM has been proved to be robust with respect to highly noisy data and thus ideally suitable for processing raw nanopore data directly. Unfortunately, its performance is somehow sensitive to the initial parameters usually preset arbitrarily. To overcome this problem, we use the Fuzzy c-Means (FCM) algorithm to initialize the HMM parameters automatically. Then we use the Viterbi training algorithm to optimize the HMM. Finally, the application results on both the simulated and experimental data are presented to demonstrate the practicability of the developed method for accurate detection of the nanopore current blockade events. The proposed method enables detection of the nanopore events at the highest bandwidth of the commercial instruments to extract the true useful information about the single molecules under analysis.
Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay
Feb 24, 2017   Science Advances
Marbouty M, Baudry L, Cournac A, Koszul R
Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay
Feb 24, 2017
Science Advances
The biochemical activities of microbial communities, or microbiomes, are essential parts of environmental and animal ecosystems. The dynamics, balance, and effects of these communities are strongly influenced by phages present in the population. Being able to characterize bacterium-phage relationships is therefore essential to investigate these ecosystems to the full extent of their complexity. However, this task is currently limited by (i) the ability to characterize complete bacterial and viral genomes from a complex mix of species and (ii) the difficulty to assign phage sequences to their bacterial hosts. We show that both limitations can be circumvented using meta3C, an experimental and computational approach that exploits the physical contacts between DNA molecules to infer their proximity. In a single experiment, dozens of bacterial and phage genomes present in a complex mouse gut microbiota were assembled and scaffolded de novo. The phage genomes were then assigned to their putative bacterial hosts according to the physical contacts between the different DNA molecules, opening new perspectives for a comprehensive picture of the genomic structure of the gut flora. Therefore, this work holds far-reaching implications for human health studies aiming to bridge the virome to the microbiome.
Ultrasonic Measurement of Dynamic Muscle Behavior for Poststroke Hemiparetic Gait
Feb 24, 2017   BioMed Research International
Chen X, Zhang X, Shi W, Wang J, Xiang Y, Zhou Y, Yang WZ
Ultrasonic Measurement of Dynamic Muscle Behavior for Poststroke Hemiparetic Gait
Feb 24, 2017
BioMed Research International
Quantitative evaluation of the hemiparesis status for a poststroke patient is still challenging. This study aims to measure and investigate the dynamic muscle behavior in poststroke hemiparetic gait using ultrasonography. Twelve hemiparetic patients walked on a treadmill, and EMG, joint angle, and ultrasonography were simultaneously recorded for the gastrocnemius medialis muscle. Pennation angle was automatically extracted from ultrasonography using a tracking algorithm reported previously. The characteristics of EMG, joint angle, and pennation angle in gait cycle were calculated for both (affected and unaffected) sides of lower limbs. The results suggest that pennation angle could work as an important morphological index to continuous muscle contraction. The change pattern of pennation angle between the affected and unaffected sides is different from that of EMG. These findings indicate that morphological parameter extracted from ultrasonography can provide different information from that provided by EMG for hemiparetic gait.
PEGylated graphene oxide elicits strong immunological responses despite surface passivation
Feb 24, 2017   Nature Communications
Luo N, Weber JK, Wang S, Luan B, Yue H, Xi X, Du J, Yang Z, Wei W, Zhou R, Ma G
PEGylated graphene oxide elicits strong immunological responses despite surface passivation
Feb 24, 2017
Nature Communications
Engineered nanomaterials promise to transform medicine at the bio-nano interface. However, it is important to elucidate how synthetic nanomaterials interact with critical biological systems before such products can be safely utilized in humans. Past evidence suggests that polyethylene glycol-functionalized (PEGylated) nanomaterials are largely biocompatible and elicit less dramatic immune responses than their pristine counterparts. We here report results that contradict these findings. We find that PEGylated graphene oxide nanosheets (nGO-PEGs) stimulate potent cytokine responses in peritoneal macrophages, despite not being internalized. Atomistic molecular dynamics simulations support a mechanism by which nGO-PEGs preferentially adsorb onto and/or partially insert into cell membranes, thereby amplifying interactions with stimulatory surface receptors. Further experiments demonstrate that nGO-PEG indeed provokes cytokine secretion by enhancing integrin β
Computational methods using genome-wide association studies to predict radiotherapy complications and to identify correlative molecular processes
Feb 24, 2017   Scientific Reports
Oh JH, Kerns S, Ostrer H, Powell SN, Rosenstein B, Deasy JO
Computational methods using genome-wide association studies to predict radiotherapy complications and to identify correlative molecular processes
Feb 24, 2017
Scientific Reports
The biological cause of clinically observed variability of normal tissue damage following radiotherapy is poorly understood. We hypothesized that machine/statistical learning methods using single nucleotide polymorphism (SNP)-based genome-wide association studies (GWAS) would identify groups of patients of differing complication risk, and furthermore could be used to identify key biological sources of variability. We developed a novel learning algorithm, called pre-conditioned random forest regression (PRFR), to construct polygenic risk models using hundreds of SNPs, thereby capturing genomic features that confer small differential risk. Predictive models were trained and validated on a cohort of 368 prostate cancer patients for two post-radiotherapy clinical endpoints: late rectal bleeding and erectile dysfunction. The proposed method results in better predictive performance compared with existing computational methods. Gene ontology enrichment analysis and protein-protein interaction network analysis are used to identify key biological processes and proteins that were plausible based on other published studies. In conclusion, we confirm that novel machine learning methods can produce large predictive models (hundreds of SNPs), yielding clinically useful risk stratification models, as well as identifying important underlying biological processes in the radiation damage and tissue repair process. The methods are generally applicable to GWAS data and are not specific to radiotherapy endpoints.
Toward deterministic and semiautomated SPADE analysis
Feb 24, 2017   Cytometry. Part A : The Journal Of The International Society For Analytical Cytology
Qiu P
Toward deterministic and semiautomated SPADE analysis
Feb 24, 2017
Cytometry. Part A : The Journal Of The International Society For Analytical Cytology
SPADE stands for spanning-tree progression analysis for density-normalized events. It combines downsampling, clustering and a minimum-spanning tree to provide an intuitive visualization of high-dimensional single-cell data, which assists with the interpretation of the cellular heterogeneity underlying the data. SPADE has been widely used for analysis of high-content flow cytometry data and CyTOF data. The downsampling and clustering components of SPADE are both stochastic, which lead to stochasticity in the tree visualization it generates. Running SPADE twice on the same data may generate two different tree structures. Although they typically lead to the same biological interpretation of subpopulations present in the data, robustness of the algorithm can be improved. Another avenue of improvement is the interpretation of the SPADE tree, which involves visual inspection of multiple colored versions of the tree based on expression of measured markers. This is essentially manual gating on the SPADE tree and can benefit from automated algorithms. This article presents improvements of SPADE in both aspects above, leading to a deterministic SPADE algorithm and a software implementation for semiautomated interpretation. © 2017 International Society for Advancement of Cytometry.© 2017 International Society for Advancement of Cytometry.
Real-time characterization of FM-AM modulation in a high-power laser facility using an RF-photonics system and a denoising algorithm
Feb 24, 2017   Applied Optics
Huang C, Lu X, Jiang Y, Wang X, Qiao Z, Fan W
Real-time characterization of FM-AM modulation in a high-power laser facility using an RF-photonics system and a denoising algorithm
Feb 24, 2017
Applied Optics
FM-AM modulation of high-power lasers significantly affects laser performance. Therefore, precise measurement of the FM-AM modulation depth is necessary. The subsequent FM-AM modulation generated by group velocity dispersion when the laser pulse propagates through a fiber affects the measurement accuracy. In order to eliminate this effect, a waveform-acquisition module is proposed that converts a broad-spectrum pulse of 1053 nm to a narrow-spectrum pulse of 1550 nm, without affecting the waveform. In addition, a signal-processing algorithm based on the orthogonal matching pursuit method is implemented to remove the sampling noise from the waveform. In this way, the signal-to-noise ratio of the measurement can be readily improved. Both theoretical and experimental results indicate that the proposed FM-AM modulation detection system is effective and economical. It can measure the FM-AM modulation depth precisely, and therefore shows considerable promise for future applications in high-power lasers.
A novel method of micro-tomography geometric angle calibration with random phantom
Feb 24, 2017   Journal Of X-ray Science And Technology
Li H, Hong W, Mou X, Liu Y
A novel method of micro-tomography geometric angle calibration with random phantom
Feb 24, 2017
Journal Of X-ray Science And Technology
The objective of this study is to develop and test the feasibility of applying a machine learning method for geometry calibration of angles in micro-tomography systems. Increasing importance of micro-tomography systems are manifested with escalating applications in various scenarios including but not limited to oral and maxillofacial surgery, vascular and intervention radiology, among other specific applications for purposes of diagnosis and treatments planning. There is possibility, however, actual pathology is confused by artifact of tissue structures after volume reconstruction as a result of CT construction errors. A Kernel Ridge Regression algorithm for micro-tomography geometry estimation and its corresponding phantom is developed and tested in this study. Several projection images of a rotating Random Phantom of some steel ball bearings in an unknown geometry with gantry angle information were utilized to calibrate both in-plane and out-plane rotation of the detector. The described method can also be expanded to calibrate other parameters of CT construction effortlessly. Using computer simulation, the study results validated that geometry parameters of micro-tomography system were accurately calibrated.
Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expression patterns and evolutional conservation in Sus scrofa
Feb 24, 2017   Scientific Reports
Tang Z, Wu Y, Yang Y, Yang YT, Wang Z, Yuan J, Yang Y, Hua C, Fan X, Niu G, Zhang Y, Lu ZJ, Li K
Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expression patterns and evolutional conservation in Sus scrofa
Feb 24, 2017
Scientific Reports
Despite modest sequence conservation and rapid evolution, long non-coding RNAs (lncRNAs) appear to be conserved in expression pattern and function. However, analysis of lncRNAs across tissues and developmental stages remains largely uncharacterized in mammals. Here, we systematically investigated the lncRNAs of the Guizhou miniature pig (Sus scrofa), which was widely used as biomedical model. We performed RNA sequencing across 9 organs and 3 developmental skeletal muscle, and developed a filtering pipeline to identify 10,813 lncRNAs (9,075 novel). Conservation patterns analysis revealed that 57% of pig lncRNAs showed homology to humans and mice based on genome alignment. 5,455 lncRNAs exhibited typical hallmarks of regulatory molecules, such as high spatio-temporal specificity. Notably, conserved lncRNAs exhibited higher tissue specificity than pig-specific lncRNAs and were significantly enriched in testis and ovary. Weighted co-expression network analysis revealed a set of conserved lncRNAs that are likely involved in postnatal muscle development. Based on the high degree of similarity in the structure, organization, and dynamic expression of pig lncRNAs compared with human and mouse lncRNAs, we propose that these lncRNAs play an important role in organ physiology and development in mammals. Our results provide a resource for studying animal evolution, morphological complexity, breeding, and biomedical research.
Intrinsic disorder in biomarkers of insulin resistance, hypoadiponectinemia, and endothelial dysfunction among the type 2 diabetic patients
Feb 24, 2017   Intrinsically Disordered Proteins
Al-Jiffri OH, Al-Sharif FM, Al-Jiffri EH, Uversky VN
Intrinsic disorder in biomarkers of insulin resistance, hypoadiponectinemia, and endothelial dysfunction among the type 2 diabetic patients
Feb 24, 2017
Intrinsically Disordered Proteins
Type 2 diabetes mellitus (T2DM) is a chronic and progressive disease that is strongly associated with various complications including cardiovascular diseases and related mortality. The present study aimed to analyze the abundance and functionality of intrinsically disordered regions in several biomarkers of insulin resistance, adiponectin, and endothelial dysfunction found in the T2DM patients. In fact, in comparison to controls, obese T2DM patients are known to have significantly higher levels of inter-cellular adhesion molecule (iCAM-1), vascular cell adhesion molecule (vCAM-1), and E-selectin, whereas their adiponectin levels are relatively low. Bioinformatics analysis revealed that these selected biomarkers (iCAM-1, vCAM-1, E-selectin, and adiponectin) are characterized by the noticeable levels of intrinsic disorder propensity and high binding promiscuity, which are important features expected for proteins serving as biomarkers. Within the limit of studied groups, there is an association between insulin resistance and both hypoadiponectinemia and endothelial dysfunction.
Integration of EGA secure data access into Galaxy
Feb 24, 2017   F1000Research
Hoogstrate Y, Zhang C, Senf A, Bijlard J, Hiltemann S,   . . . . . .   , A Meijer G, Stubbs A, Rambla J, Spalding D, Abeln S
Integration of EGA secure data access into Galaxy
Feb 24, 2017
F1000Research
High-throughput molecular profiling techniques are routinely generating vast amounts of data for translational medicine studies. Secure access controlled systems are needed to manage, store, transfer and distribute these data due to its personally identifiable nature. The European Genome-phenome Archive (EGA) was created to facilitate access and management to long-term archival of bio-molecular data. Each data provider is responsible for ensuring a Data Access Committee is in place to grant access to data stored in the EGA. Moreover, the transfer of data during upload and download is encrypted. ELIXIR, a European research infrastructure for life-science data, initiated a project (2016 Human Data Implementation Study) to understand and document the ELIXIR requirements for secure management of controlled-access data. As part of this project, a full ecosystem was designed to connect archived raw experimental molecular profiling data with interpreted data and the computational workflows, using the CTMM Translational Research IT (CTMM-TraIT) infrastructure http://www.ctmm-trait.nl as an example. Here we present the first outcomes of this project, a framework to enable the download of EGA data to a Galaxy server in a secure way. Galaxy provides an intuitive user interface for molecular biologists and bioinformaticians to run and design data analysis workflows. More specifically, we developed a tool -- ega_download_streamer - that can download data securely from EGA into a Galaxy server, which can subsequently be further processed. This tool will allow a user within the browser to run an entire analysis containing sensitive data from EGA, and to make this analysis available for other researchers in a reproducible manner, as shown with a proof of concept study.  The tool ega_download_streamer is available in the Galaxy tool shed: https://toolshed.g2.bx.psu.edu/view/yhoogstrate/ega_download_streamer.
Nonlinear image registration with bidirectional metric and reciprocal regularization
Feb 23, 2017   PloS One
Ying S, Li D, Xiao B, Peng Y, Du S, Xu M
Nonlinear image registration with bidirectional metric and reciprocal regularization
Feb 23, 2017
PloS One
Nonlinear registration is an important technique to align two different images and widely applied in medical image analysis. In this paper, we develop a novel nonlinear registration framework based on the diffeomorphic demons, where a reciprocal regularizer is introduced to assume that the deformation between two images is an exact diffeomorphism. In detail, first, we adopt a bidirectional metric to improve the symmetry of the energy functional, whose variables are two reciprocal deformations. Secondly, we slack these two deformations into two independent variables and introduce a reciprocal regularizer to assure the deformations being the exact diffeomorphism. Then, we utilize an alternating iterative strategy to decouple the model into two minimizing subproblems, where a new closed form for the approximate velocity of deformation is calculated. Finally, we compare our proposed algorithm on two data sets of real brain MR images with two relative and conventional methods. The results validate that our proposed method improves accuracy and robustness of registration, as well as the gained bidirectional deformations are actually reciprocal.
Synthetic Gene Circuits Learn to Classify
Feb 23, 2017   Cell Systems
Didovyk A, Tsimring LS
Synthetic Gene Circuits Learn to Classify
Feb 23, 2017
Cell Systems
An efficient computational algorithm is developed to design microRNA-based synthetic cell classifiers and to optimize their performance.Copyright © 2017 Elsevier Inc. All rights reserved.
Molecular mechanisms of cooperative binding of transcription factors Runx1-CBFβ-Ets1 on the TCRα gene enhancer
Feb 23, 2017   PloS One
Kasahara K, Shiina M, Fukuda I, Ogata K, Nakamura H
Molecular mechanisms of cooperative binding of transcription factors Runx1-CBFβ-Ets1 on the TCRα gene enhancer
Feb 23, 2017
PloS One
Ets1 is an essential transcription factor (TF) for several important physiological processes, including cell proliferation and differentiation. Its recognition of the enhancer region of the TCRα gene is enhanced by the cooperative binding of the Runx1-CBFβ heterodimer, with the cancelation of phosphorylation-dependent autoinhibition. The detailed mechanism of this interesting cooperativity between Ets1 and the Runx1-CBFβ heterodimer is still largely unclear. Here, we investigated the molecular mechanisms of this cooperativity, by using molecular dynamics simulations. Consequently, we detected high flexibility of the loop region between the HI2 and H1 helices of Ets1. Upon Runx1-CBFβ heterodimer binding, this loop transiently adopts various sub-stable conformations in its interactions with the DNA. In addition, a network analysis suggested an allosteric pathway in the molecular assembly and identified some key residues that coincide with previous experimental studies. Our simulations suggest that the cooperative binding of Ets1 and the Runx1-CBFβ heterodimer alters the DNA conformation and induces sub-stable conformations of the HI2-H1 loop of Ets1. This phenomenon increases the flexibility of the regulatory module, including the HI2 helix, and destabilizes the inhibitory form of this module. Thus, we hypothesize that this effect facilitates Ets1-DNA binding and prevents the phosphorylation-dependent DNA binding autoinhibition.
Clinical evaluation of new automatic coronary-specific best cardiac phase selection algorithm for single-beat coronary CT angiography
Feb 23, 2017   PloS One
Wang H, Xu L, Fan Z, Liang J, Yan Z, Sun Z
Clinical evaluation of new automatic coronary-specific best cardiac phase selection algorithm for single-beat coronary CT angiography
Feb 23, 2017
PloS One
The aim of this study was to evaluate the workflow efficiency of a new automatic coronary-specific reconstruction technique (Smart Phase, GE Healthcare-SP) for selection of the best cardiac phase with least coronary motion when compared with expert manual selection (MS) of best phase in patients with high heart rate. A total of 46 patients with heart rates above 75 bpm who underwent single beat coronary computed tomography angiography (CCTA) were enrolled in this study. CCTA of all subjects were performed on a 256-detector row CT scanner (Revolution CT, GE Healthcare, Waukesha, Wisconsin, US). With the SP technique, the acquired phase range was automatically searched in 2% phase intervals during the reconstruction process to determine the optimal phase for coronary assessment, while for routine expert MS, reconstructions were performed at 5% intervals and a best phase was manually determined. The reconstruction and review times were recorded to measure the workflow efficiency for each method. Two reviewers subjectively assessed image quality for each coronary artery in the MS and SP reconstruction volumes using a 4-point grading scale. The average HR of the enrolled patients was 91.1±19.0bpm. A total of 204 vessels were assessed. The subjective image quality using SP was comparable to that of the MS, 1.45±0.85 vs 1.43±0.81 respectively (p = 0.88). The average time was 246 seconds for the manual best phase selection, and 98 seconds for the SP selection, resulting in average time saving of 148 seconds (60%) with use of the SP algorithm. The coronary specific automatic cardiac best phase selection technique (Smart Phase) improves clinical workflow in high heart rate patients and provides image quality comparable with manual cardiac best phase selection. Reconstruction of single-beat CCTA exams with SP can benefit the users with less experienced in CCTA image interpretation.
A label-free method using a weighted-phase algorithm to quantitate nanoscale interactions between molecules on DNA microarrays
Feb 23, 2017   Analytical Chemistry
Li Q, Fu R, Zhang J, Wang R, Ye J, Xue N, Lin X, Su Y, Gan W, Lu Y, Huang G
A label-free method using a weighted-phase algorithm to quantitate nanoscale interactions between molecules on DNA microarrays
Feb 23, 2017
Analytical Chemistry
White light interference is used as a label-free method to detect nanoscale changes on surfaces. However, the signal-to-noise ratio of the white light interference method is very low, thus resulting in inaccurate results. In this paper, we report a corrected label-free method based on hyperspectral interferometry to overcome the shortcoming of the white light interference method. A platform based on hyperspectral interferometry was established, and a DNA hybridization microarray was constructed to quantitate thickness variation of molecules on a solid surface. We used fluorescence resonance energy transfer (FRET) to validate the results of our method. Compared to conventional fluorescence-labeled method like FRET, our method has advantages because it does not require a fluorescent label, has a detection limit of 1.78 nm, a high accuracy and wide detection range (5-64 bp).
Edge-preserving denoising for intra-operative cone beam CT in endovascular aneurysm repair
Feb 23, 2017   Computerized Medical Imaging And Graphics : The Official Journal Of The Computerized Medical Imaging Society
Liu Y, Castro M, Lederlin M, Shu H, Kaladji A, Haigron P
Edge-preserving denoising for intra-operative cone beam CT in endovascular aneurysm repair
Feb 23, 2017
Computerized Medical Imaging And Graphics : The Official Journal Of The Computerized Medical Imaging Society
C-arm cone-beam computed tomography (CBCT) acquisition during endovascular aneurysm repair (EVAR) is an emergent technology with more and more applications. It offers real time imaging with a stationary patient and provides 3-D information to achieve guidance of intervention. However, there is growing concern on the overall radiation doses delivered to patients all along the endovascular management due to pre-, intra-, and post-operative X-ray imaging. Manufactures may have their low dose protocols to realize reduction of radiation dose, but CBCT with a low dose protocol has too many artifacts, particularly streak artifacts, and decreased contrast-to-noise ratio (CNR). To reduce noise and artifacts, a penalized weighted least-squares (PWLS) algorithm with an edge-preserving penalty is proposed. The proposed method is evaluated by quantitative parameters including a defined signal-to-noise ratio (SNR), CNR, and modulation transfer function (MTF) on clinical CBCT. Comparisons with PWLS algorithms with isotropic, TV, Huber, anisotropic penalties demonstrate that the proposed edge-preserving penalty performs well not only on edge preservation, but also on streak artifacts suppression, which may be crucial for observing guidewire and stentgraft in EVAR.Copyright © 2017 Elsevier Ltd. All rights reserved.
Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism
Feb 24, 2017   Journal Of Biotechnology
Yu J, Blom J, Sczyrba A, Goesmann A
Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism
Feb 24, 2017
Journal Of Biotechnology
The introduction of next generation sequencing has caused a steady increase in the amounts of data that have to be processed in modern life science. Sequence alignment plays a key role in the analysis of sequencing data e.g. within whole genome sequencing or metagenome projects. BLAST is a commonly used alignment tool that was the standard approach for more than two decades, but in the last years faster alternatives have been proposed including RapSearch, GHOSTX, and DIAMOND. Here we introduce HAMOND, an application that uses Apache Hadoop to parallelize DIAMOND computation in order to scale-out the calculation of alignments. HAMOND is fault tolerant and scalable by utilizing large cloud computing infrastructures like Amazon Web Services. HAMOND has been tested in comparative genomics analyses and showed promising results both in efficiency and accuracy.Copyright © 2017. Published by Elsevier B.V.
Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes
Feb 24, 2017   Nature Communications
Ryckbosch SM, Wender PA, Pande VS
Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes
Feb 24, 2017
Nature Communications
Bryostatin is in clinical trials for Alzheimer's disease, cancer, and HIV/AIDS eradication. It binds to protein kinase C competitively with diacylglycerol, the endogenous protein kinase C regulator, and plant-derived phorbol esters, but each ligand induces different activities. Determination of the structural origin for these differing activities by X-ray analysis has not succeeded due to difficulties in co-crystallizing protein kinase C with relevant ligands. More importantly, static, crystal-lattice bound complexes do not address the influence of the membrane on the structure and dynamics of membrane-associated proteins. To address this general problem, we performed long-timescale (400-500 µs aggregate) all-atom molecular dynamics simulations of protein kinase C-ligand-membrane complexes and observed that different protein kinase C activators differentially position the complex in the membrane due in part to their differing interactions with waters at the membrane inner leaf. These new findings enable new strategies for the design of simpler, more effective protein kinase C analogs and could also prove relevant to other peripheral protein complexes.Natural supplies of bryostatin, a compound in clinical trials for Alzheimer's disease, cancer, and HIV, are scarce. Here, the authors perform molecular dynamics simulations to understand how bryostatin interacts with membrane-bound protein kinase C, offering insights for the design of bryostatin analogs.
Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability
Feb 24, 2017   Science (New York, N.Y.)
Leuenberger P, Ganscha S, Kahraman A, Cappelletti V, Boersema PJ, von Mering C, Claassen M, Picotti P
Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability
Feb 24, 2017
Science (New York, N.Y.)
Temperature-induced cell death is thought to be due to protein denaturation, but the determinants of thermal sensitivity of proteomes remain largely uncharacterized. We developed a structural proteomic strategy to measure protein thermostability on a proteome-wide scale and with domain-level resolution. We applied it to Copyright © 2017, American Association for the Advancement of Science.
ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter
Feb 24, 2017   Genome Research
Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H, Coombe L, Warren RL, Birol I
ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter
Feb 24, 2017
Genome Research
The assembly of DNA sequences de novo is fundamental to genomics research. It is the first of many steps towards elucidating and characterizing whole genomes. Downstream applications, including analysis of genomic variation between species, between or within individuals critically depend on robustly assembled sequences. In the span of a single decade, the sequence throughput of leading DNA sequencing instruments has increased drastically, and coupled with established and planned large-scale, personalized medicine initiatives to sequence genomes in the thousands and even millions, the development of efficient, scalable and accurate bioinformatics tools for producing high-quality reference draft genomes is timely. With ABySS 1.0, we originally showed that assembling the human genome using short 50 bp sequencing reads was possible by aggregating the half terabyte of compute memory needed over several computers using a standardized message-passing system (MPI). We present here its re-design, which departs from MPI and instead implements algorithms that employ a Bloom filter, a probabilistic data structure, to represent a de Bruijn graph and reduce memory requirements. We benchmarked ABySS 2.0 human genome assembly using a Genome in a Bottle dataset of 250 bp Illumina paired-end and 6 kbp mate-pair libraries from a single individual. Our assembly yielded a NG50 (NGA50) scaffold contiguity of 3.5 (3.0) Mbp using less than 35 GB of RAM. This is a modest memory requirement by today's standards, and is often available on a single computer. We also investigate the use of BioNano Genomics and 10x Genomics' Chromium data to further improve the scaffold NG50 (NGA50) of this assembly to 42 (15) Mbp.Published by Cold Spring Harbor Laboratory Press.
Metabolic anchor reactions for robust biorefining
Feb 24, 2017   Metabolic Engineering
Jouhten P, Huerta-Cepas J, Bork P, Raosaheb Patil K
Metabolic anchor reactions for robust biorefining
Feb 24, 2017
Metabolic Engineering
Microbial cell factories based on renewable carbon sources are fundamental to a sustainable bio-economy. The economic feasibility of producer cells requires robust performance balancing growth and production. However, the inherent competition between these two objectives often leads to instability and reduces productivity. While algorithms exist to design metabolic network reduction strategies for aligning these objectives, the biochemical basis of the growth-product coupling has remained unresolved. Here, we reveal key reactions in the cellular biochemical repertoire as universal anchor reactions for aligning cell growth and production. A necessary condition for a reaction to be an anchor is that it splits a substrate into two or more molecules. By searching the currently known biochemical reaction space, we identify 62 C-C cleaving anchor reactions, such as isocitrate lyase (EC 4.1.3.1) and L-tryptophan indole-lyase (EC 4.1.99.1), which are relevant for biorefining. The here identified anchor reactions mark network nodes for basing growth-coupled metabolic engineering and novel pathway designs.Copyright © 2017. Published by Elsevier Inc.
Anatase (101)-like Structural Model Revealed for Metastable Rutile TiO2(011) Surface
Feb 23, 2017   ACS Applied Materials & Interfaces
Xu M, Shao S, Gao B, Lv J, Li Q, Wang Y, Wang H, Zhang L, Ma Y
Anatase (101)-like Structural Model Revealed for Metastable Rutile TiO2(011) Surface
Feb 23, 2017
ACS Applied Materials & Interfaces
Titanium dioxide has been widely used as efficient transition metal oxide photocatalyst. However, its photocatalytic activity is limited to ultraviolet spectrum range due to the deficient large bandgap beyond 3 eV. Efforts towards to reduce the bandgap for achieving a broader spectrum range of light absorption are attempted with a success on the experimental synthesis of dopant-free metastable surface structure of rutile-type TiO2 (011) 21. This new surface phase possesses a much reduced bandgap of ~2.1 eV, showing a great potential for an excellent photocatalyst covering a wide range of visible light. There is an urge to establish the atomistic structure of this metastable surface for understanding the physical cause for the bandgap reduction and for future design of better photocatalyst. We here report the computational investigations in an effort to unravel this surface structure via swarm structure-searching simulations. The established structure adopts the anatase (101)-like structure model, where the topmost two-fold O atoms form a quasi-hexagonal surface pattern, and bonded with unsaturated five-fold and four-fold Ti atoms in the next layer. The predicted anatase (101)-like surface model can naturally explain the experimental observation of STM image, the electronic bandgap, and the oxidation state of Ti4+. Dangling bonds on the anatase (101)-like surface are rich, making it a superior photocatalyst. First-principles molecular dynamics simulations has approved the high photocatalystic activity by showing that water and formic acid molecules dissociate spontaneously on this anatase (101)-like surface.

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