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https://www.readbyqxmd.com/read/27914056/parallel-computational-protein-design
#1
Yichao Zhou, Bruce R Donald, Jianyang Zeng
Computational structure-based protein design (CSPD) is an important problem in computational biology, which aims to design or improve a prescribed protein function based on a protein structure template. It provides a practical tool for real-world protein engineering applications. A popular CSPD method that guarantees to find the global minimum energy solution (GMEC) is to combine both dead-end elimination (DEE) and A* tree search algorithms. However, in this framework, the A* search algorithm can run in exponential time in the worst case, which may become the computation bottleneck of large-scale computational protein design process...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913670/screening-for-chemical-modulators-for-lrrk2
#2
REVIEW
Heather Mortiboys
After the discovery of leucine-rich repeat kinase 2 (LRRK2) as a risk factor for sporadic Parkinson's disease (PD) and mutations in LRRK2 as a cause of some forms of familial PD, there has been substantial interest in finding chemical modulators of LRRK2 function. Most of the pathogenic mutations in LRRK2 are within the enzymatic cores of the protein; therefore, many screens have focused on finding chemical modulators of this enzymatic activity. There are alternative screening approaches that could be taken to investigate compounds that modulate LRRK2 cellular functions...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27911849/scalable-manufacturing-of-biomimetic-moldable-hydrogels-for-industrial-applications
#3
Anthony C Yu, Haoxuan Chen, Doreen Chan, Gillie Agmon, Lyndsay M Stapleton, Alex M Sevit, Mark W Tibbitt, Jesse D Acosta, Tony Zhang, Paul W Franzia, Robert Langer, Eric A Appel
Hydrogels are a class of soft material that is exploited in many, often completely disparate, industrial applications, on account of their unique and tunable properties. Advances in soft material design are yielding next-generation moldable hydrogels that address engineering criteria in several industrial settings such as complex viscosity modifiers, hydraulic or injection fluids, and sprayable carriers. Industrial implementation of these viscoelastic materials requires extreme volumes of material, upwards of several hundred million gallons per year...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911167/recommendations-for-a-nomenclature-system-for-reporting-methylation-aberrations-in-imprinted-domains
#4
David Monk, Joannella Morales, Johan T den Dunnen, Silvia Russo, Franck Court, Dirk Prawitt, Thomas Eggermann, Jasmin Beygo, Karin Buiting, Zeynep Tümer
The analysis of DNA methylation has become routine in the pipeline for diagnosis of imprinting disorders, with many publications reporting aberrant methylation associated with imprinted differentially methylated regions (DMRs). However, comparisons between these studies are routinely hampered by the lack of consistency in reporting sites of methylation evaluated. To avoid confusion surrounding nomenclature, special care is needed to communicate results accurately, especially between scientists and other health care professionals...
December 2, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27910641/real-time-energy-measurement-of-high-repetition-rate-ultrashort-laser-pulses-using-pulse-integration-and-fpga-processing
#5
Qi-Jie Tang, Dong-Xu Yang, Jian Wang, Yi Feng, Hong-Fei Zhang, Teng-Yun Chen
Real-time energy measurement using pulse integration method for high repetition rate ultrashort laser pulses based on FPGA (Field-Programmable Gate Array) and high-speed pipeline ADC (Analog-to-Digital Convertor) is introduced in this paper. There are two parts contained in this method: pulse integration and real-time data processing. The pulse integration circuit will convert the pulse to the step type signals which are linear to the laser pulse energy. Through the real-time data processing part, the amplitude of the step signals will be obtained by ADC sampling and conducting calculation in real time in FPGA...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910131/whole-exome-association-of-rare-deletions-in-multiplex-oral-cleft-families
#6
Jack Fu, Terri H Beaty, Alan F Scott, Jacqueline Hetmanski, Margaret M Parker, Joan E Bailey Wilson, Mary L Marazita, Elisabeth Mangold, Hasan Albacha-Hejazi, Jeffrey C Murray, Alexandre Bureau, Jacob Carey, Stephen Cristiano, Ingo Ruczinski, Robert B Scharpf
By sequencing the exomes of distantly related individuals in multiplex families, rare mutational and structural changes to coding DNA can be characterized and their relationship to disease risk can be assessed. Recently, several rare single nucleotide variants (SNVs) were associated with an increased risk of nonsyndromic oral cleft, highlighting the importance of rare sequence variants in oral clefts and illustrating the strength of family-based study designs. However, the extent to which rare deletions in coding regions of the genome occur and contribute to risk of nonsyndromic clefts is not well understood...
December 1, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/27909578/advances-in-analyzing-rna-diversity-in-eukaryotic-transcriptomes-peering-through-the-omics-lens
#7
REVIEW
Sushant Bangru, Auinash Kalsotra
Alternative splicing, polyadenylation, and chemical modifications of RNA generate astonishing complexity within eukaryotic transcriptomes. The last decade has brought numerous advances in sequencing technologies that allow biologists to investigate these phenomena with greater depth and accuracy while reducing time and cost. A commensurate development in biochemical techniques for the enrichment and analysis of different RNA variants has accompanied the advancement of global sequencing analysis platforms. Here, we present a detailed overview of the latest biochemical methods, along with bioinformatics pipelines that have aided in identifying different RNA variants...
2016: F1000Research
https://www.readbyqxmd.com/read/27909575/a-step-by-step-workflow-for-low-level-analysis-of-single-cell-rna-seq-data
#8
Aaron T L Lun, Davis J McCarthy, John C Marioni
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise and data complexity. The differences between scRNA-seq and bulk RNA-seq data mean that the analysis of the former cannot be performed by recycling bioinformatics pipelines for the latter. Rather, dedicated single-cell methods are required at various steps to exploit the cellular resolution while accounting for technical noise...
2016: F1000Research
https://www.readbyqxmd.com/read/27908674/renaissance-of-protein-crystallization-and-precipitation-in-biopharmaceuticals-purification
#9
REVIEW
Raquel Dos Santos, Ana Luísa Carvalho, A Cecília A Roque
The current chromatographic approaches used in protein purification are not keeping pace with the increasing biopharmaceutical market demand. With the upstream improvements, the bottleneck shifted towards the downstream process. New approaches rely in Anything But Chromatography methodologies and revisiting former techniques with a bioprocess perspective. Protein crystallization and precipitation methods are already implemented in the downstream process of diverse therapeutic biological macromolecules, overcoming the current chromatographic bottlenecks...
November 28, 2016: Biotechnology Advances
https://www.readbyqxmd.com/read/27905885/mefit-merging-and-filtering-tool-for-illumina-paired-end-reads-for-16s-rrna-amplicon-sequencing
#10
Hardik I Parikh, Vishal N Koparde, Steven P Bradley, Gregory A Buck, Nihar U Sheth
BACKGROUND: Recent advances in next-generation sequencing have revolutionized genomic research. 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumina, Inc., is being used to characterize the composition and dynamics of extremely complex/diverse microbial communities. For this analysis on the Illumina platform, merging and quality filtering of paired-end reads are essential first steps in data analysis to ensure the accuracy and reliability of downstream analysis...
December 1, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27905871/phyinformr-phylogenetic-experimental-design-and-phylogenomic-data-exploration-in-r
#11
Alex Dornburg, J Nick Fisk, Jules Tamagnan, Jeffrey P Townsend
BACKGROUND: Analyses of phylogenetic informativeness represent an important step in screening potential or existing datasets for their proclivity toward convergent or parallel evolution of molecular sites. However, while new theory has been developed from which to predict the utility of sequence data, adoption of these advances have been stymied by a lack of software enabling application of advances in theory, especially for large next-generation sequence data sets. Moreover, there are no theoretical barriers to application of the phylogenetic informativeness or the calculation of quartet internode resolution probabilities in a Bayesian setting that more robustly accounts for uncertainty, yet there is no software with which a computationally intensive Bayesian approach to experimental design could be implemented...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27905027/erratum-to-grape-a-graphical-pipeline-environment-for-image-analysis-in-adaptive-magnetic-resonance-imaging
#12
Refaat E Gabr, Getaneh B Tefera, William J Allen, Amol S Pednekar, Ponnada A Narayana
No abstract text is available yet for this article.
November 30, 2016: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/27904880/microbial-community-patterns-associated-with-automated-teller-machine-keypads-in-new-york-city
#13
Holly M Bik, Julia M Maritz, Albert Luong, Hakdong Shin, Maria Gloria Dominguez-Bello, Jane M Carlton
In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the "urban microbiome" may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads...
November 2016: MSphere
https://www.readbyqxmd.com/read/27904445/endovascular-treatment-of-unruptured-aneurysms-of-cavernous-and-ophthalmic-segment-of-internal-carotid-artery-with-flow-diverter-device-pipeline
#14
Marko Jevsek, Charbel Mounayer, Tomaz Seruga
BACKGROUND: Intra-arterial treatment of aneurysms by redirecting blood flow is a newer method. The redirection is based on a significantly more densely braided wire stent. The stent wall keeps the blood in the lumen of the stent and slows down the turbulent flow in the aneurysms. Stagnation of blood in the aneurysm sac leads to the formation of thrombus and subsequent exclusion of the aneurysm from the circulation. The aim of the study was to evaluate flow diverter device Pipeline for broad neck and giant aneurysm treatment...
December 1, 2016: Radiology and Oncology
https://www.readbyqxmd.com/read/27903644/a-reference-data-set-of-5-4-million-phased-human-variants-validated-by-genetic-inheritance-from-sequencing-a-three-generation-17-member-pedigree
#15
Michael A Eberle, Epameinondas Fritzilas, Peter Krusche, Morten Källberg, Benjamin L Moore, Mitchell A Bekritsky, Zamin Iqbal, Han-Yu Chuang, Sean J Humphray, Aaron L Halpern, Semyon Kruglyak, Elliott H Margulies, Gil McVean, David R Bentley
Improvement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalog of high-confidence variants called in a set of genomes for use as a benchmark. We generated deep, whole-genome sequence data of 17 individuals in a three-generation pedigree and called variants in each genome using a range of currently available algorithms. We used haplotype transmission information to create a phased "Platinum" variant catalog of 4.7 million single-nucleotide variants (SNVs) plus 0...
November 30, 2016: Genome Research
https://www.readbyqxmd.com/read/27902994/targeted-immunomodulatory-therapy-an-overview
#16
Ashley L Lefebvre, Laura McAuliffe
Monoclonal antibodies and other biologic response modifiers have allowed for targeted drug therapy in managing various autoimmune diseases. A number of immune pathways have been exploited in the development of targeted immunomodulatory therapies, including cytokine-directed therapies such as tumor necrosis factor-alpha and interleukins, integrins, B-cells, and co-stimulation modulators. With new targeted therapies in the pipeline, more options are becoming available for treatment of autoimmune diseases. [Full article available at http://rimed...
December 1, 2016: Rhode Island Medical Journal
https://www.readbyqxmd.com/read/27902792/rascaf-improving-genome-assembly-with-rna-sequencing-data
#17
Li Song, Dhruv S Shankar, Liliana Florea
Abundant but short second-generation sequencing reads make assembly difficult, leading to fragmented genomes and gene annotations. Gene structure information from RNA sequences can be used to improve the completeness and contiguity of an assembly, but bioinformatics methods have been lacking. Rascaf is a highly efficient tool leveraging long-range continuity information from intron spanning RNA sequencing (RNA-seq) read pairs to detect new contig connections. It determines a heaviest path in an exon block graph that simultaneously represents a gene and the underlying contig relationships...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27901159/a-portable-and-reconfigurable-multi-organ-platform-for-drug-development-with-onboard-microfluidic-flow-control
#18
J R Coppeta, M J Mescher, B C Isenberg, A J Spencer, E S Kim, A R Lever, T J Mulhern, R Prantil-Baun, J C Comolli, J T Borenstein
The drug development pipeline is severely limited by a lack of reliable tools for prediction of human clinical safety and efficacy profiles for compounds at the pre-clinical stage. Here we present the design and implementation of a platform technology comprising multiple human cell-based tissue models in a portable and reconfigurable format that supports individual organ function and crosstalk for periods of up to several weeks. Organ perfusion and crosstalk are enabled by a precision flow control technology based on electromagnetic actuators embedded in an arrayed format on a microfluidic platform...
November 30, 2016: Lab on a Chip
https://www.readbyqxmd.com/read/27900698/mining-microbial-signals-for-enhanced-biodiscovery-of-secondary-metabolites
#19
F Jerry Reen, Jose A Gutiérrez-Barranquero, Fergal O'Gara
The advent of metagenomics based biodiscovery has provided researchers with previously unforeseen access to the rich tapestry of natural bioactivity that exists in the biosphere. Unhindered by the "culturable bottleneck" that has severely limited the translation of the genetic potential that undoubtedly exists in nature, metagenomics nonetheless requires ongoing technological developments to maximize its efficacy and applicability to the discovery of new chemical entities.Here we describe methodologies for the detection and isolation of quorum sensing (QS) signal molecules from metagenomics libraries...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27899963/recent-perspectives-of-epithelial-ovarian-carcinoma
#20
Xiao-Ying Zhang, Pei-Ying Zhang
Epithelial ovarian tumours have been reported to mainly arise from the simple cuboidal surface epithelium of the ovary, and account for 75% of all ovarian tumours, and 90-95% of ovarian malignancies. Epithelial ovarian carcinoma (EOC) is responsible for the highest number of deaths in women due to gynecologic malignancy, with a low 5-year relative survival of only 44%. The possible reasons for these low survival rates are the high incidence of chemoresistance found with EOC and a lack of consideration of the high degree of heterogeneity of EOC in the current standard of care...
November 2016: Oncology Letters
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