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Computational and Structural Biotechnology Journal

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https://www.readbyqxmd.com/read/30214695/intermediate-levels-of-antibiotics-may-increase-diversity-of-colony-size-phenotype-in-bacteria
#1
Lewis Lee, Van M Savage, Pamela J Yeh
Antibiotics select for resistant bacteria whose existence and emergence is more likely in populations with high phenotypic and genetic diversity. Identifying the mechanisms that generate this diversity can thus have clinical consequences for drug-resistant pathogens. We show here that intermediate levels of antibiotics are associated with higher levels of phenotypic diversity in size of colony forming units (cfus), within a single bacterial population. We examine experimentally thousands of populations of bacteria subjected to different disturbance levels that are created by varying antibiotic concentrations...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30181841/advances-in-human-placental-biomechanics
#2
REVIEW
R Plitman Mayo
Pregnancy complications are a major clinical concern due to the related maternal and fetal morbidity. Many are caused through defective placentation, but research into placental function is difficult, principally because of the ethical limitations associated with the in-vivo organ and the difficulty of extrapolating animal models. Perfused by two separate circulations, the maternal and fetal bloodstreams, the placenta has a unique structure and performs multiple complex functions. Three-dimensional imaging and computational modelling are becoming popular tools to investigate the morphology and physiology of this organ...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30181840/a-blockchain-based-notarization-service-for-biomedical-knowledge-retrieval
#3
Athina-Styliani Kleinaki, Petros Mytis-Gkometh, George Drosatos, Pavlos S Efraimidis, Eleni Kaldoudi
Biomedical research and clinical decision depend increasingly on scientific evidence realized by a number of authoritative databases, mostly public and continually enriched via peer scientific contributions. Given the dynamic nature of biomedical evidence data and their usage in the sensitive domain of biomedical science, it is important to ensure retrieved data integrity and non-repudiation. In this work, we present a blockchain-based notarization service that uses smart digital contracts to seal a biomedical database query and the respective results...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30128085/biophysics-of-tumor-microenvironment-and-cancer-metastasis-a-mini-review
#4
REVIEW
Bashar Emon, Jessica Bauer, Yasna Jain, Barbara Jung, Taher Saif
The role of tumor microenvironment in cancer progression is gaining significant attention. It is realized that cancer cells and the corresponding stroma co-evolve with time. Cancer cells recruit and transform the stromal cells, which in turn remodel the extra cellular matrix of the stroma. This complex interaction between the stroma and the cancer cells results in a dynamic feed-forward/feed-back loop with biochemical and biophysical cues that assist metastatic transition of the cancer cells. Although biochemistry has long been studied for the understanding of cancer progression, biophysical signaling is emerging as a critical paradigm determining cancer metastasis...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30108685/fhirchain-applying-blockchain-to-securely-and-scalably-share-clinical-data
#5
Peng Zhang, Jules White, Douglas C Schmidt, Gunther Lenz, S Trent Rosenbloom
Secure and scalable data sharing is essential for collaborative clinical decision making. Conventional clinical data efforts are often siloed, however, which creates barriers to efficient information exchange and impedes effective treatment decision made for patients. This paper provides four contributions to the study of applying blockchain technology to clinical data sharing in the context of technical requirements defined in the "Shared Nationwide Interoperability Roadmap" from the Office of the National Coordinator for Health Information Technology (ONC)...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30105090/in-silico-prediction-of-large-scale-microbial-production-performance-constraints-for-getting-proper-data-driven-models
#6
REVIEW
Julia Zieringer, Ralf Takors
Industrial bioreactors range from 10.000 to 700.000 L and characteristically show different zones of substrate availabilities, dissolved gas concentrations and pH values reflecting physical, technical and economic constraints of scale-up. Microbial producers are fluctuating inside the bioreactors thereby experiencing frequently changing micro-environmental conditions. The external stimuli induce responses on microbial metabolism and on transcriptional regulation programs. Both may deteriorate the expected microbial production performance in large scale compared to expectations deduced from ideal, well-mixed lab-scale conditions...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30105089/mechanical-and-systems-biology-of-cancer
#7
REVIEW
Fabian Spill, Chris Bakal, Michael Mak
Mechanics and biochemical signaling are both often deregulated in cancer, leading toincreased cell invasiveness, proliferation, and survival. The dynamics and interactions of cytoskeletal components control basic mechanical properties, such as cell tension, stiffness, and engagement with the extracellular environment, which can lead to extracellular matrix remodeling. Intracellular mechanics can alter signaling and transcription factors, impacting cell decision making. Additionally, signaling from soluble and mechanical factors in the extracellular environment, such as substrate stiffness and ligand density, can modulate cytoskeletal dynamics...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30101004/authenticating-health-activity-data-using-distributed-ledger-technologies
#8
James Brogan, Immanuel Baskaran, Navin Ramachandran
The on-demand digital healthcare ecosystem is on the near horizon. It has the potential to extract a wealth of information from "big data" collected at the population level, to enhance preventive and precision medicine at the patient level. This may improve efficiency and quality while decreasing cost of healthcare delivered by professionals. However, there are still security and privacy issues that need to be addressed before algorithms, data, and models can be mobilized safely at scale. In this paper we discuss how distributed ledger technologies can play a key role in advancing electronic health, by ensuring authenticity and integrity of data generated by wearable and embedded devices...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30069285/a-family-of-novel-cyclophilins-conserved-in-the-mimivirus-genus-of-the-giant-dna-viruses
#9
REVIEW
Sailen Barik
The cyclophilin (abbreviated here as CYN) family represents a large group of protein prolyl isomerase (PPIase), many of which are also chaperones that promote proper folding of a large variety of client proteins. Over the past few years, megaviruses with giant DNA genomes were discovered and placed in the order Megavirales . Recently, the first complete genome sequence of Acanthamoebaae polyphaga mimivirus, a member of the Mimiviridae family of the Megavirales order, revealed a novel CYN that lacked PPIase activity and contained unique peptide insertions...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30069284/blockchain-technology-for-healthcare-facilitating-the-transition-to-patient-driven-interoperability
#10
REVIEW
William J Gordon, Christian Catalini
Interoperability in healthcare has traditionally been focused around data exchange between business entities, for example, different hospital systems. However, there has been a recent push towards patient-driven interoperability, in which health data exchange is patient-mediated and patient-driven. Patient-centered interoperability, however, brings with it new challenges and requirements around security and privacy, technology, incentives, and governance that must be addressed for this type of data sharing to succeed at scale...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30069283/following-ribosome-footprints-to-understand-translation-at-a-genome-wide-level
#11
REVIEW
Guillermo Eastman, Pablo Smircich, José R Sotelo-Silveira
Protein translation is a key step in gene expression. The development of Ribosome Profiling has allowed the global analysis of this process at sub-codon resolution. In the last years the method has been applied to several models ranging from bacteria to mammalian cells yielding a surprising amount of insight on the mechanism and the regulation of translation. In this review we describe the key aspects of the experimental protocol and comment on the main conclusions raised in different models.
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30050664/functional-prediction-of-hypothetical-transcription-factors-of-escherichia-coli-k-12-based-on-expression-data
#12
Emanuel Flores-Bautista, Carenne Ludeña Cronick, Anny Rodriguez Fersaca, Mario Alberto Martinez-Nuñez, Ernesto Perez-Rueda
The repertoire of 304 DNA-binding transcription factors (TFs) in Escherichia coli K-12 has been described recently, with 196 TFs experimentally characterized and 108 proteins predicted by sequence comparisons. Based on 303 expression profile patterns retrieved from the Colombos database 12 clusters were identified, including hypothetical and experimentally characterized TFs, using a spectral clustering algorithm based on a 3NN graph built using 14 principal components that represent 65% of the variance of the expression data...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30026889/current-perspectives-of-the-chicken-gastrointestinal-tract-and-its-microbiome
#13
REVIEW
Daniel Borda-Molina, Jana Seifert, Amélia Camarinha-Silva
The microbial communities inhabiting the gastrointestinal tract (GIT) of chickens are essential for the gut homeostasis, the host metabolism and affect the animals' physiology and health. They play an important role in nutrient digestion, pathogen inhibition and interact with the gut-associated immune system. Throughout the last years high-throughput sequencing technologies have been used to analyze the bacterial communities that colonize the different sections of chickens' gut. The most common methodologies are targeted amplicon sequencing followed by metagenome shotgun sequencing as well as metaproteomics aiming at a broad range of topics such as dietary effects, animal diseases, bird performance and host genetics...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30026888/prediction-of-dyslipidemia-using-gene-mutations-family-history-of-diseases-and-anthropometric-indicators-in-children-and-adolescents-the-caspian-iii-study
#14
Hamid R Marateb, Mohammad Reza Mohebian, Shaghayegh Haghjooy Javanmard, Amir Ali Tavallaei, Mohammad Hasan Tajadini, Motahar Heidari-Beni, Miguel Angel Mañanas, Mohammad Esmaeil Motlagh, Ramin Heshmat, Marjan Mansourian, Roya Kelishadi
Dyslipidemia, the disorder of lipoprotein metabolism resulting in high lipid profile, is an important modifiable risk factor for coronary heart diseases. It is associated with more than four million worldwide deaths per year. Half of the children with dyslipidemia have hyperlipidemia during adulthood, and its prediction and screening are thus critical. We designed a new dyslipidemia diagnosis system. The sample size of 725 subjects (age 14.66 ± 2.61 years; 48% male; dyslipidemia prevalence of 42%) was selected by multistage random cluster sampling in Iran...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30026887/highlighting-clinical-metagenomics-for-enhanced-diagnostic-decision-making-a-step-towards-wider-implementation
#15
REVIEW
Jessica D Forbes, Natalie C Knox, Christy-Lynn Peterson, Aleisha R Reimer
Clinical metagenomics (CMg) is the discipline that refers to the sequencing of all nucleic acid material present within a clinical specimen with the intent to recover clinically relevant microbial information. From a diagnostic perspective, next-generation sequencing (NGS) offers the ability to rapidly identify putative pathogens and predict their antimicrobial resistance profiles to optimize targeted treatment regimens. Since the introduction of metagenomics nearly a decade ago, numerous reports have described successful applications in an increasing variety of biological specimens, such as respiratory secretions, cerebrospinal fluid, stool, blood and tissue...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30002791/lung-cancer-therapy-targeting-histone-methylation-opportunities-and-challenges
#16
REVIEW
Yuchen Chen, Xinran Liu, Yangkai Li, Chuntao Quan, Ling Zheng, Kun Huang
Lung cancer is one of the most common malignancies. In spite of the progress made in past decades, further studies to improve current therapy for lung cancer are required. Dynamically controlled by methyltransferases and demethylases, methylation of lysine and arginine residues on histone proteins regulates chromatin organization and thereby gene transcription. Aberrant alterations of histone methylation have been demonstrated to be associated with the progress of multiple cancers including lung cancer. Inhibitors of methyltransferases and demethylases have exhibited anti-tumor activities in lung cancer, and multiple lead candidates are under clinical trials...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30002790/taxonomy-and-evolution-of-aspergillus-penicillium-and-talaromyces-in-the-omics-era-past-present-and-future
#17
REVIEW
Chi-Ching Tsang, James Y M Tang, Susanna K P Lau, Patrick C Y Woo
Aspergillus , Penicillium and Talaromyces are diverse, phenotypically polythetic genera encompassing species important to the environment, economy, biotechnology and medicine, causing significant social impacts. Taxonomic studies on these fungi are essential since they could provide invaluable information on their evolutionary relationships and define criteria for species recognition. With the advancement of various biological, biochemical and computational technologies, different approaches have been adopted for the taxonomy of Aspergillus , Penicillium and Talaromyces ; for example, from traditional morphotyping, phenotyping to chemotyping (e...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/30002789/protein-sequences-recapitulate-genetic-code-evolution
#18
Hervé Seligmann
Several hypotheses predict ranks of amino acid assignments to genetic code's codons. Analyses here show that average positions of amino acid species in proteins correspond to assignment ranks, in particular as predicted by Juke's neutral mutation hypothesis for codon assignments. In all tested protein groups, including co- and post-translationally folding proteins, 'recent' amino acids are on average closer to gene 5' extremities than 'ancient' ones. Analyses of pairwise residue contact energies matrices suggest that early amino acids stereochemically selected late ones that stablilize residue interactions within protein cores, presumably producing 5'-late-to-3'-early amino acid protein sequence gradients...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29977482/corrigendum-to-a-gene-module-based-eqtl-analysis-prioritizing-disease-genes-and-pathways-in-kidney-cancer
#19
M Q Yang, D Li, W Yang, Y Zhang, J Liu, W Tong
[This corrects the article DOI: 10.1016/j.csbj.2017.09.003.].
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29977481/ctdna-and-ctcs-in-liquid-biopsy-current-status-and-where-we-need-to-progress
#20
REVIEW
Martin H D Neumann, Sebastian Bender, Thomas Krahn, Thomas Schlange
We discuss the current status of liquid biopsy and its advantages and challenges with a focus on pre-analytical sample handling, technologies and workflows. The potential of circulating tumor cells and circulating tumor DNA is pointed out and an overview of corresponding technologies is given.
2018: Computational and Structural Biotechnology Journal
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