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Computational cell biology

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https://www.readbyqxmd.com/read/28524227/computational-approaches-for-interpreting-scrna-seq-data
#1
REVIEW
R Rostom, V Svensson, S A Teichmann, G Kar
The recent developments in high throughput single-cell RNA sequencing technology (scRNA-seq) have enabled the generation of vast amounts of transcriptomic data at cellular resolution. With these advances come new modes of data analysis, building on high-dimensional data mining techniques. Here, we consider biological questions for which scRNA-seq data is used, both at a cell and gene level, and describe tools available for these types of analyses. This is an exciting and rapidly evolving field, where clustering, pseudotime inference, branching inference and gene-level analyses are particularly informative areas of computational analysis...
May 19, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28523006/virtual-plant-tissue-building-blocks-for-next-generation-plant-growth-simulation
#2
Dirk De Vos, Abdiravuf Dzhurakhalov, Sean Stijven, Przemyslaw Klosiewicz, Gerrit T S Beemster, Jan Broeckhove
Motivation: Computational modeling of plant developmental processes is becoming increasingly important. Cellular resolution plant tissue simulators have been developed, yet they are typically describing physiological processes in an isolated way, strongly delimited in space and time. Results: With plant systems biology moving toward an integrative perspective on development we have built the Virtual Plant Tissue (VPTissue) package to couple functional modules or models in the same framework and across different frameworks...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28521011/translation-initiation-events-on-structured-eukaryotic-mrnas-generate-gene-expression-noise
#3
Estelle Dacheux, Naglis Malys, Xiang Meng, Vinoy Ramachandran, Pedro Mendes, John Eg McCarthy
Gene expression stochasticity plays a major role in biology, creating non-genetic cellular individuality and influencing multiple processes, including differentiation and stress responses. We have addressed the lack of knowledge about posttranscriptional contributions to noise by determining cell-to-cell variations in the abundance of mRNA and reporter protein in yeast. Two types of structural element, a stem-loop and a poly(G) motif, not only inhibit translation initiation when inserted into an mRNA 5΄ untranslated region, but also generate noise...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520533/a-fully-automated-high-throughput-zebrafish-behavioral-ototoxicity-assay
#4
Douglas W Todd, Rohit C Philip, Maki Niihori, Ryan A Ringle, Kelsey R Coyle, Sobia F Zehri, Jordan A Mudery, Ross H Francis, Jeffrey J Rodriguez, Abraham Jacob
Zebrafish animal models lend themselves to behavioral assays that can facilitate rapid screening of ototoxic, otoprotective, and otoregenerative drugs. Structurally similar to human inner ear hair cells, the mechanosensory hair cells on their lateral line allow the zebrafish to sense water flow and orient head-to-current in a behavior called rheotaxis. This rheotaxis behavior deteriorates in a dose-dependent manner with increased exposure to the ototoxin cisplatin, thereby establishing itself as an excellent biomarker for anatomic damage to lateral line hair cells...
May 18, 2017: Zebrafish
https://www.readbyqxmd.com/read/28515787/a-computational-approach-for-the-functional-classification-of-the-epigenome
#5
Francesco Gandolfi, Anna Tramontano
BACKGROUND: In the last decade, advanced functional genomics approaches and deep sequencing have allowed large-scale mapping of histone modifications and other epigenetic marks, highlighting functional relationships between chromatin organization and genome function. Here, we propose a novel approach to explore functional interactions between different epigenetic modifications and extract combinatorial profiles that can be used to annotate the chromatin in a finite number of functional classes...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28511910/synthesis-and-biological-research-of-novel-azaacridine-derivatives-as-potent-dna-binding-ligands-and-topoisomerase-ii-inhibitors
#6
Dan Li, Zigao Yuan, Shaopeng Chen, Cunlong Zhang, Lu Song, Chunmei Gao, Yuzong Chen, Chunyan Tan, Yuyang Jiang
DNA and DNA-related enzymes are one of the most effective and common used intracellular anticancer targets in clinic and laboratory studies, however, most of DNA-targeting drugs suffered from toxic side effects. Development of new molecules with good antitumor activity and low side effects is important. Based on computer aided design and our previous studies, a series of novel azaacridine derivatives were synthesized as DNA and topoisomerases binding agents, among which compound 9 displayed the best antiproliferative activity with an IC50 value of 0...
May 4, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28510023/protein-rna-interactions-structural-biology-and-computational-modeling-techniques
#7
REVIEW
Susan Jones
RNA-binding proteins are functionally diverse within cells, being involved in RNA-metabolism, translation, DNA damage repair, and gene regulation at both the transcriptional and post-transcriptional levels. Much has been learnt about their interactions with RNAs through structure determination techniques and computational modeling. This review gives an overview of the structural data currently available for protein-RNA complexes, and discusses the technical issues facing structural biologists working to solve their structures...
December 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28508359/evolving-relevance-of-neuroproteomics-in-alzheimer-s-disease
#8
Simone Lista, Henrik Zetterberg, Sid E O'Bryant, Kaj Blennow, Harald Hampel
Substantial progress in the understanding of the biology of Alzheimer's disease (AD) has been achieved over the past decades. The early detection and diagnosis of AD and other age-related neurodegenerative diseases, however, remain a challenging scientific frontier. Therefore, the comprehensive discovery (relating to all individual, converging or diverging biochemical disease mechanisms), development, validation, and qualification of standardized biological markers with diagnostic and prognostic functions with a precise performance profile regarding specificity, sensitivity, and positive and negative predictive value are warranted...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28504946/essential-protein-detection-by-random-walk-on-weighted-protein-protein-interaction-networks
#9
Bin Xu, Jihong Guan, Yang Wang, Zewei Wang
Essential proteins are critical to the development and survival of cells. Identification of essential proteins is helpful for understanding the minimal set of required genes in a living cell and for designing new drugs. To detect essential proteins, various computational methods have been proposed based on protein-protein interaction (PPI) networks. However, protein interaction data obtained by highthroughput experiments usually contain high false positives, which negatively impacts the accuracy of essential protein detection...
May 12, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28504682/testing-for-differential-abundance-in-mass-cytometry-data
#10
Aaron T L Lun, Arianne C Richard, John C Marioni
When comparing biological conditions using mass cytometry data, a key challenge is to identify cellular populations that change in abundance. Here, we present a computational strategy for detecting 'differentially abundant' populations by assigning cells to hyperspheres, testing for significant differences between conditions and controlling the spatial false discovery rate. Our method (http://bioconductor.org/packages/cydar) outperforms other approaches in simulations and finds novel patterns of differential abundance in real data...
May 15, 2017: Nature Methods
https://www.readbyqxmd.com/read/28500031/labeling-glycans-on-living-cells-by-a-chemoenzymatic-glycoengineering-approach
#11
Ruben T Almaraz, Yanhong Li
Structural glycobiology has traditionally been a challenging field due to a limited set of tools available to investigate the diverse and complexity of Glycan molecules. However, we cannot ignore that glycans play critical roles in health as well as in disease, are present in more than 50% of all proteins and on over 80% of all surface proteins. Chemoenzymatic Glycoengineering (CEG) methods are a powerful set of tools to synthesize complex glycans but its full potential has not been explored in cell biology yet...
May 12, 2017: Biology Open
https://www.readbyqxmd.com/read/28499168/novel-imidazo-4-5-c-1-2-6-thiadiazine-2-2-dioxides-as-antiproliferative-trypanosoma-cruzi-drugs-computational-screening-from-neural-network-synthesis-and-in%C3%A2-vivo-biological-properties
#12
Angela Guerra, Pedro Gonzalez-Naranjo, Nuria E Campillo, Javier Varela, María L Lavaggi, Alicia Merlino, Hugo Cerecetto, Mercedes González, Alicia Gomez-Barrio, José A Escario, Cristina Fonseca-Berzal, Gloria Yaluf, Jorge Paniagua-Solis, Juan A Páez
A new family of imidazo[4,5-c][1,2,6]thiadiazine 2,2-dioxide with antiproliferative Trypanosoma cruzi properties was identified from a neural network model published by our group. The synthesis and evaluation of this new class of trypanocidal agents are described. These compounds inhibit the growth of Trypanosoma cruzi, comparable with benznidazole or nifurtimox. In vitro assays were performed to study their effects on the growth of the epimastigote form of the Tulahuen 2 strain, as well as the epimastigote and amastigote forms of CL clone B5 of Trypanosoma cruzi...
May 1, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28498871/towards-implementation-of-cellular-automata-in-microbial-fuel-cells
#13
Michail-Antisthenis I Tsompanas, Andrew Adamatzky, Georgios Ch Sirakoulis, John Greenman, Ioannis Ieropoulos
The Microbial Fuel Cell (MFC) is a bio-electrochemical transducer converting waste products into electricity using microbial communities. Cellular Automaton (CA) is a uniform array of finite-state machines that update their states in discrete time depending on states of their closest neighbors by the same rule. Arrays of MFCs could, in principle, act as massive-parallel computing devices with local connectivity between elementary processors. We provide a theoretical design of such a parallel processor by implementing CA in MFCs...
2017: PloS One
https://www.readbyqxmd.com/read/28497009/false-positive-positron-emission-tomography-computed-tomography-scans-in-treated-head-and-neck-cancers
#14
Michael K Cheung, Shawn Y Ong, Uma Goyal, Betsy C Wertheim, Charles C Hsu, Sun K Yi
OBJECTIVE: Positron emission tomography/computed tomography (PET/CT) imaging for head and neck cancers (HNC) is commonly utilized for post-treatment assessment. Though PET/CT in this setting has been reported to have high negative predictive values (> 90%), positive predictive values have been reported at approximately 50%, leading to high rates of false positivity (FP) and troubling management decisions for both patient and practitioner. The objective of this study was to identify patient, disease, treatment and imaging factors that might be associated with a higher likelihood of FP on initial post-treatment PET/CT imaging for patients treated for HNC...
April 10, 2017: Curēus
https://www.readbyqxmd.com/read/28494968/bistability-and-nonmonotonic-induction-of-the-lac-operon-in-the-natural-lactose-uptake-system
#15
Dominique Zander, Daniel Samaga, Ronny Straube, Katja Bettenbrock
The Escherichia coli lac operon is regulated by a positive feedback loop whose potential to generate an all-or-none response in single cells has been a paradigm for bistable gene expression. However, so far bistable lac induction has only been observed using gratuitous inducers, raising the question about the biological relevance of bistable lac induction in the natural setting with lactose as the inducer. In fact, the existing experimental evidence points to a graded rather than an all-or-none response in the natural lactose uptake system...
May 9, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28494433/electrospun-ultrathin-pbat-nhap-fibers-influenced-the-in-vitro-and-in-vivo-osteogenesis-and-improved-the-mechanical-properties-of-neoformed-bone
#16
Gabriela F Santana-Melo, Bruno V M Rodrigues, Edmundo da Silva, Ritchelli Ricci, Fernanda R Marciano, Thomas J Webster, Luana M R Vasconcellos, Anderson O Lobo
Combining polyester scaffolds with synthetic nanohydroxyapatite (nHAp), which is bioactive and osteoconductive, is a plausible strategy to improve bone regeneration. Here, we propose the combination of PBAT [poly(butylene-adipate-co-terephthalate)] and synthetic nHAp (at 3 and 5wt%). PBAT is a relatively a new polymer with low crystallinity and attractive biodegradability and mechanical properties for orthopedic applications, however, with a still underexplored potential for in vivo applications. Then, we performed a careful biological in vitro and in vivo set of experiments to evaluate the influence of PBAT containing two different nHAp loads...
April 27, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28494185/functional-analysis-of-rare-variants-in-mismatch-repair-proteins-augments-results-from-computation-based-predictive-methods
#17
Sanjeevani Arora, Peter J Huwe, Rahmat Sikder, Manali Shah, Amanda J Browne, Randy Lesh, Emmanuelle Nicolas, Sanat Deshpande, Michael J Hall, Roland L Dunbrack, Erica A Golemis
The cancer-predisposing Lynch Syndrome (LS) arises from germline mutations in DNA mismatch repair (MMR) genes, predominantly MLH1, MSH2, MSH6,and PMS2. A major challenge for clinical diagnosis of LS is the frequent identification of variants of uncertain significance (VUS) in these genes, as it is often difficult to determine variant pathogenicity, particularly for missense variants. Generic programs such as SIFT and PolyPhen-2, and MMR gene-specific programs such as PON-MMR and MAPP-MMR, are often used to predict deleterious or neutral effects of VUS in MMR genes...
May 11, 2017: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/28493881/shinyheatmap-ultra-fast-low-memory-heatmap-web-interface-for-big-data-genomics
#18
Bohdan B Khomtchouk, James R Hennessy, Claes Wahlestedt
BACKGROUND: Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets, especially across single-cell sequencing studies. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well as programming acumen. Since heatmaps are used to depict high-dimensional numerical data as a colored grid of cells, efficiency and speed have often proven to be critical considerations in the process of successfully converting data into graphics...
2017: PloS One
https://www.readbyqxmd.com/read/28492659/ensemble-clustering-of-phosphoproteomic-data-identifies-differences-in-protein-interactions-and-cell-cell-junction-integrity-of-her2-overexpressing-cells
#19
Katherine E Schaberg, Venktesh S Shirure, Elizabeth A Worley, Steven C George, Kristen M Naegle
Overexpression of HER2, a receptor tyrosine kinase of the ERBB family, in breast cancer is related to increased cancer progression and aggressiveness. A breast epithelial cell model with the single perturbation of HER2 overexpression is capable of replicating the increased aggressiveness of HER2 overexpressing cancers. In previous work, Wolf-Yadlin and colleagues (Wolf-Yadlin et al., Mol. Syst. Biol., 2006, 2) measured the proximal tyrosine phosphorylation dynamics of the parental and HER2 overexpressing cells (24H) in response to EGF...
May 11, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28487402/biological-functions-controlled-by-manganese-redox-changes-in-mononuclear-mn-dependent-enzymes
#20
REVIEW
Wen Zhu, Nigel G J Richards
Remarkably few enzymes are known to employ a mononuclear manganese ion that undergoes changes in redox state during catalysis. Many questions remain to be answered about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II), the nature of the dioxygen species involved in the catalytic mechanism, and how these enzymes acquire Mn(II) given that many other metal ions in the cell form more stable protein complexes. Here, we summarize current knowledge concerning the structure and mechanism of five mononuclear manganese-dependent enzymes: superoxide dismutase, oxalate oxidase (OxOx), oxalate decarboxylase (OxDC), homoprotocatechuate 3,4-dioxygenase, and lipoxygenase (LOX)...
May 9, 2017: Essays in Biochemistry
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