keyword
MENU ▼
Read by QxMD icon Read
search

Computational cell biology

keyword
https://www.readbyqxmd.com/read/27914063/episweep-computationally-driven-reengineering-of-therapeutic-proteins-to-reduce-immunogenicity-while-maintaining-function
#1
Yoonjoo Choi, Deeptak Verma, Karl E Griswold, Chris Bailey-Kellogg
Therapeutic proteins are yielding ever more advanced and efficacious new drugs, but the biological origins of these highly effective therapeutics render them subject to immune surveillance within the patient's body. When recognized by the immune system as a foreign agent, protein drugs elicit a coordinated response that can manifest a range of clinical complications including rapid drug clearance, loss of functionality and efficacy, delayed infusion-like allergic reactions, more serious anaphylactic shock, and even induced auto-immunity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27911038/quantitating-the-cell-turning-images-into-numbers-with-imagej
#2
REVIEW
Ellen T Arena, Curtis T Rueden, Mark C Hiner, Shulei Wang, Ming Yuan, Kevin W Eliceiri
Modern biological research particularly in the fields of developmental and cell biology has been transformed by the rapid evolution of the light microscope. The light microscope, long a mainstay of the experimental biologist, is now used for a wide array of biological experimental scenarios and sample types. Much of the great developments in advanced biological imaging have been driven by the digital imaging revolution with powerful processors and algorithms. In particular, this combination of advanced imaging and computational analysis has resulted in the drive of the modern biologist to not only visually inspect dynamic phenomena, but to quantify the involved processes...
December 2, 2016: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/27909575/a-step-by-step-workflow-for-low-level-analysis-of-single-cell-rna-seq-data
#3
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/27903820/agent-based-modelling-in-synthetic-biology
#4
REVIEW
Thomas E Gorochowski
Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903590/anterior-cruciate-ligament-derived-stem-cells-transduced-with-bmp2-accelerate-graft-bone-integration-after-acl-reconstruction
#5
Yohei Kawakami, Koji Takayama, Tomoyuki Matsumoto, Ying Tang, Bing Wang, Yutaka Mifune, James H Cummins, Ryan J Warth, Ryosuke Kuroda, Masahiro Kurosaka, Freddie H Fu, Johnny Huard
BACKGROUND: Strong graft-bone integration is a prerequisite for successful graft remodeling after reconstruction of the anterior cruciate ligament (ACL) using soft tissue grafts. Novel strategies to accelerate soft tissue graft-bone integration are needed to reduce the need for bone-tendon-bone graft harvest, reduce patient convalescence, facilitate rehabilitation, and reduce total recovery time after ACL reconstruction. HYPOTHESIS: The application of ACL-derived stem cells with enhanced expression of bone morphogenetic protein 2 (BMP2) onto soft tissue grafts in the form of cell sheets will both accelerate and improve the quality of graft-bone integration after ACL reconstruction in a rat model...
November 30, 2016: American Journal of Sports Medicine
https://www.readbyqxmd.com/read/27902924/simple-mechanisms-of-early-life-simulation-model-on-the-origin-of-semi-cells
#6
Adrian Klein, Martin Bock, Wolfgang Alt
The development of first cellular structures played an important role in the early evolution of life. Early evolution of life probably took place on a molecular level in a reactive environment. The iron-sulfur theory postulates the formation of cell-like structures on catalytic surfaces. Experiments show that H2S together with FeS and other metallic centers drive auto-catalytic surface reactions, in which organic molecules such as pyruvic and amino acids occur. It is questionable which mechanisms are needed to form cell-like structures under these conditions...
November 27, 2016: Bio Systems
https://www.readbyqxmd.com/read/27901061/inter-individual-variability-and-modeling-of-electrical-activity-a-possible-new-approach-to-explore-cardiac-safety
#7
Jean-Yves Le Guennec, Jérôme Thireau, Aude Ouillé, Julien Roussel, Jérôme Roy, Serge Richard, Sylvain Richard, Eric Martel, Pascal Champéroux
Safety pharmacology aims to predict rare side effects of new drugs. We explored whether rare pro-arrhythmic effects could be linked to the variability of the effects of these drugs on ion currents and whether taking into consideration this variability in computational models could help to better detect and predict cardiac side effects. For this purpose, we evaluated how intra- and inter-individual variability influences the effect of hERG inhibition on both the action potential duration and the occurrence of arrhythmias...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900575/glycosaminoglycanomics-where-we-are
#8
Sylvie Ricard-Blum, Frédérique Lisacek
Glycosaminoglycans regulate numerous physiopathological processes such as development, angiogenesis, innate immunity, cancer and neurodegenerative diseases. Cell surface GAGs are involved in cell-cell and cell-matrix interactions, cell adhesion and signaling, and host-pathogen interactions. GAGs contribute to the assembly of the extracellular matrix and heparan sulfate chains are able to sequester growth factors in the ECM. Their biological activities are regulated by their interactions with proteins. The structural heterogeneity of GAGs, mostly due to chemical modifications occurring during and after their synthesis, makes the development of analytical techniques for their profiling in cells, tissues, and biological fluids, and of computational tools for mining GAG-protein interaction data very challenging...
November 30, 2016: Glycoconjugate Journal
https://www.readbyqxmd.com/read/27897006/session-introduction
#9
Nikolay Samusik, Nima Aghaeepour, Sean Bendall
Recent technological developments allow gathering single-cell measurements across different domains (genomic, transcriptomics, proteomics, imaging etc). Sophisticated computational algorithms are required in order to harness the power of single-cell data. This session is dedicated to computational methods for single-cell analysis in various biological domains, modelling of population heterogeneity, as well as translational applications of single cell data.
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27897001/differential-pathway-dependency-discovery-associated-with-drug-response-across-cancer-cell-lines
#10
Gil Speyer, Divya Mahendra, Hai J Tran, Jeff Kiefer, Stuart L Schreiber, Paul A Clemons, Harshil Dhruv, Michael Berens, Seungchan Kim
The effort to personalize treatment plans for cancer patients involves the identification of drug treatments that can effectively target the disease while minimizing the likelihood of adverse reactions. In this study, the gene-expression profile of 810 cancer cell lines and their response data to 368 small molecules from the Cancer Therapeutics Research Portal (CTRP) are analyzed to identify pathways with significant rewiring between genes, or differential gene dependency, between sensitive and non-sensitive cell lines...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27894336/curcumin-and-long-chain-omega-3-polyunsaturated-fatty-acids-for-prevention-of-type-2-diabetes-cop-d-study-protocol-for-a-randomised-controlled-trial
#11
Rohith N Thota, Shamasunder H Acharya, Kylie A Abbott, Manohar L Garg
BACKGROUND: Lifestyle interventions, including increase in physical activity and dietary counselling, have shown the ability to prevent type 2 diabetes (T2D) in high-risk state individuals, but the prevalence is still skyrocketing in Australia, in line with global prevalence. Currently, no medicines are approved by the Therapeutic Goods Administration in Australia for the management of prediabetes. Therefore, there is a need of developing a safer, biologically efficacious and cost-effective alternative for delaying the transition of individual health state from prediabetes into T2D...
November 29, 2016: Trials
https://www.readbyqxmd.com/read/27891096/systematic-characterization-of-dynamic-parameters-of-intracellular-calcium-signals
#12
Laurent Mackay, Nicholas Mikolajewicz, Svetlana V Komarova, Anmar Khadra
Dynamic processes, such as intracellular calcium signaling, are hallmark of cellular biology. As real-time imaging modalities become widespread, a need for analytical tools to reliably characterize time-series data without prior knowledge of the nature of the recordings becomes more pressing. The goal of this study is to develop a signal-processing algorithm for MATLAB that autonomously computes the parameters characterizing prominent single transient responses (TR) and/or multi-peaks responses (MPR). The algorithm corrects for signal contamination and decomposes experimental recordings into contributions from drift, TRs, and MPRs...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27888928/analytical-prediction-of-sub-surface-thermal-history-in-translucent-tissue-phantoms-during-plasmonic-photo-thermotherapy-pptt
#13
Purbarun Dhar, Anup Paul, Arunn Narasimhan, Sarit K Das
Knowledge of thermal history and/or distribution in biological tissues during laser based hyperthermia is essential to achieve necrosis of tumour/carcinoma cells. A semi-analytical model to predict sub-surface thermal distribution in translucent, soft, tissue mimics has been proposed. The model can accurately predict the spatio-temporal temperature variations along depth and the anomalous thermal behaviour in such media, viz. occurrence of sub-surface temperature peaks. Based on optical and thermal properties, the augmented temperature and shift of the peak positions in case of gold nanostructure mediated tissue phantom hyperthermia can be predicted...
December 2016: Journal of Thermal Biology
https://www.readbyqxmd.com/read/27887656/looking-beyond-the-cancer-cell-for-effective-drug-combinations
#14
Jonathan R Dry, Mi Yang, Julio Saez-Rodriguez
Combinations of therapies are being actively pursued to expand therapeutic options and deal with cancer's pervasive resistance to treatment. Research efforts to discover effective combination treatments have focused on drugs targeting intracellular processes of the cancer cells and in particular on small molecules that target aberrant kinases. Accordingly, most of the computational methods used to study, predict, and develop drug combinations concentrate on these modes of action and signaling processes within the cancer cell...
November 25, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27887644/copenhagen-comorbidity-in-hiv-infection-cocomo-study-a-study-protocol-for-a-longitudinal-non-interventional-assessment-of-non-aids-comorbidity-in-hiv-infection-in-denmark
#15
Andreas Ronit, Judith Haissman, Ditte Marie Kirkegaard-Klitbo, Thomas Skårup Kristensen, Anne-Mette Lebech, Thomas Benfield, Jan Gerstoft, Henrik Ullum, Lars Køber, Andreas Kjær, Klaus Kofoed, Jørgen Vestbo, Børge Nordestgaard, Jens Lundgren, Susanne Dam Nielsen
BACKGROUND: Modern combination antiretroviral therapy (cART) has improved survival for people living with HIV (PLWHIV). Non-AIDS comorbidities have replaced opportunistic infections as leading causes of mortality and morbidity, and are becoming a key health concern as this population continues to age. The aim of this study is to estimate the prevalence and incidence of non-AIDS comorbidity among PLWHIV in Denmark in the cART era and to determine risk factors contributing to the pathogenesis...
November 26, 2016: BMC Infectious Diseases
https://www.readbyqxmd.com/read/27885191/-modeling-and-simulation-of-trabecular-pattern-formation-in-a-cancellous-bone-defect-under-mechanical-forces
#16
Taiji Adachi
Understanding regeneration of the trabecular structure in cancellous bone defects is an important issue in bone tissue engineering and regenerative medicine. Biochemical and biomechanical viewpoints are indispensable for understanding the fundamental mechanism that underlies the regeneration of the trabecular structure. In vitro observations of the Turing pattern-like bone differentiation into osteoblasts from human mesenchymal stem cells suggest that mathematical modeling and simulation based on a reaction-diffusion system model would help us to understand the mechanism of trabecular pattern formation during cancellous bone regeneration...
2016: Clinical Calcium
https://www.readbyqxmd.com/read/27879272/quantification-of-pathway-crosstalk-reveals-novel-synergistic-drug-combinations-for-breast-cancer
#17
Samira Jaeger, Ana Igea, Rodrigo Arroyo, Victor Alcalde, Begoña Canovas, Modesto Orozco, Angel R Nebreda, Patrick Aloy
Combinatorial therapeutic approaches are an imperative to improve cancer treatment, since it is critical to impede compensatory signaling mechanisms that can engender drug resistance to individual targeted drugs. Currently approved drug combinations result largely from empirical clinical experience and cover only a small fraction of a vast therapeutic space. Here we present a computational network biology approach, based on pathway crosstalk inhibition, to discover new synergistic drug combinations for breast cancer treatment...
November 22, 2016: Cancer Research
https://www.readbyqxmd.com/read/27875779/novel-pyrimidine-2-4-dione-1-2-3-triazole-and-furo-2-3-d-pyrimidine-2-one-1-2-3-triazole-hybrids-as-potential-anti-cancer-agents-synthesis-computational-and-x-ray-analysis-and-biological-evaluation
#18
Tomislav Gregorić, Mirela Sedić, Petra Grbčić, Andrea Tomljenović Paravić, Sandra Kraljević Pavelić, Mario Cetina, Robert Vianello, Silvana Raić-Malić
Regioselective 1,4-disubstituted 1,2,3-triazole tethered pyrimidine-2,4-dione derivatives (5-23) were successfully prepared by the copper(I)-catalyzed click chemistry. While known palladium/copper-cocatalyzed method based on Sonogashira cross-coupling followed by the intramolecular 5-endo-dig ring closure generated novel 6-alkylfuro[2,3-d]pyrimidine-2-one-1,2,3-triazole hybrids (24b-37b), a small library of their 5-alkylethynyl analogs (24a-37a) was synthesized and described for the first time by tandem terminal alkyne dimerization and subsequent 5-endo-trig cyclization, which was additionally corroborated with computational and X-ray crystal structure analyses...
November 14, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27874013/crystal-structure-of-fabz-acp-complex-reveals-a-dynamic-seesaw-like-catalytic-mechanism-of-dehydratase-in-fatty-acid-biosynthesis
#19
Lin Zhang, Jianfeng Xiao, Jianrong Xu, Tianran Fu, Zhiwei Cao, Liang Zhu, Hong-Zhuan Chen, Xu Shen, Hualiang Jiang, Liang Zhang
Fatty acid biosynthesis (FAS) is a vital process in cells. Fatty acids are essential for cell assembly and cellular metabolism. Abnormal FAS directly correlates with cell growth delay and human diseases, such as metabolic syndromes and various cancers. The FAS system utilizes an acyl carrier protein (ACP) as a transporter to stabilize and shuttle the growing fatty acid chain throughout enzymatic modules for stepwise catalysis. Studying the interactions between enzymatic modules and ACP is, therefore, critical for understanding the biological function of the FAS system...
December 2016: Cell Research
https://www.readbyqxmd.com/read/27872707/biochemical-characterization-of-pe_pgrs61-family-protein-of-mycobacterium-tuberculosis-h37rv-reveals-the-binding-ability-to-fibronectin
#20
Monu, Laxman S Meena
OBJECTIVES: The periodic binding of protein expressed by Mycobacterium tuberculosis H37Rv with the host cell receptor molecules i.e. fibronectin (Fn) is gaining significance because of its adhesive properties. The genome sequencing of M. tuberculosis H37Rv revealed that the proline-glutamic (PE) proteins contain polymorphic GC-rich repetitive sequences (PGRS) which have clinical importance in pathogenesis events when the host encounters M. tuberculosis H37Rv. The functional parts of PE_PGRS family proteins, have not been extensively studied in tuberculosis biology...
October 2016: Iranian Journal of Basic Medical Sciences
keyword
keyword
20424
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"