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https://www.readbyqxmd.com/read/29232700/sygl-1-and-lst-1-link-niche-signaling-to-puf-rna-repression-for-stem-cell-maintenance-in-caenorhabditis-elegans
#1
Heaji Shin, Kimberly A Haupt, Aaron M Kershner, Peggy Kroll-Conner, Marvin Wickens, Judith Kimble
Central questions in regenerative biology include how stem cells are maintained and how they transition from self-renewal to differentiation. Germline stem cells (GSCs) in Caenorhabditis elegans provide a tractable in vivo model to address these questions. In this system, Notch signaling and PUF RNA binding proteins, FBF-1 and FBF-2 (collectively FBF), maintain a pool of GSCs in a naïve state. An open question has been how Notch signaling modulates FBF activity to promote stem cell self-renewal. Here we report that two Notch targets, SYGL-1 and LST-1, link niche signaling to FBF...
December 12, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29232689/a-computational-model-for-regulation-of-nanoscale-glucan-exposure-in-candida-albicans
#2
Michael J Wester, Jia Lin, Aaron K Neumann
Candida albicans is a virulent human opportunistic pathogen. It evades innate immune surveillance by masking an immunogenic cell wall polysaccharide, β-glucan, from recognition by the immunoreceptor Dectin-1. Glucan unmasking by the antifungal drug caspofungin leads to changes in the nanostructure of glucan exposure accessible to Dectin-1. The physical mechanism that regulates glucan exposure is poorly understood, but it controls the nanobiology of fungal pathogen recognition. We created computational models to simulate hypothetical physical processes of unmasking glucan in a biologically realistic distribution of cell wall glucan fibrils...
2017: PloS One
https://www.readbyqxmd.com/read/29232568/prior-systemic-treatment-increased-the-incidence-of-somatic-mutations-in-metastatic-breast-cancer
#3
Takeo Fujii, Naoko Matsuda, Miho Kono, Kenichi Harano, Huiqin Chen, Rajyalakshmi Luthra, Sinchita Roy-Chowdhuri, Aysegul A Sahin, Chetna Wathoo, Aron Y Joon, Debu Tripathy, Funda Meric-Bernstam, Naoto T Ueno
BACKGROUND: Understanding the biology of breast cancer is important for guiding treatment strategies and revealing resistance mechanisms. Our objectives were to investigate the relationship between previous systemic therapy exposure and mutational spectrum in metastatic breast cancer and to identify clinicopathological factors associated with identified frequent somatic mutations. METHODS: Archival tissues of patients with metastatic breast cancer were subjected to hotspot molecular testing by next-generation sequencing...
December 9, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/29232518/theoretical-study-on-the-photoinduced-electron-transfer-mechanisms-of-different-peroxynitrite-probes
#4
Li Li, Minghui Zan, Xingwang Qie, Juan Yue, Peng Miao, Mingfeng Ge, Zhimin Chang, Zheng Wang, Fuquan Bai, Hong-Xing Zhang, James Kit Ferri, Wen-Fei Dong
The development of probes for rapid and selective detection of peroxynitrite in vivo is of great importance in biological science. We investigate different photoinduced electron transfer (PET) processes of two generations of peroxynitrite probes. Each has fluorescein and phenol moieties; one is conjugated by an ether linkage while the other is conjugated via an amine linkage. Using theoretical calculations, we demonstrated that the PET in the probe with an ether linkage occurs from the benzoic acid to the xanthene moiety...
December 12, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/29232515/parametrization-and-benchmark-of-the-long-range-corrected-dftb2-for-organic-molecules
#5
Quan Van Vuong, Jissy Akkarapattiakal Kuriappan, Maximilian Kubillus, Julian Kranz, Thilo Mast, Thomas A Niehaus, Stephan Irle, Marcus Elstner
We present the parametrization and benchmark of long-range corrected second-order DFTB, LC-DFTB2, for organic and biological molecules. The LC-DFTB2 model not only improves fundamental orbital energy gaps, but also ameliorates the DFT self-interaction error and overpolarization problem, and further improves charge-transfer excited states significantly. Electronic parameters for the construction of the DFTB2 Hamiltonian as well as repulsive potentials were optimized for molecules containing C, H, N, and O chemical elements...
December 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29232504/a-genetic-toolbox-for-modulating-the-expression-of-heterologous-genes-in-the-cyanobacterium-synechocystis-sp-pcc-6803
#6
Bo Wang, Carrie Eckert, Pin-Ching Maness, Jianping Yu
Cyanobacteria, genetic models for photosynthesis research for decades, have recently become attractive hosts for producing renewable fuels and chemicals, owing to their genetic tractability, relatively fast growth, and their ability to utilize sunlight, fix carbon dioxide and, in some cases, fix nitrogen. Despite significant advances, there is still an urgent demand for synthetic biology tools in order to effectively manipulate genetic circuits in cyanobacteria. In this study, we have compared a total of 17 natural and chimeric promoters, focusing on expression of the ethylene-forming enzyme (EFE) in the cyanobacterium Synechocystis sp...
December 12, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29232104/the-effects-of-biological-fluids-on-colloidal-stability-and-sirna-delivery-of-a-ph-responsive-micellar-nanoparticle-delivery-system
#7
Dominic W Malcolm, Jomy J Varghese, Janet E Sorrells, Catherine E Ovitt, Danielle S W Benoit
Nanoparticles (NP) interact with complex protein milieus in biological fluids, and these interactions have profound effects on NP physicochemical properties and function. Surprisingly, most studies neglect the impact of these interactions, especially with respect to NP-mediated siRNA delivery. Here, the effects of serum on colloidal stability and siRNA delivery of a pH-responsive micellar NP delivery system were characterized. Results show cationic NP-siRNA complexes aggregate in  2% serum in buffer, but are stable in serum-free media...
December 12, 2017: ACS Nano
https://www.readbyqxmd.com/read/29231847/natural-knockouts-natural-selection-knocked-out
#8
Peter Borger
In functional genomics studies, research is dedicated to unveiling the function of genes using gene-knockouts, model organisms in which a gene is artificially inactivated. The idea is that, by knocking out the gene, the provoked phenotype would inform us about the function of the gene. Still, the function of many genes cannot be elucidated, because disruption of conserved sequences, including protein-coding genes, often does not directly affect the phenotype. Since the phenomenon was first observed in the early nineties of the last century, these so-called 'no-phenotype knockouts' have met with great skepticism and resistance by died-in-the-wool selectionists...
December 12, 2017: Biology
https://www.readbyqxmd.com/read/29231764/relevance-of-chronotype-for-eating-patterns-in-adolescents
#9
Sarah Roßbach, Tanja Diederichs, Ute Nöthlings, Anette E Buyken, Ute Alexy
During adolescence, a shift from morningness to eveningness occurs, yet school continues to start early in the morning. Hence, adolescents are at risk for social jetlag, i.e. a discrepancy between biological and social timing. It remains to be determined whether chronotype associates with daily and daytime-specific eating patterns during this potentially critical period. Therefore, the aim of the present study was to investigate whether chronotype is decisive for daily eating patterns [total energy intake (TEI, kcal), total macronutrient intake (% of TEI), eating occasion frequency (n/day), meal frequency (n/day), snack frequency (n/day), duration of nightly fasting], or daytime-specific eating patterns [morning (before 11 am) energy intake (% of TEI), morning macronutrient intake (% of morning energy intake), regular breakfast skipping (no morning energy intake at least on 2 of 3 days, yes/no), evening (after 6 pm) energy intake (% of TEI), evening macronutrient intake (% of evening energy intake), regular dinner skipping (no evening energy intake at least on 2 of 3 days, yes/no)] in German adolescents...
December 12, 2017: Chronobiology International
https://www.readbyqxmd.com/read/29231335/-review-on-skin-temperature-of-acupoints
#10
REVIEW
Ziyi Yang, Mengyuan Zhou, Xing Wang, Yunyun Zhao, Zhifeng Chen, Yi Lan, Tao Xu, Yu Zhao, Ling Zhao
We retrieve and analyze the articles on body surface temperature of acupoints in the recent 50 years. Surface temperatures have been compared between acupoints and nonacupoints, and among acupoints in different states. The impacts of interventions for acupoint temperature are explored, including acupuncture,moxibustion and cupping, etc. We summarize the features and the rules of acupoint skin temperature. It is considered that there exists distribution rule for healthy people's acupoint skin temperature. That means acupoints have higher surface temperature than nonacupoints...
January 12, 2017: Zhongguo Zhen Jiu, Chinese Acupuncture & Moxibustion
https://www.readbyqxmd.com/read/29231177/hindrances-to-precise-recovery-of-cellular-forces-in-fibrous-biopolymer-networks
#11
Yunsong Zhang, Jingchen Feng, Shay I Heizler, Herbert Levine
How cells move through the three-dimensional extracellular matrix (ECM) is of increasing interest in attempts to understand important biological processes such as cancer metastasis. Just as in motion on flat surfaces, it is expected that experimental measurements of cell-generated forces will provide valuable information for uncovering the mechanisms of cell migration. However, the recovery of forces in fibrous biopolymer networks may suffer from large errors. Here, within the framework of lattice-based models, we explore possible issues in force recovery by solving the inverse problem: how can one determine the forces cells exert to their surroundings from the deformation of the ECM? Our results indicate that irregular cell traction patterns, the uncertainty of local fiber stiffness, the non-affine nature of ECM deformations and inadequate knowledge of network topology will all prevent the precise force determination...
December 12, 2017: Physical Biology
https://www.readbyqxmd.com/read/29231176/tensorcalculator-exploring-the-evolution-of-mechanical-stress-in-the-ccmv-capsid
#12
Olga Kononova, Farkhad Maksudov, Kenneth A Marx, Valeri Barsegov
A new computational methodology for accurate numerical calculation of the Cauchy stress tensor, stress invariants, principal stress components, von Mises and Tresca tensors is developed. The methodology is based on the atomic stress approach which permits the calculation of stress tensors, widely used in continuum mechanics modeling of materials properties, using the output from the MD simulations of discrete atomic and Cα-based coarse-grained structural models of biological particles. The methodology mapped into software package TensorCalculator was successfully applied to the empty Cowpea Chlorotic Mottle virus (CCMV) shell to explore the evolution of mechanical stress in this mechanically-tested specific example of a soft virus capsid...
December 12, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29231174/the-influence-of-substrate-roughness-patterning-curvature-and-compliance-in-peeling-problems
#13
Lucas Brely, Federico Bosia, Nicola M Pugno
Biological adhesion, in particular the mechanisms by which animals and plants "stick" to surfaces has been widely studied in recent years, and some of the structural principles have been successfully applied to bioinspired adhesives. However, modelling of adhesion such as in single or multiple peeling theories, have in most cases been limited to ideal cases and due consideration of the role of substrate geometry and mechanical properties has been limited. In this paper, we propose a numerical model to evaluate these effects, including substrate roughness, patterning, curvature and deformability...
December 12, 2017: Bioinspiration & Biomimetics
https://www.readbyqxmd.com/read/29231142/crispr-cas-in-medicinal-chemistry-applications-and-regulatory-concerns
#14
Aliuska Duardo-Sanchez
A rapid search in scientific publication's databases shows how the use of CRISPR-Cas genome editions' technique has considerably expanded, and its growing importance, in modern molecular biology. Just in pub-med platform, the search of the term gives more than 3000 results. Specifically, in Drug Discovery, Medicinal Chemistry and Chemical Biology in general CRISPR method may have multiple applications. Some of these applications are: resistance-selection studies of antimalarial lead organic compounds; investigation of druggability; development of animal models for chemical compounds testing, etc...
December 11, 2017: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/29230881/variance-component-analysis-to-assess-protein-quantification-in-biomarker-discovery-application-to-maldi-tof-mass-spectrometry
#15
Catherine Mercier, Amna Klich, Caroline Truntzer, Vincent Picaud, Jean-François Giovannelli, Patrick Ducoroy, Pierre Grangeat, Delphine Maucort-Boulch, Pascal Roy
Controlling the technological variability on an analytical chain is critical for biomarker discovery. The sources of technological variability should be modeled, which calls for specific experimental design, signal processing, and statistical analysis. Furthermore, with unbalanced data, the various components of variability cannot be estimated with the sequential or adjusted sums of squares of usual software programs. We propose a novel approach to variance component analysis with application to the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) technology and use this approach for protein quantification by a classical signal processing algorithm and two more recent ones (BHI-PRO 1 and 2)...
December 12, 2017: Biometrical Journal. Biometrische Zeitschrift
https://www.readbyqxmd.com/read/29230875/kinetics-of-plasma-cell-free-dna-and-creatine-kinase-in-a-canine-model-of-tissue-injury
#16
I J Wilson, R K Burchell, A J Worth, S E Burton, K R Gedye, K J Clark, K R Crosse, M Jack, T F Odom, S J De Grey, K M S McGlade, S C Tomlin, N Lopez-Villalobos, A Gal
BACKGROUND: Cell-free DNA (cfDNA) comprises short, double-stranded circulating DNA sequences released from damaged cells. In people, cfDNA concentrations correlate well with disease severity and tissue damage. No reports are available regarding cfDNA kinetics in dogs. OBJECTIVES/HYPOTHESIS: Cell-free DNA will have a short biological half-life and would be able to stratify mild, moderate, and severe tissue injury. Our study aims were to determine the kinetics and biological half-life of cfDNA and to contrast them with those of creatine kinase (CK)...
December 12, 2017: Journal of Veterinary Internal Medicine
https://www.readbyqxmd.com/read/29230865/glial-source-of-nitric-oxide-in-epileptogenesis-a-target-for-disease-modification-in-epilepsy
#17
REVIEW
Shaunik Sharma, Sreekanth Puttachary, Thimmasettappa Thippeswamy
Epileptogenesis is the process of developing an epileptic condition and/or its progression once it is established. The molecules that initiate, promote, and propagate remarkable changes in the brain during epileptogenesis are emerging as targets for prevention/treatment of epilepsy. Epileptogenesis is a continuous process that follows immediately after status epilepticus (SE) in animal models of acquired temporal lobe epilepsy (TLE). Both SE and epileptogenesis are potential therapeutic targets for the discovery of anticonvulsants and antiepileptogenic or disease-modifying agents...
December 12, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/29230701/estimating-intermittent-individual-spawning-behavior-via-disaggregating-group-data
#18
Joel Nishimura, Rebecca Smith, Kathleen Jensen, Gerald Ankley, Karen Watanabe
In order to understand fish biology and reproduction, it is important to know the fecundity patterns of individual fish, as frequently established by recording the output of mixed-sex groups of fish in a laboratory setting. However, for understanding individual reproductive health and modeling purposes it is important to estimate individual fecundity from group fecundity. We created a multistage method that disaggregates group-level data into estimates for individual-level clutch size and spawning interval distributions...
December 11, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/29230566/a-rate-reduced-neuron-model-for-complex-spiking-behavior
#19
Koen Dijkstra, Yuri A Kuznetsov, Michel J A M van Putten, Stephan A van Gils
We present a simple rate-reduced neuron model that captures a wide range of complex, biologically plausible, and physiologically relevant spiking behavior. This includes spike-frequency adaptation, postinhibitory rebound, phasic spiking and accommodation, first-spike latency, and inhibition-induced spiking. Furthermore, the model can mimic different neuronal filter properties. It can be used to extend existing neural field models, adding more biological realism and yielding a richer dynamical structure. The model is based on a slight variation of the Rulkov map...
December 11, 2017: Journal of Mathematical Neuroscience
https://www.readbyqxmd.com/read/29230441/detection-of-a%C3%AE-plaque-associated-astrogliosis-in-alzheimer-s-disease-brain-by-spectroscopic-imaging-and-immunohistochemistry
#20
Francesca Palombo, Francesco Tamagnini, J Charles G Jeynes, Sara Mattana, Imogen Swift, Jayakrupakar Nallala, Jane Hancock, Jonathan T Brown, Andrew D Randall, Nick Stone
Recent work using micro-Fourier transform infrared (μFTIR) imaging has revealed that a lipid-rich layer surrounds many plaques in post-mortem Alzheimer's brain. However, the origin of this lipid layer is not known, nor is its role in the pathogenesis of Alzheimer's disease (AD). Here, we studied the biochemistry of plaques in situ using a model of AD. We combined FTIR, Raman and immunofluorescence images, showing that astrocyte processes co-localise with the lipid ring surrounding many plaques. We used μFTIR imaging to rapidly measure chemical signatures of plaques over large fields of view, and selected plaques for higher resolution analysis with Raman microscopy...
December 12, 2017: Analyst
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