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promoter dynamics

Jejoong Yoo, Aleksei Aksimentiev
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity...
March 16, 2018: Physical Chemistry Chemical Physics: PCCP
Andrea L Metti, John R Best, C Elizabeth Shaaban, Mary Ganguli, Caterina Rosano
Background: physical function (PF) and physical activity (PA) both decline as adults age and have been linked to negative outcomes, including dementia, depression and cardiovascular diseases. Although declines in each are associated with numerous negative outcomes, the longitudinal relationship between these two measures is unclear. Objective: to examine the dynamic, bidirectional associations between declines in PF and PA. Design: prospective cohort...
March 13, 2018: Age and Ageing
Zhiyi Qin, Peter Stoilov, Xuegong Zhang, Yi Xing
Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5' Untranslated Regions (5'UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to identify the 5' ends of transcripts. We developed a computational pipeline SEASTAR that identifies first exons from RNA-seq data alone then quantifies and compares alternative first exon usage across multiple biological conditions...
March 13, 2018: Nucleic Acids Research
Danuta Gutowska-Owsiak, Jorge Bernardino de La Serna, Marco Fritzsche, Aishath Naeem, Ewa I Podobas, Michael Leeming, Huw Colin-York, Ryan O'Shaughnessy, Christian Eggeling, Graham S Ogg
Epidermal stratification critically depends on keratinocyte differentiation and programmed death by cornification, leading to formation of a protective skin barrier. Cornification is dynamically controlled by the protein filaggrin, rapidly released from keratohyalin granules (KHGs). However, the mechanisms of cornification largely remain elusive, partly due to limitations of the observation techniques employed to study filaggrin organization in keratinocytes. Moreover, while the abundance of keratins within KHGs has been well described, it is not clear whether actin also contributes to their formation or fate...
March 15, 2018: Cell Death & Disease
Bivas Panigrahi, Chang-Hung Lu, Neha Ghayal, Chia-Yuan Chen
The zebrafish sperm activation profoundly depends upon the homogeneous mixing of the sperm cells with its diluent in a quick succession as it alters the cell's extracellular medium and initiates their motility. Manual stirring, the traditional method for zebrafish sperm activation is tedious, time-consuming, and has a poor outcome. In this aspect, an artificial cilia embedded serpentine microfluidic is designed through which hydrodynamic factors of the microfluidic environment can be precisely regulated to harness uniform mixing, hence ensuring a superior sperm activation...
March 15, 2018: Scientific Reports
Zhijian Zhao, Mengping Zhang, Xiaolu Duan, Yiwen Chen, Ermao Li, Lianming Luo, Wenqi Wu, Zhenwei Peng, Hui-Juan Qiu, Guohua Zeng
Transient receptor potential melastatin 7 (TRPM7) is important for the tumorigenesis and progression of several cancers. However, little is known about TRPM7 expression and its clinical significance in clear cell renal cell carcinoma (ccRCC). The expression dynamics of TRPM7 was examined in a clinical cohort of RCC specimens by quantitative PCR (qPCR), immunoblotting and immunohistochemical (IHC) staining. A series of in vitro and in vivo assays were performed to elucidate the function of TRPM7 in RCC and the underlying mechanisms...
March 15, 2018: Molecular Cancer Research: MCR
Oriane Blanquie, Frank Bradke
Recent years have seen cytoskeleton dynamics emerging as a key player in axon regeneration. The cytoskeleton, in particular microtubules and actin, ensures the growth of neuronal processes and maintains the singular, highly polarized shape of neurons. Following injury, adult central axons are tipped by a dystrophic structure, the retraction bulb, which prevents their regeneration. Abnormal cytoskeleton dynamics are responsible for the formation of this growth-incompetent structure but pharmacologically modulating cytoskeleton dynamics of injured axons can transform this structure into a growth-competent growth cone...
March 12, 2018: Current Opinion in Neurobiology
Ciarán L Kelly, George M Taylor, Andrew Hitchcock, Antonio Torres-Méndez, John T Heap
Cyanobacteria are important for fundamental studies of photosynthesis and have great biotechnological potential. In order to better study and fully exploit these organisms, the limited repertoire of genetic tools and parts must be expanded. A small number of inducible promoters have been used in cyanobacteria, allowing dynamic external control of gene expression through the addition of specific inducer molecules. However, the inducible promoters used to date suffer from various drawbacks including toxicity of inducers, leaky expression in the absence of inducer and inducer photolability, the latter being particularly relevant to cyanobacteria which, as photoautotrophs, are grown under light...
March 15, 2018: ACS Synthetic Biology
Marta Martínez-Calle, Bárbara Olmeda, Paul Dietl, Manfred Frick, Jesús Pérez-Gil
The release of pulmonary surfactant by alveolar type II (ATII) cells is essential for lowering surface tension at the respiratory air-liquid interface, stabilizing the lungs against physical forces tending to alveolar collapse. Hydrophobic surfactant protein (SP)-B ensures the proper packing of newly synthesized surfactant particles, promotes the formation of the surface active film at the alveolar air-liquid interface and maintains its proper structure along the respiratory dynamics. We report that membrane-associated SP-B efficiently induces secretion of pulmonary surfactant by ATII cells, at the same level as potent secretagogues such as ATP...
March 15, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
Yong Yang, Brent A Langellier, Ivana Stankov, Jonathan Purtle, Katherine L Nelson, Ana V Diez Roux
OBJECTIVES: Daily transport may impact depression risk among older adults through several pathways including facilitating the ability to meet basic needs, enabling and promoting contact with other people and nature, and promoting physical activity (e.g. through active transportation such as walking or walking to public transit). Both daily transport and depression are influenced by the neighborhood environment. To provide insights into how transport interventions may affect depression in older adults, we developed a pilot agent-based model to explore the contribution of daily transport and neighborhood environment to older adults' depression in urban areas...
March 15, 2018: Aging & Mental Health
Alessandro Bosco, Justine Schneider, Donna Maria Coleston-Shields, Lidia Sousa, Martin Orrell
OBJECTIVES: Good interaction with family caregivers helps maintain positive identity in people with dementia. However, research in this area is limited. We aimed to systematically review the dyadic experience of dementia caring. METHOD: We searched on five databases: MedLine, EMBASE, PsycInfo, ASSIA, and CINAHL. Eligible studies employed qualitative or mixed method design, reported the experience of dyads of dementia with no comorbid organic or psychiatric disorders...
March 15, 2018: Aging & Mental Health
Dominik Linz, R Doug McEvoy, Martin R Cowie, Virend K Somers, Stanley Nattel, Patrick Lévy, Jonathan M Kalman, Prashanthan Sanders
Importance: Obstructive sleep apnea (OSA) is the most common clinically significant breathing abnormality during sleep. It is highly prevalent among patients with atrial fibrillation (AF), and it promotes arrhythmogenesis and impairs treatment efficacy. Observations: The prevalence of OSA ranges from 3% to 49% in population-based studies and from 21% to 74% in patients with AF. Diagnosis and treatment of OSA in patients with AF requires a close interdisciplinary collaboration between electrophysiologists, cardiologists, and sleep specialists...
March 14, 2018: JAMA Cardiology
Josette M Northcott, Ivory S Dean, Janna K Mouw, Valerie M Weaver
The tumor microenvironment is a dynamic landscape in which the physical and mechanical properties evolve dramatically throughout cancer progression. These changes are driven by enhanced tumor cell contractility and expansion of the growing tumor mass, as well as through alterations to the material properties of the surrounding extracellular matrix (ECM). Consequently, tumor cells are exposed to a number of different mechanical inputs including cell-cell and cell-ECM tension, compression stress, interstitial fluid pressure and shear stress...
2018: Frontiers in Cell and Developmental Biology
Elizabeth J Lawrence, Göker Arpağ, Stephen R Norris, Marija Zanic
Cytoplasmic Linker-Associated Proteins (CLASPs) are microtubule-associated proteins essential for microtubule regulation in many cellular processes. However, the molecular mechanisms underlying CLASP activity are not understood. Here, we use purified protein components and Total Internal Reflection Fluorescence (TIRF) microscopy to investigate the effects of human CLASP2 on microtubule dynamics in vitro We demonstrate that CLASP2 suppresses microtubule catastrophe and promotes rescue without affecting the rates of microtubule growth or shrinkage...
March 14, 2018: Molecular Biology of the Cell
Cecilia Siliansky de Andreazzi, Paulo R Guimarães, Carlos J Melián
Studies have shown the potential for rapid adaptation in coevolving populations and that the structure of species interaction networks can modulate the vulnerability of ecological systems to perturbations. Although the feedback loop between population dynamics and coevolution of traits is crucial for understanding long-term stability in ecological assemblages, modelling eco-evolutionary dynamics in species-rich assemblages is still a challenge. We explore how eco-evolutionary feedbacks influence trait evolution and species abundances in 23 empirical antagonistic networks...
March 14, 2018: Proceedings. Biological Sciences
Megan Sjodt, Ramsay Macdonald, Joanna D Marshall, Joseph Clayton, John S Olson, Martin L Phillips, David A Gell, Jeff Wereszczynski, Robert T Clubb
Staphylococcus aureus is a leading cause of life-threatening infections in the United States. It actively acquires the essential nutrient iron from human hemoglobin (Hb) using the iron-regulated surface-determinant (Isd) system. This process is initiated when the closely related bacterial IsdB and IsdH receptors bind to Hb and extract its hemin through a conserved tri-domain unit that contains two NEAr iron Transporter (NEAT) domains that are connected by a helical linker domain. Previously, we demonstrated that the tri-domain unit within IsdH (IsdHN2N3 ) triggers hemin release by distorting Hb's F-helix...
March 14, 2018: Journal of Biological Chemistry
Thenappan Thenappan, Mark L Ormiston, John J Ryan, Stephen L Archer
Pulmonary hypertension is defined as a resting mean pulmonary artery pressure of 25 mm Hg or above. This review deals with pulmonary arterial hypertension (PAH), a type of pulmonary hypertension that primarily affects the pulmonary vasculature. In PAH, the pulmonary vasculature is dynamically obstructed by vasoconstriction, structurally obstructed by adverse vascular remodeling, and pathologically non-compliant as a result of vascular fibrosis and stiffening. Many cell types are abnormal in PAH, including vascular cells (endothelial cells, smooth muscle cells, and fibroblasts) and inflammatory cells...
March 14, 2018: BMJ: British Medical Journal
Sandra Infante Villamil, Roger Huerlimann, Christina Morianos, Zoltan Sarnyai, Gregory E Maes
Obesity and other lifestyle diseases in modern society can be related to historical dietary changes from diets balanced in omega-6 and omega-3 to the unbalanced "Western-type" diet. It is recognized that diet influences the murine and human gut microbiome, and most research indicates that microbial diversity and composition are altered by high-fat diets (HFDs). However, good knowledge about the effects of early exposure to HFD on the maturation and structure of the bacterial community is limited. Using mice as model, we hypothesized that an HFD alters the early dynamic of the gut bacterial community toward an unstable/unhealthy state...
February 2018: Nutrition Research
Justine Lebeau, Jaclyn M Saunders, Vivian W R Moraes, Aparajita Madhavan, Nicole Madrazo, Mary C Anthony, R Luke Wiseman
Endoplasmic reticulum (ER) stress is transmitted to mitochondria and is associated with pathologic mitochondrial dysfunction in diverse diseases. The PERK arm of the unfolded protein response (UPR) protects mitochondria during ER stress through the transcriptional and translational remodeling of mitochondrial molecular quality control pathways. Here, we show that ER stress also induces dynamic remodeling of mitochondrial morphology by promoting protective stress-induced mitochondrial hyperfusion (SIMH). ER-stress-associated SIMH is regulated by the PERK arm of the UPR and activated by eIF2α phosphorylation-dependent translation attenuation...
March 13, 2018: Cell Reports
Chandan Kumar Choudhury, Sidong Tu, Igor Luzinov, Sergiy Minko, Olga Kuksenok
Designing biomaterials capable of functioning in harsh environments is vital for a range of applications. Using molecular dynamics simulations, we show that conjugating lysozymes with a copolymer [poly(GMA-stat-OEGMA)] comprising of glycidyl methacrylate (GMA) and oligo(ethylene glycol) methyl ether methacrylate (OEGMA) results in a dramatic increase of stability of these enzymes at high temperatures provided that the concentration of the copolymer in the close vicinity of the enzyme exceeds a critical value...
March 14, 2018: Biomacromolecules
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