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Nils Krietenstein, Megha Wal, Shinya Watanabe, Bongsoo Park, Craig L Peterson, B Franklin Pugh, Philipp Korber
Chromatin remodelers regulate genes by organizing nucleosomes around promoters, but their individual contributions are obfuscated by the complex in vivo milieu of factor redundancy and indirect effects. Genome-wide reconstitution of promoter nucleosome organization with purified proteins resolves this problem and is therefore a critical goal. Here, we reconstitute four stages of nucleosome architecture using purified components: yeast genomic DNA, histones, sequence-specific Abf1/Reb1, and remodelers RSC, ISW2, INO80, and ISW1a...
October 20, 2016: Cell
Raffaela Torggler, Daniel Papinski, Thorsten Brach, Levent Bas, Martina Schuschnig, Thaddäus Pfaffenwimmer, Sabrina Rohringer, Tamara Matzhold, David Schweida, Andrea Brezovich, Claudine Kraft
Autophagy is a potent cellular degradation pathway, and its activation needs to be tightly controlled. Cargo receptors mediate selectivity during autophagy by bringing cargo to the scaffold protein Atg11 and, in turn, to the autophagic machinery, including the central autophagy kinase Atg1. Here we show how selective autophagy is tightly regulated in space and time to prevent aberrant Atg1 kinase activation and autophagy induction. We established an induced bypass approach (iPass) that combines genetic deletion with chemically induced dimerization to evaluate the roles of Atg13 and cargo receptors in Atg1 kinase activation and selective autophagy progression...
October 20, 2016: Molecular Cell
Deepa Khare, Nobukata Mitsuda, Seungchul Lee, Won-Yong Song, Daehee Hwang, Masaru Ohme-Takagi, Enrico Martinoia, Youngsook Lee, Jae-Ung Hwang
Plants reorganize their root architecture to avoid growth into unfavorable regions of the rhizosphere. In a screen based on chimeric repressor gene-silencing technology, we identified the Arabidopsis thaliana GeBP-LIKE 4 (GPL4) transcription factor as an inhibitor of root growth that is induced rapidly in root tips in response to cadmium (Cd). We tested the hypothesis that GPL4 functions in the root avoidance of Cd by analyzing root proliferation in split medium, in which only half of the medium contained toxic concentrations of Cd...
October 21, 2016: New Phytologist
Tabitha Bucher, Elena Kartvelishvily, Ilana Kolodkin-Gal
This work assesses different methodologies to study the impact of small molecule biofilm inhibitors, such as D-amino acids, on the development and resilience of Bacillus subtilis biofilms. First, methods are presented that select for small molecule inhibitors with biofilm-specific targets in order to separate the effect of the small molecule inhibitors on planktonic growth from their effect on biofilm formation. Next, we focus on how inoculation conditions affect the sensitivity of multicellular, floating B...
October 9, 2016: Journal of Visualized Experiments: JoVE
Chai Kobkitsuksakul, Pakorn Jiarakongmun, Ekachat Chanthanaphak, Sirintara Pongpech
PURPOSE: The classic symptoms and signs of carotid cavernous sinus fistula or cavernous sinus dural arteriovenous fistula (AVF) consist of eye redness, exophthalmos, and gaze abnormality. The angiography findings typically consist of arteriovenous shunt at cavernous sinüs with ophthalmic venous drainage with or without cortical venous reflux. In rare circumstances, the shunts are localized outside the cavernous sinus, but mimic symptoms and radiography of the cavernous shunt. We would like to present the other locations of the arteriovenous shunt, which mimic the clinical presentation of carotid cavernous fistulae, and analyze venous drainages...
October 21, 2016: Diagnostic and Interventional Radiology: Official Journal of the Turkish Society of Radiology
Petr Stadlbauer, Liuba Mazzanti, Tristan Cragnolini, David J Wales, Philippe Derreumaux, Samuela Pasquali, Jiri Sponer
G-quadruplexes are the most important non-canonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)n, have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradicting models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach the thermodynamics equilibrium...
October 21, 2016: Journal of Chemical Theory and Computation
Bruce Wen, Kirby R Campbell, Karissa Tilbury, Oleg Nadiarnykh, Molly A Brewer, Manish Patankar, Vikas Singh, Kevin W Eliceiri, Paul J Campagnola
Remodeling of the collagen architecture in the extracellular matrix (ECM) has been implicated in ovarian cancer. To quantify these alterations we implemented a form of 3D texture analysis to delineate the fibrillar morphology observed in 3D Second Harmonic Generation (SHG) microscopy image data of normal (1) and high risk (2) ovarian stroma, benign ovarian tumors (3), low grade (4) and high grade (5) serous tumors, and endometrioid tumors (6). We developed a tailored set of 3D filters which extract textural features in the 3D image sets to build (or learn) statistical models of each tissue class...
October 21, 2016: Scientific Reports
Xin Wang, Thor E Friis, Paul P Masci, Ross W Crawford, Wenbo Liao, Yin Xiao
The quality of hematomas are crucial for successful early bone defect healing, as the structure of fibrin clots can significantly influence the infiltration of cells, necessary for bone regeneration, from adjacent tissues into the fibrin network. This study investigated if there were structural differences between hematomas from normal and delayed healing bone defects and whether such differences were linked to changes in the expression of IL-1β. Using a bone defect model in rats, we found that the hematomas in the delayed healing model had thinner fibers and denser clot structures...
October 21, 2016: Scientific Reports
Satoru Kondo, Takashi Yoshida, Kenichi Ohki
A minicolumn is the smallest anatomical module in the cortical architecture, but it is still in debate whether it serves as functional units for cortical processing. In the rodent primary visual cortex (V1), neurons with different preferred orientations are mixed horizontally in a salt and pepper manner, but vertical functional organization was not examined. In this study, we found that neurons with similar orientation preference are weakly but significantly clustered vertically in a short length and horizontally in the scale of a minicolumn...
October 21, 2016: Nature Communications
Gustavo Rios, Evgueniy V Lubenov, Derrick Chi, Michael L Roukes, Athanassios G Siapas
Computations in brain circuits involve the coordinated activation of large populations of neurons distributed across brain areas. However, monitoring neuronal activity in the brain of intact animals with high temporal and spatial resolution has remained a technological challenge. Here we address this challenge by developing dense, three-dimensional (3-D) electrode arrays for electrophysiology. The 3-D arrays constitute the front-end of a modular and configurable system architecture that enables monitoring neuronal activity with unprecedented scale and resolution...
October 21, 2016: Nano Letters
Xiayin Yao, Deng Liu, Chunsheng Wang, Peng Long, Gang Peng, Yong-Sheng Hu, Hong Li, Liquan Chen, Xiaoxiong Xu
High energy and power densities are the greatest challenge for all-solid-state lithium batteries due to the poor interfacial compatibility between electrodes and electrolytes as well as low lithium ion transfer kinetics in solid materials. Intimate contact at the cathode/solid electrolyte interface and high ionic conductivity of solid electrolyte are crucial to realize high-performance all-solid-state lithium batteries. Here we report a general interfacial architecture, i.e. Li7P3S11 electrolyte particles anchored on cobalt sulfide nanosheets, by an in situ liquid-phase appraoch...
October 21, 2016: Nano Letters
Lei Sun, Sarah S Park, Dennis Sheberla, Mircea Dinca
Electrically conductive metal-organic frameworks (MOFs) are emerging as a subclass of porous materials that can have a transformative effect on electronic and renewable energy devices. Systematic advances in these materials depend critically on the accurate and reproducible characterization of their electrical properties. This is made difficult by the numerous techniques available for electrical measurements and the dependence of metrics on device architecture and numerous external variables. These challenges, common to all types of electronic materials and devices, are especially acute for porous materials, whose high surface area make them even more susceptible to interactions with contaminants in the environment...
October 21, 2016: Journal of the American Chemical Society
Joan Yw Liu, Cheryl Reeves, Beate Diehl, Antonietta Coppola, Aliya Al-Hajri, Chandrashekar Hoskote, Salim Al Mughairy, Mohamed Tachrount, Michael Groves, Zuzanna Michalak, Kevin Mills, Andrew W McEvoy, Anna Miserocchi, Sanjay M Sisodiya, Maria Thom
OBJECTIVE: This study reports on a novel brain pathology in young patients with Frontal Lobe Epilepsy that is distinct from Focal Cortical Dysplasia. METHODS: Surgical specimens from twenty young adults with frontal lobe epilepsy (mean age, 30 years) were investigated with histological/immunohistochemical markers for cortical laminar architecture, mammalian target of rapamycin pathway activation and inhibition, cellular autophagy, and synaptic vesicle-mediated trafficking as well as proteomics analysis...
October 20, 2016: Annals of Neurology
Percival G Matthews, Mark R Lewis
Although many researchers theorize that primitive numerosity processing abilities may lay the foundation for whole number concepts, other classes of numbers, like fractions, are sometimes assumed to be inaccessible to primitive architectures. This research presents evidence that the automatic processing of nonsymbolic magnitudes affects processing of symbolic fractions. Participants completed modified Stroop tasks in which they selected the larger of two symbolic fractions while the ratios of the fonts in which the fractions were printed and the overall sizes of the compared fractions were manipulated as irrelevant dimensions...
October 20, 2016: Cognitive Science
Brendan D Crawford, Christopher E Gillies, Catherine C Robertson, Matthias Kretzler, Edgar Otto, Virginia Vega-Wagner, Matthew G Sampson
BACKGROUND: More than 30 genes can harbor rare exonic variants sufficient to cause nephrotic syndrome (NS), and the number of genes implicated in monogenic NS continues to grow. However, outside the first year of life, the majority of affected patients, particularly in ancestrally mixed populations, do not have a known monogenic form of NS. Even in those children classified with a monogenic form of NS, there is phenotypic heterogeneity. Thus, we have only discovered a fraction of the heritability of NS-the underlying genetic factors contributing to phenotypic variation...
October 20, 2016: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
Klaus-Peter Stein, Isabel Wanke, Neriman Oezkan, Yuan Zhu, I Erol Sandalcioglu, Michael Forsting, Ulrich Sure
BACKGROUND: Multiple AVMs are exceptionally rare lesions and only a few larger series have been published, including other vascular pathologies, such as arterio-venous fistulae (AVF) or patients with hereditary syndromes. Our study presents clinical, angiographic, and therapeutic characteristics of patients harboring sporadic multiple AVMs. METHODS: Basic demographic data, vascular architecture, clinical presentation, treatment strategies, and treatment outcome were analyzed retrospectively from patients with cerebral AVMs treated in our department between 1990 and 2015...
October 20, 2016: Acta Neurochirurgica
Kishan A Manani, Kim Christensen, Nicholas S Peters
Atrial fibrillation (AF) increases the risk of stroke by a factor of 4-5 and is the most common abnormal heart rhythm. The progression of AF with age, from short self-terminating episodes to persistence, varies between individuals and is poorly understood. An inability to understand and predict variation in AF progression has resulted in less patient-specific therapy. Likewise, it has been a challenge to relate the microstructural features of heart muscle tissue (myocardial architecture) with the emergent temporal clinical patterns of AF...
October 2016: Physical Review. E
Eitaro Aihara, Andrea L Matthis, Rebekah A Karns, Kristen A Engevik, Peihua Jiang, Jiang Wang, Bruce R Yacyshyn, Marshall H Montrose
BACKGROUND & AIMS: The peptic ulcer heals through a complex process, although the ulcer relapse often occurs several years later after healing. Our hypothesis is that even after visual evidence of healing of gastric ulceration, the regenerated epithelium is aberrant for an extended interval, increasing susceptibility of the regenerated epithelium to damage and further diseases. METHODS: Gastric ulcers were induced in mice by serosal topical application of acetic acid...
September 2016: Cellular and Molecular Gastroenterology and Hepatology
Richard J McMurtrey
Biomaterials are becoming an essential tool in the study and application of stem cell research. Various types of biomaterials enable three-dimensional culture of stem cells, and, more recently, also enable high-resolution patterning and organization of multicellular architectures. Biomaterials also hold potential to provide many additional advantages over cell transplants alone in regenerative medicine. This article describes novel designs for functionalized biomaterial constructs that guide tissue development to targeted regional identities and structures...
January 2016: Journal of Tissue Engineering
Yaohong Wang, Sudeep P George, Swati Roy, Eric Pham, Amin Esmaeilniakooshkghazi, Seema Khurana
In the small intestine, epithelial cells are derived from stem cells in the crypts, migrate up the villus as they differentiate and are ultimately shed from the villus tips. This process of proliferation and shedding is tightly regulated to maintain the intestinal architecture and tissue homeostasis. Apoptosis regulates both the number of stem cells in the crypts as well as the sloughing of cells from the villus tips. Previously, we have shown that villin, an epithelial cell-specific actin-binding protein functions as an anti-apoptotic protein in the gastrointestinal epithelium...
October 21, 2016: Scientific Reports
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