bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parkinson’s disease associated mutation E46K of α-synuclein triggers the formation of a novel fibril structure
Authors: Zhao Kun , Li Yaowang , Liu Zhenying , Long Houfang , Zhao Chunyu , Luo Feng , Sun Yunpeng , Tao Youqi , Su Xiao-dong , Li Dan , Li Xueming , Liu Cong 
Published: December 2019

ABSTRACTα-Synuclein (α-syn) amyloid fibril, as the major component of Lewy bodies and pathological entity spreading in human brain, is closely associated with Parkinson’s disease (PD) and other synucleinopathies. Several single amino-acid mutations (e.g. E46K) of α-syn have been identified causative to the early onset of familial PD. Here, we determined the cryo-EM structure of a full-length α-syn fibril formed by N-terminal acetylated E46K mutant α-syn (Ac-E46K). The fibril structure represents a new fold of α-syn, which demonstrates that the E46K mutation breaks the electrostatic interactions in the wild type (WT) α-syn fibril and thus triggers the rearrangement of the overall structure. Furthermore, we show that the Ac-E46K fibril is less resistant to harsh conditions and protease cleavage, and more prone to be fragmented with a higher capability of seeding fibril formation than that of the WT fibril. Our work provides a structural view to the severe pathology of the PD familial mutation E46K of α-syn and highlights the importance of electrostatic interactions in defining the fibril polymorphs.
Establishment of a novel method for the production of chimeric mouse embryos using oil droplets
Authors: Imai Hiroyuki , Tsuda Soichiro , Iwamori Tokuko , Ono Etsuro 
Published: December 2019

AbstractThe production of chimeric animals is frequently necessary for the constructing genetically modified animals, and has gained popularity in regenerative medicine in the recent years for the reconstruction of xenogeneic organs. The aggregation method and the injection method are generally used for producing chimeric mice. In the aggregation method, the chimeras are produced by co-culturing embryos and stem cells, and keeping them physically adhered. In the injection method, the chimeras are produced by injecting stem cells into the zona pellucida using microcapillaries. These methods only focus on the generation of chimeric animals, and are not expected to produce reproducible results or allow quantitative evaluation.This study aimed to establish a novel method for producing chimeric embryos via droplets for improving on the conventional methods that are used for producing chimeric embryos. In this study, the embryonic stem cells and embryos were successfully isolated in the droplets, and the emergence of chimeric embryos was confirmed by co-culture for 6 hours. By this method, the control and operability of stem cell numbers can be regulated, and the method allows better reproducibility and quantification during the production of chimeric embryos. In addition to the conventional methods for producing chimeric embryo, the novel method described herein could be employed for the efficient production of chimeric animals.
Influence of Strontium on the Physical, Mechanical and In-Vitro Bioactivity of Glass Ionomer Cements
Authors: Li Yiyu 
Published: December 2019

AbstractIn this work, we investigated the effects of strontium incorporation in the glass phase of glass ionomer cements (GIC). Three different glass compositions were synthesized with 0, 5, and 10 mol% of SrO addition. GICs were prepared by the addition of 50 wt% polyacrylic acid (PAA) at powder to liquid ratio of 1:1.5. Initial characterization on the cement series was to study their rheological behavior. Cements represented working times between 50-64 seconds and setting times of 356-452 seconds. Rheological results indicated that the addition of strontium decreases the working and setting times of the cements. To analyze the mechanical properties, compressive and flexural strength studies were performed after 1, 10, and 30 days incubation in simulated body fluid. The compressive strength of the cements increased as a function of incubation time, with the strontium containing compositions showing the highest strength at 34 MPa and after 30 days of incubation. Biaxial flexural strength of the cements was not significantly affected by the composition and maturation time and ranged between 13.4 to 16.3 MPa. In-vitro bioactivity of the cements was analyzed using SBF trials and after 1, 10, and 30 days incubation periods. Strontium containing cements, showed higher solubility with higher amounts of calcium phosphate surface depositions only after 10 days incubation. The elemental identifications of the surface depositions indicated high amounts of Ca, P and Zn are present on the surface of SBF incubated samples.
Allosteric feed-forward activation of AP-2viaFCHO-BMP2K axis promotes clathrin-mediated endocytosis
Authors: Ramesh Shikha T. , Navyasree Kolaparamba V. , Ashok Anjitha B. , Qathoon Nishada , Mohanty Suryasikha , Swain Rajeeb K. , Umasankar Perunthottathu K. 
Published: December 2019

AbstractSpatio-temporal regulation of central adaptor complex, AP-2 is pivotal for clathrin-mediated endocytosis (CME). We recently discovered that FCHO proteins trigger clathrin-coated pit (CCP) formation by allosterically activating AP-2 on plasma membrane (Umasankaret al., 2014). Here, we demonstrate that this activation promotes AP-2 phosphorylationviarecruitment and stabilization of BMP-2 inducible kinase (BMP2K), abona fideAP-2 kinase leading to CCP maturation. Accordingly, BMP2K mislocalizes and degrades in FCHO knockout/ AP-2 depleted cells. Functional inactivation of kinase impairs AP-2 phosphorylation leading to altered lattice morphology and CME phenotypes reminiscent of CCP maturation defects. Reexpression of FCHO rescues AP-2 phosphorylation defects in FCHO knockout cells implying membrane activation of AP-2 is a prerequisite for kinase function. Furthermore, gain- and loss-of function phenotypes of FCHO and BMP2K are analogous and mirror altered AP-2 functions during zebrafish embryogenesis. Together, our findings reveal anin vivoallosteric feed-forward axis for operation of CME.
iASPP contributes to cortex rigidity, astral microtubule capture and mitotic spindle positioning
Authors: Mangon Aurélie , Salaün Danièle , Lala Bouali Mohamed , Quitard Sabine , Isnardon Daniel , Audebert Stéphane , Puech Pierre-Henri , Verdier-Pinard Pascal , Badache Ali 
Published: December 2019

AbstractThe microtubule plus-end binding protein EB1 is the core of a complex protein network which regulates microtubule dynamics during important biological processes such as cell motility and mitosis. We found that iASPP, an inhibitor of p53 and predicted regulatory subunit of the PP1 phosphatase, associates with EB1 at microtubule plus-ends via a SxIP motif. iASPP silencing or mutation of the SxIP motif led to defective microtubule capture at the leading edge of migrating cells, and at the cortex of mitotic cells leading to abnormal positioning of the mitotic spindle. These effects were recapitulated by the knockdown of Myosin-Ic (Myo1c), identified as a novel partner of iASPP. Moreover, iASPP or Myo1c knockdown cells failed to round up during mitosis because of defective cortical rigidity. We propose that iASPP, together with EB1 and Myo1c, contributes to mitotic cell cortex rigidity, allowing astral microtubule capture and appropriate positioning of the mitotic spindle.
AUTS2 regulation of synapses for proper synaptic inputs and social communication
Authors: Hori Kei , Yamashiro Kunihiko , Nagai Taku , Shan Wei , Egusa Saki F. , Shimaoka Kazumi , Go Yasuhiro , Tatsumoto Shoji , Yamada Mitsuyo , Shiraishi Reika , Kanno Kouta , Miyashita Satoshi , Sakamoto Asami , Abe Manabu , Sakimura Kenji , Sone Masaki , Sohya Kazuhiro , Kunugi Hiroshi , Yamada Kiyofumi , Hoshino Mikio 
Published: December 2019

AbstractImpairments in synapse development are thought to cause numerous psychiatric disorders.Autism susceptibility candidate 2(AUTS2) gene has been associated with various psychiatric disorders, such as autism and intellectual disabilities. Although roles for AUTS2 in neuronal migration and neuritogenesis have been reported, its involvement in synapse regulation remains unclear. In this study, we found that excitatory synapses were specifically increased in theAuts2-deficient primary cultured neurons as well asAuts2mutant forebrains. Electrophysiological recordings and immunostaining showed increases in excitatory synaptic inputs as well as c-fos expression inAuts2mutant brains, suggesting that an altered balance of excitatory and inhibitory inputs enhances brain excitability.Auts2mutant mice exhibited autistic-like behaviors including impairments in social interaction and altered vocal communication. Together, these findings suggest that AUTS2 regulates excitatory synapse number to coordinate E/I balance in the brain, whose impairment may underlie the pathology of psychiatric disorders in individuals withAUTS2mutations.
Characterization of eyes, photoreceptors and opsins in developmental stages of the chaetognath Spadella cephaloptera
Authors: Wollesen Tim , Rodríguez Monje Sonia Victoria , Oel Adam Phillip , Arendt Detlev 
Published: December 2019

AbstractThe phylogenetic position of chaetognaths has been debated for decades, however recently they have been grouped into the Gnathifera, sister taxon to the Lophotrochozoa. Chaetognaths possess photoreceptor cells that are anatomically unique and arranged remarkably different in the eyes of the various species. Studies investigating eye development and underlying gene regulatory networks are so far missing.In order to gain insights into the development and the molecular toolkit of chaetognath photoreceptors and eyes a new transcriptome of the epibenthic species Spadella cephaloptera was searched for opsins. Our screen revealed single-copies of xenopsin and peropsin and gene expression analyses demonstrated that only xenopsin is expressed in photoreceptor cells of the developing lateral eyes. Adults likewise exhibit two xenopsin+ photoreceptor cells in each of their lateral eyes. Beyond that, a single cryptochrome gene was uncovered and found co-expressed with xenopsin in some photoreceptor cells of the lateral developing eye. In addition, it is co-expressed with peropsin in the cerebral ganglia, a condition reminiscent of a non-visual photoreceptive zone in the apical nervous system of the annelid Platynereis dumerilii that performs circadian entrainment and melatonin release. Cryptochrome expression was also detected in cells of the corona ciliata, a circular organ in the posterior dorsal head region that has been attributed several functions arguing for an involvement of this organ in circadian entrainment. Our study demonstrates the importance to investigate representatives of the Gnathifera, a clade that has been neglected with respect to developmental studies and that might contribute to unravel the evolution of spiralian and bilaterian body plans.
On the use of calcium deconvolution algorithms in practical contexts
Authors: Evans Mathew H. , Petersen Rasmus S. , Humphries Mark D. 
Published: December 2019

AbstractCalcium imaging is a powerful tool for capturing the simultaneous activity of large populations of neurons. Here we determine the extent to which our inferences of neural population activity, correlations, and coding depend on our choice of whether and how we deconvolve the calcium time-series into spike-driven events. To this end, we use a range of deconvolution algorithms to create nine versions of the same calcium imaging data obtained from barrel cortex during a pole-detection task. Seeking suitable values for the deconvolution algorithms’ parameters, we optimise them against ground-truth data, and find those parameters both vary by up to two orders of magnitude between neurons and are sensitive to small changes in their values. Applied to the barrel cortex data, we show that a substantial fraction of the processing methods fail to recover simple features of population activity in barrel cortex already established by electrophysiological recordings. Raw calcium time-series contain an order of magnitude more neurons tuned to features of the pole task; yet there is also qualitative disagreement between deconvolution methods on which neurons are tuned to the task. Finally, we show that raw and processed calcium time-series qualitatively disagree on the structure of correlations within the population and the dimensionality of its joint activity. Collectively, our results show that properties of neural activity, correlations, and coding inferred from calcium imaging are sensitive to the choice of if and how spike-evoked events are recovered. We suggest that quantitative results obtained from population calcium-imaging be verified across multiple processed forms of the calcium time-series.
A Nanomule Peptide-siRNA Conjugate that Traverses the Intact Blood Brain Barrier and Attenuates Stroke
Authors: Eyford Brett A. , Singh Chaahat S.B. , Abraham Thomas , Munro Lonna , Choi Kyung Bok , Hildebrandt Rhonda , Hill Tracy , Welch Ian , Okon Mark , Vitalis Timothy Z. , Gabathuler Reinhard , Gordon Jacob A. , Adomat Hans , Guns Emma S.T. , Lu Chieh-Ju , Pfeifer Cheryl G. , Tian Mei Mei , Jefferies Wilfred A. 
Published: December 2019

AbstractThe blood-brain barrier (BBB), hinders the distribution of therapeutics, intended for treatment of diseases of the brain. A twelve-amino acid peptide, termed MTfp, was derived from MTf, and retains the ability to cross the BBB intact and ferry cargo into intacellular organelles within neurons, glia and microglia in the brain. A novel MTfp-siRNA peptide-oligonucleotide conjugate (POC), directed against NOX4, a gene known to potentiate ischemic stroke, was chemically synthesized. The MTfp-NOX4 siRNA POC traversed the BBB, resulting in the knockdown of NOX4 expression in the brain. Following induction of ischemic stroke, animals treated with the POC exhibited significantly smaller infarcts; accompanied by significant protection against neurological deterioration and improved recovery. The data demonstrates that the MTfp portion, of this novel POC, can facilitate BBB transcytosis; where the siRNA moiety can elicit effective therapeutic knockdown of a gene associated with a disease of the central nervous system (CNS). This is a general platform to transport therapeutics to the CNS and thereby, offers new avenues for potential treatments of neuropathologies that are currently refractory to existing therapies.
Insights into the ligand-free structure of cyclic diguanosine monophosphate I riboswitch of Vibrio cholerae using molecular dynamics simulation
Authors: Kumari Priyanka , Som Anup 
Published: December 2019

AbstractRiboswitches are key cis regulatory elements present at 5’ UTRs of mRNAs. They play a critical role in gene expression regulation at transcriptional and translational level by binding selectively to specific ligands followed by conformational changes. Ligands bind to the aptamer of riboswitches and their complex structures have been solved, but ligand-free riboswitches structures are not available which is important to understand specific ligand binding mechanism. In this paper, an all atom 150 nano-second (ns) molecular dynamics (MD) simulations of cyclic diguanosine monophosphate (c-di-GMP I) riboswitch aptamer domain from Vibrio cholerae were carried out to study ligand-free c-di-GMP I riboswitch aptamer structure and the binding mechanism. The Principle component analysis, cross correlation dynamics analysis and trajectory analyses revealed that the ligand-free structure has stable conformation with folded P2, P3 and an open P1 helix which opens the ligand binding helix-join-helix while the ligand-bound structure shows less deviation and remains as closed structure compared to the ligand-free structure. The junction residues significantly showed anti-correlated motions with each other elucidating the open conformation of the ligand-free aptamer of riboswitch. The identified key residues involved in binding are A18, G20, C46, A47 and C92.HighlightsThe c-di-GMP I riboswitch regulates the essential genes involved in the virulence of human bacterial pathogen V. Cholera.A 150 ns molecular dynamics run was performed to find a ligand-free stable structure of c-di-GMP I riboswitch aptamer.The trajectory analysis resulted in stable conformation of ligand-free structure with folded P2, slightly open P3 and an unwind P1 helix.The atomic level analyses through cross correlation dynamics and RMSF values showed the opening of catalytic pocket and unwinding P1 helix.The identified key residues involved in binding are A18, G20, C46, A47 and C92 at the catalytic pocket.
Voluntary wheel running has no impact on brain and liver mitochondrial DNA copy number or mutation measures in the PolG mouse model of aging
Authors: Maclaine Kendra D. , Stebbings Kevin A. , Llano Daniel A. , Rhodes Justin S. 
Published: December 2019

AbstractThe mitochondrial theory of aging attributes much of the aging process to mitochondrial DNA damage. The PolGAD257A/D257A(PolG) mutant mouse was created to explore the mitochondrial theory of aging and carries a mutated proofreading region of polymerase gamma, which exclusively transcribes the mitochondrial genome. As a result, PolG mice accumulate mitochondrial DNA (mtDNA) mutations which leads to premature aging including hair loss, weight loss, kyphosis, increased rates of apoptosis, organ damage, and eventually, an early death at around 12 months. Exercise has been reported to decrease skeletal muscle mtDNA mutations and normalize protein levels in PolG mice. However, brain mtDNA changes with exercise in PolG mice have not been explored. We found no effects of exercise on mtDNA mutations or copy number in brain or liver in PolG mice, despite effects on body mass. Our results suggest that mitochondrial mutations play little role in exercise-brain interactions in the PolG model of accelerated aging. In addition to evaluating the effect of exercise on mtDNA outcomes, we also implemented novel methods for mtDNA extraction and measuring mtDNA mutations to improve efficiency and accuracy.
In Situ Processing and Efficient Environmental Detection iSPEED of pests and pathogens of trees using point-of-use real-time pcr
Authors: Capron Arnaud , Stewart Don , Hrywkiw Kelly , Allen Kiah , Feau Nicolas , Bilodeau Guillaume , Tanguay Philippe , Cusson Michel , Hamelin Richard C. 
Published: December 2019

AbstractThe increase in global trade is responsible for a surge in foreign invasive species introductions across the world. Early detection and surveillance activities are essential to prevent future invasions. Molecular diagnostics by DNA testing has become an integral part of this process. However, for environmental applications, there is a need for cost-effective and efficient point-of-use DNA testing that would allow for the collection of results in real-time away from laboratory facilities. To achieve this requires the development of simple and fast sample processing and DNA extraction, room-temperature stable reagents and a portable instrument. We conducted a series of tests using a crude buffer-based DNA extraction protocol and lyophilized, pre-made, reactions to address the first two requirements. We chose to demonstrate the use of this approach with organisms that cover a broad spectrum of known undesirable insects and pathogens: the ascomycete Sphaerulina musiva, the oomycete Phytophthora ramorum, the basidiomycetes Cronartium ribicola and Cronartium comandrae and the insect Lymantria dispar. Tests performed from either infected leaf material or spores (pathogens), or legs and antenna (insects). We were able to obtain positive amplification for the targeted species in all the samples tested. The shelf-life of the lyophilized reactions was assessed, confirming the stability of over a year at room temperature. Finally, successful tests conducted with portable thermocyclers and disposable plastics, demonstrating the suitability of the method, named in Situ Processing and Efficient Environment Detection (iSPEED), for field testing. This kit is ideally adapted to field testing as it fits in a backpack and can be carried to remote locations.
Regulation of heterotopic ossification through local inflammatory monocytes in a mouse model of aberrant wound healing
Authors: Sorkin Michael , Huber Amanda K. , Hwang Charles , Carson William F. , Menon Rajasree , Li John , Vasquez Kaetlin , Pagani Chase , Patel Nicole , Li Shuli , Visser Noelle D , Niknafs Yashar , Loder Shawn , Scola Melissa , Nycz Dylan , Gallagher Katherine , McCauley Laurie K. , Xu Jiajia , James Aaron W. , Agarwal Shailesh , Kunkel Stephen , Mishina Yuji , Levi Benjamin 
Published: December 2019

AbstractHeterotopic ossification (HO) is an aberrant regenerative process with ectopic bone induction in response to musculoskeletal trauma, in which mesenchymal stem cells (MSC) differentiate into osteochondrogenic cells instead of myocytes or tenocytes. Despite frequent cases of hospitalized musculoskeletal trauma, the inflammatory responses and cell population dynamics that regulate subsequent wound healing and tissue regeneration are still unclear. Here we examine, using a mouse model of trauma-induced HO, the local microenvironment of the initial post-injury inflammatory response. Single cell transcriptome analyses identify distinct monocyte/macrophage populations at the injury site, with their dynamic changes over time elucidated using trajectory analyses. Mechanistically, transforming growth factor beta-1 (TGFβ1)-producing monocytes/macrophages are associated with HO and aberrant chondrogenic progenitor cell differentiation, while CD47-activating peptides that reduce systemic TGFβ levels help ameliorate HO. Our data thus implicate CD47 activation as a novel therapeutic approach for modulating monocyte/macrophage phenotypes, MSC differentiation and HO formation during wound healing.
The Euler Characteristic and Topological Phase Transitions in Complex Systems
Authors: de Amorim Filho Edgar C. , Moreira Rodrigo A. , Santos Fernando A N 
Published: December 2019

AbstractIn this work, we use methods and concepts of applied algebraic topology to comprehensively explore the recent idea of topological phase transitions (TPT) in complex systems. TPTs are characterized by the emergence of nontrivial homology groups as a function of a threshold parameter. Under certain conditions, one can identify TPT’s via the zeros of the Euler characteristic or by singularities of the Euler entropy. Recent works provide strong evidence that TPTs can be interpreted as a complex network’s intrinsic fingerprint. This work illustrates this possibility by investigating some classic network and empirical protein interaction networks under a topological perspective. We first investigate TPT in protein-protein interaction networks (PPIN) using methods of topological data analysis for two variants of the Duplication-Divergence model, namely, the totally asymmetric model and the heterodimerization model. We compare our theoretical and computational results to experimental data freely available for gene co-expression networks (GCN) of Saccharomyces cerevisiae, also known as baker’s yeast, as well as of the nematode Caenorhabditis elegans. Supporting our theoretical expectations, we can detect topological phase transitions in both networks obtained according to different similarity measures. Later, we perform numerical simulations of TPTs in four classical network models: the Erdős-Renyi model, the Watts-Strogatz model, the Random Geometric model, and the Barabasi-Albert. Finally, we discuss some perspectives and insights on the topic. Given the universality and wide use of those models across disciplines, our work indicates that TPT permeates a wide range of theoretical and empirical networks.