bluuebunny/crossref_metadata_2025_split huggingface dataset:
CyanoGate: A Golden Gate modular cloning suite for engineering cyanobacteria based on the plant MoClo syntax
Authors: Vasudevan Ravendran , Gale Grant A.R. , Schiavon Alejandra A. , Puzorjov Anton , Malm John , Gillespie Michael D. , Vavitsas Konstantinos , Zulkower Valentin , Wang Baojun , Howe Christopher J. , Lea-Smith David , McCormick Alistair J. 
Published: October 2018

ABSTRACTRecent advances in synthetic biology research have been underpinned by an exponential increase in available genomic information and a proliferation of advanced DNA assembly tools. The adoption of plasmid vector assembly standards and parts libraries has greatly enhanced the reproducibility of research and exchange of parts between different labs and biological systems. However, a standardised Modular Cloning (MoClo) system is not yet available for cyanobacteria, which lag behind other prokaryotes in synthetic biology despite their huge potential in biotechnological applications. By building on the assembly library and syntax of the Plant Golden Gate MoClo kit, we have developed a versatile system called CyanoGate that unites cyanobacteria with plant and algal systems. We have generated a suite of parts and acceptor vectors for making i) marked/unmarked knock-outs or integrations using an integrative acceptor vector, and ii) transient multigene expression and repression systems using known and novel replicative vectors. We have tested and compared the CyanoGate system in the established model cyanobacteriumSynechocystissp. PCC 6803 and the more recently described fast-growing strainSynechococcus elongatusUTEX 2973. The system is publicly available and can be readily expanded to accommodate other standardised MoClo parts.
Coverage and timeliness of vaccination and the validity of routine estimates: Insights from a Vaccine Registry in Kenya
Authors: Adetifa Ifedayo M.O. , Karia Boniface , Mutuku Alex , Bwanaali Tahreni , Makumi Anne , Wafula Jackline , Chome Martina , Mwatsuma Pauline , Bauni Evasius , Hammitt Laura L , Mataza Christine , Tabu Collins , Kamau Tatu , William Thomas N. , G. Scott J. Anthony 
Published: October 2018

AbstractThe benefits of childhood vaccines are critically dependent on vaccination coverage. We used a vaccine registry (as gold standard) in Kenya to quantify errors in routine coverage methods (surveys and administrative reports), to estimate the magnitude of survivor bias, contrast coverage with timeliness and use both measures to estimate population immunity.We found coverage surveys in the 2nd year of life overestimate coverage by 2%. Compared to mean coverage in infants, static coverage at 12 months was exaggerated by 7–8% for third doses of oral polio, pentavalent (Penta3) and pneumococcal conjugate vaccines, and by 24% for the measles vaccine. Surveys and administrative coverage also underestimated the proportion of the fully immunised child by 10–14%. For BCG, Penta3 and measles, timeliness was 23–44% higher in children born in a health facility but 20–37% lower in those who first attended during vaccine stock outs.Coverage surveys in 12–23 month old children overestimate protection by ignoring timeliness, and survivor and recall biases.
Multimodal interferometric imaging of nanoscale structure and macromolecular motion uncovers UV induced cellular paroxysm
Authors: Gladstein Scott , Almassalha Luay M. , Cherkezyan Lusik , Chandler John E. , Eshein Adam , Eid Aya , Zhang Di , Wu Wenli , Bauer Greta M. , Stephens Andrew D. , Morochnik Simona , Subramanian Hariharan , Marko John F. , Ameer Guillermo A. , Szleifer Igal , Backman Vadim 
Published: October 2018

AbstractWe present a multimodal label-free interferometric imaging platform for measuring intracellular nanoscale structure and macromolecular dynamics in living cells with a sensitivity to macromolecules as small as 20nm and millisecond temporal resolution. We validate this system by pairing experimental measurements of nanosphere phantoms with a novel interferometric theory. Applying this system in vitro, we explore changes in higher-order chromatin structure and dynamics that occur due to cellular fixation, stem cell differentiation, and ultraviolet (UV) light irradiation. Finally, we discover a new phenomenon, cellular paroxysm, a near-instantaneous, synchronous burst of motion that occurs early in the process of UV induced cell death. Given this platform’s ability to obtain nanoscale sensitive, millisecond resolved information within live cells without concerns of photobleaching, it has the potential to answer a broad range of critical biological questions about macromolecular behavior in live cells, particularly about the relationship between cellular structure and function.
Bridging the spatiotemporal scales of macromolecular transport in crowded biomimetic systems
Authors: Regan Kathryn , Wulstein Devynn , Rasmussen Hannah , McGorty Ryan , Robertson-Anderson Rae M. 
Published: October 2018

AbstractCrowding plays a key role in the transport and conformations of biological macromolecules. Gene therapy, viral infection and transfection require DNA to traverse the crowded cytoplasm, including a heterogeneous cytoskeleton of filamentous proteins. Given the complexity of cellular crowding, the dynamics of biological molecules can be highly dependent on the spatiotemporal scale probed. We present a powerful platform that spans molecular and cellular scales by coupling single-molecule conformational tracking (SMCT) and selective-plane illumination differential dynamic microscopy (SPIDDM). We elucidate the transport and conformational properties of large DNA, crowded by custom-designed networks of actin and microtubules, to link single-molecule conformations with ensemble DNA transport and cytoskeleton structure. We show that actin crowding leads to DNA compaction and suppression of fluctuations, combined with anomalous subdiffusion and heterogeneous transport, whereas microtubules have much more subdued impact across all scales. Interestingly, in composite networks of both filaments, microtubules primarily govern single-molecule DNA dynamics whereas actin governs ensemble transport.
Straightjacket/α2δ3deregulation is associated with cardiac conduction defects in Myotonic Dystrophy type 1
Authors: Plantié Emilie , Nakamori Masayuki , Renaud Yoan , Huguet Aline , Choquet Caroline , Dondi Cristiana , Miquerol Lucile , Takahashi Masanori , Gourdon Geneviève , Junion Guillaume , Jagla Teresa , Zmojdzian Monika , Jagla Krzysztof 
Published: October 2018

ABSTRACTCardiac conduction defects decrease life expectancy in myotonic dystrophy type 1 (DM1), a complex toxic CTG repeat disorder involving misbalance between two RNA- binding factors, MBNL1 and CELF1. How this pathogenic DM1 condition translates into cardiac conduction disorders remains poorly understood. Here, we simulated MBNL1 and CELF1 misbalance in theDrosophilaheart and identified associated gene deregulations using TU-tagging based transcriptional profiling of cardiac cells. We detected deregulations of several genes controlling cellular calcium levels and among them increased expression ofstraightjacket/α2δ3that encodes a regulatory subunit of a voltage-gated calcium channel.Straightjacketoverexpression in the fly heart leads to asynchronous heart beating, a hallmark of affected conduction, whereas cardiacstraightjacketknockdown improves these symptoms in DM1 fly models. We also show that ventricularα2δ3expression is low in healthy mice and humans but significantly elevated in ventricular muscles from DM1 patients with conduction defects. Taken together, this suggests that reducing thestraightjacket/α2δ3transcript levels in ventricular cardiomyocytes could represent a strategy to prevent conduction defects and in particular intraventricular conduction delay associated with DM1 pathology.
Redistribution of a glucuronoxylomannan epitope towards the capsule surface coincides with Titanisation in the human fungal pathogenCryptococcus neoformans
Authors: Probert Mark , Zhou Xin , Goodall Margaret , Johnston Simon A. , Bielska Ewa , Ballou Elizabeth R. , May Robin C. 
Published: October 2018

AbstractDisseminated infections with the fungal speciesCryptococcus neoformansor, less frequently,C. gattii,are a leading cause of mortality in immunocompromised individuals. Central to the virulence of both species is an elaborate polysaccharide capsule that consists predominantly of glucuronoxylomannan (GXM). Due to its abundance, GXM is an ideal target for host antibodies, and several monoclonal antibodies (mAbs) have previously been derived using purified GXM or whole capsular preparations as antigen. In addition to their application in the diagnosis of cryptococcosis, anti-GXM mAbs are invaluable tools for studying capsule structure. In this study, we report the production and characterisation of a novel anti-GXM mAb, Crp127, that unexpectedly reveals a role for GXM remodelling during the process of fungal Titanisation. We show that Crp127 recognises a GXM epitope in anO-acetylation dependent, but xylosylation-independent, manner. The epitope is differentially expressed by the four main serotypes ofCryptococcus neoformansandgattii,is heterogeneously expressed within clonal populations ofC. gattiiserotype B strains and is typically confined to the central region of the enlarged capsule. Uniquely, however, this epitope redistributes to the capsular surface in Titan cells, a recently recognised subset of giant fungal cells that are produced in the host lung and are critical for successful infection. Crp127 therefore highlights hitherto unexpected features of cryptococcal morphological change and may hold significant therapeutic potential in differentially identifying cryptococcal strains and subtypes.ImportanceCryptococcus neoformansandCryptococcus gattiiare the etiological agents of cryptococcosis, an invasive fungal infection responsible for approximately 200,000 deaths each year and 15% of AIDS-related deaths annually. Whilst the main virulence factor for both species is a highly variable polysaccharide capsule, formation of Titan cells also underlies the pathogenesis ofC. neoformans.Previous studies have shown that capsule composition differs between yeast and Titan cells, however no clear distinctions in the expression or localisation of specific capsular epitopes have been made. In this study, we characterise a novel monoclonal antibody (mAb) specific to a capsular epitope that is differentially distributed throughout the capsules produced by yeast and Titan cells. Whilst this epitope is found within the midzone of yeast capsules, the presentation of this epitope on the surface of Titan cell capsules may represent a way in which these cell types are perceived differently by the immune system.
Immune regeneration in irradiated mice is not impaired by the absence of DPP9 enzymatic activity
Authors: Gall Margaret G. , Zhang Hui Emma , Cook Adam , Jolly Christopher J. , McCaughan Geoffrey W. , Roediger Ben , Gorrell Mark D. 
Published: October 2018

AbstractThe ubiquitous intracellular protease dipeptidyl peptidase 9 (DPP9) has roles in antigen presentation and B cell signaling. To investigate the importance of DPP9 in immune regeneration, primary and secondary chimeric mice were created in irradiated recipients using fetal liver cells and adult bone marrow cells, respectively, using wild-type (WT) and DPP9 gene-knockin (DPP9S729A) enzyme-inactive mice. Immune cell reconstitution was assessed at 6 and 16 weeks post-transplant. Primary chimeric mice successfully regenerated neutrophils, natural killer, T and B cells, irrespective of donor cell genotype. There were no significant differences in total myeloid cell or neutrophil numbers between DPP9-WT and DPP9S729A-reconstituted mice. There were fewer B cells in the DPP9S729A-origin compared to DPP9 WT-origin mice in primary chimeric mice. In secondary chimeric mice, cells of DPP9S729A-origin cells displayed enhanced engraftment compared to WT. However, we observed no differences in myeloid or lymphoid lineage reconstitution between WT and DPP9S729A donors, indicating that hematopoietic stem cell (HSC) engraftment and self-renewal is not diminished by the absence of DPP9 enzymatic activity. This is the first report on transplantation of bone marrow cells that lack DPP9 enzymatic activity.
Proteomic Profile of TGF-β1 treated Lung Fibroblasts identifies Novel Markers of Activated Fibroblasts in the Silica Exposed Rat Lung
Authors: Na Mao , Hong Xu , Fuyu Jin , Dingjie Xu , Sales Dominic , Hui Zhang , Zhongqiu Wei , Shifeng Li , Xuemin Gao , Wenchen Cai , Dan Li , Guizhen Zhang , Bonan Zhang , Lijuan Zhang , Shumin Li , Ying Zhu , Jin Wang , Mingwang Rui , Summer Ross , Fang Yang 
Published: October 2018

ABSTRACTWe performed liquid chromatography-tandem mass spectrometry (LC-MS/MS) on control and TGF-β1-exposed rat lung fibroblasts to identify proteins differentially expressed between cell populations. A total of 1648 proteins were found to be differentially expressed in response to TGF-β1 treatment and 196 proteins were expressed at ≥ 1.2 fold relative to control. Guided by these results, we next determined whether similar changes in protein expression were detectable in the rat lung after chronic exposure to silica dust. Of the five proteins selected for further analysis, we found that levels of all proteins were markedly increased in the silica-exposed rat lung, including the proteins for the very low density lipoprotein receptor (VLDLR) and the transmembrane (type I) heparin sulfate proteoglycan called syndecan 2 (SDC2). Because VLDLR and SDC2 have not, to our knowledge, been previously linked to the pathobiology of silicosis, we next examined whether knockdown of either gene altered responses to TGF-β1 in MRC-5 lung fibroblasts. Interestingly, we found knockdown of either VLDLR or SDC2 dramatically reduced collagen production to TGF-β1, suggesting that both proteins might play a novel role in myofibroblast biology and pathogenesis of silica-induced pulmonary fibrosis. In summary, our findings suggest that performing LC-MS/MS on TGF-β1 stimulated lung fibroblasts can uncover novel molecular targets of activated myofibroblasts in silica-exposed lung.HighlightsWe identified 196 proteins differentially expressed between control and TGF-β1 treated fibroblastsby LC-MS/MS.Several proteins identified by LC-MS/MS were also found to be differentially expressed in whole lung tissues and isolated fibroblasts after chronic exposure to silica dust, including the very low density lipoprotein receptor (VLDLR) and the transmembrane type I heparan sulfate proteoglycan called syndecan 2Knockdown of SDC2 or VLDLR markedly inhibited collagen production in MRC-5 fibroblasts, suggesting a novel pathogenic role for these proteins in myofibroblast biology.
In vivo characterisation of fluorescent proteins in budding yeast
Authors: Botman Dennis , de Groot Daan Hugo , Schmidt Phillipp , Goedhart Joachim , Teusink Bas 
Published: October 2018

AbstractFluorescent proteins (FPs) are widely used in many organisms, but are commonly characterised in vitro. However, the in vitro properties may poorly reflect in vivo performance. Therefore, we characterised 27 FPs in vivo using Saccharomyces cerevisiae as model organism. We linked the FPs via a T2A peptide to a control FP, producing equimolar expression of the 2 FPs from 1 plasmid. Using this strategy, we characterised the FPs for brightness, photostability, photochromicity and pH-sensitivity, achieving a comprehensive in vivo characterisation. Many FPs showed different in vivo properties compared to existing in vitro data. Additionally, various FPs were photochromic, which affects readouts due to complex bleaching kinetics. Finally, we codon optimized the best performing FPs for optimal expression in yeast, and found that codon-optimization alters FP characteristics. These FPs improve experimental signal readout, opening new experimental possibilities. Our results may guide future studies in yeast that employ fluorescent proteins.
Motor context dominates output from Purkinje cell functional regions during reflexive visuomotor behaviours
Authors: Knogler Laura D. , Kist Andreas M. , Portugues Ruben 
Published: October 2018

SUMMARYThe cerebellum integrates sensory stimuli and motor actions to enable smooth coordination and motor learning. Here we harness the innate behavioral repertoire of the larval zebrafish to characterize the spatiotemporal dynamics of feature coding across the entire Purkinje cell population during visual stimuli and the reflexive behaviors that they elicit. Population imaging reveals three spatially-clustered regions of Purkinje cell activity along the rostrocaudal axis. Complementary single-cell electrophysiological recordings assign these Purkinje cells to one of three functional phenotypes that encode a specific visual, and not motor, signal via complex spikes. In contrast, simple spike output of most Purkinje cells is strongly driven by motor-related tail and eye signals. Interactions between complex and simple spikes show heterogeneous modulation patterns across different Purkinje cells, which become temporally restricted during swimming episodes. Our findings reveal how sensorimotor information is encoded by individual Purkinje cells and organized into behavioral modules across the entire cerebellum.
Fate-mapping within human kidney organoids reveals conserved mammalian nephron progenitor lineage relationships
Authors: Howden Sara E , Vanslambrouck Jessica M , Wilson Sean B , Tan Ker Sin , Little Melissa H 
Published: October 2018

AbstractWhile mammalian kidney morphogenesis has been well documented, human kidney development is poorly understood. Here we combine reprogramming, CRISPR/Cas9 gene-editing and organoid technologies to study human nephron lineage relationships in vitro. Early kidney organoids contained a SIX2+ population with a transcriptional profile akin to human nephron progenitors. Lineage-tracing using gene-edited induced pluripotent stem cell (iPSC) lines revealed that SIX2-expressing cells contribute to nephron formation but not to the putative collecting duct epithelium. However, Cre-mediated temporal induction of the SIX2+ lineage revealed a declining capacity for these cells to contribute to nephron formation over time. This suggests human kidney organoids, unlike the developing kidney in vivo, lack a nephron progenitor niche capable of both self-renewal and ongoing nephrogenesis. Nonetheless, human iPSC-derived kidney tissue maintains previously identified lineage relationships supporting the utility of pluripotent stem cell-derived kidney organoids for interrogating the molecular and cellular basis of early human development.
IRE1α is critical for kaempferol induced neuroblastoma differentiation
Authors: Abdullah Ahmad , Talwar Priti , Ravanan Palaniyandi 
Published: October 2018

AbstractNeuroblastoma is an embryonic malignancy arises out of the neural crest cells of the sympathetic nervous system. It is the most common childhood tumor and well known for its spontaneous regression via the process of differentiation. The induction of differentiation using small molecule modulators such as all trans retinoic acid is one of the treatment strategies to treat the residual disease. In this study, we have reported the effect of kaempferol, a phytoestrogen in inducing differentiation of neuroblastoma cellsin vitro. Treatment of neuroblastoma cells with kaempferol reduced the proliferation and enhanced apoptosis along with the induction of neuritogenesis. Analysis of the expression of neuron specific markers such as β III tubulin, neuron specific enolase and NRDG1 (N-myc down regulated gene 1) revealed the process of differentiation accompanying kaempferol induced apoptosis. Further analysis on understanding the molecular mechanism of action showed that the activity of kaempferol happened through the activation of the endoribonuclease activity of IRE1α (Inositol requiring enzyme 1 alpha), an endoplasmic reticulum (ER) resident transmembrane protein. Thein silicodocking analysis and biochemical assays using recombinant human IRE1α confirms the binding of kaempferol to the ATP binding site of IRE1α and thereby activating ribonuclease activity. Treatment of cells with the small molecule inhibitor STF083010 which specifically targets and inhibits the endoribonuclease activity of IRE1α showed reduced expression of neuron specific markers and curtailed neuritogenesis. The knock down of IRE1α using plasmid based shRNA lentiviral particles also showed diminished changes in the change in morphology of the cells upon kaempferol treatment. Thus our study suggests that kaempferol induces differentiation of neuroblastoma cells via the IRE1α-XBP1 pathway.
Modulation of Resting Connectivity Between the Mesial Frontal Cortex and Basal Ganglia
Authors: Popa Traian , Morris Laurel S. , Hunt Rachel , Deng Zhi-De , Horovitz Silvina , Mente Karin , Shitara Hitoshi , Baek Kwangyeol , Hallett Mark , Voon Valerie 
Published: October 2018

AbstractThe mesial prefrontal cortex, cingulate cortex and the ventral striatum are key nodes of the human mesial fronto-striatal circuit involved in decision-making and executive function and pathological disorders. Here we ask whether deep wide-field repetitive transcranial magnetic stimulation (rTMS) targeting the mesial prefrontal cortex (MPFC) influences resting state functional connectivity. In Study 1, we examined functional connectivity using resting state multi-echo and independent components analysis in 154 healthy subjects to characterize default connectivity in the MPFC and mid-cingulate cortex (MCC). In Study 2, we used inhibitory, 1 Hz deep rTMS with the H7-coil targeting MPFC and dorsal anterior cingulate (dACC) in a separate group of 20 healthy volunteers and examined pre-and post-TMS functional connectivity using seed-based and independent components analysis. In Study 1, we show that MPFC and MCC have distinct patterns of functional connectivity with MPFC–ventral striatum showing negative, whereas MCC–ventral striatum showing positive functional connectivity. Low-frequency rTMS decreased functional connectivity of MPFC and dACC with the ventral striatum. We further showed enhanced connectivity between MCC and ventral striatum. These findings emphasize how deep inhibitory rTMS using the H7-coil can influence underlying network functional connectivity by decreasing connectivity of the targeted MPFC regions, thus potentially enhancing response inhibition and decreasing drug cue reactivity processes relevant to addictions. The unexpected finding of enhanced default connectivity between MCC and ventral striatum may be related to the decreased influence and connectivity between the MPFC and MCC. These findings are highly relevant to the treatment of disorders relying on the mesioprefrontal–cingulo–striatal circuit.