bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate MS-based Rab10 phosphorylation stoichiometry determination as readout for LRRK2 activity in Parkinson’s disease
Authors: Karayel Özge , Tonelli Francesca , Winter Sebastian Virreira , Geyer Phillip E. , Fan Ying , Sammler Esther M. , Alessi Dario R. , Steger Martin , Mann Matthias 
Published: October 2019

AbstractPathogenic mutations in the Leucine-rich repeat kinase 2 (LRRK2) are the predominant genetic cause of Parkinson’s disease (PD). They increase its activity, resulting in augmented Rab10-Thr73 phosphorylation and conversely, LRRK2 inhibition decreases pRab10 levels. However, there is no assay to quantify pRab10 levels for drug target engagement or patient stratification. We developed an ultra-sensitive targeted mass spectrometry (MS)-based assay for determining Rab10-Thr73 phosphorylation stoichiometry in human samples. It uses synthetic stable isotope-labeled (SIL) analogues for both phosphorylated and non-phosphorylated tryptic peptides surrounding Rab10-Thr73 to directly derive the percentage of Rab10 phosphorylation from attomole amounts of the endogenous phosphopeptide. We test the reproducibility of our assay by determining Rab10-Thr73 phosphorylation stoichiometry in human neutrophils before and after LRRK2 inhibition. Compared to healthy controls, neutrophils of LRRK2 G2019S and VPS35 D620N carriers robustly display 1.4-fold and 3.7-fold increased pRab10 levels, respectively. Our generic MS-based assay further establishes the relevance of pRab10 as a prognostic PD marker and is a powerful tool for determining LRRK2 inhibitor efficacy and for stratifying PD patients for LRRK2 inhibitor treatment.
A hierarchical framework for segmenting movement paths
Authors: Getz Wayne M. 
Published: October 2019

AbstractComparative applications of animal movement path analyses are hampered by the lack of a comprehensive framework for linking structures and processes conceived at different spatio-temporal scales. Although many analyses begin by generating step-length (SL) and turning-angle (TA) distributions from relocation time-series data—some of which are linked to ecological, landscape, and environmental covariates—the frequency at which these data are collected may vary from sub-seconds to several hours, or longer. The kinds of questions that may be asked of these data, however, are very much scale-dependent. It thus behooves us to clarify how the scale at which SL and TA data are collected and relate to one another, as well as the kinds of ecological questions that can be asked. Difficulties arise because the information contained in SL and TA time series is not semantically aligned with the physiological, ecological, and sociological factors that influence the structure of movement paths. I address these difficulties by classifying movement types at salient temporal scales using two different kinds of vocabularies. The first is the language derived from behavioral and ecological concepts. The second is the language derived from mathematically formulated stochastic walks. The primary tools for analyzing these walks are fitting time-series and stochastic-process models to SL and TA statistics (means, variances, correlations, individual-state and local environmental covariates), while paying attention to movement patterns that emerge at various spatial scales. The purpose of this paper is to lay out a more coherent, hierarchical, scale-dependent, appropriate-complexity framework for conceptualizing path segments at different spatio-temporal scales and propose a method for extracting a simulation model, referred to as M3, from these data when at a relatively high frequencies (ideally minute-by-minute). Additionally, this framework is designed to bridge biological and mathematical movement ecology concepts; thereby stimulating the development of conceptually-rooted methods that facilitates the formulation of our M3model for simulating theoretical and analyzing empirical data, which can then be used to test hypothesis regarding mechanisms driving animal movement and make predications of animal movement responses to management and global change.
Kinesin KIF18A is a novel PUM regulated target promoting mitotic progression and survival of human male germ cell line - TCam-2
Authors: Smialek Maciej Jerzy , Kuczynska Bogna , Ilaslan Erkut , Janecki Damian Mikolaj , Sajek Marcin Piotr , Kusz-Zamelczyk Kamila , Jaruzelska Jadwiga 
Published: October 2019

ABSTRACTRegulation of proliferation, apoptosis and cell cycle is crucial for the physiology of germ cells. Their malfunction contributes to infertility and germ cell tumours. Kinesin KIF18A is an important germ cell specific regulator which downregulates apoptosis while promoting cell proliferation in animal models. Whereas regulation of KIF18A expression was studied at the transcriptional level, its posttranscriptional regulation has not been extensively explored. Due to the presence of two PUM Binding Elements (PBEs) within 3’UTR,KIF18AmRNA is a potential target of PUMs, well known RNA-binding proteins involved in posttranscriptional gene regulation (PTGR). We investigated that possibility in TCam-2 cells originating from seminoma, representing human male germ cells. We conducted RNA co-immunoprecipitation combined with RT-qPCR, as well as luciferase reporter assay by applying appropriate luciferase construct encoding the wild typeKIF18A3’UTR, upon PUM1 and PUM2 overexpression or knockdown. We found that KIF18A is repressed by PUM1 and PUM2. To study how this regulation influences KIF18A function in TCam-2 cells, MTS proliferation assay, apoptosis and cell cycle, analysis using flow cytometry was performed uponKIF18AsiRNA knockdown. We uncovered that KIF18A significantly influences proliferation, apoptosis and cell cycle, these effects being opposite to PUM effects in TCam-2 cells. We propose that repression by PUM proteins may represent one of mechanisms influencing KIF18A level in controlling proliferation, cell cycle and apoptosis in TCam-2 cells. To the best of our knowledge, this paper identifies the first mammalian functionally germ cell specific gene that is regulated by Pum proteins via 3’UTR.
Repetita iuvant: repetition facilitates online planning of sequential movements
Authors: Ariani Giacomo , Kwon Young Han , Diedrichsen Jörn 
Published: October 2019

AbstractBeyond being essential for long-term motor-skill development, movement repetition has immediate benefits on performance, increasing speed and accuracy of a second execution. While repetition effects have been reported for single reaching movements, it has yet to be determined whether they also occur for movement sequences, and what aspects of sequence production are improved. We addressed these questions in two behavioral experiments using a discrete sequence production (DSP) task in which human volunteers had to perform short sequences of finger movements. In Experiment 1, we presented participants with randomly varying sequences and manipulated 1) whether the same sequence was repeated on successive trials, and 2) whether participants had to execute the sequence (Go), or not (No-Go). We establish that sequence repetition led to immediate improvements in speed without associated accuracy costs. The largest benefit was observed in the middle part of a sequence, suggesting that sequence repetition facilitated online planning. This claim was further supported by Experiment 2, in which we kept a set of sequences fixed throughout the experiment, thus allowing participants to develop sequence-specific learning: once the need for online planning decreased, the benefit of repetition disappeared. Finally, we found that repetition-related improvements only occurred for the trials that had been preceded by sequence production, suggesting that action selection and sequence pre-planning may not be sufficient to reap the benefits of repetition. Together, these results show that repetition can enhance representations at the level of movement sequences (rather than of individual movements) and facilitate online planning.New & NoteworthyEven for overlearned motor skills such as reaching, movement repetition improves performance. How brain processes associated with motor planning or execution benefit from repetition, however, remains unclear. Here we report the novel finding of repetition effects for sequential movements. Our results show that repetition benefits are tied to improved online planning of upcoming sequence elements. We also highlight how actual movement experience appears to be more beneficial than mental rehearsal for observing short-term repetition effects.
Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the Sodalis genus
Authors: Hall Rebecca J. , Thorpe Stephen , Thomas Gavin H. , Wood A. Jamie 
Published: October 2019

1AbstractInsect-bacterial symbioses are ubiquitous, but there is still much to uncover about how these relationships establish, persist and evolve. The tsetse endosymbiont Sodalis glossinidius displays intriguing metabolic adaptations to its microenvironment, but the process by which this relationship evolved remains to be elucidated. The recent chance discovery of the free-living secies of the Sodalis genus, S. praecaptivus, provides a serendipitous starting point from which to investigate the evolution of this symbiosis. Here, we present a flux balance model for S. praecaptivus. Metabolic modelling is used in combination with a multi-objective evolutionary algorithm to explore the trajectories that S. glossinidius may have undertaken after becoming internalised. The time-dependent loss of key genes is shown to influence the evolved populations, providing possible targets for future in vitro genetic manipulation. This method provides an unusually detailed perspective on possible evolutionary trajectories for S. glossinidius in this fundamental process of evolutionary and ecological change.
Targeting the PI5P4K lipid kinase family in cancer using novel covalent inhibitors
Authors: Sivakumaren Sindhu Carmen , Shim Hyeseok , Zhang Tinghu , Ferguson Fleur M. , Lundquist Mark R. , Browne Christopher M. , Seo Hyuk-Soo , Paddock Marcia N. , Manz Theresa D. , Jiang Baishan , Hao Ming-Feng , Krishnan Pranav , Wang Diana G. , Yang T. Jonathan , Kwiatkowski Nicholas P. , Ficarro Scott B. , Cunningham James M. , Marto Jarrod A. , Dhe-Paganon Sirano , Cantley Lewis C. , Gray Nathanael S. 
Published: October 2019

SummaryThe PI5P4Ks have been demonstrated to be important for cancer cell proliferation and other diseases. However, the therapeutic potential of targeting these kinases is understudied due to a lack of potent, specific small molecules available. Here we present the discovery and characterization of a novel pan-PI5P4K inhibitor, THZ-P1-2, that covalently targets cysteines on a disordered loop in PI5P4Kα/β/γ. THZ-P1-2 demonstrates cellular on-target engagement with limited off-targets across the kinome. AML/ALL cell lines were sensitive to THZ-P1-2, consistent with PI5P4K’s reported role in leukemogenesis. THZ-P1-2 causes autophagosome clearance defects and upregulation in TFEB nuclear localization and target genes, disrupting autophagy in a covalent-dependent manner and phenocopying the effects of PI5P4K genetic deletion. Our studies demonstrate that PI5P4Ks are tractable targets, with THZ-P1-2 as a useful tool to further interrogate the therapeutic potential of PI5P4K inhibition and inform drug discovery campaigns for these lipid kinases in cancer metabolism and other autophagy-dependent disorders.
Contribution of fungal microbiome to intestinal physiology, early-life immune development and mucosal inflammation in mice
Authors: van Tilburg Bernardes Erik , Pettersen Veronika Kuchařová , Gutierrez Mackenzie W. , Laforest-Lapointe Isabelle , Jendzjowsky Nicholas G. , Cavin Jean-Baptiste , Vicentini Fernando A. , Keenan Catherine M. , Ramay Hena R. , Samara Jumana , MacNaughton Wallace K. , Wilson Richard J. A. , Kelly Margaret M. , McCoy Kathy D. , Sharkey Keith A. , Arrieta Marie-Claire 
Published: October 2019

AbstractGut microbiomes make major contributions to the physiological and immunological development of the host, but the relative importance of their bacterial and fungal components, and how they interact, remain largely unknown. We applied carefully controlled experiments in gnotobiotic mice colonized with defined communities of bacteria, fungi, or both to differentiate the direct role of fungi on microbiome assembly, host development, and susceptibility to colitis and airway inflammation. Our results revealed that fungal colonization alone was insufficient to promote the intestinal anatomic and physiological changes seen in mice colonized by bacteria, and had limited impact on the fecal metabolome. However, fungal colonization promoted major shifts in bacterial microbiome ecology, and had an independent effect on the innate and adaptive immune development in young mice. Fungi further exacerbated some aspects of the inflammatory effects of the bacterial community during OVA-induced airway inflammation by promoting macrophage infiltration in the airway. Our results demonstrate a dominant ecological and physiological role of bacteria in gut microbiomes, but highlight fungi as an ecological factor shaping the assembly of the bacterial community and a direct capacity to impact immune system and modulate disease susceptibility. These findings demonstrate that studies focused on bacteria alone provide an incomplete portrayal on microbiome ecology and functionality, and prompt for the inclusion of fungi in human microbiome studies.
Cortical contraction drives the 3D patterning of epithelial cell surfaces
Authors: van Loon Aaron P. , Erofeev Ivan S. , Maryshev Ivan V. , Goryachev Andrew B. , Sagasti Alvaro 
Published: October 2019

ABSTRACTCellular protrusions create complex cell surface topographies, but biomechanical mechanisms regulating their formation and arrangement are largely unknown. To study how protrusions form, we focused on the morphogenesis of microridges, elongated actin-based structures projecting from the apical surfaces of zebrafish skin cells that are arranged in labyrinthine patterns. Microridges form by accreting simple finger-like precursors. Live imaging demonstrated that microridge morphogenesis is linked to apical constriction. A non-muscle myosin II (NMII) reporter revealed pulsatile contractions of the actomyosin cortex; inhibiting NMII demonstrated that contractions are required for apical constriction and microridge formation. A biomechanical model suggested that contraction reduces surface tension to permit the fusion of precursors into microridges. Indeed, reducing surface tension with hyperosmolar media promoted microridge formation. In anisotropically stretched cells, microridges formed by precursor fusion along the stretch axis, which computational modeling explained as a consequence of stretch-induced cortical flow. Collectively, our results demonstrate how contraction within the 2D plane of the cortex patterns 3D cell surfaces.SUMMARYMicroridges, elongated 3D protrusions arranged in maze-like patterns on zebrafish skin cells, form by the accretion of simple precursor projections. Modeling and in vivo experiments showed that cortical contractions promote the coalescence of precursors into microridges by reducing membrane tension.
The Impact of Cross-Species Gene Flow on Species Tree Estimation
Authors: Jiao Xiyun , Flouris Thomas , Rannala Bruce , Yang Ziheng 
Published: October 2019

ABSTRACTRecent analyses of genomic sequence data suggest cross-species gene flow is common in both plants and animals, posing challenges to species tree inference. We examine the levels of gene flow needed to mislead species tree estimation with three species and either episodic introgressive hybridization or continuous migration between an outgroup and one ingroup species. Several species tree estimation methods are examined, including the majority-vote method based on the most common gene tree topology (with either the true or reconstructed gene trees used), the UPGMA method based on the average sequence distances (or average coalescent times) between species, and the full-likelihood method based on multi-locus sequence data. Our results suggest that the majority-vote method is more robust to gene flow than the UPGMA method and both are more robust than likelihood assuming a multispecies coalescent (MSC) model with no cross-species gene flow. A small amount of introgression or migration can mislead species tree methods if the species diverged through speciation events separated by short time intervals. Estimates of parameters under the MSC with gene flow suggest theAnopheles gambiaAfrican mosquito species complex is an example where gene flow greatly impacts species phylogeny.
Toward a genetic system in the marine cyanobacteriumProchlorococcus
Authors: Laurenceau Raphaël , Bliem Christina , Osburne Marcia S. , Becker Jamie W. , Biller Steven J. , Cubillos-Ruiz Andres , Chisholm Sallie W. 
Published: October 2019

ABSTRACTAs the smallest and most abundant primary producer in the oceans, the cyanobacteriumProchlorococcusis of interest to diverse branches of science. For the past 30 years, research on this minimal phototroph has led to a growing understanding of biological organization across multiple scales, from the genome to the global ocean ecosystem. Progress in understanding drivers of its diversity and ecology, as well as molecular mechanisms underpinning its streamlined simplicity, has been hampered by the inability to manipulate these cells genetically.Multiple attempts have been made to develop an efficient genetic transformation method forProchlorococcusover the years; all have been unsuccessful to date, despite some success with their close relative,Synechococcus. To avoid the pursuit of unproductive paths, we report here what has not worked in our hands, as well as our progress developing a method to screen the most efficient electroporation parameters for optimal DNA delivery intoProchlorococcuscells. We also report a novel protocol for obtaining axenic colonies and a new method for differentiating live and dead cells. The electroporation method can be used to optimize DNA delivery into any bacterium, making it a useful tool for advancing transformation systems in other genetically recalcitrant microorganisms.
Methionyl-tRNA synthetase inhibitor has potentin vivoactivity in a novelGiardia lamblialuciferase murine infection model
Authors: Michaels Samantha A. , Shih Han-Wei , Zhang Bailin , Navaluna Edelmar D. , Zhang Zhongsheng , Ranade Ranae M. , Gillespie J. Robert , Merritt Ethan A. , Fan Erkang , Buckner Frederick S. , Paredez Alexander R. , Ojo Kayode K. 
Published: October 2019

AbstractObjectivesMethionyl-tRNA synthetase (MetRS) inhibitors are under investigation for the treatment of intestinal infections caused byGiardia lamblia. To properly analyze the therapeutic potential of the MetRS inhibitor1717, experimental tools including a robust cell-based assay and a murine model of infection were developed based on novel strains ofG. lambliathat employ luciferase reporter systems to quantify viable parasites.MethodsSystematic screening of Giardia-specific promoters and luciferase variants led to the development of a strain expressing the click beetle green luciferase. Further modifying this strain to express NanoLuc created a dual reporter strain capable of quantifying parasites in both the trophozoite and cyst stages. These strains were used to develop a high throughput cell assay and a mouse infection model. A library of MetRS inhibitors was screened in the cell assay and1717was tested for efficacy in the mouse infection model.ResultsCell viability inin vitrocompound screens was quantified via bioluminescence readouts while infection loads in mice were monitored with noninvasive whole-animal imaging and fecal analysis. Compound1717was effective in clearing mice ofGiardiainfection in 3 days at varying doses, which is supported by data from enzymatic and phenotypic cell assays.ConclusionsThe newin vitroandin vivoassays based on luciferase expression by engineeredG. lambliastrains are useful for the discovery and development of new therapeutics for giardiasis. MetRS inhibitors, as validated by1717, have promising anti-giardiasis properties that merit further study as alternative therapeutics.
End lateral extension path strategy for intersection in wire and arc additive manufactured 2319 aluminum alloy
Authors: Li Runsheng , Zhang Haiou , Dai Fusheng , Huang Cheng , Wang Guilan 
Published: October 2019

Purpose
Large-scale aircraft parts usually with many frame features, which consist of intersections. Profile and tensile properties of junctions in wire and arc additive manufacturing (WAAM) are significantly affected by path strategies. The purpose of this paper is to propose a novel path strategy for intersections in WAAM and compare it with commonly used ones.

Design/methodology/approach
Three typical intersections including T crossing (TC), square crossing (SC) and arbitrary-angle crossing (AAC) were built up with two commonly used path strategies (parallel and oscillation) and a proposed method named end lateral extension (ELE) which extends the weld track along the crossed direction. A robotic system and cold metal transfer (CMT) process were used to deposit Al-6.3Cu (2319) alloy. The profile of the bead was scanned by laser vision sensor. Tightened ratio (r), inter-layer height increment (Δh) and deviation to the fitting plane (df) are calculated based on the point cloud. Tensile tests were done for all built intersections.

Findings
Comparison to the commonly used path strategies, the proposed ELE method eliminated the tightened defects at the intersection, achieved a more stable inter-layer height increment (Δh) and improved the profile quality with a lower deviation to the fitting plane (df). Tensile tests show that the proposed strategy has exhibited favorable tensile properties.

Originality/value
In this paper, a novel path strategy named ELE is proposed, which provides a new path choice for fabricating intersections by WAAM.
A priori models and inversion of gravity gradient data in hilly terrain
Authors: Pedersen Laust B. , Kamm Jochen , Bastani Mehrdad 
Published: October 2019

ABSTRACTThe increased popularity of airborne measurements of the gravity gradient tensor for resource studies and geological mapping has resulted in a new awareness of the importance of terrain effects. In these measurements, the terrain effect often overwhelms that of the underlying crust and it becomes important to formulate a strategy for taking it into account when presenting the data and when inverting the data into density models. Using newly acquired data from Northern Sweden, we first attempted to estimate a variable terrain density model by inverting the data using a terrain model with a laterally varying density. Using data weights related to the topography variations, we find the best estimate of the lateral variation of the terrain density. We translate this model into a full three‐dimensional model such that all columns have the same vertical centre of mass as estimated from inspecting the radially averaged power spectrum of the area. This then defines a reference model for subsequent three‐dimensional inversion of the gravity gradient tensor dataset. We tested this approach first on synthetic data calculated from the measured topography including two density anomalies before we applied it to the measured data. The result is a model in which the surface density variations are propagated downwards in a systematic manner now in better agreement with measured densities of rock samples in the area.