bluuebunny/crossref_metadata_2025_split huggingface dataset:
Context-dependent role of vinculin in neutrophil adhesion, motility and trafficking
Authors: Wilson Zachary S. , Witt Hadley , Hazlett Lauren , Harman Michael , Neumann Brittany M. , Whitman Andrew , Patel Mohak , Ross Robert S. , Franck Christian , Reichner Jonathan S. , Lefort Craig T. 
Published: November 2019

AbstractNeutrophils are innate immune effector cells that traffic from the peripheral blood to extravascular sites of inflammation. β2 integrins are involved during multiple phases of neutrophil recruitment, including the transition from rolling to arrest, firm attachment and motility within the vasculature. Following neutrophil arrest, adhesion stabilization occurs as the neutrophil interacts with the endothelial surface and crawls into a favorable position for extravasation. The cytoskeletal protein vinculin has been implicated in other cell types as a regulator of adhesion strength by promoting focal adhesion maturation and as a sensor of the mechanical properties of the microenvironment. Neutrophils express vinculin but do not form mature focal adhesions. Here, we characterize the role of vinculin in β2 integrin-dependent neutrophil adhesion, motility, mechanosensing, and recruitment. We observe that knockout of vinculin attenuates, but does not completely abrogate, neutrophil adhesion, spreading, and crawling under static conditions. In the presence of forces from fluid flow, vinculin was not required for neutrophil adhesion or migration. Vinculin deficiency only mildly attenuated neutrophil traction stresses and spreading on stiff, but not soft, polyacrylamide gels indicating a minor role for vinculin in the mechanosensing of the neutrophil as compared to slower moving mesenchymal cells that form mature focal adhesions. Consistent with these findings, we observe in vivo neutrophil recruitment into the inflamed peritoneum of mice remains intact in the absence of vinculin. Together, these data suggest that while vinculin regulates some aspects of neutrophil adhesion and spreading, it may be dispensable for neutrophil recruitment and motility in vivo.
Signal to Noise Ratio as a Cross-Platform Metric for Intraoperative Fluorescence Imaging
Authors: Gharia Asmaysinh , Papageorgiou Efthymios P. , Giverts Simeon , Park Catherine , Anwar Mekhail 
Published: November 2019

AbstractReal-time molecular imaging to guide curative cancer surgeries is critical to ensure removal of all tumor cells, however visualization of microscopic tumor foci remains challenging. Wide variation in both imager instrumentation and molecular labeling agents demands a common metric conveying the ability of a system to identify tumor cells. Microscopic disease, comprised of a small number of tumor cells, has a signal on par with the background, making the use of signal (or tumor) to background ratio inapplicable in this critical regime. Therefore, a metric that incorporates the ability to subtract out background, evaluating the signal itself relative to the sources of uncertainty, or noise is required. Here we introduce the signal-to-noise ratio (SNR) to characterize the ultimate sensitivity of an imaging system, and optimize factors such as pixel size. Variation in the background (noise) are due to electronic sources, optical sources, and spatial sources (heterogeneity in tumor marker expression, fluorophore binding, diffusion). Here we investigate the impact of these noise sources and ways to limit its effect on SNR. We use empirical tumor and noise measurements to procedurally generate tumor images and run a monte carlo simulation of microscopic disease imaging to optimize parameters such as pixel size.
Branch point control at malonyl-CoA node: A computational framework to uncover the design principles of an ideal genetic-metabolic switch
Authors: Xu Peng 
Published: November 2019

AbstractLiving organism is an intelligent system encoded by hierarchically-organized information to perform precisely-controlled biological functions. Biophysical models are important tools to uncover the design rules underlying complex genetic-metabolic circuit interactions. Based on a previously engineered synthetic malonyl-CoA switch (Xu et al, PNAS 2014), we have formulated nine differential equations to unravel the design principles underlying an ideal metabolic switch to improve fatty acids production in E. coli. By interrogating the physiologically accessible parameter space, we have determined the optimal controller architecture to configure both the metabolic source pathway and metabolic sink pathway. We determined that low protein degradation rate, medium strength of metabolic inhibitory constant, high metabolic source pathway induction rate, strong binding affinity of the transcriptional activator toward the metabolic source pathway, weak binding affinity of the transcriptional repressor toward the metabolic sink pathway, and a strong cooperative interaction of transcriptional repressor toward metabolic sink pathway benefit the accumulation of the target molecule (fatty acids). The target molecule (fatty acid) production is increased from 50% to 10-folds upon application of the autonomous metabolic switch. With strong metabolic inhibitory constant, the system displays multiple steady states. Stable oscillation of metabolic intermediate is the driving force to allow the system deviate from its equilibrium state and permits bidirectional ON-OFF gene expression control, which autonomously compensates enzyme level for both the metabolic source and metabolic sink pathways. The computational framework may facilitate us to design and engineer predictable genetic-metabolic switches, quest for the optimal controller architecture of the metabolic source/sink pathways, as well as leverage autonomous oscillation as a powerful tool to engineer cell function.
Wolbachia successfully replicate in a newly established horn fly, Haematobia irritans irritans (L.) (Diptera: Muscidae) cell line
Authors: Madhav Mukund , Brown Geoff , Morgan Jess A.T. , Asgari Sassan , McGraw Elizabeth A. , Munderloh Ulrike G. , Kurtti Timothy J. , James Peter 
Published: November 2019

AbstractBACKGROUNDHaematobia spp., horn flies (HF) and buffalo flies (BF), are economically important ectoparasites of dairy and beef cattle. Control of these flies relies mainly on the treatment of cattle with chemical insecticides. However, the development of resistance to commonly used compounds is compromising the effectiveness of these treatments and alternative methods of control are required. Wolbachia are maternally transmitted endosymbiotic bacteria of arthropods that cause various reproductive distortions and fitness effects, making them a potential candidate for use in the biological control of pests.RESULTSHere we report the successful establishment of a continuous HF cell line (HIE-18) from embryonic cells and its stable transinfection with Wolbachia strain wAlbB native to mosquitoes, and wMel and wMelPop native to Drosophila melanogaster. The established HIE-18 cells are typically round and diploid with ten chromosomes (2n = 10) or tetraploid with 20 chromosomes (4n=20) having a doubling time of 67.2 hours. Wolbachia density decreased significantly in the HIE-18 cells in the first 48 hours of infection, possibly due to overexpression of antimicrobial peptides through the Imd immune signalling pathway. However, density recovered after this time and stably Wolbachia-infected HIE-18 cell lines have now all been subcultured more than 50 times as persistently infected lines.CONCLUSIONThe amenability of HF to infection with different strains of Wolbachia suggests the potential for use of Wolbachia in novel approaches for the control of Haematobia spp. Further, the availability of the HIE-18 cell line will provide an important resource for the study of genetics, host-parasite interactions and chemical resistance in Haematobia populations.
Determination of Cas9/dCas9 associated toxicity in microbes
Authors: Misra Chitra Seetharam , Bindal Gargi , Sodani Megha , Wadhawan Surbhi , Kulkarni Savita , Gautam Satyendra , Mukhopadhyaya Rita , Rath Devashish 
Published: November 2019

AbstractThe CRISPR-Cas9 system has been used extensively in eukaryotic and prokaryotic systems for various applications. In case of the latter, a couple of previous studies had shown Cas9 protein expression associated toxicity. We studied the same in five microbes, viz Escherichia coli, Salmonella typhimurium, Mycobacterium smegmatis, Xanthomonas campestris and Deinococcus radiodurans. Transformation efficiency of plasmids carrying genes coding for Cas9 or dCas9 was used to gauge toxicity associated with Cas9 protein expression. Results showed differential levels of Cas9 toxicity among the bacteria and lower transformation efficiency for cas9/dcas9 bearing plasmids compared to controls in general. This indicated lethal effect of Cas9/dCas9 expression. While E. coli and S. typhimurium seemed to tolerate Cas9/dCas9 fairly well, in GC rich microbes, M. smegmatis, X. campestris and D. radiodurans, Cas9/dCas9 associated toxicity was acute.
Transplacental innate immune training via maternal microbial exposure: the XBP1-ERN1 axis in programming dendritic cell precursors
Authors: Mincham Kyle T. , Jones Anya C. , Bodinier Marie , Scott Naomi M. , Lauzon-Joset Jean-Francois , Stumbles Philip A. , Bosco Anthony , Holt Patrick G. , Strickland Deborah H. 
Published: November 2019

AbstractWe recently reported that the offspring of mice treated during pregnancy with the microbial-derived immunomodulator OM-85 manifest striking resistance postnatally to allergic airways inflammation, and localised the potential treatment target to the fetal cDC progenitor compartment which expands to increase the pool of precursors available at birth, enabling accelerated postnatal seeding of the lung mucosal cDC network required for establishment of immunological homeostasis in the airways. Here, we profile maternal OM-85 treatment-associated transcriptomic signatures in fetal bone marrow, and identify a series of immunometabolic pathways which provide essential metabolites for accelerated myelopoiesis, that are hallmarks of classical “immune training”. In addition, the cDC progenitor compartment displayed treatment-associated activation of the XBP1-ERN1 signalling axis which has previously been shown to be essential for tissue survival of cDC, particularly within the lung microenvironment. Our forerunner studies indicate uniquely rapid turnover of airway mucosal cDCs at baseline, with further large-scale upregulation of population dynamics during aeroallergen and/or pathogen challenge. XBP1-ERN1 signalling plays a key role in mitigation of ER stress-associated toxicity which frequently accompanies DC hyper-activation during intense immunoinflammatory responses, and we suggest that enhanced capacity for XBP1-ERN1-dependent cDC survival within the airway mucosal tissue microenvironment may be a crucial element of the OM-85-mediated transplacental “innate immune training” process which results in enhanced resistance to airway inflammatory disease during the high-risk early postnatal period.
Toxin-antitoxin gene pairs found in Tn3family transposons appear to be an integral part of the transposition module
Authors: Lima-Mendez Gipsi , Alvarenga Danillo Oliveira , Ross Karen , Hallet Bernard , Van Melderen Laurence , Varani Alessandro M. , Chandler Michael 
Published: November 2019

AbstractMuch of the diversity of prokaryotic genomes is contributed by the tightly controlled recombination activity of transposons (Tn). The Tn3family is arguably one of the most widespread transposon families. Members carry a large range of passenger genes incorporated into their structures. Family members undergo replicative transposition using a DDE transposase to generate a cointegrate structure which is then resolved by site-specific recombination between specific DNA sequences (res) on each of the two Tn copies in the cointegrate. These sites also carry promoters controlling expression of the recombinase and transposase. We report here that a number of Tn3members encode a type II toxin-antitoxin (TA) system, typically composed of a stable toxin and a labile antitoxin that binds the toxin and inhibits its lethal activity. This system serves to improve plasmid maintenance in a bacterial population and, until recently, was believed to be associated with bacterial persistence. At least six different TA gene pairs are associated with various Tn3members. Our data suggest that several independent acquisition events have occurred. In contrast to most Tn3family passenger genes which are generally located away from the transposition module, the TA gene pairs abut theressite upstream of the resolvase genes. Although their role when part of Tn3family transposons is unclear, this finding suggests a potential role for the embedded TA in stabilizing the associated transposon with the possibility that TA expression is coupled to expression of transposase and resolvase during the transposition process itself.ImportanceTransposable Elements (TEs) are important in genetic diversification due to their recombination properties and their ability to promote horizontal gene transfer. Over the last decades, much effort has been made to understand TE transposition mechanisms and their impact on prokaryotic genomes. For example, the Tn3family is ubiquitous in bacteria, moulding their host genomes by thepaste-and-copymechanism. In addition to the transposition module, Tn3members often carry additional passenger genes (e.g., conferring antibiotic or heavy metal resistance and virulence) and three were previously known to carry a toxin-antitoxin (TA) system often associated with plasmid maintenance; however, the role of TA systems within the Tn3family is unknown. The genetic context of TA systems in Tn3members suggests that they may play a regulatory role in ensuring stable invasion of these Tn during transposition.
Robotic light touch assists human balance control during maximum forward reaching
Authors: Johannsen Leif , Potwar Karna , Saveriano Matteo , Endo Satoshi , Lee Dongheui 
Published: November 2019

AbstractObjectiveWe investigated how light interpersonal touch (IPT) provided by a robotic system supports human individuals performing a challenging balance task compared to IPT provided by a human partner.BackgroundIPT augments the control of body balance in contact receivers without a provision of mechanical body weight support. The nature of the processes governing the social haptic interaction, whether they are predominantly reactive or predictive, is uncertain.MethodTen healthy adult individuals performed maximum forward reaching (MFR) without visual feedback while standing upright. We evaluated their control of reaching behaviour and of body balance during IPT provided by either another human individual or by a robotic system in two alternative control modes (reactive vs predictive).ResultsChanges in reaching behaviour under the robotic IPT, such as lower speed and straighter direction were linked to reduced body sway. MFR of the contact receiver was influenced by the robotic control mode such as that a predictive mode reduced movement variability and increased postural stability to a greater extend in comparison to human IPT. The effects of the reactive robotic system, however, more closely resembled the effects of IPT provided by human contact provider.ConclusionThe robotic IPT system was as supportive as human IPT. Robotic IPT seemed to afford more specific adjustments, such as trading reduced speed for increased accuracy, to meet the intrinsic demands and constraints of the robotic system. Possibly, IPT provided by a human contact provider reflected reactive interpersonal postural coordination more similar to the robotic system’s follower mode.PrécisInterpersonal touch support by a robotic system was evaluated against support provided a human partner during maximum forward reaching.Human contact receivers showed comparable benefits in their reaching postural performance between the support conditions.Coordination with the robotic system, nevertheless, afforded specific adaptations in the reaching behaviour.
DoUble resin casting micro computed tomography (DUCT) reveals biliary and vascular pathology in a mouse model of Alagille syndrome
Authors: Hankeova Simona , Salplachta Jakub , Zikmund Tomas , Kavkova Michaela , Van Hul Noemi , Brinek Adam , Smekalova Veronika , Laznovsky Jakub , Jaros Josef , Bryja Vitezslav , Lendahl Urban , Ellis Ewa , Hannezo Edouard , Kaiser Jozef , Andersson Emma R 
Published: November 2019

ABSTRACTBACKGROUND AND AIMSAlagille syndrome, like several other liver diseases, is characterized by malformation of lumenized structures, such as the circulatory or biliary systems. Liver architecture has typically been studied through 2D sections and, more recently, using thick tissue sections combined with immunofluorescence. We aimed to develop a robust method to image, digitalize and quantify 3D architecture of the biliary and vascular systems in tandem.METHODSThe biliary and portal vein trees of the mouse liver were injected with Microfil resin, followed by microCT scanning. Tomographic data was segmented and analyzed using a MATLAB script we wrote to investigate length, volume, tortuosity, branching, and the relation between the vascular and biliary systems. Double resin casting micro computed tomography (DUCT) was applied to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), in which the biliary system is absent at postnatal stages, but regenerates by adulthood. Phenotypes discovered using DUCT were validated with cumbersome consecutive liver sections from mouse and human liver including patients with Alagille syndrome.RESULTSDUCT revealed tortuous bile ducts either placed further from portal veins, or ectopically traversing the parenchyma and connecting two portal areas, in Jag1Ndr/Ndr mice. Furthermore, bile ducts either ended abruptly, or branched independently of portal vein branching, with bifurcations placed hilar or peripheral to portal vein branches. The branching defects, parenchymal bile ducts, and blunt endings were confirmed in patient samples.CONCLUSIONDUCT is a powerful technique, which provides computerized 3D reconstruction of casted networks. It exposes and quantifies previously unknown vascular and biliary phenotypes in mouse models, revealing new phenotypes in patients.Abstract Figure
Endogenous sugar level is associated with differential heat tolerance in onion bulb scales
Authors: Galsurker Ortal , Kelly Gilor , Doron-Faigenboim Adi , Aruchamy Kalaivani , Salam Bolaji Babajide , Teper-Bamnolker Paula , Lers Amnon , Eshel Dani 
Published: November 2019

AbstractPostharvest heat treatment stimulates desiccation and browning of outer scales of onion (Allium cepa. L) bulb to dry papery skins. Inner scales resist the heat treatment, as evidenced by high moisture levels. During heating, inner scales showed increasing soluble sugar levels followed by higher osmolarity, vs. a dramatic decrease in both in the outer scales. Exogenous feeding of outer scales with sucrose, glucose or fructose solutions before heat treatment reduced water loss during heating, suggesting a role for soluble sugars in water retention and therefore, heat tolerance. Vacuolar invertase (VInv) is a key enzyme regulating the levels of sucrose, glucose and fructose in plant tissue.VInv-silencing in potato plants prevented the accumulation of reducing sugars in heated leaves, increasing water loss. In onion outer scales, VInv activity increased during heating but reducing sugars decreased, possibly due to their rapid metabolism during scale senescence to form skin. Transcriptomic analysis demonstrated upregulation of genes involved in lignin biosynthesis and secondary cell-wall formation in outer scales during heat exposure, and upregulation of genes involved in energy-related pathways in inner scales. This study reveals the dual role of soluble sugars in different onion scales, as osmoprotectants or building blocks, under heat stress.HighlightHexose formation in the inner scales of onion is associated with heat tolerance, while in the outer scales, the hexoses are metabolized for onion skin formation.
Sex differences in alternative reproductive tactics in response to predation risk in tree crickets
Authors: Torsekar Viraj R. , Balakrishnan Rohini 
Published: November 2019

AbstractPredation risk has been hypothesised to drive the evolution of alternative mate-search strategies, but few empirical studies have examined this. In crickets, mate-search involves acoustic signalling by males and acoustic-mediated movement by females. It is unclear whether predators affect fitness of both sexes directly, by reducing survival, or indirectly, by affecting mate-searching. We empirically examined effects of increased predation risk on mate-searching behaviour and survival of male and female tree crickets, and their effects on mating success, using field-enclosure experiments with tree cricketsOecanthus henryiand their primary predator, green lynx spiders,Peucetia viridans. Crickets were allocated into three treatments with differential levels of predation risk. Increased predation risk strongly reduced survival, and thereby mating success, for both sexes. With increasing predation risk, males reduced calling and increased movement towards neighbouring callers, which had negative effects on mating success. Using simulations, we found male movement was significantly directed towards other calling males implying a switch to satellite strategies. Female movement behaviour, however, remained unaltered. Males and females thus differed in their response to comparable levels of predation risk, showing that the role of predation as a driver of alternative mate search strategies is sex and strategy-specific.
Minimal genome-wide human CRISPR-Cas9 library
Authors: Gonçalves Emanuel , Thomas Mark , Behan Fiona M , Picco Gabriele , Pacini Clare , Allen Felicity , Sharma Mamta , Jackson David A. , Price Stacey , Beaver Charlotte M. , Dovey Oliver , Parry-Smith David , Iorio Francesco , Parts Leopold , Yusa Kosuke , Garnett Mathew J 
Published: November 2019

AbstractCRISPR guide-RNA libraries have been iteratively optimised to provide increasingly efficient reagents, although their large size is a barrier for many applications. We designed an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9), by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 42% reduction in size compared to other libraries while preserving assay sensitivity and specificity. MinLibCas9 increases the dynamic range of CRISPR-Cas9 loss-of-function screens and extends their application to complex models and assays.