bluuebunny/crossref_metadata_2025_split huggingface dataset:
From spikes to intercellular waves: tuning intercellular Ca2+signaling dynamics modulates organ size control
Authors: Soundarrajan Dharsan K. , Huizar Francisco J. , Paravitorghabeh Ramezan , Robinett Trent , Zartman Jeremiah J. 
Published: June 2019

AbstractInformation flow within and between cells depends in part on calcium (Ca2+) signaling dynamics. However, the biophysical mechanisms that govern emergent patterns of Ca2+signaling dynamics at the organ level remain elusive. Recent experimental studies in developingDrosophilawing imaginal discs demonstrate the emergence of four distinct patterns of Ca2+activity: Ca2+spikes, intercellular Ca2+transients, tissue-level Ca2+waves, and a global “fluttering” state. Here, we used a combination of computational modeling and experimental approaches to identify two different populations of cells within tissues that are connected by gap junctional proteins. We term these two subpopulations “initiator cells” defined by elevated levels of Phospholipase C (PLC) activity and “standby cells,” which exhibit baseline activity. We found that the strength of hormonal stimulation and extent of gap junctional communication jointly determine the predominate class of Ca2+signaling activity. Further, single-cell Ca2+spikes are stimulated by insulin, while intercellular Ca2+waves depend on Gαq activity. Our computational model successfully recapitulates how the dynamics of Ca2+transients varies during organ growth. Phenotypic analysis of perturbations to Gαq and insulin signaling support an integrated model of cytoplasmic Ca2+as a dynamic reporter of overall tissue growth. Further, we show that perturbations to Ca2+signaling tune the final size of organs. This work provides a platform to further study how organ size regulation emerges from the crosstalk between biochemical growth signals and heterogeneous cell signaling states.Author SummaryCalcium (Ca2+) is a universal second messenger that regulates a myriad of cellular processes such as cell division, cell proliferation and apoptosis. Multiple patterns of Ca2+signaling including single cell spikes, multicellular Ca2+transients, large-scale Ca2+waves, and global “fluttering” have been observed in epithelial systems during organ development. Key molecular players and biophysical mechanisms involved in formation of these patterns during organ development are not well understood. In this work, we developed a generalized multicellular model of Ca2+that captures all the key categories of Ca2+activity as a function of key hormonal signals. Integration of model predictions and experiments reveals two subclasses of cell populations and demonstrates that Ca2+signaling activity at the organ scale is defined by a general decrease in gap junction communication as organ growth. Our experiments also reveal that a “goldilocks zone” of optimal Ca2+activity is required to achieve optimal growth at the organ level.
Pneumococcal Colonisation is an Asymptomatic Event in Healthy Adults using an Experimental Human Colonisation Model
Authors: Trimble Ashleigh , Connor Victoria , Robinson Ryan E , Hancock Carole A , Wang Duolao , Gordon Stephen B , Ferreira Daniela M , Wright Angela D , Collins Andrea M 
Published: June 2019

AbstractIntroductionPneumococcal colonisation is regarded as a pre-requisite for developing pneumococcal disease. In children previous studies have reported colonisation to be a symptomatic event and described a relationship between symptom severity/frequency and colonisation density. The evidence for this in adults is lacking in the literature. This study uses an experimental human pneumococcal challenge model to explore whether pneumococcal colonisation (or co-colonisation with a respiratory virus) is a symptomatic event in healthy adults.MethodsHealthy volunteers aged 18-50 were recruited and inoculated intra-nasally with either Streptococcus pneumoniae (serotypes 6B, 23F) or saline as a control. Respiratory viral swabs were obtained prior to inoculation. Nasal and non-nasal symptoms were then assessed using a modified Likert score between 1 (no symptoms) to 7 (cannot function). The rate of symptoms reported between groups was compared and a correlation analysis performed.ResultsData from 54 participants were analysed. 46 were inoculated with S. pneumoniae (29 with 6B, 17 with 23F) and 8 received saline. In total, 14 became experimentally colonised (30.4%), all of which were inoculated with 6B serotype. There was no statistically significant difference in nasal (p= 0.45) or non-nasal symptoms (p=0.28) between the pneumococcal inoculation group and the saline group. There was no direct correlation between colonisation density and symptom severity in those who were colonised. In the 22% (12/52) who were co-colonised with pneumococcus and respiratory viruses there was no statistical difference in either nasal or non-nasal symptoms (virus positive p=0.74 and virus negative p=1.0).ConclusionPneumococcal colonisation is asymptomatic in healthy adults, regardless of bacterial density or viral co-colonisation.
Preconditioning cathodal transcranial direct current stimulation facilitates the neuroplastic effect of subsequent anodal transcranial direct current stimulation applied during cycling in young adults
Authors: Pourmajidian Maryam , Lauber Benedikt , Sidhu Simranjit K 
Published: June 2019

AbstractThe study aimed to examine the effect of a priming cathodal transcranial direct current stimulation (ctDCS) before subsequent anodal-tDCS (atDCS) was applied during low workload cycling exercise on the corticospinal responses in young healthy individuals. Eleven young subjects participated in two sessions receiving either priming ctDCS or sham stimulation, followed by atDCS while cycling (i.e. ctDCS-atDCS, sham-atDCS) at 1.2 times their body weight (84 ± 20 W) in a counterbalanced double-blind design. Corticospinal excitability was measured with motor evoked potentials (MEPs) elicited via transcranial magnetic stimulation with the intensity set to produce an MEP amplitude of 1 mV in a resting hand muscle at baseline (PRE), following priming tDCS (POST-PRIMING) and post atDCS combined with cycling exercise (POST-TEST). There was a significant interaction between time and intervention (P < 0.01) on MEPs. MEPs increased from PRE (1.0 ± 0.06 mV) to POST-TEST (1.3 ± 0.06 mV) during ctDCS-atDCS (P < 0.001) but did not change across time during sham-atDCS (1.0 ± 0.06 mV, P > 0.7). Furthermore, MEPs were higher in ctDCS-atDCS compared to sham-atDCS (P < 0.01) at both POST-PRIMING (ctDCS-atDCS: 1.1 ± 0.06, sham-atDCS: 1.0 ± 0.06) and POST-TEST (ctDCS-atDCS: 1.3 ± 0.06, sham-atDCS: 1.0 ± 0.06). These outcomes demonstrate that cathodal tDCS priming can enhance corticospinal excitability following anodal tDCS applied in combination with cycling exercise. The findings have implications for the application of tDCS in combination with cycling exercise in rehabilitation and sporting contexts.
Simplified high-throughput methods for deep proteome analysis on the timsTOF Pro
Authors: Sandow Jarrod J , Infusini Giuseppe , Dagley Laura F , Larsen Rune , Webb Andrew I 
Published: June 2019

AbstractRecent advances in mass spectrometry technology have seen remarkable increases in proteomic sequencing speed, while improvements to dynamic range have remained limited. An exemplar of this is the new timsTOF Pro instrument, which thanks to its trapped ion mobility, pushes effective fragmentation rates beyond 100Hz and provides accurate CCS values as well as impressive sensitivity. Established data dependent methodologies underutilize these advances by relying on long analytical columns and extended LC gradients to achieve comprehensive proteome coverage from biological samples. Here we describe the implementation of methods for short packed emitter columns that fully utilize instrument speed and CCS values by combining rapid generation of deep peptide libraries with enhanced matching of single shot data dependent sample analysis. Impressively, with only a 17 minute separation gradient (50 samples per day), the combination of high performance chromatography and CCS enhanced library based matching resulted in an average of 5,931 protein identifications within individual samples, and 7,244 proteins cumulatively across replicates from HeLa cell tryptic digests. Additionally, an ultra-high throughput setup utilizing 5 min gradients (180 samples per day) yielded an average of 3,666 protein identifications within individual samples and 4,659 proteins cumulatively across replicates. These workflows are simple to implement on available technology and do not require complex software solutions or custom-made consumables to achieve high throughput and deep proteome analysis from biological samples.
CAMIO for deletion analysis of endogenous DNA sequences in multicellular organisms
Authors: Chen Hui-Min , Marques Jorge Garcia , Sugino Ken , Wei Dingjun , Miyares Rosa Linda , Lee Tzumin 
Published: June 2019

AbstractThe genome is the blueprint for an organism. Interrogating the genome, especially locating critical cis-regulatory elements, requires deletion analysis. This is conventionally performed using synthetic constructs, making it cumbersome and non-physiological. Thus, we createdCas9-mediatedArrayedMutagenesis of IndividualOffspring (CAMIO) to achieve high-throughput analysis of native DNA. CAMIO utilizes CRISPR that is spatially restricted to generate independent deletions. Controlled by recombination, a single guide RNA is stochastically chosen from a set targeting a specific DNA region. Combining two sets increases variability, leading to either indels at 1-2 target sites or inter-target deletions. Cas9 restriction to male germ cells elicits autonomous double-strand-break repair, consequently creating offspring with diverse mutations. Thus, from a single population cross, we can obtain a deletion matrix covering a large expanse of DNA at both coarse and fine resolution. We demonstrate the ease and power of CAMIO by mapping 5’UTR sequences crucial forchinmo’spost-transcriptional regulation.
Zebrafish Dscaml1 is Essential for Retinal Patterning and Function of Oculomotor Subcircuits
Authors: Ma Manxiu , Ramirez Alexandro D. , Wang Tong , Roberts Rachel L. , Harmon Katherine E. , Schoppik David , Sharma Avirale , Kuang Christopher , Goei Stephanie L. , Gagnon James A. , Zimmerman Steve , Tsai Shengdar Q. , Reyon Deepak , Joung J. Keith , Aksay Emre R. F. , Schier Alexander F. , Pan Y. Albert 
Published: June 2019

AbstractDown Syndrome Cell Adhesion Molecules (dscam and dscaml1) are essential regulators of neural circuit assembly, but their roles in vertebrate neural circuit function are still mostly unexplored. We investigated the role of dscaml1 in the zebrafish oculomotor system, where behavior, circuit function, and neuronal activity can be precisely quantified. Loss of zebrafish dscaml1 resulted in deficits in retinal patterning and light adaptation, consistent with its known roles in mammals. Oculomotor analyses showed that mutants have abnormal gaze stabilization, impaired fixation, disconjugation, and faster fatigue. Notably, the saccade and fatigue phenotypes in dscaml1 mutants are reminiscent of human ocular motor apraxia, for which no animal model exists. Two-photon calcium imaging showed that loss of dscaml1 leads to impairment in the saccadic premotor pathway but not the pretectum-vestibular premotor pathway, indicating a subcircuit requirement for dscaml1. Together, we show that dscaml1 has both broad and specific roles in oculomotor circuit function, providing a new animal model to investigate the development of premotor pathways and their associated human ocular disorders.
Caenorhabditis elegansExhibits Positive Gravitaxis
Authors: Chen Wei-Long , Ko Hungtang , Chuang Han-Sheng , Bau Haim H. , Raizen David 
Published: June 2019

AbstractWhether or not the micro swimmerCaenorhabditis eleganssenses and respond to gravity is unknown. We find thatC. elegansaligns its swimming direction with that of the gravity vector (positive gravitaxis). When placed in an aqueous solution that is denser than the animals, they still orient downwards, indicating that non-uniform mass distribution and/or hydrodynamic effects are not responsible for animal’s downward orientation. Paralyzed worms and worms with globally disrupted sensory cilia do not change orientation as they settle in solution, indicating that gravitaxis is an active behavior that requires gravisensation. Other types of sensory driven orientation behaviors cannot explain our observed downward orientation. Like other neural behaviors, the ability to respond to gravity declines with age. Our study establishes gravitaxis in the micro swimmerC. elegansand suggests thatC. eleganscan be used as a genetically tractable system to study molecular and neural mechanisms of gravity sensing and orientation.Significance StatementUnderstanding how animals respond to gravity is not only of fundamental scientific interest, but has clinical relevance, given the prevalence of postural instability in aged individuals. Determining whetherC. elegansresponds to gravity is important for mechanistic studies of gravity sensing in an experimentally tractable animal, for a better understanding of nematode ecology and evolution, and for studying biological effects of microgravity. Our experiments, which indicate thatC. eleganssenses and responds to gravity, set the stage for mechanistic studies on molecular mechanisms of gravity sensing.
Adaptive and Innate Immune Cell Responses in Tendons and Lymph Nodes After Tendon Injury and Repair
Authors: Noah Andrew C , Li Thomas M , Martinez Leandro M , Wada Susumu , Swanson Jacob B , Disser Nathaniel P , Sugg Kristoffer B , Rodeo Scott A , Lu Theresa T , Mendias Christopher L 
Published: June 2019

AbstractTendon injuries are a common clinical condition with limited treatment options. The cellular components of the innate system, such as neutrophils and macrophages, have been well studied in tendon injuries. However the adaptive immune system, comprised of specialized lymphocytes, plays an important role in orchestrating the healing of numerous tissues but less is known about these cells in tendon healing. To gain a greater understanding of the biological processes that regulate tendon healing, we sought to determine how the cellular components of the adaptive and innate immune system respond to a tendon injury using two-month old male mice. We determined that the lymphatic vasculature is present in the epitenon and superficial regions of Achilles tendons. We then created an acute Achilles tenotomy followed by repair, and collected tendons and draining lymph nodes one, two, and four weeks after injury. Using flow cytometry and histology, after tendon injury we observed a robust adaptive immune cell response that followed an initial innate immune cell response. There was an accumulation of monocytes, neutrophils, and macrophages one week after injury that declined thereafter. Dendritic cells and CD4+ T cells peaked two weeks after injury, while B cells and CD8+ T cells progressively increased over time. In parallel, immune cells of the draining popliteal lymph node demonstrated a similarly coordinated response to the injury. These results suggest that there is an adaptive immune response to tendon injury and adaptive immune cells may play a role in regulating tendon healing.
GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences
Authors: Gabrielaite Migle , Marvig Rasmus L. 
Published: June 2019

AbstractBacterial gene loss and acquisition is a well-known phenomenon which contributes to bacterial adaptation through changes in important phenotypes such as virulence, antibiotic resistance and metabolic capability. While advances in DNA sequencing have accelerated our ability to generate short-read genome sequencing to disentangle phenotypic changes caused by gene loss and acquisition, the short-read genome sequencing often results in fragmented genome assemblies as a basis for identification of gene loss and acquisition events. However, sensitive and precise determination of gene content change for fragmented genome assemblies remain challenging as analysis needs to account for cases when only a fragment of the gene is assembled or when the gene assembly is split in more than one contig.We developed GenAPI, a command-line tool that is designed to compare the gene content of bacterial genomes for which only fragmented genome assemblies are available. GenAPI, unlike other available tools of similar purpose, accounts for genome assembly imperfections and aims to compensate for them. We tested the performance of GenAPI on three different datasets to show that GenAPI has high sensitivity while it maintains precision when dealing with partly assembled genes in both simulated and real datasets. Furthermore, we compared and evaluated the performance of GenAPI with six popular tools for gene presence-absence identification. While we find that the compared tools have the same precision and recall rates when analyzing complete genome sequences, GenAPI performs better than the other tools on fragmented genome assemblies.
Silver nanoparticle induced oxidative stress augments anticancer gut bacterial metabolites production
Authors: Bhalla Prerna , Rengaswamy Raghunathan , Karunagaran Devarajan , Suraishkumar G. K. , Sahoo Swagatika 
Published: June 2019

AbstractColorectal cancer (CRC) is the fourth leading cause of mortality, world-wide. Gut bacterial dysbiosis being one of the major causes of CRC onset. Gut microbiota produced metabolites, e.g. folate and butyrate play crucial roles in cancer progression and treatment, and thus, need to be considered for effective CRC management. A potential cancer therapy, i.e., use of silver nanoparticles (AgNPs), imparts cytotoxic effects by inducing high intracellular reactive oxygen species (ROS) levels. However, the simultaneous interactions of AgNPs with gut microbiota to aid CRC treatment has not been reported thus far. Therefore, in this study, variation of intracellular ROS concentrations, in Enterococcus durans (E. durans), a representative gut microbe, was studied in the presence of low AgNP concentrations (25 ppm). Increases were observed in intracellular hydroxyl radical and extracellular folic acid concentrations by 48% and 52%, respectively, at the 9thhour of microbial growth. To gain a systems level understanding of ROS metabolism in E. durans, genome scale metabolic network reconstruction and modeling was adopted. In silico modeling reconfirmed the critical association between ROS and folate metabolism. Further, amino acids, energy metabolites, nucleotides, and butyrate were found to be important key players. Consequently, the anticancer effect of folic acid was experimentally studied on HCT116 (i.e., colon cancer cell line), wherein, its viability was reduced to 79% via folate present in the supernatants from AgNP treated E. durans cultures. Thus, we suggest that the inter-relationship between gut bacteria and AgNP-based cancer treatment can be used to design robust and effective cancer therapies.
YY males of the dioecious plantMercurialis annuaare fully viable but produce largely infertile pollen
Authors: Li Xinji , Veltsos Paris , Cossard Guillaume , Gerchen Jörn , Pannell John R. 
Published: June 2019

SummaryThe suppression of recombination during sex-chromosome evolution is thought to be favoured by linkage between the sex-determining locus and sexually-antagonistic loci, and leads to the degeneration of the chromosome restricted to the heterogametic sex. Despite substantial evidence for genetic degeneration at the sequence level, the phenotypic effects of the earliest stages of sex-chromosome evolution are poorly known. Here, we compare the morphology, viability and fertility between XY and YY individuals produced by crossing seed-producing males in the dioecious plantMercurialis annuaL., which has young sex chromosomes with limited X-Y sequence divergence. We found no significant difference in viability or vegetative morphology between XY and YY males. However, electron microscopy revealed clear differences in pollen anatomy, and YY males were significantly poorer sires in competition with their XY counterparts. Our study suggests either that the X chromosome is required for full male fertility inM. annua, or that male fertility is sensitive to the dosage of relevant Y-linked genes. We discuss the possibility that the maintenance of male-fertility genes on the X chromosome might have been favoured in recent population expansions, which selected for the ability of females to produce pollen in the absence of males.
Liquid-liquid phase separation and aggregation of the prion protein globular domain modulated by a high-affinity DNA aptamer
Authors: Matos Carolina O. , Passos Yulli M. , do Amaral Mariana J. , Macedo Bruno , Tempone Matheus , Bezerra Ohanna C. L. , Moraes Milton O. , Almeida Marcius S. , Weber Gerald , Missailidis Sotiris , Silva Jerson L. , Pinheiro Anderson S. , Cordeiro Yraima 
Published: June 2019

ABSTRACTStructural conversion of cellular prion protein (PrPC) into scrapie PrP (PrPSc) and subsequent aggregation are key events for the onset of Transmissible Spongiform Encephalopathies (TSEs). Experimental evidences support the role of nucleic acids (NAs) in assisting the protein conversion process. Here, we used the SELEX methodology to identify two 25-mer DNA aptamers against the globular domain of recombinant murine PrP (rPrP90-231), namely A1 and A2. High-affinity binding of A1 and A2 to rPrP was verified by ITC. Aptamers structure was characterized by theoretical predictions, CD, NMR and SAXS, revealing that A1 adopts a hairpin conformation. Aptamer binding caused dynamic aggregation of rPrP90-231, resulting from the ability of rPrP90-231to undergo liquid-liquid phase separation (LLPS). While free rPrP90-231phase separated into large droplets, aptamer binding increased the amount but reduced the size of the condensates. Strikingly, a modified A1 aptamer that does not adopt a hairpin structure induced transition to an ordered state, suggestive of amyloid formation on the surface of the droplets. Our results describe for the first time PrP:NA interaction leading to LLPS and modulation of this effect depending on NA structure and binding stoichiometry, shedding light on the role of NAs in PrP misfolding and TSEs.
Transient invaders can induce shifts between alternative stable states of microbial communities
Authors: Amor Daniel R. , Ratzke Christoph , Gore Jeff 
Published: June 2019

AbstractMicrobial dispersal often leads to the arrival of outsider organisms into ecosystems. When their arrival give rise to successful invasions, outsider species establish within the resident community, which can dramatically alter the ecosystem. Seemingly less influential, the potential impact of unsuccessful invaders that interact only transiently with the community has remained largely ignored. Here, we experimentally demonstrate that such transient invasions can perturb the stability of microbial ecosystems and induce a lasting transition to an alternative stable state, even when the invader species itself does not survive the transition. First, we develop a mechanistic understanding of how environmental changes caused by such transient invaders can drive a community shift in a simple, bistable model system. Beyond this, we show that transient invaders can also induce switches between stable states in more complex communities isolated from natural soil samples. Our results demonstrate that short-term interactions with an invader species can induce lasting shifts in community composition and function.One Sentence SummaryTransient invaders can cause lasting shifts in community composition and function.