bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flow cytometry method for absolute counting and single-cell phenotyping of mycobacteria
Authors: Barr David A. , Omollo Charles , Mason Mandy , Koch Anastasia , Wilkinson Robert J. , Lalloo David G. , Meintjes Graeme , Mizrahi Valerie , Warner Digby F. , Davies Gerry 
Published: May 2021

AbstractDetection and accurate quantitation of viableMycobacterium tuberculosisis fundamental to understanding mycobacterial pathogenicity, tuberculosis (TB) disease progression and outcomes; TB transmission; drug action, efficacy and drug resistance. Despite this importance, methods for determining numbers of viable bacilli are limited in accuracy and precision owing to inherent characteristics of mycobacterial cell biology – including the tendency to clump, and “differential” culturability – and technical challenges consequent on handling an infectious pathogen under biosafe conditions. We developed an absolute counting method for mycobacteria in liquid cultures using a bench-top flow cytometer, and the low-cost fluorescent dyes Calcein-AM (CA) and SYBR-gold (SG). During exponential growth CA+ cell counts are highly correlated with CFU counts and can be used as a real-time alternative to simplify the accurate standardisation of inocula for experiments. In contrast to CFU counting, this method can detect and enumerate cell aggregates in samples, which we show are a potential source of variance and bias when using established methods. We show that CFUs comprise a sub-population of intact, metabolically active mycobacterial cells in liquid cultures, with CFU-proportion varying by growth conditions. A pharmacodynamic application of the flow cytometry method, exploring kinetics of fluorescent probe defined subpopulations compared to CFU is demonstrated. Flow cytometry derivedMycobacterium bovis BCGtime-kill curves differ for rifampicin and kanamycin versus isoniazid and ethambutol, as do the relative dynamics of discrete morphologically-distinct subpopulations of bacilli revealed by this high-throughput single-cell technique.
Mesenchymal Lineage Heterogeneity Underlies Non-Redundant Functions of Pancreatic Cancer-Associated Fibroblasts
Authors: Helms Erin J. , Berry Mark W. , Chaw R. Crystal , DuFort Chris C. , Sun Duanchen , Onate M. Kathrina , Oon Chet , Bhattacharyya Sohinee , Sanford-Crane Hannah , Horton Wesley , Finan Jennifer M. , Sattler Ariana , Makar Rosemary , Dawson David W. , Xia Zheng , Hingorani Sunil R. , Sherman Mara H. 
Published: May 2021

AbstractCancer-associated fibroblast (CAF) heterogeneity is increasingly appreciated, but the origins and functions of distinct CAF subtypes remain poorly understood. The abundant and transcriptionally diverse CAF population in pancreatic ductal adenocarcinoma (PDAC) is thought to arise from a common cell of origin, pancreatic stellate cells (PSCs), with diversification resulting from cytokine and growth factor gradients within the tumor microenvironment. Here we analyzed the differentiation and function of PSCs during tumor progressionin vivo. Contrary to expectations, we found that PSCs give rise to a numerically minor subset of PDAC CAFs. Targeted ablation of PSC-derived CAFs within their host tissue revealed non-redundant functions for this defined CAF population in shaping the PDAC microenvironment, including production of specific components of the extracellular matrix. Together, these findings link stromal evolution from distinct cells of origin to transcriptional heterogeneity among PDAC CAFs, and demonstrate unique functions for CAFs of a defined cellular origin.Statement of significanceBy tracking and ablating a specific CAF population, we find that a numerically minor CAF subtype from a defined cell of origin plays unique roles in establishing the pancreatic tumor microenvironment. Together with prior studies, this work suggests that mesenchymal lineage heterogeneity as well as signaling gradients diversify PDAC CAFs.
Group size and modularity interact to shape the spread of infection and information through animal societies
Authors: Evans Julian C , Hodgson David J , Boogert Neeltje J , Silk Matthew J 
Published: May 2021

AbstractSocial interactions between animals can provide many benefits, including the ability to gain useful environmental information through social learning. However, these social contacts can also facilitate the transmission of infectious diseases through a population. Animals engaging in social interactions must therefore face a trade-off between the potential informational benefits and the risk of acquiring disease. In order to understand how this trade-off can influence animal sociality, it is necessary to quantify the effects of different social structures on individuals’ likelihood of acquiring information versus infection Theoretical models have suggested that modular social networks, associated with the formation of groups or sub-groups, can slow spread of infection by trapping it within particular groups. However these social structures will not necessarily impact the spread of information in the same way if its transmission is considered as a “complex contagion”, e.g. through individuals copying the majority (conformist learning). Here we use simulation models to demonstrate that modular networks can promote the spread of information relative to the spread of infection, but only when the network is fragmented and group sizes are small. We show that the difference in transmission between information and disease is maximised for more well-connected social networks when the likelihood of transmission is intermediate. Our results have important implications for understanding the selective pressures operating on the social structure of animal societies, revealing that highly fragmented networks such as those formed in fission-fusion social groups and multilevel societies can be effective in modulating the infection-information trade-off for individuals within them.Significance statementRisk of infection is commonly regarded as one of the costs of animal social behaviours, while the potential for acquiring useful information is seen as a benefit. Balancing this risk of infection with the potential to gain useful information is one of the key trade-offs facing animals that engage in social interactions. In order to better understand this trade-off, it is necessary to quantify how different social structures can promote access to useful information while minimising risk of infection. We used simulations of disease and information spread to examine how group sizes and social network fragmentation influences both these transmission processes. Our models find that more subdivided networks slow the spread of disease far more than infection, but only group sizes are small. Our results demonstrate that showing that fragmented social structures can be more effective in balancing the infection-information trade-off for individuals within them.
ACTIVATION LOOP PHOSPHORYLATION OF A NON-RD RECEPTOR KINASE INITIATES PLANT INNATE IMMUNE SIGNALING
Authors: Bender Kyle W. , Couto Daniel , Kadota Yasuhiro , Macho Alberto P. , Sklenar Jan , Bjornson Marta , Petriello Annalise , Farre Maria Font , Schwessinger Benjamin , Ntoukakis Vardis , Stransfeld Lena , Jones Alexandra M.E. , Menke Frank L.H. , Zipfel Cyril 
Published: May 2021

AbstractReceptor kinases (RKs) play fundamental roles in extracellular sensing to regulate development and stress responses across kingdoms. In plants, leucine-rich repeat receptor kinases (LRR-RKs) function primarily as peptide receptors that regulate myriad aspects of plant development and response to external stimuli. Extensive phosphorylation of LRR-RK cytoplasmic domains is among the earliest detectable responses following ligand perception, and reciprocal transphosphorylation between a receptor and its co-receptor is thought to activate the receptor complex. Originally proposed based on characterization of the brassinosteroid receptor, the prevalence of complex activation via reciprocal transphosphorylation across the plant RK family has not been tested. Using the LRR-RK ELONGATION FACTOR TU RECEPTOR (EFR) as a model RK, we set out to understand the steps critical for activating RK complexes. While the EFR cytoplasmic domain is an active protein kinasein vitroand is phosphorylated in a ligand-dependent mannerin vivo, catalytically deficient EFR variants are functional in anti-bacterial immunity. These results reveal a non-catalytic role for the EFR cytoplasmic domain in triggering immune signaling and indicate that reciprocal transphoshorylation is not a ubiquitous requirement for LRR-RK complex activation. Rather, our analysis of EFR along with a detailed survey of the literature suggests a distinction between LRR-RK complexes with RD- versus non-RD protein kinase domains. Based on newly identified phosphorylation sites that regulate the activation state of the EFR complexin vivo, we propose that LRR-RK complexes containing a non-RD protein kinase may be regulated by phosphorylation-dependent conformational changes of the ligand-binding receptor which could initiate signaling in a feed-forward fashion either allosterically or through driving the dissociation of negative regulators of the complex.
The potential of aquatic haematophagous, liquidosomatophagous and macrophagous leeches as a tool for iDNA characterisation
Authors: Lynggaard Christina , Oceguera-Figueroa Alejandro , Kvist Sebastian , Gilbert M Thomas P , Bohmann Kristine 
Published: May 2021

AbstractLeeches play important roles in food webs due to their abundance, diversity and feeding habits. Studies using invertebrate-derived DNA (iDNA) extracted from leech gut contents to target vertebrate DNA have focused on the Indo-Pacific region and mainly leveraged the leech family Haemadipsidae, composed of haematophagous terrestrial leeches, while the aquatic haematophagous, liquidosomatophagous and macrophagous counterparts have largely been disregarded. While there is general knowledge regarding the taxonomic groups that leeches prefer to feed on, detailed taxonomic resolution is still missing and therefore, their potential use for monitoring animals is not known. In this study, 116 non-haemadipsid leeches belonging to 12 species and spanning the three feeding habits were collected in Mexico and Canada. We used DNA metabarcoding to investigate their diet and assess their potential use for vertebrate monitoring. We detected vertebrate taxa from five orders including fish, turtles and birds in the diet of the aquatic haematophagous leeches; eight invertebrate orders of annelids, arthropods and molluscs in the liquidosomatophagous leeches; and ten orders of invertebrates belonging to Arthropoda and Annelida, as well as one vertebrate and one parasitic nematode, in the macrophagous leeches. These results show the potential use of iDNA from the gut content of aquatic haematophagous leeches for retrieving vertebrate taxa, and from macrophagous and liquidosomatophagous counterparts for invertebrates. Our study provides information about the dietary range of the freshwater leeches and the non-haemadipsid terrestrial leech and proof-of-concept for the use of non-haemadipsid leeches for animal monitoring, expanding our knowledge of the use of iDNA from leech gut contents to North America.
The interplay of spatial scale and landscape transformation moderates the abundance and intraspecific variation in the ecomorphological traits of a phyllostomid bat
Authors: Ramírez-Mejía Andrés F. , Urbina-Cardona J. Nicolás , Sánchez Francisco 
Published: May 2021

ABSTRACTLand-use intensification imposes selective pressures that systematically change the frequency of wild population phenotypes. Growing evidence is biased towards the comparison of populations from discrete categories of land uses, ignoring the role of landscape emerging properties on the phenotype selection of wild fauna. Across the largest urban-rural gradient of the Colombian Orinoquia, we measured ecomorphological traits of 216 individuals of the Flat-faced Fruit-eating BatArtibeus planirostris, to evaluate the scale of effect at which landscape transformation better predicts changes in phenotype and abundance of an urban-tolerant species. Forest percentage at 1.25 km was the main predictor affecting abundance, wing aspect ratio, and body mass of this phyllostomid; but the direction of the effect differed between abundance and ecomorphological traits. Although landscape factors explained changes in the forearm length at all spatial scales, the effect was sex-dependent and the most important predictor was forest percentage at 0.5 km. Our results indicate that landscape elements and spatial scale interact to shape ecomorphological traits and the abundance ofA. planirostris. Interestingly, the scale of effect was congruent among all biological responses. A pattern that likely arises since species’ abundance can reflect the variation on phenotype under different environmental filters across landscape scenarios.
Symbiont-conferred immunity interacts with the effects of parasitoid genotype and intraguild predation to shape pea aphid immunity in a clone-specific fashion
Authors: Purkiss Samuel Alexander , Khudr Mouhammad Shadi , Aguinaga Oscar Enrique , Hager Reinmar 
Published: May 2021

AbstractHost-parasite interactions represent complex co-evolving systems in which genetic variation within a species can significantly affect selective pressure on traits in the other (for example via inter-species indirect genetic effects). While often viewed as a two-species interaction between host and parasite species, some systems are more complex due to the involvement of symbionts in the host that influence its immunity, enemies of the host, and the parasite through intraguild predation. However, it remains unclear what the joint effects of intraguild predation, defensive endosymbiosis, within-species genetic variation and indirect genetic effects on host immunity are. We have addressed this question in an important agricultural pest system, the pea aphidAcyrthosiphon pisum, which shows significant intraspecific variability in immunity to the parasitoid waspAphidius ervidue to immunity conferring endosymbiotic bacteria. In a complex experiment involving a quantitative genetic design of the parasitoid, two ecologically different aphid lineages and the aphid lionChrysoperla carneaas an intraguild predator, we demonstrate that aphid immunity is affected by intraspecific genetic variation in the parasitoid and the aphid, as well as by associated differences in the defensive endosymbiont communities. Using 16s rRNA sequencing, we identified secondary symbionts that differed between the lineages. We further show that aphid lineages differ in their altruistic behaviour once parasitised whereby infested aphids move away from the clonal colony to facilitate predation. The outcome of these complex between-species interactions not only shape important host-parasite systems but have also implications for understanding the evolution of multitrophic interactions, and aphid biocontrol.
Corticohippocampal circuit dysfunction in a mouse model of Dravet syndrome
Authors: Mattis Joanna , Somarowthu Ala , Goff Kevin M. , Yom Jina , Sotuyo Nathaniel P. , McGarry Laura M. , Feng Huijie , Kaneko Keisuke , Goldberg Ethan M. 
Published: May 2021

AbstractDravet syndrome (DS) is a neurodevelopmental disorder defined by treatment-resistant epilepsy, autism spectrum disorder, and sudden death, due to pathogenic variants inSCN1Aencoding the Nav1.1 sodium channel subunit. Convergent data suggest hippocampal dentate gyrus (DG) pathology. We found that optogenetic stimulation of entorhinal cortex was ictogenic in DS (Scn1a+/-) but not wild-type mice in vivo. Two-photon calcium imaging in brain slice demonstrated profound impairment in filtering of perforant path input by DG in young adultScn1a+/-mice due to enhanced excitatory input to granule cells. Excitability of parvalbumin interneurons (PV-INs) was near-normal and selective activation of PV-INs rescued circuit impairments. This demonstrates developmental reorganization of hippocampal circuitry that can be modulated by recruitment of functional PV-INs, suggesting potential therapeutic approaches towards seizure modulation. The identified circuit abnormality mirrors that seen in models of chronic temporal lobe epilepsy, suggesting convergent mechanisms linking genetic and acquired causes of temporal lobe-onset seizures.
Convergence of proprioceptive and visual feedback on neurons in primary motor cortex
Authors: Cross Kevin P. , Cook Douglas J. , Scott Stephen H. 
Published: May 2021

SummaryAn important aspect of motor function is our ability to rapidly generate goal-directed corrections for disturbances to the limb or behavioural goal. Primary motor cortex (M1) is a key region involved in feedback processing, yet we know little about how different sources of feedback are processed by M1. We examined feedback-related activity in M1 to compare how different sources (visual versus proprioceptive) and types of information (limb versus goal) are represented. We found sensory feedback had a broad influence on M1 activity with ∼73% of neurons responding to at least one of the feedback sources. Information was also organized such that limb and goal feedback targeted the same neurons and evoked similar responses at the single-neuron and population levels indicating a strong convergence of feedback sources in M1.
Modeling in yeast how rDNA introns slow growth and increase desiccation tolerance in lichens
Authors: Armaleo Daniele , Chiou Lilly 
Published: May 2021

AbstractWe define a molecular connection between ribosome biogenesis and desiccation tolerance in lichens, widespread symbioses between specialized fungi (mycobionts) and unicellular phototrophs. Our experiments test whether the introns present in the nuclear ribosomal DNA of lichen mycobionts contribute to their anhydrobiosis. Self-splicing introns are found in the rDNA of several eukaryotic microorganisms, but most introns populating lichen rDNA are unable to self-splice, being either degenerate group I introns lacking the sequences needed for catalysis, or spliceosomal introns ectopically present in rDNA. Although all introns are eventually removed from rRNA by the splicing machinery of the mycobiont, Northern analysis of its RNA indicates that they are not removed quickly during rRNA transcription but are still present in early post-transcriptional processing and ribosome assembly stages, suggesting that delayed splicing interferes with ribosome assembly. To study the phenotypic repercussions of lichen introns in a model system, we used CRISPR to introduce a spliceosomal intron from the rDNA of the lichen fungusCladonia grayiinto all nuclear rDNA copies of the yeastSaccharomyces cerevisiae, which lacks rDNA introns. Three intron-bearing yeast mutants were constructed with the intron inserted either in the 18S rRNA genes, the 25S rRNA genes, or in both. The mutants removed the introns correctly but had half the rDNA genes of the wildtype strain, grew 4.4 to 6 times slower, and were 40 to 1700 times more desiccation tolerant depending on intron position and number. Intracellular trehalose, a disaccharide implicated in desiccation tolerance, was detected, but at low concentration. Overall, our data suggest that the constitutive interference of the intron splicing machinery with ribosome assembly and the consequent lowering of the cytoplasmic concentration of ribosomes and proteins are the primary causes of slow growth and increased desiccation tolerance in the yeast mutants. The relevance of these findings for slow growth and desiccation tolerance in lichens is discussed.
Mechanisms Underlying WNT-mediated Priming of Human Embryonic Stem Cells
Authors: Yoney Anna , Bai Lu , Brivanlou Ali H. , Siggia Eric D. 
Published: May 2021

AbstractEmbryogenesis is guided by a limited set of signaling pathways dynamically expressed in different places. How a context dependent signaling response is generated has been a central question of developmental biology, which can now be addressed within vitromodels of human embryos that are derived from embryonic stem cells (hESCs) called gastruloids. Our previous work demonstrated that during early self-organization of gastruloids, cells chronicle signaling hierarchy. Only cells that have been exposed (primed) by WNT signaling can respond to subsequent Activin exposure and differentiate to mesendodermal (ME) fates. Here, we show that WNT priming does not alter SMAD2 binding nor its chromatin opening, but rather, acts by inducing the expression of the SMAD2 co-factor, EOMES. Expression of EOMES is sufficient to replace WNT upstream of Activin-mediated ME differentiation, thus unveiling the mechanistic basis for priming and cellular memory in early development.
Time-reversal symmetric component of the flagellar beat enhances the translational and rotational velocities of isolated Chlamydomonas flagella
Authors: Gholami A. , Ahmad R. , Bae A. , Pumir A. , Bodenschatz E. 
Published: May 2021

AbstractThe beating of cilia and flagella is essential to perform many important biological functions, including generating fluid flows on the cell surface or propulsion of micro-organisms. In this work, we analyze the motion of isolated and demembranated flagella from green algaeChlamydomonas reinhardtii, which act as ATP-driven micro-swimmers. The waveform of theChlamydomonasbeating flagella has an asymmetric waveform that is known to involve the superposition of a static component, corresponding to a fixed, intrinsic curvature, and a dynamic wave component traveling in the base-to-tip direction at the fundamental beat frequency, plus higher harmonics. Here, we demonstrate that these modes are not sufficient to reproduce the observed flagella waveforms. We find that two extra modes play an essential role to describe the motion: first, a time-symmetric mode, which corresponds to a global oscillation of the axonemal curvature, and second, a secondary tip-to-base wave component at the fundamental frequency that propagates opposite to the dominant base-to-tip wave, albeit with a smaller amplitude. Although the time-symmetric mode cannot, by itself, contribute to propulsion (scallop theorem), it does enhance the translational and rotational velocities of the flagellum by approximately a factor of 2. This mode highlights a long-range coupled on/off activity of force-generating dynein motors and can provide further insight into the underling biology of the ciliary beat.