bluuebunny/crossref_metadata_2025_split huggingface dataset:
ResQ, a release factor-dependent ribosome rescue factor in the Gram-positive bacterium Bacillus subtilis
Authors: Shimokawa-Chiba Naomi , Müller Claudia , Fujiwara Keigo , Beckert Bertrand , Ito Koreaki , Wilson Daniel N. , Chiba Shinobu 
Published: August 2019

SummaryRescue of the ribosomes from dead-end translation complexes, such as those on truncated (non-stop) mRNA, is essential for the cell. Whereas bacteria use trans-translation for ribosome rescue, some Gram-negative species possess alternative and release factor (RF)-dependent rescue factors, which enable an RF to catalyze stop codon-independent polypeptide release. We now discover that the Gram-positive Bacillus subtilis has an evolutionarily distinct ribosome rescue factor named ResQ. Genetic analysis shows that B. subtilis requires the function of either trans-translation or ResQ for growth, even in the absence of proteotoxic stresses. Biochemical and cryo-EM characterization demonstrates that ResQ binds to non-stop stalled ribosomes, recruits homologous RF2, but not RF1, and induces its transition into an open active conformation. Although ResQ is distinct from E. coli ArfA, they use convergent strategies in terms of mode of action and expression regulation, indicating that many bacteria may have evolved as yet unidentified ribosome rescue systems.
A Canal-Associated Neuron cAMP signalling pathway that regulatesC. eleganslarval development
Authors: Chien Jason , Wolf Fred W. , Grosche Sarah , Yosef Nebeyu , Garriga Gian , Mörck Catarina 
Published: August 2019

ABSTRACTCaenorhabditis eleganslarval development requires the function of the two Canal-Associated Neurons (CANs): killing the CANs by laser microsurgery or disrupting their development by mutating the geneceh-10results in early larval arrest. How these cells promote larval development, however, remains a mystery. In screens for mutations that bypass CAN function, we identified the genekin-29,which encodes a member of the Salt-Inducible Kinase (SIK) family and a component of a conserved pathway that regulates variousC. elegansphenotypes. Likekin-29loss, gain-of-function mutations in genes that may act upstream ofkin-29or growth in cyclic-AMP analogs bypassedceh-10larval arrest, suggesting that a conserved adenylyl cyclase/PKA pathway inhibits KIN-29 to promote larval development and that loss of CAN function results in dysregulation of KIN-29 and larval arrest. The adenylyl cyclase ACY-2 mediates CAN-dependent larval development:acy-2mutant larvae arrested development with a similar phenotype toceh-10mutants, and the arrest phenotype was suppressed by mutations inkin-29. ACY-2 is predominantly expressed in the CANs, and we provide evidence that theacy-2functions in the CANs to promote larval development. By contrast, cell-specific expression experiments suggest thatkin-29acts in both the hypodermis and neurons, but not in the CANs. Based on our findings, we propose that cAMP produced by ACY-2 in the CANs acts in neighboring neurons and hypodermal cells where it activates PKA and inhibits KIN-29 to promote larval development. We discuss how this conserved pathway could be partitioned between two cells.
Intercellular communication controls agonist-induced calcium oscillations independently of gap junctions in smooth muscle cells
Authors: Stasiak S.E. , Jamieson R.R. , Bouffard J. , Cram E.J. , Parameswaran H. 
Published: August 2019

AbstractWe report the existence of a unique mode of communication among human smooth muscle cells (SMCs) where they use force to frequency modulate long-range calcium waves. An important consequence of this mechanical signaling is that changes in stiffness of the underlying extracellular matrix can interfere with the frequency modulation of Ca2+ waves causing healthy SMCs to falsely perceive a much higher agonist dose than they actually received. This distorted sensing of contractile agonist dose on stiffer matrices is absent in isolated SMCs, even though the isolated cells can sense matrix rigidity. We show that intercellular communication that enables this collective Ca2+ response does not involve transport across gap junctions or extracellular diffusion of signaling molecules. The aberrant communication between cells that distorts the individual cell's perception of contractile stimulus can explain the sudden, exaggerated narrowing of the lumen when exposed to low dose of inhaled agonists in diseases like asthma.
Detection and quantification of GPCR mRNA: An assessment and implications of data from high-content methods
Authors: Sriram Krishna , Wiley Shu Z. , Moyung Kevin , Gorr Matthew W. , Salmerón Cristina , Marucut Jordin , French Randall P. , Lowy Andrew M. , Insel Paul A. 
Published: August 2019

AbstractG protein-coupled receptors (GPCRs) are the largest family of membrane receptors and targets for approved drugs. Analysis of GPCR expression is thus important for drug discovery and typically involves mRNA-based methods. We compared transcriptomic cDNA [Affymetrix] microarrays, RNA-seq and qPCR-based TaqMan arrays for their ability to detect and quantify expression of endoGPCRs (non-chemosensory GPCRs with endogenous agonists). In human pancreatic cancer-associated fibroblasts, RNA-seq and TaqMan arrays yielded closely correlated values for GPCR number (~100) and expression levels, as validated by independent qPCR. By contrast, the microarrays failed to identify ~30 such GPCRs and generated data poorly correlated with results from those methods. RNA-seq and TaqMan arrays also yielded comparable results for GPCRs in human cardiac fibroblasts, pancreatic stellate cells, cancer cell lines and pulmonary arterial smooth muscle cells. The magnitude of mRNA expression for several Gq/11-coupled GPCRs predicted cytosolic calcium increase and cell migration by cognate agonists. RNA-seq also revealed splice variants for endoGPCRs. Thus, RNA-seq and qPCR-based arrays are better suited than microarrays for assessing GPCR expression and can yield results predictive of functional responses--findings that have implications for GPCR biology and drug discovery.Abstract Graphic
BiofilmQ, a software tool for quantitative image analysis of microbial biofilm communities
Authors: Hartmann Raimo , Jeckel Hannah , Jelli Eric , Singh Praveen K. , Vaidya Sanika , Bayer Miriam , Vidakovic Lucia , Díaz-Pascual Francisco , Fong Jiunn C.N. , Dragoš Anna , Besharova Olga , Nadell Carey D. , Sourjik Victor , Kovács Ákos T. , Yildiz Fitnat H. , Drescher Knut 
Published: August 2019

AbstractBiofilms are now considered to be the most abundant form of microbial life on Earth, playing critical roles in biogeochemical cycles, agriculture, and health care. Phenotypic and genotypic variations in biofilms generally occur in three-dimensional space and time, and biofilms are therefore often investigated using microscopy. However, the quantitative analysis of microscopy images presents a key obstacle in phenotyping biofilm communities and single-cell heterogeneity inside biofilms. Here, we present BiofilmQ, a comprehensive image cytometry software tool for the automated high-throughput quantification and visualization of 3D and 2D community properties in space and time. Using BiofilmQ does not require prior knowledge of programming or image processing and provides a user-friendly graphical user interface, resulting in editable publication-quality figures. BiofilmQ is designed for handling fluorescence images of any spatially structured microbial community and growth geometry, including microscopic, mesoscopic, macroscopic colonies and aggregates, as well as bacterial biofilms in the context of eukaryotic hosts.
Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation
Authors: Amamoto Ryoji , Garcia Mauricio D. , West Emma R. , Choi Jiho , Lapan Sylvain W. , Lane Elizabeth A. , Perrimon Norbert , Cepko Constance L. 
Published: August 2019

ABSTRACTRecent transcriptional profiling technologies are uncovering previously-undefined cell populations and molecular markers at an unprecedented pace. While single cell RNA (scRNA) sequencing is an attractive approach for unbiased transcriptional profiling of all cell types, a complementary method to isolate and sequence specific cell populations from heterogeneous tissue remains challenging. Here, we developed Probe-Seq, which allows deep transcriptional profiling of specific cell types isolated using RNA as the defining feature. Dissociated cells are labelled using fluorescent in situ hybridization (FISH) for RNA, and then isolated by fluorescent activated cell sorting (FACS). We used Probe-Seq to purify and profile specific cell types from mouse, human, and chick retinas, as well as the Drosophila midgut. Probe-Seq is compatible with frozen nuclei, making cell types within archival tissue immediately accessible. As it can be multiplexed, combinations of markers can be used to create specificity. Multiplexing also allows for the isolation of multiple cell types from one cell preparation. Probe-Seq should enable RNA profiling of specific cell types from any organism.
Ctf4 organizes sister replisomes and Pol α into a replication factory
Authors: Yuan Zuanning , Georgescu Roxana , de Luna Almeida Santos Ruda , Zhang Daniel , Bai Lin , Yao Nina Y. , Zhao Gongpu , O’Donnell Michael E. , Li Huilin 
Published: August 2019

ABSTRACTThe current view is that eukaryotic replisomes are independent. Here we show that Ctf4 tightly dimerizes CMG helicase, with an extensive interface involving Psf2, Cdc45, and Sld5. Interestingly, Ctf4 binds only one Pol α-primase. Thus, Ctf4 may have evolved as a trimer to organize two helicases and one Pol α-primase into a replication factory. In the 2CMG-Ctf43-1Pol α-primase factory model, the two CMGs nearly face each other, placing the two lagging strands toward the center and two leading strands out the sides. The single Pol α-primase is centrally located and may prime both sister replisomes. The Ctf4-coupled-sister replisome model is consistent with cellular microscopy studies revealing two sister forks of an origin remain attached and are pushed forward from a protein platform. The replication factory model may facilitate parental nucleosome transfer during replication.
Simulating metagenomic stable isotope probing datasets with MetaSIPSim
Authors: Barnett Samuel E. , Buckley Daniel H. 
Published: August 2019

AbstractBackgroundDNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and binning of these targeted genomes. However, empirical development of metagenomic-SIP methods is hindered by the complexity and cost of these studies. We developed a toolkit, ‘MetaSIPSim,’ to simulate sequencing read libraries for metagenomic-SIP experiments. MetaSIPSim is intended to generate datasets for method development and testing. To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment.ResultsThrough simulation we show that metagenomic-SIP improves the assembly and binning of isotopically labeled genomes relative to a conventional metagenomic approach. Improvements were dependent on experimental parameters and on sequencing depth. Community level G+C content impacted the assembly of labeled genomes and subsequent binning, where high community G+C generally reduced the benefits of metagenomic-SIP. Furthermore, when a high proportion of the community is isotopically labeled, the benefits of metagenomic-SIP decline. Finally, the choice of gradient fractions to sequence greatly influences method performance.ConclusionsMetagenomic-SIP is a valuable method for recovering isotopically labeled genomes from complex communities. We show that metagenomic-SIP performance depends on optimization of experimental parameters. MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data.
KAT2-mediated acetylation switches the mode of PALB2 chromatin association to safeguard genome integrity
Authors: Fournier Marjorie , Bleuyard Jean-Yves , Couturier Anthony M. , Ellins Jessica , Hester Svenja , Smerdon Stephen J. , Tora László , Esashi Fumiko 
Published: August 2019

SummaryThe tumour suppressor PALB2 stimulates error-free repair of DNA breaks, whilst its steady-state chromatin association protects active genes from genotoxic stress. Here, we report that the lysine acetyltransferases 2A and 2B (KAT2A/B), commonly known to promote transcriptional activation, acetylate the PALB2 chromatin association motif (ChAM), providing a dynamic regulatory mechanism for PALB2. ChAM acetylation within a cluster of seven lysine residues (7K), detected in the chromatin-enriched fraction in undamaged cells, enhanced its association with nucleosomes while decreasing its non-specific binding to naked DNA. DNA damage triggered a rapid deacetylation of ChAM and a concomitant increase in PALB2 mobility. Significantly, a 7K-null mutation, which hindered ChAM binding to both nucleosomes and DNA, conferred deficiency in DNA repair and hypersensitivity to the anti-cancer drug olaparib. Thus, our study reveals a unique mechanism mediated by KAT2A/B-dependent acetylation of a non-histone protein, which fine-tunes the DNA damage response and hence promotes genome stability.
Modulation of sensory behavior and food choice by an enteric bacteria-produced neurotransmitter
Authors: O’Donnell Michael P. , Fox Bennett W. , Chao Pin-Hao , Schroeder Frank C. , Sengupta Piali 
Published: August 2019

AbstractAnimals coexist in commensal, pathogenic or mutualistic relationships with complex communities of diverse organisms including microbes1. Some bacteria produce bioactive neurotransmitters which have been proposed to modulate host nervous system activity and behaviors2. However, the mechanistic basis of this microbiota-brain modulation and its physiological relevance is largely unknown. Here we show that inC. elegans, the neuromodulator tyramine (TA) produced by gut-colonizing commensalProvidenciabacteria can bypass the requirement for host TA biosynthesis to manipulate a host sensory decision. Bacterially-produced TA is likely converted to octopamine (OA) by the host tyramine beta-hydroxylase enzyme. OA, in turn, targets the OCTR-1 receptor on the ASH/ASI sensory neurons to modulate an aversive olfactory response. We identify genes required for TA biosynthesis inProvidencia, and show that these genes are necessary for modulation of host behavior. We further find thatC. eleganscolonized byProvidenciapreferentially select these bacteria in food choice assays, and that this selection bias requires bacterially-produced TA. Our results demonstrate that a neurotransmitter produced by gut microbiota mimics the functions of the cognate host molecule to override host control of a sensory decision, thereby promoting fitness of both host and microbe.
Live-cell assays for cell stress responses reveal new patterns of cell signaling caused by mutations in rhodopsin, α-synuclein and TDP-43
Authors: Harlen Kevin M. , Roush Elizabeth C. , Clayton Joseph E. , Martinka Scott , Hughes Thomas E. 
Published: August 2019

ABSTRACTMany neurodegenerative diseases induce high levels of sustained cellular stress and alter a number of cellular processes. Genetically-encoded fluorescent biosensors are effective tools to examine neuronal activity and signaling in living cells. To examine how different mutations associated with neurodegenerative disease affect cell stress and signaling we created live-cell assays for ER-mediated cell stress and second messenger signaling. Analysis of the rhodopsin P23H mutation, the most common mutation in autosomal dominant Retinitis Pigmentosa, revealed increased cell stress levels compared to wild type rhodopsin. Moreover, this increase in cell stress correlated with blunted Ca2+signaling in a stress dependent manner. Analysis of single cell Ca2+signaling profiles revealed unique Ca2+signaling responses exist in cells expressing wild type or P23H mutants, further supporting the notion that second messenger signaling is affected by cell stress. To explore the use of the ER-stress biosensor in other neurodegenerative diseases we examined how various mutants of α-synuclein and TDP-43 affected ER-mediated cell stress. Mutants of both α-synuclein and TDP-43 associated with Parkinson’s Disease and ALS demonstrated increases in ER-mediated cell stress. This increased cell stress was accompanied by changes in phosphodiesterase activity. Both HEK293T and SH-SY5Y cells expressing these proteins displayed a shift towards increased cAMP degradation rates, likely due to increased phosphodiesterase activity. Together these data illustrate how biosensors can provide nuanced, new views of neurodegenerative disease processes.
Untangling the effects of cellular composition on coexpression analysis
Authors: Farahbod Marjan , Pavlidis Paul 
Published: August 2019

AbstractBackgroundCoexpression analysis is one of the most widely used methods in genomics, with applications to inferring regulatory networks, predicting gene function, and interpretation of transcriptome profiling studies. Most studies use data collected from bulk tissue, where the effects of cellular composition present a potential confound. However, the impact of composition on coexpression analysis have not been studied in detail. Here we examine this issue for the case of human brain RNA analysis.ResultsWe found that for most genes, differences in expression levels across cell types account for a large fraction of the variance of their measured RNA levels in brain (median R2= 0.64). We then show that genes that have similar expression patterns across cell types will have correlated RNA levels in bulk tissue, due to the effect of variation in cellular composition. We demonstrate that much of the coexpression in the bulk tissue can be attributed to this effect. We further show how this composition-induced coexpression masks underlying intra-cell-type coexpression observed in single-cell data. Attempt to correct for composition yielded mixed results.ConclusionsThe dominant coexpression signal in brain can be attributed to cellular compositional effects, rather than intra-cell-type regulatory relationships, and this is likely to be true for other tissues. These results have important implications for the relevance and interpretation of coexpression in many applications.
Cooperation, only for high rewards – a solvable task-based study on free-ranging dogs
Authors: Bhattacharjee Debottam , Sarkar Rohan , Sau Shubhra , Babu Daisy , Albal Asawari , Mehta Diksha , Bhadra Anindita 
Published: August 2019

AbstractThe benefits of group living mostly surpass the disadvantages like sharing of resources and competition over food, space and mates, driving the evolution of social organization. Group living can be facilitated by social tolerance and cooperation among the group members. Social canids (e.g. wolves) display cooperative breeding, hunting, and prosocial activities in different contexts. Unlike cooperative pack-living wolves (Canis lupus lupus), their descendants, domesticated dogs (Canis lupus familiaris), show varying levels of associations from solitary to stable social groups. Free-ranging dogs are group-living but prefer to forage solitarily, hence providing an excellent opportunity for investigating social tolerance and coordinated task performance among the members in various situations. We tested 113 adult-only groups of free-ranging dogs in three different tasks to investigate group responses and performance in problem-solving situations in the presence of an unfamiliar human. Task 1 (unfamiliar, single food reward) and 2 (familiar, single food reward) examined group responses and cooperation from the perspective of familiarity, while Task 3 (familiar, multiple food rewards) enabled us to test whether increased food rewards promote social tolerance and food sharing among the group members. Regardless of significantly higher performance in Task 2 compared to Task 1, cooperation and food sharing were significantly lower in both. Task 3 revealed a strong positive correlation between food sharing and social tolerance, but not between success and social tolerance, suggesting a tendency for cooperation. We conclude that context-dependent cooperation and tolerance among group members facilitate group-living in free-ranging dogs.Significance statementGroup living is a common phenomenon in the animal world where the members of a group show social tolerance and co-operative behaviours towards each other. This need for cooperative intents increases manifolds while groups face different problem-solving situations in their day to day lives. Here, we tested a large number of free-ranging dog groups to understand general cooperative intents such as social tolerance and food sharing in different problem-solving conditions. We found shreds of evidence of context-dependent cooperation and social tolerance among group members with minimal display of aggression. It is not adaptive for the dogs to fight or display aggression over resources. Alternatively, use of subtle cues such as display of dominance and subordination seem to be more plausible mechanisms for the development of efficient scavenging strategies and maintaining hierarchy.
Phylogenetic weighting does little to improve the accuracy of evolutionary coupling analyses
Authors: Hockenberry Adam J. , Wilke Claus O. 
Published: August 2019

AbstractHomologous sequence alignments contain important information about the constraints that shape protein family evolution. Correlated changes between different residues, for instance, can be highly predictive of physical contacts within three-dimensional structures. Detecting such co-evolutionary signals via direct coupling analysis is particularly challenging given xsthe shared phylogenetic history and uneven sampling of different lineages from which protein sequences are derived. Current best practices for mitigating such effects include sequence-identity-based weighting of input sequences and post-hoc re-scaling of evolutionary coupling scores. However, numerous weighting schemes have been previously developed for other applications, and it is unknown whether any of these schemes may better account for phylogenetic artifacts in evolutionary coupling analyses. Here, we show across a dataset of 150 diverse protein families that the current best practices out-perform several alternative sequence- and tree-based weighting methods. Nevertheless, we find that sequence weighting in general provides only a minor benefit relative to post-hoc transformations that re-scale the derived evolutionary couplings. While our findings do not rule out the possibility that an as-yet-untested weighting method may show improved results, the similar predictive accuracies that we observe across distinct weighting methods suggests that there may be little room for further improvement on top of existing strategies.