bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probability-based methods for outlier detection in replicated high-throughput biological data
Authors: Smith Matthew S. , Devarajan Karthik 
Published: August 2020

AbstractA problem that arises frequently in high-throughput biological studies is the assessment of technical reproducibility of data obtained under homogeneous experimental conditions. This is an important problem considering the significant growth in the number of high-throughput technologies that have become available to the researcher in the past decade. Although certain ad hoc and graphical methods for determining data quality have been in existence, these methods lack statistical rigor and are not broadly applicable across different technologies. There is an inherent need for the quantitative evaluation of the reproducibility of technical replicates from high-throughput compound and siRNA screening, next-generation sequencing and other modern “omics” studies. To this end, we have developed an approach that accounts for technical variability and potential asymmetry that arise naturally in the distribution of replicate data, and aids in the identification of outliers. Our methods for outlier detection rely on flexible statistical models, employ maximum likelihood methods for estimation and are broadly applicable to a variety of high-throughput biological studies. We discuss an adaptation of these methods when there are multiple replicates as well as current limitations to these techniques. We illustrate our methods using experimental data from high-throughput compound screening and protein expression studies as well as simulated data. Our methods are implemented in the R package replicateOutliers and are currently available at github.com/matthew-seth-smith/replicateOutliers.
Macrophages promote endothelial-to-mesenchymal transition via MT1-MMP/TGFβ1 after myocardial infarction
Authors: Alonso-Herranz Laura , Sahún-Español Álvaro , Gonzalo Pilar , Gkontra Polyxeni , Núñez Vanessa , Cedenilla Marta , Villalba-Orero María , Inserte Javier , Clemente Cristina , García-Dorado David , Arroyo Alicia G , Ricote Mercedes 
Published: August 2020

ABSTRACTMacrophages produce factors that participate in cardiac repair and remodeling after myocardial infarction (MI); however, how these factors crosstalk with other cell types mediating repair is not fully understood. In this study, we demonstrated that cardiac macrophages increased expression ofMmp14(MT1-MMP) 7 days post-MI. Specific macrophage-targeting of MT1-MMP (MT1-MMPΔLysMmice) attenuates post-MI cardiac dysfunction, reduces fibrosis, and preserves the cardiac capillary network. Mechanistically, we showed that MT1-MMP activates latent TGFβ1 in macrophages, leading to paracrine SMAD2-mediated signaling in endothelial cells and endothelial-to-mesenchymal transition (EndMT). Post-MI MT1-MMPΔLysMhearts contained fewer cells undergoing EndMT than their wild-type counterparts, and MT1-MMP-deficient macrophages showed a reduced ability to induce EndMT in co-cultures with endothelial cells. Our results demonstrate the contribution of EndMT to cardiac fibrosis and adverse remodeling post-MI and identify macrophage MT1-MMP as a key regulator of this process. The identified mechanism has potential as a therapeutic target in ischemic heart disease.
SETD1B controls cognitive function via cell type specific regulation of neuronal identity genes
Authors: Michurina Alexandra , Sakib Sadman , Kerimoglu Cemil , Krüger Dennis Manfred , Kaurani Lalit , Islam Rezaul , Centeno Tonatiuh Pena , Cha Julia , Xu Xingbo , Zeisberg Elisabeth M. , Kranz Andrea , Stewart Francis Adrian , Fischer Andre 
Published: August 2020

ABSTRACTHistone-3-lysine-4-methylation (H3K4me) is mediated by six different lysine methyltransferases (KMTs). Amongst these enzymes SET domain containing 1b (SETD1B) has been linked to intellectual disability but its role in the adult brain has not been studied yet. Here we show that mice lackingSetd1bfrom excitatory neurons of the adult forebrain exhibit severe memory impairment. By combining neuron-specific ChIP-seq, RNA-seq and single cell RNA-seq approaches we show thatSetd1bcontrols the expression of neuronal-identity genes with a broad H3K4me3 peak linked to learning and memory processes. Our data furthermore suggest that basal neuronal gene-expression is ensured by other H3K4 KMTs such asKmt2aandKmt2bwhile the additional presence ofSetd1bat the single cell level provides transcriptional consistency to the expression of genes important for learning & memory.
Individual human genomes frequently contain variants that have evolutionary couplings
Authors: Martell Henry J , Griffin Darren K , Wass Mark N 
Published: August 2020

ABSTRACTCoevolution has been widely studied between species and has an important role in our understanding of biological function. For proteins there has recently been interest in the identification of positions within proteins that have coevolved including their use for modelling protein structure. Such studies focus on the identification of coevolving positions (or evolutionary couplings) within multiple sequence alignments of proteins from many species. Here, we exploit large human genome resources to investigate if it is possible to use genetic variation data from a single species, human, to identify positions within proteins that have coevolved. We combine the 1000 genome project genetic variation data with protein structural data to identify variant-variant interactions within individual human genomes. We find >4,000 combinations of variants that are located close in 3D protein structure and >1,200 in protein-protein interfaces. Many variant combinations include compensatory amino acid changes (e.g. maintaining charge/functional groups), thus supporting that these are coevolutionary events. Our study highlights that it is possible to identify coevolution within a single species. Given the important role that genetic variation plays in causing disease it is important for variant interpretation and precision medicine to consider the gestalt effects of variants rather than individual variants in isolation.
Multi-omics approach highlights differences between functional RLP classes inArabidopsis thaliana
Authors: Steidele C. , Stam R. 
Published: August 2020

AbstractThe receptor-like protein (RLP) family is a complex gene family with 57 members inArabidopsis thaliana. Some members of the RLP family are known to be involved in basal developmental processes, whereas others have found to be involved in defence responses. However, functional data is to date, only available for a small subset of RLPs, leaving the remaining ones classified as RLPs of unknown function. Using publicly available datasets, we annotated those RLPs of unknown functions as either likely defence-related or likely fulfilling a more basal function in plants. Using these categories, we can identify important characteristics that differ between the RLP sub classes. We find the two classes differ in abundance on both transcriptome and proteome level, physical clustering in the genome and putative interaction partners. However, the classes do not differ in the genetic diversity of their individual members in accessible pan-genome data. Our work has several implications for work related to functional studies on RLPs as well as for the understanding of RLP gene family evolution. Using our annotations, we can make suggestions of which RLPs can be identified as potential immune receptors using genetics tools, which can be useful for disease studies. The lack of differences in nucleotide diversity between the two RLP subclasses further suggests that non-synonymous diversity of gene sequences alone cannot distinguish defence from developmental genes. By contrast, differences in transcript and protein abundance or clustering at genomic loci might also allow for functional annotations and characterisation in other plant species.
Improved reference genome uncovers novel sex-linked regions in the guppy (Poecilia reticulata)
Authors: Fraser Bonnie A. , Whiting James R. , Paris Josephine R. , Weadick Cameron J. , Parsons Paul J. , Charlesworth Deborah , Bergero Roberta , Bemm Felix , Hoffmann Margarete , Kottler Verena A. , Liu Chang , Dreyer Christine , Weigel Detlef 
Published: August 2020

AbstractTheory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favour the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male colour patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female guppy. Here, we present a new guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing (SMRT) and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.
Theory of genetic oscillations with external noisy regulation
Authors: Negrete Jose , Lengyel Iván M. , Rohde Laurel , Desai Ravi A. , Oates Andrew C. , Jülicher Frank 
Published: August 2020

AbstractWe present a general theory of noisy genetic oscillators with externally regulated production rate. The observables that characterize the genetic oscillator are discussed, and it is shown how their statistics depend on the statistics of the external regulator. We show that these observables have generic features that are observed in two different experimental systems: the expression of the circadian clock genes in fibroblasts, and in the transient and oscillatory dynamics of the segmentation clock genes observed in cells disassociated from zebrafish embryos. Our work shows that genetic oscillations with diverse biological contexts can be understood in a common framework based on delayed negative feedback system, and slow regulator dynamics.
Light stimuli and circadian clock affect neural development inDrosophila melanogaster
Authors: Dapergola Eleni , Menegazzi Pamela , Raabe Thomas , Hovhanyan Anna 
Published: August 2020

AbstractEndogenous clocks enable organisms to adapt their physiology and behavior to daily variation in environmental conditions. Metabolic processes in cyanobacteria to humans are effected by the circadian clock, and its dysregulation causes metabolic disorders. In mouse andDrosophilawere shown that the circadian clock directs translation of factors involved in ribosome biogenesis and synchronizes protein synthesis. However, the role of clocks inDrosophilaneurogenesis and the potential impact of clock impairment on neural circuit formation and function is less understood. Here we demonstrate that light stimuli or circadian clock causes a defect in neural stem cell growth and proliferation accompanied by reduced nucleolar size. Further, we define that light and clock independently affect the InR/TOR growth regulatory pathway due to the effect on regulators of protein biosynthesis. Altogether, these data suggest that alterations in growth regulatory pathways induced by light and clock are associated with impaired neural development.
Determination of the amount of insecticide picked up by mosquitoes from treated nets
Authors: Kristan Mojca , Lines Jo , Kaur Harparkash 
Published: August 2020

ABSTRACTBackgroundInsecticides used in vector control mostly rely on vectors being exposed through contact with treated surfaces, yet little is known about the amount picked up by the insect. Measuring this amount is relevant not only for determining the actual doses that are lethal to the mosquito, but also for understanding effects on the physiology and vector competence of mosquitoes. Insecticides at sub-lethal doses can affect both parasites developing inside mosquitoes and mosquito microbiota, hence it is important to understand the processes by which parasites are exposed to insecticide inside the insect. These doses will inevitably depend on the amount of insecticide that mosquitoes pick up when they come into contact with treated nets.MethodsThree to five days old non-blood fed femaleAnopheles coluzziimosquitoes were exposed to a long-lasting insecticidal net (PermaNet 2.0 containing 55 mg/m2deltamethrin), using a wire ball frame, for 0.5-5.0 minutes. Our in-house developed colorimetric test was used to visually detect the amount of deltamethrin on different parts of the mosquito (legs, heads, thoraxes, abdomens) following exposure to the net. The amount of insecticide picked up by mosquitoes from the net over a range of exposure times was measured using a high-performance liquid chromatography with diode array detection (HPLC-DAD).ResultsThe colorimetric test, designed to only detect the type 2 pyrethroids (i.e deltamethrin, α-cypermethrin and λ-cyhalothrin) on fabrics (e.g. ITNs) and sprayed walls, was successfully used for the first time to detect deltamethrin on mosquitoes following exposure to the net. The confirmatory HPLC-DAD analysis determined that after 2 min exposure up to 12 ng of deltamethrin adhered to mosquitoes following exposure to PermaNet 2.0 (mean = 5.2 ng/mosquito, SE = 1.9) and that the final dose depends on the length of exposure time.ConclusionsThis study demonstrated the potential of a screening (type 2 pyrethroid colorimetric test) and a confirmatory test (HPLC-DAD) to determine the amount of insecticide that adheres to mosquitoes on contact with treated surfaces. This has implications for a precise lethal dose determination and detection of specific insecticide that causes the greatest mosquito mortality in circumstances where mixtures of insecticides may be used to maximise effectiveness of interventions.
Membrane composition and lipid to protein ratio modulate amyloid kinetics of yeast prion protein
Authors: Bandyopadhyay Arnab , Sannigrahi Achinta , Chattopadhyay Krishnananda 
Published: August 2020

AbstractUnderstanding of prion aggregation in membrane environment may help to ameliorate neurodegenerative complications caused by the amyloid forms of prions. Here, we investigated the membrane binding induced aggregation of yeast prion protein Sup35. Using the combination of fluorescence correlation spectroscopy (FCS) at single molecule resolution and other biophysical studies, we establish that lipid composition and lipid/protein ratio are key modulators of the aggregation kinetics of Sup35. In the presence of zwitterionic membrane, Sup35 exhibited a novel biphasic aggregation kinetics at lipid/protein ratio ranging between 20:1 and 70:1 (termed here as the Optimum Lipid Concentration, OLC). In ratios below (Low Lipid Concentration, LLC) and above (ELC, Excess Lipid Concentration) that range, the aggregation was found to be monophasic. In contrast, in the presence of negatively charged membrane, we did not observe any bi-phasic aggregation kinetics in the entire range of protein to lipid ratios. The toxicity of the aggregates formed within OLC range was found to be greater. Our results provide a mechanistic description of the role that membrane-concentration/composition-modulated-aggregation may play in neurodegenerative diseases.
Suppress me if you can: neurofeedback of the readiness potential
Authors: Schultze-Kraft Matthias , Jonany Vincent , Binns Thomas Samuel , Soch Joram , Blankertz Benjamin , Haynes John-Dylan 
Published: August 2020

AbstractVoluntary movements are usually preceded by a slow, negative-going brain signal over motor areas, the so-called readiness potential (RP). To date, the exact nature and causal role of the RP in movement preparation have remained heavily debated. One important open question is whether people can exert conscious control over their RP, for example by learning to suppress it. If people were able to initiate spontaneous movements without eliciting an RP, this would challenge the idea that the RP is a necessary stage of the causal chain leading up to a voluntary movement. We tested the ability of participants to control the magnitude of their RP in a neurofeedback experiment. Participants performed self-initiated movements and after every movement they were provided with immediate feedback about the magnitude of their RP. They were asked to find a mental strategy to perform voluntary movements such that the RPs were as small as possible. We found no evidence that participants were able to to willfully modulate or suppress their RPs while still eliciting voluntary movements. This suggests that the RP might be an involuntary component of voluntary action over which people cannot exert conscious control.
Specification of oxytocinergic and vasopressinergic circuits in the developing mouse brain
Authors: Madrigal Verdú M. Pilar , Jurado Sandra 
Published: August 2020

AbstractOxytocin (OXT) and arginine vasopressin (AVP) support sex-specific and context-appropriate social behaviors. Although alterations of these systems underlie the appearance of neuropsychiatric disorders, their formation and developmental dynamics remain largely unknown. Using novel brain clearing techniques and 3D imaging, we have reconstructed the specification of oxytocinergic and vasopressinergic circuits in the developing mouse brain with unprecedented cellular resolution. A systematic quantification indicates that OXT and AVP neurons in the hypothalamus display distinctive dynamics, but also share common features as a high cellular plasticity from embryonic to early postnatal stages. Our findings reveal new insights into the appearance and consolidation of neuropeptidergic systems in the developing CNS which is a critical step to unveil brain formation and function.
Single-molecule studies of conformational states and dynamics in the ABC importer OpuA
Authors: Tassis Konstantinos , Vietrov Ruslan , de Koning Matthijs , de Boer Marijn , Gouridis Giorgos , Cordes Thorben 
Published: August 2020

AbstractThe current model of active transport via ABC importers is mostly based on structural, biochemical and genetic data. We here establish single-molecule Förster-resonance energy transfer (smFRET) assays to monitor the conformational states and heterogeneity of the type-I ABC importer OpuA fromLactococcus lactis.We present data probing both intradomain distances that elucidate conformational changes within the substrate-binding domain (SBD) OpuAC, and interdomain distances between SBDs or transmembrane domains. Using the methodology, we studied ligand-binding mechanisms as well as ATP and glycine betaine dependences of conformational changes. Our study expands the scope of smFRET investigations towards a class of so far unstudied ABC importers, and paves the way for a full understanding of their transport cycle in the future.
Acat1gene KO restores TGN cholesterol deficiency in mutant NPC1 cells and expands mutantNpc1mouse lifespan
Authors: Rogers Maximillian A. , Chang Catherine C.Y. , Maue Robert A. , Melton Elaina M. , Peden Andrew A. , Garver William S. , Huang Mitchell M. , Schroen Peter W. , Chang Ta-Yuan 
Published: August 2020

AbstractNiemann-Pick type C (NPC) is a neurological disorder with no cure. NPC proteins deliver cholesterol from endosomes to other compartments including trans-Golgi network (TGN) and endoplasmic reticulum (ER). Acyl-coenzyme A:cholesterol acyltransferase 1 (ACAT1) is a resident ER enzyme that converts cholesterol to cholesteryl esters for storage. Here, we report the surprising finding that in a mutantNpc1mice,Acat1-deficiency delayed the onset of weight loss and declining motor skill, prolonged lifespan, delayed Purkinje neuron death, and improved hepatosplenic pathology. Furthermore, syntaxin 6, a cholesterol-binding t-SNARE normally localized to TGN, is mislocalized in mutant NPC cells. However, upon ACAT1 inhibition this mislocalization is corrected, and increase the level of a few proteins further downstream. Our results imply that ACAT1 inhibition diverts a cholesterol storage pool in a way that replenished the low cholesterol level in NPC-deficient TGN. Taking together, we identify ACAT1 inhibition as a potential therapeutic target for NPC treatment.
Evolution of multiple postzygotic barriers between species of theMimulus tilingiicomplex
Authors: Sandstedt Gabrielle D. , Wu Carrie A. , Sweigart Andrea L. 
Published: August 2020

ABSTRACTSpecies are often defined by their ability to interbreed (i.e., Biological Species Concept), but determining how and why reproductive isolation arises between new species can be challenging. In theMimulus tilingiispecies complex, three species (M. caespitosa,M. minor, andM. tilingii) are largely allopatric and grow exclusively at high elevations (>2000m). The extent to which geographic separation has shaped patterns of divergence among the species is not well understood. In this study, we determined that the three species are morphologically and genetically distinct, yet recently diverged (<400kya). Additionally, we performed reciprocal crosses within and between the species and identified several strong postzygotic reproductive barriers, including hybrid seed inviability, F1 hybrid necrosis, and F1 hybrid male and female sterility. In this study, such postzygotic barriers are so strong that a cross between any species pair in theM. tilingiicomplex would cause nearly complete reproductive isolation. We consider how geographical and topographical patterns may have facilitated the evolution of several postzygotic barriers and contributed to speciation of closely related members within theM. tilingiispecies complex.
Bioorthogonal red and far-red fluorogenic probes for wash-free live-cell and super-resolution microscopy
Authors: Werther Philipp , Yserentant Klaus , Braun Felix , Grussmayer Kristin , Navikas Vytautas , Yu Miao , Zhang Zhibin , Ziegler Michael J. , Mayer Christoph , Gralak Antoni J. , Busch Marvin , Chi Weijie , Rominger Frank , Radenovic Aleksandra , Liu Xiaogang , Lemke Edward A. , Buckup Tiago , Herten Dirk-Peter , Wombacher Richard 
Published: August 2020

AbstractSmall-molecule fluorophores enable the observation of biomolecules in their native context with fluorescence microscopy. Specific labelling via bioorthogonal tetrazine chemistry confers minimal label size and rapid labelling kinetics. At the same time, fluorogenic tetrazine-dye conjugates exhibit efficient quenching of dyes prior to target binding. However, live-cell compatible long-wavelength fluorophores with strong fluorogenicity have been difficult to realize. Here, we report close proximity tetrazine-dye conjugates with minimal distance between tetrazine and fluorophore. Two synthetic routes give access to a series of cell permeable and impermeable dyes including highly fluorogenic far-red emitting derivatives with electron exchange as dominant excited state quenching mechanism. We demonstrate their potential for live-cell imaging in combination with unnatural amino acids, wash-free multi-colour and super-resolution STED and SOFI imaging. These dyes pave the way for advanced fluorescence imaging of biomolecules with minimal label size.