bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local PI(4,5)P2pool dynamics detected by the coincidence biosensor tubbyCT maintain the integrity of ER-PM junctions during PLC signaling
Authors: Thallmair Veronika , Schultz Lea , Evers Saskia , Goecke Christian , Thallmair Sebastian , Leitner Michael G. , Oliver Dominik 
Published: September 2020

ABSTRACTPhosphoinositides (PIs) are important signaling molecules and determinants of membrane identity in the eukaryotic plasma membrane, where they multi-task in divergent signaling pathways. Signaling pleiotropy likely depends on distinct PI pools in the same membrane, although the physical definition of such pools has remained ambiguous. PI(4,5)P2, specifically, is also the precursor for the second messengers in the Gq/PLC pathway, IP3and DAG, and is broken down by PLCβ during signaling. Endoplasmic reticulum-plasma membrane contact sites (ER-PM junctions) have emerged as central hubs for lipid transport between both membranes, and specifically for PI homeostasis by supplying the PM with phosphatidylinositol.Here we show that the tubby protein, by virtue of its C-terminal tubby-domain, preferentially localizes to ER-PM junctions by binding to both PI(4,5)P2and the ER-PM tether E-Syt3. Under conditions of vigorous PI(4,5)P2consumption by PLCβ, additional recruitment of tubby revealed an increase of a local PI(4,5)P2pool fed by local synthesis through PI kinases. Inhibition of this pool-filling process led to the release of the ER-PM tethers, E-Syts, from the membrane and hence to loss of integrity of the ER-PM contact sites.We conclude that spatiotemporal metabolic channeling of PI synthesis initiated by non-vesicular transport in the ER-PM junctions specifies a local pool of PI(4,5)P2that is pivotal for the maintenance of homeostatic functions during global depletion of PI(4,5)P2. The findings further suggest that the tubby-like proteins (TULPs), so far known to impact on energy homeostasis and obesity through primary cilia signaling, have an additional function at ER-PM junctions.HIGHLIGHTSThe tubby domain preferentially assembles into ER-PM junctions due to coincidence detection of PI(4,5)P2and E-Syt3Tubby recruitment reveals an increase of a local pool of PI(4,5)P2in ER-PM junctions during PLCβ signalingJunctional PI(4,5)P2dynamics require local synthesis of PI(4,5)P2Local PI(4,5)P2supply is required for integrity of ER-PM junctions during PLCβ activity.
Population dynamics of GC-changing mutations in humans and great apes
Authors: Bergman Juraj , Schierup Mikkel Heide 
Published: September 2020

AbstractBackgroundThe nucleotide composition of the genome is a balance between origin and fixation rates of different mutations. For example, it is well-known that transitions occur more frequently than transversions, particularly at CpG sites. Differences in fixation rates of mutation types are less explored. Specifically, recombination-associated GC-biased gene conversion (gBGC) may differentially impact GC-changing mutations, due to differences in their genomic distributions and efficiency of mismatch repair mechanisms. Given that recombination evolves rapidly across species, we explore gBGC of different mutation types across human populations and among great ape species.ResultsWe report a stronger correlation between GC frequency and recombination for transitions than for transversions. Notably, CpG transitions are most strongly affected by gBGC. We show that the strength of gBGC differs for transitions and transversions but that its overall strength is positively correlated with effective population sizes of human populations and great ape species, with some notable exceptions, such as a stronger effect of gBGC on non-CpG transitions in populations of European descent. We study the dependence of gBGC dynamics on flanking nucleotides and show that some mutation types evolve in opposition to the gBGC expectation, likely due to hypermutability of specific nucleotide contexts.ConclusionsDifferences in GC-biased gene conversion are evident between different mutation types, and dependent on sex-specific recombination, population size and flanking nucleotide context. Our results therefore highlight the importance of different gBGC dynamics experienced by GC-changing mutations and their impact on nucleotide composition evolution.
Processing of novel food reveal payoff and rank-biased social learning in a wild primate
Authors: Canteloup C. , Cera M.B. , Barrett B.J. , van de Waal E. 
Published: September 2020

AbstractSocial learning – learning from others – is the basis for behavioural traditions. Different social learning strategies (SLS), where individuals biasedly learn behaviours based on their content or who demonstrates them, may increase an individual’s fitness and generate behavioural traditions. While SLS have been mostly studied in isolation, their interaction and the interplay between individual and social learning is less understood. We performed a field-based open diffusion experiment in a wild primate. We provided two groups of vervet monkeys with a novel food, unshelled peanuts, and documented how three different peanut opening techniques spread within the groups. We analysed data using hierarchical Bayesian dynamic learning models that explore the integration of multiple SLS with individual learning. We i) report evidence of social learning compared to strictly individual learning, ii) show that vervets preferentially socially learn the technique that yields the highest observed payoff and iii) also bias attention toward individuals of higher rank. This shows that behavioural preferences can arise when individuals integrate social information about the efficiency of a behaviour alongside cues related to the rank of a demonstrator. When these preferences converge to the same behaviour in a group, they may result in stable behavioural traditions.
A chromosome-level genome assembly for the Pacific oyster (Crassostrea gigas)
Authors: Peñaloza Carolina , Gutierrez Alejandro P. , Eory Lel , Wang Shan , Guo Ximing , Archibald Alan L. , Bean Tim P. , Houston Ross D. 
Published: September 2020

AbstractThe Pacific oyster (Crassostrea gigas) is a marine bivalve species with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available forC. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. In the current study, high coverage long and short read sequence data generated on Pacific Biosciences and Illumina platforms from a single female individual specimen was used to generate an initial assembly, which was then scaffolded into 10 pseudo chromosomes using both Hi-C sequencing and a high density SNP linkage map. The final assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously publishedC. gigasassembly. The new assembly was annotated using Pacific Biosciences Iso-Seq and Illumina RNA-Seq data, identifying 30K putative protein coding genes, with an average of 3.9 transcripts per gene. Annotation of putative repeat elements highlighted an inverse relationship with gene density, and identified putative centromeres of the metacentric chromosomes. An enrichment ofHelitronrolling circle transponsable elements was observed, suggesting their potential role in shaping the evolution of theC. gigasgenome. This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for genetic improvement ofC. gigasin aquaculture breeding programmes.
Integrated structure-function dataset reveals key mechanisms underlying photochromic fluorescent proteins
Authors: De Zitter Elke , Hugelier Siewert , Duwé Sam , Vandenberg Wim , Tebo Alison G. , Van Meervelt Luc , Dedecker Peter 
Published: September 2020

AbstractPhotochromic fluorescent proteins have become versatile tools in the life sciences, though our understanding of their structure-function relation is limited. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, yet differ only in one or two mutations. We also determined 43 different crystal structures of these mutants. Correlation and principal component analysis of the spectroscopic and structural properties confirmed the complex relationship between structure and spectroscopy, suggesting that the observed variability does not arise from a limited number of mechanisms, but also allowed us to identify consistent trends and to relate these to the spatial organization around the chromophore. We find that particular changes in spectroscopic properties can come about through multiple different underlying mechanisms, of which the polarity of the chromophore environment and hydrogen bonding of the chromophore are key modulators. Furthermore, some spectroscopic parameters, such as the photochromism, appear to be largely determined by a single or a few structural properties, while other parameters, such as the absorption maximum, do not allow a clear identification of a single cause. We also highlight the role of water molecules close to the chromophore in influencing photochromism. We anticipate that our dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.
LSD1 promotes secretory cell specification to driveBRAFmutant colorectal cancer
Authors: Miller Samuel A. , Policastro Robert A. , Sriramkumar Shruthi , Lai Tim , Huntington Thomas D. , Ladaika Christopher A , Zentner Gabriel E. , O’Hagan Heather M. 
Published: September 2020

AbstractDespite the connection to distinct mucus-containing colorectal cancer (CRC) histological subtypes, the role of secretory cells, including goblet and enteroendocrine (EEC) cells, in CRC progression has been underexplored. Analysis of TCGA and single cell RNA sequencing data demonstrates that multiple secretory progenitor populations are enriched inBRAF-mutant CRC patient tumors and cell lines. Enrichment of EEC progenitors inBRAF-mutant CRC is maintained by DNA methylation and silencing ofNEUROD1, a key gene required for differentiation of EECs. Mechanistically, secretory cells and the factors they secrete, such as Trefoil factor 3, are shown to promote colony formation and activation of cell survival pathways in the entire cell population. We further identify LSD1 as a critical regulator of secretory cell specificationin vitroand in a colon orthotopic xenograft model, where LSD1 loss reduces tumor growth and metastasis. This work establishes EEC progenitors, in addition to goblet cells, as targetable populations inBRAF-mutant CRC and identifies LSD1 as a therapeutic target in secretory lineage-containing CRC.
Host immune responses after suprachoroidal delivery of AAV8 in nonhuman primate eyes
Authors: Chung Sook Hyun , Mollhoff Iris Natalie , Mishra Alaknanda , Sin Tzu-Ni , Ngo Taylor , Ciulla Thomas , Sieving Paul , Thomasy Sara M. , Yiu Glenn 
Published: September 2020

AbstractThe suprachoroid is a potential space located between the sclera and choroid of the eye which provides a novel route for ocular drug or viral vector delivery. Suprachoroidal injection of AAV8 using transscleral microneedles enables widespread transgene expression in eyes of nonhuman primates, but may cause intraocular inflammation. We characterized the host humoral and cellular immune responses after suprachoroidal delivery of AAV8 expressing green fluorescent protein (GFP) in rhesus macaques, and found that it can induce a mild chorioretinitis that resolves after systemic corticosteroid administration, with recovery of photoreceptor morphology but persistent immune cell infiltration after 3 months. Suprachoroidal AAV8 triggered B-cell and T-cell responses against GFP, but only mild antibody responses to the viral capsid as compared to intravitreal injections of the same vector and dose. Systemic biodistribution studies showed lower AAV8 levels in liver and spleen after suprachoroidal injection compared with intravitreal delivery. Our findings suggest that suprachoroidal AAV8 primarily triggers host immune responses to GFP, likely due to sustained transgene expression in scleral fibroblasts outside the blood-retinal barrier, but elicits less humoral immune reactivity to the viral capsid than intravitreal delivery due to lower egress into systemic circulation. Thus, suprachoroidal AAV delivery of human transgenes may have significant translational potential for retinal gene therapy.
RNA helicase DDX5 enables STAT1 mRNA translation and interferon signaling in hepatitis B virus replicating hepatocytes
Authors: Sun Jiazeng , Wu Guanhui , Wang Wen-Hung , Zhang Zhengtao , Merle Philippe , Hui Lijian , Yang Danzhou , Andrisani Ourania 
Published: September 2020

ABSTRACTObjectiveRNA helicase DDX5 is downregulated during hepatitis B virus (HBV) replication, and poor prognosis HBV-related hepatocellular carcinoma (HCC). The objective of this study is to understand the significance of DDX5 downregulation during HBV infection and poor prognosis HCC, as it pertains to therapy of chronically HBV-infected patients with HCC. IFN-α therapy is effective only for a subgroup of HBV-infected patients, for reasons not understood. Herein, we investigated a novel mechanism of STAT1 translational control, involving DDX5-mediated resolution of a G-quadruplex structure, located at the 5’UTR of STAT1 mRNA, enabling STAT1 translation.Design and ResultsMolecular, pharmacologic, and biophysical assays were used together with cellular model of HBV replication, HCC cell lines, and HBV-related liver tumors. We observed, the protein level of DDX5 correlated with that of transcription factor STAT1. We show, DDX5 regulates STAT1 mRNA translation by resolving a G-quadruplex (rG4) RNA structure, proximal to the 5’ end of STAT1 5’UTR. We employed luciferase reporter assays comparing wild type (WT) vs. mutant (MT) rG4 sequence, rG4-stabilizing compounds, CRISPR/Cas9 editing of the rG4 sequence, and circular dichroism determination of rG4 structure. Ribonucleoprotein assays identified direct DDX5 binding to WT but not MT rG4. Importantly, liver cancer cell lines expressing low DDX5 exhibited reduced interferon response, while immunohistochemistry of HBV-related HCCs exhibiting absence of DDX5, also lacked STAT1.ConclusionDDX5 resolves a G-quadruplex structure in 5’UTR of STAT1 mRNA, enabling STAT1 translation. DDX5 is a key regulator of the dynamic range of interferon response during innate immunity and adjuvant IFN-α therapy.
Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with local ancestry and archaic introgression
Authors: Natri Heini M. , Hudjashov Georgi , Jacobs Guy , Kusuma Pradiptajati , Saag Lauri , Darusallam Chelzie Crenna , Metspalu Mait , Sudoyo Herawati , Cox Murray P. , Romero Irene Gallego , Banovich Nicholas E. 
Published: September 2020

AbstractLack of diversity in human genomics limits our understanding of the genetic underpinnings of complex traits, hinders precision medicine, and contributes to health disparities. To map genetic effects on gene regulation in the underrepresented Indonesian population, we have integrated genotype, gene expression, and CpG methylation data from 115 participants across three island populations that capture the major sources of genomic diversity on the region. In a comparison with a European dataset, we identify 166 uniquely Indonesia-specific eQTLs, highlighting the benefits of performing association studies on non-European populations. By combining local ancestry and archaic introgression inference eQTLs and methylQTLs, we identify regulatory loci driven by modern Papuan ancestry as well as introgressed Denisovan and Neanderthal variation. GWAS colocalization connects QTLs detected here to hematological traits. Our findings illustrate how local ancestry and archaic introgression drive variation in gene regulation across genetically distinct and in admixed populations.
Runx1 Shapes the Chromatin Landscape Via a Cascade of Direct and Indirect Targets
Authors: Hass Matthew R. , Brisette Daniel , Parameswaran Sreeja , Pujato Mario , Donmez Omer , Kottyan Leah C. , Weirauch Matthew T. , Kopan Raphael 
Published: September 2020

AbstractRunt-related transcription factor 1 (Runx1) can act as both an activator and a repressor. Here we show that CRISPR-mediated deletion ofRunx1in an embryonic kidney-derived cell (mK4) results in large-scale genome-wide changes to chromatin accessibility and gene expression. Open chromatin regions near down-regulated loci are enriched for Runx sites, remain bound by Runx2, but lose chromatin accessibility and expression inRunx1knockout cells. Unexpectedly, regions near upregulated genes are depleted of Runx sites and are instead enriched for Zeb transcription factor binding sites. Re-expressing Zeb2 inRunx1knockout cells restores suppression. These data confirm that Runx1 activity is uniquely needed to maintain open chromatin at many loci, and demonstrate that genome-scale derepression is an indirect consequence of losing Runx1-dependent Zeb expression.
Mg2+-binding shifts the IM30 activity from membrane protection to membrane destabilization
Authors: Junglas Benedikt , Axt Amelie , Siebenaller Carmen , Sonel Hilal , Hellmann Nadja , Weber Stefan A.L. , Schneider Dirk 
Published: September 2020

ABSTRACTThe inner membrane-associated protein of 30 kDa (IM30) is essential in chloroplasts and cyanobacteria. The spatio-temporal cellular localization of the protein appears to be highly dynamic and triggered by internal as well as external stimuli, mainly light intensity. A soluble fraction of the protein is localized in the cyanobacterial cytoplasm or the chloroplast stroma, respectively. Additionally, the protein attaches to the thylakoid membrane as well as to the chloroplast inner envelope or the cyanobacterial cytoplasmic membrane, respectively, especially under conditions of membrane stress. IM30 is involved in thylakoid membrane biogenesis and/or maintenance, where it either stabilizes membranes and/or triggers membrane-fusion processes. These apparently contradicting processes have to be tightly controlled and separated spatiotemporally in chloroplasts and cyanobacteria. The latter process depends on Mg2+-binding to IM30; yet, it still is unclear how Mg2+-loaded IM30 interacts with membranes and promotes membrane fusion. Here we show that interaction of Mg2+with IM30 results in increased binding of IM30 to native as well as model membranes. Via Atomic Force Microscopy in liquid, IM30-induced bilayer defects were observed in solid-supported bilayers in presence of Mg2+. The observed interaction of IM30 with membrane surfaces differs dramatically from previously observed membrane-stabilizing, carpet-like structures in the absence of Mg2+. Mg2+-induced alterations of the IM30 structure switches the IM30 activity from a membrane-stabilizing to a membrane-destabilizing function, a crucial step in membrane fusion.
Variable inbreeding depression may explain associations between the mating system and herbicide resistance
Authors: Van Etten Megan , Soble Anah , Baucom Regina S 
Published: September 2020

AbstractInbreeding depression is a central parameter underlying mating system variation in nature and one that can be altered by environmental stress. Although a variety of systems show that inbreeding depression tends to increase under stressful conditions, we have very little understanding across most organisms how the level of inbreeding depression may change as a result of adaptation to stressors. In this work we examined the potential that inbreeding depression varied among lineages ofIpomoea purpureaartificially evolved to exhibit divergent levels of herbicide resistance. We examined inbreeding depression in a variety of fitness-related traits in both the growth chamber and in the field. We paired our examination of inbreeding depression in fitness-related traits with an examination of gene expression changes associated with the level of herbicide resistance, breeding history (inbred or outcrossed), and the interaction of the breeding system and the level of herbicide resistance. We found that, while inbreeding depression was present across many of the traits, lineages artificially selected for increased herbicide resistance often showed no evidence of inbreeding depression in the presence of herbicide, and in fact, showed evidence of outbreeding depression in some traits compared to non-selected control lines and lineages selected for increased herbicide susceptibility. Further, at the transcriptome level, the resistant selection lines had differing patterns of gene expression according to breeding type (inbred vs outcrossed) compared to the control and susceptible selection lines. Our data together indicate that inbreeding depression may be lessened in populations that are adapting to regimes of strong selection.
Degeneracy and stability in neural circuits of dopamine and serotonin neuromodulators: A theoretical consideration
Authors: Behera Chandan K. , Joshi Alok , Wang Da-Hui , Sharp Trevor , Wong-Lin KongFatt 
Published: September 2020

AbstractDegenerate neural circuits perform the same function despite being structurally different. However, it is unclear whether neural circuits with interacting neuromodulator sources can themselves be degenerate while maintaining the same neuromodulatory function. Here, we address this by computationally modelling the neural circuits of neuromodulators serotonin and dopamine, local glutamatergic and GABAergic interneurons, and their possible interactions, under reward/punishment-based conditioning tasks. The neural modelling is constrained by relevant experimental studies of the VTA or DRN system using e.g. electrophysiology, optogenetics, and voltammetry. We first show that a single parsimonious, sparsely connected neural circuit model can recapitulate several separate experimental findings that indicated diverse, heterogeneous, distributed and mixed DRN-VTA neuronal signalling in reward and punishment tasks. The inability for this model to recapitulate all observed neuronal signalling suggests potentially multiple circuits acting in parallel. Then using computational simulations and dynamical systems analysis, we demonstrate that several different stable circuit architectures can produce the same observed network activity profile, hence demonstrating degeneracy. Due to the extensive D2-mediated connections in the investigated circuits, we simulate D2 receptor agonist by increasing the connection strengths emanating from the VTA DA neurons. We found that the simulated D2 agonist can distinguish among sub-groups of the degenerate neural circuits based on substantial deviations in specific neural populations’ activities in reward and punishment conditions. This forms a testable model prediction using pharmacological means. Overall, this theoretical work suggests the plausibility of degeneracy within neuromodulator circuitry and has important implication for the stable and robust maintenance of neuromodulatory functions.