bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circulating extracellular vesicles in lung cancer patients are not enriched in tumor-derived DNA fragments as revealed by whole genome sequencing
Authors: Moldovan Norbert , Verkuijlen Sandra , van der Pol Ymke , Bosch Leontien , van Weering Jan R.T. , Bahce Idris , Pegtel D. Michiel , Mouliere Florent 
Published: July 2022

AbstractLiquid biopsies contain multiple analytes that can be mined to improve the detection and management of cancer. Beyond cell-free DNA (cfDNA), mutations have been detected in DNA associated with extracellular vesicles (EV-DNA). The genome-wide composition and structure of EV-DNA are poorly characterized, and it remains undecided whether circulating EVs are enriched in tumor signal compared to unfractionated cfDNA.Here, using whole genome sequencing from selected lung cancer patients with a high cfDNA tumor content (>5%), we determined that the tumor fraction and heterogeneity are comparable between DNA associated with EVs and matched plasma cfDNA. DNA in EV fractions, obtained with standardized size-exclusion chromatography, are comprised of short ∼150-180 bp fragments and long >1000 bp fragments that are poor in tumor signal. Other fractions only exhibit short fragments with similar tumor DNA content. The composition in bases at the end of EV-DNA fragments, as well as their fragmentation patterns are similar to plasma cfDNA. Mitochondrial DNA is relatively enriched in EV fractions.Our results highlight that cfDNA in plasma is of dual nature, either bound to proteins (including the nucleosome) but also associated to EV. cfDNA associated to small EV (including exosomes) is however not preferentially enriched in tumor signal.
Strong effects of temperature, population and age-at-maturity genotype on maturation probability for Atlantic salmon in a common garden setting
Authors: Åsheim Eirik R. , Debes Paul V , House Andrew , Niemelä Petri T. , Siren Jukka P. , Erkinaro Jaakko , Primmer Craig R 
Published: July 2022

ABSTRACTAge at maturity is a key life history trait and involves a trade-off between survival risk and reproductive investment, has close connections to fitness, and is an important factor for population structures. Temperature can have a dramatic influence on life history in ectotherms, but this influence may differ between populations. While an increasing number of studies have examined population-dependent reactions with temperature, few have investigated this in the context of maturation timing.Atlantic salmon is a highly relevant study species for improving understanding of this topic as it displays considerable variation in life-history strategies, including maturation timing. Additionally, a large amount of this variation in maturation timing has been associated with a genomic region including the strong candidate genevgll3, but the effect of this gene in the context of different environments and populations has not been studied.Using a large-scale common-garden experiment, we find strong effects of temperature, population, andvgll3genotype on maturation in 2-year-old male Atlantic salmon. Observed maturation probability was 4.8 times higher in individuals reared at a mean temperature of 8.6°C compared to 6.9°C. This temperature effect was population-specific and was higher in the southern population compared to the northern population, potentially due to a higher intrinsic growth in the southern population as well as growth-temperature interaction.The early-maturationvgll3*E associated with a significantly higher maturation probability, but there was novgll3-interaction with temperature or population.Both body condition and body mass associated strongly with maturation; the body-condition association was stronger in fish carrying thevgll3*E allele, and the body mass association was only present in the warm treatment.Our findings demonstrate that the relative effect ofvgll3on maturation timing is similar for two populations and two thermal environments and gives new perspectives on the relative effect ofvgll3compared to such influences. Additionally, we show that populations can vary in their response to temperature change in terms of maturation timing, and that high intrinsic growth could potentially be associated with higher thermal sensitivity for life history variation.
The serine/threonine kinase Back seat driver prevents cell fusion to maintain cell identity
Authors: Yang Shuo , Johnson Aaron N. 
Published: July 2022

AbstractCell fate specification is essential for every major event of embryogenesis, and subsequent cell maturation ensures individual cell types acquire specialized functions. The mechanisms that regulate cell fate specification have been studied exhaustively, and each technological advance in developmental biology ushers in a new era of studies aimed at uncovering the most fundamental processes by which cells acquire unique identities. What is less appreciated is that mechanisms are in place to ensure cell identity is maintained throughout the life of the organism. The body wall musculature in the Drosophila embryo is a well-established model to study cell fate specification, as each hemisegment in the embryo generates and maintains thirty muscles with distinct identities. Here we show the serine/threonine kinase Back seat driver (Bsd), which regulates muscle morphogenesis, also maintains cell identity. Once specified, the thirty body wall muscles fuse with mononucleate muscle precursors that lack a specific identity to form multinucleate striated muscles. Importantly, body wall muscles do not fuse with each other and thereby maintain distinct identities. We show that Bsd prevents inappropriate fusion among the thirty body wall muscles. Thus, the regulation of cell fusion is one mechanism that maintains cell identity.
Synergism of interferon-beta with antiviral drugs against SARS-CoV-2 variants
Authors: Bojkova Denisa , Stack Richard , Rothenburger Tamara , Kandler Joshua D , Ciesek Sandra , Wass Mark N. , Michaelis Martin , Cinatl Jindrich 
Published: July 2022

AbstractOmicron BA.1 variant isolates were previously shown to replicate less effectively in interferon-competent cells and to be more sensitive to interferon treatment than a Delta isolate. Here, an Omicron BA.2 isolate displayed intermediate replication patterns in interferon-competent Caco-2-F03 cells when compared to BA.1 and Delta isolates. Moreover, BA.2 was less sensitive than BA.1 and similarly sensitive as Delta to betaferon treatment. Delta and BA.1 displayed similar sensitivity to the approved anti-SARS-CoV-2 drugs remdesivir, nirmatrelvir, EIDD-1931 (the active metabolite of molnupiravir) and the protease inhibitor aprotinin, whereas BA.2 was less sensitive than Delta and BA.1 to EIDD-1931, nirmatrelvir and aprotinin. Nirmatrelvir, EIDD-1931, and aprotinin (but not remdesivir) exerted synergistic antiviral activity in combination with betaferon, with some differences in the extent of synergism detected between the different SARS-CoV-2 variants. In conclusion, even closely related SARS-CoV-2 (sub)variants can differ in their biology and in their response to antiviral treatments. Betaferon combinations with nirmatrelvir and, in particular, with EIDD-1931 and aprotinin displayed high levels of synergism, which makes them strong candidates for clinical testing. Notably, effective antiviral combination therapies are desirable, as a higher efficacy is expected to reduce resistance formation.
Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA
Authors: Keil Philipp , Wulf Alexander , Kachariya Nitin , Reuscher Samira , Hühn Kristin , Silbern Ivan , Altmüller Janine , Stehle Ralf , Zarnack Kathi , Sattler Michael , Urlaub Henning , Sträßer Katja 
Published: July 2022

ABSTRACTRNA-binding proteins (RBPs) control every RNA metabolic process by multiple protein-RNA and protein-protein interactions. Their roles have largely been analyzed by crude mutations, which abrogate multiple functions at once and likely impact the structural integrity of the large messenger ribonucleoprotein particle (mRNP) assemblies, these proteins often function in. Using UV-induced RNA-protein crosslinking and subsequent mass spectrometric analysis, we first identified more than 100in vivoRNA crosslinks in 16 nuclear mRNP components inS. cerevisiae. For functional analysis, we chose Npl3, for which we determined crosslinks in its two RNA recognition motifs (RRM) and in the flexible linker region connecting the two. Using NMR and structural analyses, we show that both RRM domains and the linker uniquely contribute to RNA recognition. Interestingly, mutations in these regions cause different phenotypes, indicating distinct functions of the different RNA-binding domains of Npl3. Notably, thenpl3-Linkermutation strongly impairs recruitment of several mRNP components to chromatin and incorporation of further mRNP components into nuclear mRNPs, establishing a function of Npl3 in nuclear mRNP assembly. Taken together, we determined the specific function of the RNA-binding activity of the nuclear mRNP component Npl3, an approach that can be applied to many RBPs in any RNA metabolic process.
RNA structure landscape ofS. cerevisiaeintrons
Authors: Rangan Ramya , Huang Rui , Hunter Oarteze , Pham Phillip , Ares Manuel , Das Rhiju 
Published: July 2022

AbstractPre-mRNA secondary structures are hypothesized to play widespread roles in regulating RNA processing pathways, but these structures have been difficult to visualizein vivo. Here, we characterizeS. cerevisiaepre-mRNA structures through transcriptome-wide dimethyl sulfate (DMS) probing, enriching for low-abundance pre-mRNA through splicing inhibition. We cross-validate structures found from phylogenetic and mutational studies and identify new structures within the majority of probed introns (102 of 161). We find widespread formation of “zipper stems” between the 5’ splice site and branch point, “downstream stems” between the branch point and the 3’ splice site, and previously uncharacterized long stems that distinguish pre-mRNA from spliced mRNA. Multi-dimensional chemical mapping reveals examples where intron structures can formin vitrowithout the presence of binding partners, and structure ensemble prediction suggests that such structures appear in introns across theSaccharomycesgenus. We develop a high-throughput functional assay to characterize variants of RNA structure (VARS-seq) and we apply the method on 135 sets of stems across 7 introns, identifying structured elements that alter retained intron levels at a distance from canonical splice sites. This transcriptome-wide inference of intron RNA structures suggests new ideas and model systems for understanding how pre-mRNA folding influences gene expression.
Longitudinal in vivo monitoring of axonal integrity after brain injury
Authors: Chornyy Sergiy , Borovicka Julie A. , Patel Davina , Shin Min-Kyoo , Vázquez-Rosa Edwin , Miller Emiko , Wilson Brigid , Pieper Andrew A. , Dana Hod 
Published: July 2022

AbstractTraumatic brain injury-induced axonal degeneration leads to acute and chronic neuropsychiatric impairment, neuronal death, and accelerated neurodegenerative diseases of aging, including Alzheimer’s and Parkinson’s diseases. Thus, there is much interest in developing treatments that protect axons after injury. For this endeavor, extended comprehensive evaluation of axonal integrity in experimental systems is required to evaluate the efficacy of putative interventions in preclinical models. However, traditional histological tissue proccessing techniques are logistically prohibitive for assessments of long-term pathology. Here, we report a new method of longitudinally monitoring the functional activity of thalamocortical axons before and after injury in vivo in the same animal over an extended period of time. Specifically, we expressed an axonal-targeting genetically-encoded calcium indicator in the mouse dorsolateral geniculate nucleus and then recorded axonal activity patterns in the visual cortex in response to visual stimulation. We demonstrate the utility of this method for assessing in vivo aberrant axonal activity patterns after traumatic brain injury, as well as for evaluating the therapuetic efficacy of the neuroprotective P7C3-A20 pharmacologic agent in vivo. We found that P7C3-A20 treatment minimized most, but not all, of the pathological changes in axonal activity patterns after traumatic brain injury.
Non-trivial dynamics in a model of glial membrane voltage driven by open potassium pores
Authors: Janjic Predrag , Solev Dimitar , Kocarev Ljupco 
Published: July 2022

AbstractDespite the molecular evidence that the nearly linear steady-state current-voltage relationship in mammalian astrocytes reflects a total current resulting from more than one differently regulated K+ conductances, detailed ODE models of membrane voltage Vm are still lacking. Repeated experimental results of deregulated expressions of major K+ channels in glia, Kir4.1, in models of neurodegenerative disease, as well as their altered rectification when assembling heteromeric Kir4.1/Kir5.1 channels have motivated us to attempt a detailed model incorporating the weaker potassium K2P-TREK1 current, in addition to Kir4.1, and study the stability of the resting state Vr. The main question is whether with a deregulated Kir conductivity the nominal resting state Vr remains stable, and the cell retains a trivial, potassium electrode behavior with Vm following EK. The minimal 2-dimensional model near Vr showed that certain alterations of Kir4.1 current may result in multistability of Vm if the typically observed K+ currents - Kir, K2P, and non-specific potassium leak are present. More specifically, a decrease or loss of outward Kir4.1 conductance (turning the channels into inwardly rectifying) introduces instability of Vr, near EK. That happens through robustly observed fold bifurcation giving birth to a second, much more depolarized stable resting state Vdr > −10 mV. Realistic time series were used to perturb the membrane model, from recordings of glial Vm during electrographic seizures. Simulations of the perturbed system by constant currents through gap-junctions and transient seizure-like discharges as local field potentials led to depolarization of the astrocyte and switching of Vm between the two stable states, in a downstate – upstate manner. If the prolonged depolarizations near Vdr prove experimentally plausible, such catastrophic instability would impact all aspects of the glial function, from metabolic support to membrane transport and practically all neuromodulatory roles assigned to glia.Statement of SignificanceThe almost linear current-voltage relationship of most glial membranes results from multiple non-linear potassium leaky-pore, or background conductances. The corresponding channel types develop and deregulate independently, some of them asymmetrically – deregulate differently in different Vm ranges. Effect of those deregulations on whole-cell voltage responses has not been treated. We developed a minimal ODE model of voltage dynamics incorporating detailed models of the different potassium currents based on electrophysiological recordings. Parametrically inducing some of the reported deregulations of Kir current in glia resulted in instability of the nominal resting membrane potential and appearence of a second much more depolarized resting state. If prolonged glial depolarizations prove plausible such bistability would change the present beliefs about glial Vm dynamics.
α-syn overexpression, NRF2 suppression, and enhanced ferroptosis create a vicious cycle of neuronal loss in Parkinson’s disease
Authors: Anandhan A , Chen W , Nguyen N , Madhavan L , Dodson M , Zhang DD 
Published: July 2022

AbstractParkinson’s disease (PD) is the second most common neurodegenerative disorder, affecting millions each year. Most PD cases (∼90%) are sporadic, resulting from the age-dependent accumulation of pathogenic effects. One key pathological hallmark of PD progression is the accumulation of alpha-synuclein (α-syn), which has been shown to negatively affect neuronal function and viability. Here, using 3- and 6-month-old Nrf2+/+ and Nrf2-/- mice overexpressing human α-syn (PD model), we show that loss of NRF2 increases markers of ferroptosis across PD-relevant brain regions. Increased ferroptosis was associated with an age- and genotype-dependent increase in α-syn pathology and behavioral deficits. Finally, we demonstrate that α-syn overexpression sensitizes neuronal cells and ex vivo brain slices to ferroptosis induction, which may be due to α-syn suppression of NRF2 at the protein level. Altogether, these results indicate that NRF2 is a critical anti-ferroptotic mediator of neuronal survival, and that the vicious cycle of α-syn overexpression and NRF2 suppression, leading to enhanced neuronal ferroptotic cell death, could represent a targetable and currently untapped means of preventing PD onset and progression.
GARP complex controls Golgi physiology by stabilizing COPI machinery and Golgi v-SNAREs
Authors: Khakurel Amrita , Kudlyk Tetyana , Pokrovskaya Irina , D’Souza Zinia , Lupashin Vladimir V. 
Published: July 2022

AbstractGARP is an evolutionary conserved heterotetrameric protein complex that is thought to tether endosome-derived vesicles and promotes their fusion in thetrans-Golgi network. We have previously discovered the GARP’s role in maintaining Golgi glycosylation machinery. To further investigate the importance of the GARP complex for Golgi physiology, we employed Airyscan superresolution and electron microscopy, as well as the unbiased quantitative proteomic analysis of Golgi in RPE1 cells. Bothcisandtrans-Golgi compartments were significantly enlarged in GARP deficient cells with pronounced alterations of TGN morphology. In GARP-KO cells, proteomic analysis revealed a depletion of a subset of Golgi resident proteins, including Ca2+binding proteins, glycosylation enzymes, and v-SNAREs. We validated proteomics studies and discovered that two Golgi-resident proteins SDF4 and ATP2C1, related to Golgi calcium homeostasis, as well as intra-Golgi v-SNAREs GOSR1 and BET1L, are significantly depleted in GARP-KO cells. To test if SNARE depletion is responsible for the Golgi defects in GARP deficient cells, we created and analyzed GOSR1 and BET1L KO cell lines. Since GARP-KO was more deleterious to the Golgi physiology than SNARE-KOs, we have investigated other components of intra-Golgi vesicular trafficking, particularly COPI vesicular coat and its accessory proteins. We found that COPI is partially relocalized to the ERGIC compartment in GARP-KO cells. Moreover, COPI accessory proteins GOLPH3, ARFGAP1, GBF1 were displaced from the membrane and BIG1 was relocated to endolysosomal compartment in GARP-KO cells. We propose that the dysregulation of COPI machinery along with degradation of intra-Golgi v-SNAREs and alteration of Golgi Ca2+homeostasis are the major driving factors for the instability of Golgi resident proteins and glycosylation defects in GARP deficient cells.
Displacement experiments provide evidence for path integration in Drosophila
Authors: Titova Anna V. , Kau Benedikt E. , Tibor Shir , Mach Jana , Vo-Doan T. Thang , Wittlinger Matthias , Straw Andrew D. 
Published: July 2022

ABSTRACTLike many other animals, insects are capable of returning to previously visited locations using path integration. Recently, Drosophila has been added to the list of insects thought capable of this navigational memory. Existing experimental evidence, however, has a potential confound. Here we show that pheromones deposited at the site of reward might enable flies to find previously rewarding locations even without memory. Thus, we designed an experiment to determine if flies can use path integration memory despite potential pheromonal cues by displacing the flies shortly after an optogenetic reward. We found that rewarded flies returned to the location predicted by a memory-based model. Several analyses are consistent with path integration as the mechanism by which flies returned to the reward. We conclude that while pheromones may often be important in fly navigation and must be carefully controlled in future experiments, Drosophila may indeed be capable of performing path integration.
The chromatin landscape of the euryarchaeonHaloferax volcanii
Authors: Marinov Georgi K. , Bagdatli S. Tansu , Wu Tong , He Chuan , Kundaje Anshul , Greenleaf William J. 
Published: July 2022

AbstractArchaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations first made in their archaeal ancestors. One of the most notable such features is nucleosomal chromatin, although archaeal histones and chromatin differ significantly from those of eukaryotes. Despite increased interest in archaeal histones in recent years, the properties of archaeal chromatin have been little studied using genomic tools. Here, we adapt the ATAC-seq assay to archaea and use it to map the accessible landscape of the genome of the euryarchaeoteHaloferax volcanii. We integrate the resulting datasets with genome-wide maps of active transcription and single-stranded DNA (ssDNA) and find that whileH. volcaniipromoters exist in a preferentially accessible state, unlike most eukaryotes, modulation of transcriptional activity is not associated with changes in promoter accessibility. Applying orthogonal single-molecule footprinting methods, we quantify the absolute levels of physical protection ofH. volcanii, and find thatHaloferaxchromatin is similarly or only slightly more accessible, in aggregate, than that of eukaryotes. We also evaluate the degree of coordination of transcription within archaeal operons and make the unexpected observation that some CRISPR arrays are associated with highly prevalent ssDNA structures. These results provide a foundation for the future functional studies of archaeal chromatin.
Benchmarking Differential Abundance Analysis Methods for Correlated Microbiome Sequencing Data
Authors: Yang Lu , Chen Jun 
Published: July 2022

AbstractDifferential abundance analysis (DAA) is one central statistical task in microbiome data analysis. A robust and powerful DAA tool can help identify highly confident microbial candidates for further biological validation. Current microbiome studies frequently generate correlated samples from different microbiome sampling schemes such as spatial and temporal sampling. In the past decade, a number of DAA tools for correlated microbiome data (DAA-c) have been proposed. Disturbingly, different DAA-c tools could sometimes produce quite discordant results. To recommend the best practice to the field, we performed the first comprehensive evaluation of existing DAA-c tools using real data-based simulations. Overall, the linear model-based methods LinDA, MaAsLin2, and LDM are more robust than methods based on generalized linear models. The LinDA method is the only method that maintains reasonable performance in the presence of strong compositional effects.