bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cortical miR-709 links glutamatergic signaling to NREM sleep EEG slow waves in an activity-dependent manner
Authors: Kompotis Konstantinos , Mang Géraldine M. , Hubbard Jeffrey , Jimenez Sonia , Emmenegger Yann , Polysopoulos Christos , Hor Charlotte N. , Wigger Leonore , Hébert Sébastien S. , Mongrain Valérie , Franken Paul 
Published: September 2022

AbstractMicroRNAs (miRNAs) are key post-transcriptional regulators of gene expression that have been implicated in a plethora of neuronal processes. Nevertheless, their role in regulating brain activity in the context of sleep has so far received little attention. To test their involvement, we deleted mature miRNAs in post-mitotic neurons at two developmental ages, i.e., in early adulthood using conditionalDicerknockout (cKO) mice and in adult mice using an inducible conditionalDicercKO (icKO) line. In both models, electroencephalographic (EEG) activity was affected and the response to sleep deprivation (SD), altered; while rapid-eye-movement sleep (REMS) rebound was compromised in both, EEG delta (1-4 Hz) power during non-REM sleep (NREMS) was reduced in cKO mice and increased in icKO mice. We subsequently investigated the effects of SD on the miRNA transcriptome and found that the expression of 48 forebrain miRNAs was affected, in particular, the activity-dependent miRNA miR-709.In vivoinhibition of miR-709 in the brain increased EEG power during NREMS in the slow-delta (0.75-1.75 Hz) range, particularly after periods of prolonged wakefulness. Transcriptome analysis of primary cortical neuronsin vitrorevealed that miR-709 regulates endosomal trafficking and glutamatergic receptor activity. A subset of the genes involved in glutamatergic transmission was affected also in the cortices of sleep-deprived, miR-709-inhibited mice. Our data implicate miRNAs in the regulation of EEG activity and indicate that miR-709 links neuronal excitability during wakefulness to brain synchrony during sleep, likely through the regulation of endosomal trafficking and glutamatergic signaling.Significance StatementMicroRNAs (miRNAs) are key regulators of gene expression playing vital roles both in postnatal brain development and its functioning in adult organisms. Here, we highlight a fundamental role for miRNAs in shaping EEG slow waves, which reflect synchronous neuronal firing, characteristic of NREM sleep (NREMS) in the adult murine cortex. Disruption of the miRNA-biogenesis machinery affected brain synchrony differently, depending on when it occurred during development. Moreover, sleep deprivation altered the expression of several miRNAs in a brain-region specific manner. Among those, we identified miR-709 to affect the expression of genes involved in endosomal-trafficking and glutamatergic-transmission, thereby linking neuronal activity during wakefulness to slow EEG waves during subsequent sleep. The current study causally implicates this specific miRNA and the molecular pathways it targets in modifying the generation of NREMS EEG slow waves, which are important in synaptic plasticity and brain functioning.
The carnitine shuttle links mitochondrial metabolism to histone acetylation and lipogenesis
Authors: Izzo Luke , Trefely Sophie , Demetriadou Christina , Drummond Jack , Mizukami Takuya , Kuprasertkul Nina , Farria Aimee , Nguyen Phuong , Reich Lauren , Shaffer Joshua , Affronti Hayley , Carrer Alessandro , Andrews Andrew , Capell Brian C. , Snyder Nathaniel W. , Wellen Kathryn E. 
Published: September 2022

ABSTRACTAcetyl-CoA is a central metabolite used for lipid synthesis in the cytosol and histone acetylation in the nucleus, among other pathways. The two major precursors to acetyl-CoA in the nuclear-cytoplasmic compartment are citrate and acetate, which are processed to acetyl-CoA by ATP-citrate lyase (ACLY) and acyl-CoA synthetase short-chain 2 (ACSS2), respectively. While some evidence has suggested the existence of additional routes to nuclear-cytosolic acetyl-CoA, such pathways remain poorly defined. To investigate this, we generated cancer cell lines lacking both ACLY and ACSS2. Unexpectedly, and in contrast to observations in fibroblasts, ACLY and ACSS2 double knockout (DKO) cancer cells remain viable and proliferate, maintain pools of cytosolic acetyl-CoA, and are competent to acetylate proteins in both cytosolic and nuclear compartments. Using stable isotope tracing, we show that both glucose and fatty acids feed acetyl-CoA pools and histone acetylation in DKO cells. Moreover, we provide evidence for the carnitine shuttle and carnitine acetyltransferase (CrAT) as a substantial pathway to transfer two-carbon units from mitochondria to cytosol independent of ACLY. Indeed, in the absence of ACLY, glucose can feed fatty acid synthesis in a carnitine responsive and CrAT-dependent manner. This work defines a carnitine-facilitated route to produce nuclear-cytosolic acetyl-CoA, shedding light on the intricate regulation and compartmentalization of acetyl-CoA metabolism
Inter-organelle crosstalk supports acetyl-coenzyme A homeostasis and lipogenesis under metabolic stress
Authors: Kuna Ramya S , Kumar Avi , Galvez Hector , Wessendorf-Rodriguez Karl A , Green Courtney R , McGregor Grace H , Cordes Thekla , Shaw Reuben J , Svensson Robert U , Metallo Christian M 
Published: September 2022

AbstractProliferating cells rely on acetyl-CoA to support membrane biogenesis and acetylation. Several organelle-specific pathways are available for provision of acetyl-CoA as nutrient availability fluctuates, so understanding how cells maintain acetyl-CoA flux under such stresses is critically important. To this end we applied13C isotope tracing cell lines deficient in these mitochondrial (ATP-citrate lyase; ACLY-), cytosolic, (acetyl-CoA synthetase (ACSS2-), and peroxisomal (peroxisomal biogenesis factor 5; PEX5-) dependent pathways. ACLY knockout in multiple cell lines reduced fatty acid synthesis and increased reliance on extracellular lipids or acetate. Knockout of both ACLY and ACSS2 (DKO) severely stunted but did not entirely block proliferation, suggesting alternate pathways can support acetyl-CoA homeostasis. Metabolic tracing and PEX5 knockout studies link peroxisomal oxidation of exogenous lipids as a major source of acetyl-CoA for lipogenesis and histone acetylation, highlighting a role for inter-organelle crosstalk in supporting cell survival in response to nutrient fluctuations.TeaserWe quantify how acetyl-CoA metabolism is supported by distinct pathways spanning mitochondria, cytosol, and peroxisomes using comprehensive tracing applied to knockout cells.
Ceg1 depletion reveals mechanisms governing degradation of non-capped RNAs
Authors: Zanin Onofrio , Hebenstreit Daniel , Grzechnik Pawel 
Published: September 2022

ABSTRACTMost functional eukaryotic mRNAs contain a 7-methylguanosine (m7G) cap which serves as a platform that recruits proteins to support essential biological functions such as mRNA processing, nuclear export and translation. Although capping is accomplished during the first steps of transcription the fate and turnover of uncapped transcripts have not been studied extensively. Here, we employed fast nuclear depletion of the capping enzymes inSaccharomyces cerevisiaeto uncover the turnover of the transcripts that failed to be capped. We show that the levels of non-capped mRNAs are determined principally by the abundance of their synthesis. Nuclear depletion of the capping enzymes increases the levels of lowly expressed mRNAs and decreases mRNAs that are highly transcribed altogether mimicking the effects observed in cells lacking the predominantly cytoplasmic 5’-3’ exonuclease Xrn1. The nuclear 5’-3’ exonuclease Rat1 is not involved in the degradation of cap-defective transcripts and the lack of the capping does not affect the distribution of RNA Polymerase II on the chromatin. Our data indicate that the mRNAs that failed to be capped are not directed to a specific quality-control pathway and that the 5’ cap role is associated with the Xrn1-dependent buffering of the cellular mRNA levels, along with protecting from 5’-3’ degradation.
Viral proteins and virus-like particles of the LTR5_Hs endogenous retrovirus in human primordial germ cell-like cells
Authors: Kobayashi Mutsumi , Kobayashi Misato , Kreuzer Johannes , Zaniewski Eric , Kim Jae Jung , Shioda Keiko , Hagihara Hikari , Odajima Junko , Nakashoji Ayako , Zheng Yi , Fu Jianping , Ericsson Maria , Kawamura Kazuhiro , Stott Shannon L. , Irimia Daniel , Haas Wilhelm , Wu Chin-Lee , Tokuyama Maria , Shioda Toshi 
Published: September 2022

ABSTRACTThe hominoid-specific endogenous retrovirus LTR5_Hs is transcriptionally activated in human primordial germ cell-like cells (hPGCLCs), a pluripotent stem cell-derived cell culture model of PGCs. Here, taking the unique advantage of our novel cell culture method to obtain large amounts of pure hPGCLCs, we performed proteomics profiling of hPGCLCs and detected various viral proteins produced from the LTR5_Hs RNA via ribosomal frameshifting. We also present transmission electron microscopy images of 100-nm diameter virus-like particles (VLPs) assembled at the surface of hPGCLCs. Compared to hPGCLCs, expression of LTR5_Hs RNA is far weaker in human seminomas, the germ cell tumors resembling PGCs. Re-analysis of published single cell RNA-seq data of human embryos revealed strong activation of LTR5_Hs in migrating PGCs but suppressed in PGCs upon they reach the gonadal anlagen. In the microfluidics-supported polarized embryoids mimicking peri-implantation stages of human embryos, LTR5_Hs RNA was detected by RNA in situ hybridization in NANOG+/TFAP2C+/SOX17+ cells resembling freshly emerged PGCs. These results support that human germ cells produce LTR5_Hs proteins and VLPs during their earliest stages of normal development until their settlement in the gonadal anlagen.SUMMARY STATEMENTThe hominoid-specific endogenous retrovirus LTR5_Hs is activated in a cell culture model resembling early-stage human primordial germ cells, producing not only viral RNA but also retrovirus proteins and virus-like particles.
FLAIRR-seq: A novel method for single molecule resolution of near full-length immunoglobulin heavy chain repertoires
Authors: Ford Easton E. , Tieri David , Rodriguez Oscar , Francoeur Nancy , Soto Juan , Kos Justin , Peres Ayelet , Gibson William , Silver Catherine A. , Deikus Gintaras , Hudson Elizabeth , Woolley Cassandra R. , Beckmann Noam , Charney Alexander , Mitchell Thomas C. , Yaari Gur , Sebra Robert P. , Watson Corey T. , Smith Melissa L. 
Published: September 2022

AbstractCurrent Adaptive Immune Receptor Repertoire Sequencing (AIRR-seq) strategies resolve expressed antibody (Ab) transcripts with limited resolution of the constant region. Here we present a novel near full-length AIRR-seq (FLAIRR-Seq) method that utilizes targeted amplification by 5’ rapid amplification of cDNA ends (RACE), combined with single molecule, real-time sequencing to generate highly accurate (>Q40, 99.99%) IG heavy chain transcripts. FLAIRR-seq was benchmarked by comparing IG heavy chain variable (IGHV), diversity (IGHD), and joining (IGHJ) gene usage, complementarity-determining region 3 (CDR3) length, and somatic hypermutation to matched datasets generated with standard 5’ RACE AIRR-seq and full-length isoform sequencing. Together these data demonstrate robust, unbiased FLAIRR-seq performance using RNA samples derived from peripheral blood mononuclear cells, purified B cells, and whole blood, which recapitulated results generated by commonly used methods, while additionally resolving novel IG heavy chain constant (IGHC) gene features. FLAIRR-seq data provides, for the first time, simultaneous, single-molecule characterization of IGHV, IGHD, IGHJ, and IGHC region genes and alleles, allele-resolved subisotype definition, and high-resolution identification of class-switch recombination within a clonal lineage. In conjunction with genomic sequencing and genotyping of IGHC genes, FLAIRR-seq of the IgM and IgG repertoires from 10 individuals resulted in the identification of 32 unique IGHC alleles, 28 (87%) of which were previously uncharacterized. Together, these data demonstrate the capabilities of FLAIRR-seq to characterize IGHV, IGHD, IGHJ, and IGHC gene diversity for the most comprehensive view of bulk expressed Ab repertoires to date.
Healthcare system overstretch and in-hospital mortality of intubated COVID-19 patients in Greece: an updated analysis, September 2020 to April 2022
Authors: Lytras Theodore 
Published: September 2022

AbstractBackgroundOur previous analysis showed how in-hospital mortality of intubated COVID-19 patients in Greece is adversely affected by patient load and regional disparities. We aimed to update this analysis to include the large “delta” and “omicron” waves that affected Greece during 2021-2022, while also considering the effect of vaccination.MethodsAnonymized surveillance data were analyzed from all COVID-19 patients in Greece intubated between 1 September 2020 and 4 April 2022, and followed up until 17 May 2022. Poisson regression was used to estimate the hazard of dying as a function of fixed and time-varying covariates.ResultsMortality was significantly higher above 400 patients, with an adjusted Hazard Ratio of 1.22, 95% CI: 1.09-1.38), rising progressively up to 1.48 (95% CI: 1.31-1.69) for 800+ patients. Hospitalization away from Attica region was also independently associated with increased mortality, as was hospitalization after 1 September 2021 (HR=1.21, 95% CI: 1.09-1.36). Vaccination did not affect the mortality of these already severely ill patients.ConclusionOur results confirm that in-hospital mortality of severely ill COVID-19 patients is adversely affected by high patient load and regional disparities, and point to a further significant deterioration after 1 September especially away from Attica and Thessaloniki. This highlights the need for urgent strengthening of healthcare services in Greece, ensuring equitable and high-quality care for all.
A novel, ssDNA Bidnavirus in the giant freshwater prawn Macrobrachium rosenbergii
Authors: Gangnonngiw Warachin , Bunnontae Malinee , Kayansamruaj Pattanapon , Senapin Saengchan , Srisala Jiraporn , Flegel Timothy W. , Wongprasert Kanokpan 
Published: September 2022

AbstractA purported parvovirus producing circular, eosinophilic inclusions in the nuclei of tubule epithelial cells of the hepatopancreas (HP) of the giant freshwater prawn Macrobrachium rosenbergii (Mr) was first reported from Malaysia in 1994. In 2009, similar inclusions in Mr from Thailand were confirmed to contain single-stranded DNA (ssDNA). In 2021, Mr samples showing similar HP inclusions were reported to give positive PCR test results for decapod Hepanhamaparvovirus (DHPV) using universal DHPV primers designed from many viral isolates of 3 penaeid shrimp species. However, the matching DNA probe revealed positive in situ hybridization (ISH) results with host HP nuclei only, and not with the intranuclear inclusions. At the time, the negative ISH result with the intranuclear inclusions has not been further elucidated. Here we describe metagenomic analysis and de novo assembly from 2016 samples of Mr with similar intranuclear inclusions that showed negative PCR test results using the DHPV universal primers. Genomes identified through metagenomics have revealed a novel ssDNA genome sequence of 6,723 bases that was confirmed by a single PCR amplicon. ISH using specific probes derived from this genome sequence demonstrated the ssDNA presented in both grossly normal nuclei and in the intranuclear inclusions. Tests with archived DNA from the samples used in the 2021 publication yielded positive PCR results for both DHPV and the novel sequence, suggesting that the shrimp had dual infections. Phylogenetic analysis of the novel sequence revealed no relationship to any known DHPV type. Instead, the sequence most closely matched the polymerase B gene in the V1 fragment from Bombyx mori bidensovirus 2 (BmBDV2) is characterized by 2 ssDNA genome fragments and has been classified in the family Bidnaviridae. The 2 BmBDV2 fragments V1 and V2 each produce their own independent capsid protein genes and virions. In contrast, the new Mr virus is independent with a single 6,723 base ssDNA genome, and we propose the name Macrobrachium hepatopancreatic bidnavirus (MHBV).
Scaffold and structural diversity of the secondary metabolite space of medicinal fungi
Authors: Vivek-Ananth R.P. , Sahoo Ajaya Kumar , Baskaran Shanmuga Priya , Samal Areejit 
Published: September 2022

AbstractMedicinal fungi including mushrooms have well documented therapeutic uses. The MeFSAT database provides a curated library of more than 1800 secondary metabolites produced by medicinal fungi for potential use in high throughput screening (HTS) studies. In this study, we perform a cheminformatics based investigation of the scaffold and structural diversity of the secondary metabolite space of medicinal fungi, and moreover, perform a detailed comparison with approved drugs, other natural product libraries and semi-synthetic libraries. We find that the secondary metabolite space of MeFSAT has similar or higher scaffold diversity in comparison to other natural product libraries analysed here. Notably, 94% of the scaffolds in the secondary metabolite space of MeFSAT are not present in the approved drugs. Further, we find that the secondary metabolites of medicinal fungi, on the one hand are structurally far from the approved drugs, while on the other hand are close in terms of molecular properties to approved drugs. Lastly, chemical space visualization using dimensionality reduction methods showed that the secondary metabolite space has minimal overlap with the approved drug space. In a nutshell, our results underscore that the secondary metabolite space of medicinal fungi is a valuable resource for identifying potential lead molecules for natural product based drug discovery.
Ecological change and conflict reduction led to the evolution of a transformative social behavior in ants
Authors: Meurville Marie-Pierre , Silvestro Daniele , LeBoeuf Adria C. 
Published: September 2022

AbstractBehavioral innovations can be ecologically transformative for lineages that perform them and for their associated communities. Many ecologically dominant, superorganismal, and speciose ant lineages use a mouth-to-mouth fluid exchange behavior – trophallaxis – to share both exogenously sourced and endogenously produced materials across their colonies, while lineages that are less abundant, less cooperative and less speciose tend not to perform this behavior. How and why this behavior evolved and fixed in only some ant lineages remains unclear and whether this trait enables ants’ ecological dominance is not yet understood. Here we show that trophallaxis evolved in two major events ~110 Ma in lineages that today encompass 36% of ants, and in numerous smaller and more recent events. We found that trophallaxis evolved early only in ant lineages that had reduced intra-colonial conflict by losing workers ability to reproduce. Our causal models indicate that this signature behavior of superorganismal ants required social cooperation and ecological opportunism, and likely contributed to the large colony sizes and speciation patterns of the ants that use it and dominate our landscapes today. We hypothesize that the early evolution of trophallaxis was brought about by a major shift in terrestrial ecosystems through the origin and diversification of flowering plants and the consequent opportunistic inclusion of nectar and sap-sucker honeydew in the ant diet.
Thetrans-zeatin-type side-chain modification of cytokinins controls rice growth
Authors: Kiba Takatoshi , Mizutani Kahori , Nakahara Aimi , Takebayashi Yumiko , Kojima Mikiko , Hobo Tokunori , Osakabe Yuriko , Osakabe Keishi , Sakakibara Hitoshi 
Published: September 2022

AbstractCytokinins (CKs), a class of phytohormones with vital roles in growth and development, occur naturally with various side-chain structures, includingN6-(Δ2-isopentenyl)adenine-,cis-zeatin- andtrans-zeatin (tZ)-types. Recent studies in a model dicot plantArabidopsisdemonstrated that tZ-type CKs are biosynthesized via cytochrome P450 monooxygenase (P450) CYP735A, and have a specific function in shoot growth promotion. Although the function of some of these CKs has been demonstrated in a few dicotyledonous plant species, the significance of these variations and their biosynthetic mechanism and function in monocots and in plants with distinctive side-chain profiles thanArabidopsis, such asOryza sativa(rice), remain elusive. In this study, we characterizedCYP735A3andCYP735A4to investigate the role of tZ-type CKs in rice. Complementation test of theArabidopsisCYP735A-deficient mutant and CK profiling of loss-of-function rice mutant,cyp735a3 cyp735a4, demonstrated thatCYP735A3andCYP735A4encode P450s required for tZ-type side-chain modification in rice.CYP735Asare expressed in both roots and shoots. Thecyp735a3 cyp735a4mutants exhibited growth retardation concomitant with reduction in CK activity in both roots and shoots, indicating that tZ-type CKs function in growth promotion of both organs. Expression analysis revealed that tZ-type CK biosynthesis is negatively regulated by auxin, abscisic acid, and cytokinin and positively by dual nitrogen nutrient signals, namely glutamine-related and nitrate-specific signals. These results suggest that the physiological role of tZ-type CKs in rice is different from that inArabidopsisand they control growth of both roots and shoots in response to internal and environmental cues in rice.
Supercharged PGR5-dependent cyclic electron transfer compensates for mis-regulated chloroplast ATP synthase
Authors: Degen Gustaf E. , Jackson Philip J. , Proctor Matthew S. , Zoulias Nicholas , Casson Stuart A. , Johnson Matthew P. 
Published: September 2022

AbstractThe light reactions of photosynthesis couple electron and proton transfers across the thylakoid membrane, generating NADPH, and proton motive force (pmf) that powers the endergonic synthesis of ATP by ATP synthase. ATP and NADPH are required for CO2 fixation into carbohydrates by the Calvin-Benson-Bassham cycle (CBBC). The dominant ΔpH component of the pmf also plays a photoprotective role in regulating photosystem II (PSII) light harvesting efficiency, through non-photochemical quenching (NPQ), and cytochrome b6f (cytb6f) to photosystem I (PSI) electron transfer, via photosynthetic control. ΔpH can be adjusted by increasing the proton influx into the thylakoid lumen via upregulation of cyclic electron transfer (CET) or decreasing proton efflux via downregulation of ATP synthase conductivity (gH+). The interplay and relative contributions of these two elements of ΔpH control to photoprotection are not well understood. Here, we show that an Arabidopsis ATP synthase mutant (hope2) with 40% higher proton efflux, has supercharged CET. Double crosses of hope2 with the CET-deficient pgr5 and ndho lines reveal that PGR5-dependent CET is the major pathway contributing to higher proton influx. PGR5-dependent CET allows hope2 to maintain wild-type levels of ΔpH, CO2 fixation and NPQ, however photosynthetic control remains absent, and PSI is acceptor-side limited. Therefore, high CET in the absence of ATP synthase regulation is insufficient for PSI photoprotection.