bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microglial amyloid beta clearance is driven by PIEZO1 channels
Authors: Konttinen Henna , Sitnikova Valeria , Ishchenko Yevheniia , Shakirzyanova Anastasia , Giudice Luca , Ugidos Irene F , Gómez-Budia Mireia , Korvenlaita Nea , Ohtonen Sohvi , Belaya Irina , Fazaludeen Feroze , Mikhailov Nikita , Gotkiewicz Maria , Ketola Kirsi , Lehtonen Šárka , Koistinaho Jari , Kanninen Katja M , Hernández Damian , Pébay Alice , Giugno Rosalba , Korhonen Paula , Giniatullin Rashid , Malm Tarja 
Published: March 2022

ABSTRACTBackgroundMicroglia are the endogenous immune cells of the brain and act as sensors of pathology to maintain brain homeostasis and eliminate potential threats. In Alzheimer’s disease (AD), toxic amyloid beta (Aβ) accumulates in the brain and forms stiff plaques. In late-onset AD accounting for 95% of all cases, this is thought to be due to reduced clearance of Aβ. Human genome-wide association studies and animal models suggest that reduced clearance results from aberrant function of microglia. While the impact of neurochemical pathways on microglia have been broadly studied, mechanical receptors regulating microglial functions remain largely unexplored.MethodsHere we showed that a mechanotransduction ion channel, PIEZO1, is expressed and functional in human and mouse microglia. We used a small molecule agonist, Yoda1, to study how activation of PIEZO1 affects AD-related functions in human induced pluripotent stem cell (iPSC) -derived microglia-like cells (iMGL) under controlled laboratory experiments. Cell survival, metabolism, phagocytosis and lysosomal activity were assessed using real-time functional assays. To evaluate the effect of activation of PIEZO1 in vivo, 5-month-old 5xFAD male mice were infused daily with Yoda1 for two weeks through intracranial cannulas. Microglial Iba1 expression and Aβ pathology were quantified with immunohistochemistry and confocal microscopy. Published human and mouse AD datasets were used for in-depth analysis of PIEZO1 gene expression and related pathways in microglial subpopulations.ResultsWe show that PIEZO1 orchestrates Aβ clearance by enhancing microglial survival, phagocytosis, and lysosomal activity. Aβ inhibited PIEZO1-mediated calcium transients, whereas activation of PIEZO1 with a selective agonist, Yoda1, improved microglial phagocytosis resulting in Aβ clearance both in human and mouse models of AD. Moreover, PIEZO1 expression was associated with a unique microglial transcriptional phenotype in AD as indicated by assessment of cellular metabolism, and human and mouse single cell datasets.ConclusionThese results indicate that the compromised function of microglia in AD could be improved by controlled activation of PIEZO1 channels resulting in alleviated Aβ burden. Pharmacological regulation of these mechanoreceptors in microglia could represent a novel therapeutic paradigm for AD.GRAPHICAL ABSTRACT
Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages
Authors: Putzeys Leena , Boon Maarten , Lammens Eveline-Marie , Kuznedelov Konstantin , Severinov Konstantin , Lavigne Rob 
Published: March 2022

ABSTRACTRNA sequencing has become the method of choice to study the transcriptional landscape of phage-infected bacteria. However, short-read RNA sequencing approaches generally fail to capture the primary 5’ and 3’ boundaries of transcripts, confounding the discovery of key transcription initiation and termination events as well as operon architectures. Yet, the elucidation of these elements is crucial for the understanding of the strategy of transcription regulation during the infection process, which is currently lacking beyond a handful of model phages. To this end, we developed ONT-cappable-seq, a specialized long-read RNA sequencing technique that allows end-to-end sequencing of primary prokaryotic transcripts using the Nanopore sequencing platform. We applied ONT-cappable-seq to study transcription of Pseudomonas aeruginosa phage LUZ7, obtaining a comprehensive genome-wide map of viral transcription start sites, terminators, and complex operon structures that fine-regulate gene expression. Our work provides new insights in the RNA biology of a non-model phage, unveiling distinct promoter architectures, putative small non-coding viral RNAs, and the prominent regulatory role of terminators during infection. The robust workflow presented here offers a framework to obtain a global, yet fine-grained view of phage transcription and paves the way for standardized, in depth transcription studies for microbial viruses or bacteria in general.
Zhx2 is a candidate gene underlying oxymorphone metabolite brain concentration associated with state-dependent oxycodone reward
Authors: Beierle Jacob A. , Yao Emily J. , Goldstein Stanley I. , Lynch William B. , Scotellaro Julia L. , Sena Katherine D. , Wong Alyssa L. , Linnertz Colton A , Averin Olga , Moody David E. , Reilly Christopher A. , Peltz Gary , Emili Andrew , Ferris Martin T. , Bryant Camron D. 
Published: March 2022

ABSTRACTUnderstanding the pharmacogenomics of opioid metabolism and behavior is vital to therapeutic success as mutations can dramatically alter therapeutic efficacy and addiction liability. We found robust, sex-dependent BALB/c substrain differences in oxycodone behaviors and whole brain concentration of oxycodone metabolites. BALB/cJ females showed robust state-dependent oxycodone reward learning as measured via conditioned place preference when compared to the closely related BALB/cByJ substrain. Accordingly, BALB/cJ females also showed a robust increase in brain concentration of the inactive metabolite noroxycodone and the active metabolite oxymorphone compared to BALB/cByJ mice. Oxymorphone is a highly potent full agonist at the mu opioid receptor that could enhance drug-induced interoception and state-dependent oxycodone reward learning. Quantitative trait locus (QTL) mapping in a BALB/c F2 reduced complexity cross revealed one major QTL on chromosome 15 underlying brain oxymorphone concentration that explained 32% of the female variance. BALB/cJ and BALB/cByJ differ by fewer than 10,000 variants which can greatly facilitate candidate gene/variant identification. Hippocampal and striatal cis-expression QTL (eQTL) and exon-level eQTL analysis identifiedZhx2, a candidate gene coding for a transcriptional repressor with a private BALB/cJ retroviral insertion that reduces Zhx2 expression and sex-dependent dysregulation of CYP enzymes. Whole brain proteomics corroborated the Zhx2 eQTL and identified upregulated CYP2D11 that could increase brain oxymorphone in BALB/cJ females. To summarize, Zhx2 is a highly promising candidate gene underlying brain oxycodone metabolite levels. Future studies will validateZhx2and its site of action using reciprocal gene editing and tissue-specific viral manipulations in BALB/c substrains.Significance StatementOur findings show genetic variation can result in sex-specific alterations in whole brain concentrations of bioactive opioid metabolites following oxycodone administration, and reinforces the need for sex as a biological factor in pharmacogenomic studies. The co-occurrence of female-specific increased oxymorphone and state-dependent reward learning suggests that this minor yet potent and efficacious metabolite of oxycodone could increase opioid interoception and drug-cue associative learning of opioid reward which has implications for cue-induced relapse of drug-seeking behavior.
If this title is funny, will you cite me? Citation impacts of humour and other features of article titles in ecology and evolution
Authors: Heard Stephen B. , Cull Chloe A. , White Easton R. 
Published: March 2022

AbstractTitles of scientific papers pay a key role in their discovery, and “good” titles engage and recruit readers. A particularly interesting aspect of title construction is the use of humour, but little is known about whether funny titles boost or limit readership and citation of papers. We used a panel of volunteer scorers to assess title humour for 2,439 papers in ecology and evolution, and measured associations between humour scores and subsequent citation (both self-citation and citation by others). Papers with funnier titles were cited less often, but this appears to result from a confound with paper importance. Self-citation data suggest that authors give funnier titles to papers they consider less important. After correction for this confound, papers with funny titles have significantly higher citation rates, suggesting that humour recruits readers. We also examined associations between citation rates and several other features of titles. Inclusion of acronyms and taxonomic names was associated with lower citation rates, while assertive-statement phrasing and presence of colons, question marks, and political regions were associated with somewhat higher citation rates. Title length had no effect on citation. Our results suggest that scientists can use creativity with titles without having their work condemned to obscurity.
A microfluidic-based model of nociceptor sensitization reveals a direct activation of sensory axons by prostaglandin E2
Authors: Kimourtzis Georgios , Rangwani Natasha , Jenkins Bethan J. , McNaughton Peter A. , Raouf Ramin 
Published: March 2022

AbstractProstaglandin E2 (PGE2) is one of the major contributors to inflammatory pain hyperalgesia, however, the extent to which it modulates the activity of the nociceptive axons is incompletely understood. We used a microfluidic cell culture platform to investigate the changes in responsiveness of sensory axons following treatment with PGE2. We show that the application of PGE2 to fluidically isolated axons leads to sensitization of their responses to depolarising stimuli, and the inclusion of zatebradine, a blocker of HCN channels, blocks this enhancement. However, unexpectedly, we also found that the application of PGE2 to the axons elicited a direct and persistent spiking activity in the sensory neurons. We demonstrate that this persistent activity is due to a direct depolarization of axons by PGE2, which is inhibited by Nav1.8 sodium channel blockers but is mainly refractory to Nav1.7 channel blockade. Both the persistent activity and the membrane depolarization in the axons are abolished by the EP4 receptor inhibitor and a blocker of cAMP synthesis. Our data indicate that PGE2/EP4/cAMP pathway culminates in a sustained depolarization in the sensory axons, leading to the generation of action potentials propagating to the soma. PGE2 therefore, not only mediates nociceptor sensitization but can directly elicit discharges in nociceptive axons, hence redefining its role as a pain mediator in inflammatory conditions.One Sentence SummaryProstaglandin E2 can depolarise nociceptive axons in the absence of any noxious stimuli leading to a sustained activation of pain sensing neurons.
Condensin positioning at telomeres by shelterin proteins drives sister-telomere disjunction in anaphase
Authors: Colin Léonard , Reyes Céline , Berthezene Julien , Maestroni Laetitia , Modolo Laurent , Toselli Esther , Chanard Nicolas , Schaak Stephane , Cuvier Olivier , Gachet Yannick , Coulon Stéphane , Bernard Pascal , Tournier Sylvie 
Published: March 2022

ABSTRACTThe localization of condensin along chromosomes is crucial for their accurate segregation in anaphase. Condensin is enriched at telomeres but how and for what purpose had remained elusive. Here we show that fission yeast condensin accumulates at telomere repeats through the balancing acts of Taz1, a core component of the shelterin complex that ensures telomeric functions, and Mit1, a nucleosome-remodeler associated with shelterin. We further show that condensin takes part in sister-telomere separation in anaphase, and that this event can be uncoupled from the prior separation of chromosome arms, implying a telomere-specific separation mechanism. Consistent with a cis-acting process, increasing or decreasing condensin occupancy specifically at telomeres modifies accordingly the efficiency of their separation in anaphase. Genetic evidence suggests that condensin promotes sister-telomere separation by counteracting cohesin. Thus, our results reveal a shelterin-based mechanism that enriches condensin at telomeres to drive in cis their separation during mitosis.
Increased male investment in sperm competition results in reduced maintenance of gametes
Authors: Koppik Mareike , Baur Julian , Berger David 
Published: March 2022

SummaryMale animals often show higher mutation rates than their female conspecifics. A hypothesis for this male-bias is that competition over fertilization of female gametes leads to increased male investment into reproduction at the expense of maintenance and repair, resulting in a trade-off between male success in sperm competition and offspring quality. Here, we provide evidence for this hypothesis by harnessing the power of experimental evolution to study effects of sexual selection on the male germline in the seed beetleCallosobruchus maculatus. We first show that 50 generations of evolution under strong sexual selection, coupled with experimental removal of natural selection resulted in males that are more successful in sperm competition. We then show that these males produce progeny of lower quality if engaging in socio-sexual interactions prior to being challenged to surveil and repair experimentally induced damage in their germline, and that the presence of male competitors alone can be enough to elicit this response. We identify 18 candidate genes that showed differential expression in response to the induced germline damage, with several of these previously implicated in processes associated with DNA repair and cellular maintenance. These genes also showed significant expression changes across socio-sexual treatments of fathers and predicted the reduction in quality of their offspring, with expression of one gene also being strongly correlated to male sperm competition success. Sex differences in expression of the same 18 genes indicate a substantially higher female investment in germline maintenance. While more work is needed to detail the exact molecular underpinnings of our results, our findings provide rare experimental evidence for a trade-off between male success in sperm competition and germline maintenance. This suggests that sex-differences in the relative strengths of sexual and natural selection are causally linked to male mutation bias. The tenet advocated here, that the choices of an individual can affect plasticity of its germline and the resulting genetic quality of subsequent generations, has several interesting implications for mate choice processes.
A role of Lck annular lipids in the steady upkeep of active Lck in T cells
Authors: Porciello Nicla , Cipria Deborah , Masi Giulia , Lanz Anna-Lisa , Milanetti Edoardo , Grottesi Alessandro , Howie Duncan , Cobbold Steve P. , Schermelleh Lothar , He Hai-Tao , D’Abramo Marco , Destainville Nicolas , Acuto Oreste , Nika Konstantina 
Published: March 2022

AbstractTheoretical work suggests that collective spatiotemporal behaviour of integral membrane proteins (IMPs) can be modulated by annular lipids sheathing their hydrophobic moiety. Here, we present evidence for this prediction in a natural membrane by investigating the mechanism that maintains steady amount of active isoform of Lck kinase (LckA) by Lck trans-autophosphorylation offset by the phosphatase CD45. We gauged experimental suitability by quantitation of CD45 and LckAsubcellular localisation, LckAgeneration as a function of Lck and pharmacological perturbation. Steady LckAwas challenged by swapping Lck membrane anchor with structurally divergent ones expected to substantially modify Lck annular lipids, such as that of Src or the transmembrane domains of LAT, CD4, palmitoylation-defective CD4 and CD45, respectively. The data showed only small alteration of LckA, except for CD45 hydrophobic anchor that thwarted LckA, due to excessive lateral proximity to CD45. The data are best explained by annular lipids facilitating or penalising IMPs’ lateral proximity, hence modulating IMPs protein-protein functional interactions. Our findings can contribute to improve the understanding of biomembranes’ organisation.
Strategies to Identify and Edit Improvements in Synthetic Genome Segments Episomally
Authors: Rudolph Alexandra , Nyerges Akos , Chiappino-Pepe Anush , Landon Matthieu , Baas-Thomas Maximilien , Church George 
Published: March 2022

ABSTRACTGenome engineering projects often utilize bacterial artificial chromosomes (BACs) to carry multi-kilobase DNA segments on low copy number vectors. However, DNA synthesis and amplification have the potential to impose mutations on the contained DNA segments that can in turn reduce or prevent viability of the final strain. Here, we describe improvements to a multiplex automated genome engineering (MAGE) protocol to improve recombineering frequency and multiplexability. This protocol was applied to ‘recoding’ an Escherichia coli strain to swap out seven codons to synonymous alternatives genome-wide. Ten 44,402 to 47,179 bp de novo synthesized BAC-contained DNA segments from the recoded strain were unable to complement deletion of the corresponding 33 to 61 wild type genes using a single antibiotic resistance marker. Next-Generation Sequencing was used to identify 1-7 non-recoding mutations in essential genes per segment, and MAGE in turn proved a useful strategy to repair these mutations on the BAC-contained recoded segment when both the recoded and wild type copies of the mutated genes had to exist by necessity during the repair process. This strategy could be adapted to mutation identification and repair for other large-scale genome engineering projects, or for incorporation of small genetic engineering sites for quick protocol adjustments.
Hepatocyte-specific loss of LAP2α protects against diet-induced hepatic steatosis and steatohepatitis in male mice
Authors: Upadhyay Kapil K. , Choi Eun-Young K. , Foisner Roland , Omary M. Bishr , Brady Graham F. 
Published: March 2022

AbstractThere is increasing evidence for the importance of the nuclear envelope in lipid metabolism, nonalcoholic fatty liver disease (NAFLD), and nonalcoholic steatohepatitis (NASH). Human mutations in LMNA, encoding A-type nuclear lamins, cause early-onset insulin resistance and NASH, while hepatocyte-specific deletion of Lmna predisposes to NASH with fibrosis in male mice. Given that variants in the gene encoding LAP2α, a nuclear protein that regulates lamin A/C, were previously identified in patients with NAFLD, we sought to determine the role of LAP2α in NAFLD using a mouse genetic model. Hepatocyte-specific Lap2a-knockout (Lap2α(ΔHep)) mice and littermate controls were fed normal chow or high-fat diet (HFD) for 8 weeks or 6 months. In contrast to what was observed with hepatocyte-specific Lmna deletion, male Lap2a(ΔHep) mice showed no increase in hepatic steatosis or NASH compared to controls. Rather, Lap2a(ΔHep) mice demonstrated reduced hepatic steatosis, particularly after long-term HFD, with decreased susceptibility to diet-induced NASH. Accordingly, whereas pro-steatotic genes Cidea, Mogat1, and Cd36 were upregulated in Lmnα-KO mice, they were downregulated in Lap2α(ΔHep) mice, and there was a trend toward decreases in pro-inflammatory and pro-fibrotic genes. These data indicate that hepatocyte-specific Lap2a deletion protects against hepatic steatosis and NASH in mice; therefore, LAP2α might represent a potential therapeutic target in human NASH.Brief SummaryLoss of LAP2α in mouse hepatocytes protected against diet-induced hepatic steatosis and NASH.
Alpha-1 Antitrypsin Limits Neutrophil Extracellular Trap Disruption of Airway Epithelial Barrier Function
Authors: Hudock KM , Collins MS , Imbrogno M , Kramer EL , Brewington JJ , Ziady A , Zhang N , Snowball J , Xu Y , Carey BC , Horio Y , O’Grady SM , Kopras EJ , Meeker J , Morgan H , Ostmann AJ , Skala E , Siefert ME , Na CL , Gollomp K , Mangalmurti N , Trapnell BC , Clancy JP 
Published: March 2022

AbstractNeutrophil extracellular traps contribute to lung injury in cystic fibrosis and asthma, but the mechanisms are poorly understood. We sought to understand the impact of human NETs on barrier function in primary human bronchial epithelial and a human airway epithelial cell line. We demonstrate that NETs disrupt airway epithelial barrier function by decreasing transepithelial electrical resistance and increasing paracellular flux, partially by NET-induced airway cell apoptosis. NETs selectively impact the expression of tight junction genes claudins 4, 8 and 11. Bronchial epithelia exposed to NETs demonstrate visible gaps in E-cadherin staining, a decrease in full-length E-cadherin protein and the appearance of cleaved E-cadherin peptides. Pretreatment of NETs with alpha-1 antitrypsin (A1AT) inhibits NET serine protease activity, limits E-cadherin cleavage, decreases bronchial cell apoptosis and preserves epithelial integrity. In conclusion, NETs disrupt human airway epithelial barrier function through bronchial cell death and degradation of E-cadherin, which are limited by exogenous A1AT.
Location of the TEMPO moiety of TEMPO-PC in phosphatidylcholine bilayers is membrane phase-dependent
Authors: Kim Seonghoon , Hyeon Changbong 
Published: March 2022

AbstractThe (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) moiety tethered to the headgroup of phosphatidylcholine (PC) lipid is employed in spin labeling electron paramagnetic resonance (EPR) spectroscopy to probe the water dynamics near lipid bilayer interfaces. Due to its amphiphilic character, however, TEMPO spin label could partition between aqueous and lipid phases, and may even be stabilized in the lipid phase. Accurate assessment of the TEMPO-PC configuration in bilayer membranes is essential for correctly interpreting the data from measurements. Here, we carry out all-atom molecular dynamics (MD) simulations of TEMPO-PC probe in single-component lipid bilayers at varying temperatures, using two standard MD force fields. We find that for DPPC membrane whose gel-to-fluid lipid phase transition occurs at 314 K, TEMPO is stabilized above (below) the bilayer interface if the membrane is in the gel (fluid) phase. For bilayers made of unsaturated lipids, DOPC and POPC, which adopt the fluid phase at ambient temperature, TEMPO is unequivocally stabilized inside the bilayers. Our finding of membrane phase-dependent positioning of TEMPO moiety highlights the importance of assessing the packing order and fluidity of lipids under a given measurement condition.