bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD5L constraints acute and systemic inflammation and can be a novel potent therapeutic agent against sepsis
Authors: Oliveira Liliana , Gomes Ana P. , Santos Rita F. , Cardoso Marcos S. , Nóvoa Ana , Luche Hervé , Gartner Fátima , Malissen Bernard , Mallo Moisés , Carmo Alexandre M. 
Published: March 2022

AbstractThe global burden of sepsis, with an estimated 49 million cases and 11 million deaths in 2017, often passes unnoticed to the general public even though it is the direct cause of nearly 20% of all deaths worldwide. This unawareness is perhaps due to misconceptions, or miscoding in the reporting of the ultimate causes of death, as in many diseases it is not the actual infectious agent that causes the biggest harm. Rather, it is the uncontrolled inflammation leading to septic shock that is the most menacing manifestation associated with many infections, and becomes deadly serious once it has passed the stage where anti-microbial drugs no longer have any effect to inactivate or destroy the pathogen. Here we show that the combined anti-bacterial and anti-inflammatory properties of the scavenger receptor cysteine-rich (SRCR) protein CD5L contribute to a remarkable therapeutic effect of the protein to fight sepsis, such that when exogenously administered in C57BL/6 mice with induced lethal-grade sepsis, it can be a very effective curative agent to treat this condition. The resistance conferred by CD5L to polybacterial-induced sepsis using the cecal ligation and puncture (CLP) model is consistent with the reported observations that CD5L physically binds and inactivates diverse species and strains of bacteria. Accordingly, our CD5L-knockout mice are significantly more susceptible to experimentally-induced mid-grade CLP than wild-type animals. We show that CD5L is centered on promoting neutrophil recruitment and activation, overall contributing to reducing the bacteria burden of the animals. However, the dramatic susceptibility of CD5L-deficient animals is not necessarily correlated only with pathogen load, as these mice are also extremely susceptible to sterile sepsis induced by nonlethal doses of LPS. Notwithstanding the observed capacity of CD5L to directly bind to a broad range of pathogens, typical of many PRRs, our evidence suggests that the anti-inflammatory properties of the protein are at least as important as its pathogen-binding potential, and can, and should, be explored to treat the deadly inflammation storm that is sepsis.
The ADP-heptose biosynthesis enzyme GmhB is a conserved Gram-negative bacteremia fitness factor
Authors: Holmes Caitlyn L. , Smith Sara N. , Gurczynski Stephen J. , Severin Geoffrey B. , Unverdorben Lavinia V. , Vornhagen Jay , Mobley Harry L. T. , Bachman Michael A. 
Published: March 2022

ABSTRACTKlebsiella pneumoniae is a leading cause of Gram-negative bacteremia, which is a major source of morbidity and mortality worldwide. Gram-negative bacteremia requires three major steps: primary site infection, dissemination to the blood, and bloodstream survival. Since K. pneumoniae is a leading cause of healthcare-associated pneumonia, the lung is a common primary infection site leading to secondary bacteremia. K. pneumoniae factors essential for lung fitness have been characterized, but those required for subsequent bloodstream infection are unclear. To identify K. pneumoniae genes associated with dissemination and bloodstream survival, we performed insertion site sequencing (InSeq) using a pool of >25,000 transposon mutants in a murine model of bacteremic pneumonia. This analysis revealed the gene gmhB as important for either dissemination from the lung or bloodstream survival. In Escherichia coli, GmhB is a partially redundant enzyme in the synthesis of ADP-heptose for the lipopolysaccharide (LPS) core. To characterize its function in K. pneumoniae, an isogenic knockout strain (ΔgmhB) and complemented mutant were generated. During pneumonia, GmhB did not contribute to lung fitness and did not alter normal immune responses. However, GmhB enhanced bloodstream survival in a manner independent of serum susceptibility, specifically conveying resistance to spleen-mediated killing. In a tail-vein injection of murine bacteremia, GmhB was also required by K. pneumoniae, E. coli and Citrobacter freundii for optimal bloodstream survival. Together, this study identifies GmhB as a conserved Gram-negative bacteremia fitness factor that acts through LPS-mediated mechanisms to enhance bloodstream survival.IMPORTANCEKlebsiella pneumoniae frequently causes healthcare-associated infections including pneumonia and bacteremia. This is particularly concerning due to emerging antimicrobial resistance and the propensity for bacteremia to initiate sepsis, which has high mortality and is the most expensive hospital-treated condition. Defining mechanisms of bloodstream survival is critical to understanding the pathology of bacteremia and identifying novel targets for future therapies. In this study, we identified the K. pneumoniae enzyme GmhB as a bloodstream-specific fitness factor that enables the bacteria to survive in the spleen but is dispensable in the lung. Furthermore, GmhB is also needed by the related bacterial pathogens Escherichia coli and Citrobacter freundii to cause bacteremia. Conserved bacteremia fitness factors such a GmhB could be the basis for future therapeutics that would alleviate significant disease caused by from multiple diverse pathogens.
Biallelic and gene-wide genomic substitution for endogenous intron and retroelement mutagenesis in human cells
Authors: Ohno Tomoyuki , Akase Taichi , Kono Shunya , Kurasawa Hikaru , Takashima Takuto , Aizawa Yasunori 
Published: March 2022

AbstractFunctional annotation of the vast noncoding landscape of the diploid human genome still remains a major challenge of genomic research. An efficient, scarless, biallelic, and gene-wide mutagenesis approach is needed for direct investigation of the functional significance of endogenous long introns in gene regulation. Here we established a genome substitution platform, the Universal Knock-in System or UKiS, that meets these requirements. For proof of concept, we first used UKiS on the longest intron of TP53 in the pseudo-diploid cell line HCT116. Complete deletion of the intron, its substitution with mouse and zebrafish syntenic introns, and specific removal of retrotransposon-derived elements (retroelements) were all efficiently and accurately achieved in both alleles, revealing a suppressive role of intronic Alu elements in TP53 expression. We also used UKiS for TP53 intron deletion in human induced pluripotent stem cells without losing their stemness. Furthermore, UKiS enabled biallelic removal of all introns from three human gene loci of ∼100 kb and longer to demonstrate that intron requirements for transcriptional activities vary among genes. UKiS is a new standard platform with which to pursue the design of noncoding regions for genome writing in human cells.
POPEYE directly regulates bHLH Ib genes and its own expression
Authors: Pu Meng Na , Liang Gang 
Published: March 2022

AbstractIron (Fe) is an essential trace element for plants. When suffering from Fe deficiency, plants modulate the expression of Fe deficiency responsive genes. POPEYE (PYE) is a key bHLH transcription factor involved in Fe homeostasis. However, the molecular mechanism of PYE regulating the Fe deficiency response remains elusive. We found that the over-expression ofPYEattenuates the expression of Fe deficiency responsive genes. PYE directly represses the transcription of bHLH Ib genes (bHLH38, bHLH39, bHLH100, andbHLH101) by associating with their promoters. Although PYE contains anEthylene response factor-associatedAmphiphilicRepression (EAR) motif, it does not interact with the transcriptional corepressors TOPLESS/TOPLESS-RELATED (TPL/TPRs). Subcellular localization analysis indicated that PYE localizes in both the cytoplasm and nucleus. PYE contains aNuclearExportSignal (NES) which is required for the cytoplasmic localization of PYE. The mutation of NES amplifies the repression function of PYE, resulting in downregulation of Fe deficiency responsive genes. Co-expression assays indicated that bHLH IVc members (bHLH104, bHLH105/ILR3, and bHLH115) facilitate the nuclear accumulation of PYE. Conversely, PYE indirectly represses transcription activation ability of bHLH IVc. Additionally, PYE directly negatively regulates its own transcription. This study provides insights into the complicated Fe deficiency response signaling pathway and enhances the understanding of PYE functions.Short summaryPYE is a negative regulator of Fe homeostasis; however, it was still unclear how PYE integrates the Fe deficiency response signaling. Our study shows that conditional nuclear localization of PYE is crucial for Fe homeostasis. PYE not only negatively regulates FIT-dependent Fe uptake genes by directly targeting bHLH Ib genes, but also negatively regulates its own expression.
Comparative transcriptomics of the Drosophila olfactory subsystems identifies a support cell-expressed Osiris protein required for pheromone sensing
Authors: Scalzotto Marta , Ng Renny , Cruchet Steeve , Saina Michael , Armida Jan , Su Chih-Ying , Benton Richard 
Published: March 2022

AbstractThe nose of most animals comprises multiple sensory subsystems, which are defined by the expression of different olfactory receptor families. Drosophila melanogaster antennae comprise two morphologically and functionally distinct subsystems that express Odorant receptors (Ors) or Ionotropic receptors (Irs). Although these receptors have been thoroughly characterized in this species, the subsystem-specific expression and roles of other genes are much less well-understood. Here we generate subsystem-specific transcriptomic datasets to identify hundreds of genes, encoding diverse protein classes, that are selectively enriched in either Or or Ir subsystems. Using single-cell antennal transcriptomic data and RNA in situ hybridization, we find most neuronal genes – other than sensory receptor genes – are broadly expressed within the subsystems. By contrast, we identify many non-neuronal genes that exhibit highly selective cell-type expression, revealing substantial molecular heterogeneity in the non-neuronal cellular components of these olfactory subsystems. We characterize one Or subsystem-specific non-neuronal molecule, Osiris 8 (Osi8), a conserved member of a large family of insect transmembrane proteins. Osi8 is expressed in tormogen support cells that are associated with pheromone sensing neurons. Loss of Osi8 abolishes high sensitivity neuronal responses to pheromone ligands. Together this work identifies a new protein required for insect pheromone detection, emphasizes the importance of support cells in sensory responses, and provides a resource for future characterization of other olfactory subsystem-specific genes.
Novel pathogen introduction rapidly alters evolved movement strategies, restructuring animal societies
Authors: Gupte Pratik Rajan , Albery Gregory F. , Gismann Jakob , Sweeny Amy R. , Weissing Franz J. 
Published: March 2022

AbstractAnimal sociality emerges from individual decisions on how to balance the costs and benefits of being sociable. Movement strategies incorporating social information — the presence and status of neighbours — can modulate spatial associations, helping animals avoid infection while benefiting from indirect information about their environment. When a novel pathogen is introduced into a population, it should increase the costs of sociality, selecting against gregariousness. Yet current thinking about novel pathogen introductions into wildlife neglects hosts’ potential evolutionary responses. We built an individual-based model that captures essential features of the repeated introduction, and subsequent transmission of an infectious pathogen among social hosts. Examining movements in a foraging context, widely shared by many species, we show how introducing a novel pathogen to a population provokes a rapid evolutionary transition to a dynamic social distancing movement strategy. This evolutionary shift triggers a disease-dominated ecological cascade of increased individual movement, decreased resource harvesting, and fewer social encounters. Pathogen-risk adapted individuals form less clustered social networks than their pathogen-risk naive ancestors, which reduces the spread of disease. The mix of post-introduction social movement strategies is influenced by the usefulness of social information and disease cost. Our work demonstrates that evolutionary adaptation to pathogen introductions and re-introductions can be very rapid, comparable to ecological timescales. Our general modelling framework shows why evolutionary dynamics should be considered in movement-disease models, and offers initial predictions for the eco-evolutionary consequences of wildlife pathogen spillover scenarios.
Observation of a single protein by ultrafast X-ray diffraction
Authors: Ekeberg Tomas , Assalauova Dameli , Bielecki Johan , Boll Rebecca , Daurer Benedikt J. , Eichacker Lutz A. , Franken Linda E. , Galli Davide E. , Gelisio Luca , Gumprecht Lars , Gunn Laura H. , Hajdu Janos , Hartmann Robert , Hasse Dirk , Ignatenko Alexandr , Koliyadu Jayanath , Kulyk Olena , Kurta Ruslan , Kuster Markus , Lugmayr Wolfgang , Lübke Jannik , Mancuso Adrian P. , Mazza Tommaso , Nettelblad Carl , Ovcharenko Yevheniy , Rivas Daniel E. , Samanta Amit K. , Schmidt Philipp , Sobolev Egor , Timneanu Nicusor , Usenko Sergej , Westphal Daniel , Wollweber Tamme , Worbs Lena , Xavier P. Lourdu , Yousef Hazem , Ayyer Kartik , Chapman Henry N. , Sellberg Jonas A. , Seuring Carolin , Vartanyants Ivan A. , Küpper Jochen , Meyer Michael , Maia Filipe R.N.C. 
Published: March 2022

AbstractThe idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory1, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes2. This was first demonstrated on biological samples a decade ago on the giant mimivirus3. Since then a large collaboration4has been pushing the limit of the smallest sample that can be imaged5,6. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that ofEscherichia coliGroEL which at 14 nm in diameter7is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.
A Trem2*R47H mouse model without cryptic splicing drives age- and disease-dependent tissue damage and synaptic loss in response to plaques
Authors: Tran Kristine M. , Kawauchi Shimako , Kramár Enikö A. , Rezaie Narges , Liang Heidi Yahan , Arreola Miguel , Da Cunha Celia , Phan Jimmy , Collins Sherilyn , Walker Amber , Neumann Jonathan , Milinkeviciute Giedre , Gomez-Arboledas Angela , Javonillo Dominic I. , Tran Katelynn , Gantuz Magdalena , Forner Stefania , Swarup Vivek , Tenner Andrea J. , LaFerla Frank , Wood Marcelo A. , Mortazavi Ali , MacGregor Grant R. , Green Kim N. 
Published: March 2022

ABSTRACTGenome-Wide Association Studies revealed the TREM2 R47H variant as one of the strongest genetic risk factors for late-onset Alzheimer’s Disease (AD). Unfortunately, many current TREM2*R47H mouse models are associated with cryptic mRNA splicing of the mutant allele that produces a confounding reduction in protein product. We have developed the Trem2R47H NSS (Normal Splice Site) mouse model where the Trem2 allele is expressed at a similar level to the wild-type Trem2 allele, without evidence of cryptic splicing products, and appropriate inflammatory responses to cuprizone challenge. Utilizing the 5xFAD mouse model, we report age- and disease-dependent changes in response to pathology. At an early disease stage (4 mo), homozygous Trem2R47H NSS; hemizygous 5xFAD (Trem2R47H NSS ; 5xFAD) mice have reduced size and number of microglia plus impaired interaction with plaques, that is associated with increased dystrophic neurites and axonal damage detected through plasma neurofilament light chain (NfL) level and suppressed inflammation. However, homozygosity for Trem2R47H NSS suppressed LTP deficits and presynaptic puncta loss caused by the 5xFAD transgene array. At a more advanced disease stage (12 mo,) Trem2R47H NSS ; 5xFAD mice no longer display impaired plaque-microglia interaction or suppressed inflammatory gene expression, although NfL levels remain elevated, and a unique interferon-related gene expression signature is seen. Furthermore, Trem2R47H NSS ; 5xFAD mice also display robust LTP deficits and exacerbated presynaptic loss. Collectively, we provide a Trem2R47H variant mouse without cryptic splicing, and demonstrate it has disease stage dependent effects when combined with a plaque bearing model, with an initial loss of function that ultimately resolves, giving rise to a unique interferon signature and associated tissue damage.
Resolving clonal substructure from single cell genomic data using CopyKit
Authors: Minussi Darlan Conterno , Sei Emi , Wang Junke , Schalck Aislyn , Yan Yun , Davis Alexander , Wu Hua-Jun , Bai Shanshan , Peng Cheng , Hu Min , Casasent Anna , Contreras Alejandro , Chen Hui , Hui David , Damodaran Senthil , Edgerton Mary E , Kopetz Scott , Lim Bora , Navin Nicholas 
Published: March 2022

AbstractHigh-throughput methods for single cell copy number sequencing have enabled the profiling of thousands of cells in parallel, yet there remains a significant bottleneck for data analysis. Here we present CopyKit, a comprehensive set of computational methods for the pre-processing and analysis of single cell copy number data to resolve clonal substructure and reconstruct genetic lineages in tumors. We performed single cell DNA sequencing of 2977 cells from multiple spatial regions in two liver metastasis and 7365 cells from three primary tumors with matched metastatic tissues. In the liver metastases, CopyKit resolved clonal substructure in different spatial regions, which revealed both clonal intermixing and spatial segregation in the tumor mass. In the matched metastatic colorectal and breast cancers, CopyKit resolved metastatic lineages and identified subclones and genomic events that were associated with metastases. These applications show that CopyKit is comprehensive tool for resolving copy number substructure in tumors.
Identification and quantification of α- and β-amanitin in wild mushrooms by HPLC-UV-EC and HPLC-DAD-MS detection
Authors: Barbosa Isabel , Domingues Cátia , Ramos Fernando , Barbosa Rui M. 
Published: March 2022

AbstractAmatoxins are a group of highly toxic peptides, which include α- and β-amanitin, found in several species of mushrooms (e.g.Amanita phalloides). Due to their high hepatotoxicity, they account for most deaths occurring after mushrooms ingestion. The determination of α- and β- amanitin content in wild mushrooms is invaluable for treating cases involving poisoning. In the present study, we have developed and validated an analytical method based on high-performance liquid chromatography, with in-line ultraviolet and electrochemical detection (HPLC-UV-EC), for the rapid quantification of α- and β-amanitin in wild mushroom samples collected from the Inner Center of Portugal. A reproducible and simple solid-phase extraction (SPE) using OASIS®PRIME HLB cartridges was used for sample pre-treatment, followed by chromatographic separation based on the RP-C18 column. The UV and EC chromatograms of α- and β-amanitin were recorded at 305 nm and +0.600 Vvs. Ag/AgCl, respectively. The linear quantification for both amanitins was in the range of 0.5–20.0 μg·mL-1(R2> 0.999). The LOD, calculated based on the calibration curve, was similar for UV and EC detection (0.12-0.33 μg ml.-1). Intra-day and inter-day precision were less than 13%, and the recovery ratios ranged from 89% to 117%. NineAmanita speciesand five edible mushrooms were analysed by HPLC-UV-EC, and HPLC-DAD-MS confirmed the identification of amatoxins. We find high α- and β-amanitin content inA. phalloidesand not in the other species analysed. In sum, the developed and validated method provides a simple and fast analysis of α- and β-amanitins contents in wild mushrooms and is suitable for screening and routine assessment of mushroom intoxication.HighlightsNew validated method using HPLC-UV-EC to determine α- and β-amanitin in wild mushrooms.Reproducible and fast SPE procedure for small samples.Effective sample pre-treatment with the OASIS®PRIME HLB SPE cartridge.Identification and quantification of α- and β-amanitin in wild mushroom samples from Portugal.HPLC-DAD-MS confirmation of amatoxins present in mushroom samples.Graphical abstract
Oxytocin and Emotional Tear in Dogs
Authors: Murata K. , Nagasawa M. , Onaka T. , Kanemaki S. , Nakamura K. , Tsubota K. , Mogi K. , Kikusui T. 
Published: March 2022

AbstractIn humans, tear volume increases in emotional arousal. No studies have investigated the relationship of emotional arousal and tear volume in animals. We measured tear volume in dogs before and after reunion with their owners. Tear volume increased significantly during owner, but not familiar non-owner, reunions but not during reunions with familiar non-owners. When oxytocin instillation was applied to dogs, the tear volume increased, suggesting that oxytocin can mediate the emotion-induced tear secretion in dogs. When the photos of dog’s face in which artificial tear was applied to the dog’s eyes, the positive impression of these photo increased. These suggest that emotional tear can facilitate human-dog emotional connection.
Odors drive feeding through gustatory receptor neurons inDrosophila
Authors: Wei Hong-ping , Lam Thomas Ka Chung , Kazama Hokto 
Published: March 2022

SummaryOdors are intimately tied to the taste system to aid food selection and determine the sensory experience of food. However, how smell and taste are integrated in the nervous system to drive feeding remains elusive. We show inDrosophilathat odors alone activate gustatory receptor neurons (GRNs), trigger proboscis extension reflex (PER), a canonical taste-evoked feeding behavior, and enhance food intake. Odor-evoked PER requires the function of sugar-sensing GRNs but not olfactory organs. Calcium imaging and electrophysiological recording show that GRNs directly respond to odors. Odor-evoked PER is mediated by the Gr5a receptor, and is bidirectionally modulated by olfactory binding proteins. Finally, odors and sucrose co-applied to GRNs synergistically enhance PER and food consumption. These results reveal a cell-intrinsic mechanism for odor-taste multimodal integration that takes place as early as in GRNs, indicating that unified chemosensory experience is a product of layered integration in peripheral neurons and in the brain.