bluuebunny/crossref_metadata_2025_split huggingface dataset:
A semi-automated cell tracking protocol for quantitative analyses of neutrophil swarming to sterile andS. aureuscontaminated bone implants in a mouse femur model
Authors: Lekkala Sashank , Ren Youliang , Weeks Jason , Lee Kevin , Tay Allie Jia Hui , Liu Bei , Xue Thomas , Rainbolt Joshua , Xie Chao , Schwarz Edward M. , Yeh Shu-Chi A. 
Published: December 2023

AbstractImplant-associated osteomyelitis remains a major orthopaedic problem. As neutrophil swarming to the surgical site is a critical host response to prevent infection, visualization and quantification of this dynamic behavior at the native microenvironment of infection will elucidate previously unrecognized mechanisms central to understanding the host response. We recently developed longitudinal intravital imaging of the bone marrow (LIMB) to visualize fluorescentS. aureuson a contaminated transfemoral implant and host cells in live mice, which allows for direct visualization of bacteria colonization of the implant and host cellular responses using two-photon laser scanning microscopy. To the end of rigorous and reproducible quantitative outcomes of neutrophil swarming kinetics in this model, we developed a protocol for robust segmentation, tracking, and quantifications of neutrophil dynamics adapted from Trainable Weka Segmentation and TrackMate, two readily available Fiji/ImageJ plugins. In this work,Catchupmice with tdTomato expressing neutrophils received a transfemoral pin with or without ECFP-expressing USA300 methicillin-resistantStaphylococcus aureus(MRSA) to obtain 30-minute LIMB videos at 2-, 4-, and 6-hours post-implantation. The developed semi-automated neutrophil tracking protocol was executed independently by two users to quantify the distance, displacement, speed, velocity, and directionality of the target cells. The results revealed high inter-reader reliability for all outcomes (ICC > 0.98; p > 0.05). Consistent with the established paradigm on increased neutrophil swarming during active infection, the results also demonstrated increased neutrophil speed and velocity at all measured time points, and increased displacement at later time points (6 hours) in infected versus uninfected mice (p < 0.05). Neutrophils and bacteria also exhibit directionality during migration in the infected mice. The semi-automated cell tracking protocol provides a streamlined approach to robustly identify and track individual cells across diverse experimental settings and eliminates inter-observer variability.
Spermidine suppresses DC activation via eIF5A hypusination and metabolic adaptation
Authors: Meehan Gavin R , Gunes Utku , Scales Hannah E , Finney George , Deehan Ross , Sintoris Sofia , Athanasiadou Aegli , Brewer James M 
Published: December 2023

AbstractCell metabolism plays an important role in immune effector responses and through responding to metabolic signals, immune cells can adapt and regulate their function. Arginine metabolism in Dendritic cells (DC) has been shown to reduce T cell activation; however, it is unclear how this immunosuppressive state is induced. To address this issue, we examined the immunomodulatory capacity of various metabolites from arginine metabolism. Through the use of a recently described DC:T cell interaction assay and flow cytometry we demonstrated that spermidine most significantly inhibited DC activation, preventing subsequent interactions with CD4 T cells. DC function could be restored by addition of inhibitors of spermidine metabolism via the eIF5A-hypusine axis, required for expression of some mitochondrial enzymes. We also demonstrated that the spermidine induced-immunosuppressive state protected DC against activation induced loss of mitochondrial capacity for energy generation, which was also hypusination dependent. Taken together this data demonstrates that spermidine is the key immunomodulatory component downstream of arginine metabolism and that it mediates this effect by stimulating hypusination-dependent protection of OXPHOS in DC, which in turn results in a reduced ability of DC to activate and interact with T cells. This pathway may be utilised by the immune system to regulate excessive immune responses but could also be exploited by pathogens as a method of immune evasion.
Exploring the preservation of a parasitic trace in decapod crustaceans using finite elements analysis
Authors: Wright Nathan , Klompmaker Adiël A. , Petsios Elizabeth 
Published: December 2023

AbstractThe fossil record of parasitism is poorly understood, due largely to the scarcity of strong fossil evidence of parasites. Understanding the preservation potential for fossil parasitic evidence is critical to contextualizing the fossil record of parasitism. Here, we present the first use of X-ray computed tomography (CT) scanning and finite elements analysis (FEA) to analyze the impact of a parasite-induced fossil trace on host preservation. Four fossil and three modern decapod crustacean specimens with branchial swellings attributed to an epicaridean isopod parasite were CT scanned and examined with FEA to assess differences in the magnitude and distribution of stress between normal and swollen branchial chambers. The results of the FEA show highly localized stress peaks in reaction to point forces, with higher peak stress on the swollen branchial chamber for nearly all specimens and different forces applied, suggesting a possible shape-related decrease in the preservation potential of these parasitic swellings. Broader application of these methods as well as advances in the application of 3D data analysis in paleontology are critical to understanding the fossil record of parasitism and other poorly represented fossil groups.
Tic-related behaviors inCelsr3mutant mice are contributed by alterations of striatal D3dopamine receptors
Authors: Cadeddu Roberto , Branca Caterina , Braccagni Giulia , Musci Teresa , Piras Ignazio S , Anderson Collin J , Capecchi Mario R , Huentelman Matthew J , Moos Philip J , Bortolato Marco 
Published: December 2023

AbstractThe geneCELSR3(Cadherin EGF LAG Seven-pass-G-type Receptor 3) has been recently recognized as a high-confidence risk factor for Tourette syndrome (TS). Additionally,Celsr3mutant mice have been reported to exhibit TS-related behaviors and increased dopamine release in the striatum. Building on these findings, we further characterized the neurobehavioral and molecular profile ofCelsr3mutant mice to understand better the biological mechanisms connecting the deficiency of this gene and TS-related phenotypes. Our analyses confirmed thatCelsr3mutant mice displayed grooming stereotypies and tic-like jerks, as well as sensorimotor gating deficits, which were opposed by TS therapies. Spatial transcriptomic analyses revealed widespread extracellular matrix abnormalities in the striatum ofCelsr3mutants. Single-nucleus transcriptomics also showed significant upregulation of theDrd3gene, encoding the dopamine D3receptor, in striosomal D1-positive neurons.In situhybridization and immunofluorescence confirmed dysregulated D3receptor expression, with lower levels in presynaptic striatal fibers and higher levels in striatal D1-positive neurons. Activating and blocking D3receptors amplified or decreased tic-like jerks and stereotypiesin Celsr3-deficient mice, respectively. These findings suggest that modifications of D3receptor distribution contribute to the tic-like responses associated withCelsr3deficiency.
Functional annotation hypothetical proteins: a world to be explored in drug development in Trypanosomatids
Authors: de Lima Raissa Santos , Bulla Ana Carolina Silva , da Silva Manuela Leal 
Published: December 2023

AbstractHypothetical proteins can provide an alternative pathway for finding potential targets in the development of new drugs due to the fact that many Neglected tropical diseases are caused by Trypanosomatids (Chagas Disease, Leishmaniasis, and Human African Trypanosomiasis). In this work, we focus on applying functional prediction methods based on both sequence and structure to analyze the hypothetical proteins of the pathogenic agents that cause these diseases:T. cruzi(Tcr),T. brucei brucei(Tbr),T. brucei gambiense(Tbg),L. infantum(Lif),L. donovani(Ldo), andL. braziliensis(Lbz). By consulting databases and servers, we have predicted functional domains for twenty-six proteins in Tcr, thirteen in Tbr, fifteen in Tbg, ten in Lif, and one in both Ldo and Lbz. With the goal of developing multi-target therapies, we grouped the domains according to how they are shared among the organisms and investigated those that are shared among more species. By examining the existing literature using specific search strategies, we described what has already been reported for these domains and also analyzed protein structures and sequences, describing mutations among the species and potential drug sites. The published works have unveiled that some of these domains are non-essential for trypanosomatids, like the TRX domain, while others demand further investigation due to a lack of information about metabolic processes (UFC1, Ufm1, ACBP, AAA 18, and Fe-S). Although, we have identified three noteworthy domains that hold promise as targets: TPR, which plays a crucial role in the ciliogenesis process; Nuc deoxyrib tr, essential in purine recycling and recovery mechanisms; and MIX, important for protein targeting and the assembly of complexes such as COX. These three domains are promising targets for drug development due to their conservation, their potential to affect multiple species and their exclusivity.
The Arabidopsis PPR protein EMB1006 interacts with both EMB1270 and CFM2 to facilitate plastidclpP1intron2 splicing
Authors: Zhang Liqun , Zhu Yawen , Yang Keyi , Liao Fangsheng , Wang Jiaqi , Zhou Shuya , Huang Jirong , Cui Yong-Lan , Huang Weihua 
Published: December 2023

AbstractPlastid intron splicing is an essential step for gene expression. Although many nucleus-encoded splicing factors have been identified for plastid intron splicing, how these proteins coordinately regulate intron splicing is unclear. Here we found that EMB1006, an Arabidopsis P-type PPR protein, is required for splicing several plastid introns includingclpP1intron 2 by analyzing the level of intron retention in its knockdown lines and RIP-qPCR (RNA immunoprecipitation and quantitative PCR) assay. In addition, RNA electrophoretic mobility shift assay (REMSA) showed that EMB1006 specifically binds to the sequence UUACCAAACGU close to the 3’ end ofclpP1exon 2in vitro. Furthermore, yeast two hybrid (Y2H), split luciferase complementation (Split-LUC) and semi-in vivopull-down assays showed that EMB1006 interacts with both EMB1270 and CFM2, which also interact each other. Taken together, our data indicate that EMB1006 forms a complex with EMB1270 and CFM2 to facilitateclpP1intron 2 splicing in chloroplasts.
Trying harder: how cognitive effort sculpts neural representations during working memory
Authors: Master Sarah L. , Li Shanshan , Curtis Clayton E. 
Published: December 2023

AbstractThe neural mechanisms by which motivational factors influence cognition remain unknown. Using fMRI, we tested how cognitive effort impacts working memory (WM). Participants were precued whether WM difficulty would be hard or easy. Hard trials demanded more effort as a later decision required finer mnemonic precision. Behaviorally, pupil size was larger and response times were slower on hard trials suggesting our manipulation of effort succeeded. Neurally, we observed robust persistent activity in prefrontal cortex, especially during hard trials. We found strong decoding of location in visual cortex, where accuracy was higher on hard trials. Connecting these across-region effects, we found that the amplitude of delay period activity in frontal cortex predicted decoded accuracy in visual cortex on a trial-wise basis. We conclude that the gain of persistent activity in frontal cortex may be the source of effort-related feedback signals that improve the quality of WM representations stored in visual cortex.
snPATHO-seq: unlocking the pathology archives
Authors: Wang Taopeng , Harvey Kate , Morlanes Javier Escudero , Kiedik Beata , Al-Eryani Ghamdan , Greenwald Alissa , Kalavros Nikolaos , Dezem Felipe Segato , Ma Yuling , Pita-Juarez Yered H. , Wise Kellie , Degletagne Cyril , Elz Anna , Hadadianpour Azi , Johanneson Jack , Pakiam Fiona , Ryu Heeju , Newell Evan W. , Tonon Laurie , Kohlway Andrew , Drennon Tingsheng , Abousoud Jawad , Stott Ryan , Lund Paul , Durruthy Jens , Vallejo Andres F , Kaczorowski Dominik , Warren Joanna , Butler Lisa M. , O’Toole Sandra , Plummer Jasmine , Vlachos Ioannis S , Lundeberg Joakim , Swarbrick Alexander , Martelotto Luciano 
Published: December 2023

AbstractFormalin-fixed paraffin-embedded (FFPE) samples are valuable but underutilized in single-cell omics research due to their low DNA and RNA quality. In this study, leveraging recent single-cell genomic technology advances, we introduce a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples.
KatG inactivation generates vulnerabilities in isoniazid resistant strains ofMycobacterium tuberculosis
Authors: Wang XinYue , Jowsey William J , Cheung Chen-Yi , Seeto Noon E , Waller Natalie JE , Chrisp Michael T , Peterson Amanda L , Nijagal Brunda , Fineran Peter C , Cook Gregory M , Jackson Simon A , McNeil Matthew B 
Published: December 2023

AbstractDrug-resistant strains ofMycobacterium tuberculosisare a major global health problem. Resistance to the front-line antibiotic isoniazid is often associated with mutations in thekatGencoded bifunctional catalase-peroxidase. We hypothesised that perturbed KatG activity would generate collateral vulnerabilities in INH-resistantkatGmutants, providing new pathways to combat isoniazid resistance. Here, we used whole genome CRISPRi screens, transcriptomics, and metabolomics to generate a genome-wide map of cellular vulnerabilities in aM. tuberculosis katGmutant. We discovered that metabolic and transcriptional remodelling compensates for the loss of KatG but in doing so generates vulnerabilities in ribosome biogenesis, and nucleotide and amino acid metabolism. These vulnerabilities were more sensitive to inhibition in an isoniazid-resistantkatGmutant underin vitroand host-relevant conditions and translated to clinical populations. These findings provide an experimental framework for developing novel strategies to combat antimicrobial resistance inM. tuberculosisand other bacterial pathogens.
High sugar diets can increase susceptibility to bacterial infection inDrosophila melanogaster
Authors: Darby Andrea M. , Okoro Destiny O. , Aredas Sophia , Frank Ashley M. , Pearson William H. , Dionne Marc S. , Lazzaro Brian P. 
Published: December 2023

AbstractOvernutrition with dietary sugar can worsen infection outcomes in diverse organisms including insects and humans, generally through unknown mechanisms. In the present study, we show that adultDrosophila melanogasterfed high-sugar diets became more susceptible to infection by the Gram-negative bacteriaProvidencia rettgeriandSerratia marcescens,although diet had no significant effect on infection by Gram-positive bacteriaEnterococcus faecalisorLactococcus lactis.We found thatP. rettgeriandS. marcescensproliferate more rapidly inD. melanogasterfed a high-sugar diet, resulting in increased probability of host death.D. melanogasterbecome hyperglycemic on the high-sugar diet, and we find evidence that the extra carbon availability may promoteS. marcescensgrowth within the host. However, we found no evidence that increased carbon availability directly supports greaterP. rettgerigrowth.D. melanogasteron both diets fully induce transcription of antimicrobial peptide (AMP) genes in response to infection, butD. melanogasterprovided with high-sugar diets show reduced production of AMP protein. Thus, overnutrition with dietary sugar may impair host immunity at the level of AMP translation. Our results demonstrate that dietary sugar can shape infection dynamics by impacting both host and pathogen, depending on the nutritional requirements of the pathogen and by altering the physiological capacity of the host to sustain an immune response.Author SummaryDiet has critical impact on the quality of immune defense, and high-sugar diets increase susceptibility to bacterial infection in many animals. Yet it is unknown which aspects of host and pathogen physiology are impacted by diet to influence infection dynamics. Here we show that high-sugar diets increase susceptibility to some, but not all, bacterial infections inDrosophila. We find that feeding on high sugar diet impairs the host immune response by reducing the level of antimicrobial peptides produced. The expression of genes encoding these peptides is not affected, so we infer that protein translation is impaired. We further show that flies on high-sugar diets are hyperglycemic, and that some pathogens may use the excess sugar in the host to promote growth during the infection. Thus, our study demonstrates that dietary impacts on infection outcome arise through physiological effects on both the host and pathogen.
Tracking transcription-translation coupling in real-time
Authors: Qureshi Nusrat Shahin , Duss Olivier 
Published: December 2023

AbstractA central question in biology is how macromolecular machines function cooperatively. In bacteria, transcription and translation occur in the same cellular compartment and can be physically and functionally coupled. While several recently published high-resolution structures of the ribosome-RNA polymerase (RNAP) complex provided first mechanistic insight into the coupling process, we do not know how these structural snapshots are placed along a dynamic reaction trajectory. Here, we reconstitute a complete active transcription-translation system and develop multi-color single-molecule fluorescence microscopy experiments to directly and simultaneously track transcription elongation, translation elongation and the physical and functional coupling between the ribosome and the RNAP in real-time. Our data show that the ribosome slows down while colliding with the RNAP and that coupling following a collision becomes less efficient. Unexpectedly, physical coupling can occur with hundreds of nucleotides of intervening mRNA between both machineries by mRNA looping, and increases in efficiency in presence of NusG. We detect active transcription elongation during mRNA looping and show that NusA-paused RNAPs can be activated by the ribosome by long-range physical coupling. We provide an alternative explanation on how the ribosome can rescue RNAP from frequent pausing without requiring collisions by a closely trailing ribosome. Our data mechanistically highlight an example of how macromolecular machines central to gene expression physically and functionally cooperate.
Heterogeneous collateral effects in daptomycin-resistantE. faecalis
Authors: Huynh Anh , Maltas Jeff , Wood Kevin B. 
Published: December 2023

AbstractDaptomycin, a cyclic lipopeptide antibiotic that targets the cell membrane, is an important therapeutic option for treating multi-drug-resistant infections, including vancomycin-resistant enterococci (VRE). Recent work has uncovered an array of daptomycin resistance mechanisms in enterococci, but relatively little is known about how these molecular defenses contribute to collateral effects–that is, to increased resistance or sensitivity to other drugs. In this work, we investigate collateral effects that arise during daptomycin adaptation ofE. faecalisin four independent laboratory-evolved populations. Using a combination of growth assays and both single isolate and population sequencing, we identified DAP-resistant lineages with mutations in one or more genes previously associated with DAP resistance, and these isolates are characterized by divergent phenotypic properties–including different levels of DAP resistance and different growth rates (i.e. fitness costs) in drug-free media. Interestingly, we also observed strongly divergent collateral responses to different antibiotics, particularly CRO, with collateral resistance arising in mutants harboring DAP-resistance mutations in cardiolipin synthetase (cls) or in genes linked to the two-component signaling system YxdJK (bceRor a regulated transporterycvR). By contrast, mutations inliaX, a component of a LiaFSR two-component signaling system, arose in two of the four populations, with point mutations associated with CRO-sensitivity and a large structural integration of plasmid pTEF3 associated with extreme CRO-sensitivity and a dramatically reduced growth rate. Our results reveal considerable phenotypic differences in mutations targeting the LiaSFR system and highlight trade-offs between resistance to daptomycin, collateral profiles (most notably to CRO), and drug-free growth rates in evolving lineages. As a whole, these results underscore how rich–and remarkably diverse–evolutionary dynamics can emerge even in parallel populations adapting to simple daptomycin escalation protocols.
Reconstructing Spatial Transcriptomics at the Single-cell Resolution with BayesDeep
Authors: Jiang Xi , Dong Lei , Wang Shidan , Wen Zhuoyu , Chen Mingyi , Xu Lin , Xiao Guanghua , Li Qiwei 
Published: December 2023

AbstractSpatially resolved transcriptomics (SRT) techniques have revolutionized the characterization of molecular profiles while preserving spatial and morphological context. However, most next-generation sequencing-based SRT techniques are limited to measuring gene expression in a confined array of spots, capturing only a fraction of the spatial domain. Typically, these spots encompass gene expression from a few to hundreds of cells, underscoring a critical need for more detailed, single-cell resolution SRT data to enhance our understanding of biological functions within the tissue context. Addressing this challenge, we introduce BayesDeep, a novel Bayesian hierarchical model that leverages cellular morphological data from histology images, commonly paired with SRT data, to reconstruct SRT data at the single-cell resolution. BayesDeep effectively model count data from SRT studiesviaa negative binomial regression model. This model incorporates explanatory variables such as cell types and nuclei-shape information for each cell extracted from the paired histology image. A feature selection scheme is integrated to examine the association between the morphological and molecular profiles, thereby improving the model robustness. We applied BayesDeep to two real SRT datasets, successfully demonstrating its capability to reconstruct SRT data at the single-cell resolution. This advancement not only yields new biological insights but also significantly enhances various downstream analyses, such as pseudotime and cell-cell communication.