bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vi polysaccharide and conjugated vaccines afford similar early, IgM or IgG-independent control of infection but boosting with conjugated Vi vaccines sustains the efficacy of immune responses
Authors: Jossi Siân E. , Arcuri Melissa , Alshayea Areej , Persaud Ruby R. , Marcial-Juárez Edith , Palmieri Elena , Di Benedetto Roberta , Pérez-Toledo Marisol , Pillaye Jamie , Channell Will M. , Schager Anna E. , Lamerton Rachel E. , Cook Charlotte N. , Goodall Margaret , Haneda Takeshi , Bäumler Andreas J. , Jackson-Jones Lucy H. , Toellner Kai-Michael , MacLennan Calman A. , Henderson Ian R. , Micoli Francesca , Cunningham Adam F. 
Published: January 2023

AbstractVaccination with Vi capsular polysaccharide (Vi-PS) or protein-Vi typhoid conjugate vaccine (TCV) can protect adults againstSalmonellaTyphi infections. TCVs offer better protection than Vi-PS in infants and may offer better protection in adults. Potential reasons for why TCV may be superior in adults are not fully understood. Here, we immunized wild-type (WT) mice and mice deficient in IgG or IgM with Vi-PS or TCVs (Vi conjugated to tetanus toxoid or CRM197) for up to seven months, with and without subsequent challenge with Vi-expressingSalmonellaTyphimurium. Unexpectedly, IgM or IgG alone were similarly able to reduce bacterial burdens in tissues, and this was observed in response to conjugated or unconjugated Vi vaccines and was independent of antibody being of high affinity. Only in the longer-term after immunization (>5 months) were differences observed in tissue bacterial burdens of mice immunized with Vi-PS or TCV. These differences related to the maintenance of antibody responses at higher levels in mice boosted with TCV, with the rate of fall in IgG titres induced to Vi-PS being greater than for TCV. Therefore, Vi-specific IgM or IgG are independently capable of protecting from infection and any superior protection from vaccination with TCV in adults may relate to responses being able to persist better rather than from differences in the antibody isotypes induced. These findings suggest that enhancing our understanding of how responses to vaccines are maintained may inform on how to maximize protection afforded by conjugate vaccines against encapsulated pathogens such asS. Typhi.
Metabolic rewiring of the probiotic bacteriumLacticaseibacillus rhamnosusGG contributes to cell-wall remodeling and antimicrobials production
Authors: Suissa Ronit , Olender Tsviya , Malitsky Sergey , Golani Ofra , Turjeman Sondra , Koren Omry , Meijler Michael M. , Kolodkin-Gal Ilana 
Published: January 2023

AbstractLacticaseibacillus rhamnosus GG(LGG) is a Gram-positive beneficial bacterium that resides in the human intestinal tract and belongs to the family of lactic acid bacteria (LAB). This bacterium is a widely used probiotic and was suggested to provide numerous benefits for human health. However, as in most LAB strains, the molecular mechanisms that mediate the competitiveness of probiotics under different diets remain unknown. Fermentation is a fundamental process in LAB, allowing the oxidation of simple carbohydrates (e.g., glucose, mannose) for energy production under conditions of oxygen limitation, as in the human gut. Our results indicate that fermentation reshapes the metabolome, volatilome, and proteome architecture in LGG. Furthermore, fermentation alters cell envelope remodeling and peptidoglycan biosynthesis, which leads to altered cell wall thickness, aggregation properties, and cell wall composition. In addition, fermentable sugars induced secretion of known and novel metabolites and proteins targeting the enteric pathogensEnterococcus faecalisandSalmonella Enterica serovar Typhimurium. Overall, our results link the common metabolic regulation of cell wall remodeling, aggregation to host tissues, biofilm formation in probiotic strains, and connect the production of antimicrobial effectors with metabolome reprogramming. These findings provide novel insights into the role of nutrition in the establishment of LGG in the gastrointestinal tract.
Foraging guild modulates insectivorous bat responses to habitat loss and insular fragmentation in peninsular Malaysia
Authors: Hazard Quentin C.K. , Froidevaux Jérémy S.P. , Yoh Natalie , Moore Jonathan , Senawi Juliana , Gibson Luke , Palmeirim Ana Filipa 
Published: January 2023

AbstractDespite mounting evidence on the ecological impacts of damming for biodiversity, little is known regarding its consequences in the hyper-diverse Southeast Asian tropical forests. Here we assess the effects of habitat loss and fragmentation on the diversity and activity of insectivorous bats within the hydroelectric Kenyir Lake in peninsular Malaysia. We surveyed bat assemblages on 26 islands and two mainland continuous forest sites using passive acoustic monitoring. Echolocation calls were classified into sonotypes, each corresponding to either one or multiple species, and grouped into foraging guilds. We then examined bat overall assemblage (sonotype richness, activity, and composition), guild- and sonotype-specific activity. From 9360 hours of recordings, we identified 16 bat sonotypes, including 10 forest (2854 bat passes), three edge (13 703) and three open-space foragers (3651). Sonotype richness increased towards denser forest structures (higher Normalized Difference Vegetation Index - NDVI), while species composition varied across the gradient of forest area. Forest foragers were positively affected by NDVI and negatively affected by distance to the closest neighbour, whereas edge foragers’ activity increased in smaller islands. Of the six sonotypes analysed, the activity of one forest sonotype increased with forest area, while that of one edge sonotype decreased. Ensuring habitat quality within insular forest remnants, in addition to their functional connectivity, maximises bat diversity, including the persistence of forest foraging species. Future hydropower development should therefore avoid the creation of a myriad of small, isolated, and habitat-degraded islands further characterised by altered levels of bat diversity and guild-level activity.HighlightsWe assessed the diversity of insectivorous bats in dam-induced islands in MalaysiaSpecies persistence was modulated by island size and habitat qualityForest foragers were negatively affected by island isolation and degradationEdge foragers benefited from fragmentation, increasing in activity on smaller islandsBy creating multiple small, isolated, degraded islands, damming erodes bat diversity
Ancient loss of catalytic selenocysteine spurred convergent adaptation in a mammalian oxidoreductase
Authors: Rees Jasmin , Sarangi Gaurab , Cheng Qing , Floor Martin , Andrés Aida M , Miguel Baldomero Oliva , Villà-Freixa Jordi , Arnér Elias SJ , Castellano Sergi 
Published: January 2023

AbstractSelenocysteine (Sec), the 21stamino acid specified by the genetic code, is a rare selenium-containing residue found in the catalytic site of selenoprotein oxidoreductases. Sec is analogous to the common cysteine (Cys) amino acid but its selenium atom offers physicalchemical properties not provided by the corresponding sulfur atom in Cys. Catalytic sites with Sec in selenoproteins of vertebrates are under strong purifying selection but one enzyme, Glutathione Peroxidase 6 (GPX6), independently exchanged Sec for Cys less than one hundred million years ago in several mammalian lineages. We reconstructed and assayed these ancient enzymes before and after Sec was lost and up to today, and found them to have lost their classic ability to reduce hydroperoxides using glutathione (GSH). This loss of function, however, was accompanied by bursts of amino acid changes in the catalytic domain, with protein sites concertedly changing under positive selection across distant lineages abandoning Sec in GPX6. This demonstrates that when sulfur in Cys impairs catalysis a narrow evolutionary path is followed, with epistasis and pleiotropy leading to convergent evolution and triggering enzymatic properties likely beyond those in classic GPXs. These findings are an unusual example of adaptive convergence towards unexplored oxidoreductase functions during mammalian evolution.
Crosstalk between chromatin and the transcription factor Shavenbaby defines transcriptional output along theDrosophilaintestinal stem cell lineage
Authors: Mancheno-Ferris Alexandra , Immarigeon Clément , Rivero Alexia , Depierre David , Chanard Nicolas , Fosseprez Olivier , Aughey Gabriel , Lhoumaud Priscilla , Anglade Julien , Southall Tony , Plaza Serge , Cuvier Olivier , Payre François , Polesello Cédric 
Published: January 2023

SummaryThe transcription factor Shavenbaby (Svb), the only member of the OvoL family inDrosophila, controls intestinal stem cell differentiation. Post-translational modification of Svb produces two protein isoforms, Svb-ACT and Svb-REP, which promote intestinal stem cell renewal or differentiation, respectively. Using engineered cell lines, we express either isoform to define their mode of action, and develop an unbiased method to identify Svb target genes in intestinal cells. Within a given cell type, Svb-ACT and Svb-REP antagonistically regulate the expression of a set of target genes, binding specific enhancers whose accessibility is constrained by. During intestinal differentiation, the set of target genes progressively changes, together with chromatin accessibility. Moreover, Svb-REP binding stabilizes three-dimensional enhancer-promoter loops, while influencing the local chromatin landscape to repress target genes. We propose that SvbACT-to-REP switch promotes enterocyte differentiation of intestinal stem cells through direct gene regulation and chromatin remodeling.
A defined community of core gut microbiota members promotes cognitive performance in honey bees
Authors: Cabirol Amélie , Schafer Julie , Neuschwander Nicolas , Kesner Lucie , Liberti Joanito , Engel Philipp 
Published: January 2023

AbstractThe composition of the gut microbiota has recently been identified as a cause of cognitive variability in humans and animals. Germ-free individuals and individuals exposed to an antibiotic treatment show severe alteration of their learning and memory performance measured in various cognitive tasks. While different species of bacteria are known to interact in the gut, their cumulative or synergistic effects on cognitive performance remain elusive. Here we established a defined bacterial community - composed of core members of the corbiculate bee microbiota - which enhances honey bees’ cognitive capacities. Honey bees colonized with this reconstituted community discriminated better two odours based on the presence or absence of a sucrose reward compared to germ-free individuals. They also memorized better these odour-food associations in the short-term. These cognitive improvements seem to constitute an emergent property of the community, because they could not be recapitulated by any of the community members when mono-associated in gnotobiotic bees and they were not explained by the total biomass in the gut. The identification of this community and its effect on bees open new avenues of research in neuroscience, microbiology, and ecology. Future research should help understanding how interactions between bacterial species in the community promote the host’s associative learning and memory performance.
Hypersensitivity to distractors in Fragile X syndrome from loss of modulation of cortical VIP interneurons
Authors: Rahmatullah Noorhan , Schmitt Lauren M. , De Stefano Lisa , Post Sam , Robledo Jessica , Chaudhari Gunvant R. , Pedapati Ernest , Erickson Craig A. , Portera-Cailliau Carlos , Goel Anubhuti 
Published: January 2023

SUMMARYAttention deficit is one of the most prominent and disabling symptoms in Fragile X Syndrome (FXS). Hypersensitivity to sensory stimuli contributes to attention difficulties by overwhelming and/or distracting affected individuals, which disrupts activities of daily living at home and learning at school. We find that auditory or visual distractors selectively impair visual discrimination performance in both humans and mice with FXS, but not their typically developing controls. Vasoactive intestinal polypeptide (VIP) neurons were significantly modulated by incorrect responses in the post-stimulus period during early distractor trials in WT mice, consistent with their known role as ‘error’ signals. Strikingly, however, VIP cells fromFmr1-/-mice showed little modulation in error trials, and this correlated with their poor performance on the distractor task. Thus, VIP interneurons and their reduced modulatory influence on pyramidal cells, could be a potential therapeutic target for attentional difficulties in FXS.
Evidence forin vitroextensive proliferation of adult hepatocytes and biliary epithelial cells
Authors: Katsuda Takeshi , Li Jinyang , Merrell Allyson J , Sussman Jonathan , Matsuzaki Juntaro , Ochiya Takahiro , Stanger Ben Z 
Published: January 2023

SUMMARYOver the last several years, a method has emerged which endows adult hepatocytes within vitroproliferative capacity, producing chemically-induced liver progenitors (CLiPs). However, a recent study questioned the origin of these cells, suggesting that resident liver progenitor cells, but not hepatocytes, proliferate. Here, we provide lineage tracing-based evidence that adult hepatocytes acquire proliferative capacityin vitro. Unexpectedly, we also found that the CLiP method allows biliary epithelial cells to acquire extensive proliferative capacity. Interestingly, after long-term culture, hepatocyte-derived cells (hepCLiPs) and biliary-derived cells (bilCLiPs) become similar in their gene expression patterns, and they both exhibit differentiation capacity to form hepatocyte-like cells. Finally, we provide evidence that hepCLiPs can repopulate chronically injured mouse livers, reinforcing our earlier argument that CLiPs can be a cell source for liver regenerative medicine. Moreover, this study offers bilCLiPs as a potential cell source for liver regenerative medicine.
A multiprotein signaling complex sustains AKT and mTOR/S6K activity necessary for the survival of cancer cells undergoing stress
Authors: Teran Pumar Oriana Y. , Zanotelli Matthew R. , Lin Miao-chong Joy , Schmitt Rebecca R. , Green Kai Su , Rojas Katherine S. , Hwang Irene Y. , Cerione Richard A. , Wilson Kristin F. 
Published: January 2023

SummaryThe ability of cancer cells to survive microenvironmental stresses is critical for tumor progression and metastasis; however, how they survive these challenges is not fully understood. Here, we describe a novel multiprotein complex (DockTOR) essential for the survival of cancer cells under stress, triggered by the GTPase Cdc42 and a signaling partner Dock7, which includes AKT, mTOR, and the mTOR regulators TSC1, TSC2, and Rheb. DockTOR enables cancer cells to maintain a low but critical mTORC2-dependent phosphorylation of AKT during serum deprivation by preventing AKT dephosphorylation through an interaction between phospho-AKT and the Dock7 DHR1 domain. This activity stimulates a Raptor-independent but Rapamycin-sensitive mTOR/S6K activity necessary for survival. These findings address long-standing questions of how Cdc42 signals result in mTOR activation and demonstrate how cancer cells survive conditions when growth factor-dependent activation of mTORC1 is off. Determining how cancer cells survive stress conditions could identify vulnerabilities that lead to new therapeutic strategies.
Representational geometry explains puzzling error distributions in behavioral tasks
Authors: Wei Xue-Xin , Woodford Michael 
Published: January 2023

AbstractMeasuring and interpreting errors in behavioral tasks is critical for understanding cognition. Conventional wisdom assumes that encoding/decoding errors for continuous variables in behavioral tasks should naturally have Gaussian distributions, so that deviations from normality in the empirical data indicate the presence of more complex sources of noise. This line of reasoning has been central for prior research on working memory. Here we re-assess this assumption, and find that even in ideal observer models with Gaussian encoding noise, the error distribution is generally non-Gaussian, contrary to the commonly held belief. Critically, we find that the shape of the error distribution is determined by the geometrical structure of the encoding manifold via a simple rule. In the case of a high-dimensional geometry, the error distributions naturally exhibit flat tails. Using this novel insight, we apply our theory to visual short-term memory tasks, and find that it can account for a large array of experimental data with only two free parameters. Our results call attention to the geometry of the representation as a critically important, yet underappreciated factor in determining the character of errors in human behavior.
Tool-sensed object information effectively supports vision for multisensory grasping
Authors: Camponogara Ivan , Farnè Alessandro , Volcic Robert 
Published: January 2023

AbstractTools enable humans to extend their sensing abilities beyond the natural limits of their hands, allowing them to sense objects as if they were using their hands directly. The similarities between tool-mediated and hand-based sensing entail the existence of comparable processes for integrating tool- and hand-sensed information with vision, raising the intriguing question of whether tools can support vision in bimanual object manipulations. Here we investigated this question by measuring participants’ performance while reaching for and grasping objects either held with a tool or with their hand. We found that tool-mediated sensing effectively supports vision in multisensory grasping. Even more intriguingly, tool-mediated sensing resembled hand-based sensing. In addition, by manipulating the object features (availability of position and size versus position only), we found that both tool- and hand-mediated action performance was not hindered by the absence of size information. Thus, integrating the tool-sensed position of the object with its vision is sufficient to promote a multisensory advantage in grasping. In sum, our findings indicate that multisensory integration mechanisms significantly improve grasping actions, fine-tuning contralateral hand movements even when object information is only indirectly sensed through the hand operating a tool.Significance statementTools allow extending the hands sensing capabilities beyond their anatomical limits. Here we show that object information sensed through a tool can guide bimanual object manipulations as effectively as when directly sensed by the hand. Both tool and hand sensing provide relevant object positional information that are merged with vision to improve action performance. Our findings provide evidence about the interchangeable use of tools and hands for skilled actions and open new perspectives for prosthetic applications and rehabilitative plans.
An effective sanitizer for fresh produce production:In situplasma activated water treatment inactivates pathogenic bacteria and maintains the quality of cucurbit fruit
Authors: Rothwell Joanna G. , Hong Jungmi , Morrison Stuart J. , Vyas Heema Kumari Nilesh , Xia Binbin , Mai-Prochnow Anne , McConchie Robyn , Phan-Thien Kim-Yen , Cullen Patrick J. , Carter Dee A. 
Published: January 2023

AbstractThe effect of plasma activated water (PAW) generated with a dielectric barrier discharge diffusor (DBDD) system on microbial load and organoleptic quality of cucamelons was investigated and compared to the established sanitizer, sodium hypochlorite (NaOCl). Pathogenic serotypes ofEscherichia coli,Salmonella enterica, andListeria monocytogeneswere inoculated onto the surface of cucamelons (6.5 log CFU g−1) and into the wash water (6 log CFU mL−1). PAW treatment involved 2 minutesin situwith water activated at 1500 Hz and 120 V, and air as the feed gas; NaOCl treatment was a wash with 100 ppm total chlorine; and the control treatment was a wash with tap water. PAW treatment produced a 3 log CFU g−1reduction of pathogens on the cucamelon surface without negatively impacting quality or shelf life. NaOCl treatment reduced the pathogenic bacteria on the cucamelon surface by 3-4 log CFU g−1, however, this treatment also reduced fruit shelf life and quality. Both systems reduced 6 log CFU ml−1pathogens in the wash water to below detectable limits. The critical role of superoxide anion radical (·O2−) in the antimicrobial power of DBDD-PAW was demonstrated through a scavenger assay, and chemistry modelling confirmed that ·O2−generation readily occurs in DBDD-PAW generated with the employed settings. Modelling of the physical forces produced during plasma treatment showed that bacteria likely experience strong local electric fields and polarization. We hypothesize that these physical effects synergise with reactive chemical species to produce the acute antimicrobial activity seen with thein situPAW system.ImportancePlasma activated water (PAW) is an emerging sanitizer in the fresh food industry, where food safety must be achieved without a thermal kill step. Here we demonstrate PAW generatedin situto be a competitive sanitizer technology, providing a significant reduction of pathogenic and spoilage micro-organisms while maintaining the quality and shelf life of the produce item. Our experimental results are supported by modelling of the plasma chemistry and applied physical forces, which show that the system can generate highly reactive superoxide radicals and strong electric fields that combine to produce potent antimicrobial power.In situPAW has promise in industrial applications as it only requires low power (12 W), tap water and air. Moreover, it does not produce toxic by-products or hazardous effluent waste, making it a sustainable solution for fresh food safety.