bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stable isotopes disentangle niche partitioning and species co-occurrence in a multi-level marine mutualism
Authors: Titus Benjamin M. , Froehlich Catheline Y. M. , Vondriska Clayton , Baker Ronald , Caves Eleanor M. 
Published: November 2023

AbstractEcologists have long sought general explanations for the co-occurrence of ecologically similar taxa. Niche theory explains co-occurrence via functional differences among taxa that reduce competition and promote resource partitioning. Alternatively, the unified neutral theory of biodiversity and biogeography suggests that co-occurrence can be attributed to stochastic processes, and thus, presupposes that ecologically similar species that occur in sympatry are functionally analogous. We test these alternative hypotheses in multiple dimensions using the most diverse crustacean-sea anemone symbiosis from coral reefs in the Tropical Western Atlantic. δ13C and δ15N stable isotope analyses of six crustacean symbionts that co-occur around the host anemoneBartholomea annulataexhibit highly differentiated isotopic niche space spanning three trophic levels. As multiple crustacean species within the symbiosis have been documented as cleaners that remove parasites from reef fishes, we extended our investigation into the broader cleaner community. Our stable isotope analyses of cleaners shows that only Pederson’s cleaner shrimpAncylomenes pedersoniexhibits δ15N isotopic signatures that are consistent with a dedicated cleaning lifestyle. Co-occurring species that have been previously described to clean reef fishes such asPericlimenes yucatanicus, Stenopus hispidus,andStenorhynchus seticornisall occupy trophic levels well belowAn. pedersoni. Taken together, our data are consistent with the expectations of niche theory: co-occurring symbiotic crustaceans have highly partitioned niche space with low levels of functional redundancy. Finally, our findings reinforce and extend the ecological importance ofAn. pedersonias likely the only dedicated cleaner shrimp on coral reefs in the Tropical Western Atlantic.
Unraveling cryptic diversity: Genomic approaches to study the taxonomy and evolution of Woolly-necked storks using museum specimens
Authors: Ghimire Prashant , Palacios Catalina , Tremble Jeremiah , Lamichhaney Sangeet 
Published: November 2023

AbstractThe availability of large-scale genomics data for current research in evolutionary biology has enabled a comprehensive examination of the intricate interplay between diverse evolutionary processes associated with speciation. Despite these advancements, the genomic basis of taxonomic classification remains challenging in many species, one such example being the Woolly-necked storks(Ciconia sps.). The Woolly-necked storks are distributed in Asia and Africa with a taxonomic classification(C. episcopus and C. microcelis)that has been a matter of contention and ambiguity. Asian and African Woollynecks were just recently recognized as different species based on their morphological differences, however genetic/genomic studies on Woolly-necked storks are lacking. In this study, we have used ∼70-year-old museum samples to explore the taxonomy and evolution of the Woolly-necked storks. We used a whole-genome sequencing strategy and generated 13.5 million single nucleotide polymorphisms (SNPs) that were polymorphic among populations of Asian and African Woollynecks. Our study has revealed that Asian and African Woollyneck are genetically distinct, consistent with the current taxonomic classification based on morphological features. However, we also found a high genetic divergence between the Asian subspeciesC. e. neglectaandC. e. episcopussuggesting this classification harbors cryptic diversity that requires a detailed examination to explore processes of ongoing speciation. Because taxonomic classification directly impacts conservation efforts, and there is evidence of declining populations of Asian Woollynecks in Southeast Asia, our results suggest populations-scale studies are urgent to determine the genetic, ecological, and phylogenetic diversity of these birds. Moreover, our study also provides historical genomic resources to examine genomic signatures of local adaptation associated with the distribution, ecology, and evolution of African and Asian Woollynecks.
Co-exposure to Polyethylene Fiber andSalmonella entericaTyphimurium Alters Microbiome and Metabolome ofin vitroChicken Cecal Mesocosms
Authors: Chatman Chamia C. , Olson Elena G. , Freedman Allison J. , Dittoe Dana K. , Ricke Steven C. , Majumder Erica L-W. 
Published: November 2023

ABSTRACTHumans and animals encounter a summation of exposures during their lifetime (the exposome). In recent years, the scope of the exposome has begun to include microplastics. Microplastics (MPs) have increasingly been found in locations where there could be an interaction withSalmonella entericaTyphimurium, one of the commonly isolated serovars from processed chicken. In this study, the microbiota response to a 24-hour co-exposure toSalmonella entericaTyphimurium and/or low-density polyethylene (PE) microplastics in anin vitrobroiler cecal model was determined using 16S rRNA amplicon sequencing (Illumina) and untargeted metabolomics. Community sequencing results indicated that PE fiber with and withoutS.Typhimurium yielded a lowerFirmicutes/Bacteroidesratio compared to other treatment groups, which is associated with poor gut health, and overall had greater changes to the cecal microbial community composition. However, changes in the total metabolome were primarily driven by the presence ofS.Typhimurium. Additionally, the co-exposure to PE Fiber andS. Typhimurium caused greater cecal microbial community and metabolome changes than either exposure alone. Our results indicate that polymer shape is an important factor in effects resulting from exposure. It also demonstrates that microplastic-pathogen interactions cause metabolic alterations to the chicken cecal microbiome in anin vitrochicken cecal model.IMPORTANCEResearching the exposome, a summation of exposure of one’s lifespan, will aid in determining the environmental factors that contribute to disease states. There is an emerging concern that microplastic-pathogen interactions in the gastrointestinal tract of broiler chickens may lead to an increase inSalmonellainfection across flocks and eventually increased incidence of human salmonellosis cases. In this research article, we elucidated the effects of co-exposure to polyethylene microplastics andSalmonella entericaserovar Typhimurium on the ceca microbial community.Salmonellapresence caused strong shifts in the cecal metabolome but not the microbiome. The inverse was true for polyethylene fiber. Polyethylene powder had almost no effect. The co-exposure had worse effects than either alone. This demonstrates that exposure effects to the gut microbial community are contaminant specific. When combined, the interactions between exposures exacerbate changes to the gut environment. The results herein support currentSalmonellamitigation efforts and understanding microplastics-pathogen interactions.
Spatial and temporal profiling of the complement system uncovered novel functions of the alternative complement pathway in brain development
Authors: Zhang Yingying , Watson Brianna , Rattan Ajitanuj , Lee Tyrone , Chawla Smriti , Geistlinger Ludwig , Guan Yilin , Ma Minghe , Caldarone Barbara J. , Song Wenchao , Moffitt Jeffrey R. , Carroll Michael C. 
Published: November 2023

SummaryMounting evidence implicated the classical complement pathway (CP) in normal brain development, and the pathogenesis of neuropsychiatric and neurodegenerative diseases. However the source and regulation of complement in the brain remain unclear. Using MERFISH, a spatial transcriptomic method with single-cell resolution, we established a developmental brain atlas of the complement system. We showed that the brain synthesizes essential building blocks of the complement system locally with remarkable cellular and spatial heterogeneity. We provided transcriptional evidence supporting the presence of the alternative pathway (AP), but lack of lectin pathway (LP) activity in postnatal brain development. Cell type, temporal and spatial expression patterns of genes involved indicate non-redundant functions of the CP and AP. In addition, deficiency in Masp3-driven AP resulted in developmental and cognitive defects, indicating essential functions of the AP, an observation that highlights the necessity to disentangle differential involvement of the three complement activation pathways in development and diseases.
Preventing evolutionary rescue in cancer
Authors: Patil Srishti , Ahmed Armaan , Viossat Yannick , Noble Robert 
Published: November 2023

AbstractFirst-line cancer treatment frequently fails due to initially rare therapeutic resistance. An important clinical question is then how to schedule subsequent treatments to maximize the probability of tumour eradication. Here, we provide a theoretical solution to this problem by using mathematical analysis and extensive stochastic simulations within the framework of evolutionary rescue theory to determine how best to exploit the vulnerability of small tumours to stochastic extinction. Whereas standard clinical practice is to wait for evidence of relapse, we confirm a recent hypothesis that the optimal time to switch to a second treatment is when the tumour is close to its minimum size before relapse, when it is likely undetectable. This optimum can lie slightly before or slightly after the nadir, depending on tumour parameters. Given that this exact time point may be difficult to determine in practice, we study windows of high extinction probability that lie around the optimal switching point, showing that switching after the relapse has begun is typically better than switching too early. We further reveal how treatment dose and tumour demographic and evolutionary parameters influence the predicted clinical outcome, and we determine how best to schedule drugs of unequal efficacy. Our work establishes a foundation for further experimental and clinical investigation of this evolutionarily-informed “extinction therapy” strategy.
The uniqueLegionella longbeachaecapsule favors intracellular replication and immune evasion
Authors: Schmidt Silke , Mondino Sonia , Gomez-Valero Laura , Escoll Pedro , Mascarenhas Danielle P. A. , Gonçalves Augusto , Rusniok Christophe , Sachse Martin , Nilges Maryse Moya- , Fontaine Thierry , Zamboni Dario S. , Buchrieser Carmen 
Published: November 2023

AbstractLegionella longbeachaeandLegionella pneumophilacause Legionnaires’ disease despite species-specific differences in environmental niches, disease epidemiology, and genomic content. Here, we characterized a newL. longbeachaevirulence factor, a capsule that is expressed in post-exponential growth phase as shown by electron microscopy. Analysis of the capsule compositionviaHLPC revealed the presence of a highly anionic polysaccharide absent in a capsule mutant. The capsule is crucial for replication and virulencein vivoin a mouse model of infection and in the natural hostAcanthamoeba castellanii. It has anti-phagocytic function when encountering innate immune cells, it is involved in a low cytokine responses in mice and in human monocyte derived macrophages and helps to dampen the innate immune response. TheL. longbeachaecapsule is a novel virulence factor, unique among knownLegionellaspecies, that aidsL. longbeachaeto survive in specific niches and partly confersL. longbeachaeits unique infection characteristics.
Phylogenetic analysis reveals unexplored fungal diversity on skin
Authors: Brito Pedro Nicolas , Paulino Luciana Campos 
Published: November 2023

AbstractDespite recent advances, to date there is not full knowledge of microbial diversity inhabiting various organs of human body. Skin harbors a complex microbiome that might affect our health positively and negatively. Fungal communities from skin are dominated byMalasseziayeasts. Traditionally, they were thought to be causative agents of skin diseases; however, their role is controversial, and the possible implication of specific species and subtypes remains unclear. Previously, we have conducted two fungal community surveys in healthy skin and dandruff/sebohrreic dermatitis, and have detected prevalentMalasseziaorganisms that could not be assigned to any known species. The usage of distinct ITS rDNA regions did not allow sequence comparison between studies. Here we report molecular characterization and phylogenetic analysis of unidentifiedMalasseziaorganisms, aiming to increase knowledge in fungal microbiome from skin. Findings suggested that a highly prevalent organism might belong to a novelMalasseziaspecies. Results also revealed uncertain taxonomic assignments, even in the case of accepted species. Correct assignment of species and intraspecific variants is relevant considering that specific taxa might be directly involved in disease development. Despite high prevalence, organisms might have remained undiscovered due to difficulties in culturingMalassezia. Challenges and future perspectives for skin fungal microbiome studies are discussed. We address issues to be overcome for unraveling the complete skin microbial diversity and its relation to health and disease.
eSVD-DE: Cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings
Authors: Lin Kevin Z. , Qiu Yixuan , Roeder Kathryn 
Published: November 2023

AbstractBackgroundSingle-cell RNA-sequencing (scRNA) datasets are becoming increasingly popular in clinical and cohort studies, but there is a lack of methods to investigate differentially expressed (DE) genes among such datasets with numerous individuals. While numerous methods exist to find DE genes for scRNA data from limited individuals, differential-expression testing for large cohorts of case and control individuals using scRNA data poses unique challenges due to substantial effects of human variation, i.e., individual-level confounding covariates that are difficult to account for in the presence of sparsely-observed genes.ResultsWe develop the eSVD-DE, a matrix factorization that pools information across genes and removes confounding covariate effects, followed by a novel two-sample test in mean expression between case and control individuals. In general, differential testing after dimension reduction yields an inflation of Type-1 errors. However, we overcome this by testing for differences between the case and control individuals’ posterior mean distributions via a hierarchical model. In previously published datasets of various biological systems, eSVD-DE has more accuracy and power compared to other DE methods typically repurposed for analyzing cohort-wide differential expression.ConclusionseSVD-DE proposes a novel and powerful way to test for DE genes among cohorts after performing a dimension reduction. Accurate identification of differential expression on the individual level, instead of the cell level, is important for linking scRNA-seq studies to our understanding of the human population.
Mutational destabilisation accelerates the evolution of novel sensory and network functions
Authors: Kimura Yuki , Kawai-Noma Shigeko , Umeno Daisuke 
Published: November 2023

AbstractBinding-induced folding1–4(BIF) is a promising mechanism that can be used to rapidly convert binders into sensors/regulators without allosteric design. Here we showed that allosteric regulatory proteins AraC can acquire BIF mechanism without compromising their inherent allosteric mechanisms, with high frequency upon mutations. This opened an opportunity to compare the evolutionary capacity of the allosteric and non-allosteric modes of a specific sensory protein. We found that AraC evolved novel sensory function far more rapidly in BIF mode than in allosteric mode. This newly acquired (non-allosteric) sensory function is distinguishable both in its response logic and in sensitivity from original (allosteric) one, and they can be operated simultaneously, independently, and cooperatively, allowing the construction of complex regulatory networks behaviours such as a selective NIMPLY/OR converter and width-tuneable band-pass filter. Together with its high frequency of emergence, BIF can be an overlooked evolutionary driver of the invention of novel biosensors and complex regulatory networks in nature and laboratory.
An unmanned aerial vehicle pipeline to estimate body volume at scale for ecological monitoring
Authors: Stone Thomas C , Davis Katrina J 
Published: November 2023

AbstractDemographic data are essential to construct mechanistic models to understand how populations change over time and in response to global threats like climate change. Existing demographic data are either lacking or insufficient for many species, particularly those that are challenging to study, such as marine mammals. A pipeline for collecting accurate demographic data to construct robust demographic models at scale would fill this knowledge gap for many species, including marine mammals like pinnipeds (seals, sea lions, and walruses).We introduce a non-invasive pipeline to estimate the 3D body size (volume) of species that will allow monitoring at high spatial and temporal scales. Our pipeline integrates 3D structure-from-motion photogrammetry data collected via planned flight missions using off-the-shelf, multirotor unmanned aerial vehicles (UAVs). We apply and validate this pipeline on the grey sealHalichoerus grypus, a marine species that spends much of its time at sea but is predictably observable during its annual breeding season. We investigate the optimal ground sampling distance (GSD) for surveys by calculating the success rates and accuracy of volume estimates of individuals at different elevations.We establish an optimal GSD of 0.8 cm px-1for animals similar in size to UK grey seals (∼1.4 - 2.5 m length), making our pipeline reproducible and applicable to a broad range of organisms. Volume estimates were accurate and could be made for up to 68% of hauled-out seals in the study areas. Finally, we highlight six key traits that make a species well-suited to estimating body volume following this pipeline. Good candidates include large reptiles like crocodiles, large mammals such as hippopotamus, and shrubs or bushes in deserts and Mediterranean habitats.Our pipeline accurately estimates individual body volume of marine macrovertebrates in a time-and cost-effective manner whilst minimising disturbance. Whilst the approach is applied to pinnipeds here, the pipeline is adaptable to many different taxa that are otherwise challenging to study. Our proposed approach therefore opens up previously inaccessible areas of the Tree of Life to demographic studies, which will improve our ability to protect and conserve these species into the future.
Causal Role of the Medial Prefrontal Cortex in Learning Social Hierarchy
Authors: Qu Chen , Huang Yulong , Philippe Rémi , Cai Shenggang , Derrington Edmund , Moisan Frédéric , Shi Mengke , Dreher Jean-Claude 
Published: November 2023

AbstractSocial hierarchy is a fundamental principle of social organization and an important attribute of community stability and development. Yet, little is known about the causal role of specific brain regions in learning hierarchies. Here, using transcranial direct current stimulation (tDCS), we investigated the causal role of the medial prefrontal cortex (mPFC) in learning social and non-social hierarchies. In the Training phase, participants(N=128) acquired knowledge of social and non-social hierarchy in parallel, by trial and error. During the Test phase, they were presented with two items from hierarchies that were never encountered together and required to make transitive inferences. Anodal stimulation over mPFC impaired social hierarchy learning compared with non-social learning and this modulation was influenced by the relative social rank of the members (i.e. higher or lower status). Anodal stimulation also impaired transitive inference making, but only during early blocks before learning was established. Together, our results provide causal evidence of mPFC engagement in learning social ranks by observation.
Systematic optimization of automated phosphopeptide enrichment for high-sensitivity phosphoproteomics
Authors: Bortel Patricia , Piga Ilaria , Koenig Claire , Gerner Christopher , Martinez del Val Ana , Olsen Jesper V. 
Published: November 2023

AbstractImproving coverage, robustness and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography tandem mass spectrometry (LC-MS/MS) runs from minimal peptide inputs. Here, we systematically optimized key experimental parameters for automated on-beads phosphoproteomics sample preparation with focus on low input samples. Assessing the number of identified phosphopeptides, enrichment efficiency, site localization scores and relative enrichment of multiply-phosphorylated peptides pinpointed critical variables influencing the resulting phosphoproteome. Optimizing glycolic acid concentration in the loading buffer, percentage of ammonium hydroxide in the elution buffer, peptide-to-beads ratio, binding time, sample and loading buffer volumes, allowed us to confidently identify >16,000 phosphopeptides in half-an-hour LC-MS/MS on an Orbitrap Exploris 480 using 30 µg of peptides as starting material. Furthermore, we evaluated how sequential enrichment can boost phosphoproteome coverage and showed that pooling fractions into a single LC-MS/MS analysis increased the depth. We also present an alternative phosphopeptide enrichment strategy based on stepwise addition of beads thereby boosting phosphoproteome coverage by 20%. Finally, we applied our optimized strategy to evaluate phosphoproteome depth with the Orbitrap Astral MS using a cell dilution series and were able to identify >32,000 phosphopeptides from 0.5 million HeLa cells in half-an-hour LC-MS/MS using narrow-window data-independent acquisition (nDIA).Graphical abstract
Development of a Cr-Ni-Mo alloyed stress corrosion-resistant anchor bolt steel
Authors: Du Hailong , Chen Zengyao , Wang Xiyan , Li Yongliang , Yang Renshu , Liu Zhiyong , Jin Aibing , Li Xiaogang 
Published: November 2023

Purpose
The purpose of this paper is to develop new types of anchor bolt materials by adding corrosion-resistant elements for alloying and microstructure regulation.

Design/methodology/approach
Three new anchor bolt materials were designed around the 1Ni system. The stress corrosion cracking resistance of the new materials was characterized by microstructure observation, electrochemical testing and slow strain rate tensile testing.

Findings
The strength of the new anchor bolt materials has been improved, and the stress corrosion sensitivity has been reduced. The addition of Nb makes the material exhibit excellent stress corrosion resistance under –1,200 mV conditions, but the expected results were not achieved when Nb and Sb were coupled.

Originality/value
The new anchor bolt materials designed around 1Ni have excellent stress corrosion resistance, which is the development direction of future materials. Nb allows the material to retain its ability to extend in hydrogen-evolution environments.