bluuebunny/crossref_metadata_2025_split huggingface dataset:
Winners in good times and bad times: Aerobic anoxygenic phototrophic bacteria profit from photoheterotrophy under carbon-rich and poor conditions
Authors: Piwosz Kasia , Villena-Alemany Cristian , Całkiewicz Joanna , Mujakić Izabela , Náhlík Vít , Dean Jason , Koblížek Michal 
Published: December 2023

AbstractAbstract FigureAerobic Anoxygenic Phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, and by that enhance their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light conditions to elucidate how they profit from photoheterotrophy. We found that it depends on the season. In spring, AAP bacteria induce photoheterotrophic metabolism under carbon limitation but they outperform heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. In autumn photoheterotrophy is less beneficial. In both seasons, AAP bacteria responded negatively to recalcitrant or low-energy carbon sources in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria observed in pelagic environments.
Modeling cellular self-organization in strain-stiffening hydrogels
Authors: Erhardt A.H. , Peschka D. , Dazzi C. , Schmeller L. , Petersen A. , Checa S. , Münch A. , Wagner B. 
Published: December 2023

AbstractWe develop a three-dimensional mathematical model framework for the collective evolution of cell populations by an agent-based model (ABM) that mechanically interacts with the surrounding extra-cellular matrix (ECM) modeled as a hydrogel. We derive effective two-dimensional models for the geometrical set-up of a thin hydrogel sheet to study cell-cell and cell-hydrogel mechanical interactions for a range of external conditions and intrinsic material properties. We show that without any stretching of the hydrogel sheets, cells show the well-known tendency to form long chains with varying orientations. Our results further show that external stretching of the sheet produces the expected nonlinear strain-softening or stiffening response, with, however, little qualitative variation of the over-all cell dynamics for all the materials considered. The behavior is remarkably different when solvent is entering or leaving from strain softening or stiffening hydrogels, respectively.
Chromosome fusion and programmed DNA elimination shape karyotypes of parasitic nematodes
Authors: Simmons James R. , Estrem Brandon , Zagoskin Maxim V. , Oldridge Ryan , Zadegan Sobhan Bahrami , Wang Jianbin 
Published: December 2023

AbstractA growing list of metazoans undergo programmed DNA elimination (PDE), where a significant amount of DNA is selectively lost from the somatic genome during development. In some nematodes, PDE leads to the removal and remodeling of the ends of all germline chromosomes. In several species, PDE also generates internal breaks that lead to sequence loss and an increased number of somatic chromosomes. The biological significance of these karyotype changes associated with PDE and the origin and evolution of nematode PDE remain largely unknown. Here, we assembled the single germline chromosome of the horse parasiteParascaris univalensand compared the karyotypes, chromosomal gene organization, and PDE features among ascarid nematodes. We show that PDE inParascarisconverts an XX/XY sex-determination system in the germline into an XX/XO system in the somatic cells. Comparisons ofAscaris, Parascaris,andBaylisascarisascarid chromosomes suggest that PDE existed in the ancestor of these parasites, and their current distinct germline karyotypes were derived from fusion events of smaller ancestral chromosomes. The DNA breaks involved in PDE resolve these fused germline chromosomes into their pre-fusion karyotypes, leading to alterations in genome architecture and gene expression in the somatic cells. Cytological and genomic analyses further suggest that satellite DNA and the heterochromatic chromosome arms play a dynamic role in theParascarisgermline chromosome during meiosis. Overall, our results show that chromosome fusion and PDE have been harnessed in these ascarids to sculpt their karyotypes, altering the genome organization and serving specific functions in the germline and somatic cells.
Multi-omic analysis of guided and unguided forebrain organoids reveal differences in cellular composition and metabolic profiles
Authors: Øhlenschlæger Marie S. , Jensen Pia , Havelund Jesper F. , Sutcliffe Magdalena , Elmkvist Sofie B. , Criscuolo Lucrezia , Wingett Steven W. , Jakobsen Lene A. , Brewer Jonathan , Færgeman Nils J. , Lancaster Madeline A. , Larsen Martin R. , Bogetofte Helle 
Published: December 2023

AbstractNeural organoids are invaluable model systems for studying neurodevelopment and neurological diseases. For this purpose, reproducible differentiation protocols are needed that minimize inter-organoid variability whilst generating neural organoids that physiologically resemble the brain area of interest. Currently, two main approaches are used: guided, where the differentiation towards neuroectoderm and subsequently specific CNS regions is driven by applying extrinsic signalling molecules, and unguided, where the intrinsic capability of pluripotent stem cells to generate neuroectoderm without external signalling is promoted. Despite the importance for the field, the resulting differences between these models have not been directly investigated.To obtain an unbiased comparison, we performed a multi-omic analysis of forebrain organoids generated using a guided and unguided approach focusing on proteomic, lipidomic and metabolomic differences. Furthermore, we characterised differences in phosphorylation and sialylation states of proteins, two key post-translational modifications (PTMs) in neurodevelopment, and performed single cell transcriptomics (scRNAseq). The multi-omic analysis revealed considerable differences in neuronal-, synaptic and glial content, indicating that guided forebrain organoids contain a larger proportion of neurons, including GABAergic interneurons, and synapses whereas unguided organoids contain significantly more GFAP+cells and choroid plexus. Furthermore, substantial differences in mitochondrial- and metabolic profiles were identified, pointing to increased levels of oxidative phosphorylation and fatty acid β-oxidation in unguided forebrain organoids and a higher reliance on glycolysis in guided forebrain organoids.Overall, our study comprises a thorough description of the multi-omic differences arising when generating guided and unguided forebrain organoids and provide an important resource for the organoid field studying neurodevelopment and -disease.
Genome evolution is surprisingly predictable after initial hybridization
Authors: Langdon Quinn K. , Groh Jeffrey S. , Aguillon Stepfanie M. , Powell Daniel L. , Gunn Theresa , Payne Cheyenne , Baczenas John J. , Donny Alex , Dodge Tristram O. , Du Kang , Schartl Manfred , Ríos-Cárdenas Oscar , Gutierrez-Rodríguez Carla , Morris Molly , Schumer Molly 
Published: December 2023

AbstractOver the past two decades, evolutionary biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common – not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fishXiphophorus birchmanniandX. cortezito address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past ∼40 generations of evolution. Finally, we compare our results to the well-studiedX. birchmanni×X. malinchehybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids betweenX. birchmanniandX. cortezi.
Development of novel high-resolution melting markers for the assessment of hybridization betweenMauremys sinensisandMauremys reevesiiin South Korea
Authors: Baek Hae-jun , Cheong Eujin , Kim Youngha , Koo Kyo Soung , Kim Su-Hwan , Park Chang-Deuk , Yoon Ju-Duk 
Published: December 2023

AbstractThe Chinese striped-necked turtleMauremys sinensiswas first reported in the wild in South Korea in 2012. Owing to its potential to hybridize with the native and endangeredMauremys reevesiiin South Korea, leading to ecosystem disturbance,M. sinensiswas designated as an ecosystem-disturbing species (EDS; hereafter) in 2020. Such hybridization betweenM. sinensisandM. reevesiihas previously been reported in Taiwan. To protect and conserve the native South KoreanM. reevesiipopulation, the extent of its hybridization needed to be examined. Therefore, we developed novel high-resolution melting markers to elucidate the status of hybridization betweenMauremys sinensisandMauremys reevesiiin South Korea. We identified the presence ofM. sinensis,M. reevesii, and their hybrid across 47 sites in South Korea. Among these sites, five locations were confirmed as areas of sympatry for bothM. sinensisandM. reevesii, with one hybrid individual identified at the Jeonju-si site. In total, hybrids were identified at four different sites. For more definitive species identification, blood samples were collected from the specimens and subjected to mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) gene and nuclear DNA (nDNA)R35gene analysis, leading to the identification of two more hybrids from two other sites. To date, no hybrids ofM. sinensishave been confirmed to reproduce in the wild, yet this requires further research for validation. The high-resolution melting (HRM) marker in theR35gene developed in this study yielded three distinct curves that were designated asM. sinensis,M. reevesii, andM. sinensis×M. reevesii, aligning with those of theR35gene sequencing. The novel markers developed in this study serve as a valuable tool that can be used in future research on rapid detection of hybridization.
Gene expression signatures of salinity transitions inLimia perugiae(Poeciliidae), with comparisons to other teleosts
Authors: Wilson Elizabeth J. , Barts Nick , Coffin John , Johnson James B. , Rodríguez Peña Carlos M. , Kelley Joanna L. , Tobler Michael , Greenway Ryan 
Published: December 2023

AbstractSalinity gradients act as strong environmental barriers that limit the distribution of aquatic organisms. Changes in gene expression associated with transitions between freshwater and saltwater environments can provide insight into organismal responses to variation in salinity. We used RNA-sequencing (RNA-seq) to investigate genome-wide variation in gene expression between a hypersaline population and a freshwater population of the livebearing fish speciesLimia perugiae(Poeciliidae). Our analyses of gill gene expression revealed potential molecular mechanisms underlying salinity tolerance in this species, including the enrichment of genes involved in ion transport, maintenance of chemical homeostasis, and cell signaling in the hypersaline population. We also found differences in gene expression patterns associated with cell cycle and protein folding processes between the hypersaline and freshwaterL. perugiae. Bidirectional freshwater-saltwater transitions have occurred repeatedly during the diversification of fishes, allowing for broad-scale examination of repeatable patterns in evolution. We compared transcriptomic variation inL. perugiaewith other teleosts that have made freshwater-saltwater transitions to test for convergence in gene expression. Among the four distantly related population pairs from high- and low-salinity environments that we included in our analysis, we found only ten shared differentially expressed genes, indicating little evidence for convergence. However, we found that differentially expressed genes shared among three or more lineages were functionally enriched for ion transport and immune functioning. Overall, our results—in conjunction with other recent studies— suggest that different genes are involved in salinity transitions across disparate lineages of teleost fishes.
Defining bottlenecks and opportunities for Lassa virus neutralization by structural profiling of vaccine-induced polyclonal antibody responses
Authors: Brouwer Philip J.M. , Perrett Hailee R. , Beaumont Tim , Nijhuis Haye , Kruijer Sabine , Burger Judith A. , Lee Wen-Hsin , Müller-Kraüter Helena , Sanders Rogier W. , Strecker Thomas , van Gils Marit J. , Ward Andrew B. 
Published: December 2023

SummaryLassa fever continues to be a major public health burden in endemic countries in West Africa, yet effective therapies or vaccines are lacking. The isolation of potent and protective neutralizing antibodies against the Lassa virus glycoprotein complex (GPC) justifies the development of vaccines that can elicit strong neutralizing antibody responses. However, Lassa vaccines candidates have generally been unsuccessful in doing so and the associated antibody responses to these vaccines remain poorly characterized. Here, we establish an electron-microscopy based epitope mapping pipeline that enables high-resolution structural characterization of polyclonal antibodies to GPC. By applying this method to rabbits vaccinated with a recombinant GPC vaccine and a GPC-derived virus-like particle, we reveal determinants of neutralization which involve epitopes of the GPC-C, GPC-A, and GP1-A competition clusters. Furthermore, by identifying previously undescribed immunogenic off-target epitopes, we expose challenges that recombinant GPC vaccines face. By enabling detailed polyclonal antibody characterization, our work ushers in a next generation of more rational Lassa vaccine design.
Progressive lifespan modifications in the corpus callosum following a single juvenile concussion in male mice monitored by diffusion MRI
Authors: Obenaus Andre , Noarbe Brenda P. , Lee Jeong Bin , Panchenko Polina E. , Noarbe Sean D. , Lee Yu Chiao , Badaut Jerome 
Published: December 2023

AbstractIntroductionThe sensitivity of white matter (WM) in acute and chronic moderate-severe traumatic brain injury (TBI) has been established. In concussion syndromes, particularly in preclinical rodent models, there is lacking a comprehensive longitudinal study spanning the lifespan of the mouse. We previously reported early modifications to WM using clinically relevant neuroimaging and histological measures in a model of juvenile concussion at one month post injury (mpi) who then exhibited cognitive deficits at 12mpi. For the first time, we assess corpus callosum (CC) integrity across the lifespan after a single juvenile concussion utilizing diffusion MRI (dMRI).MethodsC57Bl/6 mice were exposed to sham or two severities of closed-head concussion (Grade 1, G1, speed 2 m/sec, depth 1mm; Grade 2, G2, 3m/sec, 3mm) using an electromagnetic impactor at postnatal day 17.In vivodiffusion tensor imaging was conducted at 1, 3, 6, 12 and 18 mpi (21 directions, b=2000 mm2/sec) and processed for dMRI parametric maps: fractional anisotropy (FA), axial (AxD), radial (RD) and mean diffusivity (MD). Whole CC and regional CC data were extracted. To identify the biological basis of altered dMRI metrics, astrocyte and microglia in the CC were characterized at 1 and 12 mpi by immunohistochemistry.ResultsWhole CC analysis revealed altered FA and RD trajectories following juvenile concussion. Shams exhibited a temporally linear increase in FA with age while G1/G2 mice had plateaued FA values. G2 concussed mice exhibited high variance of dMRI metrics at 12mpi, which was attributed to the heterogeneity of TBI on the anterior CC. Regional analysis of dMRI metrics at the impact site unveiled significant differences between G2 and sham mice. The dMRI findings appear to be driven, in part, by loss of astrocyte process lengths and increased circularity and decreased cell span ratios in microglia.ConclusionFor the first time, we demonstrate progressive perturbations to WM of male mice after a single juvenile concussion across the mouse lifespan. The CC alterations were dependent on concussion severity with elevated sensitivity in the anterior CC that was related to astrocyte and microglial morphology. Our findings suggest that long-term monitoring of children with juvenile concussive episodes using dMRI is warranted, focusing on vulnerable WM tracts.
Prediction of Carbon Emissions in Guizhou Province-Based on Different Neural Network Models
Authors: Da Lian , ShiQiang Yang , Wu Yang , WenRui Ran , Min Zhang 
Published: December 2023

AbstractGlobal warming caused by greenhouse gas emissions has become a major challenge facing people all over the world. The study of regional human activities and their impacts on carbon emissions is of great significance to achieve the ambitious goal of carbon neutrality and sustainable economic development. Guizhou Province is a typical karst area in China, and its energy consumption is mainly based on fossil fuels.Therefore, it is necessary to predict and analyze its carbon emissions. In this paper, BP neural network and extreme learning machine (ELM) model, which have the advantage of nonlinear processing, will be used to predict the carbon emissions of Guizhou Province from 2020 to 2040. Based on the energy consumption data of Guizhou Province, the carbon emissions of Guizhou Province are calculated by using the conversion method and the inventory compilation method. The data show that the carbon emissions of Guizhou Province show an “S” growth trend; In this paper, 12 influencing factors of carbon emissions are selected, and five influencing factors with larger correlation are screened out by using grey correlation analysis method, and the prediction model of carbon emissions in Guizhou Province is established and simulated, and the prediction performance of BP neural network, ELM and WOA-ELM are compared respectively. Compared with ELM model and BP neural network model, the prediction accuracy of WOA-ELM model is higher; Finally, three development scenarios of carbon emissions are set by scenario analysis, which are baseline scenario, high-speed scenario and low-carbon scenario. On this basis, the size and time of peak carbon emissions in Liaoning Province from 2020 to 2040 are predicted based on WOA-ELM model. The results show that the peak value of carbon dioxide in the low carbon scenario is up to 0.98 million tons 31294 in 2033, the peak value of carbon emissions in the high speed scenario is up to 0.37 million tons 30251 in 2036, and the peak value of carbon emissions in the baseline scenario is up to 0.61 million tons 26243 in 2038. Based on the peak time and prediction results of carbon emissions under the three scenarios, the main factors contributing to the reduction of carbon emissions in Guizhou Province are analyzed, and important data basis is provided for energy conservation and emission reduction in Guizhou Province.
Detection of pathogenic bacteria in ticks from Isiolo and Kwale counties of Kenya using metagenomics
Authors: Kimemia Bryson Brian , Musila Lillian , Lang’at Solomon , Odoyo Erick , Cinkovich Stephanie , Abuom David , Yalwala Santos , Khamadi Samoel , Johnson Jaree , Garges Eric , Ojwang Elly , Eyase Fredrick 
Published: December 2023

AbstractTicks are arachnid ectoparasites which rank second only to mosquitoes in the transmission of human diseases including bacteria responsible for anaplasmosis, ehrlichiosis, spotted fevers, and Lyme disease among other febrile illnesses. Due to paucity of data on bacteria transmitted by ticks in Kenya, this study undertook a bacterial metagenomic-based characterization of ticks collected from Isiolo, a semi-arid pastoralist County in Eastern Kenya, and Kwale, a coastal County with monsoon climate on the southern Kenyan border with Tanzania. A total of 2,918 ticks belonging to 3 genera and 10 species were pooled and screened in this study. Tick identification was confirmed through the sequencing of Cytochrome C Oxidase Subunit 1 (COI) gene. Bacterial 16S rRNA gene PCR amplicons obtained from the above samples were sequenced using the MinION (Oxford Nanopore Technologies) platform. The resulting reads were demultiplexed in Porechop, followed by trimming and filtering in Trimmomatic before clustering using Qiime2-VSearch. A SILVA database pretrained naïve Bayes classifier was used to taxonomically classify the Operational Taxonomic Units (OTUs). The bacteria of clinical interest detected in pooled tick assays were as follows:Rickettsia spp.59.43% of pools,Coxiella burnetii37.88%,Proteus mirabilis5.08%,Cutibacterium acnes6.08% andCorynebacterium ulcerans2.43%. These bacteria are responsible for spotted fevers, query fever (Q-fever), urinary tract infections, skin and soft tissue infections, eye infections and diphtheria-like infections in humans, respectively.P. mirabilis, C. acnesandC. ulceranswere detected only in Isiolo. Additionally, COI sequences allowed for the identification ofRickettsiaandCoxiellaspecies to strain level in some of the pools. Diversity analysis revealed that the tick genera had high levels of Alpha diversity but the differences between the microbiomes of the three tick genera studied were not significant. The detection ofCutibacterium acnes, commonly associated with human skin flora suggests that the ticks may have contact with humans potentially exposing them to bacterial infections. The findings in this study highlight the need for further investigation into the viability of these bacteria and the competency of ticks to transmit them. Clinicians in these high-risk areas also need to be appraised for them to include Rickettsial diseases and Q-fever as part of their differential diagnosis.