bluuebunny/crossref_metadata_2025_split huggingface dataset:
Field monitoring and hydraulic modelling quantify untreated wastewater as dominant source of AMR in a small river running through a big city
Authors: Sonkar Vikas , Kashyap Arun , Pallarés-Vega Rebeca , Sasidharan Sai Sugitha , Modi Ankit , Uluseker Cansu , Jambu Sangeetha Chandrakalabai , Mohapatra Pranab Kumar , Larsen Joshua , Graham David , Thatikonda Shashidhar , Kreft Jan-Ulrich 
Published: December 2024

AbstractAntimicrobial resistance (AMR) is a silent pandemic, which is transmitted and spread through the environment. Few of many studies on waterborne AMR spread have characterised the prevalence, sources, and transport of AMR in adequate detail to inform mathematical modelling and exposure risk assessments. Here, we quantified taxonomic and resistance genes (ARGs), sensitive and resistant bacteria (ARBs), and environmental conditions in water and sediment samples at ten locations along the Musi River through Hyderabad, a city renowned for antimicrobial manufacturing, to develop a hydraulic model for AMR spread in the catchment. In the dry season, absolute water column ARG and ARB abundances increased rapidly upon entering the city, then declined downstream. In the wet season, the increase and decline of AMR levels was more gradual. Clustering and ordination of ARGs separated the river into three stretches: upstream, city, and downstream. Most ARGs and water quality indicators differed significantly between stretches and seasons (p<0.05; PERMANOVA). Linear Discriminant Analysis showed that various water quality parameters, such as lower dissolved oxygen and elevated total nitrogen, can distinguish between AMR-polluted and less-polluted sites and might be good proxies to detect AMR hotspots. Modelling showed that 60%-80% of river water in the city was untreated wastewater, suggesting municipal wastewater dominated AMR in the river, not manufacturing sources. This will be a typical situation where wastewater treatment is insufficient and dilution in receiving water bodies limited, highlighting the urgent need for improved wastewater management to make rivers like the Musi safer for use, such as irrigation, reducing AMR exposures across wider environments.HighlightsWithin the city, the concentration of ARGs and ARBs increases in the dry seasonClustering and ordination of ARGs separates upstream, city and downstream stretchesPERMANOVA shows stretches and seasons are significantly differentLDA can discriminate stretches and seasons based on water quality parametersPoint source load calculations indicate 60-80% of river water is untreated wastewater
HYDRA: HYdrogel Dispensing with Robotic Automation for high throughput drug testing
Authors: Torchia Eloisa , Di Sante Moises , Horda Bohdana , Mihajlovic Marko , Zimmermann Julius , Pezzotti Melissa , Cimetta Elisa , Gabriele Sylvain , Auricchio Ferdinando , Lind Johan Ulrik , Enrico Alessandro , Pasqualini Francesco Silvio 
Published: December 2024

ABSTRACTThe poor predictivity of traditional cell culture platforms hampers drug research and development efficiency. While organoids and organs-on-chip mitigate this problem by introducing biomimetic in-vitro microenvironments in late pre-clinical stages, there is a lack of biomimetic platforms in earlier stages, particularly for high-throughput imaging screening (HTS). Something as simple as a thin hydrogel layer would provide physiological stiffness and native-like biochemical cues. However, casting hydrogels inside the small-diameter wells of HTS plates creates high-curvature menisci that negatively affect cell seeding and microscopy readouts. Here, we present a solution to this problem: HYdrogel Dispensing with Robotic Automation or HYDRA. This method allows automatic dispensing and aspiration of hydrogel precursors while preventing meniscus formation. Using this approach, we can produce gelatin hydrogels with tunable stiffnesses and thickness at room temperature and in commercial HTS plates. Then, we validate HYDRA in dose-response studies for anti-cancer drugs nocodazole and paclitaxel using genetically engineered epithelial cells (HaCaT) and imaging-based HTS readout methods such as phase holography and fluorescence microscopy. Taken together, this work shows that pharmaceutical companies can readily apply HYDRA with their current infrastructure to produce more biomimetic and predictive HTS platforms.
Synergistic activation of the human phosphate exporter XPR1 by KIDINS220 and inositol pyrophosphate
Authors: Zuo Peng , Wang Weize , Dai Zonglin , Zheng Jiye , Yu Shang , Wang Guangxi , Yin Yue , Liang Ling , Yin Yuxin 
Published: December 2024

AbstractInorganic phosphate (Pi) is fundamental to life, and its intracellular concentration must be tightly regulated to prevent toxicity. XPR1, the only known phosphate exporter, plays a crucial role in maintaining this delicate balance. However, the mechanisms underlying the function and regulation of XPR1 remain elusive until now. Here we present cryo-electron microscopy structures of the human XPR1-KIDINS220 complex in both substrate-free closed states and substrate-bound outward-open states, as well as the structure of an XPR1 mutant alone in a substrate-bound inward-facing state. In the presence of inositol hexaphosphate (InsP6) and phosphate, the XPR1-KIDINS220 complex adopts an outward-open conformation. InsP6 binds both the SPX domain and the peripheral juxtamembrane regions of XPR1, indicative of an active phosphate-export state. Conversely, in the absence of either phosphate or InsP6, the complex assumes a closed state, where the extracellular half of transmembrane 9 occupies the outward cavity, and a C-terminal plug-in loop blocks the intracellular cavity. Notably, XPR1 without KIDINS220 adopts a closed state despite the presence of phosphate and InsP6. The functional mutagenesis experiments further demonstrate that InsP6, whose concentrations fluctuate in response to Pi availability, functions synergistically with KIDINS220 to regulate the phosphate export activity of XPR1. These findings not only elucidate the intricate mechanisms of cellular phosphate regulation but also hold promise for the development of targeted therapies for ovarian cancer, where XPR1 plays a significant role.
Whole-transcriptome analysis of BLV-infected cows reveals downregulation of immune response genes in high proviral loads cows
Authors: Petersen MI , Suarez Archilla G , Miretti MM , Trono KG , Carignano HA 
Published: December 2024

AbstractBovine leukemia virus (BLV) is a retrovirus that infects cattle, causing bovine enzootic leukosis, a chronic disease characterized by the proliferation of infected B cells. BLV proviral load (PVL) is a key determinant of disease progression and transmission risk. Cattle can exhibit distinct phenotypes of low PVL (LPVL) or high PVL (HPVL), which remain stable throughout their lifetime. Differential expression analysis revealed 1,908 differentially expressed genes (DEGs) between HPVL and LPVL animals, including 774 downregulated (DReg) and 1134 upregulated (UReg) genes. Functional enrichment analysis revealed that DReg genes were associated primarily with immune response pathways. Conversely, the UReg genes were enriched in processes related to cell cycle regulation, mitotic division, and DNA biosynthesis. Protein□protein interaction analysis revealed six highly interconnected clusters. Interestingly, a cluster was enriched for sphingolipid metabolism, a process critical to enveloped virus infection and immune receptor signaling. These findings provide valuable insights into the molecular mechanisms of BLV infection, suggesting potential markers for disease monitoring and targets for therapeutic intervention.
Functional specialization of MITF, TFEB and TFE3 drives radically distinct adaptive gene expression programs in melanoma
Authors: Dias Diogo , Oliveira Erica , Martí-Díaz Román , Andrews Sarah , Chocarro-Calvo Ana , Bellini Alice , Mosteo Laura , Vivas García Yurena , Chauhan Jagat , Li Linxin , García-Martinez José Manuel , Rodriguez-López José Neptuno , Maria-Engler Silvya Stuchi , García-Jiménez Custodia , Sanchez-del-Campo Luis , Louphrasitthiphol Pakavarin , Goding Colin R 
Published: December 2024

AbstractWithin cells multiple related transcription factors targeting the same sequences may co-exist, leading to potential regulatory cooperativity, redundancy or competition. Yet the differential roles and biological functions of co-targeting transcription factors is poorly understood. In melanoma, three highly-related transcription factors are co-expressed: The mTORC1-regulated TFEB and TFE3, that are key effectors of a wide range of metabolic and microenvironmental cues; and MITF, that controls melanoma phenotypic identity. Here we reveal the functional specialization of MITF, TFE3 and TFEB and their impact on cancer progression. Notably, although all bind the same sequences, each regulates radically different and frequently opposing gene expression programs to coordinate differentiation, metabolic reprogramming, protein synthesis, and expression of immune modulators. The results uncover a hierarchical cascade in which microenvironmental stresses, including glucose limitation, lead MITF, TFEB and TFE3 to drive distinct biologically important transcription programs that underpin phenotypic transitions in cancer.
Ephrin-A5 or EphA7 stimulation is anti-proliferative for human rhabdomyosarcomain vitro
Authors: Cecchini A. , Ceccon L. , Chen A. , Schwesig J. C. , Cornelison DDW 
Published: December 2024

AbstractRhabdomyosarcoma (RMS) is a tumor which resembles skeletal muscle. Current treatments are limited to surgery and non-targeted chemotherapy, highlighting the need for alternative therapies. Differentiation therapy uses molecules that act to shift the tumor cells’ phenotype from proliferating to differentiated, which in the case of skeletal muscle includes exit from the cell cycle and potentially fusion into myofibers. We previously identified EphA7 expressed on terminally differentiated myocytes as a potent driver of skeletal muscle differentiation: stimulation of ephrin-A5-expressing myoblasts with EphA7 causes them to undergo rapid, collective differentiation. We therefore tested EphA7 as a candidate molecule for differentiation therapy on human RMS (hRMS) cell lines. Surprisingly, EphA7 had a lesser effect than ephrin-A5, a difference explained by the divergent suite of Ephs and ephrins expressed by hRMS. We show that in hRMS ephrin-A5 binds and signals to EphA8 and EphA7 binds and signals to ephrin-A2, and that Fc chimeras of both molecules are potent inhibitors of hRMS proliferation. These results identify key differences between hRMS and normal muscle cells and support further research into Eph:ephrin signaling as potential differentiation therapies.Summary statementThis study identifies EphA7 and ephrin-A5 as external regulators of rhabdomyosarcoma proliferation, highlighting ephrin-A5 as a potential candidate for differentiation therapy in future cancer treatments.
Auditory brainstem responses to speech-in-noise reflect selective attention, comprehension, and subjective listening effort
Authors: Mankel K. , Comstock D. C. , Bormann B. M. , Das S. , Sagiv D. , Brodie H. , Miller L. M. 
Published: December 2024

AbstractThe auditory brainstem plays a crucial role in speech-in-noise listening, refining numerous acoustic features such as pitch and spatial location under continual descending influence from cortex. However, the difficulty of characterizing brainstem activity during continuous speech listening has obscured its functional role in ecologically valid contexts—not only the effects of selective attention on neural responses, but also their impact on comprehension and listening effort. Here, we evaluate the role of the brainstem on speech-in-noise perception and selective attention using a continuous, speech-based stimulus with embedded chirps (Cheech) that rapidly and effectively evokes auditory brainstem responses (ABRs) while participants listen to short story narratives. The Cheech-modified stories were presented alone or in the presence of another spatially separated talker, and neural responses were measured throughout by EEG. Both word-level detection performance and narrative-level comprehension were evaluated, as well as subjective reports of listening effort. ABR wave V was modulated by the presence of a competing talker, selective attention for the target versus masker, and the talker gender. Additionally, faster wave V peak latencies and larger amplitudes were associated with identification of the target words embedded within the stories, while faster latencies additionally related to better comprehension question accuracy and lower subjective listening effort. Collectively, our results provide clear evidence for the influence of brainstem encoding processes on individual speech-listening behaviors, including the ability to selectively attend to and comprehend target speech in the presence of a competing talker.Significance statementThis study highlights the crucial role of the brainstem in speech-in-noise perception and higher-level language abilities like comprehension and subjective listening effort. Through the use of a novel speech stimulus blended with embedded chirps (Cheech) to evoke brainstem responses while listening to short story narratives, we show how selective attention influences subcortical processes. Faster and more robust subcortical processes, in turn, were associated with more successful speech-listening performance across multiple behavioral metrics. These findings advance our understanding of how the brainstem supports selective attention and speech perception in challenging listening environments.
More fungi than legs: the first fungal microbiome for a fungus-eating millipede (Colobognatha)
Authors: Macias Angie , Lovett Brian , Jusino Michelle , Cole Lauren , Kasson Matt T. 
Published: December 2024

AbstractFungi are widely consumed across the animal kingdom for nutritional and defensive benefits. Millipedes, among the first air-breathing land animals, were also among the first terrestrial fungivores. As detritus-eating omnivores, most millipedes regularly consume fungi. Millipede diets diverged ∼200 million years ago, when obligate fungivorous millipedes (subterclass Colobognatha) diverged from their detritivorous counterparts. Despite their global distribution and uncommon diet, little is known about the association between Colobognaths and the fungi they consume. In 2019, surveys of fungal communities associated with the ColobognathBrachycybe lecontiirevealed associations with at least 176 genera of culturable fungi. Given the known biases of culture-based approaches, a more comprehensive survey ofB. lecontii’s fungal microbiome using amplicon sequencing was undertaken. In this study, we generated amplicon sequence data to look for associations between fungi andB. lecontii, and to determine if patterns of fungal diversity are millipede- or habitat-driven. Altogether, the fungal microbiome ofB. lecontiiencompassed 620 fungal genera and 100 orders. Despite much greater observed fungal diversity in the amplicon-based study, sampling was likely not sufficient to capture the full diversity of fungi associated withB. lecontii. Taxonomic and functional diversity were significantly influenced by site and colony, indicating that community structure is shaped by geography and habitat. It remains unknown whether these findings are representative of the larger patterns of fungal diversity for the entire millipede subterclass. Nevertheless, the obligate fungivorous lifestyle employed by these long-extant animals may provide important clues regarding fungal diversity and function.
Demonstrating Soft X-Ray Tomography in the lab for correlative cryogenic biological imaging using X-rays and light microscopy
Authors: O’Connor Stephen , Rogers David , Kobylynska Maryna , Geraets James , Thaysen Katja , Egebjerg Jacob Marcus , Brink Madeleen C. , Herbsleb Louisa , Salakova Michaela , Fuchs Leon , Alves Frauke , Feldmann Claus , Ekman Axel , Sheridan Paul , Fyans William , McEnroe Tony , O’Reily Fergal , Fahy Kenneth , Fleck Roland A. , Wüstner Daniel , Simpson Jeremy C. , Walter Andreas , Kapishnikov Sergey 
Published: December 2024

AbstractSoft X-ray tomography (SXT) enables native-contrast three-dimensional (3D) imaging of fully hydrated, cryogenically preserved biological samples, revealing ultrastructural details without the need for staining, embedding, or sectioning. Traditionally available only at synchrotron facilities, recent advances in laser-driven plasma sources have led to the development of compact soft X-ray microscopes, such as the SXT-100. The SXT-100 achieves imaging resolutions down to 54 nm full-pitch, with tomograms acquired in 30 minutes to two hours. Integrated with an epifluorescence microscope, the SXT-100 facilitates correlative workflows by bridging fluorescence and electron microscopy while preserving the structural integrity of vitrified samples. We demonstrate the capabilities of the SXT-100 through various use cases, including imagingEuglena gracilis, Saccharomyces cerevisiaeyeast cells, and nanoparticles in mammalian cells. The relatively short tomogram acquisition times, the virtually non-destructive nature of soft X-ray tomography, and its quantitative imaging capabilities underscore its potential as a powerful tool for advanced biological imaging. Future developments promise enhanced throughput and deeper integration with emerging correlative imaging modalities, and a wider variety of sample types including tissue.
Systematic Plasmid Engineering for Targeted Carotenoid Synthesis in Bacteria
Authors: Furubayashi Maiko 
Published: December 2024

AbstractCarotenoids are natural pigments known for their vibrant colors and roles in various biological functions, such as antioxidant activity, photosynthesis, and radiation tolerance. The microbial production of carotenoids through heterologous expression of biosynthetic genes on engineered plasmid has facilitated the exploration of these functions. However, the complexity of creating carotenoid pathway plasmids has limited the number of available constructs, despite the vast diversity of carotenoids found in nature. This study aims to overcome these challenges by developing a platform for the systematic creation of plasmids that efficiently produce specific carotenoids in bacteria. A novel strategy, called Slot Assignment Cloning (SA-Clo), which applies the modular cloning (MoClo) method, was introduced. Using this strategy, plasmids for 17 carotenoids were constructed, including lycopene, β-carotene, zeaxanthin, canthaxanthin, astaxanthin, phytoene, δ-carotene, ε-carotene, α-carotene, violaxanthin, isorenieratene, several C30carotenoids, and non-natural C50-carotenoids. These plasmids enable the targeted and specific production of carotenoids, streamlining future studies on lesser-known carotenoids and their applications.
Gametocyte production and transmission fitness of African and AsianPlasmodium falciparumisolates with differential susceptibility to artemisinins
Authors: Proellochs Nicholas I. , Andolina Chiara , Ramjith Jordache , Stoter Rianne , van Gemert Geert-Jan , Graumans Wouter , Campino Susana , Vanheer Leen N. , Okitwi Martin , Tumwebaze Patrick K. , Conrad Melissa D. , Clark Taane G. , Fidock David A. , Menard Didier , Mok Sachel , Bousema Teun 
Published: December 2024

AbstractThe emergence ofPlasmodium falciparumparasites partially resistant to artemisinins (ART-R) poses a significant threat to recent gains in malaria control. ART-R has been associated with PfKelch13 (K13) mutations, which differ in fitness costs. This study investigates the gametocyte production and transmission fitness of African and AsianP. falciparumisolates with different K13 genotypes across multiple mosquito species. We tested three ART-sensitive (ART-S) isolates (NF54, NF135, NF180) and three ART-R isolates (ARN1G, 3815, PAT-023) for sexual conversion and transmission toAnopheles stephensi, An. gambiaeandAn. coluzzii. ART-R levels were quantifiedin vitrousing the Ring-stage Survival Assay (RSA), and the transmission-reducing effects of dihydroartemisinin (DHA) on mature gametocytes were assessed. Results showed that ART-S parasite lines consistently produced gametocytes and transmitted effectively in all three mosquito species. ART-R isolates showed variability: ARN1G maintained high transmission levels, whereas 3815 showed limited transmission potential despite higher sporozoite loads inAn. coluzzii. The African ART-R isolate PAT-023 demonstrated low gametocyte commitment but was transmitted efficiently in bothAn. gambiaeandAn. coluzzii. DHA exposure reduced mosquito infectivity for all isolates, regardless of K13 genotype. These findings, based on a limited number of field isolates, suggest that ART-R parasites remain transmissible across differentAnophelesspecies. However, K13 mutations do not appear to confer a direct transmission advantage. This study highlights the complexity of ART-R dynamics and underscores the need for further research to inform malaria control strategies in regions where ART-R parasites are circulating.
Network Segregation During Episodic Memory Shows Age-Invariant Relations with Memory Performance From 7 to 82 Years
Authors: Grydeland Håkon , Sneve Markus H. , Roe James M. , Raud Liisa , Ness Hedda T. , Folvik Line , Amlien Inge , Geier Oliver M. , Sørensen Øystein , Vidal-Pineiro Didac , Walhovd Kristine B. , Fjell Anders M. 
Published: December 2024

AbstractLower episodic memory capability, as seen in development and aging compared with younger adulthood, may partly depend on lower brain network segregation. Here, our objective was twofold: (1) test this hypothesis using within- and between-network functional connectivity (FC) during episodic memory encoding and retrieval, in two independent samples (n=734, age 7-82 years). (2) Assess associations with age and the ability to predict memory comparing task-general FC and memory-modulated FC. In a multiverse-inspired approach, we performed tests across multiple analytic choices. Results showed that relationships differed based on these analytic choices, were often weak, and mainly present in the cohort with the most data. Significant relationships indicated that (i) memory-modulated FC predicted memory performance and associated with memory in an age-invariant manner. (ii) In line with the so- called neural dedifferentiation view, task-general FC showed lower segregation with higher age in adults which was associated with worse memory performance. In development, although there were only weak signs of a neural differentiation, that is, gradually higher segregation with higher age, we observed similar lower segregation-worse memory relationships. This age-invariant relationships between FC and episodic memory suggest that network segregation is pivotal for memory across the healthy lifespan.Declarations of interestnone.HighlightsWithin- and between network functional connectivity predict memory performance.Multiverse-inspired analyses showed varying results depending on analytic choices.Memory associations particularly in the cohort with most data were age-invariant across the lifespan.Dedifferentiation might be better characterized as degrees of differentiation.