bluuebunny/crossref_metadata_2025 huggingface dataset:
Carcass size, not source or taxon, dictates breeding performance and carcass use in a burying beetle
Authors: Hsu Gen-Chang , Lin Wei-Jiun , Hsieh Chi-Heng , Lee Yue-Jia , Sun Syuan-Jyun
Published: October 2024

Small vertebrate carcasses represent critical resources for many terrestrial organisms, including burying beetles, which rely on carcasses for survival and breeding. Carcass attributes can influence the reproduction of burying beetles, yet most studies on their breeding ecology have used laboratory-reared carcasses of limited sizes. We conducted breeding and feeding experiments using a wide size range of lab (laboratory mice) and wild carcasses (wild mammals, birds and reptiles) to investigate how carcass size, source and taxon affect various breeding outcomes (e.g. clutch size, brood size and brood mass) of the burying beetle
Nicrophorus nepalensis
. Our results reveal a hump-shaped relationship between carcass size and breeding performance, with optimal breeding outcomes occurring on medium-sized carcasses. Furthermore, despite the variation in carcass tissue nutritional composition, breeding outcomes and larval growth did not differ between the two carcass sources or among the three wild carcass taxa. Finally, we found a larval quality–quantity trade-off across the range of carcasses examined, with carcass size shaping the larval life-history traits. Overall, these results elucidate how carcass resources may influence the breeding performance of burying beetles. Importantly, our study provides solid evidence validating decades of research using lab carcasses to study the reproductive ecology of burying beetles.
Fossil amphibian offers insights into the interplay between monsoons and amphibian evolution in palaeoequatorial Late Triassic systems
Authors: So Calvin , Kufner Aaron M. , Pardo Jason D. , Edwards Caian L. , Price Brandon R. , Bevitt Joseph J. , LeClair-Diaz Amanda , St. Clair Lynette , Mann Josh , Teran Reba , Lovelace David M.
Published: October 2024

The severe greenhouse climate and seasonality of the early to mid-Late Triassic are thought to have limited terrestrial diversity at lower latitudes, but direct adaptations to these harsh conditions remain limited in vertebrates at the palaeoequator. Here, we presentNinumbeehan dookoodukahgen. et sp. nov., an early amphibian with specialized adaptations for seasonal estivation from the upper Jelm Formation of the Late Triassic of Wyoming, USA.Ninumbeehanare found in an association of vertebrate estivation burrows across a locally dense horizon, offering insights into the evolution and ecology of vertebrates amid the challenging conditions of low-latitude Late Triassic ecosystems. Estivation chambers were excavated within point bar deposits of an ephemeral river system, recording the cyclical signature of Triassic megamonsoons and documenting a vertebrate response to annual climate extremes across tens to hundreds of seasons. Phylogenetic analysis recoversNinumbeehanwithin a group of temnospondyls characterized by fossorial adaptation, underscoring the widespread adoption of burrowing and estivation in total group Lissamphibia.Ninumbeehanhints at the pivotal role seasonal dynamics played in shaping amphibian evolution.
Interactions between soil and other environmental variables modulate forest expansion and ecotone dynamics in humid savannas of Central Africa
Authors: Sagang Le Bienfaiteur Takougoum , Tcheferi Imma , Ploton Pierre , Libalah Moses , Simo-Droissart Murielle , Sirri Nelly , Dauby Gilles , Ngansop Eric , Bissek Jean Pierre , Kamdem Narcisse , Mofack Gislain I. I. , Zebaze Donatien , Leblanc Hugo , Djonko Fabrice , Sonké Bonaventure , Barbier Nicolas , Couteron Pierre
Published: October 2024

Forest expansion into savanna is a pervasive phenomenon in West and Central Africa, warranting comparative studies under diverse environmental conditions. We collected vegetation data from the woody and grassy components within 73 plots of 0.16 ha distributed along a successional gradient from humid savanna to forest in Central Africa. We associated spatially collocated edaphic parameters and fire frequency derived from remote sensing to investigate their combined influence on the vegetation. Soil texture was more influential in shaping savanna structure and species distribution than soil fertility, with clay-rich soils promoting higher grass productivity and fire frequency. Savanna featuring woody aboveground biomass surpassing 40 Mg ha
−1
could escape the grass–fire feedback loop, by depressing grass biomass below 4 Mg ha
−1
. This thicker woody layer also favoured the establishment of fire-tolerant forest pioneers, which synergically contributed to the expansion of forests. Conversely, savannas below this fire suppression threshold sustained a balance between trees and grasses through the grass–fire feedback mechanism. This hysteresis loop, particularly pronounced on clayey soils, suggests that the contrast between grassy savanna and young forests might represent alternative ecosystem states, although savannas with low woody biomass remained vulnerable to forest edge encroachment.
Population trends are more strongly linked to environmental change and species traits in birds than mammals
Authors: Ma Xiaoming , Dong Rongan , Hughes Alice , Corlett Richard T. , Svenning Jens-Christian , Feng Gang
Published: October 2024

Changes in land use and climate directly impact species populations. Species with divergent characteristics may respond differently to these changes. Therefore, understanding species’ responses to environmental changes is fundamental for alleviating biodiversity loss. However, the relationships between land use changes, climate changes, species' intrinsic traits and population changes at different spatial scales have not been tested. In this study, we analysed the effects of land use and climate changes from different time periods and species traits on the population change rates of 2195 bird and mammal populations in 577 species recorded in the Living Planet Database at global, tropical and temperate scales. We hypothesized that both bird and mammal populations will decline owing to climate and land use changes, especially phylogenetically young and small-bodied species. We found that bird population trends were more closely related to environmental changes and phylogenetic age than those of mammals at global and temperate scales. Mammal population trends were not significantly correlated with land use or climate changes but were with longevity at global and temperate scales. Given the divergent responses of bird and mammal populations to these explanatory variables, different conservation strategies should be considered for these taxa and for different regions.
The Palaeozoic assembly of the holocephalan body plan far preceded post-Cretaceous radiations into the ocean depths
Authors: Brownstein Chase D. , Near Thomas J. , Dearden Richard P.
Published: October 2024

Among cartilaginous fishes,
Holocephali
represents the species-depauperate, morphologically conservative sister to sharks, rays and skates and the last survivor of a once far greater Palaeozoic and Mesozoic diversity. Currently, holocephalan diversity is concentrated in deep-sea species, suggesting that this lineage might contain relictual diversity that now persists in the ocean depths. However, the relationships of living holocephalans to their extinct relatives and the timescale of their diversification remain unclear. Here, we reconstruct the evolutionary history of holocephalans using comprehensive morphological and DNA sequence datasets. Our results suggest that crown holocephalans entered and diversified in deep (below 1000 m) ocean waters after the Cretaceous–Palaeogene mass extinction, contrasting with the hypothesis that this ecosystem has acted as a refugium of ancient cartilaginous fishes. These invasions were decoupled from the evolution of key features of the holocephalan body plan, including crushing dentition, a single frontal clasper, and holostylic jaw suspension, during the Palaeozoic Era. However, these invasions considerably postdated the appearance of extant holocephalan families 150 million years ago during a major period of biotic turnover in oceans termed the Mesozoic Marine Revolution. These results clarify the origins of living holocephalans as the recent diversification of a single surviving clade among numerous Palaeozoic lineages.
A systematic review of laboratory investigations into the pathogenesis of avian influenza viruses in wild avifauna of North America
Authors: Gonnerman Matthew , Leyson Christina , Sullivan Jeffery D. , Pantin-Jackwood Mary J. , Spackman Erica , Mullinax Jennifer M. , Prosser Diann J.
Published: October 2024

The lack of consolidated information regarding the response of wild bird species to infection with avian influenza virus (AIV) is a challenge to both conservation managers and researchers alike, with related sectors also impacted, such as public health and commercial poultry. Using two independent searches, we reviewed published literature for studies describing wild bird species experimentally infected with avian influenza to assess host species’ relative susceptibility to AIVs. Additionally, we summarize broad-scale parameters for elements such as shedding duration and minimum infectious dose that can be used in transmission modelling efforts. Our synthesis shows that waterfowl (i.e. Anatidae) compose the vast majority of published AIV pathobiology studies, whereas gulls and passerines are less represented in research despite evidence that they also are susceptible and contribute to highly pathogenic avian influenza disease dynamics. This study represents the first comprehensive effort to compile available literature regarding the pathobiology of AIVs in all wild birds in over a decade. This database can now serve as a tool to all researchers, providing generalized estimates of pathobiology parameters for a variety of wild avian families and an opportunity to critically examine and assess what is known and identify where further insight is needed.
Behavioural responses of a trans-hemispheric migrant to climate oscillation
Authors: Siddiqi-Davies Katrina , Wynn Joe , Padget Oliver , Lewin Patrick , Gillies Natasha , Morford Joe , Fisher-Reeves Lewis , Jaggers Paris , Morgan Greg , Danielsen Jóhannis , Kirk Holly , Fayet Annette , Shoji Akiko , Bond Sarah , Syposz Martyna , Maurice Lou , Freeman Robin , Dean Ben , Boyle David , Guilford Tim
Published: October 2024

Large-scale climatic fluctuations, such as the El Niño–Southern Oscillation, can have dramatic effects on ocean ecosystem productivity. Many mobile species breeding in temperate or higher latitudes escape the extremes of seasonal climate variation through long-distance, even trans-global migration, but how they deal with, or are affected by, such longer phased climate fluctuations is less understood. To investigate how a long-lived migratory species might respond to such periodic environmental change we collected and analysed a 13 year biologging dataset for a trans-equatorial migrant, the Manx shearwater (
Puffinus puffinus
). Our primary finding was that in El Niño years, non-breeding birds were at more northerly (lower) latitudes than in La Niña years, a response attributable to individual flexibility in migratory destinations. Daily time spent foraging varied in concert with this latitudinal shift, with birds foraging less in El Niño years. Secondarily, we found that in subsequent breeding, a hemisphere away, El Niño years saw a reduction in foraging time and chick provisioning rates: effects that could not be attributed to conditions at their breeding grounds in the North Atlantic. Thus, in a highly migratory animal, individuals may adjust to fluctuating non-breeding conditions but still experience cascading carry over effects on subsequent behaviour.
Mechanism of N-Myc Downstream Regulated Gene-1 regulating Integrin expression to inhibit gastric cancer metastasis
Authors: Wanga Tengkai , Ma Wenlong , Zhang Di , Lv Fenxiao , Zeng Yunqing , Zheng Yuan , Liu Mingru , Lu Jiaoyang
Published: October 2024

Background

N-myc downstream regulated gene-1 (NDRG1), the first member of the NDRG family, is widely distributed in various tissues and organs. In gastric cancer, the hypo-expression of NDRG1 has been positively associated with malignant biological behavior and poor prognosis. In-depth investigation of the potential regulatory mechanism of NDRG1 on gastric cancer is crucial for understanding the pathogenesis of this disease, identifying new therapeutic targets, and developing personalized treatment strategies. This study aims to explore the significance of NDRG1 in regulating the expression of integrins during the progression of gastric cancer.

Methods

The expression of NDRG1 in gastric cancer was analyzed using R software v4.0.3, Boxplot, and the Kaplan-Meier Plotter. Stable cell lines with NDRG1 knockdown and overexpression were subjected to wound healing assays, transwell migration assays, CCK8 assays, and colony formation assays, in order to determine the effects of NDRG1 on the migration and proliferation of gastric cancer cells. Western blotting was employed to examine the impact of NDRG1 on the expression of integrin-related proteins. Immunostaining was used to comprehensively analyze the in vitro experimental results.

Results

The mRNA and protein levels of NDRG1 were downregulated substantially in gastric cancer, which was inversely correlated with the malignancy of pathological behavior and poor prognosis in gastric cancer. Knockdown of the NDRG1 gene significantly enhanced the proliferation and migration capabilities of gastric cancer cells, whereas overexpression of NDRG1 reduced their metastatic potential and inhibited both migration and proliferation. NDRG1 was found to regulate the expression of fibronectin 1, which in turn influenced the expression of a series of integrins, including αv, α5, β1, and β3. This regulatory mechanism may play a crucial role in the early distant metastasis observed in gastric cancer.

Conclusions

This study demonstrated that NDRG1 could regulate the expression levels of integrins through specific signaling pathways, thereby interfering the adhesive and migratory capacities of gastric cancer cells. NDRG1 could serve as a valuable biomarker for the diagnosis and prognosis of gastric cancer, offering new potential targets for its treatment.
Xpert MTB/RIF Ultra resistant and MTBDRplussusceptible rifampicin results in people with tuberculosis: utility of FluoroType MTBDR and deep sequencing
Authors: Ghebrekristos Yonas , Ahmed Aysha , Beylis Natalie , Singh Sarishna , Opperman Christoffel , Naufal Fahd , Folkerts Megan , Engelthaler David , Auma Erick , Venter Rouxjeane , Booley Ghowa , Metcalfe John , Warren Robin , Theron Grant
Published: October 2024

Background

Xpert MTB/RIF Ultra (Ultra)-detected rifampicin-resistant tuberculosis (TB) is often programmatically confirmed using MTBDRplus. There are limited data on discordant results, including re-tested using newer methods like FluoroType MTBDR (FT-MTBDR) and targeted deep sequencing.

Methods

MTBDRplusrifampicin-susceptible isolates from people with Ultra rifampicin-resistant sputum were identified from a South African programmatic laboratory. FT-MTBDR and single molecule-overlapping reads deep (SMOR;rpoB, inhA, katG) on isolate DNA were done (SMOR reference standard).

Findings

Between 01/04/2021-30/09/2022, 8% (109/1347) of Ultra rifampicin-resistant specimens were MTBDRplus-susceptible. Of 89% (97/109) isolates with a sequenceablerpoB, SMOR resolved most in favour of Ultra [79% (77/97)]. Sputum with lower mycobacterial load was associated with Ultra false-positive resistance [46% (11/24) of “very low” Ultras had false-resistance vs. 12% (9/73; p=0.0004) in those ≥“low”], as were Ultra heteroresistance calls (all wild type probes, ≥1 mutant probe) [62% (23/37 vs. 25% (15/60) for Ultra without heteroresistance calls; p=0.0003]. Of the 91% (88/97) of isolates successfully tested by FT-MTBDR, 55% (48/88) were FT-MTBDR rifampicin-resistant and 45% (40/88) susceptible, translating to 69% (47/68) sensitivity and 95% (19/20) specificity. In the 91% (99/109) of isolates withinhAandkatGsequenced, 62% (61/99) were SMOR isoniazid-susceptible.

Interpretation

When Ultra and MTBDRplusrifampicin results are discordant, Ultra is more likely to be correct and FT-MTBDR agrees more with Ultra than MTBDRplus, however, lower load and the Ultra heteroresistance probe pattern were risk factors for Ultra false rifampicin-resistant results. Most people with Ultra-MTBDRplusdiscordant resistance results were isoniazid-susceptible. These data have implications for drug-resistant TB diagnosis.

Funding

This work was supported by European & Developing Countries Trial Partnerships (EDCTP2; RIA2020I-3305, CAGE-TB), National Institutes of Health (D43TW010350; U01AI152087; U54EB027049; R01AI136894).
A mixed-methods analysis of the implementation of a new community long-COVID service during the 2020 pandemic: learning from practice
Authors: Williams Stefanie L , Beadle Emily , Williams Paul , Master Harsha , Casarin Annalisa
Published: October 2024

Introduction

The rapidly increasing prevalence of long-COVID (LC), the multisystem complexity of the condition and high patient symptom burden, necessitated an immediate need to develop new clinics for assessment and management. This article reports on the rapid implementation of a reactive and responsive LC care pathway. We mapped patients’ journey through this pathway, identifying the services that were activated according to prevalent symptoms, and assessed the barriers and facilitators to its implementation and delivery, from the perspective of health care professionals (HCPs) and LC patients using the Theoretical Domains Framework (TDF).

Methods

Mixed methods study, including retrospective quantitative cross-sectional analysis of patient data and semi-structured qualitative interviews. One hundred and sixteen patients who attended long-COVID clinic in Hertfordshire, UK, in the first 5 months of its existence, consented for their data to be analysed for the quantitative study. Six HCPs and five patients participated in semi-structured interviews.

Results

Patients were referred into the service an average of 5.75 months post initial COVID-19 infection. 82% of patients required onward referral to other HCPs, most commonly pulmonary rehabilitation, chronic fatigue specialists, and the specialist COVID-19 Rehab general practitioner embedded within the service. Patients reported having rehabilitation needs, moderate depression and anxiety, and difficulties performing usual activities of daily living at point of care. The TDF domains most relevant to the implementation of the LC pathway werebeliefs about capabilities, environmental context and resources, knowledge, and reinforcement.

Discussion

Our study provides novel insight into the development of a reactive multidisciplinary care pathway. Key drivers for successful implementation of LC services were identified, such as leadership, multidisciplinary teamwork, transferable skills, and knowledge exchange. Barriers to rapid set up of the service included funding constraints and the rapid evolution of an emergency context.
AtTOC159 Receptors are Targeted to the Chloroplast Outer Membrane by a β-Signal and Galactolipid-Specific Transit Peptide-Like Sequence at the C-Terminus
Authors: Fish Michael , Saudan George , Chuong Simon D. X. , Jelokhani-Niaraki Masoud , Smith Matthew D.
Published: October 2024

Chloroplasts, the essential organelles responsible for photosynthesis, rely on the coordinated import of nuclear-encoded proteins for their biogenesis and function. TOC159 receptors are critical components of the translocon at the outer membrane of chloroplasts (TOC complex), responsible for recognizing and importing preproteins. However, the mechanisms by which TOC159 itself is targeted and integrated into the chloroplast outer envelope are only partially understood. In this study, we explore the structural aspects of the C-terminal membrane (M) domain ofArabidopsis thalianaTOC159, with a focus on its role in chloroplast outer envelope targeting and TOC complex integration. Structural predictions using AlphaFold and far-UV circular dichroism (CD) spectroscopy experiments suggested that the M domain forms an integral β-barrel that fuses with the β-barrel of TOC75, forming a hybrid channel at the chloroplast outer envelope. We identified a novel bi-partite targeting signal within the M domain, composed of a C-terminal β-signal with the consensus sequence G-Q-Φ-[ST]-Φ-[RK]-X-[SN]-[ST] and a transit peptide (TP)-like sequence. Using fluorescence microscopy and mutational analyses, we demonstrated that the β-signal is essential for chloroplast targeting, while the TP-like sequence enhances targeting ejiciency. Furthermore, CD spectroscopy and Langmuir-Blodgett trough experiments revealed that the TP-like sequence preferentially interacts with galactolipids unique to the chloroplast outer membrane, particularly sulfoquinovosyl diacylglycerol (SQDG), facilitating chloroplast outer envelope targeting specificity. Overall, our findings provide a deeper understanding of TOC159 receptor targeting mechanisms, TOC complex biogenesis and highlight the broader significance of lipid-mediated targeting in intracellular protein trajicking. These results pave the way for future studies on the role of TP-like sequences in chloroplast outer membrane protein targeting and other novel targeting pathways more generally.
Differential gene expression analysis identifies a group of defensin like peptides fromSolanum chacoenseovules within vitropollen tube attraction activity
Authors: Liu Yang , Joly Valentin , Sabar Mohamed , Matton Daniel Philippe , Morse David
Published: October 2024

Solanum chacoenseis a wild potato species with superior genetic resistance to diseases and pests that has been extensively used for introgression into cultivated potato. One determinant of crossing success between wild and cultivated potato species is the effective ploidy of the parents. However, little is known about whether other, prezygotic level, breeding barriers exist. We hypothesize ovular pollen tube guidance may serve as such a checkpoint. Tests for species-specific pollen tube guidance using semi-in vivoassays suggested a positive correlation between species-specificity and taxonomic distance. RNA-seq of ovules hand dissected from wild type plants at anthesis and two days before anthesis, as well as from afrk1mutant lacking an embryo sac identified a list of 284 embryo sac-dependent genes highly expressed in mature ovules and poorly expressed in all other samples. Among these are 17Solanumchacoensecysteine-richproteins (ScCRPs), considered to be good candidates since CRPs are ovular pollen tube attractants in other species. A group of three cloned and purified ScCRP2 sequences belonging to the DEFL protein family showed moderate levels ofin vitropollen tube attraction activity in functional assays. We conclude that ScCRP2s are good candidates for ovular pollen tube guidance inS. chacoense.

Highlights

This work introduces key characteristics of pollen tube guidance inSolanum chacoense, identifies candidate attractants through transcriptome subtraction and reportsin vitropollen tube attraction activity for three defensin-like peptides.
Breaking Free: Development of Circular AAV Cargos for Targeted Seamless Integration in the Liver
Authors: Estes Brett J.G. , Gandhi Nisha , Von Stetina Jessica , Paudel Dev , Nan Angela X. , Amin Parth , Rose Joshua , Wu Shuai , Zheng Kangni , Zhang Yijun , Cochrane Jesse C. , Finn Jonathan D. , Xie Jenny
Published: October 2024

Recent advancements in gene insertion have shifted from DNA repair-dependent mechanisms to more precise approaches, enhancing safety and predictability for editing outcomes. Integrase-mediated programmable genomic integration (I-PGI) utilizes a DNA cargo to insert transgenes in a targeted, unidirectional manner.In vivo, where nuclear delivery of DNA is challenging, adeno-associated virus (AAV) can act as the cargo vector. While I-PGI does not require DNA double-stranded breaks (DSBs) for activity, linear DNA cargo, like AAV, stimulates DNA end joining activity after integration. To mitigate potential risks from DSBs with linear viral cargo, we developed two circular genome types capable of seamless gene insertion in non-dividing cells. We first harnessed the orthogonal property of large serine integrases to produce circle-AAV (cAAV) from linear viral genomes in cells. cAAV demonstrated faithful seamless cargo integration in primary human hepatocytes (PHH) and robust DSB-free insertion structuresin vivo. We then investigated the delivery of packaged circular AAV cargo (AAV.AD), which eliminates the need for enzymatic manipulation in the cell. AAV.AD proved to be a viable cargo for I-PGI, exhibiting functional integration in PHH andin vivo, that resulted in seamless insertion structures. Together, these findings provide the first reported evidence of DSB-free programmable genomic integration using integrase and AAV cargo, addressing a previously unrecognized challenge in the field.
Harnessing Smartphone RGB Imagery and LiDAR Point Cloud for Enhanced Leaf Nitrogen and Shoot Biomass Assessment - Chinese Spinach as a Case Study
Authors: Harikumar Aravind , Shenhar Itamar , Pebes-Trujillo Miguel R. , Qin Lin , Moshelion Menachem , He Jie , Ng Kee Woei , Gavish Matan , Herrmann Ittai
Published: October 2024

Accurate estimation of leaf nitrogen concentration and shoot dry-weight biomass in leafy vegetables is crucial for crop yield management, stress assessment, and nutrient optimization in precision agriculture. However, obtaining this information often requires access to reliable plant physiological and biophysical data, which typically involves sophisticated equipment, such as high-resolution in-situ sensors and cameras. In contrast, smartphone-based sensing provides a cost-effective, manual alternative for gathering accurate plant data.

In this study, we propose an innovative approach for estimating leaf nitrogen concentration and shoot biomass by integrating smartphone RGB imagery with Light Detection and Ranging (LiDAR) data, usingAmaranthus dubius(Chinese spinach) as a case study. The influence of varying nitrogen dosages on individual spectral and structural features derived from smartphone RGB imagery and LiDAR data was modeled. Additionally, the spectral indices from RGB imagery and structural indices from LiDAR data were combined to model both leaf nitrogen concentration and shoot biomass.

The performance of crop parameter modeling was evaluated using support vector regression, random forest regression, and lasso regression. Results demonstrate that the combined use of smartphone RGB imagery and LiDAR data can accurately estimate leaf total reduced nitrogen concentration, leaf nitrate concentration, and shoot dry-weight biomass, with average relative root mean square errors as low as 0.06, 0.16, and 0.05, respectively. Furthermore, the optimal nitrogen dosage for maximizing biomass yield in Chinese spinach was also estimated using the smartphone data. This study lays the groundwork for smartphone-based estimate leaf nitrogen concentration and shoot biomass, supporting accessible precision agriculture practices.
EGF and IgA in maternal milk, donor milk and milk fortifiers in the Neonatal Intensive Care Unit setting
Authors: Tamar Christian , Greenfield Kara , McDonald Katya , Levy Emily , Brumbaugh Jane , Knoop Kathryn
Published: October 2024

Human milk contains a variety of factors that positively contribute to neonatal health, including epidermal growth factor (EGF) and immunoglobulin A (IgA). When maternal milk cannot be the primary diet, maternal milk alternatives like donor human milk or formula can be provided. Donor human milk is increasingly provided to infants born preterm or low birth weight with the aim to supply immunological factors at similar concentrations to maternal milk. We sought to assess the concentrations of human EGF and IgA in the diet and stool of neonates between exclusive maternal milk, donor human milk, or formula-based diets. Using a prospective cohort study, we collected samples of diet and stool weekly from premature and low birth weight neonates starting at 10 days postnatal through five weeks of life while admitted to a neonatal intensive care unit (NICU). Compared to formula, there was significantly more EGF in both the milk and the stool of the infants fed human milk. Donor milk pooled from multiple donors contained similar concentrations of EGF and IgA to maternal milk, which was also significantly more compared to formula diets. Maternal milk fortified with fortifier derived from human milk contained significantly more EGF and IgA compared to unfortified maternal milk or maternal milk fortified with fortifier derived from bovine milk. Further analysis of human milk-derived fortifiers confirmed these fortifiers contained significant concentrations of EGF and IgA, contributing to an increased concentration of those factors when added to maternal milk compared to bovine milk-derived fortifiers. These findings illustrate how the choice of diet for a newborn, and even how that diet is modified through fortifiers or pasteurization before ingestion, impacts the beneficial biomolecules the infant receives from feeding.
Semi-supervised Contrastive Learning for Bioactivity Prediction using Cell Painting Image Data
Authors: Bushiri Pwesombo David , Beese Carsten , Schmied Christopher , Sun Han
Published: October 2024

Morphological profiling has recently demonstrated remarkable potential for identifying the biological activities of small molecules. Alongside the fully supervised and self-supervised machine learning methods recently proposed for bioactivity prediction from Cell Painting image data, we introduce here a semi-supervised contrastive (SemiSupCon) learning approach. This approach combines the strengths of using biological annotations in supervised contrastive learning and leveraging large unannotated image datasets with self-supervised contrastive learning. SemiSupCon enhances downstream prediction performance of classifying MeSH pharmacological classifications from PubChem, as well as mode of action and biological target annotations from the Drug Repurposing Hub across two publicly available Cell Painting datasets. Notably, our approach has effectively predicted the biological activities of several unannotated compounds, and these findings were validated through literature searches. This demonstrates that our approach can potentially expedite the exploration of biological activity based on Cell Painting image data with minimal human intervention.
Origin of Ewing sarcoma by embryonic reprogramming of neural crest to mesoderm
Authors: Vasileva Elena , Arata Claire , Luo Yongfeng , Burgos Ruben , Gage Crump J. , Amatruda James F.
Published: October 2024

Ewing sarcoma is a malignant small round blue cell tumor of bones and soft tissues caused by chromosomal translocations that generate aberrant fusion oncogenes, most frequently EWSR1::FLI1. The cell of origin and mechanisms of EWSR1::FLI1-driven transformation have remained unresolved, largely due to lack of a representative animal model. By developing a zebrafish Ewing sarcoma model, we provide evidence for a neural crest origin of this cancer. Neural crest-derived cells uniquely tolerate expression of EWSR1::FLI1 and targeted expression of EWSR1::FLI1 in these cells generates Ewing sarcomas. Single-cell analysis of tumor initiation shows that EWSR1::FLI1 reprograms neural crest-derived cells to a mesoderm-like state, strikingly resulting in ectopic fins throughout the body. By profiling chromatin accessibility and genome-wide EWSR1::FLI1 binding, we find that the fusion oncogene hijacks developmental enhancers for neural crest to mesoderm reprogramming during cancer initiation. These findings show how a single mutation profoundly alters embryonic cell fate decisions to initiate a devastating childhood cancer.
Benchmarking HelixFold3-Predicted Holo Structures for Relative Free Energy Perturbation Calculations
Authors: Furui Kairi , Ohue Masahito
Published: October 2024

AlphaFold2 demonstrated remarkable capabilities for protein structure prediction. However, it is limited to downstream tasks, such as ligand docking and free energy calculations, as it cannot predict holo structures with bound ligands. AlphaFold3, a state-of-the-art protein structure prediction model, can predict the binding structures of complexes with proteins, nucleic acids, small molecules, ions, and modified residues with cutting-edge performance. However, AlphaFold3 does not currently provide access to some functions, such as the prediction of protein-ligand complex structures. To reduce the enormous costs in early small molecule drug discovery, verifying the utility of protein-ligand complex prediction methods, such as AlphaFold3, in downstream tasks like free energy perturbation calculations is crucial. In this study, we evaluated HelixFold3, designed to emulate AlphaFold3, in predicting holo and apo structures' complex formations and examined its utility in free energy perturbation calculations. Regarding the complex structure prediction performance of the 8 targets from Wang \etal's FEP benchmark, HelixFold3 showed superior performance to AlphaFold2 and existing methods. Predicting a holo structure rather than an apo structure resulted in higher binding site prediction accuracy. Furthermore, using HelixFold3 predicted structures in practical situations, where binding free energies of all derivatives were estimated, both structures achieved accuracies comparable to crystal structures. Additionally, novel derivatives not included in the training data were accurately predicted, demonstrating that free energy calculations using these novel structures are sufficiently usable.
Tuning and validation of a virtual mechanical testing pipeline for condylar stress fracture risk assessment in Thoroughbred racehorses
Authors: Irandoust Soroush , Whitton R. Christopher , Henak Corinne R. , Muir Peter
Published: October 2024

Condylar stress fracture of the third metacarpal/metatarsal bone (MC3/MT3) in Thoroughbred racehorses is a common catastrophic injury, putting racehorse and jockey safety at risk. Microdamage forms in the distal MC3 and may result in strain elevation and higher risk of stress fracture, directly and through focal osteolysis resulting from the associated process of repair by remodeling in the condylar parasagittal grooves (PSG). Standing computed tomography (sCT) is a practical screening tool for detection of fatigue-induced structural changes, but the clinical interpretation remains subjective. The goal of this study was to develop and validate a sCT-based subject-specific finite element analysis (FEA) pipeline for virtual mechanical testing of the distal MC3. Twelve (n=12) MC3 condyles with availableex vivostrain were selected. Half of the specimens were used for tuning of the Young’s modulus in fatigue sites, and the other half to examine validity of the pipeline for prediction of PSG strain. The tuned model improved prediction of strain and predicted higher strain in bones with PSG lysis over the untuned model, which is an essential feature for a diagnostic screening tool. The presented pipeline is expected to assist clinicians with interpretation of sCT-detectable structural changes and ultimately condylar fracture risk assessment.
Site-specific free energy surface parameters from single-molecule fluorescence measurements of exciton-coupled (iCy3)2dimer probes positioned at DNA replication fork junctions
Authors: Maurer Jack , Albrecht Claire S. , von Hippel Peter H. , Marcus Andrew H.
Published: October 2024

Single-stranded (ss) – double-stranded (ds) DNA replication forks and primer-template junctions are important recognition sites for the assembly and function of proteins involved in DNA replication, recombination and repair. DNA ‘breathing’ – i.e., thermally-induced local fluctuations of the sugar-phosphate backbones and bases – can populate metastable conformational macrostates at positions near such junctions and likely play key roles in the functional interactions of the regulatory proteins that bind at these sites. Recently, Maureret al. (1) performed polarization-sweep single-molecule fluorescence (PS-SMF) studies on exciton-coupled (iCy3)2dimer-labeled ss-dsDNA fork constructs, which revealed that the nucleobases and backbones immediately adjacent to the dimer probes undergo conformational fluctuations on time scales ranging from hundreds-of-microseconds to hundreds-of-milliseconds. The local conformations sensed by the dimer probes consist of four quasi-stable macrostates whose populations and dynamics depend on dimer probe position relative to these junctions. Here we present theoretical analyses of these PS-SMF data that quantify the relative stabilities and activation barriers of the free energy surfaces (FESs) of site-specific DNA ‘breathing’ events at key positions within these junctions. Our results suggest a detailed molecular picture for DNA ‘breathing’ at these positions, thus providing insights into understanding the molecular mechanisms of the proteins that operate at these sites.
Unveiling Humoral and Cellular Immune Responses to SARS-CoV-2 in Head and Neck Cancer: A Comparative Study of Vaccination and Natural Infection in Romania
Authors: Marutescu Luminita , Enea Alexandru , Antoniadis Nefeli-Maria , Neculae Marian , Costea Diana Antonia , Popa Marcela , Dragu Elena , Codrici Elena , Ristoiu Violeta , Galateanu Bianca , Hudita Ariana , Pircalabioru Gratiela Gradisteanu , Filali-Mouhim Abdelali , Lazar Veronica , Chifiriuc Carmen , Grigore Raluca , Ancuta Petronela
Published: October 2024

Background: To fill the knowledge gap regarding the antiviral immunity in oncologic patients, we performed a comparative study on natural/vaccine-induced SARS-CoV-2 immunity in head and neck cancer (HNC) in Romania. Methods: Blood was collected from HNC (n=49) and controls (n=14), stratified as vaccinated (RNA/adenovirus-based vaccines), convalescent, and hybrid immunity. Plasma IgG/IgA antibodies (Abs) against Spike (S1/S2), receptor binding domain (RBD), and nucleocapsid (NC), and cytokines were quantified using the MILLIPLEX; technology. The frequency/phenotype/isotype of RBD-specific B-cells were studied by flow cytometry using tetramers (Tet++). Cell proliferation in response to Spike/NC peptides was monitored by carboxyfluorescein succinimidyl ester (CFSE) assay. A longitudinal follow-up was performed on n=25 HNC. Findings: Levels of S1/S2/RBD-specific IgG/IgA Abs were similarly high in HNC and controls, but significantly increased in convalescent/hybrid versus vaccinated HNC. NC-specific IgG/IgA Abs were only detected in convalescent/hybrid immunity groups. The frequency of Tet++ B-cells in HNC was similar to controls, irrespective of the immunization status, and correlated positively with RBD IgG/IgA Abs and negatively with the time since immunization (TSI). Compared to total B-cells, Tet++ were enriched in CD27+ memory phenotype and IgG/IgA isotype. A linear regression model identified Spike S2 IgG and NC IgA Abs as strong positive predictors of Tet++ frequencies, while IL-6 was a marginally significant negative predictor. Tet++ frequency remained stable at median TSI of 341 versus 117 days, despite a decline in memory phenotype. Interpretation: HNC participants mount efficient and durable SARS-CoV-2 humoral immunity, with RBD-specific IgG/IgA Abs and Tet++ B-cells representing the major immunization outcomes.
Sirtuin2 blockade inhibits replication of Human Immunodeficiency Virus-1 andMycobacterium tuberculosisin macrophages and humanized mice
Authors: Singh Vipul. K. , Mishra Abhishek , Truong Khangy , Bohorquez Jose Alejandro , Sharma Suman , Khan Arshad , Bracher Franz , Zhang Kangling , Endsley Janice , Endsley Mark , Rice Andrew P. , Kimata Jason T. , Yi Guohua , Jagannath Chinnaswamy
Published: October 2024

Coinfections withMycobacterium tuberculosis(Mtb) and HIV-1 present a critical health challenge and require treatment for survival. We found that human M1 macrophages inhibit Mtb growth, while M2 macrophages, characterized by elevated Sirt2 expression, permit Mtb growth. Further, we found that HIV-1 augmented Sirt2 gene expression in MФs. Therefore, we explored the therapeutic potential of sirtuin-modulating drugs in MФs. Sirtinol, a Sirt2 inhibitor, significantly reduced HIV-1 growth in M0, M1, and M2-MФs by >1 log10 over 7 days. Conversely, individual doses of resveratrol and SRT1460, which activate Sirt1, did not affect HIV-1. However, their combination showed a strong synergistic inhibition of HIV-1. The combination of sirtinol with resveratrol was neither synergistic nor antagonistic. Sirtinol upregulatediNOSandATG5mRNA in HIV-1 infected MФs in a phenotype-dependent manner. In a humanized mouse model (Hu-NSG-SGM3) co-infected with Mtb H37Rv and the HIV-1 BAL strain, treatment with sirtinol alone, or in combination with combination antiretroviral therapy (cART), showed promising results; Sirtinol alone reduced Mtb growth, while its combination with cART effectively inhibited HIV-1 replication in the organs. We propose that Sirt2 blockade and Sirt1-activation represent a novel dual therapeutic strategy for treating HIV-1 and Mtb coinfections.
Identification of diagnostic KASP markers for selection of crown rust resistance in oats
Authors: Nguyen Duong T. , Lewis David , Henningsen Eva C. , Mago Rohit , Sperschneider Jana , Dodds Peter N. , Figueroa Melania
Published: October 2024

Oat crown rust, caused byPuccinia coronataf. sp.avenae, poses a significant threat to global oat production (Avena sativaL.). Molecular markers are essential to assist in the integration of multiple resistance genes into a single oat cultivar to achieve genetic resistance durability. Here, we validated previously reported markers for the race-specific resistance genesPc39,Pc45/PcKM,Pc54, andPc68, and developed new KASP markers closely linked to these loci. These markers were subsequently screened across a collection of 150 oat cultivars. Analysis of molecular marker data, pedigree information, and disease resistance profile indicated several oat cultivars likely carryingPc39andPc68. Newly identified carriers ofPc68include the cultivars Galileo and Graza80, while Warrego, Kowari, Possum, Forester, Drummond, Hokonui, Glider, and Culgoa were identified as potential carriers ofPc39. Discrepancies between the previous postulation ofPcgene carriers and our phenotyping and genotyping analysis were also found. For example, the oat line Glider was previously postulated to carryPc58orPc59,but it was positive for thePc39-associated marker and had a similar resistance profile toPc39carriers. These findings underscore the importance of the utilisation of molecular markers in tracking the resistance genes in breeding germplasm.

Key message

This study has developed and validated KASP molecular markers associated with crown rust resistance genesPc39,Pc45/PcKM,Pc54, andPc68that could be used for marker-assisted selection in oats.
The epidemiology of Brucellosis and Q fever in a cross-sectional serosurvey of occupationally exposed groups in peri-urban Lomé, Togo
Authors: Kerr Charlotte L. , Patassi Akouda , Pato Pidemnéwé S. , Guitian Javier , Diop Sylvie Audrey , Mangtani Punam , Nguipdop-Djomo Patrick
Published: October 2024

Background

Brucellaspecies andCoxiella burnetiihave been detected in livestock populations in Togo. Populations exposed to livestock ruminants through occupation may be at increased risk of infection.

Methods/Principal Findings

A cross-sectional serosurvey was conducted in 108 abattoir and 81 dairy farm workers (from 52 dairy farms) in peri-urban Lomé, Togo in 2019-2020. Sera were tested using the Rose Bengal plate agglutination test (RBT) and the indirect Brucella IgG Enzyme-Linked Immunosorbent Assay (ELISA) for Brucella, and the IgG ELISA forCoxiella burnetiiin Phase 1 and in Phase 2. Fresh bulk milk from farms were tested using an indirect milk ELISA for Brucella IgG.

Eighteen workers (9.5%, 95% CI 5.5-16.0) were Brucella seropositive. Twenty-eight percent (95% CI 22.5-34.3) of workers were seropositive forC. burnetii. Twenty of fifty-one farms which gave milk samples tested positive for Brucella (39.2%, 95% CI 26.6 - 53.4%).

Farmworkers had nearly twice the odds of being Brucella seropositive compared to abattoir workers (OR 1.93, 95% CI: 0.94-3.93, p=0.07). In farmworkers, working on farms with animal ill health, a positive milk test, participating in small animal husbandry and assisting with cattle abortion were all associated with increased odds of seropositivity. Workers who consumed unboiled milk at least every month were more likely to be seropositive (OR 3.79, 95% CI: 2.34-6.13, p<0.001) while participants who consumed fermented milk and cheese had greater odds of being seropositive forC.burnetii(OR 1.59, 95% CI: 1.26-2.00, p<0.001 and OR 1.70, 95% CI: 0.97-2.98, p=0.07 respectively).

Conclusions

Livestock workers in peri-urban Lome have been exposed to bothBrucellaandCoxiella burnetiidbacteria. The widespread consumption of unboiled dairy products and lack of PPE use is of concern as both dairy consumption and participation in animal husbandry activities have been seen to increase odds of seropositivity for both pathogens.

Author summary

Human and animal health are inextricably linked, particularly for those who live and work closely with animals. Brucellosis and Q fever are two zoonotic diseases transmitted through animal contact and dairy product consumption, which cause non-specific fevers and for which diagnostic tests are lacking in many LMIC contexts. Previous studies have shown that both bacteria circulate in livestock in Togo. We undertook a survey in dairy farm and abattoir workers in peri-urban Lomé, Togo, and found that 9.5% and 28% of workers were seropositive forBrucellaandC.burnetiirespectively. We found that risk factors included animal husbandry practices and consumption of dairy products. Mitigating practices such as the use of PPE and boiling milk are simple ways that livestock workers could protect themselves from these and other zoonotic disease.
Untangling age and menopausal status reveals no effect of menopause on white matter hyperintensity volume
Authors: Wezel Denise , Parent Olivier , Costantino Manuela , Sifi Lina , Pigeau Grace , Gervais Nicole J. , McQuarrie Ann , Maranzano Josefina , Devenyi Gabriel Allan , Dadar Mahsa , Chakravarty M. Mallar
Published: October 2024

Background and objectives

White matter hyperintensities (WMHs) are radiological abnormalities indicative of cerebrovascular dysfunction associated with increased risk for cognitive decline and increase in prevalence in older age. However, there are known sex-differences as older females harbour higher WMH burden than males. Some have hypothesized that the increase in this dementia-related risk factor is related to the menopausal transition.

Methods

To untangle the effects of age and menopause, we leveraged a large sample from the UK Biobank (n = 10,519) to investigate differences in WMH volumes across the menopausal transition using a strict age-matching procedure.

Results

Surprisingly, we find increased WMH volumes in premenopausal women compared to postmenopausal women when simply correcting for age with linear models, but we find no effect in the age-matched sample. Menopause-related characteristics, such as age at menopause or hormone replacement therapy, did not replicate previous literature reporting an association with WMH volumes. Cardiovascular lifestyle variables, such as smoking and blood pressure, were significant predictors of WMH volume in the full sample without age-matching. These effects varied by menopausal status only for days of moderate activity.

Discussion

In sum, our findings in a well-powered study suggest that previous reports of menopause-related differences in WMH burden are potentially confounded by age. We further show that the effect of positive lifestyle factors on brain health, as indexed with WMH burden, generally does not change after menopause. Factors other than the menopausal transition are likely at play in explaining the difference in WMH burden between males and females in later life.