bluuebunny/crossref_metadata_2025 huggingface dataset:
Seasonal Variations and Challenges in Estimating Populations and Identifying Species of Korean Ungulates Using Drone-Derived Thermal Orthomosaic Maps
Authors: Kim Jinhwi , Woo Donggul
Published: January 2025

Thermal drones offer significant time and labor savings in estimating wild ungulate populations. Among available methods, Thermal Infrared (TIR) orthomosaic maps have shown potential for animal counting and population estimation. In this study, we assessed the feasibility of counting Korean ungulates in March and June using TIR and RGB orthomosaic maps, aiming to compare population estimates across season and identify the appropriate Ground Sampling Distance (GSD). The average estimated population was 25.3 ± 4.2 individuals (range: 18–29) in March and 28.2 ± 9.1 individuals (range: 14–40) in June. The average counting error was 4.1 (95% CI: 1.3–6.9) across the orthomosaic maps, with no substantial difference between March and June (P = 0.75). Counting errors increased when RGB GSD exceeded 2.5 cm/pix and TIR GSD exceeded 7.5 cm/pix, suggesting that these thresholds may guide future GSD selection for more accurate population estimates. We measured 149 thermal marks for species identification across three ungulate species. MANOVA revealed strong effects of species (P < 0.001) and posture (P < 0.001) on body measurements, but variations in posture limited the effectiveness of thermal mark measurements for species identification. This issue was especially prominent in lying positions, where species overlap occurred. Further data collection on thermal measurements from TIR orthomosaic maps, particularly from a perpendicular angle and across diverse environments and postures, could improve the accuracy of thermal methods for species identification.
High-dose DFMO alters protein translation in neuroblastoma
Authors: Franson Andrea T. , Liu Kangning , Vemu Rohan , Scadden Elizabeth , Li Yimei , Vu Annette , Hogarty Michael D.
Published: January 2025

DFMO has been studied as a cancer therapeutic at doses ranging from 500-9,000 mg/m2/day. Lower doses are favored for cancer prevention studies while higher doses, often with chemotherapy, are studied in refractory cancers. DFMO inhibits the rate-limiting enzyme in polyamine synthesis, ornithine decarboxylase (ODC), an oncogene transcriptionally regulated by MYC.MYCgenes are the principal oncogenic drivers of neuroblastoma, andODC1is co-amplified in a subset with dismal outcome, so DFMO is a rational therapeutic candidate. Low-dose DFMO has now been FDA-approved for high-risk patients though the mechanisms for its anti-tumor activity, and the exposures required to elicit them, remain obscure. We sought to define biomarkers of activity across exposures achieved in the clinic with low through high-dose DFMO. Polyamines support protein translation by providing spermidine, which is essential to hypusinate (and activate) the elongation factor, eIF5A. Selective binding of polyamines with tRNA and rRNA provide eIF5A-independent mechanisms of translation support. We show that low-dose DFMO does not extend survival in mouse modelsin vivonor alter translation biomarkersin vitro. High-dose DFMO consistently extends survival in neuroblastoma models, and, in a subset of neuroblastoma cell lines, inhibits eIF5A hypusination and global translation at achievable concentrations. However, the concentration required to engage these changes across many cell lines exceeded that achievable even with high-dose DFMO. No correlation was seen amongMYCNand/orODC1copy number and sensitivity to DFMO. Combining high-dose DFMO with additional agents to further deplete tumor polyamines may be necessary to fully engage polyamine-depletion effects on tumors, and more granular measures of translation, including codon-resolution ribosome profiling, may be required to define these effects.

STATEMENT OF TRANSLATIONAL RELEVANCE

Low-dose DFMO is approved by the FDA for the treatment of neuroblastoma. The depletion of tumor polyamines has been shown to have activity against tumors with activatedMYCsignaling, like neuroblastoma, yet the degree of polyamine depletion required, the mechanisms by which this impedes tumor progression, and the DFMO exposures required to enable these are poorly understood. Here we evaluate alterations in protein translation as putative mechanisms for DFMO activity. Translation biomarkers and colony formation can be inhibited by DFMOin vitroat exposures achievablein vivowith high-dose DFMO. Similarly, high-dose DFMO, but not low-dose DFMO, extends neuroblastoma-prone mouse survival. These findings support studying DFMO at higher doses and in therapeutic combinations that further augment polyamine depletion within tumors.
Efficacy of Deferoxamine Mesylate in Serum and Serum-Free Media: Adult Schwann Cell Survival Following Hydrogen Peroxide Induced Cell Death
Authors: Ma Yee H.E. , Putta Abhinay R. , Chan Cyrus H. H. , Vidman Stephen , Monje Paula , Plant Giles W.
Published: January 2025

Schwann cell (SC) transplantation shows promise in treating spinal cord injury as a pro-regenerative agent to allow host endogenous neurons to bridge over the lesion. However, SC transplants face significant oxidative stress facilitated by ROS in the lesion leading to poor survival. Deferoxamine Mesylate (DFO) is a neuroprotection agent shown to reduce H2O2induced cell death in serum containing conditions, here we show that DFO is not necessary to induce neuroprotection under serumfree conditions by cell survival quantification and phenotypic analysis via immunohistochemistry, Hif1a and collagen IV quantification via whole cell corrected total cell fluorescence, and cell death transcript changes via RT-qPCR. Our results indicate survival of SC regardless of DFO pretreatment in serum-free conditions and an increased survival facilitated by DFO in serum containing conditions. Furthermore, our results showed strong nuclear expression of Hif1a in serum-free conditions regardless of DFO pretreatment and a nuclear expression of Hif1a in DFO treated SCs in serum conditions. Transcriptomic analysis reveals upregulation of autophagy transcripts in SCs grown in serum-free media relative to SCs in serum conditions, with and without DFO and H2O2. Thus, indicating a pro-repair and regenerative state of the SCs in serum free conditions. Overall, results indicate the protectiveness of chemically defined medium in enhancing SC survival against ROS induced cell deathin vitro.
Nanodomain distribution and function of PIN-FORMED auxin efflux carriers in the plasma membrane of tobacco cells are defined by their interactions with the cell wall
Authors: Stelate Ayoub , Malinska Katerina , Tihlarikova Eva , Muller Karel , Vaculikova Roberta , Knirsch Martina , Vondrakova Zuzana , Vlcak Erik , Retzer Katarzyna , Neubergerova Michaela , Pleskot Roman , Harant Karel , Filimonenko Vlada , Schwarzerova Katerina , Nedela Vilem , Petrasek Jan
Published: January 2025

Plant development is under the morphogenic control of auxin. In addition to biosynthesis and metabolism, auxin concentration gradients are maintained by directional intercellular transport via PIN-FORMED (PIN) auxin efflux carriers. Although the structure-function properties of PINs have been described, it is still unclear whether individual members of PIN family could localize differently within the plasma membrane (PM) and whether their nanodomain distribution defines their function. To address this, we used cultured tobacco cells (Nicotiana tabacum L., cv. BY-2) and revealed by RNA-seq and RT-qPCR the cell stage-specific presence of transcripts of tobacco PIN homologs. We used high-resolution light microscopy and two independent immunoelectron microscopy techniques in cell lines expressing functional GFP-tagged inducible versions of NtPIN11T, NtPIN2T and NtPIN3bT. We show that NtPINs are distributed within specific PM nanodomains and that removal of the cell wall alters their appearance. By a series of in vivo microscopic observations, we provide evidence that NtPIN11T is the most homogenously distributed and the least mobile NtPIN. Pharmacological treatments suggested that the immobilization of NtPIN11T depends on the actin and microtubular cytoskeleton and the cell wall composition. Using comparative co-immunoprecipitation (co-IP) analysis of isolated membrane fractions for all three NtPINs we finally identified several novel interaction partners indicating a preferential association of NtPIN11T with cell wall GPI-anchored arabinogalactan proteins. In conclusion, our results suggest a model in which specific immobilization of PINs through interactions with the cell wall affects their function.
Eg5 Inhibitor SB743921 Causes p53-Dependent Cell Cycle Arrest, Senescence and Death in Tumor Cells
Authors: Abramenko Iaroslav E. , Khamidullina Alvina I. , Kiryukhina Tamara A. , Tvorogova Anna V. , Pavlenko Nataliya G. , Bruter Alexandra V. , Tatarskiy Victor V.
Published: January 2025

Mitotic inhibitors, such as Vinca alkaloids and taxanes, are one of the most effective chemotherapeutic agents used in the clinic. Despite their advantages, there are drawbacks to their use – primarily development of resistance and a high rate of side-effects, including damage to non-proliferating tissues. A range of new inhibitors targeting mitosis, whose activity does not depend on the binding to tubulin, are currently tested in clinical trials. Among such agents, inhibitors of Eg5 kinesin are highly promising due to their high activity and specificity. Here we show that compared to other drugs that target mitosis, an Eg5 inhibitor, SB743921, preferentially eliminatesTP53-mutated cells and induces irreversible senescence, even after the drug washout, regardless of the p53 status. These effects are not defined by the immediate block of mitosis where SB743921 and a clinically used mitotic inhibitor Ixabepilone induce similar rates of mitotic arrest, apoptosis and induction of p53 and p21, but rather a long-term reaction, with absence of proteins required for replication, such as Cyclin A, E2F1, pRB. While after the washout Ixabepilone-treated cells can exit senescence and resume proliferation, cells treated with SB743921 did not exit the senescent state and did not resume proliferation as based on SA-β-galactosidase staining and EdU incorporation. The remaining senescent cells were effectively eliminated by Bcl2/Bcl-xL/Bcl- w inhibitor ABT-263, showing a potential of the combinational therapy with senolytic drugs. In total, we show the capacity of Eg5-targeting drugs for therapy of high-riskTP53-mutated tumors, which are potentially resistant to clinically approved mitotic inhibitors.
TIME-CoExpress: Temporal Trajectory Modeling of Dynamic Gene Co-expression Patterns Using Single-Cell Transcriptomics Data
Authors: Yang Shuyi , Bussing Anderson , Marra Giampiero , Brinkmeier Michelle L. , Camper Sally A. , Davis Shannon W. , Ho Yen-Yi
Published: January 2025

The rapid advancements of single-cell RNA sequencing (scRNAseq) technology provide high-resolution views of transcriptomic activity within a single cell. Most routine analyses of scRNAseq data focus on individual genes; however, the one-gene-at-a-time analysis is likely to miss meaningful genetic interactions. Gene co-expression analysis addresses this issue by identifying coordinated gene expression changes in response to cellular conditions, such as developmental or temporal trajectory. Identifying differential co-expression gene combinations along the cell temporal trajectory using scRNAseq data can provide deeper insight into the biological processes. Existing approaches for gene co-expression analysis assume a restrictive linear change of gene co-expression. In this paper, we propose a copula-based approach with proper data-driven smoothing functions to model non-linear gene co-expression changes along cellular temporal trajectories. Our proposed approach provides flexibility to incorporate characteristics such as over-dispersion and zero-inflation rate observed in scRNAseq data into the modeling framework. We conducted a series of simulation analyses to evaluate the performance of the proposed algorithm. We demonstrate the implementation of the proposed algorithm using a scRNAseq dataset and identify differential co-expression gene pairs along cell temporal trajectory in pituitary embryonic development comparingNxn−/−mutated versus wild-type mice.
Bioengineered visible polymeric mesh to enhance urogynaecological health
Authors: Houshyar Shadi , Quigley Anita , Cole Ivan , Yin Hong , Zizhou Rumbidzai E , Saha Tanushree , Pirogova Elena , Yeung Justin M , Mohsenipour Mitra , Mirabedini Azadeh , Subejano Edden , Shindler Anya E , Wood Jennifer L , Franks Ashley E , Hill-Yardin Elisa L
Published: January 2025

Pelvic floor disorders, including pelvic organ prolapse and stress urinary incontinence, are prevalent health concerns, affecting approximately 50% of females over their lifetime, with about 75% of women over 65 years of age being impacted. Traditional surgical interventions, such as transvaginal mesh implants, have led to numerous complications, resulting in their prohibition in several countries. This study introduces an innovative composite mesh designed to mitigate these issues by combining polymethylmethacrylate and thermoplastic polyurethane, further enhanced with iodine-doped carbon nanoparticles to enable visibility via medical imaging. The mesh is coated with 2-methacryloyloxyethyl phosphorylcholine polymer to prevent protein adsorption and promote tissue regeneration. In vitro studies showed high cell viability and low protein adsorption, indicating excellent biocompatibility. Implantation of mesh (with or without iodine) in mice revealed no adverse effects on overall animal health. Mouse spleen weight (an indicator of inflammation) was similar between groups; however, levels of some cytokines (i.e., IL-10, IL-17A and GM-CSF) were elevated following implantation of iodinated mesh in mice suggesting that further refinement of the composite mesh is required. Analysis of the fecal microbiome, which is correlated with physiological states, showed that sham and iodinated mesh implant groups maintained consistent microbial profiles with stable diversity (richness and evenness) measures over time. In contrast, the non-iodinated mesh group exhibited decreased species richness post mesh implantation, likely due to a distinct starting microbiome composition prior to implantation. This research is envisaged to contribute to a safer and more effective solution for treating pelvic floor disorders, providing non-invasive post-implantation monitoring and enhanced mechanical compatibility of surgical mesh with native tissue. Our findings demonstrate that this composite mesh possesses mechanical properties that closely mimic human tissue, ensuring biocompatibility, strength, and flexibility without stimulating significant inflammatory or foreign body responses.
Depicting pathogenesis of osteomyelitis by single cell RNA-sequencing and an involvement ofMorrbidin the autoinflammatory disease
Authors: Huo Qingran , Ding Jiayu , Zhou Hongxi , He Hang , Cai Lorie Chen , Liu Jingjing , Dong Ge , Cai Zhigang
Published: January 2025

Autoinflammatory diseases (AIDs) are defined as abnormal activation of the innate immune system leading to spontaneous and uncontrolled inflammation. The AIDs affect bone tissue and lead to chronic recurrent multifocal osteomyelitis (CRMO). However, the etiology and treatment of CRMO remain elusive. A mouse strain,Pstpip2cmo/cmo(cmo:chronic multifocal osteomyelitis), exhibits phenotypic characteristics similar to human CRMO.Morrbidis a long non-coding RNA gene and has been indicated in leukemogenesis in our previous studies. In this study, we demonstrated thatMorrbidandPstpip2are co-expressed in mature myeloid cells and hypothesized a role ofMorrbidin osteomyelitis. ThePstpip2−/−mice have the same phenotype asPstpip2cmo/cmo,mimicking CRMO, while loss ofMorrbidinPstpip2−/−mice significantly inhibited the initiation and progression of CRMO symptoms, as well as the dysregulated activation of myeloid cells and the excessive release of inflammatory cytokines. Furthermore, single-cell RNA-sequencing (scRNA-seq) analysis from thePstpip2−/−mice and the compound mutant mice supports that reduction of osteoclasts and inflammatory cells caused byMorrbidloss. The study systematically profiles the etiology of CRMO by scRNA-seq and warrants that inhibiting the lifespan of inflammatory myeloid cells by targetingMorrbidis an effective therapeutic strategy for osteomyelitis.

Highlights

We generated a frameshift mutant mouse strainPstpip2−/−, which have a classic CRMO-like phenotype as same asPstpip2cmo/cmoand could be used for testing various anti-inflammation perturbations.

Loss ofMorrbidsignificantly inhibited the autoinflammatory symptoms inPstpip2−/−mice, suggesting thatMorrbidis a novel target for mitigating CRMO.

scRNA-seq analysis of the affected bone marrow cells inPstpip2−/−revealed the abnormalities of osteoclasts (OC), neutrophils (NE) and granulocyte macrophage progenitors (GMP) in both their fractions and inflammatory activities.

Upon loss ofMorrbid, we observed reduced composition and proliferation of OC and decreased activity ofNfkb2andRelain the compound mutants.
E2F1 Suppresses EBV Lytic Reactivation through Cellular and Viral Transcriptional Networks
Authors: Biswas Joyanta , Ali SK Asif , Malik Samaresh , Nag Subhadeep , Mukherjee Piyali , Saha Abhik
Published: January 2025

Latent EBV infection is causally associated with various B-cell malignancies, while periodic lytic-cycle replication is essential for sustaining viral progeny. Lytic cycle induction represents a promising therapeutic strategy for EBV-associated neoplasms. Therefore, uncovering the mechanisms that regulate EBV lytic-cycle reactivation is pivotal for understanding viral pathogenesis and advancing novel therapies. Our genome-wide transcriptomic analysis reveals that E2F1 expression is transcriptionally activated during EBV latent infection in B-lymphocytes but significantly suppressed during lytic cycle reactivation. While ectopic E2F1 expression suppresses lytic replication, E2F1 depletion markedly accelerates this process. Mechanistically, we establish that E2F1 and the lytic transactivator BZLF1 form a negative transcriptional feedback loop, tightly controlling viral lytic replication. Furthermore, E2F1 positively regulates c-Myc expression and together they repress the leaky BZLF1 expression during latency. Importantly, c-Myc does not influence E2F1 expression, nor does BZLF1 modulate c-Myc transcription, underlining a distinct regulatory hierarchy. In sum, our findings reveal that EBV tightly controls the latent-to-lytic switch through precise regulation of E2F1 expression, positioning E2F1 as a pivotal regulator of both cellular and viral gene expression.

Synopsis

EBV coordinates the latent-to-lytic switch by sensing E2F1 abundance, which acts as a crucial transcriptional regulator of both cellular and viral gene expressions.

During EBV latent infection, E2F1 promotes c-Myc transcription, and together they suppress EBV lytic cycle transactivator BZLF1 expression.

E2F1 and BZLF1 form a negative feedback loop in order to control each other’s transcriptions.

BZLF1-driven controlled E2F1 expression successively inhibits c-Myc level, thereby stimulating EBV lytic cycle reactivation.

BZLF1 does not regulate c-Myc, nor does c-Myc reciprocally regulate E2F1, emphasizing a unidirectional regulatory hierarchy.
Unmasking Epstein-Barr Role in Gastric Carcinogenesis: A Gene Expression Approach to Virus-Positive Tumors
Authors: Santos da Silva Valeria Cristiane , Pereira Diego , Avelar Daniel de Souza , Silva Jéssica Manoelli Costa da , Mourão Ronald Matheus da Silva , Silva Rubem Ferreira da , Marcon Davi Josué , Magalhães Leandro , Vidal Amanda Ferreira , Neotti Tatiane , Anaissi Ana Karyssa Mendes , Barra Williams Fernandes , Casseb Samir Mansour , Ribeiro dos Santos Andrea Kely Campos , Demachki Samia , Ishak Geraldo , Assumpção Paulo Pimentel de , Moreira Fabiano , Burbano Rommel Mario Rodriguez
Published: January 2025

Human gammaherpesvirus 4 or Epstein-Barr virus (EBV) is an oncogenic virus linked to malignancies like gastric adenocarcinoma. Notably, EBV infection induces genetic and epigenetic modifications that play a crucial role in oncogenesis and tumor progression, underscoring the importance of analyzing viral gene expression in the context of gastric cancer (GC) to elucidate its unique characteristics. This study aimed to perform a molecular characterization of EBV gene expression using next-generation sequencing (NGS). The analysis included human gene expression patterns in EBV-positive and EBV-negative samples and the expression of viral genes in EBV-positive samples. The study received approval from the Ethics and Research Committee of João de Barros Barreto University Hospital under reference number 47580121.9.0000.5634. It utilized 76 tumor tissue samples from patients with gastric cancer who had undergone surgical resection, and both fresh and paraffin-embedded samples were gathered for total RNA sequencing (RNA-seq) and in situ hybridization (ISH). The RNA-seq was conducted in a pair-end manner on the NextSeq® platform (Illumina®, US). The NextSeq® 500 MID Output V2 kit - 150 cycles (Illumina®) were utilized following the manufacturer's instructions. ISH targeting RNA-1 of EBER1 (Y5200, DAKO, Carpinteria) was performed using the automated Dako system.  Molecular characterization was conducted using the Kraken2 software. Subsequently, to elucidate the mechanisms through which EBV may influence gastric cancer, we analyzed the patterns of human gene expression in EBV-positive and EBV-negative samples. Of the 76 samples, 8 were classified as EBV-positive according to the applied methodology. Our analysis identified approximately 834 differentially expressed genes, 92 of which exhibited an AUC > 0.85. These genes are implicated in tumor progression, cellular metabolism, and both innate and adaptive immune responses. Additionally, viral genes expressed in the positive samples were evaluated, and we found manifestations of both lytic phase and latent phase genes. Finally, our study presents an efficient strategy for molecular classification of EBV-positive gastric cancer based on NGS and shows the effects of EBV on human gene expression.
Fexinidazole and Corallopyronin A targetWolbachia-infected sheath cells present in filarial nematodes
Authors: Chappell Laura , Peguero Ricardo , Conner William R , Fowler Sommer , Cooper Brandon , Pfarr Kenneth , Hoerauf Achim , Lustigman Sara , Sakanari Judy , Sullivan William
Published: January 2025

The discovery of the endosymbiotic bacteriaWolbachiaas an obligate symbiont of filarial nematodes has led to antibiotic-based treatments for filarial diseases. While lab and clinical studies have yielded promising results, recent animal studies reveal thatWolbachialevels may rebound following treatment with suboptimal doses of the antibiotic rifampicin. Previous work showed that a likely source of the bacterial rebound in females were dense clusters ofWolbachiain ovarian tissue. The number, size, and density of theseWolbachiaclusters were not diminished despite antibiotic treatment. Here we define the cellular characteristics of theWolbachiaclusters inBrugia pahangi(wBp) and identify drugs that also target them. We have evidence that theWolbachiaclusters originate from newly formed sheath cells adjacent to the ovarian Distal Tip Cells. The dramatically enlarged volume of an infected sheath cell is strikingly similar to endosymbiont-induced bacteriocytes found in many insect species. Ultrastructural analysis reveals that the clusteredWolbachiapresent within the sheath cells exhibit a distinct morphology and form direct connections with the oocyte membrane and possibly the cytoplasm. This includes membrane-based channels providing a connection betweenWolbachia-infected sheath cells and oocytes. We also determined that theWolbachiawithin the sheath cells are either quiescent or replicating at a very low rate. Screens of known antibiotics and other drugs revealed that two drugs, Fexinidazole and Corallopyronin A, significantly reduced the number of clusteredWolbachialocated within the sheath cells.
The expression of IL-35 in the prophase of liver failure and its preliminary exploration for the mechanism of immunoregulation by IL-35 and glucocorticoids
Authors: Wang Yan , Zhang Xin-chi , Xiong Yu-fan , Li Xin-yi , Huang Xiao-ping , Gu Jing , Sun Wei , Chen Li , Gan Jian-he
Published: January 2025

Background and Aims: To determine appropriate dosages for mice models in liver failure prophase and explore IL-35 and cytokine levels. Also, investigate changes in Treg/Th17 ratio, IL-35, and IL-17 in patients with HBV-induced liver failure before and after treatment. Methods: We induced liver failure in mice with different doses of concanavalin and assessed severity through serum biochemistry and pathology. Mice were divided into control, model, IL-35 plasmid, anti-IL-35, and dexamethasone groups. IL-35 and IL-17 expressions in liver tissue were evaluated via immunohistochemistry, fluorescence staining, and ELISA. Treg/Th17 ratio and IL-35 and IL-17 levels in peripheral blood of patients were measured using flow cytometry and ELISA, compared to 22 healthy individuals. Results: The optimal dose for the liver failure model was 20μg/kg concanavalin. The IL-35 plasmid and dexamethasone groups showed significantly lower serum TBil, ALT, AST, IL-4, IL-17, TNF-α, and liver histopathology scores compared to the model group, while the anti-IL-35 group showed higher levels (P<0.05). In HBV-PLF patients, TBil, ALT, and AST significantly decreased, and PTA increased after glucocorticoid treatment (P<0.05). Treg/Th17 ratio was lower in HBV-PLF patients compared to the healthy group (P<0.05), with higher IL-35 and IL-17 levels (P<0.05). Post-treatment, Treg increased and Th17 decreased significantly; IL-17 and Treg/Th17 ratios increased, while IL-35 decreased (P<0.05). IL-35 positively correlated with the Treg/Th17 ratio. Conclusions: 20μg/kg concanavalin proper dose for mice model. IL-35 may protect in liver failure. Glucocorticoids help maintain immune balance, prevent failure, increase ratios and IL-35 in HBV-PLF patients, and IL-35 related to Treg/Th17 balance.
Western red cedar (Thuja plicata) beehives have no impact on honey bee (Apis mellifera) overwintering colony survival or detoxification enzyme expression
Authors: McAfee Alison , Tarpy David R , Foster Leonard J
Published: January 2025

In North America, wooden honey bee hives are most often constructed from pine, but some companies also produce and sell boxes made of western red cedar (Thuja plicata) as a result of its local availability and desirable properties. However, there is debate within the beekeeping community about whether cedar is a safe hive material for bees, since resins within the wood are known to be insecticidal or insect deterrents. There is very little empirical evidence to support or refute these arguments. Here, we recorded health metrics of honey bee nucleus colonies hived in western red cedar and pine boxes (n = 10 each) to determine if the type of wood affects colony outcomes. Colonies were produced and introduced into these boxes in late July, with monitoring continued until the following spring. We found no significant differences in adult bee populations, brood areas, orVarroamite prevalence among colonies hived in cedar versus pine boxes at either the end of summer (September 1st) or spring (April 1st) assessments. Overwintering survival was identical in the two groups at 90%. Hemolymph detoxification enzyme expression differed strongly between callow (day-old) workers and foragers but did not differ with hive material. Overall, we did not find evidence that hiving honey bee colonies in boxes constructed of western red cedar has any negative or positive effect on bee physiology or colony outcomes.
TGR5-mediated Ca2+signaling in cholangiocytes
Authors: Chen Xuanmeng , Al-Shebel Amr , Pebrier Thibault , Tordjmann Thierry , Dellis Olivier
Published: January 2025

The Bile Acid TGR5 receptor is well known to active the cAMP pathways leading to CFTR activation and Cl−ions secretion, needed for bile alkalinization and hydration. However, during cystic fibrosis development, only 10 to 15% of the patients present liver defect due to bile duct disorders, meaning that another process should compensate for the loss of CFTR activity. Interestingly, TGR5 stimulation has also been reported to mobilize Ca2+ions. Using normal human cholangiocytes and cholangiocarcinoma cell lines, we confirmed by using a specific agonist, that TGR5 stimulation induced a Ca2+release from the endoplasmic reticulum and an influx of extracellular Ca2+ions. Next, this Ca2+mobilization allows an ATP (and UTP) release, leading to the activation of P2Y receptors, reinforcing this Ca2+mobilization. This study shows that activation of the BA receptor TGR5 has the capacity to induce the two main intracellular pathways, cAMP and IP3-Ca2+in cholangiocytes. From our data, we speculate that the pathway we described will allow activation of the Ca2+-activated Cl−channels TMEM16A, in parallel to CFTR in non-CF cells, or to compensate in part or in totality the loss of CFTR in CF patients.

HIGHLIGHTS

Bile acid receptor TGR5 induces Ca2+mobilization in cholangiocytes

Ca2+ions come from the endoplasmic reticulum and from the extracellular medium

P2Y receptors are trans-activated by TGR5 and reinforce the Ca2+mobilization

This Ca2+pathways might compensate the CFTR defect in CF patients
Flavodiiron protein activity outcompetes cyclic electron transport when expressed in angiosperm Nicotiana tabacum
Authors: Rizzetto Nicholas , Traverso Eleonora , Sabia Andrea , Fiorin Filippo , Francese Carlotta , Trainotti Livio , Morosinotto Tomas , Alboresi Alessandro
Published: January 2025

In conditions of excess illumination, alternative electron transport pathways in the thylakoid membranes protect the photosynthetic apparatus against damage from eventual over-reduction. Two main pathways downstream of photosystem I (PSI) enable alternative electron flow, mitigating PSI acceptor-side limitation, while contributing to ATP biosynthesis without reducing NADP+ to NADPH: cyclic electron transport (CET) and pseudo-cyclic electron transport (PCET). Flavodiiron proteins (FLV) are crucial enzymes in PCET, found in all photosynthetic organisms but lost during the evolution of angiosperms. The absence of FLV coding sequences in angiosperm genomes raises intriguing questions about their role and function in photosynthetic organisms. Previous studies utilizing heterologous expression have already demonstrated that FLV can function in angiosperms. In this study, Physcomitrium patens FLVA and FLVB coding sequences were stably expressed in wild-type Nicotiana tabacum, a model crop species. Transgenic lines exhibited significantly increased PCET rates, with FLV-dependent electron transport competing for electrons with CET, particularly under sudden increases in light intensity that limited acceptor side limitation. These findings indicate that FLVs are not only active but also play a critical role in protecting from over-reduction the photosynthetic apparatus of Nicotiana tabacum under fluctuating light conditions.
CD33KO-CD33-mesothelin loop CAR design avoids fratricide and improves efficacy of iNK cells against acute myeloid leukemia
Authors: Wang Yao , Zheng Xiujuan , Wang Zhiqian , Xiao Ziyun , Lin Yunqing , Zhang Fan , Liu Yanhong , Liu Pengcheng , Weng Qitong , Zhang Leqiang , Xia Chengxiang , Huang Dehao , Liu Lijuan , Zhu Yanping , Zhang Qi , Qi Hanmeng , Chen Yi , Shen Yiyuan , Zhang Chenyuan , Xu Jiacheng , Zhao Yaoqin , Wu Jiaxin , Wang Tongjie , Zhang Mengyun , Li Minming , Qian Wenbin , Liang Aibin , Du Xin , Yang Wenyu , Chen Qi , Zhu Xiaofan , Hu Fangxiao , Wang Jinyong
Published: January 2025

Acute myeloid leukemia (AML) patients are often older, which brings challenges of endurance and persistent efficacy of autologous CAR-T cell therapies. Allogenic CAR-NK cell therapies may offer reduced toxicities and enhanced anti-leukemic potential against AML. In this study, we designed a novel CD33-mesothelin loop CAR (Loop CAR) and evaluated its anti-tumor efficacy in human umbilical cord blood-derived NK (UCB-NK) cells and human pluripotent stem cell-derived NK (hPSC-iNK) cells. The Loop CAR exhibited superior cytotoxicity against dual-antigen-positive tumor cell lines and primary AML cells. To further avoid fratricide caused by endogenous CD33 expression in NK cells, we established a hPSC-derived cell line via knockout of CD33 gene (CD33KO) and engineered Loop CAR. Rather than enforced expression of exogenous CD16, we generated abundant mature CD33KO-Loop CAR-iNK cells highly expressing endogenous CD16 via an organoid induction approach. This innovative strategy effectively mitigated NK cell fratricide and significantly enhanced CD33 and mesothelin-mediated specific cytotoxicity. Moreover, the CD33KO-Loop CAR-iNK cells demonstrated superior tumor-killing activity in AML xenograft mice and significantly prolonged survival. hPSC-derived CD33KO-Loop CAR-iNK cells possess unique advantages and translational potential for treating AML.
MeQTL Mapping in African American Hepatocytes Reveals Shared Genetic Regulators of DNA Methylation and Gene Expression
Authors: Carver Kathryn , Clark Carolina , Zhong Yizhen , Yang Guang , Mishra Mrinal , Alarcon Cristina , Perera Minoli
Published: January 2025

Methylation quantitative trait loci (meQTL) mapping can provide insight into the genetic architecture underlying the epigenome by identifying single-nucleotide polymorphisms (SNPs) associated with differential methylation at methylation sites (CpGs) across the genome. Given that the epigenetic architecture underlying differences in gene expression can vary across racial populations, performing epigenomic studies in African Americans is crucial for understanding the interplay between genetic variation, DNA methylation, and gene expression in this understudied group. By performing cis-meQTL mapping in African American hepatocytes, we identified 410,186 cis-meQTLs associated with methylation at 24,425 CpGs in the liver. Through colocalization analysis, we found that 18,206 of these meQTLs are also colocalized with known liver eQTLs. Additionally, we found that using African American eQTL data results in an increased ability to detect additional colocalized variants that exhibit strong differences in allele frequency between people of European and African ancestry. Furthermore, the presence of smaller linkage disequilibrium blocks in African Americans allows us to identify narrower genomic regions of potentially causal variants compared to when data from Europeans is used. Importantly, these colocalized SNPs are significantly enriched for genetic associations with lipid and inflammatory traits in the GWAS catalog, suggesting that DNA methylation may contribute to the etiologies of these diseases. Furthermore, while it is generally presumed that the genetic regulation of DNA methylation is shared between blood and liver, we found that only 5.4% of African American liver meQTLs colocalize with blood meQTLs. Overall, our results reveal that studying African American populations results in the identification of additional genetic and epigenetic factors that may regulate gene expression in the liver, thereby expanding our understanding of gene regulation in African Americans.
Single-cell and spatial transcriptomics reveal the pathogenesis of chronic granulomatous disease in a natural model
Authors: Yu Hanzhi , Zhang Guorong , Ma Yunxi , Ding Jiayu , Liu Jingjing , Zhou Zhiliang , Jiao Shaozhuo , Dong Ge , Cai Zhigang
Published: January 2025

Genetic defects in NOX2 can cause chronic granulomatous disease (CGD), characterized by increased susceptibility to infections and pronounced inflammatory responses that lead to granuloma formation. We developed a CGD model usingNcf2-/-mice through controlled environmental exposure. Unlike in specific pathogen-free environment, these mice spontaneously developed pulmonary granulomas under clean-grade conditions. Employing single-cell RNA sequencing, we observed an expansion of neutrophils and monocyte-derived macrophages (MDMs) within the lung tissue, identifying pro-inflammatory NOS2high-neutrophils and a distinct MDMs subset marked by NOS2 and ARG1. Spatial transcriptomics demonstrated that NOS2high-neutrophils were located at the core area, while the MDMs subset was positioned at the periphery, facilitating extracellular matrix remodeling. Pharmacological targeting of MIF, deletion of the pro-survival geneMorrbid, and elimination ofIl1r1all suppressed granuloma formation by mitigating inflammation. This study underscores how environmental control can establish a natural CGD model, elucidates the mechanisms of granuloma formation, and develops potent therapeutic interventions.

Highlights

Through installing a mutation in a NOX2 subunit geneNcf2and changing the husbandry environment, we generated a natural CGD mouse model with progressive pulmonary granuloma formation.

NOS2highneutrophils located in the core region of CGD lung granulomas, exhibit a pro-inflammatory transcriptional profile.

Monocyte-derived macrophages marked byNos2andArg1are located at the periphery of granulomas and exhibit a profibrotic transcriptional profile.

The transcriptomic studies assist the development of three effective perturbations for treating the rare disease CGD via targetingIl1r1, Morrbid,andMifrespectively.
Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings
Authors: Brière Galadriel , Stosskopf Thomas , Loire Benjamin , Baudot Anaïs
Published: January 2025

In recent years, Knowledge Graphs (KGs) have gained significant attention for their ability to organize complex biomedical knowledge into entities and relationships. Knowledge Graph Embedding (KGE) models facilitate efficient exploration of KGs by learning compact data representations. These models are increasingly applied to biomedical KGs for link prediction, for instance to uncover new therapeutic uses for existing drugs.

While numerous KGE models have been developed and benchmarked for link prediction, existing evaluations often over-look the critical issue of data leakage. Data leakage leads the model to learn patterns it would not encounter when deployed in real-world settings, artificially inflating performance metrics and compromising the overall validity of benchmark results. In machine learning, data leakage can arise when (1) there is inadequate separation between training and test sets, (2) the model leverages illegitimate features, or (3) the test set does not accurately reflect real-world inference scenarios.

In this study, we implement a systematic procedure to control train-test separation for KGE-based link prediction and demonstrate its impact on models’ performance. In addition, through permutation experiments, we investigate the potential use of node degree as an illegitimate predictive feature, finding no evidence of such leveraging. Finally, by evaluating KGE models on a curated dataset of rare disease drug indications, we demonstrate that performance metrics achieved on real-world drug repurposing tasks are substantially worse than those obtained on drug-disease indications sampled from the KG.
Stratification along tropical forest succession enhances pollinator diversity via functionally unique canopies
Authors: Diniz Ugo Mendes , Böttger Dennis , Brehm Gunnar , Lalama Sabine Fernanda Viteri , Frühholz Kilian , Pitz Maximilian , Windl Julia , Rasmussen Claus , Keller Alexander , Leonhardt Sara Diana
Published: January 2025

Vertical stratification is among the main drivers of biodiversity in forests. Canopies are a key spatial component for primary consumers due to a higher concentration of resources, but methodological constraints impair a proper assessment of canopy communities. Therefore, the occupancy of key animal groups along the forest’s vertical axis and the role of stratification in forest succession remains little understood. In this work, we investigated the stratification of pollinator abundance, (functional) diversity, and composition along a succession chronosequence in a lowland rainforest ecosystem. Moths, social diurnal bees, and nocturnal bees were more abundant and diverse in canopies, while orchid bees showed an inverse trend across parameters, suggesting taxa-specific responses. Late successional and old-growth forests were similarly diverse, suggesting that stratification establishes fast. Moreover, canopy- bearing successional and old-growth forests were more diverse than early successional plots across all groups. For moths and partially for bees, stratification enhanced diversity in old-growth and late-successional forests via species turnover between canopy and understory. Plot isolation, elevation, and canopy height had overall little effect on the variance between canopy and understory, potentially indicating a more prominent role of resource composition than environmental and local plot variables. Moreover, canopies harbored different pollinator compositions than understories. In particular, smaller, shorter-tongued, slower-flying, light-colored bees, and cryptic moths were associated with the canopy, suggesting that the relative role of interaction, dispersal and response traits in pollinator stratification is also group-dependent. Our study underlines the importance of stratification in leveraging diversity along forest succession, with a trait-driven, group-specific divergence of pollinator communities between forest strata. These results highlight the importance of considering canopies to improve sampling completeness and fully assess ecosystem biodiversity.
Comprehensive mutational characterization of the calcium-sensing STIM1 EF-hand reveals residues essential for structure and function
Authors: Kamath Nisha D , Matreyek Kenneth A
Published: January 2025

Calcium signaling is a fundamental molecular means of cellular regulation. Store operated calcium entry (SOCE) is a major intracellular signaling module, wherein calcium release from the endoplasmic reticulum triggers transmembrane STIM1 proteins to conformationally shift and oligomerize to prompt calcium influx from the extracellular environment. STIM1 senses ER calcium concentrations with its canonical EF-hand domain, and missense variants can dysregulate SOCE and cause Tubular Aggregate Myopathy, Stormorken Syndrome or immunodeficiency. Few STIM1 EF-hand variants are characterized, obscuring how STIM1 sequence controls its function, and hampering clinical interpretation of STIM1 variants observed in patients. We leveraged fitness costs caused by overexpression of STIM1 variants in cultured human cells to functionally characterize 706 of the 720 possible single amino acid variants of the STIM1 canonical EF-hand. The calcium-coordinating EF-hand residues exhibited varying mutational patterns. The trailing helix possessed a core of immutable residues, even depleting during library propagation in bacteria, implicating residues normally restraining STIM1 aggregation. The leading helix only exhibited toxicity in cells with endogenous STIM1, implicating a multimerization-dependent STIM1 regulatory module. No cytotoxic STIM1 variants were observed in healthy human populations. Some disease-associated variants had low scores, but most pathogenic variants were not overtly cytotoxic in our assay. We demonstrate that orthogonal measurements for STIM1 oligomerization, cytoplasmic calcium influx, and cellular stress complement the cytotoxicity phenotypes to enhance variant understanding. Collectively, these data reveal the complex molecular roles embedded in the STIM1 canonical EF-hand sequence for its function in promoting calcium signaling through SOCE.
Reprogramming of alveolar macrophages by intestinal segmented filamentous bacteria protects mice from lethal bacterial pneumoniae following influenza infection
Authors: Ngo Vu L. , Lieber Carolin M. , Abo Hirohito , Kuczma Michal , Plemper Richard K. , Gewirtz Andrew T.
Published: January 2025

The most severe outcomes of respiratory viral infection (RVI) result from secondary bacterial infection, which RVI promotes via depletion of alveolar macrophages (AM). Colonization of the intestine by the common but non-ubiquitous commensal, segmented filamentous bacteria (SFB), reprograms AM to resist RVI-induced depletion. Hence, we examined if SFB against secondary infection byS. pneumoniae,H. influenzae, orS. aureus,following primary infection by influenza virus (IAV). Indeed, SFB colonization conferred strong post-IAV protection against these lethal bacterial pathogens. AM depletion and transplant studies indicated that SFB reprogramming these cells was necessary and sufficient for such protection. Assay of AM,ex vivo, from SFB-colonized mice argued their protection against secondary bacterial infection was not only due to their withstanding IAV-induced depletion. Rather, AM from SFB-colonized mice displayed complement-dependent increases in phagocytosis and killing of these bacteria. Furthermore, AM from SFB-colonized mice stably held their enhanced anti-bacterial phenotype even when transplanted into an inflamed interferon-rich post IAV-environment. Thus, SFB, and perhaps gut microbiota composition in general influences proneness to bacterial pneumonia, especially post-RVI.

One Sentence summary

SFB colonization stably changed the phenotype of alveolar macrophages resulting in sustained clearance of bacterial pathogens even amidst an inflamed interferon-rich immune suppressed lung.
Comparative proteomics uncovers distinct biomarkers, protein networks and defense responses in tomato during beneficial and pathogenic microbial interactions
Authors: Singh Dhananjaya Pratap , Maurya Sudarshan , Reddy Suresh Yerasu , Prabha Ratna , Shukla Renu , Sarma Birinchi K , Satnami Lovkush , Rai Nagendra
Published: January 2025

The molecular mechanisms underlying plant responses to beneficial and pathogenic microbial interactions has been uncovered in tomato at the proteomic level. Our study employed LC-MS-based proteomics to investigate differential protein regulation in tomato plants during interactions with beneficial bacteria (Bacillus subtilis BV7) versus pathogenic fungus (Alternaria solani). Comparative analysis revealed distinct protein signatures characterizing each interaction: 232 unique proteins in BV7-treated plants versus 96 in pathogen-infected plants, with 54 proteins shared between treatments. BV7 inoculation enhanced proteins involved in photosynthesis and primary metabolism, with PSI-K emerging as the top biomarker (score 2.53), while pathogen infection triggered focused defense responses with Cytochrome b559 (score 2.38) as the key biomarker. Metabolic pathway analysis demonstrated that BV7 uniquely enhanced vitamin metabolism (thiamine, riboflavin, folate) and energy production pathways, while pathogen infection activated defense-related phenylpropanoid biosynthesis. Analysis of defense enzymes showed pathogen infection induced highest activities of PAL (39.4 U h-1 g-1 fw), SOD (29.9 U mg-1 protein), POD (3.18 microg-1 fw min-1), APx (15.58 U mg-1 protein), and GPx (71.51 U mg-1 protein), while BV7 maintained moderate enzyme levels, suggesting balanced growth-defense responses. The shared proteins between treatments indicate a common molecular framework potentially contributing to induced systemic resistance. These findings provide novel insights into plant-microbe interactions at the molecular level, identifying specific protein biomarkers and metabolic pathways that could be targeted for enhancing crop productivity and disease resistance. The results have significant implications for developing biological control strategies and improving sustainable agricultural practices.