bluuebunny/crossref_metadata_2025 huggingface dataset:
DP427 DEFICIENCY AND ITS IMPACT ON THUNDER SOUND-INDUCED FREEZING RESPONSES IN DUCHENNE MUSCULAR DYSTROPHY DOGS
Authors: Takeuchi *Eri , Imamura Michihiro , Kikusui Takefumi , Sekiguchi Masayuki , Aoki Yoshitsugu
Published: February 2025

Background

Duchenne muscular dystrophy (DMD) is an X-linked neuromuscular disease characterized by progressive muscle wasting caused by a mutation in the DMD gene which encodes dystrophin protein. Approximately 30% of DMD patients show cognitive deficits and psychiatric symptoms. In the brain, Dp427 dystrophin isoform is localized to a subset of GABAergic synapses in the amygdala and hippocampus. We previously reported that the number of GABAA receptor α2 clusters was reduced in the basolateral amygdala (BLA) of dystrophic mdx mice. This resulted in impaired GABAergic transmission in the BLA and a freezing response to threat. However, the characterization of brain Dp427 deficiency and its impact on brain phenotypes still need to be better understood. Canine X-linked muscular dystrophy in Japan (CXMDJ), a middle-sized and emotionally expressive model of DMD, is suitable for examining the neurobehavior associated with brain Dp427 deficiency.

Aims & Objectives

We aim to elucidate the molecular mechanism of brain Dp427 and the impact of its absence on brain phenotypes in CXMDJ.

Method

CXMDJ and wild-type littermates were observed in the thunder sound-induced fear response behavior. In this study, we used the open field apparatus consisting of an aluminum canine circle (W240 × L240 × H120 cm). Dogs were placed in a carrier cage, and the test was started when the door was opened. A reward was placed on the diagonal, and a thunder sound (110-140 dB) was presented when the dog approached the reward. A video camera was mounted on the ceiling to record each dog's behavior. Images were analyzed using image analysis software (Move-tr/2D). An electrocardiogram (ECG) measurement was recorded during the sound-induced fear response behavior to evaluate the emotional state.

Results

CXMDJ exhibited enhanced anxiety-like behavior in the open field test. The measurement of heart rate variability revealed decreased parasympathetic nerve activity in CXMDJ during the open field test. Moreover, CXMDJ showed an increased freezing behavior and decreased total distance traveled in the sound-induced fear response compared to wild-type littermates. This result suggests that CXMDJ exhibits enhanced fear behavior associated with brain Dp427 deficiency.

Discussion & Conclusion

We showed that CXMDJ exhibited highly anxiety-like behavior and freezing response. It is postulated that the absence of Dp427 in the amygdala may contribute to heightened anxiety and fear levels in CXMDJ.
Comparison of Sequencing-by-Synthesis and Avidity Base Chemistry Next-Generation Sequencing Platforms in Identifying Somatic Variants of Hematological Malignancies
Authors: Lim Min Hui , Kim Juwuk , Tu Zheng Jin , Cheng Yu-Wei
Published: February 2025

Background

This study evaluates the performance of the Illumina NextSeq™ 550 and the Element Biosciences AVITI™ next-generation sequencing (NGS) system, in detecting single nucleotide variants (SNVs) and gene fusions.

Methods

A set of 66 NGS libraries, consisting of 33 DNA, 24 cDNA, and triplicates of 3 control libraries, were prepared from bone marrow samples targeting 63 genes and related fusions, and initially sequenced using the NextSeq 550 in the Cleveland Clinic's molecular diagnostic laboratory. The same libraries were subsequently sequenced on the AVITI. The resulting data were analyzed using a combination of Cleveland Clinic developed pipelines and ArcherDx virtual machine software.

Results

The study found that all 105 SNVs and 39 gene fusions identified by the NextSeq 550 were also detected in the AVITI, demonstrating a high degree of concordance between the platforms. The analyses revealed R2 values of 0.86 for read depth and 0.96 for VAF of the 105 DNA variants, and 0.95 for read depth and 0.97 for fusion percentage of the 39 fusion variants. In the reproducibility studies, the VAF and fusion percentage of all variants were within 2 standard deviations of the mean when the same positive controls were sequenced 3 times on the AVITI.

Conclusions

These results indicate that the NextSeq 550 and the AVITI provide comparable performance in terms of accuracy and sensitivity for variant detection. Notably, the AVITI chemistry requires substantially lower PhiX input than the NextSeq 550 needs for this application. This results in substantial cost and efficiency benefits.
Efficacy of supplemental amino acids with Corynebacterium glutamicum cell mass on growth and health of nursery pigs
Authors: Cheng Yi-Chi , Duarte Marcos Elias , Kim Sung Woo
Published: February 2025

Removing filtration and crystallization provides amino acids with reduced purity because Corynebacterium glutamicum cell mass (CGCM) is not removed. This study aimed to evaluate nutritional and functional values of granulated Threonine (Thr) and Valine (Val) with CGCM in diets for growth performance, jejunal mucosa-associated microbiota, nutrient digestibility, and health of nursery pigs. Seventy-two newly weaned pigs (28 d-of-age; initial body weight (BW) of 8.2 ± 0.4 kg) were allotted to 9 treatments (n = 8) based on a randomized complete block design with sex and initial BW as blocks. Treatments consisted of a basal diet with different levels of standardized ileal digestible (SID) Thr and Val: NC (SID Thr and SID Val at 70% of NRC requirement), CT (95% SID Thr using crystalline Thr); CV (95% SID Val using crystalline Val); PT (95% SID Thr using ThrPro); PV (95% SID Val using ValPro); HCT (5 × crystalline Thr used in CT); HCV (5 × crystalline Val used in CV); HPT (5 × ThrPro used in PT); HPV (5 × ValPro used in PV). Diets were fed to nursery pigs for 25 d in 2 phases (10 d and 15 d, respectively). Feed intake and BW were recorded at the end of each phase. Blood samples were collected to measure serum proteins, metabolites, and electrolytes on d 21. Pigs were euthanized at d 25 to collect liver and jejunal tissues for morphological evaluation and jejunal mucosa to measure intestinal health biomarkers. Data were analyzed by SAS using MIXED procedure. Pigs with 95% SID Thr or 95% SID Val tended to have greater average daily gain (P = 0.078) and gross energy digestibility (P = 0.058), had greater (P < 0.05) jejunal villus height, and had lower (P < 0.05) plasma urea nitrogen and liver fibrosis than pigs with 70% SID Thr or 70% SID Val, respectively. Pigs fed a diet with HAAPro had increased (P < 0.05) alpha diversity of jejunal mucosa-associated microbiota than pigs fed a diet with AAPro. Pigs fed a diet with HAAPro had increased (P < 0.05) relative abundance of Bifidobacterium and decreased (P < 0.05) relative abundance of Comamonas than pigs fed a diet with AAPro. In conclusion, increasing the supplementation of AAPro by five folds than typical level did not negatively affect growth performance whereas beneficially modulated the jejunal mucosa-associated microbiota. Results suggest that AAPro can effectively replace the use of crystalline amino acids in pig diets whilst potentially reducing feed costs due to reduced cost of producing such amino acids.
Multi-messenger emission from magnetic reconnection in blazar jets: the case of TXS 0506+056
Authors: de Gouveia Dal Pino E M , Rodríguez-Ramírez J C , del Valle M V
Published: February 2025

Measurements from astroparticle experiments, such as the 2017 flare associated with the source TXS 0506+056, indicate that blazars act as multi-messenger (MM; radiation and neutrinos) factories. Theoretically, the particle acceleration mechanisms responsible for blazar emissions and the precise location within the jet where this occurs remain undetermined. This paper explores MM emission driven by magnetic reconnection in a blazar jet. Previous studies have shown that reconnection in the magnetically dominated regions of these relativistic jets can efficiently accelerate particles to very high energies (VHE). Assuming that turbulent-driven magnetic reconnection accelerates cosmic-ray protons and electrons by a Fermi process, we developed a lepto-hadronic radiation model without the influence of external soft-photons to explain the 2017 MM flare from TXS 0506+056. In the proposed scenario, the emission blob moves downstream in the jet from ∼2 to 4 pc from the central engine, which is a supermassive black hole (SMBH) of 3 × 108 M⊙ launching a jet with 150LEdd power. As the blob moves, we observe a sequence of spectral energy distribution (SED) profiles that match the observed arrival of the high energy neutrino and electromagnetic emission from TXS 0506+056. This arrival coincides with the high state of intermediate energy γ-rays (E ∼ 1 GeV) detection, followed by the subsequent appearance of the VHE γ-ray signal and then no further significant neutrino detection. We obtain a time delay between the neutrino and VHE events ≃ 6.4 days, which is consistent with that observed in the 2017 MM flare.
The XXL Survey LIV. X-ray luminosity function and Luminosity-Mass Relation of optically selected galaxy groups
Authors: Wood C , Maughan B J , Crossett J P , Eckert D , Pierre M , Ramos-Ceja M E , Robotham A S G , Adami C , Faccioli L , Koulouridis E , McGee S L , Pacaud F , Phillipps S
Published: February 2025

The overlap between the GAMA spectroscopic survey and the XXL X-ray survey was used to study the X-ray properties of optically-selected groups of galaxies. Forced X-ray aperture photometry was applied to an optically-selected sample of 235 groups (containing at least five member galaxies) to measure their X-ray luminosities in the regime of low signal to noise X-ray data. The sample encompasses X-ray luminosities over an order of magnitude fainter than typical X-ray selected samples, and avoids X-ray selection biases. This gives access to low mass groups where the effects of non-gravitational processes, such as AGN-feedback, should be most apparent and could inhibit their detection in an X-ray survey. We measured the X-ray luminosity function (XLF) of the sample, and found it to be consistent with the extrapolation of the XLF from X-ray selected samples at higher luminosities. The XLF was combined with a theoretical halo mass function to infer the form of the scaling relation between X-ray luminosity and mass (LM relation) for the GAMA groups. We found a slope of 1.87 ± 0.12, which is steeper than self similarity in this mass regime. When comparing with other measurements of the LM relation, we find evidence for a steepening of the slope in the low mass regime, likely due to the impact of non-gravitational processes. Our approach can be translated to eROSITA data using multi-wavelength surveys to constrain the X-ray properties of galaxy groups in the limits of high redshift and low mass.
Individualized and targeted coagulation management in bleeding trauma patients
Authors: Hofmann Nikolaus , Schöchl Herbert , Gratz Johannes
Published: February 2025

Purpose of review

This review aims to summarize current evidence on hemostatic management of bleeding trauma patients, with a focus on resuscitation strategies using either coagulation factor concentrates or fixed-ratio transfusion concepts. It discusses the potential benefits and limitations of both approaches.

Recent findings

Recent studies have shown that coagulopathy caused by massive traumatic hemorrhage often cannot be reversed by empiric treatment. During initial resuscitation, a fixed-ratio transfusion approach uses the allogeneic blood products red blood cells, plasma, and platelets to mimic ‘reconstituted whole blood’. However, this one-size-fits-all strategy risks both overtransfusion and undertransfusion in trauma patients.

Many European trauma centers have shifted toward individualized hemostatic therapy based on point-of-care diagnostics, particularly using viscoelastic tests. These tests provide rapid insight into the patient’s hemostatic deficiencies, enabling a more targeted and personalized treatment approach.

Individualized, goal-directed hemostatic management offers several advantages over fixed-ratio transfusion therapy for trauma patients. However, there is a paucity of data regarding the direct comparison of these two approaches.
Host Response Stratification in Malarial and Non-malarial Sepsis: A Prospective, Multicenter Analysis From Uganda
Authors: Cummings Matthew J. , Lutwama Julius J. , Owor Nicholas , Tomoiaga Alin S. , Ross Jesse E. , Muwanga Moses , Nsereko Christopher , Nayiga Irene , Kyebambe Stephen , Shinyale Joseph , Ochar Thomas , Nie Kai , Xie Hui , Miake-Lye Sam , Villagomez Bryan , Qi Jingjing , Reynolds Steven J. , Nakibuuka Martina Cathy , Lu Xuan , Kayiwa John , Haumba Mercy , Nakaseegu Joweria , Che Xiaoyu , Byakika-Kibwika Pauline , Wayengera Misaki , Achan Jane , Kim-Schulze Seunghee , Lipkin W. Ian , O’Donnell Max R. , Bakamutumaho Barnabas
Published: February 2025

Objectives:

Globally, the burden of sepsis is highest in malaria endemic areas of sub-Saharan Africa. The influence of malaria on biological heterogeneity inherent to sepsis in this setting is poorly understood. We sought to determine shared and distinct features of the host response in malarial and non-malarial sepsis in sub-Saharan Africa.

Design and Setting:

Analysis of Olink proteomic data from prospective observational cohort studies of sepsis conducted at public hospitals in Uganda (discovery cohort [Entebbe, urban], n = 238; validation cohort [Tororo, rural], n = 253).

Patients:

Adults (age ≥ 18 yr) hospitalized with sepsis.

Interventions:

None.

Measurements and Main Results:

The frequency of malaria-associated (malarial) sepsis was 20% in the discovery cohort and 28% in the validation cohort. In both cohorts, a shared host response was predominant, with less than or equal to 8% of proteins differentially expressed (Benjamini-Hochberg-adjusted p ≤ 0.05) between malarial and non-malarial sepsis, after adjustment for demographic variables and HIV and tuberculosis coinfection. In both cohorts, malarial sepsis was associated with increased expression of immunosuppressive proteins (interleukin-10, leukocyte immunoglobulin-like receptor B1, killer cell immunoglobulin-like receptor 3DL1), including those associated with Tcell exhaustion and apoptosis (lymphocyte activation gene 3, T cell immunoglobulin and mucin domain containing 4). A classifier model including these immunosuppressive proteins showed reasonable discrimination (area under the receiver operating characteristic curves, 0.73 [95% CI, 0.65–0.81] and 0.72 [0.65–0.79]) and calibration (Brier scores 0.14 and 0.18) for stratification of malarial sepsis in the discovery and validation cohorts, respectively.

Conclusions:

Host responses are largely conserved in malarial and non-malarial sepsis but may be distinguished by a signature of relative immunosuppression in the former. Further investigations are needed to differentiate mechanisms of malarial and non-malarial sepsis, with the goal of informing pathogen-stratified and pathogen-agnostic treatment strategies.
Incidence and management of accidental dural puncture and postdural puncture headache in parturients
Authors: Cohen Stav , Greenberger Chaim , Aptekman Boris , Rabkin Victor , Weiniger Carolyn F.
Published: February 2025

BACKGROUND

Postdural puncture headache (PDPH) is a common complication of neuraxial block resulting from either intentional dural puncture (IDP) or accidental dural puncture (ADP).

OBJECTIVES

The primary objective was to estimate the rate of PDPH and ADP following introduction of a real-time documentation system in April 2018. Secondary objectives included examining the use of epidural blood patch (EBP) and investigating risk factors associated with ADP and PDPH.

DESIGN

Retrospective cohort study.

SETTING

Secondary care at a tertiary hospital from January 2017 to April 2022.

PATIENTS

Three hundred and eleven adult parturients after neuraxial block, with PDPH or a reported ADP, were identified during the procedure or postpartum.

INTERVENTIONS

Implementation of a real-time documentation system in April 2018 to improve PDPH and ADP documentation.

MAIN OUTCOME MEASURES

Rates of PDPH and ADP, performance of epidural blood patch, and risk factors associated with PDPH and ADP.

RESULTS

The overall rate of PDPH was 0.4% (164/39888), 95% confidence intervals (CI) 0.0036 to 0.0049, and the rate of ADP was 0.9% (284/31635), 95% CI 0.0078 to 0.0099. During the real-time documentation period, the rates were 0.44% (157/35376), 95% CI 0.0038 to 0.0052, and 0.99% (279/28121), 95% CI 0.0088 to 0.0111, for PDPH and ADP respectively. Thirty-two (10.3%) cases had IDP, and 279 (89.7%) had ADP. Among 279 ADP cases, 76.3% were identified during the procedure, 10.4% suspected and 13.3% identified postpartum. Cases of ADP identified postpartum had more emergency room visits (19%). Epidural blood patch (EBP) was administered in 72% of PDPH cases, with a high first-time success rate (89.5%); 11 women received epidural blood patch after IDP.

CONCLUSIONS

Postdural puncture headache remains a significant concern. In our cohort, 13.3% of ADP cases were detected postpartum, posing an increased challenge and underscoring the critical importance of follow-up care. We confirm that epidural blood patch may be required following any neuraxial block.

TRIAL REGISTRATION

Not applicable.
Chondrocutaneous Advancement Flap and Postauricular Skin Flap: An Effective Combination for Large Helical Rim Defect Reconstruction
Authors: De Rosa Anna , Grieco Michele P. , D’Antonio Santolo , Rullo Vincenzo , Castellaneta Francesco , Fabrizio Tommaso
Published: February 2025

Background:

Defects of the ear helix are a frequent challenge in plastic surgery, with more than 5% of all skin cancers occurring in this region. The Antia-Buch flap is a single-stage reconstruction technique utilizing chondrocutaneous flaps for helix repair. However, for defects exceeding 2 cm, it can lead to auricular distortion. To address this limitation, we propose a modified Antia-Buch technique combining chondrocutaneous advancement with a postauricular skin flap to optimize outcomes.

Methods:

A retrospective review was conducted of 15 patients who underwent our modified Antia-Buch flap procedure between 2019 and 2022. This approach incorporated chondrocutaneous advancement for primary defect closure and a postauricular skin flap for improved contouring. Functional and aesthetic outcomes were assessed using a questionnaire developed in collaboration with a clinical psychologist. The questionnaire evaluated surgical satisfaction, cosmetic results, self-image, and social integration postreconstruction.

Results:

No complications, including ischemic necrosis or the need for surgical revision, were observed in any case. The technique demonstrated excellent vascularity, with no occurrences of flap failure. Patient-reported outcomes revealed high satisfaction rates, with no evidence of self-image distortion or social barriers. Aesthetic results were rated as superior, with minimal risk of auricular distortion even for larger defects.

Conclusions:

The modified Antia-Buch technique is a reliable and effective method for helical rim reconstruction, particularly for defects larger than 2 cm. It offers technical simplicity, low complication rates, patient convenience, and excellent cosmetic outcomes, making it a preferred option for many auricular defect reconstructions.
The Use of BODY-Q to Assess Factors Impacting Satisfaction and Quality-of-life Postabdominoplasty in Kenya
Authors: Nyakiongora Sarah , Laspro Matteo , Dele-Oni Oluchukwu , Abdullahi Adan A. , Nangole Ferdinand W. , Pusic Andrea L.
Published: February 2025

Background:

Massive weight loss can often lead to skin redundancy and affect a patient’s quality of life. Abdominoplasty has grown in popularity due to its cosmetic and functional effects. There is currently a paucity in the patient-reported outcome measures literature in low-resource areas. As such, this study aimed to apply the BODY-Q measure to evaluate factors impacting abdominoplasty outcomes in Kenya.

Methods:

Patients undergoing abdominoplasty were asked to complete BODY-Q scales before and after surgery. Patient demographics, medical history, and postoperative care were retrospectively collected from patient records. Inference statistics were used to assess predictors of improvement in postsurgical BODY-Q scores and seroma formation. Student t tests were used to compare means; chi-square tests were used to assess differences between proportions, and R
2 was used to determine the proportion of variance.

Results:

Thirty-nine patients underwent abdominoplasty, of whom 38 answered both surveys. Mean age and body mass index (BMI) were 38.30 (±6.35) years and 30.80 (±6.35) kg/m2, respectively. The difference in pre- and postoperative BODY-Q scores was −73.5, with an effect size of −6.67 and a minimal clinically important difference of −2.00. Positive predictors of BODY-Q score improvement were concurrent liposuction (P = 0.004), preoperative BMI (P = 0.001), and patient-rated scar quality (P = 0.003). Other factors were not significantly predictive.

Conclusions:

Kenyan patients seem to be highly satisfied with abdominoplasty procedures, which result in significant improvements in quality of life. Factors significantly associated with higher satisfaction include concurrent liposuction, higher preoperative BMI, and postoperative scar quality.
Multimodal analgesia with thoracic paravertebral block decrease pain and side effects in mastectomy patients.
Authors: Liu Pei-Chin , Su Fu-Wei , Tsai Yi-Fang , Lin Yen-Shu , Sung Chun-Sung , Tseng Ling-Ming , Teng Wei-Nung
Published: February 2025

Background:

Enhanced recovery after surgery (ERAS) protocols incorporating multimodal analgesia (MMA) have become increasingly popular for breast cancer surgery. Our study evaluated an ERAS approach that combined nonintubated general anesthesia with thoracic paravertebral block (TPVB) as part of the MMA and compared it to traditional general anesthesia (GA). Postoperative outcomes were assessed using numerical rating scale (NRS) pain scores, total analgesic consumption, and nausea and vomiting (PONV).

Methods:

We reviewed the medical records of 60 female patients aged 30–85 years who underwent unilateral mastectomy with or without sentinel lymph node biopsy (SLNB). Thirty patients received nonintubated general anesthesia with a regional block (MMA group), whereas the remaining 30 patients received conventional GA and were matched based on their anesthesia records. Postoperative analgesics, including pethidine and tramadol, were converted into intravenous morphine equivalents. We compared the groups using paired t tests for age, height, weight, operation duration, NRS scores, total analgesic dosage, and the Fisher exact test for PONV rates.

Results:

The MMA group showed significantly lower NRS scores (p < 0.001) and total analgesic consumption (p < 0.001) than the GA group. Although PONV rates were lower in the MMA group (0% vs 13%, p = 0.112), this difference was not statistically significant, likely due to the effective PONV management in the GA group with dexamethasone or 5HT-3 antagonists. There was no significant difference in pain scores (p = 0.722) or the need for additional analgesics (p = 0.419) between double- and triple-level TPVB.

Conclusion:

Nonintubated general anesthesia with TIVA and MMA using TPVB is a viable and safe alternative for breast cancer surgery. It results in reduced pain scores and analgesic needs compared with conventional GA, with PONV outcomes comparable to those managed with standard intravenous medications.
Establishing a threshold for maximum standardized uptake value on 18F-fluorodeoxyglucose PET/CT to predict high-grade lung adenocarcinoma and its prognostic significance
Authors: Huang Miao , Wang Yaqi , Yang Xin , Li Nan , Liu Bing , Li Xiang , Zhang Shanyuan , Lu Fangliang , Li Shaolei , Yan Shi , Lin Dongmei , Wu Nan
Published: February 2025

Objective:

The objective of this study is to determine an optimal threshold for the maximum standardized uptake value (SUVmax) of 18F-fluorodeoxyglucose PET/CT to predict the newly proposed high-grade tumor classification and assess its prognostic significance in invasive lung adenocarcinoma (LUAD).

Methods:

Surgical specimens from 185 patients with pathological stage I invasive LUAD in the training group, along with 90 patients in the validation group, were analyzed using the novel IASLC grading system. The receiver operating characteristic curve was used to determine the optimal SUVmax threshold and assess its predictive accuracy. Disease-free survival (DFS) and overall survival (OS) were analyzed using Kaplan–Meier survival curves and Cox regression analysis.

Results:

Linear correlation analysis demonstrated a significant positive association between SUVmax and the proportion of high-grade histological patterns (R² = 0.346, P < 0.001). The optimal SUVmax cutoff for predicting grade 3 tumors was 3.8, with an area under the curve of 0.866 in the training dataset and 0.899 in the validation dataset. Multivariate logistic regression analysis identified an SUVmax >3.8 as an independent predictor of grade 3 tumors (P < 0.001). In Cox regression analysis, SUVmax >3.8 was independently associated with reduced DFS (HR = 4.009, 95% CI: 1.568–10.250, P = 0.004) and OS (HR = 5.536, 95% CI: 1.175–26.075, P = 0.030).

Conclusion:

As a noninvasive preoperative parameter, SUVmax >3.8 is a significant indicator of high-grade tumors as classified by the IASLC grading system and is strongly associated with worse DFS and OS.
Genomic analysis reveals low genetic diversity and no continuous reintroduction of piscine myocarditis virus in farmed Atlantic salmon in the Faroe Islands
Authors: Dahl Maria Marjunardóttir , Petersen Petra Elisabeth , Christiansen Debes Hammershaimb
Published: February 2025

Piscine myocarditis virus (PMCV) is the causative agent of cardiomyopathy syndrome (CMS), a significant disease in farmed Atlantic salmon (Salmo salar L.). Although an increasing number of CMS outbreaks have been recorded in the Faroe Islands since the reemergence of CMS in 2013, overall PMCV genetic diversity, transmission pathways and evolutionary trajectories remain elusive. Here, we present a fast amplicon-based whole-genome sequencing method of PMCV directly from field samples and disclose 48 novel genomes, adding to the single genome currently available. Phylogenetic analysis revealed that genomes with a broad spatiotemporal representation of Faroese farmed salmon formed a homogenous monophyletic cluster compared to Norwegian and Irish PMCV genomes. Homogeneity of the Faroese genomes was substantiated with principal component analyses, where no spatiotemporal clustering of genotypes was found, nor any clustering based on roe or smolt origin. One genome from a returning wild salmon differed considerably from all the rest and formed an outgroup. All three ORFs exhibited signs of purifying selection, although ORF3 displayed a comparatively lower degree of selective constraint. Furthermore, no virulence-determining amino acid substitutions were identified in the Faroese genomes as no association was found between CMS cases and specific amino acid substitutions or motifs. Our data suggest that PMCV was introduced into the Faroe Islands from Norway, where brood fish is known to be infected. However, despite a steadily increasing import of Norwegian roe, our results show no continuous reintroduction of persisting PMCV strains to Faroese farmed salmon.
dar: A Consensus-Based Framework for Differential Abundance Testing in Microbiome Data
Authors: Farré-Badia Judit , Noguera-Julian Marc , Paredes Roger , Català-Moll Francesc
Published: February 2025

ThedarR package streamlines differential abundance (DA) testing in microbiome research by integrating state-of-the-art DA methods—such as DESeq2, ALDEx2, ANCOM-BC, and MetagenomeSeq—within a customizable consensus-based framework, thereby enhancing the robustness and reproducibility of DA results. Leveraging microbiome data inphyloseqorTreeSummarizedExperimentformats,darorganizes analysis steps in a modularrecipeobject, enabling users to easily incorporate preprocessing tasks such as taxonomic filtering, rarefaction, and subsetting, alongside multiple DA analysis methods. Dedicated visualization tools facilitate the definition of a consensus by illustrating the overlap among methods, empowering users to refine analysis strategies and display final results. Reproducibility is supported through functions that export and import entire analysis workflows, makingdara comprehensive solution for addressing the complex, high-dimensional nature of microbiome data.

Availability and implementation

daris an R package available from Bioconductor ≥ 3.19 (https://www.bioconductor.org/packages/dar) for R ≥ 4.4. The software is distributed under the MIT License and includes example datasets.

Contact

fcatala@irsicaixa.es

Supplementary information

Additional documentation is available athttps://microbialgenomics-irsicaixaorg.github.io/dar
Insights From Protein Frustration Analysis of BRD4-Cereblon Degrader Ternary Complexes Show Separation of Strong from Weak Degraders
Authors: Yang Tianyi , Mukhaleva Elizaveta , Wei Wenyuan , Weiss Dahlia , Ma Ning , Shanmugasundaram Veerabahu , Vaidehi Nagarajan
Published: February 2025

PROteolysis TArgeting Chimeras (PROTACs), also known as Ligand-Directed Degraders (LDDs), are an innovative class of small molecules that leverage the ubiquitin-proteasome system to induce the degradation of target proteins. Structure based design methods are not readily applicable for designing LDDs due to the dynamic nature of the ternary complexes. This study investigates the dynamic properties of five LDD-mediated BRD4-Cereblon complexes, focusing on the challenges of evaluating linker efficiency due to the difficulty in identifying suitable computational metrics that correlate well with the cooperativity or degradation propensity of LDDs. We uncovered that protein frustration, a concept originally developed to understand protein folding, calculated for the residues in the protein-protein interface of the LDD-mediated ternary complexes recapitulate the strength of degradation of the LDDs. Our findings indicated that hydrophobic residues in the interface are among the highly frustrated residues pairs, and they are crucial in distinguishing strong degraders from weak ones. By analyzing frustration patterns, we identified key residues and interactions critical to the effectiveness of the ternary complex. These insights provide practical guidelines for designing and prioritizing more efficient degraders, paving the way for the development of next-generation LDDs with improved therapeutic potential.
Identification of new interactors of eIF3f by endogenous proximity-dependent biotin labelling in human muscle cells
Authors: Tintignac Lionel , Mittal Nitish , Alam Shahidul , Ataman Meric , Ertuna Yusuf I. , Bock Thomas , Erne Beat , Zavolan Mihaela , Sinnreich Michael
Published: February 2025

Regulation of protein synthesis is central to maintaining skeletal muscle integrity and its understanding is important for the treatment of muscular and neuromuscular pathologies. The eIF3f subunit of the translation initiation factor eIF3 has a key role, as it stands at the crossroad between protein-synthesis-associated hypertrophy and MAFbx/atrogin-1-dependent. To decipher the molecular mechanisms underpinning the role of eIF3f in regulating muscle mass, we established a cellular model that enables interrogation of eIF3f functionality via identification of proximal interactors. Using CRISPR-Cas9 molecular scissors, we generated single cell clones of immortalised human muscle cells expressing eIF3f fused to the BirA biotin ligase (eIF3f-BioID1 chimera) from the endogenousEIF3Flocus. Biotinylated proteins, representing interactors of eIF3f in nanometer range distance, were identified by streptavidin pull-downs and mass spectrometry. In both proliferating and differentiated muscle cells, the eIF3f-BioID1 chimera co-sedimented with ribosomal complexes in polysome profiles and interacted mainly with components of the eIF3 complex, and with the eIF4E, eIF4G, and eIF5 initiation factors. Surprisingly, we identified several nucleus-localised interactors of eIF3f, and the immunofluorescence analyses revealed a previously unknown nuclear localization of eIF3f in both myoblasts and myotubes. We also identified novel cytoplasmic partners of eIF3f, responsible for the maintenance of skeletal muscle ultrastructure (sarcomeric/Z-disc (SYNPO2) bound proteins) and proteins of the lysosomal compartment (LAMP1). The established tagging system should be useful to further advance studies of eIF3f function in hypertrophic and atrophic conditions in skeletal muscle.
Inhibitors of the PqsR Quorum-Sensing Receptor Reveal Differential Roles for PqsE and RhlI in Control of Phenazine Production
Authors: Valastyan Julie S. , Shine Emilee E. , Mook Robert A. , Bassler Bonnie L.
Published: February 2025

Pseudomonas aeruginosais a leading cause of hospital-acquired infections and it is resistant to many current antibiotic therapies, making development of new anti-microbial treatments imperative. The cell-to-cell communication process called quorum sensing controlsP. aeruginosapathogenicity. Quorum sensing relies on the production, release, and group-wide detection of extracellular signal molecules called autoinducers. Quorum sensing enables bacteria to synchronize group behaviors.P. aeruginosapossesses multiple quorum-sensing systems that control overlapping regulons, including those required for virulence and biofilm formation. Interventions that targetP. aeruginosaquorum-sensing receptors are considered a fruitful avenue to pursue for new therapeutic advances. Here, we developed aP. aeruginosastrain that carries a bioluminescent reporter fused to a target promoter that is controlled by twoP. aeruginosaquorum-sensing receptors. The receptors are PqsR, which binds and responds to the autoinducer called PQS (2-heptyl-3-hydroxy-4(1H)-quinolone) and RhlR, which binds and responds to the autoinducer called C4-HSL (C4-homoserine lactone). We used this reporter strain to screen >100,000 compounds with the aim of identifying inhibitors of either or both the PqsR and RhlR quorum-sensing receptors. We report results for 30 PqsR inhibitors from this screen. All of the identified compounds inhibit PqsR with IC50values in the nanomolar to low micromolar range and they are readily docked into the autoinducer binding site of the PqsR crystal structure, suggesting they function competitively. The majority of hits identified are not structurally related to previously reported PqsR inhibitors. Recently, RhlR was shown to rely on the accessory protein PqsE for full function. Specifically, RhlR controls different subsets of genes depending on whether it is bound to PqsE or to C4-HSL, however, the consequences of differential regulation on the quorum-sensing output response have not been defined. PqsR regulatespqsE. That feature of the system enabled us to exploit our new set of PqsR inhibitors to show that RhlR requires PqsE to activate the biosynthetic genes for pyocyanin, a keyP. aeruginosavirulence factor, while C4-HSL is dispensable. These results highlight the promise of inhibition of PqsR as a possibleP. aeruginosatherapeutic to suppress production of factors under RhlR-PqsE control.
Delivery of caspase inhibitors through GSDMD pores to inhibit pyroptosis
Authors: Groborz Katarzyna M. , Truong Melissa E. , Stowe Irma , Lee Bettina , Jones Robert S. , Plise Emile , Levy Elizabeth S. , Kou Ponien , Lee Wyne P. , Zhang Juan , Nguyen Julia , Kalinka Malgorzata , Drag Marcin , Kayagaki Nobuhiko , Newton Kim , Poreba Marcin , Dixit Vishva M.
Published: February 2025

Caspase-1, -4, -5, and -11 activate Gasdermin D (GSDMD) to form pores in the plasma membrane. In addition to releasing interleukin (IL)-1β and IL-18, GSDMD pores cause a lytic, proinflammatory form of cell death called pyroptosis. Blocking this pathway holds therapeutic promise for the treatment of inflammatory disorders, but clinical trials of cell permeable caspase inhibitors have been unsuccessful. Here, we describe covalent inhibitors of proinflammatory caspases that are impermeable to healthy cells but effectively block caspase-1 driven pyroptosis and IL-1β secretion. Their failure to inhibit apoptosis implies inhibitor entry through GSDMD pores. Propidium iodide entered rescued cells, confirming transient membrane permeabilization via caspase-1 and GSDMD. Caspase-1 inhibition prevented rather than delayed cell death, likely due to the activation of membrane repair mechanisms neutralizing the initial GSDMD pores. Notably, inhibiting caspase-1 and -11 suppressed IL-1β and IL-18 production in a mouse model of endotoxic shock. These findings underscore the therapeutic potential of exploiting GSDMD pores for the delivery of caspase inhibitors, offering a novel strategy for treating inflammatory diseases.
Spatiotemporal analysis ofde novoKSHV infection using Crispr/Cas9-based 3D live cell imaging at single episome resolution
Authors: Günther Thomas , Weissmann Simon , Hamann Martin V. , Scheibel Henry , Bosse Jens B. , Ziegler Marion , Grundhoff Adam
Published: February 2025

Kaposi Sarcoma-associated herpesvirus (KSHV) persists as a latent episome in infected cells. While the virus efficiently infects established cell lines and primary cellsin vitro, the early events guiding establishment of latent infection and the dynamic interplay between viral episomes and host factors remain incompletely understood. Here, we describe the development and application of a CRISPR/Cas9-based 3D live cell imaging system capable of tracking single KSHV episomes in real-time. Our approach exploits the SunTag technology, wherein deactivated Cas9 (dCas9) molecules are fused to repetitive epitope arrays recognized by superfolder GFP-fused single-chain antibodies. By targeting these complexes to terminal repeat units of KSHV, we achieve high level signal amplification, allowing us not only to detect newly incoming viral genomes within the first hours ofde novoinfection, but also to follow their spatiotemporal trajectories through different stages of the viral lifecycle. Furthermore, to facilitate efficient generation of stable reporter cell lines, we adapted the transposon-based piggyBac system to combine all SunTag components into a single-vector targeting system (SunSeT).

Using these systems, we demonstrate the ability to observe both transient and stable interactions between KSHV episomes and key cellular regulators, including the variant polycomb-repressive complex 1 (vPRC) component KDM2B and the innate immune sensor IFI16. Furthermore, our platform allows detailed visualization of episodic changes in episome localization, abundance and distribution duringde novoand long-term infection, providing critical insights into how viral genome positioning and dynamics correlate with host subnuclear environments.

Overall, our study introduces a robust and adaptable imaging platform to dissect the earliest events of KSHV infection. The ability to track viral episomes in living cells offers a powerful tool to advance our understanding of the spatial and temporal regulation of individual KSHV genomes, shedding light on fundamental mechanisms of herpesvirus latency and persistence.
Persistence of large conjugative plasmids relies on the combination of active partitioning and addiction mechanisms
Authors: Effe Johannes , Santer Mario , Wang Yiqing , Feenstra Theresa E. , Hülter Nils F. , Dagan Tal
Published: February 2025

Extrachromosomal and mobile genetic elements, including transposable elements, plasmids, and accessory chromosomes, are found across all domains of life. The replication and segregation of elements integrated into the host chromosome are ensured by the host life cycle. In contrast, the persistence of autonomously replicating elements relies on their ability to remain within the host population. Here, we assess the evolutionary success of different persistence strategies of prokaryotic plasmids. Through intracellular competitions between plasmid genotypes, we find that combining active partitioning during cell division with a toxin-antitoxin (TA) system for post-segregational killing is more effective than either strategy alone. Mathematical modeling of long-term plasmid evolution, calibrated with empirical plasmid persistence probabilities, further supports these findings. A survey of enterobacterial genomes indicates that partitioning and TA systems are core features of large conjugative plasmids. Indeed, we confirm the presence of a previously unrecognized type I TA system in IncX3 plasmids, which serve as important vectors of antibiotic resistance in human pathogens. These findings suggest that large conjugative plasmids likely encode TA systems, including those yet to be identified. The combination of TA and partitioning systems emerges as the most effective strategy for the persistence of low-copy extrachromosomal elements with unstable segregation.
Functional specialisation of multisensory temporal integration in the mouse superior colliculus
Authors: Gaia Bianchini , Razafindrahaba Ines , Moglie Marcelo J. , Konstantinou George , Cano-Ferrer Xavier , Imbert Albane , Iacaruso M. Florencia
Published: February 2025

Our perception of the world depends on the brain’s ability to integrate information from multiple senses, with temporal disparities providing a critical cue for binding or segregating cross-modal signals1,2. The superior colliculus (SC) is a key site for integrating sensory modalities, but how cellular and network mechanisms in distinct anatomical regions within the SC contribute to multisensory integration remains poorly understood. Here, we recorded responses from over 5,000 neurons across the SC’s anatomical axes of awake mice during presentations of spatially coincident audiovisual stimuli with varying temporal asynchronies. Our findings revealed that multisensory neurons reliably encoded audiovisual delays and exhibited nonlinear summation of auditory and visual inputs, with nonlinearities being more pronounced when visual stimuli preceded auditory stimuli, consistent with the natural statistics of light and sound propagation. Nonlinear summation was crucial for population-level decoding accuracy and precision of AV delay representation. Moreover, enhanced population decoding of audiovisual delays in the posterior-medial SC, facilitated temporal discriminability in the peripheral visual field. Cross-correlation analysis indicated higher connectivity in the medial SC and functional specific recurrent connectivity, with visual, auditory, and multisensory neurons preferentially connecting to other neurons of the same functional subclass, and multisensory neurons receiving approximately 50 percent of the total local input from other multisensory neurons. Our results highlight the interplay between single-neuron computations, network connectivity, and population coding in the SC, where nonlinear integration, distributed representations and regional functional specialisations enables robust sensory binding and supports the accurate encoding of temporal multisensory information. Our study provides new insights into how the brain leverages both single-neuron and network-level mechanisms to represent sensory features by adapting to the statistics of the natural world.
Complex interplay between gene deletions and the environment uncovers cellular roles for genes of unknown function inEscherichia coli
Authors: Sondervorst Kaat , Nesporova Kristina , Herdman Matthew , Steemans Bart , Rosseels Joëlle , Govers Sander K.
Published: February 2025

Phenotypic outcomes can be heavily affected by environmental factors. In this study, we exploited the previously observed nutrient-dependency of cell biological phenotypic features, captured by a cross-condition image-based profiling assay ofEscherichia colideletion strains, to examine this in more detail. We identified several general principles, including the existence of a spectrum of deviating phenotypes across nutrient conditions (i.e., from nutrient- or feature-specific to pleiotropic phenotypic deviations), limited conservation of phenotypic deviations across nutrient conditions (i.e., limited phenotypic robustness), and a subset of nutrient-independent phenotypic deviations (indicative of consistent genetic determinants of specific phenotypic features). In a subsequent step, we used this cross-condition dataset to identify five genes of unknown function of which the deletion displayed either nutrient-independent phenotypic deviations or phenotypic similarities to genes of known function:yibN,yaaY,yfaQ,ybiJ, andyijD. These genes showed different levels of phylogenetic conservation, ranging from conserved across the tree of life (yibN) to only present in some genera of the Enterobacterales (yaaY). Analysis of the structural properties of the proteins encoded by these y-genes, identification of structural similarities to other proteins, and the examination of their subcellular localization yielded new insights into their contribution toE. colicell morphogenesis, cell cycle progression and cell growth. Together, our approach showcases how bacterial image-based profiling assays and datasets can serve as a gateway to reveal the function of uncharacterized proteins.

Importance

Despite unprecedented access to genomic information, predicting phenotypes based on genotypes remains notoriously difficult. One major confounding factor is the environment and its ability to modulate phenotypic outcomes. Another is the fact that a large fraction of protein-coding genes in bacterial genomes remains uncharacterized and have no known function. In this work, we use a large-scale cross-condition image-based profiling dataset to characterize nutrient-dependent phenotypic variability ofE. colideletion strains and exploit it to provide insight into the cellular role of genes of unknown function. Through our analysis, we identified five genes of unknown function that we subsequently further characterized by examining their phylogenetic conservation, predicted structural properties and similarities, and their intracellular localization. Combined, this approach highlights the potential of cross-condition image-based profiling, which extracts many cell biological phenotypic readouts across multiple conditions, to better understand nutrient-dependent phenotypic variability and uncover protein function.