bluuebunny/crossref_metadata_2025 huggingface dataset:
Surgical Treatment of Temporomandibular Joint Ankylosis: our experience with 36 cases
Authors: Rikhotso Risimati E. , Sekhoto Mmathabo G.
Published: May 2024

Aim:

To evaluate and compare outcomes of patients with temporomandibular joint ankylosis (TMJA) treated by gap arthroplasty, costochondral graft, and total alloplastic joint reconstruction.

Methodology:

A retrospective cohort study reviewed and analyzed data from patients with TMJA from January 1, 2009 to December 31, 2019, at the Maxillofacial and Oral Surgery Department, University of the Witwatersrand. Patients with TMJA were treated either with gap arthroplasty, costochondral graft, or total alloplastic joint reconstruction. Data collected included age, sex, etiology of ankylosis, sides involved, preoperation and postoperation mouth opening (MO), treatment type, complications, and revision surgery. Patients were followed up for at least 18 months after the surgical procedure. Comparison of means across the treatment groups was analyzed using paired t tests or analysis of variance test. A P value of less than 0.05 was considered statistically significant.

Results:

The study sample comprised of 36 patients [bilateral, n=22; unilateral, n=14 (21 male, 15 female)]. Trauma was the most common etiology (n=27, 75%), followed by chronic infections (n=4, 11.11%) and juvenile arthritis (n=3, 8.3%). A paired t test revealed no statistical significance between treatment modality and postoperative MO and complications over 18 months (P=0.5316 and P=0.426, respectively). The mean MO increased from 4 to 28 mm. Reankylosis was the most common complication (n=5).

Conclusions:

All 3 treatment options yield acceptable outcomes in patients with TMJA. Irrespective of surgical technique, early postoperative exercises, active physiotherapy, and follow-up are imperative for successful rehabilitation and prevention of reankylosis.
Management of Atypical M-Shaped Zygomatic Arch Fractures
Authors: Lin Yuxin , Lv Kun
Published: May 2024

Background:

M-shaped zygomatic arch fractures can usually be treated effectively through closed reduction. It consists of 2 fracture segments: the anterior zygomatic segment and the posterior temporal bone segment. In clinical practice, atypical M-shaped fractures are often encountered, in which the anterior and posterior fracture segments are discontinuous and separated. Closed reduction usually cannot achieve the desired anatomic reduction effect for this type of fracture.

Methods:

The preoperative design showed that the anatomic reduction of the posterior zygomatic arch fracture segment was hindered due to bone spurs in the most concave area of the anterior zygomatic bone fracture segment. Open reduction and fixation were performed to achieve anatomic reduction and restore facial symmetry. The fracture sites were exposed through a hemicoronal incision. After the bone spurs are removed, the posterior bone segment can be anatomically reduced. Absorbable plates were used for fixation.

Results and Discussion:

The patient’s facial appearance was restored after the surgery. The postoperative computed tomography scan showed a good alignment of the fracture. The authors believe that for patients with high requirements for facial symmetry, the presence of atypical M-shaped fractures can indicate open reduction and fixation.
The Effects of the Maxillary Movements in Angle Class 2 and 3 Malocclusion Treatment on Nose Air Flow Amount, Rate, and Resistance
Authors: Can Yücel Hüseyin , Kozanoğlu Erol , Edim Akalin Bora , Onur Sütçü Ahmet , Şentürk Erol , Emekli Ufuk
Published: May 2024

Maxillary movements performed during orthognathic surgery affect the external and internal anatomy of the nose. The functional and anatomical effects may change nasal airway parameters after the surgery, and these alterations can be examined objectively by rhinomanometry. In this study, patients who underwent maxillary orthognathic surgery were divided into 3 groups based on their surgical plans: advancement (group 1), impaction and advancement (group 2), and setdown and advancement (group 3). Preoperative and postoperative rhinomanometric data including the average nasal volume, minimum cross-sectional area, average airflow resistance of the right and left nasal passageways, and an average of both nasal passages were collected. The study included 50 patients who underwent orthognathic surgery between October 2021 and October 2022. There were 20 patients each in group 1 and group 2 and 10 patients in group 3. The average nasal passage volume increased in the advancement (group 1) and impaction–advancement (group 2) groups. In addition, the advancement (group 1) group had a decreased average airflow resistance. Setdown–advancement (group 3) group did not show a positive or negative effect on nasal airway parameters. Maxillary movements during orthognathic surgery revealed no adverse effect on nasal parameters. Moreover, advancement and impaction positively affected nasal functional and anatomical parameters.
Laparoscopic Pancreaticoduodenectomy Combined With Portal-Superior Mesenteric Vein Resection and Reconstruction: Inferior-Posterior “Superior Mesenteric Artery-First” Approach
Authors: An Baiqiang , Yue Qing , Wang Shupeng , Han Wei
Published: May 2024

Background:

Laparoscopic pancreaticoduodenectomy (LPD) with portal-superior mesenteric vein (PV/SMV) resection and reconstruction is increasingly performed. We aimed to introduce a safe and effective surgical approach and share our clinical experience with LPD with PV/SMV resection and reconstruction.

Methods:

We reviewed data for the patients undergoing LPD and open pancreaticoduodenectomy (OPD) combined with PV/SMV resection and reconstruction at the First Hospital of Jilin University between April 2021 and May 2023. The inferior-posterior “superior mesenteric artery-first” approach was used. We compared the preoperative, intraoperative, and postoperative clinicopathological data of the 2 groups to conduct a comprehensive evaluation of LPD with major vascular resection.

Results:

A cohort of 37 patients with periampullary and pancreatic tumors underwent pancreaticoduodenectomy (PD) with major vascular resection and reconstruction, consisting of 21 LPDs and 16 OPDs. The LPD group had a longer operation time (322 vs. 235 min, P=0.039), reduced intraoperative bleeding (152 vs. 325 mL, P=0.026), and lower intraoperative blood transfusion rates (19.0% vs. 50.0%, P=0.046) compared with the OPD group. The LPD group had significantly shorter operation times in end-to-end anastomosis (26 vs. 15 min, P=0.001) and artificial grafts vascular reconstruction (44 vs. 22 min, P=0.000) compared with the OPD group. There was no significant difference in the rate of R0 resection (100% vs. 87.5%, P=0.096). The length of hospital stay and ICU stay did not show significant differences between the 2 groups (15 vs. 18 d, P=0.636 and 2.5 vs. 4.5 d, P=0.726, respectively). However, the postoperative hospital stay in the LPD group was notably shorter compared with the OPD group (11 vs. 16 d, P=0.007). Postoperative complication rates, including postoperative pancreatic fistula (POPF) Grade A/B, biliary leakage, and delayed gastric emptying (DGE), were similar between the two groups (38.1% vs. 43.8%, P=0.729). In addition, 1 patient in each group developed thrombosis, with vascular patency improving after anticoagulation treatment.

Conclusion:

LPD combined with PV/SMV resection and reconstruction can be easily and safely performed using the inferior-posterior “superior mesenteric artery-first” approach in cases of venous invasion. Further studies are required to evaluate the procedure’s long-term outcomes.
Zavegepant for Acute Treatment of Migraine: A Systematic Review and Meta-analysis of Randomized Controlled Trials
Authors: Suresh Vinay , Bardhan Mainak , Dave Tirth , Shamim Muhammad Aaqib , Suresh Dilip , Satish Poorvikha , Dhakal Bishal , Bhonsale Aman , Roy Priyanka , Padhi Bijaya Kumar , Monteith Teshamae
Published: May 2024

Objective

Evaluate the safety and efficacy of zavegepant (BHV-3500), a recently approved nasal spray containing a third-generation calcitonin gene-related peptide receptor antagonist, for treating acute migraine attacks.

Methods

A comprehensive search was conducted across various databases up to 06/26/2023 to identify relevant randomized clinical trials (RCTs) on zavegepant's efficacy and safety in treatment of acute migraine attacks. Primary outcome: freedom from pain at 2 hours postdose. Safety outcomes were evaluated based on adverse events (AEs), with zavegepant 10 mg and placebo groups compared for incidence of AEs.

Results

Two RCTs, involving 2061 participants (1014 receiving zavegepant and 1047 receiving placebo), were quantitatively analyzed. An additional trial was included for qualitative synthesis. Zavegepant 10 mg exhibited a significantly higher likelihood of achieving freedom from pain at 2 hours postdose compared with the placebo group (risk ratio [RR] 1.54, 95% confidence interval [CI] 1.28 to 1.84). It also showed superior relief from the most bothersome symptoms at 2 hours postdose compared with placebo (RR 1.26, 95% CI 1.13 to 1.42). However, the zavegepant 10 mg group experienced a higher incidence of AEs compared with placebo (RR 1.78, 95% CI 1.5 to 2.12), with dysgeusia being the most reported AE (RR 4.18, 95% CI 3.05 to 5.72).

Conclusion

Zavegepant 10 mg is more effective than placebo in treating acute migraine attacks, providing compelling evidence of its efficacy in relieving migraine pain and most bothersome associated symptoms. Further trials are necessary to confirm its efficacy, tolerability, and safety in diverse clinic-based settings with varied patient populations.
Retinal Tear Following Low-Frequency Repetitive Transcranial Magnetic Stimulation for Obsessive-Compulsive Disorder
Authors: Garip Beyazit , Buzkan Burcu , Demir Suleyman
Published: May 2024

Objectives

Repetitive transcranial magnetic stimulation (rTMS) is a noninvasive form of brain stimulation that uses magnetic pulses to stimulate specific brain regions. Retina is being investigated whether the retina, which is also known as the brain's window to the outside world, is affected by the treatment.

Methods

Magventure X100 device was used for the procedure. The bilateral supplementary motor area was targeted. Procedure protocol: power: 47%, repetitive rate (frequency): 1 Hz, pulses in train duration: 300, intertrain interval (waiting time): 120 seconds, number of trains: 4, total pulses: 1200. Twenty sessions of rTMS were planned for the patient. The patient was informed about the procedure, and her consent was obtained.

Results

The Yale-Brown Obsessive-Compulsive Disorder Scale (YBOCS) score before the first session was 31, and the Brown Assessment Beliefs Scale (BABS) score was 5. The patient's YBOCS score after the 15th session was 14, and the BABS score was 0. After the implementation of the 15th session of the patient's treatment, retinal detachment developed in the right eye, and the treatment was terminated. As a result of the eye examination of the patient, it was determined that there was 1 horseshoe rupture and 2 hole-shaped ruptures in the lower half of the left eye.

Conclusions

Patients at risk for retinal detachment may require specialized treatment and close monitoring to prevent the condition from worsening. It is important to consult with an ophthalmologist for patients at risk for retinal detachment before TMS application.
Effect of Ketamine Treatment on Social Withdrawal in Autism and Autism-Like Conditions
Authors: Ralston Megan , Osman Alim , Suryadevara Pavan , Cleland Elissa
Published: May 2024

Objective

Ketamine and esketamine have been used in the field of psychiatry to alleviate conditions such as major depressive disorder. Our objective was to evaluate the current literature on the use of ketamine for symptoms of social withdrawal in autism spectrum disorder (ASD) and autism-like conditions.

Methods

A comprehensive search of PubMed and Web of Science was conducted to identify literature involving the use of ketamine to treat symptoms of autism and social withdrawal. Patients with comorbid disorders were also included.

Results

Two original studies were found, showing mixed results on the use of ketamine for ASD. The use of esketamine found no statistically significant results, whereas the use of intravenous ketamine was shown to alleviate symptoms of social withdrawal especially in the short term. Neither study reported a significant amount of serious adverse events. Five case reports were also included, showing decreased depressive symptoms and evidence of increased social condition.

Conclusions

Research on the use of ketamine for ASD and ASD-related conditions is limited. Evidence of improved social condition exists, but further studies should be conducted to increase sample power and test various doses and methods of administration.
Antifungal activity of human antimicrobial peptides targeting apoptosis in Candida auris
Authors: Shaban Siham , Patel Mrudula , Ahmad Aijaz
Published: May 2024

Introduction. Innovative antifungal therapies are of crucial importance to combat the potentially life-threatening infections linked to the multidrug-resistant fungal pathogen Candida auris. Induction of regulated cell death, apoptosis, could provide an outline for future therapeutics. Human antimicrobial peptides (AMPs), well-known antifungal compounds, have shown the ability to induce apoptosis in pathogenic fungi.

Hypothesis/Gap Statement
. Although it is known that AMPs possess antifungal activity against C. auris, their ability to induce apoptosis requires further investigations.

Aim. This study evaluated the effects of AMPs on the induction of apoptosis in C. auris.

Methods. Human neutrophil peptide-1 (HNP-1), human β-Defensins-3 (hBD-3) and human salivary histatin 5 (His 5) were assessed against two clinical C. auris isolates. Apoptosis hallmarks were examined using FITC-Annexin V/PI double labelling assay and terminal deoxynucleotidyl transferase deoxynucleotidyl transferase nick-end labelling (TUNEL) to detect phosphatidylserine externalization and DNA fragmentation, respectively. Then, several intracellular triggers were studied using JC-10 staining, spectrophotometric assay and 2′,7′-dichlorofluorescin diacetate staining to measure the mitochondrial membrane potential, cytochrome-c release and reactive oxygen species (ROS) production, respectively.

Results and conclusion. FITC-Annexin V/PI staining and TUNEL analysis revealed that exposure of C. auris cells to HNP-1 and hBD-3 triggered both early and late apoptosis, while His 5 caused significant necrosis. Furthermore, HNP-1 and hBD-3 induced significant mitochondrial membrane depolarization, which resulted in substantial cytochrome c release. In contrast to His 5, which showed minimal mitochondrial depolarization and no cytochrome c release. At last, all peptides significantly increased ROS production, which is related to both types of cell death. Therefore, these peptides represent promising and effective antifungal agents for treating invasive infections caused by multidrug-resistant C. auris.
Actinomycetota bioprospecting from ore-forming environments
Authors: Aguilar César , Alwali Amir , Mair Madeline , Rodriguez-Orduña Lorena , Contreras-Peruyero Haydeé , Modi Ramya , Roberts Carson , Sélem-Mojica Nelly , Licona-Cassani Cuauhtemoc , Parkinson Elizabeth Ivy
Published: May 2024

Natural products from Actinomycetota have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.
Androgen receptor activity inversely correlates with immune cell infiltration and immunotherapy response across multiple cancer lineages
Authors: Hu Ya-Mei , Zhao Faming , Graff Julie N. , Chen Canping , Zhao Xiyue , Thomas George V. , Wu Hui , Kardosh Adel , Mills Gordon B. , Alumkal Joshi J. , Moran Amy E. , Xia Zheng
Published: May 2024

There is now increasing recognition of the important role of androgen receptor (AR) in modulating immune function. To gain a comprehensive understanding of the effects of AR activity on cancer immunity, we employed a computational approach to profile AR activity in 33 human tumor types using RNA-Seq datasets from The Cancer Genome Atlas. Our pan-cancer analysis revealed that the genes most negatively correlated with AR activity across cancers are involved in active immune system processes. Importantly, we observed a significant negative correlation between AR activity and IFNγ pathway activity at the pan-cancer level. Indeed, using a matched biopsy dataset from subjects with prostate cancer before and after AR-targeted treatment, we verified that inhibiting AR enriches immune cell abundances and is associated with higher IFNγ pathway activity. Furthermore, by analyzing immunotherapy datasets in multiple cancers, our results demonstrate that low AR activity was significantly associated with a favorable response to immunotherapy. Together, our data provide a comprehensive assessment of the relationship between AR signaling and tumor immunity.
Single-cell and spatial atlas of steatotic liver disease-related hepatocellular carcinoma
Authors: Prawira Aldo , Xu Hang , Leow Wei Qiang , Otsuka Masayuki , Chen Ziyao , Rahbari Mohammad , Hazirah Sharifah N. , Wasser Martin , Chung Alexander , Goh Brian K.P. , Chow Pierce K.H. , Albani Salvatore , Lee Joycelyn , Lim Tony K.H. , Zhai Weiwei , Dan Yock Young , Goh George , Tai David , DasGupta Ramanuj , Heikenwalder Mathias , Chen Jinmiao , Chew Valerie
Published: May 2024

Steatotic liver disease-related hepatocellular carcinoma (SLD-HCC) poses significant challenges in liver cancer management. Our current study investigates the tumor microenvironment (TME) of SLD-HCC using single-cell transcriptomic, proteomic and spatial transcriptomic analyses. We identified altered immune-related and lipid metabolism pathways, particularly in regulatory T cells (Tregs) and cancer-associated fibroblasts (CAFs) within the SLD-HCC microenvironment, suggesting distinct cellular adaptations to a high-fat TME and general immunosuppression. Cytometry by time-of-flight revealed a cold and immunosuppressive TME depleted with CD8+T cells and enriched with Tregs, while spatial transcriptomics uncovered a unique spatial architecture with Treg/CAF clusters specifically located at the tumor margins in SLD-HCC. Crucially, we identified Treg-CAF interactions as a key mediator associated with lack of response to immunotherapy in SLD-HCC. Our findings highlight the intricate immune dynamics of SLD-HCC, indicating potential therapeutic targets to counteract immune evasion and restore anti-tumor immunity in SLD-HCC.

Highlights

The TME of SLD-HCC exhibits altered immune and lipid pathways

Immunosuppressive SLD-HCC TME is depleted with CD8+T cells and enriched with Tregs

SLD-HCC has a unique spatial architecture with Treg-CAF clusters at tumor margins

Treg-CAF interaction via TNFSF14-TNFRSF14 axis mediates immunotherapy resistance
Nutraceuticals Silybin B, resveratrol and epigallocatechin-3 gallate (EGCG) bind to cardiac muscle troponin to restore the loss of lusitropy caused by cardiomyopathy mutationsin vitro, in vivo, andin silico
Authors: Yang Zeyu , Sheehan Alice , Messer Andrew , Tsui Sharmane , Sparrow Alexander , Redwood Charles , Kren Vladimir , Gould Ian R. , Marston Steven B.
Published: May 2024

Adrenergic activation of protein kinase A (PKA) targets the thin filaments of the cardiac muscle, specifically phosphorylating cTroponin I Ser22 and Ser23, causing a higher rate of Ca2+dissociation from cTnC leading to a faster relaxation rate (lusitropy). This modulation is often suppressed by mutations that cause cardiomyopathy (uncoupling) and this could be sufficient to induce cardiomyopathy. A drug that could restore the phosphorylation-dependent modulation of relaxation rate could have the potential for treatment of these pathologies.

We found, using single thin filamentin vitromotility assays that the small molecules including silybin B, resveratrol, and epigallocatechin-3 gallate (EGCG) can restore coupling.

We performed molecular dynamics simulations of the unphosphorylated and phosphorylated cardiac Troponin core with the TNNC1 G159D mutation. We found that silybin B, EGCG, and resveratrol restored the phosphorylation-induced change in the TnC helix A/B angle and the interdomain angle to wild-type values, whilst silybin A and epicatechin gallate (ECG) did not. In unphosphorylated G159D the recoupling molecules were observed to be frequently intercalated between The N terminal peptide of Troponin I and troponin C. In contrast, the controls, silybin A, and ECG bound to the surface. All of the interactions were diminished when troponin I was phosphorylated.

We also performed studies with intact transgenic ACTC E99K mouse cells and TNNT2 R92Q-transfected guinea pig cardiomyocytes. The mutations blunt the increase in relaxation speed due to dobutamine; resveratrol, EGCG, and silybin B could restore the dobutamine response whilst silybin A did not. Thus recoupling by small molecules is demonstratedin vitro, in vivo, andin silico.
Longitudinal Prediction of Drug Response in High-Grade Serous Ovarian Cancer Organoid Cultures Aligning with Clinical Responses
Authors: Cavarzerani Enrico , Caligiuri Isabella , Bartoletti Michele , Corona Giuseppe , Perin Tiziana , Palumbo Antonio , Canzonieri Vincenzo , Rizzolio Flavio
Published: May 2024

High-grade serous ovarian cancer (HGSOC) ranks among the most aggressive gynecological malignancies. Its high mortality stems from frequent recurrence post-primary treatments and development of platinum resistance. Since, traditional drug development via animal models is time-consuming and lacks reproducibility, in precision cancer medicine, primary patient-derived organoids (PDOs) offer a solution by replicating disease pathophysiology and expediting drug screening. We developed an expandable HGSOC organoid platform for rapid drug screening and resistance testing. Our study aimed to validate the stability of seven PDO pairs in predicting drug responses over time. Organoids underwent low- and high-passage drug screenings over nine months, involving 21 conventional and FDA-approved drugs and proteomic analyses. Comparison of in vitro outcomes with clinical data confirmed the platform’s predictive capacity. Notably, a PDO with BRCA1 mutation exhibited resistance to Carboplatin and PARP inhibitors, highlighting organoid models’ clinical relevance for novel targeted therapies such as the Peptidylprolyl Cis/Trans Isomerase, NIMA-Interacting 1 (Pin1), a valuable target for HGSOC patients.
Optimizing clinical interpretability of functional evidence in epilepsy-related ion channel variants
Authors: Parthasarathy Shridhar , Cohen Stacey R. , Fitch Eryn , Vaidiswaran Priya , Ruggiero Sarah , Lusk Laina , Chisari Victoria , Lewis-Smith David , Lauxmann Stephan , Boßelmann Christian M. , Thompson Christopher H. , Wengert Eric R. , Hedrich Ulrike , Ganesan Shiva , Balagura Ganna , Krause Roland , Xian Julie , Galer Peter , Pendziwiat Manuela , Perez-Palma Eduardo , Vihinen Mauno , Hart Jennifer , Landrum Melissa J. , Lal Dennis , Cooper Edward C. , Lerche Holger , Goldberg Ethan , Brunklaus Andreas , Vanoye Carlos G. , Schorge Stephanie , George Alfred L. , Helbig Ingo
Published: May 2024

Variants in genes encoding the voltage-gated ion channels are among the most common monogenic causes of epilepsy and neurodevelopmental disorders. Functional effects of a variant are increasingly important for diagnosis and therapeutic decisions. To incorporate knowledge regarding functional consequences in formal clinical variant interpretation, we developed an approach for evaluating multiple functional measurements within the Bayesian framework of the modified ACMG/AMP guidelines. We analyzed 216 functional assessments of 191 variants inSCN1A(n=74),SCN2A(n=66),SCN3A(n=18), andSCN8A(n=33). Of 20 commonly measured biophysical parameters, the most frequent drivers of overall functional consequence were persistent current (f=0.54), voltage dependence of activation (f=0.51), and voltage dependence of fast inactivation (f=0.40) for gain-of-function and peak current (f=0.87) for loss-of-function. By comparing measurements of 23 benign variants, we determined thresholds by which published data on these four parameters conferStrongevidence of variant pathogenicity (likelihood ratio > 18.7) under the ACMG/AMP rubric. Similarly, we delineated evidence weights for the most common epilepsy-related potassium channel gene,KCNQ2, through reports of 80 pathogenic and 24 benign variants, accounting for heterozygous and homozygous experimental conditions. We collected the resulting categorization of functional data into FENICS, a biomedical ontology of 152 standardized terms for coherent annotation of electrophysiological results. Across 271 variants inSCN1A/2A/3A/8AandKCNQ2, 1,731 annotations are available in ClinVar, facilitating use of this evidence in variant classification. In summary, we introduce and apply an ACMG/AMP-calibrated framework for electrophysiological studies in epilepsy-related channelopathies to delineate the impact of functional evidence on clinical variant interpretation.
Distinct genome architecture underlies fine-scale population differentiation in two common European bumblebees (Bombus pascuorumandBombus lapidarius)
Authors: Cobb Lauren , Sydenham Markus A. K. , Nielsen Anders , Star Bastiaan
Published: May 2024

Bumblebees are keystone pollinators which facilitate the reproduction of a wide range of wild and agricultural plants. Their abundance and diversity have been severely reduced by anthropogenic stressors such as land-use change and widespread habitat fragmentation. However, we lack a comprehensive understanding of bumblebee population structure and local adaptation in response to human-altered landscapes. We here discover surprisingly fine-scaled population structure (e.g. ∼300km) within two widely occurring bumblebee species,Bombus lapidariusandBombus pascuorum, by analysing whole genome data of 106 specimens from 7 sites in Northern Europe. Our sample range encompasses a mosaic of land-use types with varying levels of habitat fragmentation and natural oceanic barriers. While the observed population structure is largely associated with reduced gene flow across natural barriers, we also detect significant divergence between populations sampled from more fragmented, agricultural landscapes. Furthermore, we identify species-specific patterns of population structure which are underpinned by distinct genomic architecture. Whereas genetic divergence inB. lapidariusis spread relatively evenly across the genome, divergence inB. pascuorumis concentrated within several megabase-sized genomic regions with significantly elevated differentiation – including a putative chromosomal inversion – which may underlie well-known colour polymorphisms across its range. Our observations reveal unexpectedly high levels of inter- and intraspecific genomic diversity within the bumblebee genus, and highlight the necessity of increasing our understanding of bumblebee population structure and connectivity to design optimal bumblebee conservation strategies.

Significance statement

Anthropogenic stressors such as habitat fragmentation have severe impacts on bumblebee abundance and diversity, yet little is known about how bumblebee populations are structured in human-altered landscapes. We analyse whole-genome data from two common bumblebee species (Bombus lapidariusandBombus pascuorum) across Northern Europe to uncover species-specific patterns of spatial population differentiation and local adaptation, including a chromosomal rearrangement inB. pascuorum. Importantly, our results imply that many of the fragmented bumblebee habitats in Europe comprise locally distinct populations with limited gene flow in between. These findings are therefore of major importance for our overall understanding of bumblebee genomic variation, connectivity and adaptation, offering fundamental insights that are required to effectively mitigate the effects of human activities on wild bee biodiversity.
Supervised and unsupervised deep learning-based approaches for studying DNA replication spatiotemporal dynamics
Authors: Ng-Kee-Kwong Julian , Philps Ben , Smith Fiona N. C. , Sobieska Aleksandra , Chen Naiming , Alabert Constance , Bilen Hakan , Buonomo Sara C. B.
Published: May 2024

In eukaryotic cells, DNA replication is organised both spatially and temporally, as evidenced by the stage-specific spatial distribution of replication foci in the nucleus. Despite the genetic association of aberrant DNA replication with numerous human diseases, the labour-intensive methods employed to study DNA replication have hindered large-scale analyses of its roles in pathological processes. In this study, we first demonstrate that a convolutional neural network trained to classify S-phase stages based on DAPI and EdU patterns could identify altered replication dynamics inRif1-deficient mouse embryonic stem cells (mESCs), revealing a skewed distribution across the various S-phase stages. Given the possible practical limitations associated with a supervised framework, we proceed to show that the abnormal replication profile ofRif1-deficient mESCs could further be detected by an unsupervised approach (based on self-supervised representation learning), which could additionally reconstruct progression through S-phase. Finally, we extend our approach to a well-characterised cellular model of inducible deregulated origin firing, involving cyclin E overexpression. Through parallel EdU- and PCNA-based analyses, we demonstrate the potential applicability of our method to patient samples, offering a means to identify the contribution of deregulated DNA replication to a plethora of pathogenic processes.
TOR signaling regulates GPCR levels on the plasma membrane and suppresses theSaccharomyces cerevisiaemating pathway
Authors: Leclerc Nicholas R. , Dunne Toby M. , Shrestha Sudati , Johnson Cory P. , Kelley Joshua B.
Published: May 2024

Saccharomyces cerevisiaerespond to mating pheromone through the GPCRs Ste2 and Ste3, which promote growth of a mating projection in response to ligand binding. This commitment to mating is nutritionally and energetically taxing, and so we hypothesized that the cell may suppress mating signaling during starvation. We set out to investigate negative regulators of the mating pathway in nutritionally depleted environments. Here, we report that nutrient deprivation led to loss of Ste2 from the plasma membrane. Recapitulating this effect with nitrogen starvation led us to hypothesize that it was due to TORC1 signaling. Rapamycin inhibition of TORC1 impacted membrane levels of all yeast GPCRs. Inhibition of TORC1 also dampened mating pathway output. Deletion analysis revealed that TORC1 repression leads to α-arrestin-directed CME through TORC2-Ypk1 signaling. We then set out to determine whether major downstream effectors of the TOR complexes also downregulate pathway output during mating. We found that autophagy contributes to pathway downregulation through analysis of strains lackingATG8. We also show that Ypk1 significantly reduced pathway output. Thus, both autophagy machinery and TORC2-Ypk1 signaling serve as attenuators of pheromone signaling during mating. Altogether, we demonstrate that the stress-responsive TOR complexes coordinate GPCR endocytosis and reduce the magnitude of pheromone signaling, in ligand-independent and ligand-dependent contexts.

One Sentence Summary

TOR signaling regulates the localization of allSaccharomyces cerevisiaeGPCRs during starvation and suppress the mating pathway in the presence and absence of ligand.
Identification of the potential function-specific sites in subunits of vertebrate neuronal nicotinic acetylcholine receptors
Authors: Zhu Zhouhai , Zhang Fengyu , Guan Ying , Pan Zhenhua , Li Meng , Wang Ju
Published: May 2024

The nicotinic acetylcholine receptors (nAChR) are complexes that are composed of subunits evolved from common ancestor. Although the subunits are similar in sequences and structures, their molecular function varies significantly. Therefore, detecting the molecular sites specific to each subunit is important to understand the property of the subunits and the receptors formed by them. As we know, the molecular sites critical to the structure and molecular function of a protein family usually are conserved in evolution, and those specific to each member of the family are often closely related to its structural and functional specificity. In this study, we analyzed the sequence specific sites in nAChR subunits by adopting the evolutionary trace method and the two-state model, and explored the relationship between structure and function in combination with the spatial location of the sites. The results showed that the detected sites in α7 subunit were closely related to ligand binding and conformational changes of the energetic coupling pathway. The conserved sites tended to be distributed in the interior of the spatial structure of protein molecules, and the sites potentially related to new functions were distributed on the surface of the spatial structure. In summary, our results could be helpful to understanding the molecular features related to the function specificity and diversity of the nAChR subunits.
An early, novel arginine methylation of KCa3.1 attenuates subsequent T cell exhaustion
Authors: Sharma Piyush , Guo Ao , Poudel Suresh , Boada-Romero Emilio , Verbist Katherine C. , Palacios Gustavo , Immadisetty Kalyan , Chen Mark J. , Haydar Dalia , Mishra Ashutosh , Peng Junmin , Babu M. Madan , Krenciute Giedre , Glazer Evan S. , Green Douglas R.
Published: May 2024

T cell receptor (TCR) engagement initiates the activation process, and this signaling event is regulated in multifaceted ways. Nutrient availability in the immediate niche is one such mode of regulation1–3. Here, we investigated how the availability of an essential amino acid methionine (Met) and TCR signaling might interplay in the earliest events of T cell activation to affect subsequent T cell fate and function. We found that limiting Met during only the initial 30 minutes of CD8+T cell activation increased Ca2+influx, Ca2+-mediated NFAT1 (Nfatc2) activation, NFAT1 promoter occupancy, and T cell exhaustion. We identified changes in the protein arginine methylome during the initial 30 min of TCR engagement and discovered a novel arginine methylation of a Ca2+-activated potassium transporter, KCa3.1, which regulates Ca2+-mediated NFAT1 signaling to ensure optimal activation. Ablation of arginine methylation in KCa3.1 led to increased NFAT1 activation, rendering T cells dysfunctional in murine tumour and infection models. Furthermore, acute Met supplementation at early stages reduced nuclear NFAT1 in tumour-infiltrating T cells and augmented their anti-tumour activity. Our findings identify a metabolic event occurring early after T cell activation that influences the subsequent fate of the cell.
ErbB2/HER2 governs CDK4 inhibitor sensitivity and timing and irreversibility of G1/S transition by altering c-Myc and cyclin D function
Authors: Ichikawa Ayaka Nagasato , Murakami Ken , Aoki Kazuhiro , Okada Mariko
Published: May 2024

Cell cycle entry and the irreversible transition from the G1 to S phase are crucial for mammalian cell proliferation. Among the ErbB family, the ErbB2/HER2 receptor is a key driver of cancer growth. However, the quantitative mechanisms underlying the ErbB2-mediated G1/S transition remain unclarified. Here, we performed an extensive time-course analysis of high and low ErbB2-expressing breast cancer cells to describe the regulatory mechanisms of the ErbB2-mediated G1/S transition. Live-cell imaging using cell cycle reporters revealed that the G1/S transition occurs 20 h after ErbB2 activation, driven primarily by the cyclin D1/CDK4-RB axis. Hsp90 is regulated by CDK4 activity and controls the stability of ErbB2 protein in a time-dependent manner. CDK4 inhibitor treatment arrested the cell cycle in most cells; a subpopulation showed a 25-h delay in G1/S entry associated with enhanced c-Myc activation. In high ErbB2-expressing cells, CDK4 inhibition led to c-Myc overactivation, a rapid decrease in cyclin D1 expression, and cell cycle arrest. Overall, we demonstrate how ErbB2 receptor levels modulate the roles of cyclin D1 and c-Myc in the G1/S transition and suggest that variations in ErbB2 levels within breast cancer tissues confer heterogeneous sensitivity to CDK4 inhibitors, potentially complicating treatment.
Automated muscle path calibration with gradient-specified optimization based on moment arm
Authors: Chen Ziyu , Hu Tingli , Haddadin Sami , Franklin David W.
Published: May 2024

Muscle path modeling is more than just routing a cable that visually represents the muscle, but rather it defines how moment arms vary with different joint configurations. The muscle moment arm is the factor that translates muscle force into joint moment, and this property has an impact on the accuracy of musculoskeletal simulation. However, it is not easy to calibrate muscle path based on moment arm, because each path is configured by various parameters while the relations between moment arm and both the parameters and joint configuration are complicated. Here, we tackle this challenge in the simple fashion of optimization, but with an emphasis on the gradient; when specified in its analytical form, optimization speed and accuracy will be improved. We explain in detail how to differentiate the enormous cost function and how our optimization is configured, then we demonstrate the performance of this method by fast and accurate replication of muscle paths from a state-of-the-art shoulder–arm model. As long as the muscle is represented as a cable wrapping around obstacles, our method could overcome difficulties in path calibration, both for developing generic models and for customizing subject-specific models.
Biallelic variants inARHGAP19cause a motor-predominant neuropathy with asymmetry and conduction slowing
Authors: Dominik Natalia , Efthymiou Stephanie , Record Christopher J. , Miao Xinyu , Lin Renee , Parmar Jevin , Scardamaglia Annarita , Maroofian Reza , Aughey Gabriel , Wilson Abigail , Lowe Simon , Curro Riccardo , Schnekenberg Ricardo P. , Alavi Shahryar , Leclaire Leif , He Yi , Zhelchenska Kristina , Bellaiche Yohanns , Gaugué Isabelle , Skorupinska Mariola , Van de Vondel Liedewei , Da’as Sahar I. , Turchetti Valentina , Güngör Serdal , Karimiani Ehsan Ghayoor , Ricaurte Camila Armirola , Topaloglu Haluk , Jordanova Albena , Zaman Mashaya , Banu Selina H. , Marques Wilson , Tomaselli Pedro José , Aynekin Busra , Cansu Ali , Per Huseyin , Güleç Ayten , Alvi Javeria Raza , Sultan Tipu , Khan Arif , Zifarelli Giovanni , Ibrahim Shahnaz , Mancini Grazia M.S. , Motazacker M. Mahdi , Brusse Esther , Lupo Vincenzo , Sevilla Teresa , Başak A Nazlı , Tekgul Seyma , Palvadeau Robin , Baets Jonathan , Parman Yesim , Çakar Arman , Horvath Rita , Haack Tobias B. , Stahl Jan-Hendrik , Grundmann-Hauser Kathrin , Park Joohyun , Züchner Stephan , Laing Nigel G. , Wilson Lindsay , Rossor Alexander M. , Polke James , Figueiredo Fernanda Barbosa , Pessoa André Luiz , Kok Fernando , Coimbra-Neto Antônio Rodrigues , França Marcondes C. , Jamshidi Yalda , Ravenscroft Gianina , Hamed Sherifa Ahmed , Chung Wendy K. , Osborn Daniel P. , Hanna Michael , Cortese Andrea , Reilly Mary M. , Jepson James E. C. , Lamarche-Vane Nathalie , Houlden Henry
Published: May 2024

Charcot-Marie-Tooth Disease is a clinically and genetically heterogeneous group of hereditary neuropathies, with over 100 causative genes identified to date. Despite progress in genetic sequencing, around a quarter of patients remain unsolved. Through international collaborations, we identified 16 recessive variants in Rho GTPase activating protein 19 (ARHGAP19) causing motor-predominant neuropathy with conduction slowing in 25 individuals from 20 unrelated multi-ancestry families. ARHGAP19 is a GTPase-activating protein with activity towards RhoA.In vitrobiochemical assays revealed that variants located within the GAP domain cause loss of GAP activity. iPSc-derived motor neurons exhibited 50% knockdown of ARHGAP19 protein.In vivogenetic perturbations of theDrosophila melanogaster ARHGAP19orthologRhoGAP54Dreduced self-driven locomotor activity and startle responses to visual stimuli. Zebrafish loss-of-function models similarly exhibited movement deficits, coupled with increased motor neuron axonal branching but shorter caudal primary motor neurons. Together, these findings establishARHGAP19as a novel cause of early-onset neuropathy through a loss-of-function mechanism.
Effects of goldenrod (Solidago giganteaAiton and S.canadensisL.) invasion on the wet meadow vegetation composition of Somogyfajsz wood pasture
Authors: Szitár Katalin , Kabai Melinda , Zimmermann Zita , Szabó Gábor , Reis Bruna Paolinelli , Somay László
Published: May 2024

In recent decades, restoring abandoned wood pastures are being rediscovered as an effective way to preserve biodiversity. Their restoration include the control of invasive plant species. In our study, we compared the vegetation composition of wet meadow patches uninvaded and invaded by giant and Canadian goldenrod in a wood pasture located in Somogyfajsz, Hungary. We sampled the vegetation of the wet meadows of the pasture in 16 pairs of 1 x 1 m invaded and uninvaded quadrats in June 2020. We studied the effect of goldenrod invasion on nature conservation value in terms of species diversity, origin of species, and Social Behaviour Types, and forage quality and quantity. The study revealed that goldenrod invasion had negative effects on species richness and community-level biomass in wet meadows, leading to a significant reduction in species diversity and total cover. Goldenrod invasion also impacted the richness and cover of both native and exotic species, with a decrease in richness but not cover, highlighting the competitive ability of goldenrods and their potential to alter vegetation composition.
GENE THERAPY PREVENTS HEPATIC MITOCHONDRIAL DYSFUNCTION IN MURINE DEOXYGUANOSINE KINASE DEFICIENCY
Authors: Keshavan Nandaki , Greenwood Miriam , Prunty Helen , Diaz Juan Antinao , Privolizzi Riccardo , Counsell John , Karlsson Anna , Waddington Simon , Karda Rajvinder , Rahman Shamima
Published: May 2024

Primary mitochondrial disorders are an uncommon cause of neonatal hepatic failure. Biallelic pathogenic variants of the gene encoding the mitochondrial localising enzyme deoxyguanosine kinase (DGUOK) cause hepatocerebral mitochondrial DNA depletion syndrome leading to acute neonatal liver failure and early mortality. There are currently no effective disease-modifying therapies. In this study, we developed an adeno-associated virus 9 (AAV9) gene therapy approach to treat a mouse model of DGUOK deficiency that recapitulates human disease. We delivered AAV9-hDGUOKgene therapy intravenously to newbornDguokknock-out mice and showed that liver dysfunction was prevented in a dose dependent manner. Unexpectedly for neonatal delivery, durable and long-lasting liver transduction and RNA expression were demonstrated. Liver mitochondrial DNA depletion, deficiencies of oxidative phosphorylation complexes I, III and IV and liver transaminitis and survival were ameliorated in a dose-dependent manner.
Insights into Ligand-Mediated Activation of an Oligomeric Ring-Shaped Gene-Regulatory Protein from Solution- and Solid-State NMR
Authors: Muzquiz Rodrigo , Jamshidi Cameron , Conroy Daniel W. , Jaroniec Christopher P. , Foster Mark P.
Published: May 2024

The 91 kDa oligomeric ring-shaped ligand binding protein TRAP (trpRNA binding attenuation protein) regulates the expression of a series of genes involved in tryptophan (Trp) biosynthesis in bacilli. When cellular Trp levels rise, the free amino acid binds to sites buried in the interfaces between each of the 11 (or 12, depending on the species) protomers in the ring. Crystal structures of Trp-bound TRAP show the Trp ligands are sequestered from solvent by a pair of loops from adjacent protomers that bury the bound ligand via polar contacts to several threonine residues. Binding of the Trp ligands occurs cooperatively, such that successive binding events occur with higher apparent affinity but the structural basis for this cooperativity is poorly understood. We used solution methyl-TROSY NMR relaxation experiments focused on threonine and isoleucine sidechains, as well as magic angle spinning solid-state NMR13C-13C and15N-13C chemical shift correlation spectra on uniformly labeled samples recorded at 800 and 1200 MHz, to characterize the structure and dynamics of the protein. Methyl13C relaxation dispersion experiments on ligand-free apo TRAP revealed concerted exchange dynamics on the µs-ms time scale, consistent with transient sampling of conformations that could allow ligand binding. Cross-correlated relaxation experiments revealed widespread disorder on fast timescales. Chemical shifts for methyl-bearing side chains in apo- and Trp-bound TRAP revealed subtle changes in the distribution of sampled sidechain rotameric states. These observations reveal a pathway and mechanism for induced conformational changes to generate homotropic Trp-Trp binding cooperativity.
Unravelling the Impact of miR-21 Overexpression on the MicroRNA Network and Cancer Pathways
Authors: Hill Meredith , Stapleton Sarah , Nguyen Phuong Thao , Sais Dayna , Deutsch Fiona , Gay Valarie , Marsh Deborah , Tran Nham
Published: May 2024

Abstract

MicroRNAs (miRNA, miRs) are small noncoding RNAs that are ubiquitously expressed in all mammalian cells. Their primary function is the regulation of nascent RNA transcripts by direct binding to regions on the target. There is now exciting data to suggest that these miRNAs can bind to other miRNAs, and this may have a broader impact on gene regulation in disease states. The oncomiR miR-21 is one of the highest-expressing miRNAs in cancer cells, and in this study, we characterise which miRNAs could be potential targets of miR-21. In cancer cells delivered with a miR-21 mimic, there was an observable shift of the miRNA milieu. We demonstrate that the miR-17-92a cluster, which harbours six miRNA members, may be a target of miR-21 regulation. Additionally, the primary transcript of miR-17-92a was reduced in the presence of miR-21. In the broader context of gene regulation, overexpression of miR-21 shifted the expression of more than 150 miRNAs, including those known to regulate genes encoding proteins in cancer pathways such as the MAPK signalling and FoxO pathways. This study expands upon our limited understanding of miR:miR regulatory network and reinforces the concept that miRNAs can regulate each other, thereby influencing broader gene regulatory networks.