bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel Genus of Virulent Phage TargetingAcinetobacter baumannii: Efficacy and Safety in a Murine Model of Pulmonary Infection
Authors: Wang JiaWang , Hu Huan , Wang QingQing , Zhu TianZhu , Ren XiaoHan , Jiang WenQian , Hou XueMei , Lin Jun , Yu XiaoLing
Published: October 2024

Acinetobacter baumannii(A.baumannii) is a notable opportunistic pathogen responsible for severe hospital-acquired infections, with multidrug-resistant strains posing significant treatment challenges. Phage therapy, which employs bacteriophages as natural bacterial antagonists, has gained renewed attention as a promising solution to combat antibiotic-resistant infections. In this study, we isolated and characterized a novel virulent phage, vB_AbaS_qsb1, which specifically lysesA.baumannii. Phylogenetic and genomic analyses indicate that vB_AbaS_qsb1 is the founding member of a previously unreported genus, which we have named asAcinibactriovirus, withAcinibactriovirus lysinusas the type species. vB_AbaS_qsb1 demonstrated robust stability across diverse temperature and pH ranges, a short latent period, and no known virulence or antibiotic resistance genes within its 54,713 bp dsDNA genome. Safety assessments showed that high-dose vB_AbaS_qsb1 induced no adverse effects in mice, with histopathology confirming its safety profile. Therapeutic experiments further indicated that vB_AbaS_qsb1 provided at least 50% protection againstA.baumannii-induced pneumonia, significantly reducing bacterial loads and inflammation markers, while maintaining high phage titers in lung tissue.This study introduces vB_AbaS_qsb1 as a promising candidate for phage therapy againstA.baumannii, offering both innovative insights and a valuable framework for future isolation, genomic characterization, and efficacy evaluation of phages targeting antibiotic-resistant bacteria.

Graphical abstract
Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of UUCG RNA Tetraloop and Other Systems
Authors: Mlýnský Vojtěch , Kührová Petra , Pykal Martin , Krepl Miroslav , Stadlbauer Petr , Otyepka Michal , Banáš Pavel , Šponer Jiří
Published: October 2024

Molecular dynamics (MD) simulations are an important and well-established tool for investigating RNA structural dynamics, but their accuracy relies heavily on the quality of the employed force field (ff). In this work, we present a comprehensive evaluation of widely used pair-additive and polarizable RNAffs using the challenging UUCG tetraloop (TL) benchmark system. Extensive standard MD simulations, initiated from the NMR structure of the 14-mer UUCG TL, revealed that mostffs did not maintain the native state, instead favoring alternative loop conformations. Notably, three very recent variants of pair-additiveffs, OL3CP–gHBfix21, DESAMBER, and OL3R2.7, successfully preserved the native structure over a 10 × 20 µs timescale. To further assess theseffs, we performed enhanced sampling folding simulations of the shorter 8-mer UUCG TL, starting from the single-stranded conformation. Estimated folding free energies (ΔG°fold) varied significantly among these threeffs, with values of 0.0 ± 0.6 kcal/mol, 2.4 ± 0.8 kcal/mol, and 7.4 ± 0.2 kcal/mol for OL3CP–gHBfix21, DESAMBER, and OL3R2.7, respectively. The ΔG°foldvalue from OL3CP–gHBfix21 was closest to experimental data, while the higher ΔG°foldvalues from DESAMBER and OL3R2.7were unexpected, suggesting an over- or underestimation of key interactions within the folded and mis(un)folded ensembles. These discrepancies led us to further test DESAMBER and OL3R2.7ffs on additional RNA and DNA systems, where further performance issues were observed. Our results emphasize the complexity of accurately modeling RNA dynamics and suggest that creating an RNAffcapable of reliably performing across a wide range of RNA motifs remains extremely challenging. In conclusion, our study provides valuable insights into the capabilities of current RNAffs and highlights key areas for futureffdevelopment.
A novel model to quantify blood transit time in cerebral arteries using ASL-based 4D magnetic resonance angiography with example clinical application in moyamoya disease
Authors: Bhogal Alex A. , Uniken-Venema Simone M. , Deckers Pieter , Versluis Maarten , Braun Kees P. , van der Zwan Albert , Siero Jeroen C.W.
Published: October 2024

Angiography is critical for visualizing cerebral blood flow in intracranial steno-occlusive diseases. Current 4D magnetic resonance angiography (MRA) techniques primarily focus on macrovascular structures, yet few have quantified hemodynamic timing. This study introduces a novel model to estimate macrovascular arterial transit time (mATT) derived from arterial spin labeling (ASL)-based 4D-MRA. We provide examples of our method that visualize mATT differences in patients with intracranial steno-occlusive disease (moyamoya and atherosclerosis) and changes in mATT resulting from the cerebrovascular reactivity response to an acetazolamide (ACZ) injection. Furthermore, we present a method that projects sparse arterial signals into a 3D native brain-region atlas space and correlate regional mATT with other hemodynamic parameters of interest such as tissue transit time and cerebrovascular reactivity. This approach offers a non-invasive, quantitative assessment of macrovascular dynamics, with potential to enhance understanding of large-vessel and tissue-level hemodynamics and augment monitoring of treatment outcomes in steno-occlusive disease patients. Furthermore, it sets the stage for more in-depth investigations of the macrovascular contribution to brain hemodynamics.
Effect of a widespread reduction in treatment duration for group A streptococcal pharyngitis on outcomes and household transmission
Authors: Bloomfield Max , Reed Hamish , Todd Sue , van der Werff Koen , Balm Michelle , Blackmore Tim
Published: October 2024

Background

the optimal treatment duration for group A streptococcal pharyngitis (GAS-P) is debated. Shorter courses appear inferior for pharyngeal GAS eradication, however the effect of this on household transmission is uncertain. In 2022 a laboratory reporting change drove reduced treatment durations for GAS-P in our region. This study sought to assess the effect of this on outcomes.

Methods

positive throat swab cultures (TSC) for GAS from two years pre-change until 21 months post-change were matched to antibiotic dispensing data. Logistic models were fitted to examine associations between treatment duration and 30-day repeat antibiotic treatment, repeat GAS-positive TSC, and hospitalisation with complications; 90-day incidence of rheumatic fever; 30-day incident household GAS-P cases.

Results

865 patients pre-change and 1604 post-change were included. Pre-change 32.8% received ≤7 days treatment, versus 60.0% post-change (p<0.01). There were no significant differences across any outcome measure at a population level between periods. When the post-change period was examined specifically, no significant differences occurred for any outcome measure for patients receiving five- or seven-days of antibiotics versus ten-days. Patients receiving no antibiotics also had similar outcomes, except for significantly higher odds of 30-day household cases (aOR 2.93, 95%-CI 1.44-5.96, p<0.01).

Conclusions

shorter treatment durations driven by a change in laboratory reporting resulted in no detectable change in GAS-P outcomes, except for more common household transmission in those receiving no treatment.
Identification of DLK1, a Notch ligand, as an immunotherapeutic target and regulator of tumor cell plasticity and chemoresistance in adrenocortical carcinoma
Authors: Sun Nai-Yun , Kumar Suresh , Kim Yoo Sun , Varghese Diana , Mendoza Arnulfo , Nguyen Rosa , Okada Reona , Reilly Karlyne , Widemann Brigitte , Pommier Yves , Elloumi Fathi , Dhall Anjali , Patel Mayank , Aber Etan , Contreras-Burrola Cristie , Kaplan Rosie , Martinez Dan , Pogoriler Jennifer , Hamilton Amber K. , Diskin Sharon J. , Maris John M. , Robey Robert W. , Gottesman Michael M. , Del Rivero Jaydira , Roper Nitin
Published: October 2024

Immunotherapeutic targeting of cell surface proteins is an increasingly effective cancer therapy. However, given the limited number of current targets, the identification of new surface proteins, particularly those with biological importance, is critical. Here, we uncover delta-like non-canonical Notch ligand 1 (DLK1) as a cell surface protein with limited normal tissue expression and high expression in multiple refractory adult metastatic cancers including small cell lung cancer (SCLC) and adrenocortical carcinoma (ACC), a rare cancer with few effective therapies. In ACC, ADCT-701, a DLK1 targeting antibody-drug conjugate (ADC), shows potentin vitroactivity among established cell lines and a new cohort of patient-derived organoids as well as robustin vivoanti-tumor responses in cell line-derived and patient-derived xenografts. However, ADCT-701 efficacy is overall limited in ACC due to high expression and activity of the drug efflux protein ABCB1 (MDR1, P-glycoprotein). In contrast, ADCT-701 is extremely potent and induces complete responses in DLK1+ACC and SCLCin vivomodels with low or no ABCB1 expression. Genetic deletion of DLK1 in ACC dramatically downregulates ABCB1 and increases ADC payload and chemotherapy sensitivity through NOTCH1-mediated adrenocortical de-differentiation. Single cell RNA-seq of ACC metastatic tumors reveals significantly decreased adrenocortical differentiation in DLK low or negative cells compared to DLK1 positive cells. This works identifies DLK1 as a novel immunotherapeutic target that regulates tumor cell plasticity and chemoresistance in ACC. Our data support targeting DLK1 with an ADC in ACC and neuroendocrine neoplasms in an active first-in-human phase I clinical trial (NCT06041516).
A Darwinian model of cultural replication over the continuum of Weismannian and Lamarckian inheritance
Authors: Zachar Istvan , Szamado Szabolcs
Published: October 2024

Universal Darwinism argues that entities capable of multiplication, variation and inheritance evolve by natural selection. Besides genetic reproduction implementing Weismannian inheritance, other adaptive systems were proposed to support Darwinian evolution, most notably culture, assuming autonomous cultural replicators akin to genes. Culture, on one hand, lacks direct template copying and inherits acquired changes, while on the other its overall behaviour is Darwinian as languages attest. The properties of culture setting it apart from biological evolution suggests a Lamarckian, while its overall behaviour a Weismannian interpretation, which is often coined as "the duality of cultural replication". According to canonical Darwinism, Lamarckian and Weismannian inheritance are disjunct mechanisms and only the latter is sufficient to maintain cumulative evolution. We resolve this apparent contradiction via a mathematical model of cultural information replication. We model the inheritance of information, cultural or genetic, as a successive set of template-based transformations of digital information between generations. We demonstrate that Lamarckian and Weismannian inheritance form a continuum and that both can reconstruct information stably for an indefinite time. Our formalism naturally unifies Lamarckian and Weismannian inheritance, proving that cultural replication, in theory, can approximate the fidelity of genetic replication. We claim that (well-defined) Lamarckian inheritance is an adequate low-level model of culture and can support population-level Darwinian evolution. We discuss the implications of our results to bridge the gap between the Lamarckian and Darwinian explanations of cultural evolution.
Evidence of opportunistic blood feeding in the parasitic nematodeHeligmosomoides bakeri
Authors: Szabo Edina K. , Wasmuth James D. , Leon-Coria Aralia , Rich Kaylee D. , Liu Holly , Finney Constance A. M.
Published: October 2024

Haem, which binds iron and oxygen, is essential for parasitic nematode growth. Nematodes lack endogenous haem synthesis pathways and acquire haem from their environment or intracellular symbionts. Genes involved in haem degradation and detoxification have been identified in parasitic nematodes who are either specialised blood feeders (haematophages) or reside in the blood stream. Targeting these genes, so limiting parasite growth and promoting parasite death, provides a new therapeutic avenue against blood feeding parasitic nematodes.

Heligmosomoides bakeri, a model intestinal parasitic nematode, has not been considered a blood feeder. Adults live in the intestinal lumen and graze on host tissue. However, the earlier larval stages enter the intestinal tissue, where they grow and moult multiple times, an oxygen demanding process. We have shown that,in vivo, likely through nematode-induced damage, many tissue-dwellingH. bakeriare in close vicinity of red blood cells. During this time, infection induces host anemia. Further, tissue-dwellingH. bakerithat have fed on blood have an increased expression of collagen genes compared to those parasites that had not fed on blood.In vitro, this translates to a growth advantage.

Our findings suggest blood feeding is more widespread among nematodes than currently described. We argue that biochemical adaptations previously considered to be limited to blood-feeders are found in other nematodes. Moreover,H. bakerican serve as a model for studying blood-feeding mechanisms and developing anthelminthic strategies to them.
Protein Kinases in Phagocytosis: Promising Genetic Biomarkers for Cancer
Authors: Arumilli Sadhika , Liu Hengrui
Published: October 2024

Cancer is a complex disease characterized by genetic and molecular diversity, often involving dysregulation of critical cellular pathways. Recent advances in pan-cancer research have highlighted the importance of shared oncogenic mechanisms across different cancer types, providing new avenues for therapeutic exploration. Protein kinases, particularly those involved in phagocytosis, play pivotal roles in cellular homeostasis and immune response. This study systematically examines the genetic alterations and expression profiles of protein kinases associated with phagocytosis across various cancer types, using data from The Cancer Genome Atlas (TCGA) and other publicly available resources. We analyzed single nucleotide variations (SNVs), copy number variations (CNVs), methylation patterns, and mRNA expression to identify recurring alterations and their associations with survival outcomes. Our findings reveal that MET and MERTK are the most frequently mutated genes, with missense mutations dominating across cancers. CNV analysis shows significant correlations with survival in cancers like UCEC, KIRP, and KIRC, while methylation analysis indicates cancer-specific regulatory patterns affecting gene expression. Differential expression analysis highlights distinct cancer-type-specific expression profiles, with genes like MET and BTK displaying significant variation. Crosstalk pathway analysis further reveals the involvement of these kinases in key cancer-related pathways, such as epithelial-mesenchymal transition (EMT) and apoptosis. Drug sensitivity analysis identifies potential therapeutic targets, with gene expression correlating significantly with cancer cell line responsiveness to specific compounds. These findings underscore the importance of the phagocytotic kinome in cancer biology and suggest potential therapeutic strategies targeting protein kinases to enhance immune response and improve treatment outcomes.
Biosynthetic characterization and combinatorial biocatalysis of the cysteine protease inhibitor E-64
Authors: Liu Mengting , Zang Xin , Vlahakis Niko W. , Rodriguez Jose A. , Ohashi Masao , Tang Yi
Published: October 2024

E-64 is an irreversible and selective cysteine protease inhibitor prominently used in chemical biology and drug discovery. In this work, we uncovered and characterized the NRPS-independent pathway responsible for biosynthesis of E-64, which is widely conserved in fungi. Heterologous reconstitution and biochemical assays show the pathway starts with epoxidation of fumaric acid to the warhead (2S,3S)-trans-epoxysuccinic acid with an α-ketoglutarate (αKG)/Fe(II)-dependent oxygenase, followed by successive condensation with anl-amino acid by an ATP-grasp enzyme, and with an amine by the first characterized amide bond synthetase from fungi. Both amide bond-forming enzymes displayed significant biocatalytic potential, including scalability, stereoselectivity towards the warhead and broader substrate scopes in forming the amide bonds. Combinatorial biocatalysis with the two amide-bond forming enzymes generated a library of cysteine protease inhibitors and led to more potent analogs towards cathepsin B. In addition, preparative synthesis of clinically relevant cysteine protease inhibitors was accomplished from a single reaction mixture. Our work highlights the importance of biosynthetic investigation for enzyme discovery and the potential of amide bond-forming enzymes as biocatalysts for a library synthesis of small molecules.
Body Fatness Increases Risk of Monoclonal Gammopathy of Undetermined Significance in the U.S. Population
Authors: Ji Mengmeng , Huber John , Wang Mei , Shih Yi-Hsuan , Lan Tuo , Wang Shi-Yi , Chang Su-Hsin
Published: October 2024

Objective

Current evidence on whether obesity is associated with MGUS remains inconsistent. This study aims to evaluate the association between objectively measured obesity markers and the risk of developing MGUS, using nationally representative data from the U.S. population.

Method

Data came from the third National Health and Nutrition Examination Survey III (1988-1994) and continuous NHANES (1999-2004). Multivariable-adjusted odds ratios (aOR) and 95% confidence intervals (CIs) for the association between the risk of developing MGUS and seven obesity markers—including baseline body mass index (BMI), maximum lifetime BMI, waist circumference (WC), waist-hip ratio (WHR), total body fat, fat-free mass, and body percentage fat—were estimated using logistic regression.

Results

In the study cohort, a total of 364 participants tested positive for MGUS, compared to 12,043 participants without MGUS. Multivariate logistic regression analysis indicates that each 1% increase in body fat percentage is associated with a 4% (aOR: 1.04, 95% CI [1.01, 1.07]) higher risk of MGUS. Each 1% increase in body fat percentage is also associated with a 6% (aOR: 1.06, 95% CI [1.02, 1.10]) higher risk of non-IgM MGUS. No statistically significant association was found between MGUS and other obesity markers, including baseline BMI, maximum lifetime BMI, WC, WHR, and fat-free mass.

Conclusion

Our findings show that obesity is associated with an increase in the risk of MGUS. However, many obesity markers, including the commonly used BMI, fail to capture this association.
Characteristics and care trajectories of older patients in temporary stays in Denmark
Authors: Harbi Hanin , Lundby Carina , Jensen Peter Bjødstrup , Larsen Søren Post , Rørbæk Linda Grouleff , Ravn-Nielsen Lene Vestergaard , Ryg Jesper , Reilev Mette , Edwards Kasper , Pottegård Anton
Published: October 2024

Background

Temporary stays for patients requiring short-term care outside the home, often following hospital discharge, has gained increasing importance. This study aimed to describe the characteristics and care trajectories of older patients in Danish temporary stays to improve care delivery and patient safety.

Methods

We conducted a descriptive study on a cohort of patients in temporary stays across 14 Danish municipalities from 2016 to 2023, using data from national health registries.

Results

We identified 11,424 patients with a median age of 81 years (interquartile range [IQR] 73-87 years); 54% were women. Patients exhibited a high level of comorbidity, with a median Charlson Comorbidity Index of 1 (IQR 0-2), and a median of 3 hospital admissions (IQR 2-6) in the year preceding their move into temporary care. The majority (70%) transitioned to temporary stays following hospital discharge, while 30% were admitted directly from their homes. The median duration of temporary stays was 24 days (IQR 11-49 days), with 9.1% staying ≥ 90 days. Additionally, 8.2% of patients were hospitalised directly from the temporary stay facility, with a median time to hospital admission of 13 days (IQR 5-28 days). Median survival after admission to a temporary stay was 23 months (IQR 3.6-57 months). Predictors of mortality included male sex, older age, higher comorbidity burden, and increased number of hospital admissions prior to temporary stay.

Conclusion

Patients in temporary stays are generally older individuals with multimorbidity and limited life expectancy. Most patients are admitted following hospital discharge, and their stays are often prolonged.
The association between outdoor ambient temperature and depression and mania: an ecological momentary assessment study
Authors: Clery P , Hayes JF , Launders N , Thompson R , Kandola A , Osborn DPJ , Lawrance EL , Jeffery A , Dykxhoorn J
Published: October 2024

Background

Environmental heat exposure can negatively impact mental health. Evidence for its effect on mood disorder symptoms is inconsistent. Current studies are limited by poor temporal and geographical resolution.

Methods

We used ecological momentary assessment (EMA) data from the smartphone appjulito investigate the association between real-time mean and maximum ambient temperature collected from smartphone geolocation, and depressive and manic symptom scales, every two weeks, in adults with depression and bipolar disorder. We used negative binomial mixed-effects regression models, controlled for demographic and weather variables, and stratified by season.

Results

We analysed data from 4,000 participants with depressive symptom scores and 2,132 with manic symptom scores, between 2021 and 2023. We found that each 1°C increase in mean daily temperature in the preceding two weeks was associated with a 0.2% reduction in depressive symptom scores (coeff 0.998, 95%CI 0.997-0.999) and a 0.4% increase in manic symptom scores (coeff 1.004, 95%CI 1.001-1.007). Associations between maximum temperature and symptom scores followed a similar pattern.

Limitations

We were unable to capture several socio-demographic covariates, had limited geographical information due to privacy regulations, and included a non-random sample.

Conclusions

We found evidence that higher temperatures were associated with increased manic symptoms and decreased depressive symptoms, indicating an important relationship between temperature and the mood disorder continuum. With global heating, there is a need to understand the impact of temperature on mood symptoms, to provide targeted clinical prevention and support. This study demonstrates potential for EMA methods to inform our understanding of these links.
Estimating the generation time for SARS-CoV-2 transmission using household data in the United States, December 2021 – May 2023
Authors: Chan Louis Yat Hin , Morris Sinead E. , Stockwell Melissa S. , Bowman Natalie M. , Asturias Edwin , Rao Suchitra , Lutrick Karen , Ellingson Katherine D. , Nguyen Huong Q. , Maldonado Yvonne , McLaren Son H. , Sano Ellen , Biddle Jessica E. , Smith-Jeffcoat Sarah E. , Biggerstaff Matthew , Rolfes Melissa A. , Talbot H. Keipp , Grijalva Carlos G. , Borchering Rebecca K. , Mellis Alexandra M. ,   RVTN-Sentinel Study Group
Published: October 2024

Background

Generation time, representing the interval between infection events in primary and secondary cases, is important for understanding disease transmission dynamics including predicting the effective reproduction number (Rt), which informs public health decisions. While previous estimates of SARS-CoV-2 generation times have been reported for early Omicron variants, there is a lack of data for subsequent sub-variants, such as XBB.

Methods

We estimated SARS-CoV-2 generation times using data from the Respiratory Virus Transmission Network – Sentinel (RVTN-S) household transmission study conducted across seven U.S. sites from December 2021 to May 2023. The study spanned three Omicron sub-periods dominated by the sub-variants BA.1/2, BA.4/5, and XBB. We employed a Susceptible-Exposed-Infectious-Recovered (SEIR) model with a Bayesian data augmentation method that imputes unobserved infection times of cases to estimate the generation time.

Findings

The estimated mean generation time for the overall Omicron period was 3.5 days (95% credible interval, CrI: 3.3-3.7). During the sub-periods, the estimated mean generation times were 3.8 days (95% CrI: 3.4-4.2) for BA.1/2, 3.5 days (95% CrI: 3.3-3.8) for BA.4/5, and 3.5 days (95% CrI: 3.1-3.9) for XBB.

Interpretation

Our study provides estimates of generation times for the Omicron variant, including the sub-variants BA.1/2, BA.4/5, and XBB. These up-to-date estimates specifically address the gap in knowledge regarding these sub-variants and are consistent with earlier studies. They enhance our understanding of SARS-CoV-2 transmission dynamics by aiding in the prediction of Rt, offering insights for improving COVID-19 modeling and public health strategies.

Funding

Centers for Disease Control and Prevention, and National Center for Advancing Translational Sciences.
De novo rates of aTrypanosoma-resistant mutation in two human populations
Authors: Melamed Daniel , Shemer Revital , Bolotin Evgeni , Yakass Michael B. , Fink-Barkai Dorit , Hiadzi Edem K. , Skorecki Karl L. , Livnat Adi
Published: October 2024

Until recently, mutation rates have only been measured as averages across many genomic positions. Recently, a method to measure mutation rates at the single-mutation resolution was applied to a narrow region in the human hemoglobin subunit beta (HBB) gene containing the site of the hemoglobin S (HbS) mutation as well as to a paralogous hemoglobin subunit delta (HBD) region, in sperm samples from sub-Saharan African and northern European donors. The HbS mutation, which protects against malaria while causing sickle-cell anemia in homozygotes originated de novo significantly more frequently in theHBBgene in Africans compared to the other three test cases combined (the EuropeanHBBgene and the European and AfricanHBDgene). Here, we apply this approach to the human apolipopro-tein L1 (APOL1) gene containing the site of the G1 1024A→G mutation, which protects against African sleeping sickness caused byTrypanosoma brucei gambiensewhile causing a substantially increased risk of chronic kidney disease (CKD) in homozygotes. We find that the 1024A→G mutation is the mutation of highest de novo origination rate and deviates most from the genome-wide average rate for its type (A→G) compared to all other observable mutations in the region, and that it originates de novo significantly more frequently in Africans than in Europeans—i.e., in the population where it is of adaptive significance. The results are inconsistent with the notion that the probability of a specific mutational event is independent of its value to the organism and underscore the importance of studying mutation rates at the single-mutation resolution.
Loop-extruder mediated rigidity can globally order bacterial chromosomes
Authors: Harju Janni , Armbruster Till , Broedersz Chase
Published: October 2024

Many bacterial chromosomes show large-scale linear order, so that a locus’s genomic position correlates with its position along the cell. In the model organismE. coli, for instance, the left and right arms of the circular chromosome lie in different cell halves. However, no mechanisms that anchor loci to the cell poles have been identified, and it remains unknown how this so-called “left-ori-right” organization arises. Here, we construct a biophysical model that explains how global chromosome order could be established via an active loop extrusion mechanism. Our model assumes that the motor protein complex MukBEF extrudes loops on most of theE. colichromosome, but is excluded from the terminal region by the protein MatP, giving rise to a partially looped ring polymer structure. Using 3D simulations of loop extrusion on a chromosome, we find that our model can display stable left-ori-right chromosomal order in a parameter regime consistent with prior experiments. We explain this behavior by considering the effect of loop extrusion on the bending rigidity of the chromosome, and derive necessary conditions for left-ori-right order to emerge. Finally, we develop a phase diagram for the system, where order emerges when the loop size is large enough and the looped region is compacted enough. Our work provides a mechanistic explanation for how loop-extruders can establish linear chromosome order inE. coli, and how this order leads to accurate gene positioning within the cell, without locus anchoring.
Loss of PKCθ-GADD45a axis drives triple-negative breast cancer cells into p53-independent senescence
Authors: Nicolle Amandine , Zhang Ye , Choesmel-Cadamuro Valérie , Wang Xiaobo , Belguise Karine
Published: October 2024

Background

PKCθ is a serine/threonine kinase that is well known for its role in the immune system. However, increasing evidence implicates PKCθ in the pathology of breast cancer. PKCθ is highly expressed in triple negative breast cancer (TNBC) cells in which it controls cell migration and invasion, while its implication in cell proliferation remains poorly understood.

Methods

To determine the function of PKCθ in cell proliferation, siRNAs were used to modulate the expression of PKCθ in TNBC cells (MDA-MB-231, MDA-MB-436, HCC1937) and cell growth was examined by clonogenic and EdU assays. β-galactosidase assay, RT-qPCR and western blot were used to characterize the senescence features. PCR microarrays and rescue experiments were conducted to investigate the underlying mechanism.

Results

We show that PKCθ inhibition leads to a growth arrest in TNBC cells harboring a p53 loss-of-function mutation. This p53-independent growth arrest is accompanied by an increased activity of senescence-associated β-galactosidase, the presence of a senescence-associated secretory phenotype, and the striking expression change of various genes implicated in cell proliferation and senescence. Thus, our data show that PKCθ silencing drives TNBC cells into a senescence-like phenotype. Mechanistically, we demonstrate that p27 is the main CDK inhibitor controlling the PKCθ loss-induced senescence. The accumulation of p27 is due to a surprising strong reduction in GADD45a expression. Indeed, similar to PKCθ silencing phenotype, GADD45a knockdown drives TNBC cells into a senescence-like phenotype.

Conclusions

Altogether, our study highlights that the loss of PKCθ-GADD45a axis triggers a p27-dependent senescence response in TNBC cells and further supports strategies targeting PKCθ as treatment for this type of aggressive breast cancer.
Structural Insights into Selective and Dual Antagonism of EP2 and EP4 Prostaglandin Receptors
Authors: Wu Yanli , Zhang Heng , Xu Jiuyin , Wu Kai , Hu Wen , Wu Canrong , Xu H. Eric
Published: October 2024

Prostaglandin E2 (PGE2) signaling through EP2 and EP4 receptors plays a crucial role in inflammation, pain, and cancer progression. Selective and dual antagonists of these receptors have shown promising therapeutic potential. However, the structural basis for their binding modes and selectivity remained unclear. Here, we present cryo-EM structures of human EP2 and EP4 receptors in complex with selective antagonists PF-04418948 and grapiprant, respectively, as well as the dual antagonist TG6-129. These structures reveal distinct binding pockets and interaction networks that govern antagonist selectivity and efficacy. Combining the structural data and functional studies, we uncover the key residues and structural features that differentiate EP2 and EP4 binding sites, including a unique π-π stacking interaction in EP2 and variations in pocket shape and charge distribution. The dual antagonist TG6-129 exhibited a novel binding mode, interacting deeply with EP2 but only shallowly with EP4 in a two-warhead manner. These findings provide a structural framework for understanding prostanoid receptor pharmacology and offer valuable insights for the rational design of improved selective and dual antagonists targeting EP2 and EP4 receptors.
Mapping the Spatial Proteome of Leukemia Cells Undergoing Fludarabine Treatment
Authors: Globisch Maria Ascencion , Gezelius Henrik , Enblad Anna Pia , Lundmark Anders , Lysenkova Wiklander Mariya A , Krali Olga , Aberg Martin , Harila Arja , Raine Amanda , Andersson Claes , Nordlund Jessica
Published: October 2024

Recent advancements in spatial biology have revolutionized our understanding of the organization and functional dynamics of cells and tissues. In this study, we applied Molecular Pixelation (MPX), a single-cell spatial proteomics assay, to investigate the modulation of the cell surface proteome in an in vitro drug screening model using the ETV6::RUNX1 acute lymphoblastic leukemia (ALL) cell line, Reh . Specifically, we focused on the in vitro response to fludarabine, a chemotherapeutic agent used prior to allogenic stem cell transplantation and chimeric antigen receptor (CAR)-T cell therapy in high-risk, refractory, or relapsed ALL patients. Using MPX, we quantified changes in protein abundance, spatial distribution, and colocalization of 76 targeted cell surface proteins in Reh cells before and after fludarabine treatment. Our analysis revealed 25 proteins with altered abundance, 24 proteins with increased polarity, and 138 protein pairs with modified colocalization following treatment. Notably, the tetraspanins CD82 and CD53, which are known for their roles in chemotherapy resistance, exhibited increased abundance, polarization, and colocalization post-treatment, suggesting their potential as a therapeutic scaffold. These findings underscore the unique ability of spatially resolved single-cell proteomics to uncover nuanced cellular responses that would otherwise remain undetected.
Step-by-Step Maturation Mechanism of Binary Toxin Pore Revealed by Cryo-EM Analysis
Authors: Yamada Tomohito , Sugita Yukihiko , Yoshida Toru , Noda Takeshi , Tsuge Hideaki
Published: October 2024

Membrane pore-forming proteins (PFPs) form ring-shaped membrane-translocating oligomers on membranes, contributing to infection, immunity, and cell death functions. Binary toxins produced by some bacteria consist of an enzymatic component that acts as a toxin and a membrane-binding component that forms a pore that delivers the enzymatic component into target cells. Cryo-electron microscopy (cryo-EM) has advanced our understanding of these translocation mechanisms by revealing several binary toxin complexes’ structures. However, the mechanisms underlying the initial pore formation remain unclear. We determined the structures of several oligomeric forms of the membrane-binding component, Ib, of the Iota toxin fromClostridium perfringensat various stages of pore formation. Structural comparisons revealed that the symmetrically arranged soluble oligomer (prepore) became a transmembrane oligomer (pore). These findings enhance our understanding of the PFP mechanisms and provide a structural basis for developing nanodevices using membrane pores.
Reliable RNA-seq analysis from FFPE specimens as a means to accelerate cancer-related health disparities research
Authors: Frederick M.J. , Perez-Bello D. , Yadollahi P. , Castro P. , Frederick A. , Frederick A. , Osman R.A. , Essien F. , Yebra I. , Hamlin A. , Ow T.J. , Skinner H.D. , Sandulache V.C.
Published: October 2024

Whole transcriptome sequencing (WTS/ RNA-Seq) is a ubiquitous tool for investigating cancer biology. RNA isolated from frozen sources limits possible studies for analysis of associations with phenotypes or clinical variables requiring long-term follow-up. Although good correlations are reported in RNA-Seq data from paired frozen and formalin fixed paraffin embedded (FFPE) samples, uncertainties regarding RNA quality, methods of extraction, and data reliability are hurdles to utilization of archival samples. We compared three different platforms for performing RNA-seq using archival FFPE oropharyngeal squamous carcinoma (OPSCC) specimens stored up to 20 years, as part of an investigation of transcriptional profiles related to health disparities. We developed guidelines to purify DNA and RNA from FFPE tissue and perform downstream RNA-seq and DNA SNP arrays. RNA was extracted from 150 specimens, with an average yield of 401.8 ng/cm2of tissue. Most samples yielded sufficient RNA reads >13,000 protein coding genes which could be used to differentiate HPV-associated from HPV-independent OPSCCs. Co-isolated DNA was used to identify patient ancestry. Utilizing the methods described in this study provides a robust, reliable, and standardized means of DNA & RNA extraction from FFPE as well as a means by which to assure the quality of the data generated.
CCG interruptions are unstable and hypermethylated in DM1 patients
Authors: Lameiras Sonia , Lampraki Eirini Maria , Kilburn Duncan , Alaeitabar Tina , Jamail Ismail , Servant Nicolas , Baulande Sylvain , Kingan Sarah , Holt Sam , Gaysinskaya Valeriya , De Sena Brandine Guilherme , Stucki David , Stojkovic Tanya , Bassez Guillaume , Furling Denis , Gourdon Geneviève , Tomé Stéphanie
Published: October 2024

Myotonic dystrophy type 1 (DM1) exhibits highly heterogeneous clinical manifestations caused by an unstable CTG repeat expansion reaching up to 4,000 CTG. The dynamics of CTG repeats and clinical variability depends on the CTG repeat number, CNG repeat interruptions, DNA methylation, somatic mosaicism, but also gene modifiers. Around 10% of the DM1 population carries triplet repeat interruptions (CCG, CGG, CTC, CAG), which differ in number and nature between DM1 families. CCG interruptions have been associated with stabilization of the CTG repeat expansions and a milder phenotype in the DM1 population. However, the dynamics and precise role of interruptions in CTG repeat instability remain relatively underexplored due to the complexities of analyzing them. In this study, we showed that the number of CCG interruptions within the expansion varies within tissues and between generations using single-molecule real-time long-read sequencing. Although the interrupted expanded alleles showed global stabilization, the CCG interruptions themselves displayed variability across generations and within somatic tissues. Importantly, our findings reveal, for the first time, CCG hypermethylation within the CTG expansion, which is linked to downstream hypermethylation of the repeat. These results support the hypothesis that methylation of CCG interruptions within the expandedDMPKalleles may contribute to the stabilization of trinucleotide repeats.
H2AK119ub dynamics controls hair follicle stem cell quiescence
Authors: Flora Pooja , Li Meng Yen , Zhou Yudong , Mercédes Maria , Zheng Xiang Yu , Galbo Phillip M. , Zheng Deyou , Ezhkova Elena
Published: October 2024

The transition of stem cells from a quiescent state to an active state is a finely tuned process that requires the dismantling of the quiescence program and the establishment of a cell cycle-promoting transcriptional landscape. Whether epigenetic processes control stem cell states to promote the regeneration of adult tissues remains elusive. In this study, we show that a repressive histone modification, H2AK119ub, is dynamic between quiescent and active hair follicle stem cells (HFSCs) in the adult murine skin. Ablation of H2AK119ub in HFSCs leads to impaired quiescence leading to premature activation and an eventual exhaustion of HFSC pool. Transcriptional and chromatin studies revealed that H2AK119ub directly represses a proliferation promoting transcriptional program in the HFSCs to preserve quiescence. Lastly, we identify that the inhibitory FGF signaling produced by the hair follicle niche keratinocytes maintains H2AK119ub in quiescent HFSCs. Together, these findings reveal that a repressive histone mark, H2AK119ub, is under the dynamic regulation of inhibitory niche signaling to prevent the untimely establishment of an activated state to preserve SC function and longevity.
Mechanistic modeling to understand variability in responses to chronic Hepatitis B treatment
Authors: Granjeon-Noriot Solène , Schneider Anne , Porte Solène , Peyronnet Emmanuel , Gómez Germán , Jacob Evgueni , Ratto Nicolas , Wang Yishu , Scalfaro Pietro , André Patrice , Kahoul Riad , Monteiro Claudio , Bruezière Lara
Published: October 2024

Chronic hepatitis B virus (HBV) remains the most common serious liver infection globally, accounting for an estimated 820,000 deaths each year. Patient responses to treatment vary widely, due to complex interplay between viral and immune system dynamics. As yet, there is no reliable way to predict response; this is one reason cure rates remain disappointingly low (<10%).

We developed a mechanistic model to simulate serum viral markers evolution during two HBV treatment mainstays - the nucleoside analog entecavir (ETV) and pegylated interferon alfa (IFN) - for a variety of patients, and identify and quantify the key processes driving variability in patient responses. Based on a detailed literature review, this model integrates key processes in chronic HBV pathophysiology and drug pharmacokinetics/dynamics and was calibrated on published data only.

Post simulation regression and classification analyses, including a global sensitivity analysis and a random forest, highlighted the importance of HBV replication cycle processes in explaining pre-treatment inter-patient variability in serum viral markers. Post-treatment with entecavir, most of the response variability could be attributed to interactions between the viral replication cycle and immune system processes. Response variability after IFN treatment, however, was more directly related to the drug mechanism of action, which includes direct antiviral effects and immune system modulation. Quantifying these measures may help to inform new drug development with identification of more direct tailored and effective HBV therapy.

Graphical Abstract

Highlights

A mechanistic model of chronic hepatitis B disease, accounting for intra-hepatocyte virus replication and an implemented immune response to entecavir and Peginterferon alfa-2a, allows for reproducing the observed variability between patients in terms of measured serum viral markers in response to treatments.

Statistical analysis of simulated virtual populations helps investigate the mechanisms involved in observed variability between patients for both baseline and responses to treatments.

Such a mechanistic model offers, via a QSP platform, new perspectives on the exploration of hepatitis B physiopathology, including treatment combinations or hepatitis D co-infection.
Probing the shape of the quark-gluon plasma droplet via event-by-event quark-gluon plasma tomography
Authors: Karmakar Bithika , Zigic Dusan , Djordjevic Magdalena , Huovinen Pasi , Djordjevic Marko , Auvinen Jussi
Published: October 2024

This study investigates quark-gluon plasma in heavy-ion collisions through two avenues: high-p⊥ frameworks and hydrodynamic modeling. Using the TRENTo model, we find that the p=0 value aligns well with high-p⊥ data, in agreement with Bayesian analysis of the low-p⊥ regime. While adjusting p values may improve a fit to a particular high-p⊥ observable, it does not permit an earlier onset of transverse expansion.

Published by the American Physical Society
2024
Tunneling time in coupled-channel systems
Authors: Guo Peng , Gasparian Vladimir , Pérez-Garrido Antonio , Jódar Esther
Published: October 2024

In present work, we present a couple-channel formalism for the description of tunneling time of a quantum particle through a composite compound with multiple energy levels or a complex structure that can be reduced to a quasi-one-dimensional multiple-channel system.

Published by the American Physical Society
2024
Thermodynamic inference of correlations in nonequilibrium collective dynamics
Authors: Chatzittofi Michalis , Golestanian Ramin , Agudo-Canalejo Jaime
Published: October 2024

The theory of stochastic thermodynamics has revealed many useful fluctuation relations, with the thermodynamic uncertainty relation (TUR) being a theorem of major interest. When many nonequilibrium currents interact with each other, a naive application of the TUR to an individual current can result in an apparent violation of the TUR bound. Here, we explore how such an apparent violation can be used to put a lower bound on the strength of correlations C as well as the number N of interacting currents in collective dynamics. This lower bound is a combined bound on C(N−1) if only one current is measured, or a bound on N if two currents are measured. Our proposed protocol allows for the inference of hidden correlations in experiment, for example when a team of molecular motors pulls on the same cargo but only one or a subset of them is fluorescently tagged. By solving analytically and numerically several models of many-body nonequilibrium dynamics, we ascertain under which conditions this strategy can be applied and the inferred bound on correlations becomes tight.

Published by the American Physical Society
2024
Synthesis and crystal structure of 1H-1,2,4-triazole-3,5-diamine monohydrate
Authors: Inoue Kazuki , Nakami Shun , Kumasaki Mieko , Matsumoto Shinya
Published: October 2024

The title compound, a hydrate of 3,5-diamino-1,2,4-triazole (DATA), C2H5N5·H2O, was synthesized in the presence of sodium perchlorate. The evaporation of H2O from its aqueous solution resulted in anhydrous DATA, suggesting that sodium perchlorate was required to precipitate the DATA hydrate. The DATA hydrate crystallizes in the P21/c space group in the form of needle-shaped crystals with one DATA and one water molecule in the asymmetric unit. The water molecules form a three-dimensional network in the crystal structure. Hirshfeld surface analysis revealed that 8.5% of the intermolecular interactions originate from H...O contacts derived from the incorporation of the water molecules.
Crystal structure and Hirshfeld surface analysis of (nitrato-κ2
O,O′)(1,4,7,10-tetraazacyclododecane-κ4
N)nickel(II) nitrate
Authors: Reibenspies Joseph , Small Nadia , Bhuvanesh Nattamai , Chiarella Gina , Salazar Vivian , Pery Bréayshia , Smith Rukiyah , Toole Deja , Hewage Shamika , Fernando Harschica , Reinheimer Eric
Published: October 2024

The crystal structure of the title compound, [Ni(C8H20N4)(NO3)]NO3, at room temperature, has monoclinic (P21/n) symmetry. The structure displays intermolecular hydrogen bonding. The nickel displays a distorted bipyramidal geometry with the symmetric bidentate bonded nitrate occupying an equatorial site. The 1,4,7,10-tetraazacyclododecane (cyclen) backbone has the [4,8] configuration, with three nitrogen-bound H atoms directed above the plane of the nitrogen atoms towards the offset nickel atom with the fourth nitrogen-bound hydrogen directed below from the plane of the nitrogen atoms. The nitrate anion O atoms are seen to hydrogen bond to the H atoms bound to the N atoms of the ligand.