bluuebunny/crossref_metadata_2025 huggingface dataset:
Large-scale application of palaeoproteomics (Zooarchaeology by Mass Spectrometry; ZooMS) in two Palaeolithic faunal assemblages from China
Authors: Wang Naihui , Xu Yang , Tang Zhuowei , He Cunding , Hu Xin , Cui Yinqiu , Douka Katerina
Published: October 2023

The application of Zooarchaeology by Mass Spectrometry (ZooMS) on Pleistocene sites in Europe and northern Asia has resulted in the discovery of important new hominin fossils and has expanded the range of identified fauna. However, no systematic, large-scale application of ZooMS on Palaeolithic sites in East Asia has been attempted thus far. Here, we analyse 866 morphologically non-diagnostic bones from Jinsitai Cave in northeast China and Yumidong Cave in South China, from archaeological horizons dating to 150–10 ka BP. Bones from both sites revealed a high degree of collagen preservation and potentially time-related deamidation patterns, despite being located in very distinct environmental settings. At Jinsitai, we identified 31 camel bones, five of which were radiocarbon dated to 37–20 ka BP. All dated specimens correspond to colder periods of Marine Isotope Stages 3 and 2. We regard the presence of camels at Jinsitai as evidence of wild camels being a megafauna taxon targeted, most likely by early modern humans, during their expansion across northeast Asia. This large-scale application of ZooMS in China highlights the potential of the method for furthering our knowledge of the palaeoanthropological and zooarchaeological records of East Asia.
Ferroptosis precedes apoptosis to facilitate specific death signalling by fatty acids
Authors: Zupo Valerio , Costantini Maria , Aflalo Eliahu D. , Levy Tom , Chalifa-Caspi Vered , Obayomi Olabiyi , Mutalipassi Mirko , Ruocco Nadia , Glaviano Francesca , Somma Emanuele , Nieri Paola , Sagi Amir
Published: October 2023

Cell death is physiologically induced by specific mediators. However, our power to trigger the process in selected cells is quite limited. The protandric shrimp
Hippolyte inermis
offers a possible answer. Here, we analyse a de novo transcriptome of shrimp post-larvae fed on diatoms. The sex ratio of diatom-fed shrimps versus shrimps fed on control diets was dramatically altered, demonstrating the disruption of the androgenic gland, and their transcriptome revealed key modifications in gene expression. A wide transcriptomic analysis, validated by real-time qPCR, revealed that ferroptosis represents the primary factor to re-shape the body of this invertebrate, followed by further apoptotic events, and our findings open biotechnological perspectives for controlling the destiny of selected tissues. Ferroptosis was detected here for the first time in a crustacean. In addition, this is the first demonstration of a noticeable effect prompted by an ingested food, deeply impacting the gene networks of a young metazoan, definitely determining its future physiology and sexual differentiation.
The emergence of division of labour through decentralized social sanctioning
Authors: Yaman Anil , Leibo Joel Z. , Iacca Giovanni , Wan Lee Sang
Published: October 2023

Human ecological success relies on our characteristic ability to flexibly self-organize into cooperative social groups, the most successful of which employ substantial specialization and division of labour. Unlike most other animals, humans learn by trial and error during their lives what role to take on. However, when some critical roles are more attractive than others, and individuals are self-interested, then there is a social dilemma: each individual would prefer others take on the critical but unremunerative roles so they may remain free to take one that pays better. But disaster occurs if all act thus and a critical role goes unfilled. In such situations learning an optimum role distribution may not be possible. Consequently, a fundamental question is: how can division of labour emerge in groups of self-interested lifetime-learning individuals? Here, we show that by introducing a model of social norms, which we regard as emergent patterns of decentralized social sanctioning, it becomes possible for groups of self-interested individuals to learn a productive division of labour involving all critical roles. Such social norms work by redistributing rewards within the population to disincentivize antisocial roles while incentivizing prosocial roles that do not intrinsically pay as well as others.
Genomic estimates of mutation and substitution rates contradict the evolutionary speed hypothesis of the latitudinal diversity gradient
Authors: Liu Haoxuan , Sun Mengyi , Zhang Jianzhi
Published: October 2023

The latitudinal diversity gradient (LDG) refers to a decrease in biodiversity from the equator to the poles. The evolutionary speed hypothesis, backed by the metabolic theory of ecology, asserts that nucleotide mutation and substitution rates per site per year are higher and thereby speciation rates are higher at higher temperatures, generating the LDG. However, prior empirical investigations of the relationship between the temperature and mutation or substitution rate were based on a few genes and the results were mixed. We here revisit this relationship using genomic data. No significant correlation between the temperature and mutation rate is found in 13 prokaryotes or in 107 eukaryotes. An analysis of 234 diverse trios of bacterial taxa indicates that the synonymous substitution rate is not significantly associated with the growth temperature. The same data, however, reveal a significant negative association between the nonsynonymous substitution rate and temperature, which is explainable by a larger fraction of detrimental nonsynonymous mutations at higher temperatures due to a stronger demand for protein stability. We conclude that the evolutionary speed hypothesis of the LDG is unsupported by genomic data and advise that future mechanistic studies of the LDG should focus on other hypotheses.
Signatures of adaptive decreased virulence of deformed wing virus in an isolated population of wild honeybees (
Apis mellifera
)
Authors: Ray Allyson M. , Gordon Emma C. , Seeley Thomas D. , Rasgon Jason L. , Grozinger Christina M.
Published: October 2023

Understanding the ecological and evolutionary processes that drive host–pathogen interactions is critical for combating epidemics and conserving species. The
Varroa destructor
mite and deformed wing virus (DWV) are two synergistic threats to Western honeybee (
Apis mellifera
) populations across the globe. Distinct honeybee populations have been found to self-sustain despite
Varroa
infestations, including colonies within the Arnot Forest outside Ithaca, NY, USA. We hypothesized that in these bee populations, DWV has been selected to produce an avirulent infection phenotype, allowing for the persistence of both host and disease-causing agents. To investigate this, we assessed the titre of viruses in bees from the Arnot Forest and managed apiaries, and assessed genomic variation and virulence differences between DWV isolates. Across groups, we found viral abundance was similar, but DWV genotypes were distinct. We also found that infections with isolates from the Arnot Forest resulted in higher survival and lower rates of symptomatic deformed wings, compared to analogous isolates from managed colonies, providing preliminary evidence to support the hypothesis of adaptive decreased viral virulence. Overall, this multi-level investigation of virus genotype and phenotype indicates that host ecological context can be a significant driver of viral evolution and host–pathogen interactions in honeybees.
Pulmonary Ventilation Analysis Using1H Ultra-Short Echo Time (UTE) Lung MRI: A Reproducibility Study
Authors: Tan Fei , Zhu Xucheng , Chan Marilynn , Deveshwar Nikhil , Willmering Matthew M. , Lustig Michael , Larson Peder E. Z.
Published: October 2023

Purpose

To evaluate methods for quantification of pulmonary ventilation with ultrashort echo time (UTE) MRI.

Methods

We performed a reproducibility study, acquiring two free-breathing1H UTE lung MRIs on the same day for six healthy volunteers. The 1) 3D + t cyclic b-spline and 2) symmetric image normalization (SyN) methods for image registration were applied after respiratory phase-resolved image reconstruction. Ventilation maps were calculated using 1) Jacobian determinant of the deformation fields minus one, termed regional ventilation, and 2) intensity percentage difference between the registered and fixed image, termed specific ventilation. We compared the reproducibility of all four method combinations via statistical analysis.

Results

Split violin plots and Bland-Altman plots are shown for whole lungs and lung sections. The cyclic b-spline registration and Jacobian determinant regional ventilation quantification provide total ventilation volumes that match the segmentation tidal volume, smooth and uniform ventilation maps. The cyclic b-spline registration and specific ventilation combination yields the smallest standard deviation in the Bland-Altman plot.

Conclusion

Cyclic registration performs better than SyN for respiratory phase-resolved1H UTE MRI ventilation quantification. Regional ventilation correlates better with segmentation lung volume, while specific ventilation is more reproducible.
The history of chromosomal instability in genome doubled tumors
Authors: Baker Toby M. , Lai Siqi , Lesluyes Tom , Yan Haixi , Verfaillie Annelien , Dentro Stefan , Lynch Andrew R. , Bowes Amy L. , Pillay Nischalan , Flanagan Adrienne M. , Swanton Charles , Tarabichi Maxime , Loo Peter Van
Published: October 2023

Tumors frequently display high chromosomal instability (CIN) and contain multiple copies of genomic regions. Here, we describe GRITIC, a generic method for timing genomic gains leading to complex copy number states, using single-sample bulk whole-genome sequencing data. By applying GRITIC to 5,656 tumors, we found that non-parsimonious evolution is frequent in the formation of complex copy number states in genome-duplicated tumors. We measured CIN before and after genome duplication in human tumors and found that late genome doubling was followed by an increase in the rate of copy number gain. Copy number gains often accumulate as punctuated bursts, commonly after genome duplication. We infer that genome duplications typically affect the selection landscape of copy number losses, while only minimally impacting copy number gains. In summary, GRITIC is a novel copy number gain timing framework that permits the analysis of copy number evolution in chromosomally unstable tumors.

Statement of significance

Complex genomic gains are associated with whole-genome duplications, which are frequent across tumors, span a large fraction of their genomes, and are linked to poorer outcomes. GRITIC infers when these gains occur during tumor development, which will help to identify the genetic events that drive tumor evolution.
β-aminopropionitrile Induces Distinct Pathologies in the Ascending and Descending Thoracic Aortic Regions of Mice
Authors: Franklin Michael K. , Sawada Hisashi , Ito Sohei , Howatt Deborah A. , Amioka Naofumi , Liang Ching-Ling , Zhang Nancy , Graf David B. , Moorleghen Jessica J. , Katsumata Yuriko , Lu Hong S. , Daugherty Alan
Published: October 2023

BACKGROUND

β-aminopropionitrile (BAPN) is a pharmacological inhibitor of lysyl oxidase and lysyl oxidase-like proteins. Administration of BAPN promotes aortopathies, although there is a paucity of data on experimental conditions to generate pathology. The objective of this study was to define experimental parameters and determine whether equivalent or variable aortopathies were generated throughout the aortic tree during BAPN administration in mice.

METHODS

BAPN was administered in drinking water for a period ranging from 1 to 12 weeks. The impacts of BAPN were first assessed with regard to dose, strain, age, and sex. BAPN-induced aortic pathological characterization was conducted using histology and immunostaining. To investigate the mechanistic basis of regional heterogeneity, ascending and descending thoracic aortas were harvested after one week of BAPN administration before the appearance of overt pathology.

RESULTS

BAPN-induced aortic rupture predominantly occurred or originated in the descending thoracic aorta in young C57BL/6J or N mice. No apparent differences were found between male and female mice. For mice surviving 12 weeks of BAPN administration, profound dilatation was consistently observed in the ascending region, while there were more heterogeneous changes in the descending thoracic region. Pathological features were distinct between the ascending and descending thoracic regions. Aortic pathology in the ascending region was characterized by luminal dilatation and elastic fiber disruption throughout the media. The descending thoracic region frequently had dissections with false lumen formation, collagen deposition, and remodeling of the wall surrounding the false lumen. Cells surrounding the false lumen were predominantly positive for α-smooth muscle actin. One week of BAPN administration compromised contractile properties in both regions equivalently, and RNA sequencing did not show obvious differences between the two aortic regions in smooth muscle cell markers, cell proliferation markers, and extracellular components.

CONCLUSIONS

BAPN-induced pathologies show distinct, heterogeneous features within and between ascending and descending aortic regions in mice.
Age at menopause and risk of ischemic stroke: a systematic review and meta-analysis
Authors: Wang Jie , Chen Ying
Published: October 2023

Background

Despite its importance in being among the top 10 causes of old women death, there is limited data on age at menopause and ischemic stroke.

Aims

We performed a systematic review and meta-analysis to estimate the effect of age at onset of menopause on ischemic stroke.

Methods

We screened four databases (PubMed, Cochrane, Web of Science, and EMBASE databases) up to July 17, 2023. This systematic review was reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines and was registered with PROSPERO (CRD42023444245). Data extraction and quality assessment were independently undertaken by two reviewers. A random-effects model was used for meta-analysis using Revman5.4 to calculate the risk ratio of the incidence of ischemic stroke. Heterogeneity was assessed using I2. Meta-regression and assessment for bias were performed.

Results

Out of 725 records identified, 10 studies were included in the qualitative synthesis and the quantitative meta-analysis. The pooled incidence rate for ischemic strokes which age at onset of menopause before 43 years old was 1.22 (95% confidence interval (CI): 1.02-1.46). The pooled incidence rate of early menopause was 1.26 (95% CI: 1.07-1.48) for ischemic stroke. The incidence rate of ischemic stroke for women with early menopause may be in an environment with a high incidence for a long time.

Conclusion

Evidence from this meta-analysis suggests that early menopause is associated with an increased risk of ischemic stroke. Age at onset of menopause before 43 years old may be the cut-off value of increased risk of ischemic stroke.
Growth couples temporal and spatial fluctuations of tissue properties during morphogenesis
Authors: Fruleux Antoine , Hong Lilan , Roeder Adrienne H. K. , Li Chun-Biu , Boudaoud Arezki
Published: October 2023

Living tissues display fluctuations – random spatial and temporal variations of tissue properties around their reference values – at multiple scales. It is believed that such fluctuations may enable tissues to sense their state or their size. Recent theoretical studies developed specific models of fluctuations in growing tissues and predicted that fluctuations of growth show long-range correlations. Here we elaborated upon these predictions and we tested them using experimental data. We first introduced a minimal model for the fluctuations of any quantity that has some level of temporal persistence or memory, such as concentration of a molecule, local growth rate, or mechanical property. We found that long-range correlations are generic, applying to any such quantity, and that growth couples temporal and spatial fluctuations, through a mechanism that we call ‘fluctuation stretching’ — growth enlarges the lengthscale of variation of this quantity. We then analysed growth data from sepals of the model plant Arabidopsis and we quantified spatial and temporal fluctuations of cell growth using the previously developed Cellular Fourier Transform. Growth appears to have long-range correlations. We compared different genotypes and growth conditions: mutants with lower or higher response to mechanical stress have lower temporal correlations and longer-range spatial correlations than wild-type plants. Finally, we used theoretical predictions to merge experimental data from all conditions and developmental stages into an unifying curve, validating the notion that temporal and spatial fluctuations are coupled by growth. Altogether, our work reveals kinematic constraints on spatiotemporal fluctuations that have an impact on the robustness of morphogenesis.

Significance Statement

How do organs and organisms grow and achieve robust shapes in the face of subcellular and cellular variability? In order to address this outstanding mystery, we investigated the variability of growth at multiple scales and we analysed experimental data from growing plant tissues. Our results support the prediction that tissue expansion couples temporal memory of growth with spatial variability of growth. Our work reveals a constraint on the spatial and temporal variability of growth that may impact the robustness of morphogenesis.
INTRAVENOUS VITAMIN C SUPPLEMENTATION IN ALLOGENEIC HEMATOPOIETIC CELL TRANSPLANT RECIPIENTS: SALUTARY IMPACT ON CLINICAL OUTCOMES
Authors: Simmons Gary , Sabo Roy , Aziz May , Martin Erika , Bernard Robyn J. , Sriparna Manjari , McIntire Cody , Krieger Elizabeth , Brophy Donald F. , Natarajan Ramesh , Fowler Alpha , Roberts Catherine H. , Toor Amir
Published: October 2023

Intravenous (IV) vitamin C improves organ function and reduces inflammation in sepsis, an inflammatory state like the post-hematopoietic stem cell transplant (SCT) milieu. The safety and efficacy of parenteral vitamin C after allogeneic hematopoietic stem cell transplant (HSCT) were evaluated in a phase I/II trial and clinical outcomes compared with a propensity score - matched historical control.

Methods

Patients with advanced hematologic malignancies were enrolled in a phase 2 clinical trial, receiving IV vitamin C, 50mg/kg/d, divided into 3 doses given on days 1-14 after HSCT, followed by 500 mg bid oral from day 15 until 6 months post-SCT.

Results

55 patients received IV vitamin C: these include 10/10 HLA-MRD and MUD (n=48) and 9/10 HLA MUD recipients (n=7). All patients enrolled were deficient in vitamin C at day 0 and had restoration to normal levels for the remainder of the course. Vitamin C recipients had lower non-relapse mortality (11% vs. 25%, p-value = 0.07) and consequently, improved survival compared to historical controls (82% vs 62% p=0.06), with no attributable grade 3 and 4 toxicities to vitamin C. Patients with myeloid malignancies had improved survival (83% vs. 54%, p=0.02) and non-relapse mortality (NRM) (10% vs. 37%, p=0.009), as well as chronic GVHD, with similar relapse rates compared to controls.

Conclusions

In patients undergoing allogeneic HSCT the administration of IV vitamin C is safe and reduces non-relapse mortality improving overall survival. Randomized trials are needed to confirm the utility of this easily available and inexpensive therapy.
Machine Learning Enables Single-Score Assessment of MASLD Presence and Severity
Authors: Chen Robert , Petrazzini Ben Omega , Nadkarni Girish , Rocheleau Ghislain , Bansal Meena , Do Ron
Published: October 2023

Metabolic dysfunction-associated steatotic liver disease (MASLD) affects 30% of the global population but is often underdiagnosed. To fill this diagnostic gap, we developed a digital score reflecting presence and severity of MASLD. We fitted a machine learning model to electronic health records from 37,212 UK Biobank participants with proton density fat fraction measurements and/or a MASLD diagnosis to generate a “MASLD score”. In holdout testing, our model achieved areas under the receiver-operating curve of 0.83-0.84 for MASLD diagnosis and 0.90-0.91 for identifying MASLD-associated advanced fibrosis. MASLD score was significantly associated with MASLD risk factors, progression to cirrhosis, and mortality. External testing in 252,725 diverse American participants demonstrated consistent results, and hepatologist chart review showed MASLD score identified probable MASLD underdiagnosis. The MASLD score could improve early diagnosis and intervention of chronic liver disease by providing a non-invasive, low-cost method for population-wide screening of MASLD.
Inferring community transmission of SARS-CoV-2 in the United Kingdom using the ONS COVID-19 Infection Survey
Authors: McCabe Ruth , Danelian Gabriel , Panovska-Griffiths Jasmina , Donnelly Christl A.
Published: October 2023

Key epidemiological parameters, including the effective reproduction number,R(t), and the instantaneous growth rate,r(t), generated from an ensemble of models, have been informing public health policy throughout the COVID-19 pandemic in the four nations of the United Kingdom of Great Britain and Northern Ireland (UK). However, estimation of these quantities became challenging with the scaling down of surveillance systems as part of the transition from the “emergency” to “endemic” phase of the pandemic.

The Office for National Statistics (ONS) COVID-19 Infection Survey (CIS) provided an opportunity to continue estimating these parameters in the absence of other data streams. We used a penalised spline model fitted to the ONS CIS test positivity estimates to produce a smoothed estimate of the prevalence of SARS-CoV-2 positivity over time. The resulting fitted curve was used to estimate the “ONS-based”R(t) andr(t) across the four nations of the UK. Estimates produced under this model are compared to government-published estimates with particular consideration given to the contribution that this single data stream can offer in the estimation of these parameters.

Depending on the nation and parameter, we found that up to 77% of the variance in the government-published estimates can be explained by the ONS-based estimates, demonstrating the value of this singular data stream to track the epidemic in each of the four nations. We additionally find that the ONS-based estimates uncover epidemic trends earlier than the corresponding government-published estimates.

Our work shows that the ONS CIS can be used to generate the key COVID-19 epidemics across the four UK nations. This is not intended as an alternative to ensemble modelling, rather it is intended as a potential solution to the aforementioned challenge faced by public health officials in the UK in early 2022.
Projections of the incidence of COVID-19 in Japan and the potential impact of a Fall 2023 COVID-19 Vaccine
Authors: Kohli M , Maschio M , Lee A , Igarashi A
Published: October 2023

Background

The study objective was to estimate the incidence of COVID-19 infection, hospitalization, and deaths in Japan from September 2023 to August 2024 and potential impact of a Fall 2023 COVID-19 vaccine for adults ≥18 years on these outcomes.

Methods

A previously developed Susceptible-Exposed-Infected-Recovered model for the United States (US) was adapted to Japan. The numbers of symptomatic infections, COVID-19– related hospitalizations, and deaths were calculated. Given differences in vaccination coverage, masking practices and social mixing patterns between the US and Japan, all inputs were updated to reflect the Japanese context. Vaccine effectiveness (VE) values are hypothetical, but predicted based on existing VE values of bivalent BA.4/BA.5 boosters against BA.4/BA.5 in Japan, from the VERSUS test-negative case-control study. Sensitivity analyses were performed.

Results

The base case model predicts overall that there will be approximately 35.2 million symptomatic COVID-19 infections, 690,000 hospitalizations, and 62,000 deaths in Japan between September 2023 and August 2024. If an updated COVID-19 vaccine is offered to all adults aged 18 years and older in Fall 2023, the model predicts that 7.3 million infections, 275,000 hospitalizations and 26,000 deaths will be prevented. If vaccines are only given to those aged 65 years and older, only 2.9 million infections, 180,000 hospitalizations and 19,000 deaths will be prevented. Sensitivity analysis results suggest that hospitalizations and deaths prevented are most sensitive to initial vaccine effectiveness (VE) against infection and hospitalizations, and the waning rate associated with VE against infection. Symptomatic infections prevented was most sensitive to initial VE against infection and VE waning.

Conclusions

Results suggest that a Fall 2023 COVID-19 vaccine would reduce total numbers of COVID-19 related infections, hospitalizations, and deaths.
A Comparative Analysis of Global Adult Tobacco Survey (GATS): Prevalence and Predictors of Tobacco Smoking in Seven Regions of India
Authors: Tikhute Vishal
Published: October 2023

Aim

This article aims to assess the prevalence of tobacco smoking among the adult study population and also explore the association between socio-demographic factors and tobacco use in the six geographical regions of India.

Methods

This is a cross-sectional comparative research design that used nationally representative population-based household GATS-1 data on tobacco use in India. Six states representing the respective six geographic regions (one state per region) of India were selected using systematic random sampling. The prevalence of tobacco smoking among the study population was calculated and used for comparison between the six regions. Logistic regression was used to assess the association between socio-demographic factors and tobacco smoking in each zone.

Results

The North-eastern, Central, and Eastern regions had a high prevalence of tobacco smoking. Further, factors such as sex, place of residence, literacy, and working status had a significant association with current use of tobacco (smoking).

Conclusion

Despite there are policies and legal frameworks to control the use and sell of tobacco in India, the prevalence of tobacco smoking is high, particularly in the North-eastern, Central, and Eastern regions of India. Policies and community-based approaches to provide health education to reduce tobacco smoking are recommended.
Integration of Capnography and Continuous Positive Airway Pressure (CPAP) in the Prehospital Setting
Authors: Sethi Sahil , Hobbs Gene , Hubbard Devin , Donnelly Kenneth , Grover Joseph M. , Rizvi Imran
Published: October 2023

BACKGROUND

Capnography is one of the most important respiratory monitoring tools used in EMS because changes to end-tidal CO2(ETCO2) generally precede blood oxygen desaturation, and waveform morphology can be used to assess bronchial patency. Many of capnography’s indications overlap with those of continuous positive airway pressure (CPAP) therapy. However, there are currently no convenient methods to administer CPAP while using capnography, and no peer-reviewed studies have examined combining the two technologies in the prehospital setting.

METHODS & FINDINGS

Two types of capnography sampler were used to investigate how ETCO2, capnogram shape, and respiration rate (RR) are affected by applying a CPAP mask both with and without oxygen flowing. A traditional nasal-oral cannula (NC) sampler, as well as a novel sampler that does not break the seal between the CPAP mask and the patient’s face (called the CPAP-Capnography Adapter, or CCA), were evaluated on a Human Patient Simulator (HPS). No significant differences between the NC and CCA were found for ETCO2and RR percent error. Placement of a CPAP mask without turning on O2increased ETCO2. During CPAP therapy, the two samplers maintained their RR measurement accuracy, but ETCO2values were significantly reduced and the capnogram depicted an increased β-angle with severe blunting of the inspiratory downstroke.

CONCLUSIONS

The HPS had set-point ETCO2and PaCO2values, indicating that the local CO2concentration at the nares was diluted during CPAP and no longer accurately reflected the simulated subject’s breathing. The compromise in waveform morphology could be overcome by further research into interpreting capnogram differences during CPAP between healthy patients and those with respiratory pathologies. However, at this time, our results show that ETCO2values and capnogram shape should be interpreted with caution during CPAP.
Changes in urinary glutathione sulfonamide (GSA) levels between admission and discharge of patients with cystic fibrosis
Authors: Blake Tamara L , Sly Peter D , Andersen Isabella , Wainwright Claire E , Reid David W , Bell Scott C , Kettle Anthony J , Dickerhof Nina
Published: October 2023

There is an urgent need to develop sensitive, non-invasive biomarkers that can track airway inflammatory activity for patients with cystic fibrosis (CF). Urinary GSA levels correlate well with GSA levels in BAL samples and other markers of neutrophilic inflammation, suggesting that this biomarker may be suitable for tracking disease activity in this population.

We recruited 102 children (median 11.5 years-old) and 64 adults (median 32.5 years-old) who were admitted to hospital for management of an acute pulmonary exacerbation and/or eradication of infectious agents such asP. aeruginosaorS. aureus. Our aim was to explore how urinary GSA levels changed across admission timepoints. Urine samples were collected at admission and discharge, and GSA measured by liquid chromatography with mass spectrometry. Paired admission-discharge results were compared using Wilcoxon signed-rank test.

Paired admission-discharge samples were available for 49 children and 60 adults. A statistically significant difference was observed between admission-discharge for children, but not for adults. Spearman’s correlation analysis identified a correlation between urinary GSA levels and age, sex, inflammatory markers, andP. aeruginosainfection for children only. Our preliminary findings suggest that urinary GSA is responsive to the resolution of an acute pulmonary exacerbation and therefore warrants further studies in this population.
Protocols for Multi-Scale Molecular Dynamics Simulations: A Comparative Study for Intrinsically Disordered Amyloid Beta in Amber & Gromacs on CPU & GPU
Authors: Smardz Pamela , Anila Midhun Mohan , Rogowski Pawel , Li Mai Suan , Różycki Bartosz , Krupa Pawel
Published: October 2023

Intrinsically disordered proteins (IDPs) present challenges to conventional experimental techniques due to their large-scale conformational fluctuations and the transient occurrence of structural elements. This work illustrates computational methods for studying IDPs at various levels of resolution. The included simulation protocol offers a step-by-step guide on how to conduct molecular dynamics (MD) simulations and analyze the results using the Amber and Gromacs packages, employing both all-atom and coarse-grained approaches. This protocol can be easily adapted to study other biomacromolecules, including folded and disordered proteins and peptides.

Furthermore, it is discussed in this work how to perform standard molecular modeling operations, such as amino-acid substitutions (mutagenesis) and insertions of residues missing in a protein structure, as well as how to incorporate post-translational modifications into the simulations, such as disulfide bonds, which are often crucial for proteins to attain their physiologically functional structure. In conventional MD studies, disulfide bonds are typically fixed at the preparation step and remain unchanged throughout the simulations, unable to break or reform. Here, in contrast, a dynamic approach is presented. It involves adequate distance restraints applied to the sulfur atoms of selected cysteine residues, allowing disulfide bonds to break and reform during the simulation.

The effectiveness of these methodologies is demonstrated by examining a model IDP, the monomeric form of 1-42 amyloid-β (Aβ42), both with and without disulfide bonds, at different levels of resolution. This study not only contributes to our understanding of the role of disulfide bonds but also provides detailed simulation protocols that can serve as a foundation for future investigations.

Given the challenges of experimental studies on intrinsically disordered proteins, this manuscript demonstrates step-by-step protocols for conducting all-atom and coarse-grained molecular dynamics simulations using two widespread packages, Amber and Gromacs. The monomeric form of 1-42 amyloid-β (Aβ42) is used as an example, from which insights into the structure, dynamics and physicochemical properties of this protein can be obtained.
Discovery of CMX990: A Potent SARS-CoV-2 3CL Protease Inhibitor Bearing a Novel Covalent Warhead
Authors: Elshan N. G. R. Dayan , Wolff Karen C. , Riva Laura , Woods Ashley K. , Grabovyi Gennadii , Wilson Katy , Rahimi Alireza , Pedroarena James , Ghorai Sourav , Gupta Anil Kumar , Nazarian Armen , Weiss Frank , Liu Yuyin , Mazumdar Wrickban , Song Lirui , Okwor Neechi , Malvin Jacqueline , Bakowski Malina A. , Beutler Nathan , Kirkpatrick Melanie G. , Gebara-Lamb Amal , Huang Edward , Nguyen-Tran Van , Chi Victor , Li Shuangwei , Rogers Thomas F. , McNamara Case W. , Chen Jian Jeffrey , Joseph Sean B. , Schultz Peter G. , Chatterjee Arnab K.
Published: October 2023

There remains a need to develop novel SARS-CoV-2 therapeutic options that improve upon existing therapies by increased robustness of response, fewer safety liabilities, and global-ready accessibility. Functionally critical viral main protease (Mpro, 3CLpro) of SARS-CoV-2 is an attractive target due to its homology within the coronaviral family, and lack thereof towards human proteases. In this disclosure, we outline the advent of a novel SARS-CoV-2 3CLproinhibitor, CMX990, bearing an unprecedented trifluoromethoxymethyl ketone warhead. Compared with the marketed drug nirmatrelvir (combination with ritonavir = PaxlovidTM), CMX990 has distinctly differentiated potency (∼5x more potent in primary cells) and humanin vitroclearance (>4x better microsomal clearance and >10x better hepatocyte clearance), with goodin vitro-in vivocorrelation. Based on its compelling preclinical profile and projected once or twice a day dosing supporting unboosted oral therapy in humans, CMX990 advanced to a Phase 1 clinical trial as an oral drug candidate for SARS-CoV-2.
Unexpected delayed incursion of highly pathogenic avian influenza H5N1 (clade 2.3.4.4b) in the Antarctic region
Authors: Lisovski Simeon , Günther Anne , Dewar Meagan , Ainley David , Aldunate Fabián , Arce Rodrigo , Ballard Grant , Bauer Silke , Belliure Josabel , Banyard Ashley C. , Boulinier Thierry , Bennison Ashley , Braun Christina , Cary Craig , Catry Paulo , Clessin Augustin , Connan Maelle , Correia Edna , Cox Aidan , Cristina Juan , Elrod Megan , Emerit Julia , Ferreiro Irene , Fowler Zoe , Gamble Amandine , Granadeiro José P. , Hurtado Joaquin , Jongsomjit Dennis , Lesage Célia , Lejeune Mathilde , Kuepfer Amanda , Lescroël Amélie , Li Amy , McDonald Ian R. , Menéndez-Blázquez Javier , Morandini Virginia , Moratorio Gonzalo , Militão Teresa , Moreno Pilar , Perbolianachis Paula , Pennycook Jean , Raslan Maryam , Reid Scott M. , Richards-Babbage Roanna , Schmidt Annie E. , Sander Martha Maria , Smyth Lucy , Soutullo Alvaro , Stanworth Andrew , Streith Léo , Tornos Jérémy , Varsani Arvind , Herzschuh Ulrike , Beer Martin , Wille Michelle
Published: October 2023

The current highly pathogenic avian influenza H5N1 panzootic has substantial impacts on wild birds and marine mammals. Although major outbreaks occurred in South America, incursion to Antarctica emerged late in the breeding season of 2023/2024 and was confined the wider region of the Antarctic Peninsula. To infer potential underlying processes, we compiled H5N1 surveillance from Antarctica and Sub-Antarctic Islands prior to the first confirmed cases.
Increased tau expression in theAPOE4blood-brain barrier model is associated with reduced anti-tau therapeutic antibody deliveryin vitro
Authors: Wasielewska Joanna M. , Bajracharya Rinie , Johnston Rebecca L. , Chaves Juliana C.S. , Pébay Alice , Oikari Lotta E. , Götz Jürgen , Nisbet Rebecca M. , White Anthony R.
Published: October 2023

Tau protein is a critical driver of neurodegeneration and an important drug target in Alzheimer’s disease (AD). Tau-specific immunotherapy has emerged as a promising treatment strategy for AD, however the therapeutic efficacy of anti-tau antibodies may be limited by their insufficient delivery across the blood-brain barrier (BBB). The apolipoprotein E4 allele (APOE4) is the strongest genetic risk factor for sporadic AD and is known to influence tau-mediated neurodegeneration. Interestingly, both tau andAPOE4have been implicated in the cerebrovascular pathology observed in AD. Yet, the crosstalk betweenAPOE4and tau at the level of the BBB and its consequences for anti-tau immunotherapeutics delivery, remain poorly understood. Here, we utilisedAPOE3- andAPOE4-carrying human iPSC-derived induced brain endothelial-like cells (iBECs) as a sporadic AD BBB model, determined the levels of endogenous tau in iBECs, and explored the transport of two novel monoclonal anti-tau antibodies, RNF5 and RN2N, across thein vitrobarrier. Our results demonstrate thatMAPTgene transcription, tau protein levels and tau phosphorylation are increased in iBECs in anAPOE4-related manner and are associated with reduced iBEC monolayer integrity and increased permeability to biologically inert fluorescent tracers. Additionally, elevated levels of intracellular tau inAPOE4cells were accompanied by the reduced passive permeability of therapeutic anti-tau antibodies through theAPOE4iBEC monolayer, which could be improved by the application of focused ultrasound and microbubble drug-delivery technology. Together, our study illustrates a new role forAPOE4and tau in human iBECs with potential implications for BBB dysfunction and anti-tau therapeutic antibody delivery.
GRAIGH: Gene Regulation accessibility integrating GeneHancer database
Authors: Martini Lorenzo , Savino Alessandro , Bardini Roberta , Di Carlo Stefano
Published: October 2023

Single-cell assays for transposase-accessible chromatin sequencing data are one of the most powerful tools for studying the epigenetic heterogeneity of cell populations. However, the chromatin accessibility landscape is not well understood and lacks a proper way to interpret it. This work proposes Gene Regulation Accessibility Integrating GeneHancer (GRAIGH), a novel approach to the interpretation of genome accessibility through the integration of the GeneHancer database information, which describes genome-wide enhancer-to-gene associations. Firstly, this paper presents the methods for integrating GeneHancer with scATAC-seq data, creating a new matrix where the features are the GeneHancer elements IDs instead of the accessibility peaks. Secondly, it investigates its capability to analyze the data and detect cellular heterogeneity. In particular, this work shows that the GeneHancer elements are selectively accessible for distinct cell types, and more importantly, their connected genes are precisely known marker genes. Moreover, it investigates the specificity of GeneHancer elements accessibility, demonstrating their high selectivity against the gene activity.
Light-driven synchronization of optogenetic clocks
Authors: Cannarsa Maria Cristina , Liguori Filippo , Pellicciotta Nicola , Frangipane Giacomo , Di Leonardo Roberto
Published: October 2023

Synthetic genetic oscillators can serve as internal clocks within engineered cells to program periodic expression. However, cell-to-cell variability introduces a dispersion in the characteristics of these clocks that drives the population to complete desynchronization. Here we introduce the optorepressilator, an optically controllable genetic clock that combines the repressilator, a three-node synthetic network in E. coli, with an optogenetic module enabling to reset, delay, or advance its phase using optical inputs. We demonstrate that a population of optorepressilators can be synchronized by transient green light exposure or entrained to oscillate indefinitely by a train of short pulses, through a mechanism reminiscent of natural circadian clocks. Furthermore, we investigate the system's response to detuned external stimuli observing multiple regimes of global synchronization. Integrating experiments and mathematical modeling, we show that the entrainment mechanism is robust and can be understood quantitatively from single cell to population level.
Evolution and Diversification of Carboxylesterase-like [4+2] Cyclases in Aspidosperma and Iboga Alkaloid Biosynthesis
Authors: DeMars Matthew D. , O’Connor Sarah E.
Published: October 2023

Monoterpene indole alkaloids (MIAs) are a large and diverse class of plant natural products, and their biosynthetic construction has been a subject of intensive study for many years. The enzymatic basis for the production of aspidosperma and iboga alkaloids, which are produced exclusively by members of the Apocynaceae plant family, has recently been discovered. Three carboxylesterase (CXE)-like enzymes fromCatharanthus roseusandTabernanthe ibogacatalyze regio- and enantiodivergent [4+2] cycloaddition reactions to generate the aspidosperma (tabersonine synthase, TS) and iboga (coronaridine synthase, CorS; catharanthine synthase, CS) scaffolds from a common biosynthetic intermediate. Here, we use a combined phylogenetic and biochemical approach to investigate the evolution and functional diversification of these cyclase enzymes. Through ancestral sequence reconstruction, we provide evidence for initial evolution of TS from an ancestral CXE followed by emergence of CorS in two separate lineages, leading in turn to CS exclusively in theCatharanthusgenus. This progression from aspidosperma to iboga alkaloid biosynthesis is consistent with the chemotaxonomic distribution of these MIAs. We subsequently generate and test a panel of chimeras based on the ancestral cyclases to probe the molecular basis for differential cyclization activity. Finally, we show through partial heterologous reconstitution of tabersonine biosynthesis using non-pathway enzymes how aspidosperma alkaloids could have first appeared as “underground metabolites” via recruitment of promiscuous enzymes from common protein families. Our results provide insight into the evolution of biosynthetic enzymes and how new secondary metabolic pathways can emerge through small but important sequence changes following co-option of preexisting enzymatic functions.
TheStaphylococcus aureusregulatory program in a human skin-like environment
Authors: Costa Flavia G. , Mills Krista B. , Crosby Heidi A. , Horswill Alexander R.
Published: October 2023

Staphylococcus aureusis a Gram-positive pathogen responsible for the majority of skin and soft tissue infections (SSTIs).S. aureuscolonizes the anterior nares of approximately 20-30% of the population and transiently colonizes the skin, thereby increasing the risk of developing SSTIs and more serious infections. Current laboratory models that mimic the skin surface environment are expensive, require substantial infrastructure, and limit the scope of bacterial physiology studies under human skin conditions. To overcome these limitations, we developed a cost-effective, open-source, chemically defined media recipe termed skin-like media (SLM) that incorporates key aspects of the human skin surface environment and supports growth of several Staphylococcal species. We utilized SLM to investigate the transcriptional response of methicillin-resistantS. aureus(MRSA) following growth in SLM compared to a commonly used laboratory media. Through RNA-seq analysis, we observed the upregulation of several virulence factors, including genes encoding functions involved in adhesion, proteolysis, and cytotoxicity. To further explore these findings, we conducted qRT-PCR experiments to determine the influence of media composition, pH, and temperature on the transcriptional response of key factors involved in adhesion and virulence. We also demonstrated that MRSA primed in SLM adhered better to human corneocytes and demonstrated adhesin-specific phenotypes that previously required genetic manipulation. These results support the potential utility of SLM as anin vitromodel for assessing Staphylococcal physiology and metabolism on human skin.

Importance

Staphylococcus aureusis the major cause of skin diseases, and its increased prevalence in skin colonization and infections present a need to understand its physiology in this environment. The work presented here outlinesS. aureusupregulation of colonization and virulence factors using a newly developed media that strives to replicate the human skin surface environment, and demonstrates roles for adhesins ClfA, SraP, and Fnbps in human corneocyte adherence.
Non-essential kinetochore proteins contribute to meiotic chromosome condensation through polo-like kinase
Authors: Trakroo Deepika , Agarwal Prakhar , Alekar Anushka , Ghosh Santanu Kumar
Published: October 2023

Chromosome condensation plays a pivotal role during faithful chromosome segregation, hence understanding the factors that drive condensation is crucial to get mechanistic insight into chromosome segregation. Previously we showed that in budding yeast, the absence of the non-essential kinetochore proteins affects chromatin-condensin association in meiosis but not in mitosis. A differential organization of the kinetochores, that we and others observed earlier during mitosis and meiosis may contribute to the meiotic-specific role. Here, with our in-depth investigation using in vivo chromosome condensation assays in cells sans a non-essential kinetochore protein, Ctf19, we establish that these proteins have roles in achieving a higher meiotic condensation without influencing much of the mitotic condensation. We further observed an accumulation of the polo-like kinase Cdc5 owing to its higher protein stability inctf19Δmeiotic cells. High Cdc5 activity causes hyper-phosphorylation of the condensin resulting in its reduced stability and concomitant decreased association with the chromatin. Overall, our findings highlight the role of Ctf19 in promoting meiotic chromosome condensation by influencing the activity of Cdc5 and thereby affecting the stability and association of condensin with the chromatin.
Spindle architecture constrains karyotype in budding yeast
Authors: Helsen Jana , Reza Md Hashim , Carvalho Ricardo , Sherlock Gavin , Dey Gautam
Published: October 2023

The eukaryotic cell division machinery must rapidly and reproducibly duplicate and partition the cell’s chromosomes in a carefully coordinated process. However, chromosome number varies dramatically between genomes, even on short evolutionary timescales. We sought to understand how the mitotic machinery senses and responds to karyotypic changes by using a series of budding yeast strains in which the native chromosomes have been successively fused. Using a combination of cell biological profiling, genetic engineering, and experimental evolution, we show that chromosome fusions are well tolerated up until a critical point. Cells with fewer than five centromeres lack the necessary number of kinetochore-microtubule attachments needed to counter outward forces in the metaphase spindle, triggering the spindle assembly checkpoint and prolonging metaphase. Our findings demonstrate that spindle architecture is a constraining factor for karyotype evolution.