bluuebunny/crossref_metadata_2025 huggingface dataset:
Human deleterious mutation rate implies high fitness variance, with declining mean fitness compensated by rarer beneficial mutations of larger effect
Authors: Matheson Joseph , Bertram Jason , Masel Joanna
Published: September 2023

Each new human has an expectedUd=2 - 10 new deleterious mutations. This deluge of deleterious mutations cannot all be purged, and therefore accumulate in a declining fitness ratchet. Using a novel simulation framework designed to efficiently handle genome-wide linkage disequilibria across many segregating sites, we find that rarer, beneficial mutations of larger effect are sufficient to compensate fitness declines due to the fixation of many slightly deleterious mutations. Drift barrier theory posits a similar asymmetric pattern of fixations to explain ratcheting genome size and complexity, but in our theory, the cause isUd>1 rather than small population size. In our simulations,Ud∼2 - 10 generates high within-population variance in relative fitness; two individuals will typically differ in fitness by 15- 40%.Ud∼2 - 10 also slows net adaptation by ∼13%-39%. Surprisingly, fixation rates are more sensitive to changes in the beneficial than the deleterious mutation rate, e.g. a 10% increase in overall mutation rate leads to faster adaptation; this puts to rest dysgenic fears about increasing mutation rates due to rising paternal age.
The universe is asymmetric, the mouse brain too
Authors: Rivera-Olvera Alejandro , Houwing Danielle J. , Ellegood Jacob , Masifi Shang , Martina Stephany LL. , Silberfeld Andrew , Pourquie Olivier , Lerch Jason P. , Francks Clyde , Homberg Judith R. , van Heukelum Sabrina , Grandjean Joanes
Published: September 2023

Hemispheric brain asymmetry is a basic organizational principle of the human brain and has been implicated in various psychiatric conditions, including autism spectrum disorder. Brain asymmetry is not a uniquely human feature and is observed in other species such as the mouse. Yet, asymmetry patterns are generally nuanced, and substantial sample sizes are required to detect these patterns. In this pre-registered study, we use a mouse dataset from the Province of Ontario Neurodevelopmental Network, which comprises structural MRI data from over 2000 mice, including genetic models for autism spectrum disorder, to reveal the scope and magnitude of hemispheric asymmetry in the mouse. Our findings demonstrate the presence of robust hemispheric asymmetry in the mouse brain, such as larger right hemispheric volumes towards the anterior pole and larger left hemispheric volumes toward the posterior pole, opposite to what has been shown in humans. This suggests the existence of species-specific traits. Further clustering analysis identified distinct asymmetry patterns in autism spectrum disorder models, a phenomenon that is also seen in atypically developing participants. Our study shows potential for the use of mouse models in studying the biological bases of typical and atypical brain asymmetry but also warrants caution as asymmetry patterns seem to differ between humans and mice.
The role of cellular filamentation in bacterial aggregation and cluster-cluster assembly
Authors: Charlton Samuel , Melaugh Gavin , Marenduzzo Davide , MacPhee Cait , Secchi Eleonora
Published: September 2023

Bacterial aggregate formation and surface accumulation are increasingly viewed as alternative pathways for biofilm colonization. However, little is known about the dynamics of bacterial aggregate cluster-cluster assembly and their subsequent microstructural and mechanical properties. To this end, we studied experimentally and computationally an aggregating bacterial system that forms a space-spanning interconnected network via cluster-cluster assembly. By controllably inducing bacterial filamentation, we aimed to understand how cell length distribution and cell surface hydrophobicity control the dynamics of aggregation and sedimentation, as well as the microstructure and mechanics of the settled bacterial networks. We found that filamentation lowers the percolation threshold, leading to gelation at a lower number density with distinct assembly dynamics and lower network connectivity. Furthermore, we analyzed the mechanical properties of the bacterial networks. Static stress tests reveal three yielding modes: discrete cluster-cluster disassembly, collective delamination, and sub-regional network fracture. The yielding modes are consistent with the gel-like viscoelastic properties of the cluster-cluster assembled networks observed during macroscale rheometry. In particular, we observe a scaling relationship between the storage modulus and the volume fraction, characteristic of an attractive rod gel. Our experimental observations are supported by Langevin dynamic simulations, providing mechanistic insights into the factors determining network self-assembly and connectivity. Our findings elucidate the gel-like structure-function dynamics in cluster-cluster aggregated bacterial systems and underscore the fundamental importance of filamentation in their properties and mechanical behavior.
Toxicity testing of two pesticides against the Carthusian snailin vitro
Authors: Bashandy A.S. , Awwad M.H
Published: September 2023

In this work, the land snail,Monacha cartusiana, was studied to assess the deadly toxic activity of two pesticides (lambda and methomyl) on this snail invitro, utilizing contact and dipping techniques. The results revealed that methomyl was more effective against snails compared with lambda in both methods of treatment. However, the contact application strategy resulted in greater death rates than the poison dipping studies. Accordingly, the mortality rate was increased by increasing concentration, with contact technique which recorded 96.3% and 69.99±15.1% deaths by dipping way on concentration 3%. For this reason, the percent Lethal Concentration fifty (LC50) was 1.30% for one day and 1.67% for seven days for methomyl by contact and dipping techniques, respectively. On the other hand, the LC50for lambda pesticide was achieved at 1.45% by contact method but was 7.51% by using the dipping application within ten days. As a result, mortality was greater after contact application than after dipping, and methomyl was disclosed to be more poisonous than lambda as a molluscicide.
Penile cavernous sinusoids are Prox1-positive hybrid vessels
Authors: Schnabellehner Sarah , Kraft Marle , Schoofs Hans , Ortsäter Henrik , Mäkinen Taija
Published: September 2023

Endothelial cells (ECs) of blood and lymphatic vessels have distinct identity markers that define their specialized functions. Recently, specialized hybrid vasculatures with both blood and lymphatic vessel-specific features have been discovered in multiple tissues. Here, we identify the penile cavernous sinusoidal (pc-S) blood vasculature as a new hybrid vascular bed expressing key lymphatic EC identity genesProx1, Vegfr3andLyve1. Using single cell transcriptome data of human corpus cavernosum tissue, we found heterogeneity within pc-S endothelia and observed distinct phenotypic alterations related to inflammation response in hybrid ECs in erectile dysfunction. Molecular, ultrastructural and functional studies further establish shared hybrid identity of pc-Ss in mouse, and reveal their morphological adaptations and ability to perform lymphatic-like function in draining high molecular weight tracers. Interestingly, we found that inhibition of the key lymphangiogenic growth factor VEGF-C did not block the development of pc-Ss in mice, distinguishing them from other lymphatic and hybrid vessels analyzed so far. Our findings provide a detailed molecular characterization of hybrid pc-Ss and pave the way for the identification of molecular targets for therapies in conditions of dysregulated penile vasculature, including erectile dysfunction.
Assessing Per- and Polyfluoroalkyl Substances (PFAS) in Fish Fillet Using Non-Targeted Analyses
Authors: Boatman Anna K. , Chappel Jessie R. , Polera Madison E. , Dodds James N. , Belcher Scott M. , Baker Erin S.
Published: September 2023

Per- and polyfluoroalkyl substances (PFAS) are a class of thousands of man-made chemicals that are persistent and highly stable in the environment. Fish consumption has been identified as a key route of PFAS exposure for humans. However, routine fish monitoring targets only a handful of PFAS, and non-targeted analyses have largely only evaluated fish from heavily PFAS-impacted waters. Here, we evaluated PFAS in fish fillets from recreational and drinking water sources in central North Carolina to assess whether PFAS are present in these fillets that would not be detected by conventional targeted methods. We used liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) to collect full scan feature data, performed suspect screening using an in-house library of 100 PFAS for high confidence feature identification, searched for additional PFAS features using non-targeted data analyses, and quantified perfluorooctane sulfonic acid (PFOS) in the fillet samples. A total of 36 PFAS were detected in the fish fillets, including 19 that would not be detected using common targeted methods, with a minimum of 6 and a maximum of 22 in individual fish. Median fillet PFOS levels were concerningly high at 11.6 to 42.3 ppb, and no significant correlation between PFOS levels and number of PFAS per fish was observed. Future PFAS monitoring in this region should target more of these 36 PFAS, and other regions not considered heavily PFAS contaminated should consider incorporating non-targeted analyses into ongoing fish monitoring studies.

SYNOPSIS

Concerningly high PFOS levels were detected in fish fillets from recreational and drinking water sources in central North Carolina. Of the 36 total PFAS identified, 19 would not be detected using routine targeted monitoring methods.

GRAPHICAL ABSTRACT

For use in table of contents only
Self-generating autocatalytic networks: structural results, algorithms, and their relevance to evolutionary processes
Authors: Huson Daniel , Xavier Joana C. , Steel Mike
Published: September 2023

The concept of an autocatalytic network of reactions that can form and persist, starting from just an available food source, has been formalised by the notion of a Reflexively-Autocatalytic and Food generated (RAF) set. The theory and algorithmic results concerning RAFs have been applied to a range of settings, from metabolic questions arising at the origin of life, to ecological networks, and cognitive models in cultural evolution. In this paper, we present new structural and algorithmic results concerning RAF sets, by studying more complex modes of catalysis that allow certain reactions to require multiple catalysts (or to not require catalysis at all), and discuss the differing ways catalysis has been viewed in the literature. We then focus on the structure and analysis of minimal RAFs, and derive structural results and polynomial-time algorithms, with applications to metabolic network data described briefly.
Meisoindigo: An Effective Inhibitor of SARS-CoV-2 Main Protease Revealed by Yeast System
Authors: Grabiński Wojciech , Kicińska Anna , Kosicka Ewa , Baranek-Grabińska Martyna , Hejenkowska Ewelina D , Budzik Joanna , Śliska Paulina , Śliwińska Weronika , Karachitos Andonis
Published: September 2023

The COVID-19 pandemic caused by SARS-CoV-2 has had a significant impact on global health and the global economy. Despite the availability of vaccines, limited accessibility and vaccine hesitancy pose challenges in controlling the spread of the disease. Effective therapeutic strategies, including antiviral drugs, are needed to combat the future spread of new SARS-CoV-2 virus variants. The main protease (Mpro) is a critical therapeutic target for COVID-19 medicines, as its inhibition impairs viral replication. However, the use of substances that inhibit Mpro may induce selection pressure. Thus, it is vital to monitor viral resistance to known drugs and to develop new drugs. Here, we have developed a yeast system for the identification of Mpro inhibitors as an alternative to costly and demanding high-biosecurity procedures. The system is based on stable expression of Mpro and does not require selection media. Yeast can be cultured on a rich carbon source, providing rapid growth and screening results. The designed tool was subsequently used to screen the FDA-Approved Drug Library. Several chemicals with Mpro inhibitory properties were identified. We found that meisoindigo, which was not previously known to have the potential to inhibit Mpro, was highly effective. Our results may promote the development of new derivatives with therapeutic properties against SARS-CoV-2 and other beta-coronaviruses.
Combinatorial Wnt signaling landscape during brachiopod anteroposterior patterning
Authors: Vellutini Bruno Cossermelli , Martín-Durán José María , Børve Aina , Hejnol Andreas
Published: September 2023

Background:Wnt signaling pathways play crucial roles in animal development. They establish embryonic axes, specify cell fates, and regulate tissue morphogenesis from the early embryo to organogenesis. It is becoming increasingly recognized that these distinct developmental outcomes depend upon dynamic interactions between multiple ligands, receptors, antagonists, and other pathway modulators, consolidating the view that a combinatorial "code" controls the output of Wnt signaling. However, due to the lack of comprehensive analyses of Wnt components in several animal groups, it remains unclear if specific combinations always give rise to specific outcomes, and if these combinatorial patterns are conserved throughout evolution.Results:In this work, we investigate the combinatorial expression of Wnt signaling components during the axial patterning of the brachiopodTerebratalia transversa. We find thatT. transversahas a conserved repertoire of ligands, receptors, and antagonists. These genes are expressed throughout embryogenesis but undergo significant upregulation during axial elongation. At this stage, Frizzled domains occupy broad regions across the body while Wnt domains are narrower and distributed in partially overlapping patches; antagonists are mostly restricted to the anterior end. Based on their combinatorial expression, we identify a series of unique transcriptional subregions along the anteroposterior axis that coincide with the different morphological subdivisions of the brachiopod larval body. When comparing these data across the animal phylogeny, we find that the expression of Frizzled genes is relatively conserved, whereas the expression of Wnt genes is more variable.Conclusions:Our results suggest that the differential activation of Wnt signaling pathways may play a role in regionalizing the anteroposterior axis of brachiopod larvae. More generally, our analyses suggest that changes in the receptor context of Wnt ligands may act as a mechanism for the evolution and diversification of the metazoan body axis.
Structure of Native Chromatin Fibres Revealed by Cryo-ETin situ
Authors: Hou Zhen , Nightingale Frank , Zhu Yanan , MacGregor-Chatwin Craig , Zhang Peijun
Published: September 2023

The structure of chromatin plays pivotal roles in regulating gene transcription, DNA replication and repair, and chromosome segregation. This structure, however, remains elusive. Using cryo-FIB and cryo-ET, we delineated the 3D architecture of native chromatin fibres in intact interphase human T-lymphoblasts and determined thein-situstructures of nucleosomes in different conformations. These chromatin fibres are not structured as uniform 30 nm one-start or two-start filaments but are composed of relaxed, variable zigzag organizations of nucleosomes connected by straight linker DNA. Nucleosomes with little H1 and linker DNA density were distributed randomly without any spatial preference. This work sets a precedent for future high-resolution investigations on native chromatin structuresin-situat both a single-nucleosome level and a population level under many different cellular conditions in health and disease.
Mechanosensing through talin 1 contributes to tissue mechanical homeostasis
Authors: Chanduri Manasa V.L. , Kumar Abhishek , Weiss Dar , Emuna Nir , Barsukov Igor , Shi Muisi , Tanaka Keiichiro , Wang Xinzhe , Datye Amit , Kanyo Jean , Collin Florine , Lam TuKiet , Schwarz Udo D. , Bai Suxia , Nottoli Timothy , Goult Benjamin T , Humphrey Jay D. , Schwartz Martin A
Published: September 2023

It is widely believed that tissue mechanical properties, determined mainly by the extracellular matrix (ECM), are actively maintained. However, despite its broad importance to biology and medicine, tissue mechanical homeostasis is poorly understood. To explore this hypothesis, we developed mutations in the mechanosensitive protein talin1 that alter cellular sensing of ECM stiffness. Mutation of a novel mechanosensitive site between talin1 rod domain helix bundles 1 and 2 (R1 and R2) shifted cellular stiffness sensing curves, enabling cells to spread and exert tension on compliant substrates. Opening of the R1-R2 interface promotes binding of the ARP2/3 complex subunit ARPC5L, which mediates the altered stiffness sensing. Ascending aortas from mice bearing these mutations show increased compliance, less fibrillar collagen, and rupture at lower pressure. Together, these results demonstrate that cellular stiffness sensing regulates ECM mechanical properties. These data thus directly support the mechanical homeostasis hypothesis and identify a novel mechanosensitive interaction within talin that contributes to this mechanism.
A Three-Stage Algorithm for Quantification of the MMSE Interlocking Pentagon Areas
Authors: Kim Namhee , Truty Timothy , Han S. Duke , Heo Moonseong , Buchman Aron S. , Bennett David A. , Tasaki Shinya
Published: September 2023

The Mini-Mental State Examination (MMSE) is a widely employed assessment tool for measuring the severity of cognitive impairment. Among the MMSE items, the pentagon copying test (PCT) requires participants to accurately replicate a sample of two interlocking pentagons. While the PCT are traditionally scored on a binary scale, there has been limited developments of granular scoring scale to assess task performance. In this paper, we present a novel three-stage algorithm, called Quantification of Interlocking Pentagons (QIP), which quantifies PCT performance by computing the areas of individual pentagons and their intersection areas, and a balance ratio between the areas of the two individual pentagons. The three stages of the QIP algorithm include: (1) detection of line segments, (2) unraveling of the interlocking pentagons, and (3) quantification of areas. The QIP algorithm was applied to 497 cases from 84 participants. Analysis of the quantified data revealed a significant inverse relationship between age and balance ratio between two pentagon areas (beta = -0.49, p = 0.0033), indicating that older age was associated with a smaller balance ratio. The QIP algorithm enhanced the scoring of performance in the PCT. It can serve as a useful tool for granular level scoring of PCT.
Foundation Models for Quantitative Biomarker Discovery in Cancer Imaging
Authors: Pai Suraj , Bontempi Dennis , Hadzic Ibrahim , Prudente Vasco , Sokač Mateo , Chaunzwa Tafadzwa L. , Bernatz Simon , Hosny Ahmed , Mak Raymond H , Birkbak Nicolai J , Aerts Hugo JWL
Published: September 2023

Foundation models represent a recent paradigm shift in deep learning, where a single large-scale model trained on vast amounts of data can serve as the foundation for various downstream tasks. Foundation models are generally trained using self-supervised learning and excel in reducing the demand for training samples in downstream applications. This is especially important in medicine, where large labeled datasets are often scarce. Here, we developed a foundation model for imaging biomarker discovery by training a convolutional encoder through self-supervised learning using a comprehensive dataset of 11,467 radiographic lesions. The foundation model was evaluated in distinct and clinically relevant applications of imaging-based biomarkers. We found that they facilitated better and more efficient learning of imaging biomarkers and yielded task-specific models that significantly outperformed their conventional supervised counterparts on downstream tasks. The performance gain was most prominent when training dataset sizes were very limited. Furthermore, foundation models were more stable to input and inter-reader variations and showed stronger associations with underlying biology. Our results demonstrate the tremendous potential of foundation models in discovering novel imaging biomarkers that may extend to other clinical use cases and can accelerate the widespread translation of imaging biomarkers into clinical settings.
Characterizing HIV status documentation among cancer patients at regional cancer centers in Malawi, Zimbabwe, and South Africa
Authors: Montaño Michalina A , Mtisi Takudzwa , Ndlovu Ntokozo , Borok Margaret , Bula Agatha , Joffe Maureen , Ignacio Rachel Bender , Chagomerana Maganizo B
Published: September 2023

Introduction

In East and Southern Africa, people with HIV (PWH) experience worse cancer-related outcomes and are at higher risk of developing certain cancers. Siloed care delivery pathways pose a substantial barrier to co-management of HIV and cancer care delivery.

Methods

We conducted cross-sectional studies of adult cancer patients at public radiotherapy and oncology units in Malawi (Kamuzu Central Hospital), Zimbabwe (Parirenyatwa Group of Hospitals), and South Africa (Charlotte Maxeke Hospital) between 2018-2019. We abstracted cancer- and HIV-related data from new cancer patient records and used Poisson regression with robust variance to identify patient characteristics associated with HIV documentation.

Results

We included 1,648 records from Malawi (median age 46 years), 1,044 records from South Africa (median age 55 years), and 1,135 records from Zimbabwe (median age 52 years). Records from all three sites were predominately from female patients; the most common cancers were cervical (Malawi [29%] and Zimbabwe [43%]) and breast (South Africa [87%]). HIV status was documented in 22% of cancer records from Malawi, 92% from South Africa, and 86% from Zimbabwe. Patients with infection-related cancers were more likely to have HIV status documented in Malawi (adjusted prevalence ratio [aPR]: 1.92, 95% confidence interval [CI]: 1.56-2.38) and Zimbabwe (aPR: 1.16, 95%CI: 1.10-1.22). Patients aged ≥60 years were less likely to have HIV status documented (Malawi: aPR: 0.66, 95% CI: 0.50-0.87; Zimbabwe: aPR: 0.76, 95%CI: 0.72-0.81) than patients under age 40 years. Patient age and cancer type were not associated with HIV status documentation in South Africa.

Conclusion

Different cancer centers have different gaps in HIV status documentation and will require tailored strategies to improve processes for ascertaining and recording HIV-related information in cancer records. Further research by our consortium to identify opportunities for integrating HIV and cancer care delivery is underway.
EEG-based Machine Learning Models for the Prediction of Phenoconversion Time and Subtype in iRBD
Authors: Jeong El , Shin Yong Woo , Byun Jung-Ick , Sunwoo Jun-Sang , Roascio Monica , Mattioli Pietro , Giorgetti Laura , Famà Francesco , Arnulfo Gabriele , Arnaldi Dario , Kim Han-Joon , Jung Ki-Young
Published: September 2023

Background

Idiopathic/Isolated rapid eye movement sleep behavior disorder (iRBD) is a prodromal stage of α-synucleinopathies and eventually phenoconverts to overt neurodegenerative diseases including Parkinson’s disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). Associations of baseline resting-state electroencephalography (EEG) with phenoconversion have been reported.

Objectives

In this study, we aimed to develop machine learning models to predict phenoconversion time and subtype using baseline EEG features in patients with iRBD.

Methods

At baseline, resting-state EEG and neurological assessments were performed on patients with iRBD. Calculated EEG features included spectral power, weighted phase lag index and Shannon entropy. Three models were used for survival prediction, and four models were used for α-synucleinopathy subtype prediction. The models were externally validated using data from a different institution.

Results

A total of 236 iRBD patients were followed-up for up to eight years (mean 3.5 years), and 31 patients converted to α-synucleinopathies (16 PD, 9 DLB, 6 MSA). The best model for survival prediction was the random survival forest model with an integrated Brier score of 0.114 and a concordance index of 0.775. The K-nearest neighbor model was the best model for subtype prediction with an area under the receiver operating characteristic curve of 0.901. EEG slowing was an important feature for both models.

Conclusions

Machine learning models using baseline EEG features can be used to predict phenoconversion time and its subtype in patients with iRBD. Further research including large sample data from many countries is needed to make a more robust model.
A powerful replicability analysis of genome-wide association studies
Authors: Li Yan , Lei Haochen , Wen Xiaoquan , Cao Hongyuan
Published: September 2023

Replicability is the cornerstone of modern scientific research. Reliable identifications of genotype-phenotype associations that are significant in multiple genome-wide association studies (GWASs) provide stronger evidence for the findings. Current replicability analysis relies on the independence assumption among single nucleotide polymorphisms (SNPs) and ignores the linkage disequilibrium (LD) structure. We show that such a strategy may produce either overly liberal or overly conservative results in practice. We develop an efficient method, ReAD, to detect replicable SNPs associated with the phenotype from two GWASs accounting for the LD structure. The local dependence structure of SNPs across two heterogeneous studies is captured by a four-state hidden Markov model (HMM) built on two sequences ofp-values. By incorporating information from adjacent locations via the HMM, our approach provides more accurate SNP significance rankings. ReAD is scalable, platform independent and more powerful than existing replicability analysis methods with effective false discovery rate (FDR) control. Through analysis of datasets from two asthma GWASs and two ulcerative colitis GWASs, we show that ReAD can identify replicable genetic loci that existing methods might otherwise miss.
How does the weekend catch-up sleep ratio affect the health and lifestyle of Korean adults? An age- and gender- matched study
Authors: Hwang In-Whi , Hwang Soo-Ji , Shen Jun-Hao , Kim Jisu , Lee Jung-Min
Published: September 2023

The purpose of this study was to investigate the association between various levels of physical activity, self-perception, cardiometabolic risk factors, and weekend catch-up sleep ratio (CSR). Using raw data from the Korea National Health and Nutrition Examination Survey 2018 – 2021, all participants were divided into three groups (< 1.0, 1.0 ≤ CSR < 1.5, or ≥ 1.5) by CSR, which is the value calculated by dividing weekend sleep time by weekday sleep time. After matching age and gender, 2,484 Korean adults were selected as study participants. Descriptive statistics, chi-square test, ANOVA, and multinomial logistic regression analysis were performed to analyze the data. The results showed a significant association between weekend CSR and socioeconomic status, physical activity, self-perception levels, and cardiometabolic risk factors. Specifically, compared to the reference group (1 ≤ CSR < 1.5), those with a CSR < 1 were 2.42 times more likely to live in a single-family house (OR = 2.42, 95% CI = 1.77 – 3.32) and 1.71 times more likely to engage in vigorous physical activity meeting WHO guidelines (OR = 1.71, 95% CI = 1.20 – 2.46). They were also 1.33 times more likely to perceive themselves as ‘obese’ (OR = 1.33, 95% CI = 1.00 – 1.76). Conversely, those in the CSR ≥ 1.5 group were 3.93 times more likely to be ‘pink-collar’ workers (OR = 3.93, 95% CI = 2.70 – 5.71), 1.72 times more likely to perceive their stress levels as ‘quite’ (OR = 1.72, 95% CI = 1.20 – 2.47), and 1.87 times more likely to have diabetes (OR = 1.87, 95% CI = 0.97 – 3.60). Alterations in CSR could indicate changes in physical activity levels, sedentary behavior duration, and other health indicators, ultimately influencing overall well-being. Therefore, a comprehensive healthcare approach incorporating CSR considerations is increasingly essential.
Data-driven Prior Elicitation for Bayes Factors in Cox Regression for Nine Subfields in Biomedicine
Authors: Linde Maximilian , Jochim Laura , Tendeiro Jorge N. , van Ravenzwaaij Don
Published: September 2023

Biomedical research often utilizes Cox regression for the analysis of time-to-event data. The pervasive use of frequentist inference for these analyses implicates that the evidence for or against the presence (or absence) of an effect cannot be directly compared and that researchers must adhere to a predefined sampling plan. As an alternative, the use of Bayes factors improves upon these limitations, which is especially important for costly and time-consuming biomedical studies. However, Bayes factors involve their own difficulty of specifying priors for the parameters of the statistical model. In this article, we develop data-driven priors for Cox regression tailored to nine subfields in biomedicine. To this end, we extracted hazard ratios and associatedx% confidence intervals from the abstracts of large corpora of already existing studies within the nine biomedical subfields. We used these extracted data to inform priors for the nine subfields. All of our suggested priors are Normal distributions with means of 0 and standard deviations closely scattered around 1. We propose that researchers use these priors as reasonable starting points for their analyses.
Disruption of maternal IgA by prenatal antibiotics precedes intestinalE. colicolonization and late-onset sepsis in neonates
Authors: McDonald Katya , Browning Danielle , Greenfield Kara G. , Lin Kathryn , Meier Josephine , Butoryak Matthew , Sasaki Alexandria , Fandozzi Eva , Hand Tim , Megli Christina , Knoop Kathryn A.
Published: September 2023

Neonates, particularly prematurely born neonates, are particularly vulnerable to enteric pathogens. Antibiotics are widely administered during pregnancy for off-label use and prevention, but the effect on neonatal physiology has not been well characterized. Maternally derived IgA provided in milk is a predominant protective measure in the intestinal lumen of the nursing offspring. The connection between the maternal intestine and mammary IgA responses has been observed, but understanding how clinical use of antibiotics effects mammary IgA remains unclear. Here we find that prenatal cephalosporin antibiotics, but not penicillins, decrease mammary IgA in dams, and limit the availability of IgA within the lumen of nursing offspring. Decreased IgA correlated with an outgrowth of commensalE. coliand increased colonization and translocation of pathogenE. coli.Moreover, antenatal cephalosporin administration was associated with increased mortality in a model of LOS that was associated with decreased mammary IgA. Futhermore, in a clinical cohort of at-risk infants, maternal broad spectrum antibiotic treatment, including cephalosporins, increased the risk of LOS in neonates in comparison to penicillin-based treatments. This was associated with reduced IgA in the milk, and we propose maternal administration of select antibiotics could disrupt mammary IgA, leading to increased risk of LOS in infants by allowing for pathogen colonization in the neonatal intestine.
Dietary road salt and monarch butterflies: minimal effects on larval growth, immunity, wing coloration, and migration to Mexico
Authors: Hund Amanda K , Mitchell Timothy S. , Ramirez Isabel , Zambre Amod , Hagg Lili , Stene Anne , Porter Karilyn , Carper Adrian , Agnew Lauren , Shephard Alex , Kobiela Megan , Oberhauser Karen , Taylor Orley R. , Snell-Rood Emilie
Published: September 2023

The spectacular migration of the monarch butterfly is under threat from the loss of habitat and the decline of their milkweed host plants. In the northern part of their range, roadsides could potentially produce millions of monarchs annually due to high densities of milkweed, however roadside milkweed can accumulate chemicals from roads, such as sodium from road salt. Controlled lab studies have shown mixed effects of sodium on monarch development: small increases can be beneficial as sodium is an important micronutrient in brain and muscle development, but large increases can sometimes decrease survival. It is unclear how dietary sodium affects performance in ecologically relevant conditions, and the migration itself. In this experiment, we raised monarchs outdoors, in migration-inducing conditions, on milkweed sprayed with three levels of sodium chloride. We released 2500 tagged monarchs and held an additional 250 for further lab assays. While our recovery rates to the wintering grounds were low (N = 7 individuals), individuals from all three sodium chloride treatments made it to Mexico. Butterflies reared on control milkweed and low salt concentrated sodium in their tissues, while those on high salt diets excreted sodium, suggesting levels were above a physiological optimum. There were no effects of treatment on wing coloration, survival, body size, immunity, or parasite prevalence. Taken together, our results suggest that monarchs are robust to levels of sodium in milkweeds found along roadsides, which is promising with respect to monarch conservation efforts that promote roadside habitat.

Significance Statement

Monarch butterflies are a flagship species for pollinator conservation, and were recently being listed as endangered by the IUCN. Roadside habitat is a target for monarch breeding habitat as they often have high densities of milkweed, the monarch hostplant. However, roadsides can also have high levels of pollutants, such as salt from deicing treatments. We reared monarch caterpillars on sodium treated milkweeds, measuring a suite of performance measures, and releasing nearly 2500 tagged monarchs for migration. We found little effect of salt on migration to Mexico, survival, body size, development time, parasite prevalence, immunity, or coloration. Monarchs appear robust to levels of sodium found in milkweed along roadsides, supporting the possibility of roadsides as habitat.
Centimeter-scale perfusable cultured meat with densely packed, highly aligned muscle fibers via hollow fiber bioreactor
Authors: Nie Minghao , Shima Ai , Takeuchi Shoji
Published: September 2023

The development of in-vitro biofabrication methods for producing cultured meat based on animal cells has been advancing, but replicating the texture of traditional meat in centimeter-scale has been a challenge. To address this, a method using a hollow fiber bioreactor (HFB) has been developed. The HFB contains semipermeable hollow fibers that act as artificial circulatory systems to deliver nutrients and oxygen uniformly to the tissue, along with microfabricated anchors for inducing cell alignment. With active perfusion, the biofabricated centimeter-scale chick muscle tissue shows elevated levels of marker protein expression and sarcomere formation across the whole tissue, along with improved texture and flavor. In the future, further scaling up of this approach using industrial robots has the potential to transform not only the cultured meat industry but also the tissue engineering fields aiming for the formation of large-scale artificial organs.
RNA binding proteins and glycoRNAs form domains on the cell surface for cell penetrating peptide entry
Authors: Perr Jonathan , Langen Andreas , Almahayni Karim , Nestola Gianluca , Chai Peiyuan , Lebedenko Charlotta G. , Volk Regan , Caldwell Reese M. , Spiekermann Malte , Hemberger Helena , Bisaria Namita , Tzelepis Konstantinos , Calo Eliezer , Möckl Leonhard , Zaro Balyn , Flynn Ryan A.
Published: September 2023

The composition and organization of the cell surface determine how cells interact with their environment. Traditionally, glycosylated transmembrane proteins were thought to be the major constituents of the external surface of the plasma membrane. Here, we provide evidence that a group of RNA binding proteins (RBPs) are present on the surface of living cells. These cell surface RBPs (csRBPs) precisely organize into well-defined nanoclusters that are enriched for multiple RBPs, glycoRNAs, and their clustering can be disrupted by extracellular RNase addition. These glycoRNA-csRBP clusters further serve as sites of cell surface interaction for the cell penetrating peptide TAT. Removal of RNA from the cell surface, or loss of RNA binding activity by TAT, causes defects in TAT cell internalization. Together, we provide evidence of an expanded view of the cell surface by positioning glycoRNA-csRBP clusters as a regulator of communication between cells and the extracellular environment.
Molecular basis of product recognition during PIP5K-mediated production of PI(4,5)P2with positive feedback
Authors: Duewell Benjamin R. , Faris Katie A. , Hansen Scott D.
Published: September 2023

The ability for cells to localize and activate peripheral membrane binding proteins is critical for signal transduction. Ubiquitously important in these signaling processes in eukaryotic cells are phosphatidylinositol phosphate (PIP) lipids, which are dynamically phosphorylated by PIP lipid kinases on intracellular membranes. Functioning primarily at the plasma membrane, phosphatidylinositol-4-phosphate 5-kinases (PIP5K) catalyze the phosphorylation of PI(4)P to generate most PI(4,5)P2lipids found in cells. Recently, we determined that PIP5K displays a positive feedback loop based on membrane-mediated dimerization and cooperative binding to its product, PI(4,5)P2. Here, we examine how two PIP5K motifs contribute to PI(4,5)P2recognition to control membrane association and catalysis. Using a combination of single molecule TIRF microscopy and kinetic analysis of PI(4)P lipid phosphorylation, we map the sequence of steps that allow PIP5K to cooperatively engage PI(4,5)P2. We find that the specificity loop regulates the rate of PIP5K membrane association and helps orient the kinase to more effectively bind PIP lipids. Attaching the PIP5K specificity loop to other peripheral membrane binding proteins can enhance their membrane binding dynamics. After correctly orienting on the membrane, PIP5K transitions to binding PIP lipids in a structural motif previously referred to as the substrate or PIP binding motif (PIPBM). Our data reveals that the PIPBM has broad specificity for anionic lipids and serves a critical role in regulating membrane association in vitro and in vivo. The strength of the interaction between the PIPBM and PIP lipids depends on the membrane density and the extent phosphorylation on the inositol head group. We propose a two-step membrane binding model where the specificity loop and PIPBM act in concert to help PIP5K orient and productively engage anionic lipids to drive the positive feedback during PI(4,5)P2production.
Stabilization of RRBP1 mRNA via an m6A-dependent manner in prostate cancer constitutes a therapeutic vulnerability amenable to small-peptide inhibition of METTL3
Authors: Feng Yuqing , Li Zenghui , Zhu Jingwei , Zou Cheng , Tian Yu , Xiong Jiangling , He Qinju , Li Wenjun , Xu Hao , Xu Bin , Shi Junfeng , Zhang Dingxiao
Published: September 2023

Mounting evidence has implicated the RNA m6A methylation catalyzed by METTL3 in a wide range of physiological and pathological processes, including tumorigenesis. The detailed m6A landscape and molecular mechanism of METTL3 in prostate cancer (PCa) remains ill-defined. We find that METTL3 is overexpressed in PCa and correlates with worse patient survival. Functional studies establish METTL3 as an oncoprotein dependent on its m6A enzymatic activity in both AR+ and AR- PCa cells. To dissect the regulatory network of m6A pathway in PCa, we map the m6A landscape in clinical tumor samples using m6A-seq and identify genome-wide METTL3-binding transcripts via RIP-seq. Mechanistically, we discover RRBP1 as a direct METTL3 target in which METTL3 stabilizesRRBP1mRNA in an m6A-dependent manner. RRBP1 positively correlates with METTL3 expression in PCa cohorts and exerts an oncogenic role in aggressive PCa cells. Leveraging the 3D structural protein-protein interaction between METTL3 and METTL14, we successfully develop two potential METTL3 peptide inhibitors (RM3 and RSM3) that effectively suppress cancer cell proliferationin vitroand tumor growthin vivo. Collectively, our study reveals a novel METTL3/m6A/RRBP1 axis in enhancing aggressive traits of PCa, which can be therapeutically targeted by small-peptide METTL3 antagonists.
A ubiquitin-specific, proximity-based labeling approach for the identification of ubiquitin ligase substrates
Authors: Mukhopadyay Urbi , Levantovsky Sophie , Gharbi Sarah , Stein Frank , Behrends Christian , Bhogaraju Sagar
Published: September 2023

Ubiquitination of proteins is central to protein homeostasis and other cellular processes including DNA repair, vesicular transport, cell-division etc. The process of ubiquitination is conserved from yeast to humans and is carried out by the sequential action of three enzymes: E1, E2 and E3. There are an estimated >600 E3 ligases in humans that execute ubiquitination of specific target proteins in a spatio-temporal manner to elicit desired signaling effects. Here, we developed a ubiquitin-specific proximity-based labeling method to selectively biotinylate substrates of a given ubiquitin ligase. Our method exploits the proximity and the relative orientation of the E3-ligase catalytic domain with respect to ubiquitin observed in the enzymatic intermediate-state structures of E3-E2∼Ub. By fusing the biotin ligase BirA and an Avi-tag variant to the candidate E3 ligase and ubiquitin, respectively, we were able to specifically enrichbona fidesubstrates and potential new substrates of a ligase using a one-step streptavidin pulldown under denaturing conditions. As proof-of-principle, we applied our method, which we named Ub-POD, to the RING E3 ligase RAD18. RAD18 ubiquitinates DNA-sliding clamp PCNA upon UV-induced DNA damage. We identified PCNA and several other critical players in the DNA damage repair pathway in a single RAD18 Ub-POD experiment. We went on to validate DNA replicase POLE as a possible new substrate of RAD18. Through RAD18 Ub-POD, we were also able to pin down the cellular localization of RAD18-mediated ubiquitination to the damaged DNA nuclear puncta using streptavidin immunofluorescence. Furthermore, we applied Ub-POD to TRAF6, another RING ubiquitin ligase involved in NF-κB signaling and successfully identified known and potentially new TRAF6 substrates. Finally, we adapted our method to the U-box-type E3 ubiquitin ligase CHIP to demonstrate that we can identify substrates of two major classes of mammalian ubiquitin ligases. We anticipate that our method and principle could be widely adapted to all classes of ubiquitin ligases to identify substrates and localize the cellular site(s) of ubiquitination.
MIC13 and SLP2 seed the assembly of MIC60-subcomplex to facilitate crista junction formation
Authors: Naha Ritam , Strohm Rebecca , Urbach Jennifer , Wittig Ilka , Reichert Andreas S. , Kondadi Arun Kumar , Anand Ruchika
Published: September 2023

The MICOS complex subunit MIC13 is essential for mitochondrial cristae organization. Mutations inMIC13cause severe mitochondrial hepato-encephalopathy displaying defective cristae morphology and loss of the MIC10-subcomplex. Here we identified stomatin-like protein 2 (SLP2) as an interacting partner of MIC13 and decipher a critical role of SLP2 as an auxiliary MICOS subunit, modulating cristae morphology. SLP2 provides a large interaction hub for MICOS subunits and loss of SLP2 leads to drastic alterations in cristae morphology. Double deletion of SLP2 and MIC13 showed reduced assembly of core MICOS subunit, MIC60 into MICOS and dispersion of MIC60-specific puncta, demonstrating a critical role of SLP2-MIC13 in MICOS assembly and crista junction (CJ) formation. We further identified that the mitochondrial i-AAA protease YME1L in coordination either with MIC13 or SLP2 differentially regulates MICOS assembly pathways thereby interlinking MIC13-specific or scaffolding-specific role of SLP2 with quality control and assembly of the MICOS complex. YME1L- depletion inMIC13KO could restore MIC10-subcomplex and reform the nascent CJ. Taken together, we propose ‘seeder’ model for MICOS assembly and CJ formation, where SLP2- MIC13 seed the assembly of MIC60 into MICOS complex and promote the formation of CJ by regulating the quality and stability of MIC10-subcomplex.
A Far-Red Fluorescent Probe to VisualizeStaphylococcus aureusin Patient Samples
Authors: Jantarug Krittapas , Tripathi Vishwachi , Morin Benedict , Iizuka Aya , Kuehl Richard , Morgenstern Mario , Clauss Martin , Khanna Nina , Bumann Dirk , Rivera-Fuentes Pablo
Published: September 2023

Staphylococcus aureus (S. aureus)is the leading bacterial cause of death in high-income countries and can cause invasive infections at various body sites. These infections are associated with prolonged hospital stays, a large economic burden, considerable treatment failure, and mortality rates. So far, there is only limited knowledge about the specific locations whereS. aureusresides in the human body during various infections. Hence, the visualization ofS. aureusholds significant importance in microbiological research. Herein, we report the development and validation of a far-red-fluorescent probe to detectS. aureusin human biopsies from deep-seated infections. This probe displays strong fluorescence and low background in human tissues, outperforming current tools forS. aureusdetection. Several applications are demonstrated, including fixed- and live-cell imaging, flow cytometry, and super-resolution bacterial imaging.

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A function of Spalt major as a sequence-specific DNA binding transcription factor mediates repression ofknirpsin theDrosophilawing imaginal disc
Authors: Ostalé Cristina M. , del Prado Alicia , Esteban Nuria , López-Varea Ana , de Celis Jose F.
Published: September 2023

The Spalt transcriptional regulators participate in a variety of cell fate decisions during multicellular development. Vertebrate Spalt proteins have been mostly associated to the organization of heterochromatic regions, but they also contribute regulatory functions through binding to A/T rich motives present in their target genes. The developmental processes in which theDrosophila spaltgenes participate are well known through genetic analysis, but the mechanism by which the Spalt proteins regulate transcription are still unknown. Furthermore, despite the prominent changes in gene expression associated to mutations in thespaltgenes, the specific DNA sequences they bind are also unknow. In this contribution we describe the analysis of a DNA fragment present in the regulatory region of theknirpsgene. Spalt proteins are candidate repressors ofknirpsexpression during the formation of the venation pattern in the wing disc, and here we identify a minimal conserved 30bp sequence that binds to Spalt major bothin vivoandin vitro. This sequence mediates transcriptional repression in the central region of the wing blade, constituting the first confirmed case of a direct regulatory interaction between Spalt major and its target DNA inDrosophila.