bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural and functional dissection of the Pacinian corpuscle reveals an active role of the inner core in touch detection
Authors: Ziolkowski Luke H. , Nikolaev Yury A. , Chikamoto Akitoshi , Oda Mai , Feketa Viktor V. , Monedero-Alonso David , Ardasheva Serafima A. , Bae Samuel S. , Xu C. Shan , Pang Song , Gracheva Elena O. , Bagriantsev Sviatoslav N.
Published: August 2024

Pacinian corpuscles are rapidly adapting mechanoreceptor end-organs that detect transient touch and high-frequency vibration. In the prevailing model, these properties are determined by the outer core, which acts as a mechanical filter limiting static and low-frequency stimuli from reaching the afferent terminal—the sole site of touch detection in corpuscles. Here, we determine the detailed 3D architecture of corpuscular components and reveal their contribution to touch detection. We show that the outer core is dispensable for rapid adaptation and frequency tuning. Instead, these properties arise from the inner core, composed of gap junction-coupled lamellar Schwann cells (LSCs) surrounding the afferent terminal. By acting as additional touch sensing structures, LSCs potentiate mechanosensitivity of the terminal, which detects touch via fast-inactivating ion channels. We propose a model in which Pacinian corpuscle function is mediated by an interplay between mechanosensitive LSCs and the afferent terminal in the inner core.

Highlights

eFIB-SEM reveals detailed 3D architecture of the entire Pacinian (Herbst) corpuscle

Inner, not outer core mediates rapid adaptation and frequency tuning

Afferent terminal detects touch via fast-inactivating ion channels

Mechanosensitive lamellar Schwann cells tune afferent terminal sensitivity to touch
MuLAN: Mutation-driven Light Attention Networks for investigating protein-protein interactions from sequences
Authors: Lombardi Gianluca , Carbone Alessandra
Published: August 2024

Understanding how proteins interact and how mutations affect these interactions is crucial for unraveling the complexities of biological systems and their evolution. Mutations can significantly alter protein behavior, impacting stability, interactions, and activity, thereby affecting cellular functions and influencing disease development and treatment effectiveness. Experimental methods for examining protein interactions are often slow and costly, highlighting the need for efficient computational strategies. We present MuLAN, a groundbreaking deep learning method that leverages light attention networks and the power of pre-trained protein language models to infer protein interactions, predict binding affinity changes, and reconstruct mutational landscapes for proteins involved in binary interactions, starting from mutational changes and directly using sequence data only. Unlike previous methods that depend heavily on structural information, MuLAN’s sequence-based approach offers faster and more accessible predictions. This innovation allows for variations in predictions based on specific partners, opening new possibilities for understanding protein behavior through their sequences. The potential implications for disease research and drug development mark a significant step forward in the computational analysis of protein interactions.
A Tale of Two Environments: Divisive Normalization and the (In)Flexibility of Choice
Authors: Kurtz-David Vered , Sinha Shreya , Alladi Vinayak , Bucher Stefan , Brandenburger Adam , Louie Kenway , Glimcher Paul , Tymula Agnieszka
Published: August 2024

The Divisive Normalization (DN) function has been described as a “canonical neural computation” in the brain that achieves efficient representations of sensory and choice stimuli. Recent theoretical work indicates that it efficiently encodes a specific class of Pareto-distributed stimuli. Does the brain shift to different encoding functions in other types of environments, or is there evidence for DN encoding in other types of environments? In this paper, using a within-subject choice experiment, we show evidence of the latter. Our subjects made decisions in two distinct choice environments with choice sets either drawn from a Pareto distribution or from a uniform distribution. Our results indicate that subjects’ choices are better described by a divisive coding strategy in both environments. Moreover, subjects appeared to calibrate a DN function to match, as closely as possible, the actual statistical properties of each environment. These results suggest that the nervous system may be constrained to use divisive representations under all conditions.

Significance Statement

How does the frequency with which we encounter different kinds of decision problems affect how the brain represents those problems? Recent empirical findings suggest that we adapt our internal representations to match the environments in which we are making choices. Theoretical work has shown that one form of internal representation, called divisive normalization, provides an optimal adaptation when making choices in a specific class of environments. Using a stylized experimental design, subjects faced two distinct choice environments, each characterized by different statistical properties. Our findings show humans appear to use the same mechanism in both environments, suggesting that a divisive representation may be a fixed feature of human cognition.
Proteolysis targeting chimera extracellular vesicles for therapeutic development treating triple negative breast cancer
Authors: Erwin Nina , De Umasankar , Xiao Yufeng , Wang Lei , Maharjan Chandra , Pan Xiaoshu , Awasthee Nikee , Zheng Guangrong , Liao Daiqing , Zhang Weizhou , He Mei
Published: August 2024

Proteolysis targeting chimeras (PROTACs) are an emerging targeted cancer therapy approach, but wide-spread clinical use of PROTAC is limited due to poor cell targeting and penetration, and instability in vivo. To overcome such issues and enhance the in vivo efficacy of PROTAC drugs, microfluidic droplet-based electroporation (µDES) was developed as a novel extracellular vesicle (EVs) transfection system, which enables the high-efficient PROTAC loading and effective delivery in vivo. Our previously developed YX968 PROTAC drug had shown the selectively degradation of HDAC3 and 8, which effectively suppresses the growth of breast tumor cell lines, including MDA-MB-231 triple negative breast cancer (TNBC) line, via dual degradation without provoking a global histone hyperacetylation. In this study, we demonstrated that µDES-based PROTAC loading in EVs significantly enhanced therapeutic function of PROTAC drug in vivo in the TNBC breast tumor mouse model. NSG mice with pre-established MDA-MB-231 tumors and treated with intraperitoneal injection of EVs for tumor inhibition study, which showed significantly higher HDAC 3 and 8 degradation efficiency and tumor inhibition than PROTAC only group. The liver, spleen, kidney, lung, heart, and brain were collected for safety testing, which exhibited improved toxicity. The EV delivery of PROTAC drug enhances drug stability and bioavailability in vivo, transportability, and drug targeting ability, which fills an important gap in current development of PROTAC therapeutic functionality in vivo and clinical translation. This novel EV-based drug transfection and delivery strategy could be applicable to various therapeutics for enhancing in vivo delivery, efficacy, and safety.
N-Acetylglucosamine Facilitates Coordinated Myoblast Flow, Forming the Foundation for Efficient Myogenesis
Authors: Satoh Masahiko S. , Rancourt Ann , St-Pierre Guillaume , Bouchard Elizabeth , Fillion Maude , Hagiwara Kana , Nakajima Kazuki , Sato Sachiko
Published: August 2024

Skeletal muscle comprises 30-40% of a mammal’s body mass, maintaining its integrity through efficient muscle fiber regeneration, which involves myoblast differentiation into myotubes. Previously, we reported that N-acetylglucosamine (GlcNAc) promotes myogenesis in C2C12 cells, although the underlying mechanisms were unclear. UDP-GlcNAc, the activated form of GlcNAc, is critical for the biosynthesis of highly branched (N-acetyllactosamine-rich) N-linked oligosaccharides, which are recognized by galectin-3 (Gal-3), facilitating dynamic cell-cell and cell-matrix interactions. In this study, we used primary myoblasts from wild-type and Gal-3 null (Gal-3KO) mice, observing myotube formation through long-term live-cell imaging and single-cell tracking. We found that GlcNAc enhances myoblast fusion in a dose-dependent manner, and the addition of Gal-3 with GlcNAc leads to the formation of larger myotubes. Gal-3KO myoblasts exhibited a reduced capacity for myotube formation, a deficiency that was rectified by supplementing with GlcNAc and Gal-3. Our results highlight the critical role of Gal-3 interaction with oligosaccharides whose synthesis was promoted by GlcNAc in facilitating myotube formation. Single-cell tracking revealed that GlcNAc and Gal-3 increase myoblast motility, creating a faster-coordinated cell flow—a directed movement of myoblasts, along which myotubes form through cell fusion. Interestingly, myoblasts contributing to myotube formation were pre-positioned along the eventual shape of the myotubes before the establishment of the coordinated flow. These myoblasts moved along the flow, paused, and even moved against the flow, suggesting that both flow and initial positioning play roles in aligning myoblasts into the shape of a myotube. Overall, our findings demonstrate that GlcNAc, in conjunction with Gal-3, enhances myotube formation by fostering an environment conducive to myoblast positioning, establishing coordinated flow, and facilitating fusion. This suggests potential therapeutic applications of GlcNAc in muscle repair and muscle disorders.
Vasculature segmentation in 3D hierarchical phase-contrast tomography images of human kidneys
Authors: Jain Yashvardhan , Walsh Claire L. , Yagis Ekin , Aslani Shahab , Nandanwar Sonal , Zhou Yang , Ha Juhyung , Gustilo Katherine S. , Brunet Joseph , Rahmani Shahrokh , Tafforeau Paul , Bellier Alexandre , Weber Griffin M. , Lee Peter D. , Börner Katy
Published: August 2024

Efficient algorithms are needed to segment vasculature in new three-dimensional (3D) medical imaging datasets at scale for a wide range of research and clinical applications. Manual segmentation of vessels in images is time-consuming and expensive. Computational approaches are more scalable but have limitations in accuracy. We organized a global machine learning competition, engaging 1,401 participants, to help develop new deep learning methods for 3D blood vessel segmentation. This paper presents a detailed analysis of the top-performing solutions using manually curated 3D Hierarchical Phase-Contrast Tomography datasets of the human kidney, focusing on the segmentation accuracy and morphological analysis, thereby establishing a benchmark for future studies in blood vessel segmentation within phase-contrast tomography imaging.
Body dissatisfaction widens the racial disparities of Benzophenone-3, a chemical biomarker of personal care and consumer product usage
Authors: Nguyen Vy Kim , Zimmerman Samuel , Colacino Justin , Jolliet Olivier , Patel Chirag J
Published: August 2024

Background

Body dissatisfaction can drive individuals to use personal care products, exposing themselves to Benzophenone-3 (BP3). Yet, no study has examined the link between body dissatisfaction and elevated chemical exposures.

Objectives

Our study examines how body dissatisfaction impacts the racial differences in BP3 exposures.

Methods

Using NHANES 2003-2016 data for 3,072 women, we ascertained body dissatisfaction with a questionnaire on weight perception. We ran two generalized linear models with log10-transformed urinary concentrations of BP3 as the outcome variable and the following main predictors: one with race/ethnicity and another combining race/ethnicity and body dissatisfaction. We also conducted stratified analyses by race/ethnicity. We adjusted for poverty income ratio, BMI, urinary creatinine, and sunscreen usage.

Results

BP3 levels in Mexican American, Other Hispanic, Other Race, non-Hispanic White, and non-Hispanic Asian women were on average 59%, 56%, 33%, 16%, and 9% higher, respectively, compared to non-Hispanic Black women. Racial differences in BP3 levels are accentuated with body dissatisfaction. For example, Other Hispanic women perceiving themselves as overweight had 69% higher BP3 levels than non-Hispanic Black women (p-value = 0.01), while those perceiving themselves as at the right weight had 32% higher levels (p-value = 0.31). Moreover, minority women perceiving themselves as overweight tended to have higher BP3 levels than those who do not. For example, BP3 levels in Other Hispanic women perceiving themselves as overweight are significantly higher compared to those who do not (73%, p-value = 0.03). In contrast, such differences in the non-Hispanic White women are minimal (-0.5%, p-value = 0.98).

Discussion

Minority women with body dissatisfaction show elevated BP3 exposure independent of sunscreen usage, implying that their elevated exposures may stem from using other personal care and consumer products. Further research is needed to determine if increases of exposure to potential toxicants occur among minority women with body dissatisfaction.

Highlights

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First integration of measures of body dissatisfaction with national chemical biomonitoring data

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Analyzed data from a diverse US nationally representative sample of 3,072 women

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Minority women with body dissatisfaction show higher BP3 levels independent of sunscreen use and BMI

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Minimal differences in BP3 levels by body dissatisfaction in non-Hispanic White women

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Developed a visualization tool to show how racial disparities widen due to body dissatisfaction
Quantifying the health impact of crop breeding: Revisiting the Disability-Adjusted Life Years Approach
Authors: Lenaerts Bert
Published: August 2024

Crop breeding, through methods like biofortification, plays a crucial role in increasing agricultural yields, contributing to a stable and healthy food supply by boosting the micronutrient content of staples, which is pivotal for combating chronic and hidden hunger, especially in rural areas. This shift towards improved nutrition can be sustainably integrated into regular diets, marking a significant stride in public health. The burden of hunger and its consequences on health are increasingly quantified using the Disability-Adjusted Life Years (DALYs) approach, which merges years of life lost and years lived with disability, offering a comprehensive view of health impacts and aiding in resource allocation despite its complexity and subjective nature. A practical formula for quantifying the health impact of biofortification was introduced by Stein et al. (2005) and Zimmermann and Qaim (2004). This entails calculating the efficacy or relative reduction in hunger burden based on the current and post-intervention nutrient intake against the recommended dietary allowances. As data on consumption and recommended intake levels are variable and not readily available, this paper proposes relying on relative estimates to bridge the data gaps and uncertainties, thus streamlining the quantification of crop breeding’s impact on diets and overall health.
Cross-site predictions of readmission after psychiatric hospitalization with mood or psychotic disorders
Authors: Ren Boyu , Yoon WonJin , Thomas Spencer , Savova Guergana , Miller Timothy , Hall Mei-Hua
Published: August 2024

Patients with mood or psychotic disorders have high rates of unplanned readmission, and predicting readmission likelihood may guide discharge decisions. In this retrospective, multi-site study, we assess the predictive power of various structured variables from electronic health records for all-cause readmission in each site separately and evaluate the generalizability of the in-site prediction models across sites. We find that the set of relevant predictors vary significantly across. For example, length of stay is strongly predictive of readmission at only three out of the four sites. We also find a general lack of cross-site generalizability of the in-site prediction models, with in-site predictions having an average F1 score of 0.666, compared to an average F1 score of 0.551 for cross-site predictions. The generalizability cannot be improved even after adjusting for differences in the distributions of predictors. These results indicate that, with this set of predictors, fitting individual models at each site is necessary to achieve reasonable prediction accuracy. Additionally, they suggest that more sophisticated predictors variables or predictive algorithms are needed to develop generalizable models capable of extracting robust insights into the root causes of early psychiatric readmissions.
An evaluation of the adequacy of Indian national and state Essential Medicines Lists (EMLs) for palliative care medical needs - a comparative analysis
Authors: Agrawal Disha , Shrinivas Divya , Sharma Parth , Rajagopal M R , Ghoshal Arun , Zadey Siddhesh
Published: August 2024

Objectives

Essential Medicines Lists (EMLs) guide the public sector procurement and supply of medications to impact access to adequate and appropriate palliative care drugs. This study evaluates the adequacy of India’s national and sub-national EMLs that can directly impact palliative care for 5.4 million patients.

Methods

In this qualitative document review, we compared Indian national, and state EMLs acquired from official government websites with the International Association for Hospice & Palliative Care (IAHPC) EML recommendations. We analysed data on the indication and formulation of drugs under the different categories of formulations present (all, some, and no), and drugs absent. Literature review and inputs from palliative care experts provided alternatives of absent medications to assess the adequacy of lists in managing the symptoms listed by IAPHC.

Results

We analysed 3 national and 25 state lists for 33 recommended drugs. The Central Government Health Services list had the maximum availability of all formulations of drugs (16 [48%]) nationally. Among states and union territories, the Delhi EML was the closest to IAHPC with 17 (52%) drugs with all formulations present. Nagaland had the most incomplete EML with only 3 (9%) drugs with all formulations present. No EML had all the recommended formulations of morphine. In one national and sixteen state EMLs, oral morphine was absent.

Conclusion

While Indian EMLs lack drugs for palliative care when compared with the IAHPC EML, symptom management is adequate. There is a need for countries with limited resources to modify the IAPHC list for their settings.

What is already known on this topic

Essential Medicines Lists (EMLs) are instrumental in guiding public sector procurement of drugs. The implementation of EMLs is known to improve drug availability and prescription practices. The rising burden of people requiring end-of-life care globally necessitates the availability of appropriate drugs for the medical management of symptoms, which can be achieved through their inclusion in local EMLs.

What this study adds

The national and sub-national EMLs of India do not fully adhere to the International Association for Hospice and Palliative Care (IAHPC) recommendations. However, they contain adequate drugs for the management of the listed symptoms. Additionally, the inclusion of various formulations of morphine remains a challenge to be addressed.

How this study might affect research, practice or policy

This study highlights the need to develop a fit-for-purpose EML for palliative care, taking into account the geographical variations in palliative care needs, and resource constraints in healthcare delivery at the state and country level.
Generation of Risk Score for Serious Non-Steroidal Anti-Inflammatory Drug (NSAID) Induced Cardiovascular Events (NAÏVE) among Active-Duty Service Members and Veterans
Authors: Atkinson Timothy J , Petway Justin , Forbes Whitney , Thorfinnson Hannah , Costantino Major Ryan C , Gressler Laura E
Published: August 2024

Importance

Cardiovascular disease (CVD) is a major global health concern, responsible for a significant proportion of deaths annually. Despite the widespread use of nonsteroidal anti-inflammatory drugs (NSAIDs) in managing various conditions, their association with cardiovascular events poses a challenge, and existing guidelines lack a reliable risk prediction tool. This study addresses the critical need for an evidence-based instrument to assess the likelihood of NSAID-induced cardiovascular events, that provides clinicians with valuable decision support to improve safety in their use for pain management, especially in patients vulnerable to cardiovascular events.

Objective

To develop a practical risk scoring tool, NSAID Induced Cardiovascular Events (NAÏVE), for estimating the risk of serious cardiovascular events associated with NSAID use.

Design

Retrospective nested case-control study

Setting

The study leveraged data from the DAVINCI database, integrating electronic health records, administrative data, and clinical data from both the Veterans Health Administration (VHA) and the Department of Defense (DoD).

Participants

The study cohort consisted of individuals with at least one NSAID pharmacy claim, with cases defined as those experiencing non-fatal myocardial infarction, non-fatal stroke, or new heart failure.

Interventions

Development of the NAÏVE risk scoring tool involved a comprehensive analysis of demographic, clinical, and prescription-related variables, including NSAID exposure, comorbidities, and medication history.

Main Outcomes/Measures

The primary outcome was the first occurrence of a cardiovascular event.

Results

The study cohort comprised 231,967 cases and 2,319,670 controls, identified from individuals with at least one NSAID pharmacy claim between October 1, 2016, and September 30, 2020. The risk index, NAÏVE, demonstrated strong discriminatory ability and calibration, with a C-statistic of 0.88. Variables such as age, NSAID exposure, comorbidities, and medication history were associated with increased odds of NSAID-induced cardiovascular events.

Conclusions/Relevance

NAÏVE is the first evidence-based risk scoring tool providing clinicians with valuable decision support for assessing the potential risk of serious cardiovascular events associated with NSAID use. It fills a crucial gap in clinical practice, allowing for transparent discussions with patients and shared decision-making regarding NSAID prescriptions. Further validation and prospective testing are warranted for broader applicability.
Chloroplastic ROS bursts initiate salicylic acid biosynthesis in plant immunity
Authors: Roussin-Léveillée Charles , St-Amand Méliane , Desbiens-Fortin Philippe , Perreault Rosaëlle , Pelletier Antoine , Gauthier Sabrina , Gaudreault-Lafleur Faye , Laforest-Lapointe Isabelle , Moffett Peter
Published: August 2024

Chloroplasts are essential centers of signal integration and transduction in plants. They are involved in the biosynthesis of primary and specialized metabolites, including salicylic acid (SA), a key defense phytohormone synthesized via the conserved chorismate biosynthetic pathway. However, the identity of the signal(s) that ultimately triggers SA induction in chloroplasts upon perception of a biotic threat has remained elusive. Here, we provide evidence of a functional link between chloroplast-derived reactive oxygen species (cROS) and SA production. We observe that inhibiting ROS bursts generated from photosystem II during plant immune activation completely abrogates the induction of SA synthesis in response to immunity-inducing signals, without affecting SA-independent immune responses. Indeed, time course analyses show that the induction of SA marker genes parallels that of cROS production during an immune response. Consistent with this, preventing cROS induction is sufficient to nullify the immune protection normally conferred by activating immunity prior to an infection. Analyses of transcriptomes and photosynthetic efficiency show that two conserved effectors from the phytopathogenPseudomonas syringae, HopM1 and AvrE1, redundantly disrupt photosynthesis and cROS bursts. These effects reduce SA accumulation and are mediated via the impact of HopM1 and AvrE1 in inducting host abscisic acid signaling. Our results suggest that a change in chloroplastic redox homeostasis induced by biotic stressors acts as an initiator of plant immunity through the production of SA, and that this response is targeted by conserved pathogen effector proteins.
Fetal liver neutrophils are responsible for the postnatal neutrophil surge
Authors: Ishiwata Ryo , Morimoto Yuji
Published: August 2024

Mammalian neonates experience an abrupt surge of blood neutrophil count within the first day of life. The postnatal neutrophil surge is regarded as a defensive reaction against infection; however, the mechanisms underlying this surge remain unclear.

The present study demonstrates that the postnatal neutrophil surge arises from the liver neutrophil pool. In rat neonates, the neutrophil surge was evident at 6 hours after birth. The proportion and immaturity of bone marrow neutrophils remained unaltered at 6 hours but increased only after the surge had peaked. In the rat fetal and neonatal livers, we observed prenatal neutrophil accumulation and acute loss of the neutrophils coinciding with the postnatal neutrophil surge. InLys-EGFPmice, an acute loss of liver neutrophils was observed within 12 hours of birth. This loss was characterized by a decrease in mature neutrophils and by perivascular neutrophil localization in the livers. Additionally, mouse fetuses exhibited an accumulation of the liver neutrophil pool during the late gestational period (e15-18), which was attributable to neutrophil-biased myeloid differentiation mediated by granulocyte-colony stimulating factor (G-CSF). The liver neutrophils exhibited characteristic transcriptomic alterations within three hours of birth, exemplified by an increase in theNos2 (iNOS) gene. The administration of a non-selective NOS inhibitor or an iNOS-selective inhibitor resulted in the inhibition of the postnatal neutrophil surge in rat neonates, accompanied by the retention of liver neutrophils.

These findings shed light on the previously unidentified source of the postnatal neutrophil surge and the stimulus initiating it.

Significance statement

Infections in newborns, particularly those occurring within the first 72 hours of life, are leading cause of mortality and morbidity. Neutrophil, a type of leukocytes, acutely increases within 24 hours after birth in the newborns’ blood. This neutrophil surge is regarded as an innate defensive system against infection; however, the mechanisms of the surge have remained unknown. Here, we examined rats and mice and found that the neutrophils accumulated in the fetal livers during the late pregnancy and were released into blood after birth. We also found a specific factor causing the release of the liver neutrophils. These findings might explain why preterm or low-birth weight newborns often lack the postnatal neutrophil surge and are thus more susceptible to infections.
Bradyrhizobium hardenbergiaesp. nov., isolated fromHardenbergia violaceain Australia, represents a novel basal lineage of theB. elkaniisupergroup
Authors: Lafay Bénédicte , Coquery Elina , Oger Philippe M.
Published: August 2024

Bradyrhizobia are widespread across the Australian continent, where they are essential to Australian ecosystems by helping legumes to compensate nutrient deficiencies and low fertility of Australian soils. Among theBradyrhizobiumgenospecies identified during a survey of Australian native rhizobia communities in 1994-1995, genospecies L appeared to be only distantly related to anyBradyrhizobiumlineages known at the time. We take advantage of the recent sequencing of the genome of strain BDV5419, the original strain corresponding toBradyrhizobiumgenospecies L, to re-assess this lineage taxonomic status. We characterized further strain BDV5419 based on morpho-physiological traits and determined its phylogenetic relationships with the type strains of the 88 currently knownBradyrhizobiumspecies based on sequence comparisons of SSU rRNA genes and complete genomes. The digital DNA–DNA hybridization relatedness with any type strain was less than 33% and both SSU rRNA gene and genome phylogenies confirmed that this strain does not belong to any formerly described species within theBradyrhizobiumgenus. Whereas its position within the lineage encompassing theB. elkaniiandB. jicamaesupergroups is unresolved in the SSU rDNA phylogeny, strain BDV5419 appears to be one of most basal lineages of theB. elkaniisupergroup in the genome comparison. All data thus support the description of the novel speciesBradyrhizobium hardenbergiaesp. nov. which type strain is BDV5419T(= CFBP 9111T= LMG 32897T), isolated from a nodule ofHardenbergia violaceaein Black Mountain Nature Reserve, in Canberra, ACT, Australia.
Alternate RNA decoding results in stable and abundant proteins in mammals
Authors: Tsour Shira , Machne Rainer , Leduc Andrew , Widmer Simon , Guez Jeremy , Karczewski Konrad , Slavov Nikolai
Published: August 2024

Amino acid substitutions may substantially alter protein stability and function, but the contribution of substitutions arising from alternate translation (deviations from the genetic code) is unknown. To explore it, we analyzed deep proteomic and transcriptomic data from over 1,000 human samples, including 6 cancer types and 26 healthy human tissues. This global analysis identified 60,024 high confidence substitutions corresponding to 8,801 unique sites in proteins derived from 1,990 genes. Some substitutions are shared across samples, while others exhibit strong tissue-type and cancer specificity. Surprisingly, products of alternate translation are more abundant than their canonical counterparts for hundreds of proteins, suggesting sense codon recoding. Recoded proteins include transcription factors, proteases, signaling proteins, and proteins associated with neurodegeneration. Mechanisms contributing to substitution abundance include protein stability, codon frequency, codon-anticodon mismatches, and RNA modifications. We characterize sequence motifs around alternatively translated amino acids and how substitution ratios vary across protein domains, tissue types and cancers. The substitution ratios are positively associated with intrinsically disordered regions and genetic polymorphisms in gnomAD, though the polymorphisms cannot account for the substitutions. Both the sequence and the tissue-specificity of alternatively translated proteins are conserved between human and mouse. These results demonstrate the contribution of alternate translation to diversifying mammalian proteomes, and its association with protein stability, tissue-specific proteomes, and diseases.
Extinction probabilities of small structured populations: adequate short-term model predictions inFolsomia candida
Authors: Van Dooren Tom J. M. , Haccou Patsy , Hermus Gerard , Tully Thomas
Published: August 2024

Population management requires predictions of extinction risk based on a general understanding of these risks and on system-specific modelling. Life tables, available for numerous populations and species, permit calculating population growth and the construction of multi-type branching process models which predict population survivorship and ultimate extinction probabilities. We exemplify this approach and tailor it to an experimental model to predict extinction probabilities per unit of time.

In age-structured populations, founders from different age classes lead to different predicted extinction probabilities. Age effects interact with environmental effects such as culling levels, which influence population growth rates. We assess the accuracy of predictions based on an age-structured matrix model, in an extinction experiment over an eight-week period on the springtailFolsomia candida, with crossed founder age and culling level treatments.

Using parameter estimates from an accessory experiment, the fit of model predictions to observed extinction probabilities was generally good. A modified branching process model which allowed culling events between and at observations reduced prediction error. However, additionally maximizing the likelihood of observed extinction probabilities based on survival and fecundity parameters, or on a parameter which concentrated fecundity within a subinterval, did not significantly reduce prediction error according to the AICc.

Our study shows that satisfactory predictions of establishment probabilities and of the initial persistence of small populations can be made using multi-type branching processes and available parameter estimates. Predictions can be improved by integrating knowledge of when events occur within intervals. This can be done without additional parameter estimation.
Predictive Dynamic Control Accurately Maps the Design Space for 2,3-Butanediol Production
Authors: Gotsmy Mathias , Erian Anna , Marx Hans , Pflügl Stefan , Zanghellini Jürgen
Published: August 2024

2,3-Butanediol is a valuable raw material for many industries. Compared to its classical production from petroleum, novel fermentation-based manufacturing is an ecologically superior alternative. To be also economically feasible, the production bioprocesses need to be well optimized.

Here, we adapted and applied a novel process optimization algorithm, dynamic control flux-balance analysis (dcFBA), for 2,3-butanediol production inE. coli. First, we performed two-stage fed-batch process simulations with varying process lengths. There, we found that the solution space can be separated into a proportionality and a trade-off region.

With the information of the simulations we were able to design close-to-optimal production processes for maximizing titer and productivity, respectively. Experimental validations resulted in a titer of 43.6±9.9 g L−1and a productivity of 1.93 ± 0.08 g L−1h−1. Subsequently, we optimized a continuous two-reactor process setup for 2,3-butanediol productivity. We found that in this mode, it is possible to increase the productivity more than threefold with minor impact on the titer and yield.

Biotechnological process optimization is cumbersome, therefore, many processes are run in suboptimal conditions. We are confident that the methods presented here, will help to make many biotechnological productions economically feasible in the future.

Highlights

Precise simulations are used to sample the process solution space.

Our simulations uncover big productivity potential in the 2,3-butanediol production.

Experiments validate the predictions and show a 2,3-butanediol productivity improvement of 104 %.
Analysis Of Respiratory Syncytial Virus Reveals Conserved Rna Secondary Structural Motifs And Impact Viral Lifecycle
Authors: Thornhill Elena M , Andrews Ryan J. , Lozier Zachary , Carino Elizabeth , Rameix-Welti Marie-Anne , Eléouët Jean-François , Moss Walter N. , Verhoeven David
Published: August 2024

An analysis that combined bioinformatics, comparative sequence/structural analysis, and experimental assays has been completed on respiratory syncytial virus (RSV). Both the genomic RNA and its reverse complement were studied using the novel bioinformatics pipeline ScanFold, which predicted 49 regions on RSV RNAs that appear to encode functional secondary structures (based on their unusually stable sequence order). Multiple motifs appear to be conserved between RSV and related virus strains, including one region within the F gene, which had a highly favorable overall prediction metric of a paired secondary structure. This motif was subjected to additional experimental analyses using SHAPE analysis to confirm ScanFold predicted secondary structure. In subsequent analysis, RSV F mRNA transcripts were made by in vitro transcription using T7 polymerase and transcripts which relaxed the predicted secondary structure yielded slightly higher mRNA transcripts and protein expression levels as wildtype F. However, using reverse genetics for comparison of viruses containing wildtype or relaxed F suggested that the predicted secondary structures may be critical for RSV replication in cells. To our knowledge, this is the first study to examine conserved RNA structures across multiple RSV strains and may help identify potential therapeutic targets to inhibit.
Opposing actomyosin pools generate cortical flows that establish epithelial polarity
Authors: Shi Yu , Ohler Lauren S. , de Jesus Bailey N. , Dickinson Daniel J.
Published: August 2024

Epithelial cell polarity, defined by distinct apical and basolateral domains, is fundamental for animal embryonic development and organ function. During organogenesis, epithelia often develop from unpolarized precursor cells. How mammalian epithelial cells establish polarityde novofrom an initially unpolarized state has remained unclear, in part due to an inability to observe this process in real time in non-transformed cellular systems. Here, we leverage recent advances in 3D spheroid culture of mouse embryonic stem cells, fluorescent protein knock-in and live imaging techniques to study the process of epithelial polarity establishment. We show that apical myosin activity, regulated by Myosin Light Chain Kinase (MLCK), is crucial for the establishment and maintenance of epithelial polarity. Actomyosin cortical flows transport ZO-1, a tight junction component that interacts with apical polarity proteins, to establish the apical membrane. A second pool of myosin, regulated by Rho kinase, localizes basally and balances apically directed flow. Our result imply that epithelial polarity emerges as a consequence of actomyosin-driven cytoskeletal rearrangements.
Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain
Authors: Bohra Darshika , Islam Zubairul , Nidharshan Sundarraj , Mazumder Aprotim , Notani Dimple
Published: August 2024

Transcription activation of genes by estrogen is driven by enhancers, which are often located within the same Topologically Associating Domain (TAD) as non-targeted promoters. We investigated how acute enhancer-driven activation affects neighbouring non-target genes within the same TAD. Using single-molecule RNA FISH (smFISH), we tracked the transcription ofTFF1(enhancer-targeted) andTFF3(non-targeted) during estrogen stimulation. We observed mutually exclusive expression patterns:TFF1expression peaked at 1 hour, whileTFF3reached its peak at 3 hours, afterTFF1’s activation had diminished. Chromatin looping data indicated that the enhancer loops withTFF1but notTFF3, suggesting thatTFF3upregulation is not due to direct enhancer-promoter interactions. CRISPR deletion of theTFF1enhancer and 1,6-hexanediol (HD) exposure revealed that theTFF1enhancer:promoter undergo Liquid-Liquid Phase Separation (LLPS), which sequesters the transcriptional machinery and inhibitsTFF3expression. As estrogen signalling wanes or LLPS is disrupted,TFF1expression declines whileTFF3expression increases. Our findings reveal that enhancer-driven activation can indirectly influence neighbouring genes, highlighting a dynamic shift in gene expression as signalling progresses.
H3K4me2 distinguishes a distinct class of enhancers during the maternal-to-zygotic transition
Authors: Hurton Matthew D. , Miller Jennifer M. , Lee Miler T.
Published: August 2024

After egg fertilization, an initially silent embryonic genome is transcriptionally activated during the maternal-to-zygotic transition. In zebrafish, maternal vertebrate pluripotency factors Nanog, Pou5f3 (OCT4 homolog), and Sox19b (SOX2 homolog) (NPS) play essential roles in orchestrating embryonic genome activation, acting as “pioneers” that open condensed chromatin and mediate acquisition of activating histone modifications. However, some embryonic gene transcription still occurs in the absence of these factors, suggesting the existence of other mechanisms regulating genome activation. To identify chromatin signatures of these unknown pathways, we profiled the histone modification landscape of zebrafish embryos using CUT&RUN. Our regulatory map revealed two subclasses of enhancers distinguished by presence or absence of H3K4me2. Enhancers lacking H3K4me2 tend to require NPS factors for de novo activation, while enhancers bearing H3K4me2 are epigenetically bookmarked by DNA hypomethylation to recapitulate gamete activity in the embryo, independent of NPS pioneering. Thus, parallel enhancer activation pathways combine to induce transcriptional reprogramming to pluripotency in the early embryo.
EML4-ALK variant-specific genetic interactions shape lung tumorigenesis
Authors: Diaz-Jimenez Alberto , Shuldiner Emily G. , Somogyi Kalman , Gonzalez Oscar , Akkas Filiz , Murray Christopher W. , Andrejka Laura , Tsai Min K. , Brors Benedikt , Sivakumar Smruthy , Sisoudiya Saumya D. , Sokol Ethan S. , Petrov Dmitri A. , Winslow Monte M. , Sotillo Rocio
Published: August 2024

Oncogenic fusions of EML4 and ALK occur in ∼5% of lung adenocarcinomas. More than 15 EML4-ALK variants with distinct breakpoints withinEML4have been identified, but the functional differences between these variants remain poorly understood. Here we use CRISPR/Cas9 somatic genome editing to generate autochthonous mouse models of the two most common EML4-ALK variants, V1 and V3, and show that V3 is more oncogenic than V1. By integrating these models with multiplexed genome editing, we quantify the effects of 29 putative tumor suppressor genes on V1- and V3-driven lung cancer growthin vivoand show that many tumor suppressor genes have dramatically variant-specific effects on tumorigenesis. Analysis of a novel dataset representing the largest human EML4-ALK lung cancer cohort to date identified alterations in the genomic landscape depending on the EML4-ALK variant. These findings demonstrate functional heterogeneity among EML4-ALK variants, suggesting that EML4-ALK variants behave more like distinct oncogenes than a uniform entity. More broadly, these findings highlight the dramatic impact of oncogenic fusions partner proteins on tumor biology.
A novel iPSC model of Bryant-Li-Bhoj neurodevelopmental syndrome demonstrates the role of histone H3.3 in neuronal differentiation and maturation
Authors: Sangree Annabel K. , Angireddy Rajesh , Bryant Laura M. , Layo-Carris Dana E. , Lubin Emily E. , Wang Xiao Min , Clark Kelly J. , Durham Emily E. , Bhoj Elizabeth J.
Published: August 2024

Background

Bryant-Li-Bhoj neurodevelopmental syndrome (BLBS) is neurogenetic disorder caused by variants inH3-3AandH3-3B,the two genes that encode the histone H3.3 protein. Ninety-nine percent of individuals with BLBS show developmental delay/intellectual disability, but the mechanism by which variants in H3.3 result in these phenotypes is not yet understood. As a result, only palliative interventions are available to individuals living with BLBS.

Methods

Here, we investigate how one BLBS-causative variant,H3-3Bp.Leu48Arg (L48R), affects neurodevelopment using an induced pluripotent stem cell (iPSC) model differentiated to 2D neural progenitor cells (NPCs), 2D forebrain neurons (FBNs), and 3D dorsal forebrain organoids (DFBOs). We employ a multi-omic approach in the 2D models to quantify the resulting changes in gene expression and chromatin accessibility. We used immunofluorescence (IF) staining to define the identities of cells in the 3D DFBOs.

Results

In the 2D systems, we found dysregulation of both gene expression and chromatin accessibility of genes important for neuronal fate, maturation, and function in H3.3 L48R compared to control. Our work in 3D organoids corroborates these findings, demonstrating altered proportions of radial glia and mature neuronal cells.

Conclusions

These data provide the first mechanistic insights into the pathogenesis of BLBS from a human-derived model of neurodevelopment, which suggest that the L48R increasesH3-3Bexpression, resulting in the hyper-deposition of H3.3 into the nucleosome which underlies changes in gene expression and chromatin accessibility. Functionally, this causes dysregulation of cell adhesion, neurotransmission, and the balance between excitatory and inhibitory signaling. These results are a crucial step towards preclinical development and testing of targeted therapies for this and related disorders.
Super-Resolution Simplified: Sub-10nm Imaging Over Large Areas and Deep Penetration via SDC-OPR and DNA-PAINT
Authors: Zaza Cecilia , Joseph Megan D. , Dalby Olivia P. L. , Walther Rhian F. , Kołątaj Karol , Chiarelli Germán , Pichaud Franck , Acuna Guillermo P. , Simoncelli Sabrina
Published: August 2024

Single molecule localization microscopy (SMLM) is constrained by selective illumination configurations to achieve high signal-to-background ratio (SBR), forcing trade-offs between penetration depth, field-of-view (FOV), and spatial resolution. We demonstrate that a Spinning Disc confocal microscope with Optical Photon Reassignment (SDC-OPR) in combination with DNA-PAINT effectively balances these limitations. This system enables high-resolution imaging through multiple cellular layers, enhancing spatial resolution while remaining practical and accessible for diverse biological applications.
A consortium-based approach to adaptive laboratory evolution ofAcinetobacter baylyiADP1 for lignin valorization
Authors: Maiti Suchismita , Singh Prashant , Vishnu Prasad J , Muthukrishnan Anantha Barathi , Blank Lars M. , Jayaraman Guhan
Published: August 2024

The utility ofAcinetobacter baylyiADP1 (ADP1) for lignin valorization has yet to be sufficiently investigated compared to other organisms such asPseudomonas,Rhodococcus,etc. In this study, a two-step Adaptive Laboratory Evolution (ALE) process was used to evolve a unique ADP1 strain (A. baylyiSAG_185). Initially, several ADP1 strains were evolved for substrate tolerance to specific lignin-related aromatics (LRAs). Subsequently, a consortium of these strains was adaptively evolved in a mixture of LRAs, which resulted in the evolution of SAG_185. This strain was capable of simultaneous utilization of multiple LRAs at higher concentrations as well as grow on a depolymerized lignin-rich residue obtained from enzymatic hydrolysis of pre-treated corncob. This is the first report on such an evolutionary strategy.

Whole-genome sequence analysis of all the evolved strains revealed large-scale mutations involving insertion sequences (IS). In particular, SAG_185 revealed a critical mutation in the vanR repressor gene, resulting in the up-regulation of vanAB genes required to convert vanillate to the key intermediate, protocatechuate (PCA). Additionally, there were two large deletions of 9kb and 38kb DNA segments, including genes for putative transcriptional regulators of LysR, MarR and AraC family. The evolved strains also showed mutations in the hcaE gene, responsible for the uptake of LRAs. The vast number of mutations in hypothetical proteins, transporter and regulatory sequences indicate the underlying effects of these regions on the uptake of multiple LRAs. Overall, our findings provide potential targets for reverse engineering of A. baylyi ADP1 for lignin valorization.

IMPORTANCE

This study shows a novel strategy for adaptive laboratory evolution, which can be generically adopted to evolve bacterial strains for taking up multiple substrates which are toxic at higher concentrations. We developed a two-step evolutionary strategy to evolve a unique strain, A. baylyi SAG_185, which could take up multiple lignin-related aromatic monomers at higher concentrations as well as grow on depolymerized lignin. Initially, individual strains were adapted to utilize single aromatic monomers at higher concentrations. After many unsuccessful attempts to adapt these strains for utilizing multiple monomers, a consortium of the five evolved strains were grown on a mixture of aromatics and adapted to utilize all the monomers at high concentrations. The adapted consortia resulted in the evolution of SAG_185. Whole-genome sequence analysis of all these strains gave rise to many interesting insights on potential genetic targets for reverse engineering of A. baylyi ADP1 for lignin valorization.