bluuebunny/crossref_metadata_2025 huggingface dataset:
An explainable map of human gastruloid morphospace reveals gastrulation failure modes and predicts teratogens
Authors: Rufo Joseph , Qiu Chongxu , Han Dasol , Baxter Naomi , Daley Gabrielle , Wilson Maxwell Z.
Published: September 2024

Human gastrulation is a critical stage of development where many pregnancies fail due to poorly understood mechanisms. Using the 2D gastruloid, a stem cell model of human gastrulation, we combined high-throughput drug perturbations and mathematical modelling to create an explainable map of gastruloid morphospace. This map outlines patterning outcomes in response to diverse perturbations and identifies variations in canonical patterning and failure modes. We modeled morphogen dynamics to embed simulated gastruloids into experimentally-determined morphospace to explain how developmental parameters drive patterning. Our model predicted and validated the two greatest sources of patterning variance: cell density-based modulations in Wnt signaling and SOX2 stability. Assigning these parameters as axes of morphospace imparted interpretability. To demonstrate its utility, we predicted novel teratogens that we validated in zebrafish. Overall, we show how stem cell models of development can be used to build a comprehensive and interpretable understanding of the set of developmental outcomes.
Nuclear body reorganization by the viral RNAkaposinpromotes Kaposi’s sarcoma-associated herpesvirus gene expression
Authors: Kleer Mariel , Johnston Michael J. , Corcoran Jennifer A.
Published: September 2024

Kaposinis the most abundantly expressed viral RNA in tumours caused by the oncogenic virus Kaposi’s sarcoma-associated herpesvirus (KSHV); however, its role in viral replication is not well understood. Here we show that during KSHV infection,kaposinactsin cisas an architectural RNA to rebuild cellular nuclear speckles (NSs) to sites proximal to the viral genome to optimize viral gene expression. We showkaposinRNA is both necessary and sufficient for NS remodelling, and ablatingkaposincolocalization with NSs using kaposin-deficient recombinant viruses impairs viral gene expression. This is the first example of an RNA (cellular or viral) capable of scaffolding NS and the first study to definekaposinas an important regulator of KSHV gene expression and, by extension, KSHV-associated disease.

Graphical Abstract

Highlights

Thekaposintranscript is the first RNA (cellular or viral) identified as sufficient to scaffold NSs.

Kaposinscaffolding of NSs requires repetitive nucleotide sequences and cellular SRRM2.

Lack ofkaposin-NS colocalization during KSHV infection impairs viral gene expression.

Kaposinfunctionsin cisto locally influence gene expression.
The molecular basis for prognosis of isoniazid resistance inMycobacterium tuberculosis
Authors: Valafar Siavash J. , Valafar Aram A. , Elmaraachli Wael
Published: September 2024

Tuberculosis (TB), a disease that kills 1.5 million people every year, is a major global public health concern. The emergence of drug resistance inM. tuberculosis, the obligate pathogen of TB is a major challenge. The emergence of resistance seems to follow an order that might be exploited for novel therapeutic strategies. In most cases resistance to isoniazid (INH) emerges first, followed by rifampicin, then either pyrazinamide or ethambutol, and finally followed by resistance to second-line drugs. For this reason, it is thought that prevention of emergence of INH resistance may help the prevention of resistance to other drugs. In this manuscript we present the prognostic potential of specific mutations in predicting the emergence of the three most common canonical INH resistance (katG315, inhA-15, and inhA-8) with the hope that majority of resistance cases can be predicted and avoided. Here we present evidence that resistance to INH occurs in steps that in most cases follow specific evolutionary trajectory. Identifying these steps can therefore be used to predict and avoid the most common INH resistance mechanism. In our approach, we used genomic and phenotypic data from over 16,000 samples collected by two large databases, the TB Portals and the CRyPTIC consortium. We used classical sensitivity and specificity values as well as a deep learning neural models to identify promising predictive mutations using TB Portals data. We then tested the prognostic potential of the identified mutations using the CRyPTIC consortium data. Here we report two mutations (Rv1258c581 indel &mshAA187V) as those carrying the highest potential for predicting the emergence of the three canonical mutations (accuracy of 73% and specificity of 96%). Our results point to a stepwise evolutionary trajectory toward the emergence of the three canonical mutations. Furthermore, the high negative predictive values provide an opportunity for clinicians to continue using INH in new regiments designed for nonresponsive patients whose samples do not contain the two precursor mutations. Finally, we present testable hypotheses describing the role of the precursor mutations in emergence of the three canonical mutations and the predicted trajectories. Mutagenesis experiments can confirm these hypotheses. Additional time course samples and analysis will undoubtedly uncover additional prognostic markers for other trajectories toward high-level INH resistance.
The Lived Experience of Infertility in Asian Americans: A Qualitative Study
Authors: Vu Michelle , Nguyen Anh-Tho Antoinette , Hyun Jinsol , Dye Timothy , Alur-Gupta Snigdha
Published: September 2024

Objective

To identify psychosocial and cultural factors among Asian American patients diagnosed with infertility that may contribute to their disparate fertility outcomes.

Design

A cross-sectional qualitative interview study was conducted with women ≥18-years-old who identified as Asian American and had a diagnosis of infertility. Semi-structured interviews were performed until thematic saturation was reached. The interviews were transcribed and coded. A codebook was developed to capture the grounded perspectives of participants. The web application Dedoose was utilized to conduct content analysis, identifying common themes and patterns.

Results

Asian Americans voice the importance of having children, emphasizing the cultural expectation to procreate. They reported that infertility caused immense mental and emotional distress, resulting in feelings of disappointment and grief. Participants noted that it is not common in their culture to talk about infertility-related issues. Religion and naturopathic remedies played a large role in helping participants adjust to their infertility journeys. Participants stated that the infertility evaluation was complicated and one particular area of frustration was the lack of individually centered treatment. Interestingly, participants expressed desire to help other Asian women who are also struggling with infertility.

Conclusion

Infertility is a difficult and complex experience for Asian American women. Parenthood is a strong expectation for people of Asian descent and results in emotional burden when complicated by infertility. Fertility concerns are considered taboo to openly discuss, which can cause additional feelings of isolation. Healthcare providers should work to address the culturally induced shame associated with infertility and provide more individualized care.
Intracellular diffusion in the cytoplasm increases with cell size in fission yeast
Authors: Tan Catherine , Lanz Michael C. , Swaffer Matthew , Skotheim Jan , Chang Fred
Published: September 2024

Diffusion in the cytoplasm can greatly impact cellular processes, yet regulation of macromolecular diffusion remains poorly understood. There is increasing evidence that cell size affects the density and macromolecular composition of the cytoplasm. Here, we studied whether cell size affects diffusion at the scale of macromolecules tens of microns in diameter. We analyzed the diffusive motions of intracellular genetically-encoded multimeric 40 nm nanoparticles (cytGEMs) in the cytoplasm of the fission yeastSchizosaccharomyces pombe. Using cell size mutants, we showed that cytGEMs diffusion coefficients decreased in smaller cells and increased in larger cells. This increase in diffusion in large cells may be due to a decrease in the DNA-to-Cytoplasm ratio, as diffusion was not affected in large multinucleate cytokinesis mutants. In investigating the underlying causes of altered cytGEMs diffusion, we found that the proteomes of large and small cells exhibited size-specific changes, including the sub-scaling of ribosomal proteins in large cells. Comparison with a similar dataset from human cells revealed that features of size-dependent proteome remodeling were conserved. These studies demonstrate that cell size is an important parameter in determining the biophysical properties and the composition of the cytoplasm.
Assessing Oxygen Perturbation and Over-Aeration Impacts on Soluble Microbial Products (SMP) Production and Release in Activated Sludge Systems
Authors: Zhou Xueyang , Manna Bharat , Lyu Boyu , Singhal Naresh
Published: September 2024

Understanding the interplay between oxygen conditions and microbial activities in an activated sludge system is crucial for the optimization of wastewater treatment processes. This study explores the influence of various aeration patterns and dissolved oxygen (DO) levels on the microbial metabolic activities, with a particular focus on the synthesis and release of soluble microbial products (SMP), and the regulation of key metabolic genes and enzymes. The activated sludge system underwent different aeration patterns, including constant aeration, continuous perturbation, and intermittent perturbation under two distinct DO levels of 2mg/L and 8mg/L. We employed a combination of multi-omics techniques (metagenomics, metaproteomics, and metabolomics) along with chemical analytical methods for comprehensive sample analysis. Our results reveal an increased intracellular accumulation of amino acids and enhanced release of protein under the conditions of oxygen perturbation. Furthermore, elevated DO levels fostered the accumulation of poly-3-hydroxybutyrate intracellularly and the release of protein and fatty acids as SMP. This outcome is associated with the abundance of key metabolic genes and enzymes, thereby highlighting the metabolic flexibility of microbes under different oxygen conditions. These findings offer valuable insights into microbial metabolic dynamics under varying oxygen conditions, thereby providing guidance for more efficient and sustainable strategies in wastewater treatment and resource recovery.

SYNOPSIS

This study explores the complex interplay between varying oxygen conditions and microbial activity in activated sludge systems, focusing on the impact on the synthesis and release of soluble microbial products (SMP). Findings highlight the significant influence of oxygen perturbation and dissolved oxygen levels on protein synthesis and fatty acid metabolic processes.
Natural variations of adult neurogenesis and anxiety predict hierarchical status of inbred mice
Authors: Grieco Fabio , Balla Atik , Larrieu Thomas , Toni Nicolas
Published: September 2024

Hierarchy provides a survival advantage to social animals in challenging circumstances. In mice, social dominance is associated with trait anxiety and reduced stress resilience which are regulated by adult hippocampal neurogenesis. Here, we tested whether adult hippocampal neurogenesis may regulate social dominance behavior. We observed that future dominant individuals exhibited higher trait anxiety and lower levels of hippocampal neurogenesis prior to social hierarchy formation, suggesting that baseline neurogenesis might predict individual social status among a group. This phenotype persisted after social hierarchy was stable. Experimentally reducing neurogenesis prior to the stabilization of social hierarchy in group-housed males increased the probability of mice to become dominant and increased anxiety. Finally, when innate dominance was assessed in socially isolated and anxiety-matched animals, mice with impaired neurogenesis displayed a dominant status toward strangers. Together, these results indicate that adult neurogenesis predicts and regulates hierarchical and situational dominance behavior along with anxiety-related behavior. These results provide a framework to study the mechanisms underlying social hierarchy and the dysregulation of dominance behavior in psychiatric diseases related to anxiety.
Rapid and reversible regulation of cell cycle progression in budding yeast using optogenetics
Authors: Koutsoumpa Andriana , Milias-Argeitis Andreas
Published: September 2024

The regulatory complexity of the eukaryotic cell cycle poses technical challenges in experiment design and data interpretation, leaving gaps in our understanding of how cells coordinate cell cycle-related processes. Traditional methods, such as knockouts and deletions are often ineffective to compensatory interactions in the cell cycle control network, while chemical agents that cause cell cycle arrest can have undesired pleiotropic effects. Synthetic inducible systems targeting specific cell cycle regulators offer potential solutions but are limited by the need for external inducers, which make fast reversibility technically challenging. To address these issues, we developed an optogenetic tool (OPTO-Cln2) that enables light-controlled and reversible regulation of G1 progression in budding yeast. Through extensive validation and benchmarking via time-lapse microscopy, we verify that OPTO-Cln2-carrying strains can rapidly toggle between normal and altered G1 progression. By integrating OPTO-Cln2 with a readout of nutrient-sensing pathways (TORC1 and PKA), we show that the oscillatory activity of these pathways is tightly coordinated with G1 progression. Finally, we demonstrate that the rapid reversibility of OPTO-Cln2 facilitates multiple cycles of synchronous arrest and release of liquid cell cultures. Our work provides a powerful new approach for studying cell cycle dynamics and the coordination of growth- with division-related processes.
Musicianship modulates cortical (but not brainstem) effects of attention on processing musical triads
Authors: MacLean Jessica , Drobny Elizabeth , Rizzi Rose , Bidelman Gavin M.
Published: September 2024

Background

Many studies have demonstrated benefits of long-term music training (i.e., musicianship) on the neural processing of sound, including simple tones and speech. However, the effects of musicianship on the encoding of simultaneously presented pitches, in the form of complex musical chords, is less well-established. Presumably, musicians’ stronger familiarity and active experience with tonal music might enhance harmonic pitch representations, perhaps in an attention-dependent manner. Additionally, attention might influence chordal encoding differently across the auditory system. To this end, we explored the effects of long-term music training and attention on processing of musical chords at brainstem and cortical levels.

Method

Young adult participants were separated into musician and nonmusician groups based on extent of formal music training. While recording EEG, listeners heard isolated musical triads that differed only in the chordal third: major, minor, and detuned (4% sharper third from major). Participants were asked to correctly identify chords via key press during active stimulus blocks and watched a silent movie during passive blocks. We logged behavioral identification accuracy and reaction times and calculated information transfer based on the behavioral chord confusion patterns. EEG data were analyzed separately to distinguish between cortical (event-related potential, ERP) and subcortical (frequency-following response, FFR) evoked responses.

Results

We found musicians were (expectedly) more accurate, though not faster, than nonmusicians in chordal identification. For subcortical FFRs, responses showed stimulus chord effects but no group differences. However, for cortical ERPs, whereas musicians displayed P2 (∼150 ms) responses that were invariant to attention, nonmusicians displayed earlier and reduced P2 during passive listening. Listeners’ degree of behavioral information transfer (i.e., success in distinguishing chords) was also better in musicians and correlated with their neural differentiation of chords, assessed via pairwise differences in the ERPs.

Conclusions

Our data suggest long-term music training strengthens even the passive cortical processing of musical sounds, supporting more automated brain processing of musical chords with less reliance on attention. Our results also suggest the degree to which listeners can behaviorally distinguish chordal triads is directly related to their neural specificity to musical sounds primarily at cortical rather than subcortical levels.
The urinary microbiome in association with diabetes and diabetic kidney disease: A systematic review
Authors: Graells Tiscar , Lin Yi-Ting , Ahmad Shafqat , Fall Tove , Ärnlöv Johan
Published: September 2024

Background

The urinary microbiome, or urobiome, is a novel area of research that has been gaining attention recently, as urine was thought to be sterile for years. There is limited information about the composition of the urobiome in health and disease. The urobiome may be affected by several factors and diseases such as diabetes, a disease that often leads to kidney damage. Thus, we need to understand the role of the urobiome to assess and monitor kidney disease related to diabetes over time.

Methods

We conducted a systematic review to summarize knowledge about the urobiome in association with diabetes mellitus and diabetic kidney disease. The search was conducted in several electronic databases until November 2024.

Results

Eighteen studies were selected including cross-sectional case-control studies, cross-sectional surveys and one prospective longitudinal study. In total, the urobiome of 1,571 people was sequenced, of which 662 people had diabetes, and of these 36 had confirmed diabetic kidney disease; 609 were healthy individuals, 179 had prediabetes or were at risk of type 2 diabetes mellitus and 121 did not have diabetes but had other comorbidities. Eight studies analysed data from females, one was focused on male data, and the other nine had mixed female-male data. Most of the studies had a small sample size, used voided midstream urine, and used 16S rRNA sequencing.

Conclusion

This systematic review summarizes trends seen throughout published data available to have a first baseline knowledge of the urinary microbiome, and its microbiota, in association with diabetes including the decreased richness and α-diversity in urinary microbiota in individuals with diabetes compared to healthy controls and the decreased α-diversity with the evolution of kidney disease independently of the cause.
Closing the gaps: testing the efficacy of carbapenem and cephalosporins in treating late-stage anthrax
Authors: Sittner Assa , Bar-David Elad , Glinert Itai , Ben-Shmuel Amir , Schlomovitz Josef , Levy Haim , Weiss Shay
Published: September 2024

Anthrax is a fatal zoonotic disease caused by exposure toBacillus anthracisspores. Treatment of systemic anthrax is usually efficient when using the right antibiotics as close as possible to exposure, preferably prior to symptoms’ onset as post exposure prophylaxis (PEP). The efficacy decreases as treatment is initiated later in disease progression. The CDC in its guidelines divides anthrax treatment to three different indications according to the progression of the disease: PEP, systemic and systemic with indications of CNS infection. While the prognosis of PEP or early treatment of systemic anthrax is very good, ingress of the bacteria into the CNS significantly decreases treatment efficacy, creating a substantial clinical challenge. Since anthrax in humans is rare, the CDC recommendations are mainly based on animal model experiments and data obtained from patients infected with other pathogens. Here we use rabbits to test the efficacy of the combined treatment of Meropenem and Doxycycline which is the first choice in the CDC recommendations for treating systemic patients with indication of CNS infection. In addition, we test the efficacy of the first-generation cephalosporin, cefazolin, in treating the different stages of the disease. We found that the combination of Doxycycline and Meropenem is highly effective in treating rabbits in our inhalation and CNS infection models. Cefazoline was efficient only as PEP or systemic stage treatment but not CNS infected animals. Our findings support the CDC recommendation of using a combination of Doxycycline and Meropenem for systemic patients with or without indications for CNS infection. We found that Cefazoline is a decent choice for PEP or early sage systemic disease but recommend considering using this antibiotic only if all other options are not available.
Molecular and Proteomic Profiles of Radioiodine Refractory Papillary Thyroid Cancer
Authors: Liu Hanqing , Wang Jiaxi , Zhou Yan , Hu Pingping , Li Lu , Yang Dan , Kong Deguang , Xu Zhiliang , Sun Yaoting , Chen Chuang
Published: September 2024

Background

Despite the generally favorable prognosis of papillary thyroid cancers (PTCs) following surgery with/without radioactive iodine (RAI) therapy, approximately one-third of patients experiencing recurrence and metastasis eventually develop resistance to RAI, leading to poor outcomes. However, the mechanisms underlying RAI-refractoriness remain elusive. This study aimed to assess the molecular and proteomic characteristics of RAI-refractory PTC (RR-PTC) for deeper insights.

Methods

The medical records were reviewed for the selection and grouping of RR-PTC patients and RAI-sensitive controls. RR-PTC patients were divided into three subgroups: continuous RAI uptake (ID), loss of uptake at the first I-131 treatment (iDF) and lost gradually (iDG). Proteomic profiling and targeted next-generation sequencing were performed on primary lesions. The incidence of gene mutations and fusions was compared across groups. Bioinformatic analysis was subsequently conducted to identify the differentially expressed proteins and enriched pathways.

Results

Forty-eight PTC patients with recurrence and/or metastasis were included. The expression profiles of the RR-PTC and control groups were similar. In the subgroup comparison, enriched pathways related to MAPK and TNF signaling were associated with negative I-131 uptake and tumor tolerance with positive I-131 uptake. TheBRAFV600Emutation was less common in the ID group, whereas theTERTpromoter mutation was more common in the iDF group.NCOA4-RETfusion was more common in the ID group.

Conclusion

The present study constructed the first proteomic profile of RR-PTC. The identified proteins and pathways may be promising biomarkers and drug targets. Gene alterations can aid in the early diagnosis of RR-PTC.
The exit of naïve pluripotency contains a lipid metabolism-induced checkpoint for genome integrity
Authors: de Souza Roshni A. , Barneda David , Karimlou Donja , Bovee Nick G.P. , Zheng Yuhan , Kahlman Eveline J.E.M. , Novo Clara Lopes , Ellis James K. , Leeke Bryony J. , Bangalore Megha Prakash , Liu Zijing , Sousa Bebiana C. , Lopez-Clavijo Andrea F. , Jansen Joop H. , Barahona Mauricio , Percharde Michelle , Keun Hector C. , Christian Mark , Marks Hendrik , Azuara Véronique
Published: September 2024

Pluripotent progenitors undergo dramatic cellular and biochemical transformations during peri-implantation development. These large-scale reprogramming events are fundamental for subsequent differentiation, but how they are integrated and co-ordinated with the preservation of genome integrity remain unknown. Here, we uncover a metabolism-induced telomere checkpoint that takes place in pluripotent progenitors as they form rosette-like epithelial structures. We show that the glycolytic switch at the exit of naïve pluripotency is preceded by an acceleration of mitochondrial respiration andde novolipogenesis, fuelling the accumulation of lipid droplets required for morphogenesis. We find that downstream of these CIDEA-promoted metabolic events is the induction of ZSCAN4, a key pluripotency-associated regulator of telomere stability. Surprisingly, the build-up of lipid droplets corresponds to a transient shortening of telomeres, which triggers the activation of an elongation mechanism via ZSCAN4. Thus, telomere homeostasis can be safeguarded as essential lipid metabolic reprogramming unfolds to drive developmental progression.
Anti-tubercular potential and pH-driven mode of action of salicylic acid derivatives
Authors: Laudouze Janïs , Francis Thomas , Forest Emma , Mies Frédérique , Bolla Jean-Michel , Crauste Céline , Canaan Stéphane , Shlyonsky Vadim , Santucci Pierre , Cavalier Jean-François
Published: September 2024

In the search for new anti-tuberculosis drugs with novel mechanisms of action, we evaluated the antimycobacterial activity of a panel of eight phenolic acids against four pathogenic mycobacterial model species, includingM. tuberculosis. We demonstrated that salicylic acid (SA), as well as the iodinated derivatives 5-iodo-salicylic acid (5ISA) and 3,5-diiodo-salicylic acid (3,5diISA), displayed promising antitubercular activities. Remarkably, using a genetically encoded mycobacterial intrabacterial pH reporter, we describe for the first time thatSA, 5ISA, 3,5diISAand the anti-inflammatory drug aspirin (ASP) act by disrupting the intrabacterial pH homeostasis ofM. tuberculosisin a dose-dependent manner underin vitroconditions mimicking the endolysosomal pH of macrophages. In contrast, the structurally related second-line anti-TB drug 4-aminosalicylic acid (PAS) had no pH-dependent activity and was strongly antagonized by L-methionine supplementation, thereby suggesting distinct modes of action. Finally, we propose thatSA, ASPand its two iodinated derivatives could restrictM. tuberculosisgrowth in a pH-dependent manner by acidifying the cytosol of the bacilli; therefore, making such compounds very attractive for further development.
Congruent brain signatures specific to phonology in fronto-temporal cortex during language production and understanding.
Authors: Dmitrieva Xenia , Anton Jean-Luc , Runnqvist Elin , Fairs Amie , Ivanova Bissera , Sein Julien , Nazarian Bruno , Dufour Sophie , Pulvermuller Friedemann , Strijkers Kristof
Published: September 2024

In this fMRI study we investigated whether language production and understanding recruit the same phoneme-specific networks. We did so by comparing the brain responses to different phoneme categories in minimal pairs: Bilabial-initial words (e.g., monkey) were contrasted to alveolar-initial words (e.g., donkey) in 37 participants performing both language production and comprehension tasks. Region-of-Interest analyses showed that the same sensorimotor networks were activated across the language modalities. In motor regions, word production and comprehension elicited the same phoneme-specific topographical activity patterns, with stronger haemodynamic activations for alveolar-initial words in the tongue cortex and stronger activations for bilabial-initial words in the lip cortex. In the posterior and middle superior temporal cortex, production and comprehension likewise resulted in similar activity patterns, with enhanced activations to alveolar- compared to bilabial-initial words. These results disagree with the classical separation between language production and understanding in neurobiological models of language, and instead advocate for a cortical organization where the same phoneme-specific acoustic-and-articulatory representations carry production and comprehension.
Transient Notch Activation Converts Pluripotent Stem Cell-Derived Cardiomyocytes Towards a Purkinje Fiber Fate
Authors: Gonzalez David M. , Dariolli Rafael , Moyett Julia , Song Stephanie , Shewale Bhavana , Bliley Jacqueline , Clarke Daniel , Ma’ayan Avi , Rentschler Stacey , Feinberg Adam , Sobie Eric , Dubois Nicole C.
Published: September 2024

Cardiac Purkinje fibers form the most distal part of the ventricular conduction system. They coordinate contraction and play a key role in ventricular arrhythmias. While many cardiac cell types can be generated from human pluripotent stem cells, methods to generate Purkinje fiber cells remain limited, hampering our understanding of Purkinje fiber biology and conduction system defects. To identify signaling pathways involved in Purkinje fiber formation, we analyzed single cell data from murine embryonic hearts and compared Purkinje fiber cells to trabecular cardiomyocytes. This identified several genes, processes, and signaling pathways putatively involved in cardiac conduction, including Notch signaling. We next tested whether Notch activation could convert human pluripotent stem cell-derived cardiomyocytes to Purkinje fiber cells. Following Notch activation, cardiomyocytes adopted an elongated morphology and displayed altered electrophysiological properties including increases in conduction velocity, spike slope, and action potential duration, all characteristic features of Purkinje fiber cells. RNA-sequencing demonstrated that Notch-activated cardiomyocytes undergo a sequential transcriptome shift, which included upregulation of key Purkinje fiber marker genes involved in fast conduction such asSCN5A, HCN4 and ID2,and downregulation of genes involved in contractile maturation. Correspondingly, we demonstrate that Notch-induced cardiomyocytes have decreased contractile force in bioengineered tissues compared to control cardiomyocytes. We next modified existingin silicomodels of human pluripotent stem cell-derived cardiomyocytes using our transcriptomic data and modeled the effect of several anti-arrhythmogenic drugs on action potential and calcium transient waveforms. Our models predicted that Purkinje fiber cells respond more strongly to dofetilide and amiodarone, while cardiomyocytes are more sensitive to treatment with nifedipine. We validated these findingsin vitro, demonstrating that our new cell-specificin vitromodel can be utilized to better understand human Purkinje fiber physiology and its relevance to disease.
Structural and functional analysis of cancer-associated missense variants in the retinoblastoma protein (Rb) pocket domain
Authors: Castro Anthony , Ruiz-Rivera Alfredo , Moorman Chad C. , Wolf-Saxon Emma R. , Mims Hailey N. , Vasquez-Meza Vanessa I. , Rangel Matthew A. , Loera Marcos M. , Bond Ian , Buchanan Seth B. , Villarreal Estela , Tripathi Sarvind , Rubin Seth M. , Burke Jason R.
Published: September 2024

The retinoblastoma tumor suppressor (Rb) is a multifunctional protein that primarily regulates the cell cycle but also has roles in cellular differentiation, DNA damage response and apoptosis. The loss of Rb is a key event in the development or progression of many cancers. Essential functions of Rb occur through its pocket domain, which is necessary for regulating binding interactions with E2F transcription factors and transcription repressors that bind via an LxCxE motif. The pocket domain is the most highly-conserved region of the multidomain protein, as well as the most frequent site of mutations. To understand what effects cancer missense mutations have on Rb’s pocket domain, we used fluorescence polarization and differential scanning fluorimetry to quantify changes, caused by 75 cancer-associated missense variants, to E2F transactivation domain (E2FTD) binding, LxCxE binding, and changes to the thermostability of the protein. We find that 43% of the missense variants we tested reduce Rb-E2FTDbinding. Many of these variants are not located at the E2F binding site, yet they destabilize the fold of the protein and show temperature-sensitive binding effects. We also find that 21% of tested mutations reduce LxCxE binding, and several mutations selectively disrupt either E2FTDor LxCxE binding. Protein X-ray crystallography of four missense variants reveals how different mutations destabilize the protein fold and inhibit E2FTDor LxCxE binding. Taken together, this work provides the first understanding of the multiple ways through which stability, structure and function of Rb’s pocket domain is altered by a large number of missense mutations seen in cancer.
Unsaturated lipids as key control points for caveola formation and disassembly
Authors: Wu Yeping , Lim Ye-Wheen , McMahon Kerrie-Ann , Martel Nick , Rae James , Lo Harriet P. , Gao Ya , Tillu Vikas , Larsson Elin , Lundmark Richard , Levic Daniel S. , Bagnat Michel , Lim Junxian , Fairlie David P. , Pol Albert , Collins Brett M. , Ariotti Nicholas , Hall Thomas E. , Parton Robert G.
Published: September 2024

Caveolae are specialized plasma membrane domains with a unique lipid composition. Recent work has implicated lipid peroxidation in triggering caveola disassembly, releasing caveolar proteins to regulate the cellular response to oxidative stress. Here we investigated the role of specific lipid species in caveola formation and response to oxidative stress. Systematic screening of lipid enzymes identified ACSL4, a critical enzyme in the synthesis of polyunsaturated fatty acid-containing lipids, and enzymes involved in the biosynthesis of pro-ferroptotic ether lipids, as key regulators of caveola formation. Omega-6 fatty acids promoted efficient caveola formation, while their oxidation or displacement by omega-3 or monounsaturated fatty acids disrupted this process. Moreover, we found that omega-6 fatty acid-containing membrane lipids were required for oxidative stress-induced caveola disassembly. These findings unveil a new model for caveola formation, highlighting specific unsaturated lipids as essential caveolar components and key control points for caveola disassembly in response to an oxidizing environment.
The accessory domains of Phospholipase D regulate its localization and activity inDrosophilaphotoreceptors
Authors: Naik Amruta , Raghu Padinjat
Published: September 2024

Phospholipase D (PLD) is activated during the response of animal cells to a large number of extracellular signals including growth factors, hormones and other extracellular stimuli. The product of PLD activity, phosphatidic acid (PA) is thought to act as a signalling molecule in cells. Since both the substrate, phosphatidylcholine and product phosphatidic acid (PA) are membrane anchored lipids, the precise localization and activation of PLD at specific locations in cells is critical. Here we report that that the precise localization ofDrosophilaPLD (dPLD) in photoreceptors is critical to maintain the structure of these cells during illumination. This localization of dPLD is dependent on its N-terminal PH domain; deletion of the PH domain (dPLDΔPH) results in mis localization of the protein, loss of functional activity anddPLDΔPHis unable to rescue the phenotypes ofdPLDloss of function. By contrast, deletion of the PX domain (dPLDΔPX) does not impact the localization of dPLD but enhances the functional activity of the protein. Thus the PH and PX domains of dPLD regulate its localization and activity respectively.
Whole-brain dynamics and hormonal shifts throughout women’s lifespan: From reproductive stages to menopausal transition and beyond
Authors: Escrichs Anira , Avila-Varela Daniela , Patow Gustavo , Pletzer Belinda , Ritter Petra
Published: September 2024

Neuroimaging studies have identified significant age-related disruptions in whole-brain dynamics, yet the influence of women’s reproductive stages and associated hormonal shifts remains underexplored. This study leverages resting-state fMRI data from the Human Connectome Project in Aging to examine brain dynamics through five reproductive stages: reproductive, late reproductive, perimenopause, early postmenopause, and late postmenopause. Our results indicate that the late reproductive stage is characterized by the highest dynamical complexity across whole-brain and resting-state networks, while brain dynamics significantly decline at menopause onset. Additionally, we employ machine learning classifiers using two approaches: (1) brain dynamics alone and (2) brain dynamics combined with follicle-stimulating hormone (FSH) and estradiol (brain-hormone model). Both models accurately distinguished reproductive stages, but the brain-hormone model outperformed the brain dynamics model. Key predictors included decreased estradiol, increased FSH, and altered brain dynamics in later life stages. These results offer a framework for assessing brain health across women’s reproductive lifespan.
Mouse PAW: reverse-translating the FINGER multimodal lifestyle intervention enhances synaptic plasticity and cognition in adult wild type female mice
Authors: Alanko Vilma , Eroli Francesca , Végvári Ákos , Solomon Alina , Hartmann Tobias , Nilsson Per , Kivipelto Miia , Maioli Silvia , Matton Anna
Published: September 2024

Background

Targeting multiple risk factors through preventive interventions can halt the onset or progression of dementia. The clinical efficacy of this approach was shown in the multimodal FINGER trial, yet knowledge of the underlying biological mechanisms is limited. In the current study, we applied for the first time a multimodal lifestyle intervention in mice to study effects on cognition and associated molecular pathways.

Methods

We have established a novel experimental model, the lifestyle intervention PAW (Prevention ofAlzheimer’s by a Multimodal Lifestyle Protocol –Working-mechanisms for Memory Gains) in mice. In this model, we combined different modalities of intervention aiming to achieve synergistic effects. The animals were given access to running wheels (voluntary exercise), Fortasyn Connect (a medical food that slows disease progression in early Alzheimer’s disease), and they were subjected to cognitive training in an IntelliCage environment (PAW group). To separately investigate the effects of pharmacological vascular management as a preventive measure, another group of mice was given Atorvastatin and Enalapril (cholesterol and blood pressure lowering pharmaceuticals, respectively) dosed in the diet (Pharma group). Control mice were housed in normal conditions. We included 12 wild type C57BL/6J female mice 6.5 months of age per group. The full intervention lasted for 8 weeks. Blood pressure was measured at baseline and the end of the intervention. All mice underwent a battery of behavioural testing after the eight weeks of intervention. Hippocampi were dissected for proteomics analysis.

Results

During the intervention, the PAW group actively participated in the intervention by learning the different cognitive training programs and by using the running wheels. At the end of the intervention, the PAW group showed a lowering of blood pressure to a similar extent as in the Pharma group (systolic 158 mmHg to 139 mmHg,p= 0.003, and 163 mmHg to 136 mmHg,p= 0.042, respectively). Furthermore, the PAW group displayed a better short-term spatial working memory compared to the control group as assessed by the spontaneous alternation in the Y maze test (66.5% and 56.7%, respectively,p= 0.036). Proteomic analysis of the hippocampi and downstream bioinformatic analysis revealed that several pathways were upregulated in the PAW mice including synaptogenesis (Z = 4.27,p= 1.26E–18) and glutamate binding, activation of AMPA receptors and synaptic plasticity (Z = 3.74,p= 3.16E–19).

Conclusions

Our findings suggest that the PAW model effectively mimics the clinical effects of multimodal lifestyle dementia prevention, and further demonstrates the activation of hippocampal-specific molecular drivers of memory gains.
Suppression of TGF-β/SMAD signaling by an inner nuclear membrane phosphatase complex
Authors: Ji Zhe , Siu Wingyan Skyla , Duenas Maria Emilia , Trost Matthias , Carvalho Pedro
Published: September 2024

Cytokines of the TGF-β superfamily control essential cell fate decisions via receptor regulated SMAD (R-SMAD) transcription factors. Ligand-induced R-SMAD phosphorylation in the cytosol triggers their activation and nuclear accumulation. We determined how R-SMADs are inactivated by dephosphorylation in the cell nucleus to counteract signaling by TGF-β superfamily ligands. We showed that R-SMAD dephosphorylation is mediated by an inner nuclear membrane associated complex containing the scaffold protein MAN1 and the CTDNEP1-NEP1R1 phosphatase. Structural prediction, domain mapping and mutagenesis revealed that MAN1 binds independently to the CTDNEP1-NEP1R1 phosphatase and R-SMADs to promote their inactivation by dephosphorylation. Disruption of this complex led to nuclear accumulation of R-SMADs and aberrant signaling, even in the absence of TGF-β ligands. These findings establish CTDNEP1-NEP1R1 as the elusive R-SMAD phosphatase and reveal the mechanistic basis for TGF-β signaling inactivation and how this process is disrupted by disease-associated MAN1 mutations.
Energetic requirements and mechanistic plasticity in Msp1-mediated substrate extraction from lipid bilayers
Authors: Smith Baylee , Gaur Deepika , Walker Nathan , Walter Isabella , Wohlever Matthew L.
Published: September 2024

AAA+ proteins are essential molecular motors involved in numerous cellular processes, yet their mechanism of action in extracting membrane proteins from lipid bilayers remains poorly understood. One roadblock for mechanistic studies is the inability to generate subunit specific mutations within these hexameric proteins. Using the mitochondrial AAA+ protein Msp1 as a model, we created covalently linked dimers with varying combinations of wild type and catalytically inactive E193Q mutations. The wide range of ATPase rates in these constructs allows us to probe how Msp1 uses the energy from ATP hydrolysis to perform the thermodynamically unfavorable task of removing a transmembrane helix (TMH) from a lipid bilayer. Ourin vitroandin vivoassays reveal a non-linear relationship between ATP hydrolysis and membrane protein extraction, suggesting a minimum ATP hydrolysis rate is required for effective TMH extraction. While structural data often supports a sequential clockwise/2-residue step (SC/2R) mechanism for ATP hydrolysis, our biochemical evidence suggests mechanistic plasticity in how Msp1 coordinates ATP hydrolysis between subunits, potentially allowing for robustness in processing challenging substrates. This study enhances our understanding of how Msp1 coordinates ATP hydrolysis to drive mechanical work and provides foundational insights about the minimum energetic requirements for TMH extraction and the coordination of ATP hydrolysis in AAA+ proteins.
Bnip3lb-driven mitophagy sustains expansion of the embryonic hematopoietic stem cell pool
Authors: Meader Eleanor , Walcheck Morgan T. , Leder Mindy R. , Jing Ran , Wrighton Paul J. , Sugden Wade W. , Najia Mohamad A. , Oderberg Isaac M. , Taylor Vivian M. , LeBlanc Zachary C. , Quenzer Eleanor D. , Lim Sung-Eun , Daley George Q. , Goessling Wolfram , North Trista E.
Published: September 2024

Embryonic hematopoietic stem and progenitor cells (HSPCs) have the unique ability to undergo rapid proliferation while maintaining multipotency, a clinically-valuable quality which currently cannot be replicated in vitro. Here, we show that embryonic HSPCs achieve this state by precise spatio-temporal regulation of reactive oxygen species (ROS) via Bnip3lb-associated developmentally-programmed mitophagy, a distinct autophagic regulatory mechanism from that of adult HSPCs. While ROS drives HSPC specification in the dorsal aorta, scRNAseq and live-imaging ofTg(ubi:mitoQC)zebrafish indicate that mitophagy initiates as HSPCs undergo endothelial-to-hematopoietic transition and colonize the caudal hematopoietic tissue (CHT). Knockdown ofbnip3lbreduced mitophagy and HSPC numbers in the CHT by promoting myeloid-biased differentiation and apoptosis, which was rescued by anti-oxidant exposure. Conversely, induction of mitophagy enhanced both embryonic HSPC and lymphoid progenitor numbers. Significantly, mitophagy activation improved ex vivo functional capacity of hematopoietic progenitors derived from human-induced pluripotent stem cells (hiPSCs), enhancing serial-replating hematopoietic colony forming potential.

HIGHLIGHTS

ROS promotes HSPC formation in the dorsal aorta but negatively affects maintenance thereafter.

HSPCs colonizing secondary niches control ROS levels via Bnip3lb-directed mitophagy.

Mitophagy protects nascent HSPCs from ROS-associated apoptosis and maintains multipotency.

Induction of mitophagy enhances long-term hematopoietic potential of iPSC-derived HSPCs.
Optimizing measurement tradeoffs in multiparameter spatial superresolution
Authors: Hervas J. R. , Sánchez-Soto L. L. , Goldberg A. Z. , Hradil Z. , Řeháček J.
Published: September 2024

The quantum Cramér-Rao bound for the joint estimation of the centroid and the separation between two incoherent point sources cannot be saturated. As such, the optimal measurements for extracting maximal information about both at the same time are not known. In this paper, we ascertain these optimal measurements for an arbitrary point spread function, in the most relevant regime of a small separation between the sources. Our measurement can be adjusted within a set of tradeoffs, allowing more information to be extracted from the separation or the centroid while ensuring that the total information is the maximum possible.

Published by the American Physical Society
2024
Polytypism of incommensurately modulated structures of crystalline bromine upon molecular dissociation under high pressure
Authors: Yin Yuqing , Aslandukov Andrey , Bykov Maxim , Laniel Dominique , Aslandukova Alena , Pakhomova Anna , Fedotenko Timofey , Zhou Wenju , Akbar Fariia Iasmin , Hanfland Michael , Glazyrin Konstantin , Giacobbe Carlotta , Bright Eleanor Lawrence , Garbarino Gaston , Jia Zhitai , Dubrovinskaia Natalia , Dubrovinsky Leonid
Published: September 2024

Polytypism of incommensurately modulated structures was hitherto unobserved. Here, it was found in solid bromine and iodine upon molecular dissociation under pressure up to 112 GPa. Single-crystal synchrotron x-ray diffraction in laser-heated diamond anvil cells revealed a number of allotropes of bromine and iodine, including polytypes of Br-IIIγ (Fmmm(00γ)s00) with γ varying within 0.18 to 0.3, coexisting at a given pressure. This finding opens a research area in the field of solid-solid phase transitions, disordered states of solid matter, and high-pressure structural studies.

Published by the American Physical Society
2024
Charge distributions of pseudoscalar and vector mesons from Dyson-Schwinger equations
Authors: Xu Y.-Z. , Raya K. , Rodríguez-Quintero J. , Segovia J.
Published: September 2024

We combine the Dyson-Schwinger/Bethe-Salpeter equations framework with modern numerical reconstruction methods to derive the three-dimensional and transverse two-dimensional charge distribution of an array of ground-state pseudoscalar and vector mesons from their elastic electromagnetic form factor in the low-momentum region. The charge radii obtained by averaging over the reconstructed charge distributions have been checked to be consistent with those calculated from the slope of the elastic electromagnetic form factor at zero transferred momentum. The capability of the reconstruction procedure for capturing a reliable low-distance charge distribution is discussed and argued to work down to distances of around 0.1 fm, such that it might be potentially applied to extract, e.g., mass densities from gravitational form factors.

Published by the American Physical Society
2024