bluuebunny/crossref_metadata_2025 huggingface dataset:
State-level structural racism and incident coronary heart disease
Authors: Safford Monika M. , Brown Tyson , Bryan Joanna , Brown Todd M. , Pinheiro Laura
Published: November 2024

Introduction

Black Americans have greater coronary heart disease (CHD) burden than White Americans, disparities that are largely socially determined. Discriminatory societal practices that systematically disadvantage Black Americans are forms of structural racism but few studies have examined structural racism and incident CHD. We sought to determine associations between three validated measures of structural racism and incident CHD, hypothesizing that greater state-level structural racism is associated with incident CHD for Black but not White individuals.

Methods

We used data from the national REasons for Geographic And Racial Differences in Stroke (REGARDS) cohort, which enrolled 30,239 Black and White community dwelling adults between 2003-7 who were contacted every 6 months with retrieval of medical records and expert adjudication of myocardial infarction and cause of death. Incident CHD was defined as myocardial infarction or death due to CHD. Structural racism variables included Black:White % living below the Federal poverty line, Black:White % uninsured, and the Dissimilarity Index (DI), a measure of residential racial segregation. Structural racism variables were dichotomized at the median. Separate race-stratified Cox proportional hazards models examined associations between each measure of structural racism and incident CHD.

Results

The 24,099 participants free of CHD at baseline included 10,286 Black and 13,813 White participants. Mean age at baseline was 64 years, 58% were women, and 47% had annual household income <$35,000. Greater structural racism was significantly associated with incident CHD for Black but not White participants. For high Black:White poverty, Black HR=1.17 (95% CI 1.01-1.35), White HR=0.93 (0.83-1.06); for high Black:White uninsurance, Black=HR 1.34 (1.06-1.70), White HR=1.20 (0.98-1.47); for high DI, Black HR=1.17 (1.01-1.35), White HR=0.99 (0.88-1.12). Findings suggest that structural racism variables indirectly influence CHD via individual-level income and education. Results were similar for men and women and for older and younger individuals. Significant associations were observed for fatal but not nonfatal CHD events.

Conclusions

Structural racism was associated with higher incidence of CHD for Black but not White individuals. If these associations are causal, changing state level laws to combat poverty in Black communities, expand Medicaid, and reduce segregation could potentially lessen Black:White disparities in CHD.
Impact of brain frailty on complications and outcomes in acute ischemic stroke
Authors: Cheng XiaoQing , Cai Wu , Li ChuYan , Shen Xi , Li JiaNan , Huang LiJun , Tang JinJing , Pang HuiMin , Luo BaiYan , Liu Ya , QianChen  , Xiao Lulu , Zhu WuSheng , Cao ZeHong , Liu XiaoYu , Zhang LongJiang , Yin XinDao , Zhang ZhiQiang , Shi Feng , Xing Wei , Lu GuangMing
Published: November 2024

BACKGROUND

This study aimed to determine the association of brain frailty with acute complications and prognosis in patients with acute ischemic stroke (AIS) due to occlusion of large vessels in the anterior circulation, and to further assess its predictive value.

METHODS AND RESULTS

This multicenter, retrospective study included patients with AIS due to large vessel occlusion in the anterior circulation. All patients underwent MRI within seven days of stroke onset, measuring subcortical and cortical atrophy and leukoaraiosis as indicators of brain frailty.The study included 1,090 patients with a median age of 64 (interquartile range, 55–73) years and a median National Institutes of Health Stroke Scale (NIHSS) score of 9 (interquartile range, 4.5–15). Multivariable logistic regression analysis showed that independent risk factors for the unfavorable clinical outcome included: NIHSS score (OR, 1.17; 95% CI, 1.13–1.22), blood glucose (OR, 1.15; 95% CI, 1.04–1.26), infarct volume (OR, 1.32; 95% CI, 1.15–1.52), subcortical atrophy (OR, 1.27; 95% CI, 1.18–1.37), severe cortical atrophy (OR, 5.46; 95% CI, 1.71–17.45), and severe leukoaraiosis (OR, 4.68; 95% CI, 1.93–11.31). However, brain frailty was not significantly associated with AIS complications (malignant cerebral edema, parenchymal hemorrhage). Including brain atrophy indicators in the model significantly improved its unfavorable clinical outcome predictive power (AUC increased from 0.762 to 0.822;p< 0.001). The results remained stable in subgroup analyses across treatment modalities.

CONCLUSIONS

Brain frailty was significantly associated with the unfavorable clinical outcome but not with acute complications. Brain frailty indicators contributed to the predictive efficacy, regardless of treatment modality.
Metabolic Polygenic Risk Scores for Prediction of Obesity, Type 2 Diabetes, and Related Morbidities
Authors: Kim Min Seo , Chen Qiuli , Sui Yang , Yang Xiong , Wang Shaoqi , Weng Lu-Chen , Cho So Mi Jemma , Koyama Satoshi , Zhu Xinyu , Yu Kang , Chen Xingyu , Zhang Rufan , Yin Wanqing , Liao Shuangqiao , Liu Zhaoqi , Alkuraya Fowzan S , Natarajan Pradeep , Ellinor Patrick T. , Fahed Akl C. , Wang Minxian
Published: November 2024

Obesity and type 2 diabetes (T2D) are metabolic diseases with shared pathophysiology. Traditional polygenic risk scores (PRS) have focused on these conditions individually, yet the single disease approach falls short in capturing the full dimension of metabolic dysfunction. We derived biologically enriched metabolic PRS (MetPRS), a composite score that uses multi-ancestry genome-wide association studies of 22 metabolic traits from over 10 million people. MetPRS, optimized to predict obesity (O-MetPRS) and T2D (D-MetPRS), was validated in the UK Biobank (UKB, n=15,000), and tested in UKB hold-out set (n=49,377), then externally tested in 3 cohorts – All of Us (n=245,394), Mass General Brigham (MGB) Biobank (n=53,306), and a King Faisal Specialist Hospital and Research Center cohort (n=6,416). O-MetPRS and D-MetPRS outperformed existing PRSs in predicting obesity and T2D across 6 ancestries (European, African, East Asian, South Asian, Latino/admixed American, and Middle Eastern). O-MetPRS and D-MetPRS also predicted morbidities and downstream complications of obesity and T2D, as well as the use of GLP-1 receptor agonists in contemporary practice. Among 37,329 MGB participants free of T2D and obesity at baseline, those in the top decile of O-MetPRS had a 103% relatively higher chance, and those in the top decile of D-MetPRS had an 80% relatively higher chance of receiving a GLP-1 receptor agonist prescription compared to individuals at the population median of MetPRS. The biologically enriched MetPRS is poised to have an impact across all layers of clinical utility, from predicting morbidities to informing management decisions.
JG2: an updated version of the Japanese population-specific reference genome
Authors: Sriwichaiin Sirawit , Makino Satoshi , Funayama Takamitsu , Otsuki Akihito , Kawashima Junko , Okamura Yasunobu , Tadaka Shu ,   the Tohoku Medical Megabank Project Study Group, Katsuoka Fumiki , Kumada Kazuki , Tsutsumi Shuichi , Kinoshita Kengo , Yamamoto Masayuki , Tamiya Gen , Takayama Jun
Published: November 2024

This study presents the construction of JG2, an updated population-specific reference genome for the Japanese population. Utilizing data from three individuals previously employed in the construction of JG1, several methodologies were employed to enhance genomic coverage and assembly quality. Hi-C sequencing technology facilitated phase-aware assembly, generating two haploid assemblies per individual and enabling improved representation of genetic variation. A meta-assembly strategy and a majority decision approach further refined assembly quality by combining the best sequences from multiple assemblies and minimizing the inclusion of rare variants. The resulting JG2 genome comprises chromosome-level sequences, mitochondrial chromosomes, and unplaced scaffolds, offering more comprehensive coverage of the Japanese genome. Comparative analyses with other reference genomes demonstrated the accuracy and representativeness of JG2, highlighting its utility for genetic research involving the Japanese population. Overall, by adopting the phased assembly technique, JG2 represents a significant advancement over the collapsed assembly-based JG1, providing researchers with a more precise and comprehensive resource for understanding the genetic landscape of the Japanese population. The sequences and annotations are available on the jMorp website (https://jmorp.megabank.tohoku.ac.jp/).
The nitrite reductase activity of xanthine oxidoreductase sustains cardiovascular health
Authors: Dyson Nicki , Khambata Rayomand S. , Parakaw Tipparat , Massimo Gianmichele , Khuat Ngan HH. , Noor Annika A. , Gee Lorna C. , Lim Ivy , Siddique Umme , Sullivan Andrew J. , Ho Jonathan W. , Rathod Krishnaraj , Barnes Michael R. , Cabrera Claudia P. , Ahluwalia Amrita
Published: November 2024

Background

Xanthine oxidoreductase (XOR) is a multi-functional enzyme that metabolises purines generating uric acid and is a generator of reactive oxygen species. Both functions have been implicated in the pathogenesis of cardiovascular disease. More recently, a third function of XOR as a nitrite reductase has been identified and been shown to play a key role in the benefits of targeting the non-canonical pathway for nitric oxide (NO) generation in the cardiovascular disease setting. This effect has been specifically attributed to XOR dependent recovery of NO levels. However, whether XOR derived NO plays any role in maintaining cardiovascular homeostasis in health is unknown. To explore this, we used global and hepatocyte-specificXdh-deleted mice to assess cardiovascular homeostasis.

Methods

Xdh+/+andXdh+/-,Xdhfl/fland Xdhfl/flAlbCre+/-(HXOR KO) mice littermates, matched for sex and age, were used for in vivo cardiovascular phenotyping; blood pressure, cardiac function, endothelial reactivity, and leukocyte trafficking. Tissues from these mice were used for biochemical measurements of nitrate, nitrite, and markers of NO downstream signalling.

Results

Xdh+/-and HXOR KO mice expressed significantly attenuated liver and plasma nitrite reductase activity and platelet cGMP levels versus littermate controls. These effects were associated with increased systolic blood pressure, left ventricular remodelling, and increased leukocyte activation. These effects were associated with and likely driven by endothelial dysfunction evident in both mouse models. This dysfunction was reflected by increased endothelial adhesion molecule expression (P-selectin), increased ischaemia-induced vasoconstriction, during vessel occlusion, and an impaired flow-mediated dilation response of the iliac artery in vivo.

Conclusions

In summary, XOR derived NO is critical for maintaining vascular homeostasis under physiological conditions and is key in mediating the benefits of dietary nitrate regimes in cardiovascular pathology
The proteomic landscape of proteotoxic stress in a fibrogenic liver disease
Authors: Rosenberger Florian A. , Mädler Sophia C. , Holtz Thorhauge Katrine , Steigerwald Sophia , Fromme Malin , Lebedev Mikhail , Weiss Caroline A. M. , Oeller Marc , Wahle Maria , Zwiebel Maximilian , Schmacke Niklas A. , Detlefsen Sönke , Boor Peter , Kaserman Joseph , Wilson Andrew , Fabián Ondřej , Fraňková Soňa , Krag Aleksander A. , Strnad Pavel , Mann Matthias
Published: November 2024

Protein misfolding diseases, including alpha-1 antitrypsin deficiency (AATD), pose significant health challenges, with their cellular progression still poorly understood1–3. We utilize spatial proteomics by mass spectrometry and machine learning to map AATD in human liver tissue. Combining Deep Visual Proteomics (DVP) with single-cell analysis4,5, we probe intact patient biopsies to resolve molecular events during hepatocyte stress in pseudo-time across fibrosis stages. We achieve unprecedented proteome depth of up to 3,800 proteins from a third of a single cell in formalin-fixed, paraffin-embedded (FFPE) tissue. This dataset revealed a potentially clinically actionable peroxisomal upregulation that precedes the canonical unfolded protein response. Our single-cell proteomics data show alpha-1 antitrypsin accumulation is largely cell-intrinsic, with minimal stress propagation between hepatocytes. We integrated proteomic data with AI-guided image-based phenotyping across multiple disease stages, revealing a terminal hepatocyte state characterized by globular protein aggregates and distinct proteomic signatures, notably including elevated TNFSF10/TRAIL expression. This phenotype may represent a critical disease progression stage. Our study offers novel insights into AATD pathogenesis and introduces a powerful methodology for high-resolution, in situ proteomic analysis of complex tissues. This approach holds potential to unravel molecular mechanisms in various protein misfolding disorders, setting a new standard for understanding disease progression at the single-cell level in human tissue.
HIRA-SETDB1-H3K9me3 axis regulate chromatin architecture in chronic myeloid leukemia cells
Authors: Shirude Mayur Balkrishna , Devarajan Anjali , Dutta Debasree
Published: November 2024

Histone cell cycle regulator A (HIRA) confers chromatin accessibility and regulates developmental hematopoiesis. But whether HIRA displays similar role in leukemia, a condition caused by abnormalities during hematopoiesis, remain elusive. Here we show that HIRA interact with heterochromatin cluster in Chronic Myeloid Leukemia, K562, cells. FRAP, FLIM-FRET and ATAC-sequencing analysis revealed increased chromatin compaction, altered spatial distribution of chromatin towards nuclear periphery and loss in chromatin accessibility at the promoter and gene bodies upon downregulation of HIRA in K562 cells. Enhanced chromatin compaction was attributed to increased histone H3K9me3 level mediated by histone methyltransferase SETDB1. Incorporation of histone H3.3 within theSETDB1promoter inHIRA-knockdown cells induced SETDB1 expression. HIRA-SETDB1-H3K9me3 axis regulate the chromatin architecture in CML cells leading to inhibition of proliferation while induction in differentiation. We anticipate that the exploration of this axis would introduce new paradigm in understanding and targeting molecules that could influence CML disease progression.
TET2-mediated epigenetic modification promotes stress senescence of pancreatic β cells in type 2 diabetes mellitus
Authors: Cai Weijuan , Song Qingqing , Mo Xiaoqing , Li Huaqian , Song Yuling , Yin Liang
Published: November 2024

Epigenetic modification plays a key role in β cell senescence. In the regulation of gene expression, there is a complex and close relationship between DNA methylation and histone modification. In order to explore its specific mechanism in T2DM β cell senescence, we used postbisulfite aptamer labeling of genome-wide bisulfite-SEQ, chromatin immunocoprecipitation-SEQ, RNA-SEQ, CRISPR/Cas9 TETs knockout, RNA interference, TET2 inhibitors, lentiviral overexpression, and gene knockout mouse models. Our study found that demethylase TET2 was localized in the islets of mice, and the expression level increased with age. TET2 knockout in pancreatic β cells can hypermethylate PTEN, up-regulate MOF and enrich H4K16ac, and reduce the level of aging markers. This study confirmed that TET2-mediated PTEN DNA methylation can promote a new mechanism of β cell senescence by regulating H4K16ac, providing a new molecular mechanism and therapeutic target for T2DM β cell senescence therapy.
Mitochondrial efficiency determines Crabtree effect across yeasts
Authors: Battjes Julius , Grigaitis Pranas , Hoving Milou , Visser Thomas D. , Stampfl Karina , Miguel Gabriela A. , van Heerden Johan , Andersen Jesper K. , Bruggeman Frank J. , Teusink Bas
Published: November 2024

Under excess glucose conditions, many yeasts switch from high-yield respiratory metabolism to low-yield fermentation, a phenomenon called the Crabtree effect in yeast, or the Warburg effect in mammalian cells. Cellular constraints and limited resources are generally believed to govern the metabolic strategies of cells to adapt to environmental conditions, but which constraints drive this switch is still under debate. Here we study the Crabtree-negative, fully respiratory yeastPichia kluyveriand compare it to the Crabtree-positive yeastSaccharomyces cerevisiaefrom a resource allocation perspective. By integrating quantitative physiology and proteomics into whole-cell proteome-constrained models, we find that the Crabtree effect is determined by the composition and catalytic efficiency of the electron transport chain. We find that the subsequent proteome efficiency of respiration versus fermentation varies between these species. The variation in parameters and composition of the respiratory machinery likely reflects the evolutionary and ecological history of these yeast species. This study advances our understanding of the role of proteome constraints and proteome efficiency in governing cellular metabolism of yeasts, and that of eukaryotic cells at large.
Transcriptional changes across tissue and time provide molecular insights into a therapeutic window of opportunity following traumatic stress exposure
Authors: McKibben Lauren A , Iyer Meghna R , Zhao Ying , Florea Roxana , Kuhl-Chimera Sophia , Deliwala Ishani H , Pan Yue , Branham Erica M , Geranton Sandrine M , McLean Samuel A , Linnstaedt Sarah D
Published: November 2024

Unfortunately, survivors of traumatic stress exposure (TSE) frequently develop adverse posttraumatic neuropsychiatric sequelae (APNS) such as chronic pain and stress/depressive symptoms. Increasing evidence indicates that there is a 'window of opportunity' following TSE in which therapeutic interventions are most effective against APNS, yet mechanisms accounting for this observation are poorly understood. Here, we aimed to better understand such mechanisms by generating snapshots of the transcriptional landscape in the early aftermath of TSE across tissues and time. Adult rats were exposed to a TSE model, single prolonged stress (SPS). Then, eight tissues (hypothalamus, left and right hippocampus, amygdala, dorsal root ganglia, spinal cord, heart, and muscle) were isolated from these animals at 2, 24, and 72 hours after SPS and in unexposed controls (n=6 per group). mRNA expression from deep sequencing was used to identify differentially expressed genes (DEGs) and biological pathways enriched over time. In all tissues except the amygdala, the highest number of DEGs was observed 2-hours post-SPS, but DEGs were detected at all timepoints and in all tissues. Some transcripts were differentially expressed in a consistent manner across multiple tissues at a time point (e.g. Fkbp5, 2 hours post-SPS), while others had tissue- or region-specific expression patterns. Stress system pathways were most represented at 2-hours post-SPS, then stress/circadian/inflammatory pathways at 24-hours, and inflammatory pathways at 72-hours. Together these findings provide insights into post-TSE transcriptional landscape dynamics and suggest specific intervention windows of opportunity. Future validation is needed across sex, age, stressor, and cell type.
AInsectID Version 1.1: an Insect Species Identification Software Based on the Transfer Learning of Deep Convolutional Neural Networks
Authors: Sadia Haleema , Alam Parvez
Published: November 2024

AInsectID Version 1.11, is a GUI operable open-source insect species identification, color processing2and image analysis software. The software has a current database of 150 insects and integrates Artificial Intelligence (AI) approaches to streamline the process of species identification, with a focus on addressing the prediction challenges posed by insect mimics. This paper presents the methods of algorithmic development, coupled to rigorous machine training used to enable high levels of validation accuracy. Our work integrates the transfer learning of prominent convolutional neural network (CNN) architectures, including VGG16, GoogLeNet, InceptionV3, MobileNetV2, ResNet50, and ResNet101. Here, we employ both fine tuning and hyperparameter optimization approaches to improve prediction performance. After extensive computational experimentation, ResNet101 is evidenced as being the most effective CNN model, achieving a validation accuracy of 99.65%. The dataset utilized for training AInsectID is sourced from the National Museum of Scotland (NMS), the Natural History Museum (NHM) London and open source insect species datasets from Zenodo (CERN’s Data Center), ensuring a diverse and comprehensive collection of insect species.
Amphiphile-engineered DNA adjuvants stimulate strong type I IFN production in lymph nodes via cytosolic danger-sensing to induce potent cellular and humoral immunity in mice and non-human primates
Authors: Steinbuck Martin P. , Seenappa Lochana M. , Zhan Wei , Palmer Erica , Jakubowski Aniela , Cabana-Puig Xavier , Jung Mimi M. , McNeil Lisa K. , Haqq Christopher M. , Fitzgerald Katherine A. , DeMuth Peter C.
Published: November 2024

Adjuvants are immuno-activators capable of shaping the magnitude and quality of antigen-specific immune responses induced by subunit immunization. Presently, there is an acute need for effective adjuvants that safely induce durable and balanced humoral and cellular responses; the latter being indispensable for protection against intracellular pathogens and cancer. Here, we iteratively optimized a novel class of Amphiphile (AMP)-modified, immunostimulatory DNA-adjuvants designed for targeted delivery to lymph nodes and enhanced stimulation of cytosolic danger-sensing pathways to generate strong adaptive immunity. AMP-DNA adjuvants induced potent IFN-I-driven inflammatory environments in mouse and NHP lymph nodes that were dependent on TBK1 signaling, leading to significantly enhanced cytokine secretion by polyfunctional CD8+and CD4+T cells in multiple tissues, and strongly elevated TH1-associated and neutralizing antibody responses, without toxicity. These results demonstrate that AMP-engineering enables lymph node-targeted DNA-adjuvants to uniquely activate cytosolic immune-signaling to generate robust adaptive responses crucial for vaccine efficacy.
Holostean genomes reveal evolutionary novelty in the vertebrate immunoproteasome that have implications for MHCI function
Authors: Barker Andi V. , Carlson Kara B. , Wcisel Dustin J. , De Allende Ian Birchler , Braasch Ingo , Fisk Michael , Dornburg Alex , Yoder Jeffrey A.
Published: November 2024

Holosteans (gars and bowfins) have emerged as valuable models for understanding early vertebrate evolution, offering insights into diverse topics ranging from genomic architecture to molecular processes. These lineages also exhibit unusual features in their immune response, combining molecular elements seen in both tetrapods and ray-finned fishes. However, the immune repertoire of holosteans remains relatively unexplored. Here, we investigate the evolution of PSMB8, a core component of the immunoproteasome responsible for cleaving intracellular proteins into peptides for presentation by MHC class I molecules. We identify two holostean PSMB8 types—S type and K type—that are unique among vertebrates. These types likely cause significant biochemical changes to the S1 binding pocket involved in antigen cleavage which could result in the presentation of novel peptides by MHC class I. Integrating comparative analyses across major ray-finned fish lineages demonstrates that bowfins and gars independently evolved the PSMB8 S type within separate PSMB8 paralog lineages, while the PSMB8-K type is an evolutionary novelty found only in gars. Our results provide new perspectives into PSMB8 haplotypes and their role in peptide antigen processing, offering unique insights into the molecular evolution of the vertebrate immunity and antigen presentation.
Androgen receptor interactions provide insight into steroid mediated metabolic shifts in endocrine resistant breast cancer
Authors: Bleach Rachel , Bozkurt Emir , Sheehan Katherine , Shirran Sally , Xin Jingqi , Agbana Stephanie , Ola Mihaela , Young Leonie , O’Reilly Michael W , Prehn Jochen HM , McIlroy Marie
Published: November 2024

Purpose

Aromatase Inhibitors (AI) are standard therapy for hormone receptor positive breast cancers in post-menopausal patients. Disease recurrence is common and previous studies suggest that the altered steroid environment may be a driver of resistance. Using label-free mass-spectrometry we explored the unique androgen receptor (AR) interactome that supervenes in AI resistant breast cancer and the associated hyperandrogenic environment.

Experimental Design

AR expression was evaluated in a primary breast cancer tissue-microarray (n=875) with nuclear and cytoplasmic localization quantified. Liquid-chromatography tandem mass-spectrometry (LC-MS/MS) analysis was utilized to identify proteins interacting with the AR in models of AI-resistance. Validation was carried out by co-immunoprecipitation and co-localisation studies. Live-cell imaging, Seahorse MitoStress Assays and flow cytometry were used to quantify changes in mitochondria and cell metabolism arising in models of AI-resistance.

Results

Utilising digital pathology we detected that abundant cytoplasmic AR protein was associated with poor survival only in the post-menopausal cohort, and most significantly, in the therapy-refractory Luminal B subtype (p=0.0085). Models of AI-resistance and androgen excess highlight diffuse AR localisation throughout the cytoplasm and nucleus accompanied by increased mitochondrial mass and membrane potential, and increased oxidative phosphorylation and glycolysis. Exploration of the AR protein interactome identified G3BP1, SLIRP, and IGFBP5 as AR protein partners which are associated with stress, adaptive metabolic response and estrogen receptor repression.

Conclusions

The findings of this study highlight the prognostic potential of cytoplasmic AR immunoreactivity in specific breast cancer subtypes and uncover novel extra-nuclear AR protein interactions that may mediate metabolic adaptations during the development of endocrine-resistance.
High-throughput development and characterization of new functional nanobodies for gene regulation and epigenetic control in human cells
Authors: Wan Jun , Thurm Abby R. , Allen Sage J. , Ludwig Connor H. , Patel Aayan N. , Bintu Lacramioara
Published: November 2024

Controlling gene expression and chromatin state via the recruitment of transcriptional effector proteins to specific genetic loci has advanced the potential of mammalian synthetic biology, but is still hindered by the challenge of delivering large chromatin regulators. Here, we develop a new method for generating small nanobodies against human chromatin regulators that can repress or activate gene expression. We start with a large and diverse nanobody library and perform enrichment against chromatin regulatory complexes using yeast display, followed by high-throughput pooled selection for transcriptional control when recruited to a reporter in human cells. This workflow allows us to efficiently select tens of functional nanobodies that can act as transcriptional repressors or activators in human cells.
Freedom of speech predicts animal welfare protection across the globe
Authors: Montalcini Camille M. , Crowther Thomas W.
Published: November 2024

The welfare of captive and wild animals is closely tied to human health, nutrition, and environmental wellbeing. Yet, until now, the global determinants of animal welfare remain unclear, as we lack quantitative global data on animal treatment. Here, by collapsing 13 indicators of animal welfare legislation across 50 major animal product-producing countries, we identify two key dimensions reflecting ‘animal welfare protection’ and ‘responsible consumption and production’. While high-income countries with lower dependence on agriculture may have more opportunity to focus on animal welfare, our analysis suggests that the level social freedoms of citizens can dramatically overwhelms this economic signal. We find that the ‘voice and accountability’ of citizens ultimately determines the extent of animal welfare protection, explaining 58% of the variation across the globe. Irrespective of environmental or economic conditions, structures that enhance political freedoms, civil liberties, and citizen participation in governance may provide the necessary foundation for developing legislation to promote animal welfare protection.
Control of electromechanical waves in engineered tissue of human iPSC-cardiomyocytes using a Halbach array and magnetic nanoparticles
Authors: Pozo Maria R. , Heinson Yuli W. , Chua Christianne J. , Entcheva Emilia
Published: November 2024

The Halbach array, originally developed for particle accelerators, is a compact arrangement of permanent magnets to create well-defined magnetic fields without heating. Here, we demonstrate its use for modulating the speed of electromechanical waves in cardiac syncytia of human stem cell-derived cardiomyocytes. At 40-50 mT magnetic field strength, a cylindrical dipolar Halbach array boosted the conduction velocity, CV, of excitation in a directional manner by up to 25% when the magnetic field was co-aligned with the electromechanical wave (but not when perpendicular to it). To observe the effects, a short-term incubation of the cardiac cell constructs with non-targeted magnetic nanoparticles, mNPs, was sufficient. This increased CV anisotropy, and the effects were most pronounced at slower pacing rates. Instantaneous formation and re-arrangement of elongated mNP clusters upon magnetic field rotation was seen, thus creating dynamic structural anisotropy that may have contributed to the directional CV effects. This approach may be useful for anti-arrhythmic control of cardiac waves.

One sentence summary

A Halbach array of permanent magnets can modulate the speed of excitation waves in human cardiac cell assemblies with magnetic nanoparticles.
Squirrel: Reconstructing semi-directed phylogenetic level-1 networks from four-leaved networks or sequence alignments
Authors: Holtgrefe Niels , Huber Katharina T. , van Iersel Leo , Jones Mark , Martin Samuel , Moulton Vincent
Published: November 2024

Phylogenetic networks model the evolutionary history of taxa while allowing for reticulate events such as hybridization and horizontal gene transfer. As is the case for phylogenetic trees, it is often not possible to infer the root location of such a network directly from biological data for several evolutionary models. Hence, we consider semi-directed (phylogenetic) networks: partially directed graphs without a root in which the directed edges represent reticulate evolutionary events. By specifying a known outgroup, the rooted topology can be recovered from such networks. We introduce the algorithm Squirrel(Semi-directed Quarnet-based Inference to Reconstruct Level-1 Networks) which constructs a semi-directed level-1 network from a full set of quarnets (four-leaf semi-directed networks). Our method also includes a heuristic to construct such a quarnet set directly from sequence alignments. To build a network from quarnets, Squirrelfirst builds a tree, after which it repeatedly solves the TravellingSalesmanProblem(TSP) to replace each high-degree vertex by a cycle. We demonstrate Squirrel’s performance on randomly generated networks and on real sequence data sets, the largest of which contains 29 aligned sequences close to 1.7 Mpb long. The resulting networks are obtained on a standard laptop within a few minutes. Lastly, we prove that Squirrelis combinatorially consistent: given a full set of quarnets coming from a triangle-free semi-directed level-1 network, it is guaranteed to reconstruct the original network. Squirrelis implemented in Python, has an easy-to-use graphical user-interface that takes sequence alignments or quarnets as input, and is freely available athttps://github.com/nholtgrefe/squirrel.
Effects of intergenerational transmission of small intestinal bacteria cultured from stunted Bangladeshi children with enteropathy
Authors: Pruss Kali M , Kao Clara , Byrne Alexandra E , Chen Robert Y , Di Luccia Blanda , Karvelyte Laura , Coskun Reyan , Lemieux Mackenzie , Nepal Keshav , Webber Daniel M , Hibberd Matthew Charles , Wang Yi , Rodionov Dmitry A. , Osterman Andrei , Maueroder Christian , Ravichandran Kodi , Barratt Michael , Ahmed Tahmeed , Gordon Jeffrey
Published: November 2024

Environmental enteric dysfunction (EED), a small intestinal disorder found at a high prevalence in stunted children, is associated with gut mucosal barrier disruption and decreased absorptive capacity due to reduced intact small intestinal villi. To test the hypothesis that intergenerational transmission of a perturbed small intestinal microbiota contributes to undernutrition by inducing EED, we characterized two consortia of bacterial strains cultured from duodenal aspirates from stunted Bangladeshi children with EED, one of which induced local and systemic inflammation in gnotobiotic female mice. Offspring of dams that received this inflammatory consortium exhibited immunologic changes along their gut that phenocopied features of EED in children. Single nucleus plus bulk RNA-sequencing revealed alterations in inter-cellular signaling pathways related to intestinal epithelial cell renewal, barrier integrity and immune function while analyses of cerebral cortex disclosed alterations in glial- and endothelial-neuronal signaling pathways that regulate neural growth/axonal guidance, angiogenesis and inflammation. Analysis of ultrasonic vocalization calls in gnotobiotic P5-P9 pups indicated increased arousal and perturbed neurodevelopment in the offspring of dams harboring the inflammation-inducing consortium. Cohousing experiments and follow-up screening of candidate disease-promoting bacterial isolates identified a strain typically found in the oral microbiota (Campylobacter concisus) as a contributor to enteropathy. Given that fetal growth was also impaired in the dams with the consortium that induced enteropathy, this preclinical model allows the effects of the human small intestinal microbiota on both pre- and postnatal development to be ascertained, setting the stage for identification of small intestinal microbiota-targeted therapeutics for (intergenerational) undernutrition.
The role of REM sleep in neural differentiation of memories in the hippocampus
Authors: McDevitt Elizabeth A. , Kim Ghootae , Turk-Browne Nicholas B. , Norman Kenneth A.
Published: November 2024

When faced with a familiar situation, we can use memory to make predictions about what will happen next. If such predictions turn out to be erroneous, the brain can adapt by differentiating the representations of the cues that generated the prediction from the mispredicted item itself, reducing the likelihood of future prediction errors. Prior work by Kim et al. (2017) found that violating a sequential association in a statistical learning paradigm triggered differentiation of the neural representations of the associated items in the hippocampus. Here, we used fMRI to test the preregistered hypothesis that this hippocampal differentiation occurs only when violations are followed by rapid eye movement (REM) sleep. In the morning, participants first learned that some items predict others (e.g., A predicts B) then encountered a violation in which a predicted item (B) failed to appear when expected after its associated item (A); the predicted item later appeared on its own after an unrelated item. Participants were then randomly assigned to one of three conditions: remain awake, take a nap containing non-REM sleep only, or take a nap with both non-REM and REM sleep. While the predicted results were not observed in the preregistered left CA2/3/DG ROI, we did observe evidence for our hypothesis in closely related hippocampal ROIs, uncorrected for multiple comparisons: In right CA2/3/DG, differentiation in the group with REM sleep was greater than in the groups without REM sleep (wake and non-REM nap); this differentiation was item-specific and concentrated in right DG. Differentiation effects were also greater in bilateral DG when the predicted item was more strongly reactivated during the violation. Overall, the results presented here provide initial evidence linking REM sleep to changes in the hippocampal representations of memories in humans.
Modelling DNA replication fork stability and collapse using chromatin fiber analysis and the R-ODD-BLOBS program
Authors: Cheng Kerenza , Aliar Kazeera , Manshaei Roozbeh , Mazalek Ali , Sabatinos Sarah A
Published: November 2024

We describe the anatomy of replication forks by comparing the lengths of synthesized BrdU-labelled DNA in wild-type,mrc1Δandcds1Δ Schizoasaccharomyces pombe. We correlated Rad51 and Cdc45 proteins relative to their positions on the fork, replicated tract, or unreplicated regions. We did this using chromatin spread pixel intensity data that was analyzed using our program: R-ODD-BLOBS. Graphs on the lengths of BrdU tract, and proteins, as well as the percentage of Rad51 and Cdc45 colocalization, were created by the program. These results were compared to the literature. The BrdU lengths detected matched current literature; cds1Δ was the longest at 8.6 px, wild-type was 7.5 px, and mrc1Δ was the shortest at 5.1 px. When colocalization of rad 51 around the fork was explored, we found that mrc1Δ uniquely had 22% more colocalization than wt at the unreplicated region of a fork. This suggests that HR was potentially detected at the forks of mrc1Δ. In this study, we summarize the usefulness of R-ODD-BLOBS in aiding in analyzing chromatin spread data which provides data on the lengths and protein colocalization and starts to paint a picture of the anatomy of a fork.

SIGNIFICANCE STATEMENT

- The dynamics of a replication fork are important to maintaining genome stability, however, current methods create an average bulk data that can conceal the heterogeneity of forks.

- This pipeline involving chromatin spread fiber, and data analysis using R-ODD-BLOBS establishes a single-molecule approach to a dynamic problem that can determine patterns like differences in synthesized DNA between conditions, and determine colocalization of proteins at different regions on chromatin, while systematically determining parameters

- This pipeline shows and quantifies patterns found in chromatin spread fibers, while maintaining the option to average out data or individually look at them
Insight Into the Molecular Parameters of PEI Promoting an Efficient Gene Delivery into Cells
Authors: Montaño González Paulina Alejandra , Tranchimand Sylvain , Rochedy Manon , Leroyer Patricia , Chapel Jean-Paul , Chevance Soizic , Schatz Christophe , Gauffre Fabienne , Loyer Pascal , Bravo Anaya Lourdes Mónica
Published: November 2024

The development of natural or synthetic polycations able to interact with nucleic acids and condense them into nanoparticles known as polyplexes, faces several unresolved challenges at the cellular level. Key issues include the intracellular trafficking of polyplexes, the endosomal escape and the release of nucleic acids into the cytosol, which are considered major bottlenecks for efficient protein expression. Here, we aim at gaining fundamental insights into the stability of polyplexes in biological media and their uptake and intracellular trafficking, while correlating data of the expression of reporter protein with both the molecular characteristics of various poly(ethylenimines) (PEI) and the physicochemical characteristics of PEI/peGFP-C3 polyplexes. For this, we chosen four samples of PEI, selected as a model polycation, with different molecular weights (Mw = 0.8, 20, 25 and 60 kg/mol) and structures (linear and branched). We found that thein vitroandin vivostability of PEI/peGFP-C3 polyplexes, their cell internalization and transfection efficiency is dependent on the variation of polycation Mw and structure, as well as the intrinsic properties of polyplexes, such as the charge ratio (R=[N+]/[P−]). A relation between the percentage of positive cells to green fluorescent protein (GFP) and the amount of internalized nucleic acid (cyanine 5-peGFP-C3) allowed revealing the molecular characteristics of PEI promoting both higher both cell internalization and GFP expression on HEK293T cells. In the long term, the outcome of this work will be to propose guidelines to help design more effective, and less cytotoxic non-viral gene carriers with a great potential for new therapeutic applications.
Social family structure and biogeography contribute to genomic divergence and cryptic speciation in the only eusocial beetle species,Austroplatypus incompertus(Curculionidae: Platypodinae)
Authors: Bickerstaff James R. M. , Jordal Bjarte H. , Riegler Markus
Published: November 2024

Eusociality in insects has arisen multiple times independently in Hymenoptera (bees, wasps, ants), Blattodea (termites) and Coleoptera (beetles). In Hymenoptera and Blattodea, the evolution of eusociality led to massive species proliferation. In the hyperdiverse Coleoptera, eusociality evolved only once, in the ancient Australian ambrosia beetle speciesAustroplatypus incompertus(Curculionidae: Platypodinae). This species occurs in mesic eucalypt forests of eastern Australia, from Victoria to northern New South Wales. Based on few individuals collected from the southern and northern edges of the species’ distribution it was initially described as two distinct species; however, the names were later synonymised as no morphological differences were found in analyses of more specimens. Recent mitochondrial haplotype analyses revealed substantial latitudinal divergence across the distribution ofA. incompertus. To address this apparent disparity between morphological and molecular data, we sequenced and analysed a SNP panel of over 6,656 biallelic markers from 187 individuals of 11 sites across 1000 km of this species’ range. Our data indicate that eusocial demographic processes such as low colony establishment success rate, limited dispersal and reliance on few reproductive individuals, together with substantial habitat fragmentation contributed to the population genetic structure of this species. We further identified that the Hunter Valley biogeographic barrier split the species into two distinct clades, with both clades in secondary close contact on the Barrington Tops plateau without any discernible admixture. Our results support the resurrection of a second species ofAustroplatypuswhich has important consequences for the evolution eusociality in Coleoptera and the systematics of Platypodinae.
Unraveling the Mysteries of Sleep: Exploring Phylogenomic Sleep Signals in the Recently Characterized Archaeal Phylum Lokiarchaeota near Loki’s Castle
Authors: Pandi-Perumal Seithikurippu R , Saravanan Konda Mani , Paul Sayan , Spence David Warren , Chidambaram Saravana Babu
Published: November 2024

Sleep is a universally conserved behavior with an elusive origin and an uncertain evolutionary purpose. Leveraging phylogenomics, we investigate the evolutionary foundations of sleep by identifying orthologs of Human sleep-related genes in the Lokiarchaeota of the Asgard superphylum. Our findings indicate a conserved suite of genes associated with energy metabolism and cellular repair, suggesting a primordial role of sleep in cellular maintenance. This data lends credence to the idea that sleep improves organismal fitness across evolutionary time by acting as a restorative process. Notably, our approach demonstrates that phylogenomics is more useful than standard phylogenetics for clarifying common evolutionary traits. By offering insight into the evolutionary history of sleep and putting forth a novel model framework for sleep research across taxa, these findings contribute to our growing understanding of the molecular foundation of sleep. This study lays the groundwork for further investigations into the importance of sleep in various organisms, which could have consequences for human health and a deeper comprehension related to the fundamental processes of life.

Graphical Abstract
Policy optimization emerges from noisy representation learning
Authors: Brenner Jonah W. , Li Chenguang , Kreiman Gabriel
Published: November 2024

Abstract

Nervous systems learn representations of the world and policies to act within it. We present a framework that uses reward-dependent noise to facilitate policy opti- mization in representation learning networks. These networks balance extracting normative features and task-relevant information to solve tasks. Moreover, their representation changes reproduce several experimentally observed shifts in the neural code during task learning. Our framework presents a biologically plausible mechanism for emergent policy optimization amid evidence that representation learning plays a vital role in governing neural dynamics. Code is available at: NeuralThermalOptimization.
Disease-linked mutations dysregulate neuronal condensate physical properties, composition, and RNA translation
Authors: Ahangama Liyanage Leshani , McCready Fraser , Chung Steve , Arsenault Jason , Wei Wei , Lin Xusheng , Wang Lu-Yang , Ellis James , Ditlev Jonathon A.
Published: November 2024

Local RNA translation is essential for development. In neurons, deficient local translation linked with mutations in scaffold proteins results in dysregulated dendrite and dendritic spine growth. However, mechanisms by which these proteins control translation and how disease-linked mutations induce aberrant translation were unclear. We use biochemical reconstitution and neuronal assays to show that mutations to the neuronal condensate scaffold shank2 cause physical hardening and altered composition of condensates; a key RNA translation-modulator FMRP is excluded from mutant condensates. Functionally, shank2 condensates repress translation while condensates composed of shank2 with intrinsically disordered region-localized missense mutations promote translation. These results demonstrate that disease-linked dysregulation of condensate physical properties and composition is an underlying mechanism of aberrant RNA translation often observed in disease.

One Sentence Summary

Disease-linked missense mutations in the postsynaptic density scaffold protein shank2 dysregulate phase separated biomolecular condensate physical properties and composition resulting in aberrant RNA translation.
Constitutive expression of CX3CR1-BAC-Cre introduces minimal off-target effects in microglia
Authors: Mroue-Ruiz Fadya H. , Desai Bhoomi , Garvin Madison , Shehu Jonila , Kamau Faith , Kar Urjoshi , Bolton Jessica L.
Published: November 2024

CX3CR1-Cre mouse lines have produced important advancements in our understanding of microglial biology. Recent studies have demonstrated the adverse effects of tamoxifen-induced CX3CR1-Cre expression during development, which include changes in microglial density, phenotype, and DNA damage, as well as anxiety-like behavior. However, the unintended effects of constitutive CX3CR1-BAC-Cre expression remain unexplored. Here, we characterized the effects of CX3CR1-BAC-Cre expression on microglia in CX3CR1-BAC-Cre+/- and CX3CR1-BAC-Cre-/-male and female littermates during early postnatal development and adulthood in multiple brain regions. Additionally, we performed anxiety-like behavior tests to assess changes caused by Cre expression. We found that CX3CR1-BAC-Cre expression causes subtle region- and sex-specific changes in microglial density, volume, and morphology during development, but these changes normalized by adulthood in all brain regions except the hippocampus. No behavioral effects were found. Our findings suggest that the constitutive-Cre model might be less detrimental than the inducible model, and highlight the need for proper controls.