bluuebunny/crossref_metadata_2025 huggingface dataset:
Mutations in Fibronectin Dysregulate Chondrogenesis in Skeletal Dysplasia
Authors: Dinesh Neha E. H. , Rousseau Justine , Mosher Deane F. , Strauss Mike , Mui Jeannie , Campeau Philippe M. , Reinhardt Dieter P.
Published: December 2023

Fibronectin (FN) is an extracellular matrix glycoprotein essential for the development and function of major vertebrate organ systems. Mutations in FN result in an autosomal dominant skeletal dysplasia termed corner fracture-type spondylometaphyseal dysplasia (SMDCF). The precise pathomechanisms through which mutant FN induces impaired skeletal development remain elusive. Here, we have generated patient-derived induced pluripotent stem cells as a cell culture model for SMDCF to investigate the consequences of FN mutations on mesenchymal stem cells (MSCs) and their differentiation into cartilage-producing chondrocytes. In line with our previous data, FN mutations disrupted protein secretion from MSCs, causing a notable increase in intracellular FN and a significant decrease in extracellular FN levels. Analyses of plasma samples from SMDCF patients also showed reduced FN in circulation. FN and endoplasmic reticulum (ER) protein folding chaperones (BIP, HSP47) accumulated in MSCs within ribosome-covered cytosolic vesicles that emerged from the ER and transitioned into lysosomes. Massive amounts of these vesicles were not cleared from the cytosol. The accumulation of intracellular FN and ER proteins elevated cellular stress markers and altered mitochondrial structure. Bulk RNA sequencing revealed a specific transcriptomic dysregulation of the patient-derived cells relative to controls. Analysis of MSC differentiation into chondrocytes showed impaired mesenchymal condensation, reduced chondrogenic markers, and compromised cell proliferation in mutant cells. FN mutant cells also displayed altered FN splice variants under chondrogenic stimuli. Moreover, FN mutant cells exhibited significantly lower transforming growth factor beta-1 (TGFβ1) expression, crucial for mesenchymal condensation. Exogenous FN or TGFβ1 supplementation effectively improved the MSC condensation and promoted chondrogenesis in FN mutant cells. These findings demonstrate the cellular consequences of FN mutations in SMDCF and explain the molecular pathways involved in the associated altered chondrogenesis.

Significance /Highlights

• SMDCF-causing mutations in fibronectin impair protein secretion in iPSC-derived mesenchymal stem cells.

• Mutant fibronectin and ER protein folding chaperones are directly exported from the rough endoplasmic reticulum into vesicles covered with ribosomes, which transition into lysosomes.

• The cells cannot clear the massive accumulation of cytosolic vesicles.

• Mutations in fibronectin impair stem cell proliferation, mesenchymal condensation, and the differentiation of MSCs into chondrocytes.

• Exogenous addition of purified fibronectin or TGFβ-1 improves mesenchymal condensation and chondrogenesis of the FN mutant stem cells.
Host-Pathogen Interactions in thePlasmodium-Infected Mouse Liver at Spatial and Single-Cell Resolution
Authors: Hildebrandt Franziska , Urrutia-Iturritza Miren , Zwicker Christian , Vanneste Bavo , Hul Noémi Van , Semle Elisa , Pascini Tales , Saarenpää Sami , He Mengxiao , Andersson Emma R. , Scott Charlotte L. , Vega-Rodriguez Joel , Lundeberg Joakim , Ankarklev Johan
Published: December 2023

Upon infecting its vertebrate host, the malaria parasite initially invades the liver where it undergoes massive replication, whilst remaining clinically silent. The spatial coordination of factors regulating immune responses and metabolic zonation during malaria infection, in the true tissue context, remains unexplored. Here, we perform spatial transcriptomics in combination with single-nuclei RNA-sequencing (snRNA-seq) over multiple time points during liver infection to delineate transcriptional programs of host-pathogen interactions acrossP. berghei-infected liver tissues. Our data suggest changes in gene expression related to lipid metabolism in response toPlasmodiuminfection in the proximity of infected hepatocytes, such as the modulation of the expression of genes involved in peroxisome proliferator-activated receptor pathway signaling. The data further indicate the presence of inflammatory hotspots with distinct cell type compositions and differential liver inflammation programs along the lobular axis in the malaria-infected tissues. Furthermore, a significant upregulation of genes involved in inflammation is observed in liver tissues of control mice injected with mosquito salivary gland components, which is considerably delayed compared toP. bergheiinfected mice. Our study establishes a benchmark for investigating transcriptome changes during host-parasite interactions in tissues, it provides informative insights regardingin vivostudy design linked to infection, and provides a useful tool for the discovery and validation ofde novointervention strategies aimed at malaria liver stage infection.
Fully automated workflow for integrated sample digestion and Evotip loading enabling high-throughput clinical proteomics
Authors: Kverneland Anders H. , Harking Florian , Vej-Nielsen Joel Mario , Huusfeldt Magnus , Bekker-Jensen Dorte B. , Svane Inge Marie , Bache Nicolai , Olsen Jesper V.
Published: December 2023

Protein identification and quantification is an important tool for biomarker discovery. With the increased sensitivity and speed of modern mass spectrometers, sample-preparation remains a bottleneck for studying large cohorts. To address this issue, we prepared and evaluated a simple and efficient workflow on the Opentrons OT-2 (OT-2) robot that combines sample digestion, cleanup and Evotip loading in a fully automated manner, allowing the processing of up to 192 samples in 6 hours. Our results demonstrate a highly sensitive workflow yielding both reproducibility and stability even at low sample inputs. The workflow is optimized for minimal sample starting amount to reduce the costs for reagents needed for sample preparation, which is critical when analyzing large biological cohorts. Building on the digesting workflow, we incorporated an automated phosphopeptide enrichment step using magnetic Ti-IMAC beads. This allows for a fully automated proteome and phosphoproteome sample preparation in a single step with high sensitivity. Using the integrated workflow, we evaluated the effects of cancer immune therapy on the plasma proteome in metastatic melanoma patients.
Metabolomics profiling reveals distinct, sex-specific signatures in the serum and brain metabolomes in the mouse models of Alzheimer’s disease
Authors: Pandey Ravi S. , Arnold Mattias , Batra Richa , Krumsiek Jan , Kotredes Kevin P. , Garceau Dylan , Williams Harriet , Sasner Michael , Howell Gareth R. , Kaddurah-Daouk Rima , Carter Gregory W.
Published: December 2023

Structured Abstract

INTRODUCTION

Increasing evidence suggests that metabolic impairments contribute to early Alzheimer’s disease (AD) mechanisms and subsequent dementia. Signals in metabolic pathways conserved across species provides a promising entry point for translation.

METHODS

We investigated differences of serum and brain metabolites between the early-onset 5XFAD and late-onset LOAD1 (APOE4.Trem2*R47H) mouse models of AD to C57BL/6J controls at six months of age.

RESULTS

We identified sex differences for several classes of metabolites, such as glycerophospholipids, sphingolipids, and amino acids. Metabolic signatures were notably different between brain and serum in both mouse models. The 5XFAD mice exhibited stronger differences in brain metabolites, whereas LOAD1 mice showed more pronounced differences in serum.

DISCUSSION

Several of our findings were consistent with results in humans, showing glycerophospholipids reduction in serum of APOE4 carriers and replicating the serum metabolic imprint of the APOE4 genotype. Our work thus represents a significant step towards translating metabolic dysregulation from model organisms to human AD.
3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes
Authors: Cordero Julio , Swaminathan Guruprasadh , Rogel-Ayala Diana G , Rubio Karla , Elsherbiny Adel , Günther Stefan , Braun Thomas , Dobreva Gergana , Barreto Guillermo
Published: December 2023

Studying the dynamics of three-dimensional (3D) chromatin structure is essential to understand biological processes in the cell nucleus. Recent publications based on integrative analysis of multi-omics studies have provided comprehensive and multilevel insights into 3D genome organization emphasizing its role during transcriptional regulation. While enhancers are regulatory elements that play a central role in the spatiotemporal control of gene expression, chromatin looping has been broadly accepted as a means for enhancer-promoter interactions allowing them to stablish cell-type-specific gene expression signatures. On the other hand, G-quadruplexes (G4s) are non-canonical DNA secondary structures that are both, enriched at promoters and related to increased gene expression. However, the role of G4s in promoter-distal regulatory elements, such as super-enhancers (SE), as well as in 3D genome organization and chromatin looping mediating long-range enhancer-promoter interactions has remained elusive. Here we show that mature microRNA 9 (miR-9) is enriched at promoters and SE of genes that are inducible by tissue growth factor beta 1 (TGFB1) signaling. Further, we found that nuclearmiR-9is required for chromatin features related to increased transcriptional activity, such as broad domains of the euchromatin histone mark H3K4me3 (histone 3 tri-methylated lysine 4) and G4s. Moreover, we show that nuclearmiR-9is required for promoter-super-enhancer looping. Our study places a nuclear microRNA in the same structural and functional context with G4s and promoter-enhancer interactions during 3D genome organization and transcriptional activation induced by TGFB1 signaling, a critical regulator of proliferation programs in cancer and fibrosis.
MCFBM: a behavioral analysis system enabling objective inference of songbirds’ attention during social interactions
Authors: Fujibayashi Mizuki , Abe Kentaro
Published: December 2023

Understanding animal behavior is crucial in behavioral neuroscience, which aims to unravel the mechanism driving these behaviors. A milestone in this field is the analysis of behavioral reactions among animals engaging in social interactions. Although many studies have revealed the fundamental roles of social interaction in social learning, the behavioral aspects of these interactions remain poorly understood, largely due to the lack of tools for analyzing complex behaviors and the attention of subjects in naturalistic, free-moving conditions. Here, we introduce a high-precision system for behavior analysis in songbirds using a marker-based motion capture technique. This system accurately tracks the body location and head direction of freely moving finches and is applicable to multiple subjects during social interaction. With this system, we have quantitatively analyzed behaviors of zebra finches (Taeniopygia guttata) related to visual attention. Our analysis revealed variations in the use of right and left eyes, as well as the duration of sight, among the individuals presented. Further analysis and comparison of their behaviors during both virtual and live presentation identified the similarities and differences in their behavioral reactions. Additionally, we observed changes in their behavioral reactions during a conditioned learning paradigm. This system provides an efficient and easy-to-use tool for advanced behavioral analysis in songbirds, providing an objective method to infer their focus of attention.
Quantitative spatial analysis of bacterial transcriptome and chromosome structural data with GRATIOSA: application to twin-supercoiled domain distribution
Authors: Pineau Maïwenn , Forquet Raphaël , Reverchon Sylvie , Nasser William , Hommais Florence , Meyer Sam
Published: December 2023

While classical models of transcriptional regulation focus on transcription factors binding at promoters, gene expression is also influenced by chromosome organization. Understanding this spatial regulation strongly benefits from integrated and quantitative spatial analyses of genome-scale data such as RNA-Seq and ChIP-Seq. We introduce Genome Regulation Analysis Tool Incorporating Organization and Spatial Architecture (GRATIOSA), a Python package making such combined analyses more automatic, systematic and reproducible. While current software focuses on initial analysis steps (read mapping and counting), GRAsTIOSA proposes an integrated framework for subsequent analyses, providing a broad range of spatially-resolved quantitative data comparisons and representations. As an example, we quantitatively assess the validity and extension of the twin-supercoiled domain model inEscherichia coligenome-wide transcription, using recent topoisomerase ChIP-Seq data. We show that topoisomerases are locally recruited by the 40% most highly expressed transcription units, with a magnitude correlating with the expression level. The recruitment of topoisomerase I extends to around 10 kb upstream, whereas DNA gyrase is recruited at least 30 kb downstream of transcription units. This organization is the primary determinant of topoisomerase I recruitment, whereas gyrase binding is additionally modulated at larger 100-200 kb length-scale. Further analyses of spatial regulation will be facilitated by GRATIOSA.
KAGE 2: Fast and accurate genotyping of structural variation using pangenomes
Authors: Grytten Ivar , Rand Knut Dagestad , Sandve Geir Kjetil
Published: December 2023

Structural variation is known to play an important and often overlooked role in regulating disease and traits, but accurately detecting structural variants from sequencing data has traditionally been difficult. However, recent improvements in high-quality genome assembly along with methodological advancements in pangenome creation have opened up the landscape for methods that use such pangenomes for structural variant calling and genotyping. We here present KAGE2, which accurately and efficiently genotypes structural variation by exploiting the availability of pangenomes that represent known variation in a population. Through comprehensive benchmarking, we highlight limitations of existing methodology and show that KAGE2 is more accurate and considerably faster than existing methods.
Flavonols improve thermotolerance in tomato pollen during germination and tube elongation by maintaining ROS homeostasis
Authors: Postiglione Anthony E. , Delange Allison M. , Ali Mohammad Foteh , Wang Eric Y. , Houben Maarten , Hahn Stacy L. , Khoury Maleana G. , Roark Colleen M. , Davis Molly , Reid Robert W. , Pease James B. , Loraine Ann E. , Muday Gloria K.
Published: December 2023

Elevated temperatures impair pollen performance and reproductive success, resulting in lower crop yields. TheSolanum lycopersicum anthocyanin reduced(are) mutant has aFLAVANONE 3 HYDROXYLASE(F3H) gene mutation resulting in impaired synthesis of flavonol antioxidants. Thearemutant has reduced pollen performance and seed set relative to the VF36 parental line, which is accentuated at elevated temperatures. Transformation ofarewith the wild-typeF3Hgene, or chemical complementation with flavonols, prevented temperature-dependent ROS accumulation in pollen and reversedare’sreduced viability, germination, and tube elongation to VF36 levels. VF36 transformed with anF3Hoverexpression construct prevented temperature driven ROS increases and impaired pollen performance, revealing thermotolerance results from elevated flavonol synthesis. Although stigmas ofarehad reduced flavonols and elevated ROS, the growth ofarepollen tubes were similarly impaired in bothareand VF36 pistils. RNA-Seq was performed at optimal and stress temperatures inare, VF36, and the VF36F3Hoverexpression line at multiple timepoints across pollen tube elongation. Differentially expressed gene numbers increased with duration of elevated temperature in all genotypes, with the largest number inare. These findings suggest potential agricultural interventions to combat the negative effects of heat-induced ROS in pollen that leads to reproductive failure.

One sentence summary

Flavonol antioxidants reduce the negative impacts of elevated temperatures on pollen performance by reducing levels of heat induced reactive oxygen species and modulation of heat-induced changes in the pollen transcriptome.
Microbiota based personalized nutrition improves hyperglycaemia and hypertension parameters and reduces inflammation: A prospective, open label, controlled, randomized, comparative, proof of concept study
Authors: Kallapura Gopalakrishna , Prakash Anthony Surya , Sankaran Kumar , Manjappa Prabhath , Chaudhary Prayagraj , Ambhore Sanjay , Dhar Debojyoti
Published: December 2023

Recent studies suggest that gut microbiota composition, abundance and diversity can influence many chronic diseases such as type 2 diabetes. Modulating gut microbiota through targeted nutrition can provide beneficial effects leading to the concept of personalized nutrition for health improvement. In this prospective clinical trial, we evaluated the impact of a microbiome-based targeted personalized diet on hyperglycaemic and hyperlipidaemic individuals. Specifically, BugSpeaks®- a microbiome profile test that profiles microbiota using next generation sequencing and provides personalized nutritional recommendation based on the individual microbiota profile was evaluated. The test arm [microbiome-based nutrition] showed a statistically significant decrease in HbA1c level [from 8.30 ± 1.12 to 6.67 ± 0.89, p<0.001] after 90 days. The test arm, also showed a 5% decline in the systolic pressure whereas the control arm showed a 7% increase. Incidentally, a sub-cohort of the test arm of patients with >130mm Hg systolic pressure showed a statistically significant decrease of systolic pressure by 14%. Interestingly, CRP level was also found to drop by 19.5%. Alpha diversity measures showed a significant increase in Shannon diversity measure [p<0.05], after the microbiome-based personalized dietary intervention. The intervention led to a minimum 2-fold [Log2 fold change] increase in beneficial species likePhascolarctobacterium succinatutens, Bifidobacterium angulatum, Levilactobacillus brevis, and a similar decrease in non-beneficial species likeAlistipes finegoldii, Sutterella faecalis. Overall, the study indicated a net positive impact of the microbiota based personalized dietary regime on the gut microbiome and correlated clinical parameters.
Geo-Demographic Trends in Nontraumatic Subarachnoid Hemorrhage-Related Mortality Among Older Adults in the United States, 1999-2020
Authors: McCandless Martin G. , Dharia Anand A. , Wicks Elizabeth E. , Camarata Paul J.
Published: December 2023

Introduction

Nontraumatic subarachnoid hemorrhage (ntSAH) often results from a ruptured aneurysm and correlates with significant morbidity and mortality, particularly among the older population. Despite its impact, limited comprehensive studies evaluate the longitudinal trends in ntSAH-related mortality in older adults in the United States (US).

Methods

The authors conducted a retrospective analysis using the CDC WONDER database from 1999 to 2020, analyzing Multiple Cause-of-Death Public Use death certificates to identify ntSAH as a contributing factor in the death of adults aged 65 years and older. We calculated age-adjusted mortality rates (AAMR) and annual percent change (APC) to examine trends across demographic variables such as sex, race/ethnicity, urbanization, and states/census region.

Results

78 260 ntSAH-related deaths (AAMR 8.50 per 100 000 individuals) occurred among older adults in the US from 1999 to 2020. The overall AAMR for ntSAH decreased from 9.98 in 1999 to 8.67 in 2020 with an APC of −0.7% (95% CI [−1.0, −0.3]). However, the authors observed a noticeable rise from 2013 to 2020 with an APC of 1.7% (95% CI [0.8, 2.6]). Sex, racial, and regional disparities were evident with higher mortality rates for ages 85 or greater (crude mortality rate 16.6), women (AAMR 9.55), non-Hispanic Asian or Pacific Islander (AAMR 12.5), and micropolitan areas (AAMR 8.99), and Western US (AAMR 8.65).

Conclusion

Mortality from ntSAH increases with age, affects women disproportionately, and occurs more often in an inpatient setting. These findings necessitate targeted, multi-dimensional health policies and clinical interventions. Specialties beyond neurosurgery can utilize this data for improved risk stratification and early treatment. Policymakers should focus on equitable resource allocation and community-level interventions to mitigate these trends effectively.
Effects of sampling methodology on phenology indices: insights from sites across India and modelling
Authors: Tiruvaimozhi Yadugiri , Teegalapalli Karthik , Reddy Abinand , Murali Akhil , Datta Aparajita , Krishnan Aparna , Ratnam Jayashree , Sankaran Mahesh , Ongole Shasank , Kasinathan Srinivasan , Raman T. R. Shankar , Ramaswami Geetha
Published: December 2023

Plant phenology is the study of timing and extent of leaf, flower, and fruit production. Phenology data are used to study drivers of cyclicity and seasonality of plant life-history stages, interactions with organisms such as pollinators, and effects of global change factors. Indices such as timing of phenological events, proportion of individuals in a particular phenophase, seasonality, and synchrony have often been used to summarise plant phenology data. However, these indices have specific utilities and limitations and may be sensitive to sampling methodology, making cross-site comparisons challenging, particularly when data collection methods vary in terms of sample size, observation frequency, and the resolution at which phenophase intensity scores/values are recorded. We use fruiting phenology data from tropical trees across five sites in India to study the effects of sampling methodology on two indices: an index of population-level synchrony (overlap), and an index of seasonality. We supplement these results with simulations of fast- and slow-changing phenologies to test for the effects of sampling methodology on these indices. We found that the overlap index is sensitive to the phenophase intensity measurement resolution—with coarser intensity measures leading to overestimation of the overlap index. The seasonality index, on the other hand, was not affected by intensity resolution. Simulations indicated that finer intensity resolution is more important than frequency of observation to accurately estimate population synchrony and seasonality for fast- and slow-changing phenophases. Based on our findings, we provide recommendations for study design of future tropical tree phenology research, particularly for long-term or cross-site studies.
Macrophage mediated mesoscale brain mechanical homeostasis mechanically imaged via optical tweezers and Brillouin microscopyin vivo
Authors: So Woong Young , Johnson Bailey , Gordon Patricia B. , Bishop Kevin S. , Gong Hyeyeon , Burr Hannah A , Staunton Jack Rory , Handler Chenchen , Sood Raman , Scarcelli Giuliano , Tanner Kandice
Published: December 2023

Tissues are active materials where epithelial turnover, immune surveillance, and remodeling of stromal cells such as macrophages all regulate form and function. Scattering modalities such as Brillouin microscopy (BM) can non-invasively access mechanical signatures at GHz. However, our traditional understanding of tissue material properties is derived mainly from modalities which probe mechanical properties at different frequencies. Thus, reconciling measurements amongst these modalities remains an active area. Here, we compare optical tweezer active microrheology (OT-AMR) and Brillouin microscopy (BM) to longitudinally map brain development in the larval zebrafish. We determine that each measurement is able to detect a mechanical signature linked to functional units of the brain. We demonstrate that the corrected BM-Longitudinal modulus using a density factor correlates well with OT-AMR storage modulus at lower frequencies. We also show that the brain tissue mechanical properties are dependent on both the neuronal architecture and the presence of macrophages. Moreover, the BM technique is able to delineate the contributions to mechanical properties of the macrophage from that due to colony stimulating factor 1 receptor (CSF1R) mediated stromal remodeling. Here, our data suggest that macrophage remodeling is instrumental in the maintenance of tissue mechanical homeostasis during development. Moreover, the strong agreement between the OT-AM and BM further demonstrates that scattering-based technique is sensitive to both large and minute structural modificationin vivo.
Cell-penetrating peptide and cationic liposomes mediated siRNA delivery to arrest growth of chronic myeloid leukemia cellsin vitro
Authors: Vysochinskaya Vera , Zabrodskaya Yana , Dovbysh Olesya , Emelyanov Anton , Klimenko Vladimir , Knyazev Nikolay , Terterov Ivan , Egorova Marya , Bogdanov Alexey , Maslov Michael , Vasin Andrey , Dubina Michael
Published: December 2023

Gene silencing through RNA interference (RNAi) is a promising therapeutic approach for a wide range of disorders, including cancer. Non-viral gene therapy, using specific siRNAs againstBCR-ABL, can be a supportive or alternative measure to traditional chronic myeloid leukemia (CML) tyrosine kinase inhibitor (TKIs) therapies, given the prevalence of clinical TKI resistance. The main challenge for such approaches remains the development of the effective delivery system for siRNA tailored to the specific disease model.

The purpose of this study was to examine and compare the efficiency of endosomolytic cell penetrating peptide (CPP) EB1 and PEG2000-decorated cationic liposomes composed of polycationic lipid 1,26-bis(cholest-5-en-3-yloxycarbonylamino)-7,11,16,20-tetraazahexacosane tetrahydrochloride (2X3) and helper lipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) for anti-bcr-abl siRNA delivery into the K562 human CML cell line. We show that both EB1 and 2X3-DOPE-DSPE-PEG2000(0.62% mol.) liposomes effectively deliver siRNA into K562 cells by endocytic mechanisms, and the use of liposomes leads to more effective inhibition of expression of the targeted gene (BCR-ABL) and cancer cell proliferation. Taken together, these findings suggest that PEG-decorated cationic liposomes mediated siRNA delivery allows an effective antisense suppression of certain oncogenes, and represents a promising new class of therapies for CML.
In-utero exposure to estrogen-mimicking bisphenols alters bone mineralization in the offspring
Authors: Varma Saikanth , Molangiri Archana , Mudavath Sreedhar , Ananthan Rajendran , Rajanna Ajumeera , Duttaroy Asim K , Basak Sanjay
Published: December 2023

Exposure to plastic-derived estrogen-mimicking endocrine-disrupting bisphenols can have a long-lasting effect on bone health. However, gestational exposure to below tolerable daily intake (TDI) of bisphenol A (BPA) and its substitute, bisphenol S (BPS), on offspring’s bone mineralization is unclear. This study examined the effects of in-utero bisphenol exposure on the growth and bone density of the offspring rats. Pregnant Wistar rats were exposed to BPA and BPS (0.0, 0.4 μg/kg bw) via oral gavage from gestational day 4 to 21. The bone density, IGF-1, osteocalcin, and calcium levels were measured by DEXA, ELISA and AAS, respectively. The bisphenol’s action on canonical BMP signaling was examined in osteoblast SaOS-2 cells. Maternal exposure to bisphenols (BPA and BPS) increased the body weight, bone mineral content, and density in the offspring aged 30 and 90 days (p<0.05). Plasma IGF-1, calcium, osteocalcin, and alkaline phosphatase activities were altered in BPA-exposed offspring (p<0.05). The bisphenols exposure to SaOS-2 cells decreased its viability in a dose-dependent manner and promoted the cell cycle progression of the S/G2-M phase (p<0.05). The expression of BMP1, BMP4, and intracellular signalling mediators SMAD1, SMAD5, and RUNX2 mRNAs was altered upon bisphenol exposure in these cells (p<0.05). The bone mineralization index and expression of extracellular matrix proteins such as ALPL, COL1A1, DMP1, and FN1 were downregulated (p<0.05). Bisphenol co-incubation with noggin decreased TGF-β1 expression, indicating its involvement in bone mineralization. Overall, exposure to bisphenols (BPA and BPS) during gestation altered growth and bone mineralization in the offspring by modulating canonical BMP/ TGF-β1 signalling mediators.

Highlights

Gestational exposure to low doses of bisphenol increases whole-body BMC and BMD in the offspring.

In-utero BPA exposure increased plasma IGF-1 and gla-type osteocalcin, a marker of osteoblast activity in the offspring.

Bisphenol exposure modulates Smad-dependent BMP signaling in the SaOS-2 cells.
Genome-wide RNA structural determination inCandidayeast pathogens
Authors: Chorostecki Uciel , Saus Ester , Gabaldón Toni
Published: December 2023

Understanding the intricate roles of RNA molecules in virulence and host-pathogen interactions can provide valuable insights into combatting infections and improving human health. Although much progress has been achieved in understanding transcriptional regulation during host-pathogen interactions in diverse species, more is needed to know about the structure of pathogen RNAs. This is particularly true for fungal pathogens, including pathogenic yeasts of theCandidagenus, which are the leading cause of hospital-acquired fungal infections. Deciphering the relation between RNA structure and their biology remains a significant gap. Despite advancements in transcriptional regulation studies, especially for fungal pathogens likeCandida, the structural aspects of pathogenic RNAs remain understudied. Our work addresses this gap by employing genome-wide structure probing to comprehensively explore the structural landscape of mRNAs and long non-coding RNAs (lncRNAs) in the four majorCandidapathogens. Specifically focusing on mRNA, we observe a robust correlation between sequence conservation and structural characteristics in orthologous transcripts, significantly when sequence identity exceeds 50%, highlighting structural feature conservation among closely related species. We investigate the impact of single nucleotide polymorphisms (SNPs) on mRNA secondary structure. SNPs within 5’ untranslated regions (UTRs) tend to occur in less structured positions, suggesting structural constraints influencing transcript regulation. Furthermore, we compare the structural properties of coding regions and UTRs, noting that coding regions are generally more structured than UTRs, consistent with similar trends in other species.

Additionally, we provide the first experimental characterization of lncRNA structures inCandida species. Most lncRNAs form independent subdomains, similar to human lncRNAs. Notably, we identify hairpin-like structures in lncRNAs, a feature known to be functionally significant. Comparing hairpin prevalence between lncRNAs and protein-coding genes, we find enrichment in lncRNAs acrossCandidaspecies, humans, andArabidopsis thaliana, suggesting a conserved role for these structures.

In summary, our study offers valuable insights into the interplay between RNA sequence, structure, and function inCandidapathogens, with implications for gene expression regulation and potential therapeutic strategies againstCandidainfections.
Relationship between advanced footwear technology longitudinal bending stiffness and energy cost of running
Authors: Rodrigo-Carranza Víctor , Hoogkamer Wouter , González-Ravé José María , González-Mohíno Fernando
Published: December 2023

Introduction/Purpose

Shoe longitudinal bending stiffness (LBS) is often considered to influence running economy (RE) and thus, running performance. However, previous results are mixed and LBS levels have not been studied in advanced footwear technology (AFT). The purpose of this study was to evaluate the isolated effects of increased LBS from curved carbon fiber plates embedded within an AFT midsole on RE and spatiotemporal parameters.

Methods

Twenty-one male trained runners completed 3 times 4 minutes at 13km/h with two experimental shoe models with a curved carbon fiber plate embedded in an AFT midsole with different LBS values (Stiff: 35.5 N/mm and Stiffest: 43.1 N/mm), and a Control condition (no carbon fiber plate: 20.1 N/mm). We measured energy cost of running (W/kg) and spatiotemporal parameters in one visit.

Results

RE improved for the Stiff shoe condition (15.71 ± 0.95 W/kg; p<0.001;n2=0.374) compared to the Control condition (16.13 ± 1.08 W/kg) and Stiffest condition (16.03 ± 1.19 W/kg). However, we found no significant differences between the Stiffest and Control conditions. Moreover, there were no spatiotemporal differences between shoe conditions.

Conclusion

Changes in LBS in AFT influences RE suggesting that moderately stiff shoes are the most effective LBS to improve RE in AFT compared to very stiff shoes and traditional, flexible shoe conditions while running at 13 km/h.
Genomic evidence for hybridization and introgression between blue peafowl and green peafowl and selection for white plumage
Authors: Wang Gang , Ban Liping , Zhang Xinye , Zhao Xiurong , Ren Xufang , Chen Anqi , Zhang Li , Lu Yan , Jiang Zhihua , Zhao Xiaoyu , Wen Junhui , Zhang Yalan , Cheng Xue , Wang Huie , Dai Wenting , Liu Yong , Ning Zhonghua , Qu Lujiang
Published: December 2023

The blue peafowl (Pavo cristatus) and the green peafowl (Pavo muticus) have significant public affection due to their stunning appearance, although the green peafowl is currently endangered. Some studies have suggested introgression between these the two species, although evidence is mixed. In this study, we successfully assembled a high-quality chromosome-level reference genome of the blue peafowl, including the autosomes, Z and W sex chromosomes as well as a complete mitochondria DNA sequence. Data from 77 peafowl whole genomes, 76 peafowl mitochondrial genomes and 33 peahen W chromosomes genomes provide the first substantial genetic evidence for recent hybridization between green and blue peafowl. We found three hybrid green peafowls in zoo samples rather than in the wild samples, with blue peafowl genomic content of 16-34%. Maternal genetic analysis showed that two of the hybrid female green peafowls contained complete blue peafowl mitochondrial genomes and W chromosomes. Hybridization of endangered species with its relatives is extremely detrimental to conservation. Some animal protection agencies release captive green peafowls in order to maintain the wild population of green peafowls. Therefore, in order to better protect the endangered green peafowl, we suggest that purebred identification must be carried out before releasing green peafowls from zoos into the wild in order to preventing the hybrid green peafowl from contaminating the wild green peafowl. In addition, we also found that there were historical introgression events of green peafowl to blue peafowl in four Zoo blue peafowl individuals. The introgressed genomic regions contain IGFBP1 and IGFBP2 genes that could affect blue peafowl body size. Finally, we identified that the nonsense mutation (g.4:12583552G>A) in the EDNRB2 gene is the genetic causative mutation for white feather color of blue peafowl (also called white peafowl), which prevents melanocytes from being transported into feathers, such that melanin cannot be deposited.
Mutational and transcriptional landscape of pediatric B-cell precursor lymphoblastic lymphoma
Authors: Kroeze Emma , Iaccarino Ingram , Kleisman Michelle M , Mondal Mayukh , Beder Thomas , Khouja Mouhamad , Hoeppner Marc P , Scheijde-Vermeulen Marijn A , Kester Lennart A , Brüggemann Monika , Baldus Claudia D , Cario Gunnar , Bladergroen Reno S , Garnier Nathalie , Attarbaschi Andishe , Verdu-Amoros Jaime , Sutton Rosemary , MacIntyre Elizabeth , Scholten Kenneth , Padilla Laura Arias , Burkhardt Birgit , Beishuizen Auke , den Boer Monique L , Kuiper Roland P , Loeffen Jan LC , Boer Judith M , Klapper Wolfram
Published: December 2023

Pediatric B-cell precursor (BCP) lymphoblastic malignancies are neoplasms with manifestation either in bone marrow/blood (BCP acute lymphoblastic leukemia, BCP-ALL) or less common in extramedullary tissue (BCP lymphoblastic lymphoma, BCP-LBL). Although both presentations are similar in morphology and immunophenotype molecular studies are virtually restricted to BCP-ALL so far. The lack of molecular studies on BCP-LBL is probably due to its rarity and the restriction to tiny, mostly formalin-fixed paraffin embedded (FFPE) tissues. Here we present the first comprehensive mutational and transcriptional analysis of what we consider the largest BCP-LBL cohort described to date (n=97). Whole exome sequencing indicates a mutational spectrum of BCP-LBL strikingly similar to that found in BCP-ALL. However, epigenetic modifiers were more frequently mutated in BCP-LBL, whereas BCP-ALL was more frequently affected by mutation in genes involved in B-cell development. Integrating copy number alterations, somatic mutations and gene expression by RNA-sequencing revealed virtually all molecular subtypes originally defined in BCP-ALL to be present in BCP-LBL too, with only 7% of lymphomas that were not assigned to a subtype. Therefore, the results here described may pave the way for molecular risk adapted treatment protocols for BCP-LBL patients.

Keypoints

Comprehensive molecular characterization of B-cell precursor lymphoblastic lymphoma allows molecular subtyping analogous to leukemias

Compared to leukemias, lymphomas show more alterations in epigenetic modifiers and less in B-cell development genes
S1 hydrophobic residues modulate voltage sensing phosphatase enzymatic function and voltage sensing
Authors: Rayaprolu Vamseedhar , Miettinen Heini M. , Baker William , Young Victoria C. , Fisher Matthew , Mueller Gwendolyn , Rankin William O. , Kelly J. Jack , Ratzan William J. , Leong Lee Min , Davisson Joshua A. , Baker Bradley J. , Kohout Susy C.
Published: December 2023

The voltage sensing domain (VSD) is a four-helix modular protein domain that converts electrical signals into conformational changes, leading to open pores and active enzymes. In most voltage sensing proteins, the VSDs do not interact with one another and the S1-S3 helices are considered mainly as scaffolding. The two exceptions are the voltage sensing phosphatase (VSP) and the proton channel (Hv). VSP is a voltage-regulated enzyme and Hv’s are channels that only have VSDs. To investigate the S1 contribution to VSP function, we individually mutated four hydrophobic amino acids in S1 to alanine (F127, I131, I134 and L137). We also combined these mutations to generate quadruple mutation designated S1-Q. Most of these mutations shifted the voltage dependence of activity to higher voltages though interestingly, not all substrate reactions were the same. The kinetics of enzymatic activity were also altered with some mutations significantly slowing down dephosphorylation. The voltage dependence of VSD motions were consistently shifted to lower voltages and indicated a second voltage dependent motion. Co-immunoprecipitation demonstrated that none of the mutations broke the VSP dimer indicating that the S1 impact could stem from intrasubunit and/or intersubunit interactions. Lastly, when the same alanine mutations were introduced into a genetically encoded voltage indicator, they dramatically altered the optical readings, making some of the kinetics faster and shifting the voltage dependence. These results indicate that the S1 helix in VSP plays a critical role in tuning the enzyme’s conformational response to membrane potential transients and influencing the function of the VSD.
The Statistical Building Blocks of Animal Movement Simulations
Authors: Getz Wayne M , Salter Richard , Sethi Varun , Cain Shlomo , Spiegel Orr , Toledo Sivan
Published: December 2023

Animal movement plays a key role in many ecological processes and has a direct influence on an individual's fitness at several scales of analysis (i.e., next-step, subdiel, day-by-day, seasonal). This highlights the need to dissect movement behavior at different spatio-temporal scales and develop hierarchical movement tools for generating realistic tracks to supplement existing single-temporal-scale simulators. In reality, animal movement paths are a concatenation of fundamental movement elements (FuMEs: e.g., a step or wing flap), but these are not generally extractable from a relocation time-series track (e.g., sequential GPS fixes) from which step-length (SL, aka velocity) and turning-angle (TA) time series can be extracted. For short, fixed-length segments of track, we generate their SL and TA statistics (e.g., means, standard deviations, correlations) to obtain segment-specific vectors that can be cluster into different types. We use the centroids of these clusters to obtain a set of statistical movement elements (StaMEs; e.g. directed fast movement versus random slow movement elements) that we use as a basis for analyzing and simulating movement tracks. Our novel concept is that sequences of StaMEs provide a basis for constructing and fitting step-selection kernels at the scale of fixed-length canonical activity modes: short fixed-length sequences of interpretable activity such as dithering, ambling, directed walking, or running. Beyond this, variable length pure or characteristic mixtures of CAMs can be interpreted as behavioral activity modes (BAMs), such as gathering resources (a sequence of dithering and walking StaMEs) or beelining (a sequence of fast directed-walk StaMEs interspersed with vigilance and navigation stops). Here we formulate a multi-modal, step-selection kernel simulation framework, and construct a 2-mode movement simulator (Numerus ANIMOVER_1), using Numerus RAMP technology. We also illustrate methods for extracting StaMEs from both simulated and real data from two barn owls ((Tyto alba)) in the Harod Valley, Israel. Overall, our new bottom-up approach to path segmentation allows us to both dissect real movement tracks and generate realistic synthetic ones, thereby providing a general tool for testing hypothesis in movement ecology and simulating animal movement in diverse contexts such as evaluating an individual's response to landscape changes, release of an individual into a novel environment, or identifying when individuals are sick or unusually stressed.
ProInterVal: Validation of Protein-Protein Interfaces through Learned Interface Representations
Authors: Ovek Damla , Keskin Ozlem , Gursoy Attila
Published: December 2023

Proteins are vital components of the biological world, serving a multitude of functions. They interact with other molecules through their interfaces and participate in crucial cellular processes. Disruptions to these interactions can have negative effects on the organism, highlighting the importance of studying protein-protein interfaces for developing targeted therapies for diseases. Therefore, the development of a reliable method for investigating protein-protein interactions is of paramount importance. In this research, we present an approach for validating protein-protein interfaces using learned interface representations. The approach involves using a graph-based contrastive autoencoder architecture and a transformer to learn representations of proteinprotein interaction interfaces from unlabeled data, then validating them through learned representations with a graph neural network. Our method achieves an accuracy of 0.91 for the test set, outperforming existing GNN-based methods. We demonstrate the effectiveness of our approach on a benchmark dataset and show that it provides a promising solution for validating protein-protein interfaces.
Ventral Pallidum and Amygdala Cooperate to Restrain Reward Approach from Overriding Defensive Behaviors
Authors: Hernández-Jaramillo Alejandra , Illescas-Huerta Elizabeth , Sotres-Bayón Francisco
Published: December 2023

Foraging decisions involve assessing potential risks and prioritizing food sources, which can be challenging when confronted with changing and conflicting circumstances. A crucial aspect of this decision-making process is the ability to actively suppress defensive reactions to threats (fear) and focus on achieving specific goals. The ventral pallidum (VP) and basolateral amygdala (BLA) are two brain regions that play key roles in regulating behavior motivated by either rewards or threats. However, it is unclear whether these regions are necessary in decision-making processes involving competing motivational drives during conflict. Our aim was to investigate the requirements of the VP and BLA for foraging choices in conflicts involving fear suppression. Here, we used a novel foraging task and pharmacological techniques to inactivate either the VP or BLA, or to disconnect these brain regions before conducting a conflict test. Our findings showed that BLA is necessary for making calculated risky choices during conflicts, whereas VP is necessary for invigorating the drive to obtain food, regardless of the presence of conflict. Importantly, our research revealed that the connection between VP and BLA is critical in limiting risk behaviors when searching for food that requires effort in conflict situations. This study provides a new perspective on the collaborative function of VP and BLA in driving behavior, aimed at achieving goals in the face of danger.
Local adaptation to mercury contamination by nitrogen-fixing rhizobia is driven by horizontal gene transfer, copy number, and enhanced gene expression
Authors: Bhat Aditi , Sharma Reena , Lucas M. Mercedes , Desigan Kumaran , Clear Michael , Mishra Ankita , Bowers Robert , Woyke Tanja , Epstein Brendan , Tiffin Peter , Pueyo José J. , Paape Tim
Published: December 2023

Mercury (Hg) is highly toxic and has the potential to cause severe health problems for foraging animals and humans when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms to prevent heavy metal translocation from roots to shoots in plants by exporting metals from nodules or compartmentalizing metal ions inside nodules. Using long-read sequencing, we assembled the genomes ofSinorhizobium medicaeandRhizobium leguminosarumfrom the Almadén mercury mine in Spain with high variation in Hg-tolerance to identify structural and transcriptomic differences between low and high Hg-tolerant strains. While independent mercury reductase A (merA) genes are prevalent in α-proteobacteria, Mer operons are rare and often vary in their gene organization. Our analyses identified multiple structurally conserved merA homologs in the genomes ofS. medicae, including a dihydrolipoamide 2-oxoglutarate dehydrogenase (D2OD), but only the strains that possessed a Mer operon exhibited hypertolerance to Hg. Using RNAseq reads mapped to the unique genome assemblies, we found the Hg-tolerant strains which possessed a Mer operon, that nearly all genes within the operon were significantly up-regulated in response to Hg stress in free-living conditions and in nodules. In both free-living and nodule environments, we found the Hg-tolerant strains with a Mer operon exhibited the fewest number of DEGs in the genome, indicating a rapid and efficient detoxification of Hg2+from the cells that reduced general stress responses to the Hg-treatment. Expression changes inS. medicaewhile inside of nodules showed that both rhizobia strain and host-plant tolerance affected the number of DEGs. Aside from Mer operon genes,nifgenes which are involved in nitrogenase activity inS. medicaeshowed significant up-regulation in the most Hg-tolerant strain while inside the most Hg-accumulating host-plant, indicating a genotype-by-genotype interaction that influences nitrogen-fixation under stress conditions. Transfer of the Mer operon to non-tolerant strains resulted in an immediate increase in Hg tolerance, indicating that the operon is solely necessary to confer hypertolerance to Hg, despite paralogous merA genes present elsewhere in the genome. This study demonstrated that the Mer operon can be exchanged via horizontal gene transfer into non-tolerant rhizobia strains naturally and experimentally.