bluuebunny/crossref_metadata_2025 huggingface dataset:
Low parental conflict, no endosperm hybrid barriers, and maternal bias in genomic imprinting in selfingDrabaspecies
Authors: Alling Renate M. , Bjerkan Katrine N. , Bramsiepe Jonathan , Nowak Michael D. , Gustafsson A. Lovisa S. , Brochmann Christian , Brysting Anne K. , Grini Paul E.
Published: January 2024

In flowering plants, a distinct post-zygotic hybridization barrier between closely related species can arise during seed maturation, resulting in embryo lethality due to abnormal endosperm development. The endosperm initially works as a nutrient sink, acquiring nutrients from adjacent tissues, but later undergoes cellularization, switching to serve as a nutrient source. In hybrid seeds, this cellularization switch can be hampered if the endosperm genomic ratio is imbalanced. Disruption in the genomic ratio can be caused when species of different ploidy are crossed, but also by crosses between species with identical ploidy, if the effective ploidy differs. One factor proposed to influence effective ploidy is the epigenetic phenomenon genomic imprinting, the parent-of-origin specific expression of alleles inherited either maternally or paternally. It has been proposed that outbreeding species exhibit higher effective ploidy compared to selfing species, as a consequence of parental conflict in resource allocation to the developing progenies. This suggests a low anticipation of endosperm-based post-zygotic hybridization barriers between selfing species of similar ploidy. Here, we show that in crosses between the diploid selfing arctic speciesDraba fladnizensis,D. nivalisandD. subcapitata, the endosperm-based post-zygotic hybridization barrier is absent, supporting low parental conflict. To investigate parent-of-origin allele specific expression, we conducted a genomic imprinting study inD. nivalisand compared to previous studies in other Brassicaceae species. We report a high number of maternally expressed genes (MEGs) and concomitantly low numbers of paternally expressed genes (PEGs). Our results suggest rapid evolution of MEGs and loss of PEGs in a mating system with low parental conflict, proposing that selfing arctic species may exhibit a generally stronger maternal expression bias as an adaptive mechanism to efficiently cope with an extreme environment.
Characterization of the skeletal muscle arginine methylome in health and disease reveals remodeling in Amyotrophic Lateral Sclerosis
Authors: Wong Julian P. H. , Blazev Ronnie , Ng Yaan-Kit , Goodman Craig A. , Montgomery Magdalene K. , Watt Kevin I. , Carl Christian S. , Watt Matthew J. , Voldstedlund Christian T. , Richter Erik A. , Crouch Peter J. , Steyn Frederik J , Ngo Shyuan T , Parker Benjamin L.
Published: January 2024

Arginine methylation is a protein post-translational modification important for the development of skeletal muscle mass and function. Despite this, our understanding of the regulation of arginine methylation under settings of health and disease remains largely undefined. Here, we investigated the regulation of arginine methylation in skeletal muscles in response to exercise and hypertrophic growth, and in diseases involving metabolic dysfunction and atrophy. We report a limited regulation of arginine methylation under physiological settings that promote muscle health, such as during growth and acute exercise, nor in disease models of insulin resistance. In contrast, we saw a significant remodeling of asymmetric dimethylation in models of atrophy characterized by the loss of innervation, including in muscle biopsies from patients with amyotrophic lateral sclerosis (ALS). Mass spectrometry-based quantification of the proteome and asymmetric arginine dimethylome of skeletal muscle from individuals with ALS revealed the largest compendium of protein changes with the identification of 793 regulated proteins, and novel site-specific changes in asymmetric dimethyl arginine (aDMA) of key sarcomeric and cytoskeletal proteins. Finally, we show thatin vivooverexpression of PRMT1 and aDMA resulted in increased fatigue resistance and functional recovery in mice. Our study provides evidence for asymmetric dimethylation as a regulator of muscle pathophysiology and presents a valuable proteomics resource and rationale for numerous methylated and non-methylated proteins, including PRMT1, to be pursued for therapeutic development in ALS.
A comparative study of influenza A M2 protein conformations in DOPC/DOPS liposomes and in nativeE. colimembranes
Authors: Sanders Griffin , Borbat Peter P. , Georgieva Elka R.
Published: January 2024

We compared the conformations of the transmembrane domain (TMD) of influenza A M2 (IAM2) protein reconstituted at pH 7.4 in DOPC/DOPS bilayers to those in isolatedE. colimembranes, having preserved its native proteins and lipids. IAM2 is a single-pass transmembrane protein known to assemble into homo-tetrameric proton channel. To represent this channel, we made a construct containing the IAM2’s TMD region flanked by the juxtamembrane residues. The single cysteine substitute, L43C, of leucine located in the bilayer polar region was paramagnetically tagged with a methanethiosulfonate nitroxide label for the ESR (electron spin resonance) study. We compared the conformations of the spin-labeled IAM2 residing in DOPC/DOPS and nativeE. colimembranes using continuous-wave (CW) ESR and double electron-electron resonance (DEER) spectroscopy. The total protein-to-lipid molar ratio spanned the range from 1:230 to 1:10,400. The CW ESR spectra corresponded to a nearly rigid limit spin label dynamics in both environments. In all cases, the DEER data were reconstructed into the distance distributions showing well-resolved peaks at 1.68 nm and 2.37 nm. The peak distance ratio was 1.41±0.2 and the amplitude ratio was 2:1. This is what one expects from four nitroxide spin-labels located at the corners of a square, indicative of an axially symmetric tetramer.

Distance modeling of DEER data with molecular modeling software applied to the NMR molecular structures (PDB: 2L0J) confirmed the symmetry and closed state of the C-terminal exit pore of the IAM2 tetramer in agreement with the NMR model. Thus, we can conclude that IAM2 TMD has similar conformations in model and nativeE. colimembranes of comparable thickness and fluidity, notwithstanding the complexity of theE. colimembranes caused by their lipid diversity and the abundance of integral and peripheral membrane proteins.
Mutation of two intronic nucleotides alters RNA structure and dynamics inhibiting MBNL1 and RBFOX1 regulated splicing of the Insulin Receptor
Authors: Nowzari Zohreh R. , Hale Melissa , Ellis Joseph , Biaesch Samantha , Vangaveti Sweta , Reddy Kaalak , Chen Alan A. , Berglund J. Andrew
Published: January 2024

Alternative splicing (AS) of Exon 11 of the Insulin Receptor (INSR) is highly regulated and disrupted in several human disorders. To better understandINSRexon 11 AS regulation, splicing activity of anINSRexon 11 minigene reporter was measured across a gradient of the AS regulator muscleblind-like 1 protein (MBNL1). The RNA-binding protein Fox-1 (RBFOX1) was added to determine its impact on MBNL1-regulated splicing. The role of the RBFOX1 UGCAUG binding site within intron 11 was assessed across the MBNL1 gradient. Mutating the UGCAUG motif inhibited RBFOX1 regulation of exon 11 and had the unexpected effect of reducing MBNL1 regulation of this exon. Molecular dynamics simulations showed that exon 11 and the adjacent RNA adopts a dynamically stable conformation. Mutation of the RBFOX1 binding site altered RNA structure and dynamics, while a mutation that created an optimal MBNL1 binding site at the RBFOX1 site shifted the RNA back to wild type. An antisense oligonucleotide (ASO) was used to confirm the structure in this region of the pre-mRNA. This example of intronic mutations shifting pre-mRNA structure and dynamics to modulate splicing suggests RNA structure and dynamics should be taken into consideration for AS regulation and therapeutic interventions targeting pre-mRNA.Abstract figure:

Model forINSRexon 11 splicing regulation through the UGCAUG motif. We propose that the UGCAUG motif, MBNL1, and RBFOX1 cooperatively regulateINSRexon 11 splicing. Mutating this UGCAUG motif is sufficient to alter RNA structural dynamics to disrupt this regulation.
Activity ofSalmonellaSPI-1 inhibits the TLR4-dependent transcriptional but not translational response during macrophage infection
Authors: Wood George , Johnson Rebecca , Brember Matt , Lastovka Filip , Tourlomousis Pani , Bryant Clare , Chung Betty Y-W
Published: January 2024

Changes in gene expression during bacterial infection are the combined result of altered transcription and translation, with the latter comparatively understudied. Gram-negative bacteria rapidly trigger cytokine gene transcription in macrophages through the activation of pathogen associated molecular pattern receptors, for example detection ofSalmonellalipopolysaccharide (LPS) from the bacterial cell envelope by Toll-like receptor 4 (TLR4). Here, through time-resolved parallel translatomic and transcriptomic profiling, we now show temporal TLR4-specific translational upregulation of cell signalling proteins in macrophages induced bySalmonella. While transcriptional upregulation of these genes is dampened through the activity of theSalmonellaSPI-1 type three secretion system, a robust translational response remains. These data reveal an important host-pathogen translational regulatory network that modifies the innate immune response of macrophages to infection.
Intrinsic and extrinsic determinants of conditional localization of Mms6 to magnetosome organelles inMagnetospirillum magneticumAMB-1
Authors: Bickley Carson D. , Komeili Arash
Published: January 2024

Magnetotactic bacteria are a diverse group of microbes that use magnetic particles housed within intracellular lipid-bounded magnetosome organelles to guide navigation along geomagnetic fields. Development of magnetosomes and their magnetic crystals inMagnetospirillum magneticumAMB-1 requires the coordinated action of numerous proteins. Most proteins are thought to localize to magnetosomes during the initial stages of organelle biogenesis regardless of environmental conditions. However, magnetite-shaping protein Mms6 is only found in magnetosomes that contain magnetic particles, suggesting that it might conditionally localize after the formation of magnetosome membranes. The mechanisms for this unusual mode of localization to magnetosomes are unclear. Here, using pulse-chase labeling, we show that Mms6 translated under non-biomineralization conditions translocates to pre-formed magnetosomes when cells are shifted to biomineralizing conditions. Genes essential for magnetite production, namelymamE, mamM,andmamOare necessary for Mms6 localization, whereasmamNinhibits Mms6 localization. MamD localization is also investigated and found to be controlled by similar cellular factors. The membrane localization of Mms6 is dependent on a glycine-leucine repeat region, while the N-terminal domain of Mms6 is necessary for retention in the cytosol and impacts conditional localization to magnetosomes. The N-terminal domain is also sufficient to impart conditional magnetosome localization to MmsF, altering its native constitutive magnetosome localization. Our work illuminates an alternative mode of protein localization to magnetosomes in which Mms6 and MamD are kept in the cytosol by MamN until biomineralization initiates, whereupon they translocate into magnetosome membranes to control the development of growing magnetite crystals.

Importance

Magnetotactic bacteria (MTB) are a diverse group of bacteria that form magnetic nanoparticles surrounded by membranous organelles. MTB are widespread and serve as a model for bacterial organelle formation and biomineralization. Magnetosomes require a specific cohort of proteins to enable magnetite formation, but how those proteins are localized to magnetosome membranes is unclear. Here, we investigate protein localization using pulse-chase microscopy and find a system of protein coordination dependent on biomineralization permissible conditions. In addition, our findings highlight a protein domain that alters the localization behavior of magnetosome proteins. Utilization of this protein domain may provide a synthetic route for conditional functionalization of magnetosomes for biotechnological applications.
Activating A1 adenosine receptor signaling boosts early pulmonary neutrophil recruitment in aged mice in response toStreptococcus pneumoniaeinfection
Authors: Simmons Shaunna R. , Herring Sydney E. , Tchalla Essi Y.I , Lenhard Alexsandra P. , Bhalla Manmeet , Bou Ghanem Elsa N.
Published: January 2024

Background:

Streptococcus pneumoniae(pneumococcus) is a leading cause of pneumonia in older adults. Successful control of pneumococci requires robust pulmonary neutrophil influx early in infection. However, aging is associated with aberrant neutrophil recruitment and the mechanisms behind that are not understood. Here we explored how neutrophil recruitment following pneumococcal infection changes with age and the host pathways regulating this.

Results:

Following pneumococcal infection there was a significant delay in early neutrophil recruitment to the lungs of aged mice. Neutrophils from aged mice showed defects in trans-endothelial migrationin vitrocompared to young controls. To understand the pathways involved, we examined immune modulatory extracellular adenosine (EAD) signaling, that is activated upon cellular damage. Signaling through the lower affinity A2A and A2B adenosine receptors had no effect on neutrophil recruitment to infected lungs. In contrast, inhibition of the high affinity A1 receptor in young mice blunted neutrophil recruitment to the lungs following infection. A1 receptor inhibition decreased expression of CXCR2 on circulating neutrophils, which is required for transendothelial migration. Indeed, A1 receptor signaling on neutrophils was required for their ability to migrate across endothelial cells in response to infection. Aging was not associated with defects in EAD production or receptor expression on neutrophils. However, agonism of A1 receptor in aged mice rescued the early defect in neutrophil migration to the lungs and improved control of bacterial burden.

Conclusions:

This study suggests age-driven defects in EAD damage signaling can be targeted to rescue the delay in pulmonary neutrophil migration in response to bacterial pneumonia.
Evolution of plant cell-type-specificcis-regulatory elements
Authors: Yan Haidong , Mendieta John P. , Zhang Xuan , Marand Alexandre P. , Liang Yan , Luo Ziliang , Minow Mark A.A. , Jang Hosung , Li Xiang , Roulé Thomas , Wagner Doris , Tu Xiaoyu , Wang Yonghong , Jiang Daiquan , Zhong Silin , Huang Linkai , Wessler Susan R. , Schmitz Robert J.
Published: January 2024

Cis-regulatory elements (CREs) are critical in regulating gene expression, and yet understanding of CRE evolution remains challenging. Here, we constructed a comprehensive single-cell atlas of chromatin accessibility inOryza sativa, integrating data from 103,911 nuclei representing 126 discrete cell states across nine distinct organs. We used comparative genomics to compare cell-type resolved chromatin accessibility betweenO. sativaand 57,552 nuclei from four additional grass species (Zea mays, Sorghum bicolor, Panicum miliaceum, andUrochloa fusca). Accessible chromatin regions (ACRs) had different levels of conservation depending on the degree of cell-type specificity. We found a complex relationship between ACRs with conserved noncoding sequences, cell-type specificity, conservation, and tissue-specific switching. Additionally, we found that epidermal ACRs were less conserved compared to other cell types, potentially indicating that more rapid regulatory evolution has occurred in the L1-derived epidermal layer of these species. Finally, we identified and characterized a conserved subset of ACRs that overlapped the repressive histone modification H3K27me3, implicating them as potentially silencer-like CREs maintained by evolution. Collectively, this comparative genomics approach highlights the dynamics of plant cell-type-specific CRE evolution.
Cardiovascular disease and Osteoporosis : A Mendelian randomization study
Authors: Wang Zhao , Zhang Shuyi , Gong Hongyang , Zhao Guoxu , Xiao Hong , Yuan Shuai , Wu Wenhao , Xu Pai , Chen Yihong , Yang Mei , Kang Chan
Published: January 2024

I.

Background

Cardiovascular disease (CVD) may have some association with osteoporosis (OP). This Mendelian randomization (MR) investigation aimed to explore the potential causal linkage between CVD and OP.

Methods

Utilizing genome-wide association study data from individuals of European descent, we pinpointed Single Nucleotide Polymorphisms (SNPs) relevant to CVD, including those for coronary heart disease (CHD) with 64,762 cases and 22,233 controls, heart failure (HF) comprising 47,309 cases against 930,014 controls, and stroke with a case-control tally of 3,611 to 18,084, to serve as the instrumental variables. Later, we searched for total body bone mineral density (BMD) statistics which were used as phenotypes for OP(sample size = 56,284). In this paper, the traditional inverse variance weighting (IVW) method, the weighted median estimation method, and the MR-Egger method are used to estimate different results. The MR-Egger intercept test, outlier (Mr-PRESSO) test and Cochran-Q statistic are used to detect potential directional pleiotropy and heterogeneity, while we also draw the scatter plot, funnel plot and forest plot. Additionally, a reverse-direction MR analysis was performed to explore the potential for reverse causation.

Results

The IVW analysis showed that CHD could significantly impact total body BMD levels, and every higher standard deviation in the risk of CHD decreased the average total body BMD by 0.0459 units in the IVW analysis(Beta = -0.0459; 95%CI = -0.0815 –-0.0104, P = 0.0113). Reverse MR analysis showed no significant correlation of the change of total body BMD on the prevalence effect of CHD. No particular relationship exists between HF and total body BMD. There was no significant effect between the changes in total body BMD induced by stroke. Reverse MR analysis revealed no significant correlation between alterations in total body BMD on stroke.

Conclusion

Our analysis points to a substantial causative link between CHD and the vulnerability to OP, potentially paving the way for innovative approaches in treating and preventing OP.
Effect of testosterone therapy on breast tissue composition and mammographic breast density in trans masculine individuals
Authors: Heng Yujing J , Baker Gabrielle M , Fein-Zachary Valerie J , Guzman-Arocho Yaileen D , Bret-Mounet Vanessa C , Massicott Erica S , Gitin Sy , Russo Paul , Tobias Adam M , Bartlett Richard A , Varma Gopal , Kontos Despina , Yaghjyan Lusine , Irwig Michael S , Potter Jennifer E , Wulf Gerburg M
Published: January 2024

Objective

Determine the association between TT and breast tissue composition and breast tissue density in trans masculine individuals (TMIs).

Design

This is a cross-sectional study.

Setting

TMIs (n=444) underwent chest-contouring surgeries to treat their gender dysphoria between 2013 and 2019 at an urban medical center.

Participants

Of the 444 TMIs, 425 had pathology images analyzed by our deep-learning algorithm to extract breast tissue composition. A subset of 42/444 TMIs had mammography prior to surgery; mammography files were available for 25/42 TMIs and analyzed using a breast density software, LIBRA.

Main Outcome(s) and Measure(s)

The first outcome was the association of duration of TT and breast tissue composition assessed by pathologists (categories of lobular atrophy and stromal composition) or by our algorithm (% epithelium, % fibrous stroma, and % fat). The second outcome is the association of TT and breast density as assessed by a radiologist (categorical variable) or by LIBRA (percent density, absolute dense area, and absolute non-dense area).

Results

Length of TT was associated with increasing degrees of lobular atrophy (p<0.001) but not fibrous content (p=0.821) when assessed by the pathologists. Every six months of TT was associated with decreased amounts of both epithelium (exp(β)=0.97, 95% CI 0.95-0.98, adjp=0.005) and stroma (exp(β)=0.99, 95% CI 0.98-1.00, adjp=0.051), but not fat (exp(β)=1.01, 95%CI 0.98-1.05,p=0.394) in fully adjusted models. There was no association between TT and radiologist’s breast density assessment (p=0.575) or LIBRA measurements (p>0.05).

Conclusions

TT decreases breast epithelium and fibrous stroma, thus potentially reducing the breast cancer risk of TMIs. Further studies are warranted to elucidate the effect of TT on breast density and breast cancer risk.

Summary Box

Very little is known about the effect of gender-affirming testosterone therapy on cancer risks, such as breast cancer.

Epidemiological studies had different conclusions about the association between testosterone and breast cancer in cisgender women (positive association) and trans masculine individuals (inverse association).

More laboratory-based research are needed to understand the effect of testosterone on breast cancer risk in the understudied trans masculine population.

Our study provides quantitative histological evidence to support prior epidemiological reports that testosterone may reduce breast cancer risk in trans masculine individuals.
Prevalence of Substance Use and related Behaviors among Tertiary Students: A Cross-sectional Survey in Yaoundé, Cameroon
Authors: Edzamba Michel Franck , Lekeumo Cheuyem Fabrice Zobel , Amani Adidja , Mossus Tatiana
Published: January 2024

Background

The use of psychoactive substances is a major global public health problem. People aged 15-24 years are more likely to abuse psychoactive substances than the general population. Substances use among youth, especially students in higher education is increasing rapidly worldwide. This study aimed to assess the prevalence of substances use among university students and to describe their behavioral profiles.

Methods

An institutional-based descriptive and cross-sectional study was conducted from September to October 2023 at the Yaoundé 1 University in Cameroon. A convenience non probabilistic sampling method were used to recruit consenting students. The data collectors were medical students who were trained for 2 days and given appropriate instructions before the survey. The data collected were reviewed and checked for completeness before being entered. All data were coded and entered into Microsoft Excel 2016. Descriptive statistics were performed using R Statistics 4.3.1. Qualitative data were collected from all participants through interviews.

Results

A total of 191 university students were enrolled in the study. The median age was 20 years. They were predominantly male (66.5%) and aged between 20-25. The prevalence of substance use was 66% for alcohol consumption, 33.5% for smoking habits and 26.7% for drug use. The main motivations for substance use were companionship, thrill-seeking and curiosity. More than a third of students were polysubstance users (35.1%). Most participants were aware of the academic consequence (85.9%) and almost all (93.7%) acknowledged the physical and psycho-social consequences of substance use.

Conclusion

There is a high rate of psychoactive substance use among university students. Therefore, effective campus-based counseling, peer education, and national surveillance systems that can monitor risky behaviors among university students should be implemented.
A One-Shot Lossless Algorithm for Cross-Cohort Learning in Mixed-Outcomes Analysis
Authors: Li Ruowang , Benz Luke , Duan Rui , Denny Joshua C. , Hakonarson Hakon , Mosley Jonathan D. , Smoller Jordan W. , Wei Wei-Qi , Lumley Thomas , Ritchie Marylyn D. , Moore Jason H. , Chen Yong
Published: January 2024

In cross-cohort studies, integrating diverse datasets, such as electronic health records (EHRs), is both essential and challenging due to cohort-specific variations, distributed data storage, and data privacy concerns. Traditional methods often require data pooling or complex data harmonization, which can reduce efficiency and limit the scope of cross-cohort learning. We introduce mixWAS, a one-shot, lossless algorithm that efficiently integrates distributed EHR datasets via summary statistics. Unlike existing approaches, mixWAS preserves cohort-specific covariate associations and supports simultaneous mixed-outcome analyses. Simulations demonstrate that mixWAS outperforms conventional methods in accuracy and efficiency across various scenarios. Applied to EHR data from seven cohorts in the US, mixWAS identified 4,534 significant cross-cohort genetic associations among traits such as blood lipids, BMI, and circulatory diseases. Validation with an independent UK EHR dataset confirmed 97.7% of these associations, underscoring the algorithm’s robustness. By enabling lossless cross-cohort integration, mixWAS improves the precision of multi-outcome analyses and expands the potential for actionable insights in healthcare research.
From Chest Pain to Coronary Functional Testing: Clinical and Economic Impact of Coronary Microvascular Dysfunction
Authors: Merdler Ilan , Wallace Ryan , Hill Andrew , Medranda Giorgio A. , Reddy Pavan , Zhang Cheng , Ozturk Sevket Tolga , Sawant Vaishnavi , Weintraub William S. , Lopez Kassandra , Ben-Dor Itsik , Waksman Ron , Hashim Hayder D. , Case Brian C.
Published: January 2024

Background

Coronary functional testing to formally diagnose coronary microvascular dysfunction (CMD) reduces cardiovascular events and alleviates angina. This study aims to investigate the extensive and complex journey that patients with CMD undergo, from the onset of chest pain to eventual diagnosis.

Methods

Data from the Coronary Microvascular Disease Registry (CMDR) were analyzed, including information on the date of first documentation of chest pain, number of non-invasive and invasive tests the patient underwent, emergency department visits, and hospitalizations. In addition, we estimated the total cost per patient. A total of 61 patients with CMD diagnosis were included in this analysis.

Results

The cohort had an average age of 65.6±9.9 years. The median time from initial chest pain symptoms to diagnosis was 0.62 (interquartile range [IQR]: 0.06-2.96) years. During this period, patients visited the emergency department a median of 1.0 (IQR: 0.0-2.0) times. Diagnostic tests included 3.0 (IQR: 2.0-6.0) electrocardiograms, 3.0 (IQR: 0.0-6.0) high-sensitivity troponin tests, and 1.0 (IQR: 1.0-2.0) echocardiograms. Prior to diagnosis of CMD, 13 (21.3%) patients had left heart catheterization without coronary functional testing. Non-invasive testing for ischemia was conducted in 43 (70.5%) patients. Alternative non-cardiac diagnoses were given to 11 (18.0%) patients during the diagnostic process, with referrals made to gastroenterology for 16 (26.2%) and pulmonology for 10 (16.4%) patients. The cost averaged $1,790±2,506 per patient.

Conclusion

Timely identification of CMD offers promising opportunities for prompt symptom alleviation, accompanied by reduced visits to the emergency department, cardiovascular testing, invasive medical procedures, and consequently reduced healthcare expenses.

Clinical Trial Registry

Coronary Microvascular Disease Registry (CMDR),clinicaltrials.gov,NCT05960474

What is Known; What the Study Adds

What is Known

- Angina pectoris is a major global health concern, impacting millions of individuals around the world.

- Coronary microvascular dysfunction (CMD) is a known etiology to cause angina.

What the Study Adds

- This study reveals the challenging journey of CMD patients from chest pain to diagnosis, showing the complexity, and overlapping symptoms of CMD, leading to under/misdiagnosis or delay in definitive diagnosis.

- Healthcare providers must improve CMD awareness and understanding to ensure timely and accurate diagnosis, minimizing patient burden and unnecessary expenses.

- Further research and awareness campaigns are crucial to optimize CMD management, leading to better healthcare outcomes and reduced economic strain.
A split-GAL4 driver line resource forDrosophilaneuron types
Authors: Meissner Geoffrey W , Vannan Allison , Jeter Jennifer , Close Kari , DePasquale Gina M , Dorman Zachary , Forster Kaitlyn , Beringer Jaye Anne , Gibney Theresa V , Hausenfluck Joanna H , He Yisheng , Henderson Kristin , Johnson Lauren , Johnston Rebecca M , Ihrke Gudrun , Iyer Nirmala , Lazarus Rachel , Lee Kelley , Li Hsing-Hsi , Liaw Hua-Peng , Melton Brian , Miller Scott , Motaher Reeham , Novak Alexandra , Ogundeyi Omotara , Petruncio Alyson , Price Jacquelyn , Protopapas Sophia , Tae Susana , Taylor Jennifer , Vorimo Rebecca , Yarbrough Brianna , Zeng Kevin Xiankun , Zugates Christopher T , Dionne Heather , Angstadt Claire , Ashley Kelly , Cavallaro Amanda , Dang Tam , Gonzalez Guillermo A , Hibbard Karen L , Huang Cuizhen , Kao Jui-Chun , Laverty Todd , Mercer Monti , Perez Brenda , Pitts Scarlett , Ruiz Danielle , Vallanadu Viruthika , Zheng Grace Zhiyu , Goina Cristian , Otsuna Hideo , Rokicki Konrad , Svirskas Robert R , Cheong Han SJ , Dolan Michael-John , Ehrhardt Erica , Feng Kai , Galfi Basel El , Goldammer Jens , Huston Stephen J , Hu Nan , Ito Masayoshi , McKellar Claire , Minegishi Ryo , Namiki Shigehiro , Nern Aljoscha , Schretter Catherine E , Sterne Gabriella R , Venkatasubramanian Lalanti , Wang Kaiyu , Wolff Tanya , Wu Ming , George Reed , Malkesman Oz , Aso Yoshinori , Card Gwyneth M , Dickson Barry J , Korff Wyatt , Ito Kei , Truman James W , Zlatic Marta , Rubin Gerald M ,   FlyLight Project Team
Published: January 2024

Techniques that enable precise manipulations of subsets of neurons in the fly central nervous system have greatly facilitated our understanding of the neural basis of behavior. Split-GAL4 driver lines allow specific targeting of cell types inDrosophila melanogasterand other species. We describe here a collection of 3060 lines targeting a range of cell types in the adultDrosophilacentral nervous system and 1373 lines characterized in third-instar larvae. These tools enable functional, transcriptomic, and proteomic studies based on precise anatomical targeting. NeuronBridge and other search tools relate light microscopy images of these split-GAL4 lines to connectomes reconstructed from electron microscopy images. The collections are the result of screening over 77,000 split hemidriver combinations. Previously published and new lines are included, all validated for driver expression and curated for optimal cell type specificity across diverse cell types. In addition to images and fly stocks for these well-characterized lines, we make available 300,000 new 3D images of other split-GAL4 lines.
Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation
Authors: Singh Pratik N. P. , Gu Wei , Madha Shariq , Lynch Allen W. , Cejas Paloma , He Ruiyang , Bhattacharya Swarnabh , Gomez Miguel M. , Oser Matthew G. , Brown Myles , Long Henry W. , Meyer Clifford A. , Zhou Qiao , Shivdasani Ramesh A.
Published: January 2024

Enteroendocrine cells (EECs), which secrete serotonin (enterochromaffin cells, EC) or a dominant peptide hormone, serve vital physiologic functions. As with any adult human lineage, the basis for terminal cell diversity remains obscure. We replicated human EEC differentiationin vitro, mapped transcriptional and chromatin dynamics that culminate in discrete cell types, and studied abundant EEC precursors expressing selected transcription factors (TFs) and gene programs. Before expressing the pre-terminal factor NEUROD1, non-replicating precursors oscillated between epigenetically similar but transcriptionally distinctASCL1+andHES6hicell states. Loss of either factor substantially accelerated EEC differentiation and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and hormone-producing cell features. Expressed late in EEC differentiation, the latter TFs mainly bindcis-elements that are accessible in undifferentiated stem cells and tailor the subsequent expression of TF combinations that specify EEC types. Thus, TF oscillations retard EEC maturation to enable accurate EEC diversification.
Definition of regulatory elements and transcription factors controlling immune cell gene expression at single cell resolution using single nucleus ATAC-seq
Authors: Yang Pengxin , Corbett Ryan , Daharsh Lance , Uribe Juber Herrera , Byrne Kristen A. , Loving Crystal L. , Tuggle Christopher
Published: January 2024

The transcriptome of porcine peripheral blood mononuclear cells (PBMC) at single cell (sc) resolution is well described, but little is understood about the cis-regulatory mechanism behind scPBMC gene expression. Here, we profiled the open chromatin landscape of porcine PBMC using single nucleus ATAC sequencing (snATAC-seq). Approximately 22% of the identified peaks overlapped with annotated transcription start sites (TSS). Using clustering based on open chromatin pattern similarity, we demonstrate that cell type annotations using snATAC-seq are highly concordant to that reported for sc RNA sequencing (scRNA-seq). The differentially accessible peaks (DAPs) for each cell type were characterized and the pattern of accessibility of the DAPs near cell type markers across cell types was similar to that of the average gene expression level of corresponding marker genes. Additionally, we found that peaks identified in snATAC-seq have the potential power to predict the cell type specific transcription starting site (TSS). We identified both transcription factors (TFs) whose binding motif were enriched in cell type DAPs of multiple cell types and cell type specific TFs by conducting transcription factor binding motif (TFBM) analysis. Furthermore, we identified the putative enhancer or promoter regions bound by TFs for each differentially expressed gene (DEG) having a DAP that overlapped with its TSS by generating cis-co-accessibility networks (CCAN). To predict the regulators of such DEGs, TFBM analysis was performed for each CCAN. The regulator TF-target DEG pair predicted in this way was largely consistent with the results reported in the ENCODE Transcription Factor Targets Dataset (TFTD). This snATAC-seq approach provides insights into the chromatin accessibility landscape of porcine PBMCs and enables discovery of TFs predicted to control DEG through binding regulatory elements whose chromatin accessibility correlates with the DEG promoter region.
RnaBench: A Comprehensive Library forIn SilicoRNA Modelling
Authors: Runge Frederic , Farid Karim , Franke Jörg K.H. , Hutter Frank
Published: January 2024

RNA is a crucial regulator in living organisms and malfunctions can lead to severe diseases. To explore RNA-based therapeutics and applications, computational structure prediction and design approaches play a vital role. Among these approaches, deep learning (DL) algorithms show great promise. However, the adoption of DL methods in the RNA community is limited due to various challenges. DL practitioners often underestimate data homologies, causing skepticism in the field. Additionally, the absence of standardized benchmarks hampers result comparison, while tackling low-level tasks requires significant effort. Moreover, assessing performance and visualizing results prove to be non-trivial and task-dependent. To address these obstacles, we introduce RnaBench (RnB), an open-source RNA library designed specifically for the development of deep learning algorithms that mitigate the challenges during data generation, evaluation, and visualization. It provides meticulously curated homology-aware RNA datasets and standardized RNA benchmarks, including a pioneering RNA design benchmark suite featuring a novel real-world RNA design problem. Furthermore, RnB offers baseline algorithms, both existing and novel performance measures, as well as data utilities and a comprehensive visualization module, all accessible through a user-friendly interface. By leveraging RnB, DL practitioners can rapidly develop innovative algorithms, potentially revolutionizing the field of computational RNA research.
Multiscale characterization of the mechanics of curved fibered structures with application to biological materials
Authors: Sanz-Herrera J.A. , Apolinar-Fernandez A. , Jimenez-Aires A. , Perez-Alcantara P. , Dominguez J. , Reina-Romo E.
Published: January 2024

Curved fibered structures are ubiquitous in nature and this organization is found in the majority of biological tissues. Indeed, the mechanical behavior of these materials is of pivotal importance in biomechanics and mechanobiology fields. In this paper, we develop a multiscale formulation to characterize the macroscopic mechanical nonlinear behavior from the microstructure of fibered matrices. From the analysis of the mechanics of a randomly curved single fiber, a fibered matrix model is built to determine the macroscopic behavior following a homogenization approach. The model is tested for tensile, compression and shear loads in a number of applications reminiscent to collagen extracellular matrices. However, any other fibered microstructures can be studied following the proposed formulation. The presented approach naturally recovers instabilities at compression as well as the strain stiffening regime, which are observed experimentally in the mechanical behavior of collagen matrices. Indeed, it was found that the bending energy associated to fiber unrolling, is the most important source of energy developed by fibers for the analyzed cases in tensile and shear in all deformation regions (except the strain stiffening region), whereas bending energy dominates at compression too during buckling. The proposed computational framework can also be used to perform multiscale simulations in the referred applications. As a result, the developed methodology may be an interesting and complementary tool to characterize the nonlinear behavior and evolution of curved fibered structures present in biology and engineered materials.
Mind the instructions: reward cues are liked first, wanted later
Authors: Prutean Nicoleta , Vermeylen Luc , Kukkonen Nanne , Steendam S. Tabitha , Eayrs Joshua O. , Krebs Ruth M. , Wiersema Jan R. , Vassena Eliana , Boehler C. Nico , Notebaert Wim
Published: January 2024

Current theories propose that mental effort is invested only when the anticipated benefits, such as rewards, outweigh the associated costs, like task difficulty. Yet, it remains unclear whether this motivational and mitigating aspect of reward processing is reflected in the evaluation of reward/difficulty cues as such, and to what extent it depends on task experience. In a pre-registered experiment (N=84), we used the affect misattribution procedure (AMP) to gauge affective evaluations of nonword cues predicting reward and task difficulty levels. Contrary to previous studies, the AMP was administered at the outset, after cue instructions, and after the cues were used in a random dot motion (RDM) task. Compared to baseline, cues predicting a larger reward were evaluated more positively after RDM task experience, and most importantly, already after cue instructions, with no difference between the two phases. This evaluative effect manifested in increased performance after larger reward cues in the RDM task. Our results suggest that AMP effects may generally capture performance expectations which are independent of task experience. Importantly, these instructed expectations of reward and difficulty play a crucial role in the evaluation and subsequent investment of mental effort.
Polygenic risk for schizophrenia converges on alternative polyadenylation as molecular mechanism underlying synaptic impairment
Authors: Raabe Florian J. , Hausruckinger Anna , Gagliardi Miriam , Ahmad Ruhel , Almeida Valeria , Galinski Sabrina , Hoffmann Anke , Weigert Liesa , Rummel Christine K. , Murek Vanessa , Trastulla Lucia , Jimenez-Barron Laura , Atella Alessia , Maidl Susanne , Menegaz Danusa , Hauger Barbara , Wagner Eva-Maria , Gabellini Nadia , Kauschat Beate , Riccardo Sara , Cesana Marcella , Papiol Sergi , Sportelli Vincenza , Rex-Haffner Monika , Stolte Sebastian J. , Wehr Michael C. , Salcedo Tatiana Oviedo , Papazova Irina , Detera-Wadleigh Sevilla , McMahon Francis J , Schmitt Andrea , Falkai Peter , Hasan Alkomiet , Cacchiarelli Davide , Dannlowski Udo , Nenadić Igor , Kircher Tilo , Scheuss Volker , Eder Matthias , Binder Elisabeth B. , Spengler Dietmar , Rossner Moritz J. , Ziller Michael J.
Published: January 2024

Schizophrenia (SCZ) is a genetically heterogenous psychiatric disorder of highly polygenic nature. Correlative evidence from genetic studies indicate that the aggregated effects of distinct genetic risk factor combinations found in each patient converge onto common molecular mechanisms. To prove this on a functional level, we employed a reductionistic cellular model system for polygenic risk by differentiating induced pluripotent stem cells (iPSCs) from 104 individuals with high polygenic risk load and controls into cortical glutamatergic neurons (iNs). Multi-omics profiling identified widespread differences in alternative polyadenylation (APA) in the 3’ untranslated region of many synaptic transcripts between iNs from SCZ patients and healthy donors. On the cellular level, 3’APA was associated with a reduction in synaptic density of iNs. Importantly, differential APA was largely conserved between postmortem human prefrontal cortex from SCZ patients and healthy donors, and strongly enriched for transcripts related to synapse biology. 3’APA was highly correlated with SCZ polygenic risk and affected genes were significantly enriched for SCZ associated common genetic variation. Integrative functional genomic analysis identified the RNA binding protein and SCZ GWAS risk gene PTBP2 as a critical trans-acting factor mediating 3’APA of synaptic genes in SCZ subjects. Functional characterization of PTBP2 in iNs confirmed its key role in 3’APA of synaptic transcripts and regulation of synapse density. Jointly, our findings show that the aggregated effects of polygenic risk converge on 3’APA as one common molecular mechanism that underlies synaptic impairments in SCZ.
Key determinants of CRISPR/Cas9 induced inversions in tomato
Authors: Grubben Jillis , Bijsterbosch Gerard , Visser Richard G.F. , Schouten Henk J.
Published: January 2024

Inversions in chromosomes occur widely within plants and suppress meiotic recombination which can be beneficial or detrimental for plant breeders. Therefore, induction or reversion of inversions via CRISPR/Cas9 has been extensively researched recently. Extensive variation in inversion induction rates and sizes have been reported, from hundreds to several million base pairs. Here, we dissect the influential factors of inversion induction efficiency using CRISPR/Cas9. By using a fixed reference gRNA, we could directly correlate gRNA mutation frequency to inversion frequency and inversion size, of inversions up to 37.5 Mb in length in tomato. Our findings indicate that the least efficient gRNA is the bottleneck for inversion induction, with inversion size having no significant influence unless the inversions were larger than 1 Mb in size. For these huge inversions, the frequency dropped astoundingly, regardless of the gRNA cutting efficiencies. We hypothesize anin plantayet unknown variant of non-homologous-end-joining (NHEJ)-based repair which utilizes active transport of damaged chromosomal sections to dedicated repair sites in the cell nucleus, where repair is finalized. We propose that large inversions are formed less frequently because the transport of these segments to the repair sites may be hampered by their sheer size.
User-friendly Oblique Plane Microscopy on a fully functional commercially available microscope base
Authors: Sirinakis George , Allgeyer Edward S. , Nashchekin Dmitry , St Johnston Daniel
Published: January 2024

In this work we present an Oblique Plane Microscope designed to work seamlessly with a commercially available microscope base. To support all the functionality offered by the microscope base, where the position of the objective lens is not fixed, we adopted a two-mirror scanning geometry that can compensate for changes to the position of the objective lens during routine microscope operation. We showed that within the expected displacement range of the 100X, 1.35 NA objective lens away from its designed position, and for most practical applications, there is no significant effect on the resolving power, or the fidelity of the 3D data produced by the microscope. Compared to the more traditional scan-lens/galvo-mirror combination, the two-mirror scanning geometry offers higher light-efficiency and a more compact footprint, which could be beneficial to all OPM designs regardless of the use of a commercial base or not.
Vestibular prepulse inhibition of the human blink reflex
Authors: Ciocca Matteo , Hosli Sarah , Hadi Zaeem , Mahmud Mohammad , Tai Yen , Seemungal Barry M
Published: January 2024

Objective

Auditory and somatosensory prepulses are commonly used to assess prepulse inhibition (PPI). The effect of a vestibular prepulse upon blink reflex (BR) excitability has not been hitherto assessed.

Methods

Twenty-two healthy subjects and two patients with bilateral peripheral vestibular failure took part in the study. Whole body yaw rotation in the dark provided a vestibular inertial prepulse. BR was electrically evoked after the end of the rotation. The area-under-the-curve (area) of the BR responses (R1, R2, and R2c) was recorded and analysed.

Results

A vestibular prepulse inhibited the R2 (p < 0.001) and R2c area (p < 0.05). Increasing the angular acceleration did not increase the R2/R2c inhibition (p>0.05). Voluntary suppression of the vestibular-ocular reflex did not affect the magnitude of inhibition (p>0.05). Patients with peripheral vestibular failure did not show any inhibition.

Conclusions

Our data support a vestibular-gating mechanism in humans.

Significance

The main brainstem nucleus mediating PPI – the pedunculopontine nucleus (PPN) – is heavily vestibular responsive, which is consistent with our findings of a vestibular-mediated PPI. Our technique may be used to interrogate the fidelity of brain circuits mediating vestibular-related PPN functions. Given the PPN’s importance in human postural control, our technique may also provide a neurophysiological biomarker of balance.

Highlights

This is the first report of a vestibular prepulse inhibition of the blink reflex.

A vestibular prepulse inhibits the R2/R2c area in healthy subjects but not in patients with bilateral peripheral vestibular failure.

Vestibular PPI is a potential neurophysiological marker of vestibular-motor integration at the brainstem level.