bluuebunny/crossref_metadata_2025 huggingface dataset:
Marked irregular myofiber shape is a hallmark of human skeletal muscle aging and is reversed by heavy resistance training
Authors: Soendenbroe Casper , Karlsen Anders , Svensson Rene B. , Kjaer Michael , Andersen Jesper L. , Mackey Abigail L.
Published: June 2023

Background

Age-related loss of strength is disproportionally greater than the loss of mass, suggesting maladaptations in the neuro-myo-tendinous system. Myofibers are often misshaped in aged and diseased muscle, but systematic analyses of large sample sets are lacking. Our aim was to investigate myofiber shape in relation to age, exercise, myofiber type, species, and sex.

Methods

Previously collected vastus lateralis muscle biopsies (n=265) from 197 males and females, covering an age-span of 20 to 97 years, were examined. The gastrocnemius and soleus muscles of 7 C57BL/6 mice were also examined. Immunofluorescence and ATPase stainings of muscle cross-sections were used to measure myofiber cross-sectional area (CSA) and perimeter, from which a shape factor index (SFI) was calculated in a fiber type specific manner (type I and II in humans; type I, IIa, IIx and IIb in mice). Heavy resistance training (RT) was performed 3 times per week for 3-4 months by a subgroup (n=59). Correlation analyses were performed comparing SFI and CSA with age, muscle mass, maximal voluntary contraction (MVC), rate of force development (RFD), and specific force (MVC/muscle mass).

Results

In human muscle, SFI was positively correlated with age for both type I (R2=0.20) and type II (R2=0.38) myofibers. When subjects were separated into age cohorts, SFI was lower for type I (p<0.001) and II (p<0.001) myofibers in Young (20-36) compared to Old (60-80), and higher for type I (p<0.05) and II (p<0.001) myofibers in the Oldest Old (>80) compared to Old. The increased SFI in old muscle was observed in myofibers of all sizes. Within all three age cohorts, type II myofibers SFI was higher than for type I myofibers (p<0.001), which was also the case in mice muscles (p<0.001). Across age cohorts, there was no difference between males and females in SFI for either type I (p=0.496/0.734) or II (p=0.176/0.585) myofibers. Multiple linear regression revealed that SFI, after adjusting for age and myofiber CSA, has independent explanatory power for 8 out of 10 indices of muscle mass and function. RT reduced SFI of type II myofibers in both Young and Old (p<0.001).

Conclusions

Here, we identify type I and II myofiber shape in humans and mice as a hallmark of muscle ageing, that independently predicts volumetric and functional assessments of muscle health. RT reverts the shape of type II myofibers, indicating that lack of neuromuscular activation might lead to myofiber deformity.
Dynamic functional connectivity in the right temporoparietal junction captures variations in autistic trait expression
Authors: Balsa Laura Bravo , Abu-Akel Ahmad , Mevorach Carmel
Published: June 2023

Background

Autistic individuals can experience difficulties with attention reorienting and Theory of Mind (ToM), which are closely associated with anterior and posterior subdivisions of the right temporoparietal junction. While the link between these processes remains unclear it is likely subserved by a dynamic crosstalk between these two subdivisions. We therefore examined the dynamic functional connectivity (dFC) between the anterior and posterior TPJ, as a biological marker of attention and ToM, to test its contribution to the manifestation of autistic trait expression in Autism Spectrum Disorder (ASD).

Methods

Two studies were conducted, exploratory (14 ASD, 15 TD) and replication (29 ASD, 29 TD), using resting-state fMRI data and the Social Responsiveness Scale (SRS) from the ABIDE repository. Dynamic Independent Component Analysis was performed in both datasets using the CONN toolbox. An additional sliding-window analysis was performed in the replication study to explore different connectivity states (from highly negatively to highly positively correlated).

Results

dynamic FC was reduced in ASD compared to TD adults in both the exploratory and replication datasets and was associated with increased SRS scores (especially in ASD). Additional regression analyses revealed that for ASD, decreased SRS autistic expression was predicted by engagement of highly negatively correlated states, while engagement of highly positively correlated states predicted increased expression.

Conclusions

These findings provided consistent evidence that the difficulties observed in ASD are associated with altered patterns of dFC between brain regions subserving attention reorienting and ToM processes.
Quantile Regression for biomarkers in the UK Biobank
Authors: Wang Chen , Wang Tianying , Wei Ying , Aschard Hugues , Ionita-Laza Iuliana
Published: June 2023

Genome-wide association studies (GWAS) for biomarkers important for clinical phenotypes can lead to clinically relevant discoveries. GWAS for quantitative traits are based on simplified regression models modeling the conditional mean of a phenotype as a linear function of genotype. An alternative and easy to apply approach is quantile regression that naturally extends linear regression to the analysis of the entire conditional distribution of a phenotype of interest by modeling conditional quantiles within a regression framework. Quantile regression can be applied efficiently at biobank scale using standard statistical packages in much the same way as linear regression, while having some unique advantages such as identifying variants with heterogeneous effects across different quantiles, including non-additive effects and variants involved in gene-environment interactions; accommodating a wide range of phenotype distributions with invariance to trait transformation; and overall providing more detailed information about the underlying genotype-phenotype associations. Here, we demonstrate the value of quantile regression in the context of GWAS by applying it to 39 quantitative traits in the UK Biobank (n> 300, 000 individuals). Across these 39 traits we identify 7,297 significant loci, including 259 loci only detected by quantile regression. We show that quantile regression can help uncover replicable but unmodelled gene-environment interactions, and can provide additional key insights into poorly understood genotype-phenotype correlations for clinically relevant biomarkers at minimal additional cost.
In silicocharacterization of five novel disease-resistance proteins inOryza sativa sp. japonicaagainst bacterial leaf blight and rice blast diseases
Authors: Dhiman Vedikaa , Biswas Soham , Shekhawat Rajveer Singh , Sadhukhan Ayan , Yadav Pankaj
Published: June 2023

Oryza sativasp.japonicais the most widely cultivated variety of rice. It has evolved several defense mechanisms, including PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI), which provide resistance against different pathogens to overcome biotic stresses. Several disease-resistance genes and proteins, such as R genes and PRR proteins, have been reported in the scientific literature which shows resistance againstXanthomonas oryzaepv.oryzae(Xoo), a causative agent for bacterial leaf blight disease (BB), andMagnaporthe oryzae(M. oryzae), causing rice blast disease (RB). Although some of these resistance proteins have been studied, the functional characterization of resistance proteins in rice is not exhaustive. In the current study, we identified five novel resistance proteins against BB and RB diseases through gene network analysis. Structure and function prediction, disease-resistance domain identification, protein-protein interaction (PPI), and pathway analysis revealed that the five new proteins played a role in the disease resistance against BB and RB.In silicomodeling, refinement, and model quality assessment were performed to predict the best structures of these five proteins, and submitted to ModelArchive for future use. The functional annotation of the proteins revealed their involvement in the bacterial disease resistance of rice. We predicted that the new resistance proteins could be localized to the nucleus and plasma membrane. This study provides insight into developing disease-resistant rice varieties by predicting novel candidate resistance proteins, which will pave the way for their future characterization and assist rice breeders in improving crop yield and addressing future food security.
Molecular Pixelation: Single cell spatial proteomics by sequencing
Authors: Karlsson Filip , Kallas Tomasz , Thiagarajan Divya , Karlsson Max , Schweitzer Maud , Navarro Jose Fernandez , Leijonancker Louise , Geny Sylvain , Pettersson Erik , Rhomberg-Kauert Jan , Granillo Marcela Gonzalez , Bunz Jessica , Dahlberg Johan , Simonetti Michele , Sathe Prajakta , Brodin Petter , Barrio Alvaro Martinez , Fredriksson Simon
Published: June 2023

The spatial distribution of cell surface proteins govern vital processes of the immune system such as inter-cell communication and mobility. However, tools for studying these at high multiplexing scale, resolution, and throughput needed to drive novel discoveries are lacking. We present Molecular Pixelation, a DNA-sequencing based method for single cell analysis to quantify protein abundance, spatial distribution, and colocalization of targeted proteins using Antibody Oligonucleotide Conjugates (AOCs). Relative locations of AOCs are inferred by sequentially associating these into local neighborhoods using DNA-pixels containing unique pixel identifier (UPI) sequences, forming >1,000 connected spatial zones per single cell in three dimensions. DNA-sequencing reads are computationally arranged into spatial single cell maps for 76 proteins without cell compartmentalization. By studying immune cell dynamics and using spatial statistics on graph representations of the data, previously known and novel patterns of protein spatial polarization and co-localization were found in chemokine-stimulated T-cells.
Ancient DNA reveals the origins of the Albanians
Authors: Davranoglou Leonidas-Romanos , Aristodemou Aris , Wesolowski David , Heraclides Alexandros
Published: June 2023

The origins of the Albanian people have vexed linguists and historians for centuries, as Albanians first appear in the historical record in the 11thcentury CE, while their language is one of the most enigmatic branches of the Indo-European family. To identify the populations that contributed to the ancestry of Albanians, we undertake a genomic transect of the Balkans over the last 8000 years, where we analyse more than 6000 previously published ancient genomes using state-of-the-art bioinformatics tools and algorithms that quantify spatiotemporal human mobility. We find that modern Albanians descend from Roman era western Balkan populations, with additional admixture from Slavic-related groups. Remarkably, Albanian paternal ancestry shows continuity from Bronze Age Balkan populations, including those known as Illyrians. Our results provide an unprecedented understanding of the historical and demographic processes that led to the formation of modern Albanians and help locate the area where the Albanian language developed.
Engineering cell and nuclear morphology on nano topography by contact-free protein micropatterning
Authors: Sarikhani Einollah , Meganathan Dhivya Pushpa , Rahmani Keivan , Tsai Ching-Ting , Marquez-Serrano Abel , Li Xiao , Santoro Francesca , Cui Bianxiao , Klausen Lasse Hyldgaard , Jahed Zeinab
Published: June 2023

Platforms with nanoscale topography have recently become powerful tools in cellular biophysics and bioengineering. Recent studies have shown that nanotopography affects various cellular processes like adhesion and endocytosis, as well as physical properties such as cell shape.

To engineer nanopillars more effectively for biomedical applications, it is crucial to gain better control and understanding of how nanopillars affect cell and nuclear physical properties, such as shape and spreading area, and impact cellular processes like endocytosis and adhesion. In this study, we utilized a laser-assisted micropatterning technique to manipulate the 2D architectures of cells on 3D nanopillar platforms. We performed a comprehensive analysis of cellular and nuclear morphology and deformation on both nanopillar and flat substrates. Our findings demonstrate precise engineering of cellular architectures through 2D micropatterning on nanopillar platforms. We show that the coupling between nuclear and cell shape is disrupted on nanopillar surfaces compared to flat surfaces. Furthermore, we discovered that cell elongation on nanopillars enhances nanopillar-induced endocytosis. These results have significant implications for various biomedical applications of nanopillars, including drug delivery, drug screening, intracellular electrophysiology, and biosensing. We believe our platform serves as a versatile tool for further explorations, facilitating investigations into the interplay between cell physical properties and alterations in cellular processes.

Graphical Abstract
Enhanced expression of Dystrophin, IGF-1, CD44 and MYH3 in plasma and skeletal muscles including Diaphragm ofmdxmice after oral administration of Neu REFIX Beta 1,3-1,6 glucan
Authors: Preethy Senthilkumar , Sakamoto Shuji , Higuchi Takuma , Ichiyama Koji , Yamamoto Naoki , Ikewaki Nobunao , Iwasaki Masaru , Dedeepiya Vidyasagar Devaprasad , Srinivasan Subramaniam , Raghavan Kadalraja , Rajmohan Mathaiyan , Senthilkumar Rajappa , Abraham Samuel JK
Published: June 2023

Introduction

Duchenne muscular dystrophy (DMD) is a rare genetic disease, causing muscle degeneration due to lack of dystrophin with inadequate muscle regeneration culminating in muscle dysfunction. The N-163 strain ofAureobasidium Pullulansproduced Beta-1,3-1,6-glucan (Neu REFIX) reported to be safe with anti-inflammatory and anti-fibrotic efficacy earlier, herein we evaluated its effects on muscle regeneration inmdxmice.

Methods

Forty-five mice in three groups (n=15 each): Group 1 (normal), Group 2 (mdxcontrol), and Group 3 (mdxfed Neu REFIX) were evaluated for 45 days. IGF-1, Dystrophin, CD44 and MYH3 in diaphragm, plasma and skeletal muscle were evaluated by ELISA and immunohistochemistry.

Results

Mean IGF-1 expression was 20.32% and 16.27% higher in plasma (p = 0.03) and diaphragm respectively in Neu-REFIX group. Mean dystrophin was higher in Neu-REFIX group by 70.3% and 4.7% in diaphragm and plasma respectively than control. H-score intensity of CD44+ was >2.0 with an MYH3-positivity 20% higher in Neu-REFIX than control.

Conclusion

Oral administration of Neu REFIX was safe. Significantly enhanced plasma IGF-1 beside increased Dystrophin, MYH3 and CD44, proving a restoration of muscle regeneration and differentiation, especially in diaphragm, makes us recommend it as a disease modifying adjuvant in both early and advanced stages of DMD.
Nest traits for the world’s birds
Authors: Sheard Catherine , Street Sally E. , Healy Susan D. , Troisi Camille A. , Clark Andrew D. , Yovcheva Antonia , Trébaol Alexis , Vanadzina Karina , Lala Kevin N.
Published: June 2023

Motivation

A well-constructed nest is a key element of successful reproduction in most species of birds, and nest-building strategies vary widely across the class. Macroecological and macroevolutionary studies tend to group nest design into a small number of discrete categories, often based on taxonomic inference. In reality, however, many species display considerable intraspecific variation in their nest-building behaviour, and broad-level categories may include many functionally distinct nest types. To address this confusion in the literature and facilitate future studies of broad-scale variation in avian parental care, we here introduce a detailed, global comparative database of nest building in birds, together with preliminary correlations between these traits and species-level environmental variables.

Main types of variable contained

We present species-level data for nest structure, location, height, material composition, sex of builder, building time, and nest dimensions.

Spatial location and grain

Global. Maps are presented at the 1°x1° level.

Time period and grain

Included species are generally extant, although we present some data for recently extinct taxa. The data was collected 2017-2021 and was drawn from secondary sources published 1992-2021.

Major taxa and level of measurement

Partial or complete trait data is presented for 8,601 species of birds, representing 36 of 36 orders and 239 of 243 families.

Software format

Data have been uploaded as Supplementary Material in .xlsx format and are separated by species and source for all traits (S1) as well as summarised at the species level for structure and location variables (S2).
A genome-wide CRISPR screen in human prostate cancer cells reveals drivers of macrophage-mediated cell killing and positions AR as a tumor-intrinsic immunomodulator
Authors: Zaalberg Anniek , Minnee Emma , Mayayo-Peralta Isabel , Schuurman Karianne , Gregoricchio Sebastian , Schaik Thijs A. van , Hoekman Liesbeth , Li Dapei , Corey Eva , Janssen Hans , Lieftink Cor , Prekovic Stefan , Altelaar Maarten , Nelson Peter S. , Beijersbergen Roderick L. , Zwart Wilbert , Bergman Andries
Published: June 2023

The crosstalk between prostate cancer (PCa) cells and the tumor microenvironment plays a pivotal role in disease progression and metastasis and could provide novel opportunities for patient treatment. Macrophages are the most abundant immune cells in the prostate tumor microenvironment (TME) and are capable of killing tumor cells. To identify genes in the tumor cells that are critical for macrophage-mediated killing, we performed a genome-wide co-culture CRISPR screen and identified AR, PRKCD, and multiple components of the NF-κB pathway as hits, whose expression in the tumor cell are essential for being targeted and killed by macrophages. These data position AR signaling as an immunomodulator, and confirmed by androgen-deprivation experiments, that rendered hormone-deprived tumor cells resistant to macrophage-mediated killing. Proteomic analyses showed a downregulation of oxidative phosphorylation in thePRKCD-andIKBKG-KOcells compared to the control, suggesting impaired mitochondrial function, which was confirmed by electron microscopy analyses. Furthermore, phosphoproteomic analyses revealed that all hits impaired ferroptosis signaling, which was validated transcriptionally using samples from a neoadjuvant clinical trial with the AR-inhibitor enzalutamide.

Collectively, our data demonstrate that AR functions together with the PRKCD and the NF-κB pathway to evade macrophage-mediated killing. As hormonal intervention represents the mainstay therapy for treatment of prostate cancer patients, our findings may have direct implications and provide a plausible explanation for the clinically observed persistence of tumor cells despite androgen deprivation therapy.
Human sodium current voltage-dependence at physiological temperature measured by coupling patch-clamp experiment to a mathematical model
Authors: Abrasheva Veronika O. , Kovalenko Sandaara G. , Slotvitsky Mihail , Scherbina Serafima A. , Aitova Aleria A. , Frolova Sheida , Tsvelaya Valeria , Syunyaev Roman A.
Published: June 2023

Voltage-gated sodium channels are crucial to action potential propagation in excitable tissues. Voltage-clamp measurements of sodium current are very challenging and are usually performed at room temperature due to the high amplitude and fast activation of the current. In this study, we measured sodium current’s voltage dependence in stem-cell-derived cardiomyocytes at physiological temperature. Although apparent activation and inactivation curves measured as the sodium current amplitude dependence on voltage step is within the range reported in previous studies, we demonstrate a systematic error in our measurements that is due to deviation of membrane potential from the command potential of the amplifier. We show how this artifact can be accounted for by the computer simulation of the patch-clamp experiment. This patch-clamp model optimization technique yields a surprising result: −11.5 mV half-activation and −87 mV half-inactivation of the sodium current. Although the half-activation is strikingly different from what was previously believed to be typical for the cardiac sodium current, we show that this estimate explains conduction velocity dependence on extracellular potassium in hyperkalemic conditions.

Key points

Voltage gated sodium currents play a crucial role in excitable tissues including neurons, cardiac and skeletal muscles.

Measurement of sodium current is challenging because of its high amplitude and rapid kinetics, especially at physiological temperature.

We have used the patch-clamp technique to measure human sodium current voltage-dependence in human induced pluripotent stem cell-derived cardiomyocytes.

The patch-clamp data was processed by optimization of the model accounting for voltage-clamp experiment artifacts, revealing a large difference between apparent parameters of sodium current and the results of the optimization.

We conclude that actual sodium current activation is extremely depolarized in comparison to previous studies.

The new sodium current model provides a better understanding of action potential propagation, we demonstrate that it explains propagation in hyperkalemic conditions.
OmicVerse: A single pipeline for exploring the entire transcriptome universe
Authors: Zeng Zehua , Ma Yuqing , Hu Lei , Liu Peng , Tan Bowen , Wang Yixuan , Xing Cencan , Xiong Yuanyan , Du Hongwu
Published: June 2023

Single-cell sequencing is frequently marred by “interruptions” due to limitations in sequencing throughput, yet bulk RNA-seq may harbor these ostensibly “interrupted” cells. In response, we introduce the single cell trajectory blending from Bulk RNA-seq (BulkTrajBlend) algorithm, a component of the OmicVerse suite that leverages a Beta-Variational AutoEncoder for data deconvolution and graph neural networks for the discovery of overlapping community. This approach proficiently interpolates and restores the continuity of “interrupted” cells within single-cell RNA sequencing dataset. Furthermore, OmicVerse provides an extensive toolkit for bulk and single cell RNA-seq analysis, offering uniform access to diverse methodologies, streamlining computational processes, fostering exquisite data visualization, and facilitating the extraction of novel biological insights to advance scientific research.
EZH2 inhibition promotes tumor immunogenicity in lung squamous cell carcinomas
Authors: DuCote Tanner J. , Song Xiulong , Naughton Kassandra J. , Chen Fan , Plaugher Daniel R. , Childress Avery R. , Edgin Abigail R. , Qu Xufeng , Liu Jinze , Liu Jinpeng , Li Fei , Wong Kwok-Kin , Brainson Christine F.
Published: June 2023

Two important factors that contribute to resistance to immune checkpoint inhibitors (ICIs) are an immune-suppressive microenvironment and limited antigen presentation by tumor cells. In this study, we examine if inhibition of the methyltransferase EZH2 can increase ICI response in lung squamous cell carcinomas (LSCCs). Ourin vitroexperiments using 2D human cancer cell lines as well as 3D murine and patient derived organoids treated with two inhibitors of the EZH2 plus interferon-γ (IFNγ) showed that EZH2 inhibition leads to expression of both major histocompatibility complex class I and II (MHCI/II) expression at both the mRNA and protein levels. ChIP-sequencing confirmed loss of EZH2-mediated histone marks and gain of activating histone marks at key loci. Further, we demonstrate strong tumor control in models of both autochthonous and syngeneic LSCC treated with anti-PD1 immunotherapy with EZH2 inhibition. Single-cell RNA sequencing and immune cell profiling demonstrated phenotypic changes towards more tumor suppressive phenotypes in EZH2 inhibitor treated tumors. These results indicate that this therapeutic modality could increase ICI responses in patients undergoing treatment for LSCC.
Single-cell transcriptomic profiling of human pancreatic islets reveals genes responsive to glucose exposure over 24 hours
Authors: Grenko Caleb M. , Bonnycastle Lori L. , Taylor Henry J. , Yan Tingfen , Swift Amy J. , Robertson Catherine C. , Narisu Narisu , Erdos Michael R. , Collins Francis S. , Taylor D. Leland
Published: June 2023

Disruption of pancreatic islet function and glucose homeostasis can lead to the development of sustained hyperglycemia, beta cell glucotoxicity, and ultimately type 2 diabetes (T2D). In this study, we sought to explore the effects of hyperglycemia on human pancreatic islet (HPI) gene expression by exposing HPIs from two donors to low (2.8mM) and high (15.0mM) glucose concentrations over 24 hours, assaying the transcriptome at seven time points using single-cell RNA sequencing (scRNA-seq). We modeled time as both a discrete and continuous variable to determine momentary and longitudinal changes in transcription associated with islet time in culture or glucose exposure. Across all cell types, we identified 1,528 genes associated with time, 1,185 genes associated with glucose exposure, and 845 genes associated with interaction effects between time and glucose. We clustered differentially expressed genes across cell types and found 347 modules of genes with similar expression patterns across time and glucose conditions, including two beta cell modules enriched in genes associated with T2D. Finally, by integrating genomic features from this study and genetic summary statistics for T2D and related traits, we nominate 363 candidate effector genes that may underlie genetic associations for T2D and related traits.
Transcription factor FfmA interacts both physically and genetically with AtrR to properly regulate gene expression in the fungusAspergillus fumigatus
Authors: Paul Sanjoy , Stamnes Mark A. , Moye-Rowley W. Scott
Published: June 2023

Transcriptional regulation of azole resistance in the filamentous fungusAspergillus fumigatusis a key step in development of this problematic clinical phenotype. We and others have previously described a C2H2-containing transcription factor called FfmA that is required for normal levels of voriconazole susceptibility and expression of an ATP-binding cassette transporter gene calledabcG1. Null alleles offfmAexhibit a strongly compromised growth rate even in the absence of any external stress. Here we employ an acutely repressible doxycycline-off form offfmAto rapidly deplete FfmA protein from the cell. Using this approach, we carried out RNA-seq analyses to probe the transcriptome ofA. fumigatuscells that have been deprived of normal FfmA levels. We found that 2000 genes were differentially expressed upon depletion of FfmA, consistent with the wide-ranging effect of this factor on gene regulation. Chromatin immunoprecipitation coupled with high throughput DNA sequencing analysis (ChIP-seq) identified 530 genes that were bound by FfmA using two different antibodies for immunoprecipitation. More than 300 of these genes were also bound by AtrR demonstrating the striking regulatory overlap with FfmA. However, while AtrR is clearly an upstream activation protein with clear sequence specificity, our data suggest that FfmA is a chromatin-associated factor that may bind to DNA in a manner dependent on other factors. We provide evidence that AtrR and FfmA interact in the cell and can influence one another’s expression. This interaction of AtrR and FfmA is required for normal azole resistance inA. fumigatus.
Evaluating the capabilities of the Astral mass analyzer for single-cell proteomics
Authors: Petrosius Valdemaras , Aragon-Fernandez Pedro , Arrey Tabiwang N. , Üresin Nil , Furtwängler Benjamin , Stewart Hamish , Denisov Eduard , Petzoldt Johannes , Peterson Amelia C. , Hock Christian , Damoc Eugen , Makarov Alexander , Zabrouskov Vlad , Porse Bo T. , Schoof Erwin M.
Published: June 2023

The complexity of human physiology arises from well-orchestrated interactions between trillions of single cells in the body. While single-cell RNA sequencing (scRNA-seq) has enhanced our understanding of cell diversity, gene expression alone does not fully characterize cell phenotypes. Additional molecular dimensions, such as proteins, are needed to define cellular states accurately. Mass spectrometry (MS)-based proteomics has emerged as a powerful tool for comprehensive protein analysis, including single-cell applications. However, challenges remain in terms of throughput and proteomic depth, in order to maximize the biological impact of single-cell proteomics by Mass Spectrometry (scp-MS) workflows. This study leverages a novel high-resolution, accurate mass (HRAM) instrument platform, consisting of both an Orbitrap and an innovative HRAM Asymmetric Track Lossless (Astral) analyzer. The Astral analyzer offers high sensitivity and resolution through lossless ion transfer and a unique flight track design. We evaluate the performance of the Thermo Scientific Orbitrap Astral MS using Data-Independent Acquisition (DIA) and assess proteome depth and quantitative precision for ultra-low input samples. Optimal DIA method parameters for single-cell proteomics are identified, and we demonstrate the ability of the instrument to study cell cycle dynamics in Human Embryonic Kidney (HEK293) cells, and cancer cell heterogeneity in a primary Acute Myeloid Leukemia (AML) culture model.
A comprehensive analysis of grazing: Improving management for environmental health
Authors: Niederman Talia E. , Xu Ashley L. , Dreiss Lindsay M.
Published: June 2023

In an effort to combat the dual climate and biodiversity crises, the international community has put forth targets to reduce emissions and protect species. Habitat degradation is at the fore in driving species extinctions and carbon loss, creating an urgent need to examine our land-use practices if we are to meet international goals. Individual nations will have differing needs and approaches to reaching these objectives based on their landscapes, industries, and levels of historic overuse. In the United States, grazing is the leading land-use, making up approximately one-third of the country. Here we present a broad-scale analysis of how grazing effects the environment and examine how this land-use plays out across the U.S. This review can help policy makers and land managers strategically assess grazing lands as we work towards a national landscape that supports equitable ecosystem services, sustainable livelihoods, and climate resilience.

Highlights

Livestock grazing can have a multitude of effects on local ecosystems often causing habitat degradation and loss. As this land-use makes up a third of U.S. lands, improving grazing practices could provide significant benefits for the environment.

To our knowledge, this is the largest review of U.S. grazing to date. We explore how grazing affects six elements of the environment across the country.

While the majority of literature discusses negative implications related to grazing, our results indicate that regions are affected differently, and that management and livestock-type also contribute to the overall environmental impact.
Clinical spine care partnerships between low- and high-resource countries: A scoping review
Authors: Lin Hannah , Halvorsen Kristin , Win Myat Thu , Yancey Michael , Rbil Nada , Chatterjee Abhinaba , Jivanelli Bridget , Khormaee Sariah
Published: June 2023

Background

Clinical collaboration between spine professionals in high-resource (HR) and low-resource (LR) countries may provide improvements in the accessibility, efficacy, and safety of global spine care. Currently, the scope and effectiveness of these collaborations remain unclear. In this review, we describe the literature on the current state of these partnerships to provide a framework for exploring future best practices.

Methods

PubMed, Embase, and Cochrane Library were queried for articles on spine-based clinical partnerships between HR and LR countries published between 2000 and March 10, 2023. This search yielded 1528 total publications. After systematic screening, nineteen articles were included in the final review.

Results

All published partnerships involved direct clinical care and 13/19 included clinical training of local providers. Most of the published collaborations reviewed involved one of four major global outreach organizations with the majority of sites in Africa. Participants were primarily physicians and physicians-in-training. Only 5/19 studies reported needs assessments prior to starting their partnerships. Articles were split on evaluative focus, with some only evaluating clinical outcomes and some evaluating the nature of the partnership itself.

Conclusions

Published studies on spine-focused clinical partnerships between HR and LR countries remain scarce. Those that are published often do not report needs assessments and formal metrics to evaluate the efficacy of such partnerships. Toward improving the quality of spine care globally, we recommend an increase in the quality and quantity of published studies involving clinical collaborations between HR and LR countries, with careful attention to reporting early needs assessments and evaluation strategies.
Computational analysis of long-range allosteric communications in CFTR
Authors: Ayca Ersoy , Bengi Altintel , Nurit Livnat Levanon , Nir Ben-Tal , Turkan Haliloglu , Oded Lewinson
Published: June 2023

Malfunction of the CFTR protein results in cystic fibrosis, one of the most common hereditary diseases. CFTR functions as an anion channel, the gating of which is controlled by long- range allosteric communications. Allostery also has direct bearings on CF treatment: the most effective CFTR drugs modulate its activity allosterically. Herein, we integrated Gaussian Network Model, Transfer Entropy, and Anisotropic Normal Mode-Langevin dynamics and investigated the allosteric communications network of CFTR. The results are in remarkable agreement with experimental observations and mutational analysis and provide extensive novel insight. We identified residues that serve as pivotal allosteric sources and transducers, many of which correspond to disease causing mutations. We find that in the ATP-free form, dynamic fluctuations of the residues that comprise the ATP binding sites facilitate the initial binding of the nucleotide. Subsequent binding of ATP then brings to the fore and focuses dynamic fluctuations that were present in a latent and diffuse form in the absence of ATP. We demonstrate that drugs that potentiate CFTR’s conductance do so not by directly acting on the gating residues, but rather by mimicking the allosteric signal sent by the ATP binding sites. We have also uncovered a previously undiscovered allosteric “hotspot” located proximal to the docking site of the phosphorylated Regulatory (R) domain, thereby establishing a molecular foundation for its phosphorylation- dependent excitatory role. This study unveils the molecular underpinnings of allosteric connectivity within CFTR and highlights a novel allosteric “hotspot” that could serve as a promising target for the development of novel therapeutic interventions.
Engineering Yeast to Improve Heterologous Abscisic Acid Production
Authors: Otto Maximilian , Gossing Michael , David Florian , Siewers Verena
Published: June 2023

Abscisic acid (ABA) is a high-value product with agricultural, medical and nutritional applications. We previously constructed an ABA cell factory by expressing the ABA metabolic pathway fromBotrytis cinereain the biotechnological workhorseSaccharomyces cerevisiae.

In this study, we aimed to improve ABA production and explored various rational engineering targets mostly focusing on increasing the activity of two rate-limiting cytochrome P450 monooxygenases of the ABA pathway, BcABA1 and BcABA2. We evaluated the effects of overexpression and knock-down of cell membrane transporters, expression of heterologous cytochrome b5, overexpression of a rate-limiting heme biosynthesis gene and overexpression or knock-out of genes involved in ER membrane homeostasis. One of the genes involved in ER membrane homeostasis,PAH1, was identified as the most promising engineering target. Knock-out ofPAH1improved ABA titers, but also caused a sever growth defect. By replacing thePAH1promoter with a weak minimal promoter, it was possible to mediate the growth defect while still improving ABA production.

In this report we were able to improve the ABA cell factory and furthermore provide valuable insights for future studies aiming to engineer cytochrome P450 monooxygenases.

One-sentence summary

In this study we explored various strategies to improve heterologous abscisic acid production inSaccharomyces cerevisiaeand identified fine-tuning of thePAH1gene as a promising engineering strategy.
CDK8 inhibitors antagonize HIV-1 reactivation and promote provirus latency in T cells
Authors: Horvath Riley M. , Brumme Zabrina L. , Sadowski Ivan
Published: June 2023

Latent HIV-1 provirus represents a barrier towards a cure for infection, but is dependent upon the host RNA Pol II machinery for expression. We find that inhibitors of the RNA Pol II mediator kinases CDK8/19, Senexin A and BRD6989, inhibit induction of HIV-1 expression in response to latency reversing agents and T cell signaling agonists. These inhibitors were found to impair recruitment of RNA Pol II to HIV-1 LTR. HIV-1 expression in response to several latency reversal agents was impaired upon disruption ofCDK8by shRNA or gene knockout. However, the effects of CDK8 depletion did not entirely mimic CDK8/19 kinase inhibition suggesting that the mediator kinases are not functionally redundant. Furthermore, treatment of CD4+PBMCs isolated from people living with HIV-1 and who are receiving ART with Senexin A inhibited induction of virus replication in response to T cell stimulation by PMA and ionomycin. These observations indicate that the mediator kinases CDK8 and CDK19, play a significant role for regulation of HIV-1 transcription, and that small molecule inhibitors of these enzymes may contribute to therapies designed to promote deep latency involving the durable suppression of provirus expression.
Structural proteomics of a bacterial mega membrane protein complex: FtsH-HflK-HflC
Authors: Akkulak Hatice , İnce H. Kerim , Goc Gunce , Lebrilla Carlito B. , Kabasakal Burak V. , Ozcan Sureyya
Published: June 2023

Recent advances in mass spectrometry (MS) yielding sensitive and accurate measurements along with developments in software tools have enabled the characterization of complex systems routinely. Thus, structural proteomics and cross-linking mass spectrometry (XL-MS) have become a useful method for structural modeling of protein complexes. Here we utilized commonly used XL-MS software tools to elucidate the protein interactions within a membrane protein complex containing FtsH, HflK, and HflC, over-expressed inE.coli. The MS data were processed using MaxLynx, MeroX, MS Annika, xiSEARCH, and XlinkX software tools. The number of identified inter- and intra-protein cross-links varied among software. Each interaction was manually checked using the raw MS and MS/MS data and distance restraints to verify inter- and intra-protein cross-links. A total of 37 inter-protein and 148 intra-protein cross-links were determined in the FtsH-HflK-HflC complex. The 59 of them were new interactions on the lacking region of recently published structures. These newly identified interactions, when combined with molecular docking and structural modeling, present opportunities for further investigation. The results provide valuable information regarding the complex structure and function to decipher the intricate molecular mechanisms underlying the mega FtsH-HflK-HflC complex.

Abstract Figure

Graphical Abstract

The overall workflow of XL-MS analysis: the steps of XL-MS studies applied to the two samples taken from different stages of purification process of mega membrane protein complex FtsH-HflC-HflK.
Oxygen production via NO dismutation in different ammonia oxidizers
Authors: Hernández-Magaña A. Elisa , Canfield Donald E. , Kraft Beate
Published: June 2023

Ammonia oxidizing archaea (AOA) are widespread and highly abundant in nature. Despite their typical aerobic metabolism, they can be abundant in ecosystems where oxygen is scarce. Recent observations revealed that the AOA isolateNitrosopumilus maritimusproduces oxygen and dinitrogen at nanomolar concentrations, upon oxygen depletion through nitric oxide (NO) dismutation. Here, we explore NO dismutation capability in other ammonia oxidizers with different phylogenetic affinities and from different environmental settings. The organisms explored include three marine AOA, one soil AOA and two soil ammonia-oxidizing bacteria (AOB). Upon oxygen depletion all isolates accumulated oxygen. In incubations with15N tracers with ongoing oxygen accumulation, the AOA strainsNitrosopumilus adriaticusandNitrosopumilus viennensisproduced46N2O from nitrite. Transient46N2O accumulation followed by30N2production was detected in the AOA strainsNitrosopumilus piranensisandNitrosopumilussp. CCS1, supporting the earlier observation that NO-dismutation is a common metabolism in AOA, albeit with physiological variations between different strains. An important physiological variable is the capability to reduce N2O to N2. The finding of oxygen production in several AOA, as well as AOB, indicates that this process is widely distributed among the tree of life and adds an explanation for their abundance in oxygen-depleted environments.
Segmental Duplications Drive the Evolution of Accessory Regions in a Major Crop Pathogen
Authors: van Westerhoven A.C. , Aguilera-Galvez C. , Nakasato-Tagami G. , Shi-Kunne X. , Martinez de la Parte E. , Chavarro-Carrero E. , Meijer H.J.G. , Feurtey A. , Maryani N. , Ordóñez N. , Schneiders H. , Nijbroek K. , Wittenberg A. H. J. , Hofstede R. , García-Bastidas F. , Sørensen E.H. , Swennen R. , Drenth A. , Stukenbrock E.H. , Kema G.H.J. , Seidl M.F.
Published: June 2023

Many pathogens evolved compartmentalized genomes with conserved core and variable accessory regions which carry effector genes mediating virulence. The fungal plant pathogenFusarium oxysporumhas such accessory regions often spanning entire chromosomes. The presence of specific accessory regions influences the host range, and horizontal transfer of some accessory regions can modify the pathogenicity of the receiving strain. However, understanding how these accessory regions evolve in strains that infect the same host remains limited.

Here, we define the pan-genome of 69 diverseFusariumstrains that cause Fusarium wilt of banana, a significant constraint to global banana production. In this diverse panel ofFusariumstrains infecting banana, we analyzed the diversity and evolution of the accessory regions.

Accessory regions inFusariumstrains infecting the same banana cultivar are highly diverse, and we could not identify any shared genomic regions and in planta induced effectors. We demonstrate that segmental duplications drive the evolution of accessory regions. Furthermore, we show that recent segmental duplications and aneuploidy occur specifically in accessory chromosomes and cause the expansion of accessory regions inF. oxysporum.

Taken together we conclude that extensive recent duplications drive the evolution of accessory regions inFusarium, which contribute to the evolution of virulence.
Impact of Point Mutation on Shiga-like Toxin 1: A Molecular Dynamics Simulation Study
Authors: Tabassum Nisat , Paul Bristi Rani , Saddam Md. , Uddin Helal Md Mostofa , Paul Susanta
Published: June 2023

The causative agent of gastroenteritis is Shiga toxin, which belongs to a functionally and structurally associated protein family despite each individual having a unique amino acid sequence. After entering the ER lumen and relocating the toxic domain to the cytoplasm, they alter the large subunit of rRNA, preventing protein synthesis and ribosomal damage. Shiga-like toxin-1 (SLT-1) subunit B targets glycolipid receptor Gb3, which plays a significant role in cytotoxicity. Though the mutational effect on subunit B is important for cytotoxicity study, we lack better understanding. Our present study targets the mutational impact of glycine protein at their 62thamino acid sequence of subunit B. For example, how it can alter the receptor-binding capacity and virulence. We used in silico method with GROMACS software suite (version 5.2, 2020.1) on Google Colab for a 100ns (100,000ps) simulation period and UCSF Chimera software for visualizing mutant and wild-type structure similarities. Surprisingly, RMSD, RMSF, and Rg trajectories from the simulation analysis indicated a more stable and compact mutant structure than the wild type. Principle component analysis (PCA) and SASA were visualized for the entire 100ns, which pointed towards homogeneity between both structures and more solvent accessibility in the mutant structure. This mutation may elevate receptor-binding and virulence capacity. Moreover, this finding can offer a better insight for future vaccine production.
Limiting Pool and Actin Architecture Controls Myosin Cluster Sizes in Adherent Cells
Authors: Chou Wen-hung , Molaei Mehdi , Wu Huini , Oakes Patrick W. , Beach Jordan R. , Gardel Margaret L.
Published: June 2023

The actomyosin cytoskeleton generates mechanical forces that power important cellular processes, such as cell migration, cell division, and mechanosensing. Actomyosin self-assembles into contractile networks and bundles that underlie force generation and transmission in cells. A central step is the assembly of the myosin II filament from myosin monomers, regulation of which has been extensively studied. However, myosin filaments are almost always found as clusters within the cell cortex. While recent studies characterized cluster nucleation dynamics at the cell periphery, how myosin clusters grow on stress fibers remains poorly characterized. Here, we utilize a U2OS osteosarcoma cell line with endogenously tagged myosin II to measure the myosin cluster size distribution in the lamella of adherent cells. We find that myosin clusters can grow with Rho-kinase (ROCK) activity alone in the absence of myosin motor activity. Time-lapse imaging reveals that myosin clusters grow via increased myosin association to existing clusters, which is potentiated by ROCK-dependent myosin filament assembly. Enabling myosin motor activity allows further myosin cluster growth through myosin association that is dependent on F-actin architecture. Using a toy model, we show that myosin self-affinity is sufficient to recapitulate the experimentally observed myosin cluster size distribution, and that myosin cluster sizes are determined by the pool of myosin available for cluster growth. Together, our findings provide new insights into the regulation of myosin cluster sizes within the lamellar actomyosin cytoskeleton.