bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-invasive and painless mid-infrared modulation increases collagen in human and mouse skin
Authors: Wang Zeyu , Zhu Jiahui , Wang Yuting , Chen Shuai , Xu Senlin , Li Yaoying , Hu Tianxing , Li Yang , Wang Xuanyue , Ji Renyue , Li Sunny C. , Yang Yan , Jia Hongbo , Chen Xiaowei , Fan Xing , Ge Lan , Zhang Jianxiong
Published: March 2024

Stimulating collagen production in skin helps to enhance vitality while decelerating aging- associated processes in skin tissue. However, current approaches to enhancing collagen production are commonly limited by accompanying pain and trauma. Here, we report that mid-infrared modulation (MIMO) at an intensity of 70 mW/cm2promotes collagen production in human or mouse skin in vivo without generating excessive heat. We found that protein levels of the collagen- degrading endopeptidase, MMP-1, were decreased in the skin of mice following MIMO treatment, whereas the collagen synthesis-related factors, TGF-β, HSP47, and HSP70, were all increased. In addition, MIMO stimulated collagen secretion in human dermal fibroblasts in vitro. This work demonstrates that MIMO is an effective, non-invasive, and painless intervention for in vivo enhancement of collagen production in the skin.

One Sentence Summary

Mid-infrared modulation promotes collagen production
Cell viscosity influences hematogenous dissemination and metastatic extravasation of tumor cells
Authors: Gensbittel Valentin , Follain Gautier , Bochler Louis , Uhlmann Klemens , Lefèbvre Olivier , Larnicol Annabel , Harlepp Sébastien , Goswami Ruchi , Girardo Salvatore , Hyenne Vincent , Mittelheisser Vincent , Kräter Martin , Balzani Daniel , Guck Jochen , Osmani Naël , Goetz Jacky G.
Published: March 2024

Metastases arise from a multi-step process during which tumor cells change their mechanics in response to microenvironmental cues. While such mechanical adaptability could influence metastatic success, how tumor cell mechanics directly impacts intravascular behavior of circulating tumor cells (CTCs) remains poorly understood. In the present study, we demonstrate how the deformability of CTCs affects hematogenous dissemination and identify the mechanical profiles that favor metastatic extravasation. Combining intravital microscopy with CTC-mimicking elastic beads and mechanically-tuned tumor cells, we demonstrate that the inherent properties of circulating objects dictate their ability to enter constraining vessels. We identify cellular viscosity as the key property that governs CTC circulation and arrest patterns. We further demonstrate that cellular viscosity is required for efficient extravasation and find that properties that favor extravasation and subsequent metastatic outgrowth can be opposite. Altogether, we identify CTC viscosity as a key biomechanical parameter that shapes several steps of metastasis.
Defining the function of disease variants with CRISPR editing and multimodal single cell sequencing
Authors: Baglaenko Yuriy , Curtis Michelle , Suqri Majd Al , Agnew Ryan , Nathan Aparna , Mire Hafsa M , Mah-Som Annelise Yoo , Liu David R. , Newby Gregory A. , Raychaudhuri Soumya
Published: March 2024

Abstract / Summary Paragraph

Genetic studies have identified thousands of individual disease-associated non-coding alleles, but identification of the causal alleles and their functions remain critical bottlenecks. Even though CRISPR-Cas editing has enabled targeted modification of DNA, inefficient editing leads to heterogeneous outcomes across individual cells, limiting the ability to detect functional consequences of disease alleles. To overcome these challenges, we present a multi-omic single cell sequencing approach that directly identifies genomic DNA edits, assays the transcriptome, and measures cell surface protein expression. We apply this approach to investigate the effects of gene disruption, deletions in regulatory regions, and non-coding single nucleotide polymorphisms. We identify the specific effects of individual SNPs, including the state-specific effects of anIL2RAautoimmune variant in primary human T cells. Multimodal functional genomic single cell assays including DNA sequencing bridge a crucial gap in our understanding of complex human diseases by directly identifying causal variation in primary human cells.
Srs2 binding to PCNA and its sumoylation contribute to RPA antagonism during the DNA damage response
Authors: Fan Jiayi , Dhingra Nalini , Yang Tammy , Yang Vicki , Zhao Xiaolan
Published: March 2024

Activation of the DNA damage checkpoint upon genotoxin treatment induces a multitude of cellular changes, such as cell cycle arrest or delay, to cope with genome stress. After prolonged genotoxin treatment, the checkpoint can be downregulated to allow cell cycle and growth resumption. In yeast, downregulation of the DNA damage checkpoint requires the Srs2 DNA helicase, which removes the ssDNA binding complex RPA and the associated Mec1 checkpoint kinase from DNA, thus dampening Mec1-mediated checkpoint. However, it is unclear whether the ‘anti-checkpoint’ role of Srs2 is temporally and spatially regulated to both allow timely checkpoint termination and to prevent superfluous RPA removal. Here we address this question by examining regulatory elements of Srs2, such as its phosphorylation, sumoylation, and protein-interaction sites. Our genetic analyses and checkpoint level assessment suggest that the RPA countering role of Srs2 is promoted by Srs2 binding to PCNA, which recruits Srs2 to a subset of ssDNA regions. RPA antagonism is further fostered by Srs2 sumoylation, which we found depends on the Srs2-PCNA interaction. Srs2 sumoylation is additionally reliant on Mec1 and peaks after Mec1 activity reaches maximal levels. Based on these data, we propose a two- step model of checkpoint downregulation wherein Srs2 recruitment to PCNA proximal ssDNA- RPA filaments and subsequent sumoylation stimulated upon Mec1 hyperactivation facilitate checkpoint recovery. This model suggests that Srs2 removal of RPA is minimized at ssDNA regions with no proximal PCNA to permit RPA-mediated DNA protection at these sites.
Arginine methylation of the p30 C/EBPα oncoprotein regulates progenitor proliferation and myeloid differentiation
Authors: Nguyen Linh T. , Zimmermann Karin , Kowenz-Leutz Elisabeth , Dörr Dorothea , Schütz Anja , Schönheit Jörg , Mildner Alexander , Leutz Achim
Published: March 2024

The transcription factor CCAAT enhancer binding protein alpha (C/EBPα) is a master regulator of myelopoiesis.CEBPAencodes a long (p42) and a truncated (p30) protein isoform from a single mRNA. Mutations that abnormally enhance expression of p30 are associated with acute myelogenous leukemia (AML). We show by mutational analysis that three highly conserved arginine residues (R140,147,154) located at the p30 C/EBPα N-terminus, previously found to be methylated, are involved in myeloid lineage commitment, progenitor proliferation, and differentiation. Replacement with lysine that retains the amino acid side chain charge enhanced progenitor proliferation, while uncharged side chains (alanine or leucine) impaired proliferation and enhanced granulopoietic differentiation. Analysis of protein-protein interactions (PPI) suggested that arginine methylation of p30 C/EBPα differentially determines its capacity to interact with SWI/SNF and MLL complexes. Pharmacological targeting of p30 C/EBPα arginine methylation may have clinical relevance in myeloproliferative and inflammatory diseases, in neutropenia, and in leukemic stem cells.
Broad-Spectrum Coronavirus Inhibitors Discovered by Modeling Viral Fusion Dynamics
Authors: Reilly Charles B. , Moore Joel , Lightbown Shanda , Paul Austin , Bernier Sylvie G. , Carlson Kenneth E. , Ingber Donald E.
Published: March 2024

Broad-spectrum therapeutics capable of inhibiting SARS-CoV-2, its variants, and related coronaviruses hold promise in curbing the spread of COVID-19 and averting future pandemics. Here, we employed a multidisciplinary approach that included molecular dynamics simulation (MDS) and artificial intelligence (AI)-based docking predictions to identify potent inhibitors that target a conserved region within the SARS-CoV-2 spike protein that mediates membrane fusion by undergoing large-scale mechanical rearrangements.In silicobinding screens honed in on this region, leading to the discovery of FDA-approved drugs and novel molecules predicted to disrupt spike protein conformational changes. These compounds significantly inhibited SARS-CoV-2 infection and blocked the entry of spike protein-bearing pseudotyped α, β, γ, δ variants as well as SARS-CoV and MERS-CoV in cultured human ACE2-expressing cells. The optimized lead compound significantly inhibited SARS-CoV2 infection in mice when administered orally.
Wrapping of single-stranded DNA by Replication Protein A and modulation through phosphorylation
Authors: Chadda Rahul , Kaushik Vikas , Ahmad Iram Munir , Deveryshetty Jaigeeth , Holehouse Alex , Sigurdsson Snorri Th.d , Bothner Brian , Dastvan Reza , Origanti Sofia , Antony Edwin
Published: March 2024

Single-stranded DNA (ssDNA) intermediates, which emerge during DNA metabolic processes are shielded by Replication Protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper, directing the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent specificity requires a comprehensive understanding of the structural conformation of ssDNA when bound to RPA. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA-ssDNA complexes using single-molecule FRET and Double Electron-Electron Resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.
A palette of bright and photostable monomeric fluorescent proteins for bacterial time-lapse imaging
Authors: Fraikin Nathan , Couturier Agathe , Lesterlin Christian
Published: March 2024

Fluorescent proteins (FPs) are pivotal for examining protein production, localization, and dynamics in live bacterial cells. However, the use of FPs in time-lapse imaging is frequently constrained by issues such as oligomerization or limited photostability. Here, we report the engineering of four new fluorescent proteins: mChartreuse (green), mJuniper (cyan), mLemon (yellow), and mLychee (red), using site-directed mutagenesis. These fluorophores outperform current standards for photostability and aggregation properties while retaining high levels of brightness in livingE. colibacteria. Starting with superfolder GFP (sfGFP), we developed mChartreuse, which shows significantly enhanced brightness, stability, and monomericity compared to other GFP variants. From mChartreuse, we derived mJuniper, a cyan fluorescent protein with rapid maturation and high photostability, and mLemon, a yellow fluorescent protein with improved photostability and brightness. We also identified a mutation that eliminates residual oligomerization in red fluorescent proteins derived fromDiscosomaspecies, such as mCherry and mApple. Incorporating this mutation into mApple, along with other substitutions, resulted in mLychee, a bright and photostable monomeric red fluorescent protein. These novel fluorescent proteins advance fluorescence time-lapse analysis in bacteria and their spectral properties match current imaging standards, ensuring seamless integration into existing research workflows.
Structure and dynamics determine G protein coupling specificity at a class A GPCR
Authors: Casiraghi Marina , Wang Haoqing , Brennan Patrick , Habrian Chris , Hubner Harald , Schmidt Maximilian F , Maul Luis , Pani Biswaranjan , Bahriz Sherif MFM , Xu Bing , White Elizabeth , Sunahara Roger K , Xiang Yang K , Lefkowitz Robert J , Isacoff Ehud Y , Nucci Nathaniel , Gmeiner Peter , Lerch Michael , Kobilka Brian K
Published: March 2024

G protein coupled receptors (GPCRs) exhibit varying degrees of selectivity for different G protein isoforms. Despite the abundant structures of GPCR-G protein complexes, little is known about the mechanism of G protein coupling specificity. The β2-adrenergic receptor is an example of GPCR with high selectivity for Gαs, the stimulatory G protein for adenylyl cyclase, and much weaker for the Gαi family of G proteins inhibiting adenylyl cyclase. By developing a new Gαi-biased agonist (LM189), we provide structural and biophysical evidence supporting that distinct conformations at ICL2 and TM6 are required for coupling of the different G protein subtypes Gαs and Gαi. These results deepen our understanding of G protein specificity and bias and can accelerate the design of ligands that select for preferred signaling pathways.
Enhanced mucosal B- and T-cell responses against SARS-CoV-2 after heterologous intramuscular mRNA prime/intranasal protein boost vaccination with a combination adjuvant
Authors: Laghlali Gabriel , Wiest Matthew J. , Karadag Dilara , Warang Prajakta , O’Konek Jessica J. , Chang Lauren A. , Park Seokchan , Farazuddin Mohammad , Landers Jeffrey J. , Janczak Katarzyna W. , García-Sastre Adolfo , Baker James R. , Wong Pamela T. , Schotsaert Michael
Published: March 2024

Current COVID-19 mRNA vaccines delivered intramuscularly (IM) induce effective systemic immunity, but with suboptimal immunity at mucosal sites, limiting their ability to impart sterilizing immunity. There is strong interest in rerouting immune responses induced in the periphery by parenteral vaccination to the portal entry site of respiratory viruses, such as SARS-CoV-2, by mucosal vaccination. We previously demonstrated the combination adjuvant, NE/IVT, consisting of a nanoemulsion (NE) and an RNA-based RIG-I agonist (IVT) induces potent systemic and mucosal immune responses in protein-based SARS-CoV-2 vaccines administered intranasally (IN). Herein, we demonstrate priming IM with mRNA followed by heterologous IN boosting with NE/IVT adjuvanted recombinant antigen induces strong mucosal and systemic antibody responses and enhances antigen-specific T cell responses in mucosa-draining lymph nodes compared to IM/IM and IN/IN prime/boost regimens. While all regimens induced cross-neutralizing antibodies against divergent variants and sterilizing immunity in the lungs of challenged mice, mucosal vaccination, either as homologous prime/boost or heterologous IN boost after IM mRNA prime was required to impart sterilizing immunity in the upper respiratory tract. Our data demonstrate the benefit of hybrid regimens whereby strong immune responses primed via IM vaccination are rerouted by IN vaccination to mucosal sites to provide optimal protection to SARS-CoV-2.
Uncovering nick DNA binding by LIG1 at the single-molecule level
Authors: Chatterjee Surajit , Chaubet Loïc , van den Berg Aafke , Mukhortava Ann , Gulkis Mitch , Çağlayan Melike
Published: March 2024

DNA ligases repair the strand breaks are made continually and naturally throughout the genome, if left unrepaired and allowed to persist, they can lead to genome instability in the forms of lethal double-strand (ds) breaks, deletions, and duplications. DNA ligase 1 (LIG1) joins Okazaki fragments during the replication machinery and seals nicks at the end of most DNA repair pathways. Yet, how LIG1 recognizes its target substrate is entirely missing. Here, we uncover the dynamics of nick DNA binding by LIG1 at the single-molecule level. Our findings reveal that LIG1 binds to dsDNA both specifically and non-specifically and exhibits diffusive behavior to form a stable complex at the nick. Furthermore, by comparing with the LIG1 C-terminal protein, we demonstrate that the N-terminal non-catalytic region promotes binding enriched at nick sites and facilitates an efficient nick search process by promoting 1D diffusion along the DNA. Our findings provide a novel single-molecule insight into the nick binding by LIG1, which is critical to repair broken phosphodiester bonds in the DNA backbone to maintain genome integrity.
Assessing Target of Rapamycin (TOR) activity in the diatomPhaeodactylum tricornutumusing commercially available materials
Authors: Tsuji Yoshinori , Ishikawa Takumi
Published: March 2024

Target of rapamycin (TOR) is a conserved protein kinase that regulates the balance between catabolic and anabolic processes in response to nutrient availability. Although the central role of TOR kinase in nutrient stress responses is well-recognized, little is known about the molecular basis of TOR signaling in ecologically important secondary algae with plastids of red algal origin, such as diatoms, as assessingin vivoTOR kinase activity is a difficult task. To assess TOR kinase activity, the phosphorylation status of downstream components, such as ribosomal protein S6 (RPS6), must be measured. Unlike for model organisms, an antibody that detects phosphorylated (P-) RPS6 in diatoms is not commercially available. Therefore, we developed a convenient method in which P-RPS6 and non-P-RPS6 were detected via Phos-tag affinity electrophoresis and immunoblotting with a commercial antibody that cross-reacts with RPS6 (both P- and non-P-RPS6) in the diatom,Phaeodactylum tricornutum. Using this Phos-tag-based method, we observed a dose-dependent decrease in the P-RPS6/total RPS6 ratio inP. tricornutumcells treated with the TOR kinase inhibitor, AZD-8055. We also observed a reduction in the P-RPS6/total RPS6 ratio during the nitrogen-deficient culture ofP. tricornutum, which indicated the inactivation of TOR kinase in response to nitrogen deficiency. Finally, we demonstrated the potential application of the Phos-tag-based method to other ecologically, evolutionarily, and industrially important secondary algae, such asNannochloropsis oceanica(Stramenopiles), the haptophyteTisochrysis lutea, andEuglena gracilis(Euglenid). As all experimental materials are commercially available, the Phos-tag-based method can be used to promote studies on TOR in diverse algae in different contexts.
The structure and diversity of the bacterial community in the overlying water of the Yangzong Lake in Yunnan
Authors: Huang Kai , Li Likun , Li Jin , Chen Han , Ma Zhiqiang , Ye Wenlong , Kong Deping , Zhang Jun
Published: March 2024

Bacteria are critical components of lake ecosystems, and understanding the characteristics of bacterial community structure and diversity indices is of significant importance for the analysis and management of lake ecology. In this study, overlying water samples were collected from Yangzong Lake in May, June, and July 2021. High-throughput sequencing and statistical analysis were employed to investigate the relationships between physicochemical factors, bacterial community structure, and diversity in the overlying water of Yangzong Lake. The results showed significant differences in oxidation-reduction potential among the sampling points. The order of oxidation-reduction potential was as follows: Yangzong DAHE > Yangzong Lake South > Yangzong Lake Middle > Yangzong Lake North, while other physicochemical factors exhibited minor differences. The number of OTUs and bacterial alpha diversity index in the overlying water of Yangzong Lake Middle were higher than those in Yangzong Lake North, Yangzong Lake South, and Yangzong DAHE. The dominant bacterial phyla in the overlying water were Actinobacteriota, Bacteroidota, and Proteobacteria. Actinobacteriota had the highest relative abundance of 34.63% in Yangzong Lake North, while Bacteroidota had the highest relative abundance of 33.79% in Yangzong Lake South, and Proteobacteria had the highest relative abundance of 27.29% in Yangzong Lake Middle. The dominant genera were hgcI_clade, CL500-29_marine_group, and Flavobacterium. Among them, hgcI_clade had the highest relative abundance of 37.56% in Yangzong Lake North, CL500-29_marine_group had the highest relative abundance of 35.22% in Yangzong Lake South, and Flavobacterium had the highest relative abundance of 42.02% in Yangzong Lake Middle. Correlation analysis revealed significant correlations between Campilobacterota at the phylum level and dissolved oxygen (DO) and total phosphorus (TP). At the genus level, Flavobacterium, Limnohabitans, and Pseudarcicella showed significant correlations with DO and TP.
WITHDRAWN: Effects of ethyl acetate fraction ofPsychotria vogelianaleaf on liver function, kidney function, and cytokines level of induced rheumatoid arthritis in albino rats
Authors: Ezean Nkiru N. , Ogbu Celestine O. , Aja Patrick M. , Uti Daniel E. , Uche Orji Obasi , Agu Peter C. , Zakari Suleiman , Zakari Hajara , Offor Christian E. , Awoke Joshua N.
Published: March 2024

WITHDRAWAL STATEMENT

The authors have withdrawn their manuscript owing to [some fundamental errors discovered in the methods and result of this study which was discovered during the review process which can obviously change our major findings and conclusion]. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Alpha-synuclein distribution and seeding activity in rectal biopsies in Parkinson’s disease
Authors: Kluge Annika , Kintrup Carmen , Kulcsarova Kristina , Schröder Katja , Welzel Julius , Heinzel Sebastian , Wedel Thilo , Böttner Martina , Lucius Ralph , Bonkat Sarah Kim , Pendziwiat Manuela , Schoch Stephan , Ellrichmann Mark , Berg Daniela , Schaeffer Eva , Cossais François
Published: March 2024

Background

Parkinson’s disease (PD) is characterized by the accumulation of alpha-synuclein (aSyn) pathology, not only in the brain but also in the gastrointestinal (GI) tract. This study investigates the use of unique aSyn antibodies and an aSyn seed amplification assay (SAA) for detecting pathological aSyn in rectal biopsy samples from PD patients and healthy individuals. These samples were preserved using formalin-fixed paraffin-embedded (FFPE) methods.

Materials and Methods

The study analyzed the seeding capacity of FFPE submucosal rectal biopsies from 24 PD patients and 20 healthy controls using an aSyn-SAA. The distribution of aSyn was examined using immunohistochemistry with antibodies targeting specific conformations and phosphorylated forms of aSyn at S129 and Y39.

Results

Pathological forms of aSyn were found in all FFPE biopsies from PD patients, as confirmed by SAA, and these were linked to the severity of motor symptoms (MDS-UPDRS-III). However, the immunoreactive patterns of conformation-specific or phosphorylated aSyn in rectal biopsies did not show notable differences between PD patients and healthy subjects.

Conclusion

Pathological aSyn strains are detectable in FFPE rectal biopsies from PD patients with high accuracy using aSyn-SAA. However, the utility of immunohistochemical detection with current antibodies for identifying pathological aSyn forms appears limited. The findings advocate the use of aSyn-SAA as a diagnostic tool for PD, contributing to a deeper understanding of the gut-brain connection in the disease.
Lingo: an automated, web-based deep phenotyping platform for language ability
Authors: Casten Lucas G. , Koomar Tanner , Elsadany Muhammad , McKone Caleb , Tysseling Ben , Sasidharan Mahesh , Tomblin J. Bruce , Michaelson Jacob J.
Published: March 2024

Background

Language and the ability to communicate effectively are key factors in mental health and well-being. Despite this critical importance, research on language is limited by the lack of a scalable phenotyping toolkit.

Methods

Here, we describe and showcase Lingo – a flexible online battery of language and nonverbal reasoning skills based on seven widely used tasks (COWAT, picture narration, vocal rhythm entrainment, rapid automatized naming, following directions, sentence repetition, and nonverbal reasoning). The current version of Lingo takes approximately 30 minutes to complete, is entirely open source, and allows for a wide variety of performance metrics to be extracted. We asked > 1,300 individuals from multiple samples to complete Lingo, then investigated the validity and utility of the resulting data.

Results

We conducted an exploratory factor analysis across 14 features derived from the seven assessments, identifying five factors. Four of the five factors showed acceptable test-retest reliability (Pearson’s R > 0.7). Factor 2 showed the highest reliability (Pearson’s R = 0.95) and loaded primarily on sentence repetition task performance. We validated Lingo with objective measures of language ability by comparing performance to gold-standard assessments: CELF-5 and the VABS-3. Factor 2 was significantly associated with the CELF-5 “core language ability” scale (Pearson’s R = 0.77, p-value < 0.05) and the VABS-3 “communication” scale (Pearson’s R = 0.74, p-value < 0.05). Factor 2 was positively associated with phenotypic and genetic measures of socieconomic status. Interestingly, we found the parents of children with language impairments had lower Factor 2 scores (p-value < 0.01). Finally, we found Lingo factor scores were significantly predictive of numerous psychiatric and neurodevelopmental conditions.

Conclusions

Together, these analyses support Lingo as a powerful platform for scalable deep phenotyping of language and other cognitive abilities. Additionally, exploratory analyses provide supporting evidence for the heritability of language ability and the complex relationship between mental health and language.
Structural factors of RGS14 regulating hormone-dependent phosphate transport mediated by NPT2A
Authors: Sneddon W. Bruce , Ramineni Suneela , Van Doorn G. Emme , Hepler John R. , Friedman Peter A.
Published: March 2024

The NPT2A sodium phosphate cotransporter-2a mediates basal and parathyroid hormone (PTH)- and fibroblast growth factor-23 (FGF23)-regulated phosphate transport in kidney proximal tubule cells. Both basal and hormone-sensitive transport require sodium hydrogen exchanger regulatory factor-1 (NHERF1), a scaffold protein with 2 PDZ domains. NPT2A binds to PDZ1. RGS14 persistently represses hormone action by binding to PDZ2. RGS14 contains an RGS domain, two Ras/Rap-binding domains (RBD1, RBD2), a G protein regulatory (GPR) motif, and a carboxy-terminal PDZ ligand. The intrinsic RGS14 domains cannot explain its regulatory effects on hormone-sensitive phosphate transport because these actions are mediated not only by the PTH receptor, a G protein-coupled receptor (GPCR) but also by fibroblast growth factor receptor-1 (FGFR1), a receptor tyrosine kinase that is not governed by G protein activity. Here, we sought to identify the RGS14 structural elements mutually controlling PTH and FGF23 action. RGS14 truncation constructs lacking upstream sequence and the RGS domain were fully functional. Removing the linker sequence between RGS and RBD1 domains was sufficient to abrogate RGS14 action. Examination of the alpha-helical linker region suggested candidate serine residues that might facilitate regulatory activities. Ser266and Ser269replacement by Ala abolished RGS14 regulatory actions on hormone-sensitive phosphate transport and binding to NHERF1. The results establish that RGS14 actions require targeted phosphorylation within the linker and an intact PDZ ligand.
Striated fibre assemblins localise in the feeding groove of the ‘typical excavate’Paratrimastix pyriformis
Authors: Heiss Aaron A. , Fang Yi-Kai , Priscila Peña-Diaz C. , Zítek Justyna , Novák Ji•í , Šmída Adam , Zelená Marie , Švagr Ezra , Hampl Vladimír
Published: March 2024

Spatial arrangement of the cytoskeleton in the cells of protists has been used for decades for taxonomy and phylogenetic inference at various levels. In contrast, the protein composition of non-microtubular structures is mostly unknown. Exceptions are system I fibres in algae, which are built of striated fiber assemblins (SFA). Interestingly, SFAs are also components of a range of other, dissimilar structures, playing a role in the cortex of ciliates, cells division in apicomplexans, and adhesion of the parasite Giardia to the intestine. In a broad bioinformatic survey, we show the presence of three ancestral eukaryotic paralogues of SFA, and note that they are present in all ‗typical excavates‘ – simple flagellates bearing a ventral feeding groove. In one representative, Paratrimastix pyriformis, we localised one of the SFA paralogues using specific antibodies and expansion microscopy. We show that it co-localises specifically with structures attached to the basal body of the posterior flagellum, namely the right microtubular root, composite fibre, and B-fibre. As the morphology of the ‗typical excavates‘ may be ancestral to eukaryotes, we speculate that the role in the development or function of this feeding apparatus may be ancestral to the protein.
Effect of shipping on the microbiome of donor mice used to reconstitute germ-free recipients
Authors: McAdams Zachary L. , Yates Jared , Turner Giedre , Dorfmeyer Rebecca A. , Wight-Carter Mary , Amos-Landgraf James , Franklin Craig L. , Ericsson Aaron C.
Published: March 2024

The gut microbiota (GM) influences multiple processes during host development and maintenance. To study these events, fecal microbiota transfer (FMT) to germ-free (GF) recipients is often performed. Mouse models of disease are also susceptible to GM-dependent effects, and cryo-repositories often store feces from donated mouse strains. Shipping live mice may affect the GM and result in an inaccurate representation of the baseline GM. We hypothesize that the use of such fecal samples for FMT would transfer shipping-induced changes in the donor GM to GF recipients. To test this, donor mice originating from two suppliers were shipped to the University of Missouri. Fecal samples collected pre- and post-shipping were used to inoculate GF mice. Pre- and post-shipping fecal samples from donors, and fecal and/or cecal contents were collected from recipients at one and two weeks post-FMT. 16S rRNA sequencing revealed supplier-dependent effects of shipping on the donor microbiome. FMT efficiency was independent of shipping timepoint or supplier, resulting in transmission of shipping-induced changes to recipient mice, however the effect of supplier-origin microbiome remained evident. While shipping may cause subtle changes in fecal samples collected for FMT, such effects are inconsistent among supplier-origin GMs and minor in comparison to other biological variables.
A mechanism that transduces lysosomal damage signals to stress granule formation for cell survival
Authors: Duran Jacob , Poolsup Suttinee , Allers Lee , Lemus Monica Rosas , Cheng Qiuying , Pu Jing , Salemi Michelle , Phinney Brett , Jia Jingyue
Published: March 2024

Lysosomal damage poses a significant threat to cell survival. Our previous work has reported that lysosomal damage induces stress granule (SG) formation. However, the importance of SG formation in determining cell fate and the precise mechanisms through which lysosomal damage triggers SG formation remains unclear. Here, we show that SG formation is initiated via a novel calcium-dependent pathway and plays a protective role in promoting cell survival in response to lysosomal damage. Mechanistically, we demonstrate that during lysosomal damage, ALIX, a calcium-activated protein, transduces lysosomal damage signals by sensing calcium leakage to induce SG formation by controlling the phosphorylation of eIF2α. ALIX modulates eIF2α phosphorylation by regulating the association between PKR and its activator PACT, with galectin-3 exerting a negative effect on this process. We also found this regulatory event of SG formation occur on damaged lysosomes. Collectively, these investigations reveal novel insights into the precise regulation of SG formation triggered by lysosomal damage, and shed light on the interaction between damaged lysosomes and SGs. Importantly, SG formation is significant for promoting cell survival in the physiological context of lysosomal damage inflicted by SARS-CoV-2 ORF3a, adenovirus infection, Malaria hemozoin, proteopathic tau as well as environmental hazard silica.
MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics
Authors: Caffrey Elisa B , Olm Matthew R , Kothe Caroline I , Evans Joshua , Sonnenburg Justin L
Published: March 2024

Fermented foods, which contain a diverse array of microbial metabolites and microbes, are increasingly recognized as potential mediators of human immune and metabolic health. While there is growing interest in characterizing the microbial landscape of fermented foods, current characterization methods typically rely on 16S rRNA sequencing or marker gene-based methods, which have low taxonomic resolution and cannot functionally characterize microbes. Here we describe MiFoDB-workflow, a metagenomics workflow for the identification of microbes associated with food fermentation based on a primary database of 675 genomes of bacteria, yeast, fungi, and common fermented food substrates. We constructed the database using metagenome-assembled genomes (MAGs) derived from metagenomic sequencing of 90 fermented foods, combined with previously-published fermented food-derived MAGs, and relevant genomes deposited in RefSeq and GenBank genomes. We demonstrate the utility of MiFoDB for high confidence genome identification, including discovery of previously uncharacterized species, strain tracking across related foods, and functional analysis in fermented foods of different substrates. The workflow streamlines high-confidence characterization of the diversity of the fermented food landscape including novel ferments, and allows strain-level tracking of microbes across time, substrates, and producers.
Towards prospective in-silico trials in atrial fibrillation: the case of polypharmacological SK and K2P channel block
Authors: Dasí Albert , Berg Lucas M , Martinez-Navarro Hector , Bueno-Orovio Alfonso , Rodriguez Blanca
Published: March 2024

Background

Virtual evaluation of medical therapy through human-based modelling and simulation can accelerate and augment clinical investigations. Treatment of the most common cardiac arrhythmia, atrial fibrillation (AF), requires novel approaches.

Objectives

To prospectively evaluate and mechanistically explain novel pharmacological therapies for atrial fibrillation through in-silico trials, considering single and combined SK and K2P channel block.

Methods

A large cohort of 1000 virtual patients was developed for simulations of AF and pharmacological action. Extensive calibration and validation with experimental and clinical data support their credibility.

Results

Sustained AF was observed in 654 (65%) virtual patients. In this cohort, cardioversion efficacy increased to 82% (534 of 654) through combined SK+K2P channel block, from 33% (213 of 654) and 43% (278 of 654) for single SK and K2P blocks, respectively. Drug-induced prolongation of tissue refractoriness, dependent on the virtual patient’s ionic current profile, explained cardioversion efficacy (atrial refractory period increase: 133.0±48.4 ms for combined vs. 45.2±43.0 and 71.0±55.3 for single SK and K2P block, respectively). Virtual patients cardioverted by SK channel block presented lower K2P densities, while lower SK densities favoured the success of K2P channel inhibition. Both ionic currents had a crucial role on atrial repolarization, and thus, a synergism resulted from the polypharmacological approach. All three strategies, including the multi-channel block, preserved atrial electrophysiological function (i.e., conduction velocity and calcium transient dynamics) and thus, its contractile properties (safety).

Conclusion

In-silico trials identify key factors determining efficacy of single vs combined SK+K2P channel block as effective and safe strategies for AF management.
Cryo-electron tomography reveals the nanoscale architecture of the actin cortex in cellular blebs
Authors: Cassani Davide A.D. , Martins Bruno , Smith Matthew B. , Medalia Ohad , Paluch Ewa K.
Published: March 2024

In animal cells, cellular deformations driving cytokinesis, migration, and epithelial constriction are driven by contractile tension in the actomyosin cortex, a thin network of actin and myosin underlying the plasma membrane. Cortical tension results from myosin-generated forces and as such, cortical myosin organization and dynamics have received significant attention. However, recent studies highlight that alongside myosin motor activity, the organization of the cortical actin network is a key regulator of tension. Yet, very little is known about the structural arrangement of cortical actin filaments. This is mostly due to the small thickness and high density of the cortex, which makes the visualization of cortical actin filaments challenging. Here, we use cryo-electron tomography (cryo-ET) to unveil the structural organization of cortical actin. As a model, we use isolated cellular blebs, which assemble an actin cortex comparable to the cortex of entire cells, but are small enough to be amenable to cryo-ET. We find that the bleb actin cortex is mostly composed of short and straight actin filaments. We then characterize cortex structural parameters, including the density of potential cross-linking and membrane attachment points. Our study unveils the nanoscale three-dimensional organization of the cortical actin network in cellular blebs. As such, it provides a quantitative framework for models of cortical tension generation, and will help understanding the nanoscale basis of cell surface contractions.
Genomic and transcriptomic analyses of the elite rice variety Huizhan provide insight into disease resistance and heat tolerance
Authors: Yang Wei , Yang Zhou , Yang Lei , Li Zheng , Zhang Zhaowu , Wei Tong , Huang Renliang , Li Guotian
Published: March 2024

Rice is an important crop and serves as a model for crop genomics and breeding studies. Here, we used Oxford Nanopore ultra-long sequencing and next-generation sequencing technologies to generate a chromosome-scale genome assembly of Huizhan, a disease-resistant and heat-tolerantindicarice variety. The final genome assembly was 395.20 Mb with a scaffold N50 of 31.87 Mb. We identified expanded gene families in Huizhan that are potentially associated with both organ growth and development, as well as stress responses. We observed that three functional rice blast resistance genes, includingPi2,PiaandPtr, and bacterial blight resistance geneXa27, likely contribute to disease resistance of Huizhan. In addition, integrated genomics and transcriptomics analyses show thatOsHIRP1,OsbZIP60, the SOD gene family, and various transcription factors are likely involved in heat tolerance of Huizhan. Results presented in this study will serve as a valuable resource for rice functional genomics studies and breeding.
Cyclocarya paliuruspolysaccharides improve high fat diet-fed mice lipid dysmetabolism through gut microbiota
Authors: Huang Chengyan , Jia Yanmei , Chai Ping , He Huizhen , Liu Wei , Cheng Lirong
Published: March 2024

Obesity is associated with low-grade chronic inflammation and intestinal dysbiosis.Cyclocarya paliurus(C.paliurus) has been shown to improve lipid metabolism and gut microbiota communities in animals and humans; however, it remains to know whetherCyclocarya paliuruspolysaccharides (CCPP) prevents obesity through gut microbiota. Here, we found that high fat diet promoted the lipid accumulation and intestinal microbiota dysbiosis in mice, while drinkCyclocarya paliuruspolysaccharides reduces body weight, inflammation, alleviated the lipid accumulation, and reversed gut microbiota dysbiosis, including the diversity of intestinal microbiota, relative abundances ofLachnospiraceae. By transplanting faeces from CP-treated mice to HFD-fed mice, the effects of anti-obesity and microbiome regulation can be transferred through gut microbiota. Our results indicate thatCyclocarya paliuruspolysaccharides can prevent gut dysbiosis and obesity-related metabolic disorders in obese individuals, the mechanism is related to the remodeling of intestinal flora.
Enhanced metabolic entanglement emerges during the evolution of an interkingdom microbial community
Authors: Scarinci Giovanni , Ariens Jan-Luca , Angelidou Georgia , Schmidt Sebastian , Glatter Timo , Paczia Nicole , Sourjik Victor
Published: March 2024

Metabolic interactions are common in microbial communities and are believed to be a key factor in the emergence of complex life forms. However, while different stages of mutualism can be observed in nature, the dynamics and mechanisms underlying the gradual erosion of independence of the initially autonomous organisms are not yet fully understood. In this study, we conducted the laboratory evolution of an engineered microbial community and were able to reproduce and molecularly track its stepwise progression towards enhanced partner entanglement. The evolution of the community both strengthened the existing metabolic interactions and led to the emergence ofde novointerdependence between partners for nitrogen metabolism, which is a common feature of natural symbiotic interactions. Selection for enhanced metabolic entanglement repeatedly occurred indirectly, via pleiotropies and trade-offs within cellular regulatory networks. This indicates that indirect selection may be a common but overlooked mechanism that drives the evolution of mutualistic communities.
Short lifespan is one’s fate, long lifespan is one’s achievement: lessons fromDaphnia
Authors: Beam Thomas , Bright Mchale , Pearson Amelia C. , Dua Ishaan , Smith Meridith , Dutta Ashit K. , Bhadra Shymal C. , Salman Saad , Strickler Caleb N. , Anderson Cora E. , Peshkin Leon , Yampolsky L. Y.
Published: March 2024

Studies of longevity and senescence rely on baseline life expectancy of reference genotypes measured in standardized conditions such as food level and group size. Variation in baseline lifespan data across labs and protocols and among genotypes can make longevity intervention studies difficult to compare, particularly when GxE interactions exist. Furthermore, extending the lifespan of a short-lived genotype or of any genotype under suboptimal conditions may be of a lesser theoretical and translational value than extending the maximal possible lifespan.Daphniais rapidly becoming a model organism of choice for longevity research complementing data obtained on traditional models. In this study we report baseline longevity of several genotypes (parthenogenetic clones) of a long-lived speciesD. magnaunder a variety of laboratory protocols, aiming to document the highest possible lifespan, factors reducing it, and physiological parameters that change with age and correlate with longevity. Combining data from 25 different experiments across two labs we report strong differences among clones of different geographic origin, moderate effects of group size and medium composition on longevity, and strong GxE with respect to food level. Specifically, short-lived clones that tend to originate from small intermittent habitats show little or no caloric restriction (CR) longevity extension, while long-lived ones expand their lifespan even further when maintained at 25% of thead libitumfood. We find no evidence of any trade-offs between longevity and fecundity across clones or correlations with age-specific feeding rate. We find that in the short-lived, CR non-responsive clones show little correlation between longevity and two measures of lipid peroxidation (LPO: lipid hydroperoxides and MDA abundance). In contrast, the long-lived, CR-responsive clones show a positive longevity correlation with lipid hydroperoxide abundance at any age, and a negative correlation with MDA concentration measured at about median lifespan. This indicates differences among genotypes in longevity-related accumulation of LPO targets, efficiency of detoxification of LPO products, and/or their effects on longevity. Our observations support the hypothesis that a long lifespan can be affected by food availability and levels of oxidative damage, while genetically determined short lifespan remains short regardless. We suggest a set of condition and genotypes to be used as a reference for longevity studies inDaphnia.
The effect of MD&A disclosures on corporate performance: a panel quantile regression analysis
Authors: Singh Vijay , Singla Himani
Published: March 2024

Purpose

The study aims to examine how the information disclosed by the managers in the management discussion and analysis (MD&A) reports varies at the different levels of corporate performance.

Design/methodology/approach

To understand this quantile effect, first OLS technique was adopted and then, the quantile regression method was applied to explore the impact of MD&A disclosures on the firm performance across the lower and upper quantiles. The sample size for the study is 490 firms’ year observations for the period 2016–2022.

Findings

The results of the study demonstrate the negative but significant relationship between MD&A disclosures and corporate performance, supporting the two management strategies of “competitive disadvantage” in case of good performance and “management impression strategy” in case of poor performance. Furthermore, with other corporate governance variables, both the size of the board and the number of independent directors on the board are positively significant only in the case of the upper quantile indicating the heterogeneity in the relationship between the performance and the MD&A disclosures. Therefore, the overall findings of the study support that these results contradict the agency theory and the stakeholders’ theory as managers are not acting well as agents on behalf of the investors and work well only when they are controlled by the large board having more independent directors.

Originality/value

To the best of the authors’ knowledge, no study so far has incorporated quantile regression to assess the effect of MD&A disclosures on company performance at various levels of the firm performance, which gives more robust insights about the viewpoint of the managers on the different level of the firm performance. In other words, this study highlights the important information as to how the information provided in the MD&A reports varies as per the good or poor performance of the companies.