Cluster Abundance Research Articles

Comparative genomics of obligate predatory bacteria belonging to phylum Bdellovibrionota highlights distribution and predicted functions of lineage-specific protein families

ABSTRACT Comparative genomics of predatory bacteria is important to understand their ecology and evolution and explore their potential to treat drug-resistant infections. We compared chromosomes of 18 obligate predators from phylum Bdellovibrionota (16 intraperiplasmic, two epibiotic) and 15 non-predatory bacteria. Phylogenetics of conserved single-copy genes and analysis of genome-wide average amino acid identity provide evidence for at least five Bdellovibrio species and support recent reclassifications of predatory taxa. To define shared and differential genome content, we grouped predicted protein sequences into gene clusters based on sequence similarity. Few gene clusters are shared by all 33 bacteria or all 18 predatory bacteria; however, we identified gene clusters conserved within lineages, such as intraperiplasmic Bdellovibrio , and not found in other bacteria. Many of these are predicted to function in cell envelope biogenesis, signal transduction, and other roles important for predatory lifestyles. Among intraperiplasmic Bdellovibrio , we detected high abundance of gene clusters predicted to encode transglycosylases, endopeptidases, and lysozymes, and we identified six gene clusters (amidase, L,D-transpeptidase, four transglycosylases) with evidence of recent gene duplication and gene family expansion. Focusing on peptidoglycan metabolism, we defined a suite of gene clusters that include peptidoglycan-degrading and -modifying enzymes and occur only in predatory bacteria, suggesting these proteins may have evolved activities specific to predation. Our analyses highlight key genome content differences between obligate predatory bacteria and non-predatory relatives and identify gene clusters that may encode enzymes adapted to predatory lifestyles. These lineage-specific proteins are strong candidates for functional characterization to clarify their role in predation. IMPORTANCE Evolution of predation as a bacterial lifestyle involves selective pressure on and adaptation of enzymes that contribute to killing and digestion of prey bacteria, in some cases from within the prey itself. Such enzymes are a hallmark of obligate predatory bacteria belonging to phylum Bdellovibrionota , which includes the well-studied predator Bdellovibrio . By comparing protein sequences of obligate predatory bacteria and their non-predatory relatives, we define key genome content differences that distinguish bacterial predators and identify lineage-specific enzymes that may have evolved unique activities due to selective pressures related to a predatory lifestyle. In addition to providing insights into the ecology and evolution of predatory bacteria, comparative genomics studies, like this, can inform efforts to develop predatory bacteria and/or their enzymes as potential biocontrol agents to combat drug-resistant bacterial infections.

Application of mass cytometry in multiparametric characterization of precancerous cervical lesions.

Cervical cancer (CC) is the fourth most common malignant tumor in women worldwide. Detecting different biomarkers together on single cells by novel method mass cytometry could contribute to more precise screening. Liquid-based cytology (LBC) cervical samples were collected (N = 53) from women categorized as normal and precancerous lesions. Human papillomavirus was genotyped by polymerase chain reaction, while simultaneous examination of the expression of 29 proteins was done by mass cytometry (CyTOF). Differences in cluster abundances were assessed with Spearman's rank correlation as well as high dimensional data analysis (t-SNE, FlowSOM). Cytokeratin (ITGA6, Ck5, Ck10/13, Ck14, Ck7) expression patterns allowed determining the presence of different cells in the cervical epithelium. FlowSOM analysis enabled to phenotype cervical cells in five different metaclusters and find new markers that could be important in CC screening. The markers Ck18, Ck18, and CD63 (Metacluster 3) showed significantly increasing associated with severity of the precancerous lesions (Spearman rank correlation rho 0.304, p = 0.0271), while CD71, KLF4, LRIG1, E-cadherin, Nanog and p53 (Metacluster 1) decreased with severity of the precancerous lesions (Spearman rank correlation rho -0.401, p = 0.0029). Other metaclusters did not show significant correlation, but metacluster 2 (Ck17, MCM, MMP7, CD29, E-cadherin, Nanog, p53) showed higher abundance in low- and high-grade intraepithelial lesion cases. CyTOF appears feasible and should be considered when examining novel biomarkers on cervical LBC samples. This study enabled us to characterize different cells in the cervical epithelium and find markers and populations that could distinguish precancerous lesions.

Secondary halo bias through cosmic time II. Reconstructing halo properties using clustering information

When constructing mock galaxy catalogs based on suites of dark matter halo catalogs generated with approximated, calibrated, or machine-learning approaches, assigning intrinsic properties for these tracers is a step of paramount importance, given that they can shape the abundance and spatial distribution of mock galaxies and galaxy clusters. We explore the possibility of assigning properties of dark matter halos within the context of calibrated or learning approaches, explicitly using clustering information. The goal is to retrieve the correct signal of primary and secondary large-scale effective bias as a function of properties reconstructed solely based on phase-space properties of the halo distribution and dark matter density field. The algorithm reconstructs a set of halo properties (such as virial mass, maximum circular velocity, concentration, and spin) constrained to reproduce both primary and secondary (or assembly) bias. The key ingredients of the algorithm are the implementation of individually-assigned large-scale effective bias, a multi-scale approach to account for halo exclusion, and a hierarchical assignment of halo properties. The method facilitates the assignment of halo properties, aiming to replicate the large-scale effective bias, both primary and secondary. This constitutes an improvement over previous methods in the literature, especially for the high-mass end population. We have designed a strategy for reconstructing the main properties of dark matter halos obtained using calibrated or learning algorithms, such that the one- and two-point statistics (on large scales) replicate the signal from detailed $N$-body simulations. We encourage the application of this strategy (or the implementation of our algorithm) for the generation of mock catalogs of dark matter halos based on approximated methods.

The SRG/eROSITA All-Sky Survey. Constraints on f(R) gravity from cluster abundances

The evolution of the cluster mass function traces the growth of the linear density perturbations and can be utilized to constrain the parameters of cosmological and alternative gravity models. In this context, we present new constraints on potential deviations from general relativity by investigating the Hu-Sawicki parametrization of the $f(R)$ gravity with the first Spectrum Roentgen Gamma (SRG)/ All-Sky Survey ( cluster catalog in the western Galactic hemisphere in combination with the overlapping Dark Energy Survey Year-3, KiloDegree Survey, and Hyper Suprime-Cam data for weak lensing mass calibration. For the first time, we present constraints obtained from cluster abundances only. When we consider massless neutrinos, we find a strict upper limit of $ f_ R0 | < -4.31$ at a 95<!PCT!> confidence level. Massive neutrinos suppress structure growth at small scales, and thus have the opposite effect of $f(R)$ gravity. We consequently investigate the joint fit of the mass of the neutrinos with the modified gravity parameter. We obtain $ f_ R0 | < -4.08$ jointly with $ m_ eV $ at a 95<!PCT!> confidence level, which is tighter than the limits in the literature utilizing cluster counts only. At $ f_ R0 |= - 6$, the number of clusters is not significantly changed by the theory. Consequently, we do not find any statistical deviation from general relativity in the study of eRASS1 cluster abundance. Deeper surveys with eROSITA, increasing the number of detected clusters, will further improve constraints on $ |f_ R0 |$ and investigate alternative gravity theories.

Novel design of hollow carbon nanocage modified with nanotubes as a bifunctional electrocatalyst for high performance Zn–air batteries

Microcavities play a crucial role as microreactors in the transport of molecular/ionic guests and the exposure of active sites, thus significantly influencing the electrocatalytic performance. This study prepares Co/N-codoped hollow carbon (HT-CoN/C) with surface-distributed carbon nanotubes by pyrolysis of PDA-coated Zn/Co bimetallic ZIF (BM-ZIF@PDA). Benefiting from the hierarchical porous structure, high specific surface area (307.17 m2 g−1) and abundant Co clusters, the HT-CoN/C exhibits remarkable bifunctional oxygen electrocatalytic activity with an overpotential of the ORR/OER processes (ΔE = 0.703 V). The density functional theory (DFT) calculations also verify that the configuration of C-coated N-coordinated Co clusters (Co4-Nx) affect the electrocatalytic activity of ORR and OER, illustrating the source of the excellent oxygen electrocatalytic activity of HT-CoN/C. The aqueous rechargeable zinc-air battery (RZAB) using HT-CoN/C as the air electrode is characterized by a superior peak power density (175 mW cm−2), a prolonged cycle life (1230 cycles/410 h at 5.0 mA cm−2) and a high open-circuit voltage (1.47 V). Meanwhile, the flexible solid-state RZAB assembled by the HT-CoN/C also exhibits a higher peak power density (117 mW cm−2) and an excellent bending performance. This work is extremely valuable for the design and synthesis of Co/N co-doped carbon electrocatalysts.

Microbial Inoculants Drive Changes in Soil and Plant Microbiomes and Improve Plant Functions in Abandoned Mine Restoration.

The application of microbial inoculants holds promise for the sustainable restoration of abandoned mine sites by affecting soil nutrients and microbial communities. However, the responses of plant microbial communities to microbial inoculants in mine restoration remain largely unknown. To bridge this knowledge gap, we conducted a 4-year field experiment at an abandoned carbonate mine site to assess the impacts of microbial inoculants on the soil-plant microbiome. Our findings revealed that microbial inoculants significantly changed roots, fine root bacterial and fungal communities. Further, no significant correlations were observed between the soil-plant nutrient content (Z-score) and microbial alpha diversity. However, a significantly positive correlation was found between the relative abundance of the keystone ecological cluster (Module #1) and soil-plant nutrient content. The application of microbial inoculants also increased complexity, albeit decreased stability of plant microbiome networks, alongside a reduction in stochastic assembly. Conversely, they decreased the complexity but increased the stability of soil microbiome networks, accompanied by an increase in stochastic assembly. Notably, the number of specifically enriched microbiome functional traits of roots and root nodules under the microbial inoculant treatments surpassed that of the control. In summary, our findings underscored the potential of microbial inoculants to enhance soil-plant functionality at abandoned mine restoration sites.

Weak-Lensing Shear-Selected Galaxy Clusters from the Hyper Suprime-Cam Subaru Strategic Program: II. Cosmological Constraints from the Cluster Abundance

We present cosmological constraints using the abundance of weak-lensing shear-selected galaxy clusters in the Hyper Suprime-Cam (HSC) Subaru Strategic Program. The clusters are selected on the aperture-mass maps constructed using the three-year (Y3) weak-lensing data with an area of ≈500deg 2, resulting in a sample size of 129 clusters with high signal-to-noise ratios ν≥4.7. Owing to the deep, wide-field, and uniform imaging of the HSC survey, this is by far the largest sample of shear-selected clusters, for which the selection solely depends on gravity and is free from any assumptions about the dynamical state and complex baryon physics. Informed by the optical counterparts, the shear-selected clusters span a redshift range of z≲0.7 with a median of z≈0.3. The lensing sources are securely selected at z≳0.7 with a median of z≈1.3, leading to nearly zero cluster member contamination. We carefully account for (1) the bias in the photometric redshift of sources, (2) the bias and scatter in the weak-lensing mass using a simulation-based calibration, and (3) the measurement uncertainty that is directly estimated on the aperture-mass maps using an injection-based method developed in a companion paper (Chen et al. submitted). In a blind analysis, the fully marginalized posteriors of the cosmological parameters are obtained as Ωm=0.50−0.24+0.28, σ8=0.685−0.088+0.161, Ŝ8≡σ8(Ωm/0.3)0.25=0.835−0.044+0.041, and σ8Ωm/0.3=0.993−0.126+0.084 in a flat ΛCDM model. We compare our cosmological constraints with other studies, including those based on cluster abundances, galaxy-galaxy lensing and clustering, and Cosmic Microwave Background observed by Planck, and find good agreement at levels of ≲2σ. [abridged]

Spatial transcriptomics of human and murine Neurofibromatosis Type I fracture pseudarthroses reveal impaired BMP signaling

Abstract Introduction/Objective In Neurofibromatosis Type 1 (NF1), caused by mutations in the NF1 tumor-suppressor gene, children form fibrotic nonunions known as pseudarthroses following long bone fractures. Here, we integrate spatial transcriptomics of human and murine samples to investigate the pathogenesis underlying pseudoarthrosis development. Methods/Case Report We performed spatial transcriptomics on 10-day post-fracture calluses from control and periosteum-specific Nf1-deficient (Nf1Postn) mice as well as a human NF1 patient pseudarthrosis specimen. Differential gene expression and SpatialTime analyses were performed. BMP signaling was validated by immunohistochemical staining of tissues for phospho-SMAD1/5/8. Results (if a Case Study enter NA) Spatial transcriptomics detected eight cell clusters, including bone, cartilage, and muscle within mouse fracture calluses. In the control, clusters involved in fracture repair were enriched for genes associated with extracellular matrix and collagen formation (progenitor and cartilage clusters), cartilage and endochondral bone processes (ossifying perichondrium cluster), and bone remodeling (woven bone cluster). Expression of TGF-beta pathway genes was highest near the fracture plane, while BMP and Wnt pathways were activated further from the fracture. In the Nf1Postn fracture, healing was significantly delayed, lacking a robust callus and with a lower abundance of reparative skeletal cell clusters. While expression of TGF-beta pathway genes was similar to control, BMP pathway expression was minimal within the Nf1Postn fracture, which was further demonstrated by a lack of phospho-SMAD1/5/8 staining. In the human pseudarthrosis, while TGF-beta pathway genes were expressed near the fracture plane as expected, there was no enrichment of BMP pathway expression in the pseudarthrosis tissue and no significant phospho-SMAD1/5/8 staining. Conclusion Spatial transcriptomics allows for the simultaneous unbiased analysis of multiple signal transduction pathways within their native tissue environment. Our analyses 1) revealed the cellular diversity required for fracture healing, 2) demonstrated the spatially-restricted expression of key morphogenetic pathways within a fracture callus, and 3) provides in situ evidence for impaired BMP pathway activation associated with NF1 fracture pseudarthroses.

Super-resolution imaging reveals the role of DDR1 cluster in NSCLC proliferation

Discoidin domain receptor 1 (DDR1), a transmembrane protein, is crucial in tumor development. Prior studies have demonstrated a significant correlation between protein cluster distribution on the cell membrane and tumor evolution. However, the precise spatial distribution characteristics of DDR1 on cell membranes and their impact on tumor development remain unclear. In this study, we conducted gene expression analysis to investigate DDR1 expression in non-small cell lung cancer (NSCLC) and its association with patient prognosis. We also employed direct stochastic optical reconstruction microscopy (dSTORM) imaging to examine DDR1's spatial distribution in NSCLC cells and tissues. Our findings indicate that DDR1 forms larger, tighter, and more abundant clusters in cancer cells and tissues compared to their normal counterparts. Notably, we observed that the enhanced aggregation of DDR1 clusters increased the likelihood of interaction with SRC, thereby activating the SRC-STAT3 signaling pathway in NSCLC cells and promoting cell proliferation. This study provides novel insights into the role of DDR1 aggregation in tumor proliferation, confirms DDR1 as a potential tumor marker, and serves as a valuable resource for future drug development.

Networks of ion-pairs are responsible for the large differences in the thermal stability of two structurally similar aminopeptidases.

Aminopeptidases are an important class of enzymes for protein metabolism. Leucyl aminopeptidase (PepL) preferably removes leucine from the N-terminus of small peptides. PepL of Lacticaseibacillus casei was observed to be thermally unstable, while a structurally similar aminopeptidase T (AmpT) of Thermus thermophilus is highly stable. To understand the molecular interaction responsible for the large difference in their stability, molecular dynamics simulations were carried out to study the thermal stability of PepL and AmpT at 300 K to 450 K temperature range over 100 ns. PepL sampled a larger conformational space with a rugged free-energy landscape, while AmpT navigated a smoother energy landscape to reach the global minimum. The RMSD, RMSF, radius of gyration and principal component analysis suggested large movements in PepL than in AmpT with an increase in temperature. Analysis of residue-interaction network revealed AmpT possessing a greater number of low, medium and high energy contacts in comparison to PepL. AmpT showed a higher abundance of ion-pair clusters and ionic residues per cluster compared to PepL. Moreover, AmpT retained a greater number of high-energy contacts at elevated temperatures. These findings showed that the inherently lower stability of PepL originates from a comparatively smaller number of contacts and can be pivotal in engineering PepL for higher stability.

Chemical abundances for a sample of FGK dwarfs in the Pleiades open cluster from APOGEE

ABSTRACT This paper presents chemical abundances of 12 elements (C, Na, Mg, Al, Si, K, Ca, Ti, V, Cr, Mn, and Fe) for 80 FGK dwarfs in the Pleiades open cluster, which span a temperature range of $\sim$2000 K in T$_{\rm eff}$, using the high-resolution (R$\sim$22 500) near-infrared SDSS (Sloan Digital Sky Survey)-IV/APOGEE (Apache Point Observatory Galactic Evolution Experiment) spectra ($\lambda$1.51–1.69 $\mu$m). Using a 1D local thermodynamic equilibrium abundance analysis, we determine an overall metallicity of [Fe/H] = +0.03 $\pm$ 0.04 dex, with the elemental ratios [$\alpha$/Fe] = +0.01 $\pm$ 0.05, [odd-z/Fe] = –0.04 $\pm$ 0.08, and [iron peak/Fe] = –0.02 $\pm$ 0.08. These abundances for the Pleiades are in line with the abundances of other open clusters at similar galactocentric distances as presented in the literature. Examination of the abundances derived from each individual spectral line revealed that several of the stronger lines displayed trends of decreasing abundance with decreasing $T_{\rm eff}$. The list of spectral lines that yield abundances that are independent of $T_{\rm eff}$ are presented and used for deriving the final abundances. An investigation into possible causes of the temperature-dependent abundances derived from the stronger lines suggests that the radiative codes and the APOGEE line list we employ may inadequately model van der Waals broadening, in particular in the cooler K dwarfs.

The R-process Alliance: Fifth Data Release from the Search for R-process-enhanced Metal-poor Stars in the Galactic Halo with the GTC* * This paper includes data gathered with the 10.4 m Gran Telescopio Canarias located at La Palma, Canary Islands, Spain.

Understanding the abundance pattern of metal-poor stars and the production of heavy elements through various nucleosynthesis processes offers crucial insights into the chemical evolution of the Milky Way, revealing primary sites and major sources of rapid neutron-capture process (r-process) material in the Universe. In this fifth data release from the R-Process Alliance (RPA), we present the detailed chemical abundances of 41 faint (down to V = 15.8) and extremely metal-poor (down to [Fe/H] = −3.3) halo stars selected from the RPA. We obtained high-resolution spectra for these objects with the HORuS spectrograph on the Gran Telescopio Canarias. We measure the abundances of light, α, Fe-peak, and neutron-capture elements. We report the discovery of five carbon-enhanced metal-poor, one limited-r, three r-I, and four r-II stars, and six Mg-poor stars. We also identify one star of a possible globular cluster origin at an extremely low metallicity at [Fe/H] = −3.0. This adds to the growing evidence of a lower-limit metallicity floor for globular cluster abundances. We use the abundances of Fe-peak elements and the α-elements to investigate the contributions from different nucleosynthesis channels in the progenitor supernovae. We find the distribution of [Mg/Eu] as a function of [Fe/H] to have different enrichment levels, indicating different possible pathways and sites of their production. We also reveal differences in the trends of the neutron-capture element abundances of Sr, Ba, and Eu of various r-I and r-II stars from the RPA data releases, which provide constraints on their nucleosynthesis sites and subsequent evolution.

Abstract C057: Pilot study of vaginal microbiome profiles among Black and White endometrial cancer survivors

Abstract Background: Lower vaginal microbiome diversity, and specifically a Lactobacillus crispatis-dominant vagitype, is associated with more favorable health outcomes. Racial variation in the vaginal microbiome has been reported in some studies, including gynecologic cancers. Racial disparities in endometrial cancer 5-year survival are stark—62% for Black women vs. 83% for White women. Cancer treatments can acutely impact the microbiome of surrounding tissues with potential impacts on quality of life in survivorship, including sexual function. The objectives of this pilot research were to assess the feasibility of self-sampling and variation in vaginal microbiome communities by race, cancer treatment, and sexual function among endometrial cancer survivors. Methods: Endometrial cancer survivors (N=50, mean=11 months from diagnosis) enrolled in the Carolina Endometrial Cancer Study were mailed Genotek vaginal microbiome self-collection kits and the validated Sexual Function-Vaginal Changes Questionnaire (SVQ) before a nurse home visit. Microbiota profiles were characterized by bacteria 16S rRNA amplicon sequencing. Vagitypes were classified as Lactobacillus-dominant and other based on relative abundance (>50% vs. ≤50%) and Ward hierarchical clustering. Results: Overall, 48 vaginal samples were obtained. We excluded samples from women who reported antibiotic use within the last month (N=8) or were missing treatment data (N=6), leaving 34 samples. Of these, 47% were from Black survivors and 53% from White. Cancer treatments were categorized as surgery only (47%) vs. any chemotherapy or radiation (53%); and did not vary by race (p >.9). Black women did not have statistically significant different alpha (Shannon p=0.9) or beta (p=0.4) diversity, or a differential proportion of Lactobacillus dominant vagitype (59% vs. 41%, p=0.3) compared to White women. Alpha (Shannon p=0.04) and beta (p=0.004) diversity varied by cancer treatment with higher microbial diversity after chemotherapy or radiation compared to surgery alone. In the surgery only group, 63% of samples were Lactobacillus dominant, compared to 17% among the chemotherapy or radiation group (p=0.006). We examined cancer treatment associations in analyses restricted to the more favorable endometroid histology (N=25), as surgery alone is associated with endometrioid histology and better prognosis. In this subgroup, 57% (8/14) of women treated with surgery only had Lactobacillus-dominant vagitypes compared to 27% (3/11) in the chemotherapy/ radiation group (p=0.1). Lactobacillus-dominant vagitype was not associated with SVQ scales (global satisfaction; changes in intimacy or interest; dryness; pain). Conclusion: Self-collection of vaginal microbiome samples is feasible in cancer survivors. In our study, Lactobacillus-dominant vagitypes were less abundant among women who were treated with more intensive cancer therapies and did not vary by race or sexual function. Radiation and chemotherapy for endometrial cancer may affect vaginal microbiome composition after treatment ends. Citation Format: Mu Jin, Tope Keku, Nikki McCoy, Jordyn Brown, Jamie Hunter, Victoria Bae-Jump, M. Andrea Azcarate-Peril, Stephanie Engle, Andy Olshan, Hazel B Nichols. Pilot study of vaginal microbiome profiles among Black and White endometrial cancer survivors [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C057.

Uncovering the Pathway of Serine Octamer Magic Number Cluster Formation during Electrospray Ionization: Experiments and Simulations.

Electrospray ionization (ESI) of serine (Ser) solution generates Ser8H+ as an abundant magic number cluster. ESI clustering of most other solutes yields nonspecific stoichiometries. It is unclear why Ser8H+ dominates in the case of Ser, and how Ser8H+ forms during ESI. Even the location of Ser8H+ formation is contentious (in solution, in ESI droplets, or elsewhere). Here we unravel key aspects of the l-Ser8H+ formation pathway. Harsh ion sampling conditions promote the collision-induced dissociation (CID) of regular ESI analytes. Unexpectedly, Ser8H+ was seemingly resistant against CID during ion sampling, despite its extremely low tandem mass spectrometry (MS/MS) stability. This unusual behavior reveals that Ser8H+ forms during ion sampling. We propose the following pathway: (1) Nonspecific Ser clusters are released when ESI droplets evaporate to dryness. These initial clusters cover a wide size range, from a few Ser to hundreds or thousands of monomers. (2) The clusters undergo dissociation during ion sampling, mostly via successive loss of neutral monomers. For any source activation voltage, there is a subpopulation of clusters for which this CID cascade tends to terminate at the octamer level, culminating in Ser8H+-dominated product distributions. Mobile proton molecular dynamics simulations were used to model the entire pathway. Ser8H+ structures formed in these simulations were consistent with ion mobility experiments. The most compact structures resembled the model of [Scutelnic, V. J. Am. Chem. Soc. 2018, 140, 7554-7560], with numerous intermolecular salt bridges and H-bonds. Our findings illustrate how the interplay of association and dissociation reactions across phase boundaries can culminate in magic number clusters.

Prebiotic effects of commercial apple juice in high-fat diet fed rat

ObjectivesApples are one of the most frequently consumed fruits and are effective in preventing lifestyle-related and other diseases. However, few studies have been conducted to evaluate health benefits of processed apple products such as juice. In this study, we analyzed the health benefits of consuming apple juice, focusing on changes in the gut microbiota, which plays an important role in maintaining human health.ResultsRats were fed apple juice ad libitum, and the relative abundances of various gut microbiota in fecal samples were analyzed. In addition, rats treated apple juice were fed with a high-fat diet, and body weight, plasma triglyceride, glucose, and cholesterol levels were measured. The relative abundance of Clostridium cluster XIV did not change with the treatment of apple juice, but the relative abundance of Clostridium cluster IV was significantly decreased. In contrast, the relative abundances of Lactobacillus and Bifidobacterium, which provide benefits to the human body, were significantly increased by 3-fold and 10-fold, respectively, with apple juice consumption. When apple juice-treated rats were fed a high-fat diet, the increase in body weight, liver fat, and blood lipid parameters were all suppressed compared to high-fat alone group.ConculusionThis study suggests that the consumption of apple juice changes the gut microbiota, exerts a prebiotic effect, and is effective in improving lifestyle-related diseases.

Constraining Cosmological Parameters Using the Splashback Radius of Galaxy Clusters

Cosmological parameters such as ΩM and σ 8 can be measured indirectly using various methods, including galaxy cluster abundance and cosmic shear. These measurements constrain the composite parameter S 8, leading to degeneracy between ΩM and σ 8. However, some structural properties of galaxy clusters also correlate with cosmological parameters, due to their dependence on a cluster’s accretion history. In this work, we focus on the splashback radius, an observable cluster feature that represents a boundary between a cluster and the surrounding Universe. Using a suite of cosmological simulations with a range of values for ΩM and σ 8, we show that the position of the splashback radius around cluster-mass halos is greater in cosmologies with smaller values of ΩM or larger values of σ 8. This variation breaks the degeneracy between ΩM and σ 8 that comes from measurements of the S 8 parameter. We also show that this variation is, in principle, measurable in observations. As the splashback radius can be determined from the same weak lensing analysis already used to estimate S 8, this new approach can tighten low-redshift constraints on cosmological parameters, either using existing data, or using upcoming data such as that from Euclid and LSST.

Characterization of piRNAs in Diploid and Triploid Pacific Oyster Gonads: Exploring Their Potential Roles in Triploid Sterility.

PIWI-interacting RNAs (piRNAs) are crucial for silencing transposable elements, germ cell development, and gametogenesis. Triploid Pacific oysters (Crassostrea gigas) are vital in the oyster aquaculture industry due to reduced fertility and rapid growth. This study integrates piRNA and mRNA expression analyses to elucidate their potential contributions to the sterility of triploid C. gigas. Bioinformatics analysis reveals a distinct U-bias at the 5' terminal of oyster piRNAs. The abundance of piRNA clusters is reduced in triploid gonads compared to diploid gonads, particularly in sterile gonads, with a significant decrease in piRNA numbers. A specific piRNA cluster is annotated with the PPP4R1 gene, which is downregulated in infertile female triploids and exhibits a negative correlation with three piRNAs within the cluster. Differential expression analysis identified 46 and 88 piRNAs in female and male comparison groups, respectively. In female sterile triploids, the expression of three target genes of differentially expressed piRNAs associated with cell division showed downregulation, suggesting the potential roles of piRNAs in the regulation of cell division-related genes, contributing to the gonad arrest observed in female triploid oysters. In male triploid oysters, piRNAs potentially interact with the target genes associated with spermatogenesis, including TSSK4, SPAG17, and CCDC81. This study provides a concise overview of piRNAs expression in oyster gonads, offering insights into the regulatory role of piRNAs in triploid sterility.

Deciphering decidual deficiencies in recurrent spontaneous abortion and the therapeutic potential of mesenchymal stem cells at single-cell resolution

BackgroundRecurrent spontaneous abortion (RSA) is a challenging condition that affects the health of women both physically and mentally, but its pathogenesis and treatment have yet to be studied in detail. In recent years, Wharton’s jelly-derived mesenchymal stem cells (WJ-MSCs) have been shown to be effective in treating various diseases. Current understanding of RSA treatment using WJ-MSCs is limited, and the exact mechanisms of WJ-MSCs action in RSA remains largely unclear. In this study, we explored the decidual deficiencies in RSA and the therapeutic potential of WJ-MSCs at single-cell resolution.MethodsThree mouse models were established: a normal pregnancy group, an RSA group, and a WJ-MSC treatment group. Decidual tissue samples were collected for single-cell RNA sequencing (scRNA-seq) and functional verification, including single-cell resolution in situ hybridization on tissues (SCRINSHOT) and immunofluorescence.ResultsWe generated a single-cell atlas of decidual tissues from normal pregnant, RSA, and WJ-MSC-treated mice and identified 14 cell clusters in the decidua on day 14. Among these cell populations, stromal cells were the most abundant cell clusters in the decidua, and we further identified three novel subclusters (Str_0, Str_1, and Str_2). We also demonstrated that the IL17 and TNF signaling pathways were enriched for upregulated DEGs of stromal cells in RSA mice. Intriguingly, cell–cell communication analysis revealed that Str_1 cell-related gene expression was greatly reduced in the RSA group and rescued in the WJ-MSC treatment group. Notably, the interaction between NK cells and other cells in the RSA group was attenuated, and the expression of Spp1 (identified as an endometrial toleration-related marker) was significantly reduced in the NK cells of the RSA group but could be restored by WJ-MSC treatment.ConclusionHerein, we implemented scRNA-seq to systematically evaluate the cellular heterogeneity and transcriptional regulatory networks associated with RSA and its treatment with WJ-MSCs. These data revealed potential therapeutic targets of WJ-MSCs to remodel the decidual subpopulations in RSA and provided new insights into decidua-derived developmental defects at the maternal–foetal interface.

Co-expression of a pair of interdependent regulators coding genes ovmZ and ovmW awakens the production of angucyclinones antibiotics in Streptomyces neyagawaensis

BackgroundMicrobial genome sequencing and analysis revealed the presence of abundant silent secondary metabolites biosynthetic gene clusters (BGCs) in streptomycetes. Activating these BGCs has great significance for discovering new compounds and novel biosynthetic pathways.ResultsIn this study, we found that ovmZ and ovmW homologs, a pair of interdependent transcriptional regulators coding genes, are widespread in actinobacteria and closely associated with the biosynthesis of secondary metabolites. Through co-overexpression of native ovmZ and ovmW in Streptomyces neyagawaensis NRRL B-3092, a silent type II polyketide synthase (PKS) gene cluster was activated to produce gephyromycin A, tetrangomycin and fridamycin E with the yields of 22.3 ± 8.0 mg/L, 4.8 ± 0.5 mg/L and 20.3 ± 4.1 mg/L respectively in the recombinant strain of S.ne/pZnWn. However, expression of either ovmZ or ovmW failed to activate this gene cluster. Interestingly, overexpression of the heterologous ovmZ and ovmW pair from oviedomycin BGC of S. ansochromogenes 7100 also led to awakening of this silent angucyclinone BGC in S. neyagawaensis.ConclusionA silent angucyclinone BGC was activated by overexpressing both ovmZ and ovmW in S. neyagawaensis. Due to the wide distribution of ovmZ and ovmW in the BGCs of actinobacteria, co-overexpression of ovmZ and ovmW could be a strategy for activating silent BGCs, thus stimulating the biosynthesis of secondary metabolites.

The infall region as a complementary probe to cluster abundance

ABSTRACT Galaxy cluster abundance measurements provide a classic test of cosmology. They are most sensitive to the evolved amplitude of fluctuations, usually expressed as $S_8 = \sigma _8\sqrt{\Omega _{\rm m}/0.3}$. Thus, abundance constraints exhibit a strong degeneracy between $\sigma _8$ and $\Omega _{\rm m}$, as do other similar low-redshift tests such as cosmic shear. The mass distribution in the infall region around galaxy clusters, where material is being accreted from the surrounding field, also exhibits a cosmological dependence, but in this case it is nearly orthogonal to the $S_8$ direction in the $\Omega _{\rm m}$–$\sigma _8$ plane, making it highly complementary to halo abundance or cosmic shear studies. We explore how weak-lensing measurements of the infall region might be used to complement abundance studies, considering three different tests. The splashback radius is a prominent feature of the infall region; we show that detection of this feature in lensing data from the Euclid survey could independently constrain $\Omega _{\rm m}$ and $\sigma _8$ to $\pm 0.05$. Another feature, the depletion radius where the bias reaches a minimum, also shows cosmological dependence, though it is challenging to observe in practice. The strongest constraints come from direct measurements of the shear profile in the infall region at 2–$4\, r_{200{\rm c}}$. Combining the latter with abundance constraints such as those reported from SRG$/$eROSITA should reduce the area of the error contours by an estimated factor of 1.2 using a sample of clusters observed by the UNIONS survey, or a factor of 3 using clusters observed by the Euclid Wide survey over a broader range of redshift.