Cluster Abundance Research Articles

Long-term dynamics of the human oral microbiome during clinical disease progression

BackgroundOral microbiome dysbiosis is linked to overt inflammation of tooth-supporting tissues, leading to periodontitis, an oral condition that can cause tooth and bone loss. Microbiome dysbiosis has been described as a disruption in the symbiotic microbiota composition’s stability that could adversely affect the host’s health status. However, the precise microbiome dynamics that lead to dysbiosis and the progression of the disease are largely unknown. The objective of our study was to investigate the long-term dynamics of periodontitis progression and its connection to dysbiosis.ResultsWe studied three different teeth groups: sites that showed disease progression, sites that remained stable during the study, and sites that exhibited a cyclic deepening followed by spontaneous recovery. Time-series analysis revealed that communities followed a characteristic succession of bacteria clusters. Stable and fluctuating sites showed high asynchrony in the communities (i.e., different species responding dissimilarly through time) and a reordering of the communities where directional changes dominated (i.e., sample distance increases over time) in the stable sites but not in the fluctuating sites.Progressing sites exhibited low asynchrony and convergence (i.e., samples distance decreases over time). Moreover, new species were more likely to be recruited in stable samples if a close relative was not recruited previously. In contrast, progressing and fluctuating sites followed a neutral recruitment model, indicating that competition between closely related species is a significant component of species-species interactions in stable samples. Finally, periodontal treatment did not select similar communities but stabilized α-diversity, centered the abundance of different clusters to the mean, and increased community rearrangement.ConclusionsHere, we show that ecological principles can define dysbiosis and explain the evolution and outcomes of specific microbial communities of the oral microbiome in periodontitis progression. All sites showed an ecological succession in community composition. Stable sites were characterized by high asynchrony, a reordering of the communities where directional changes dominated, and new species were more likely to be recruited if a close relative was not recruited previously. Progressing sites were characterized by low asynchrony, community convergence, and a neutral model of recruitment. Finally, fluctuating sites were characterized by high asynchrony, community convergence, and a neutral recruitment model.

Immune Profiling of Responses to Influenza Vaccination in Patients with Myeloproliferative Neoplasms

▪Myeloproliferative neoplasms (MPNs) are clonal stem cell neoplasms that include polycythemia vera (PV), essential thrombocythemia (ET), and myelofibrosis (MF). MPN patients are immunocompromised due to immune dysregulation from clonal hematopoiesis, heightened inflammation, and immunosuppressive treatments. Infection is a leading cause of morbidity and mortality in MPNs, and as a result annual influenza vaccination is a critical component of care. However, efficacy of the influenza vaccine in MPN patients is unclear. This study sought to identify differences between MPN patients and healthy donors in their immune response to influenza vaccination and subsequent in vitro stimulation.The Massachusetts General Hospital (MGH) maintains a tissue bank of peripheral blood and bone marrow samples collected in consented patients with hematologic malignancy, including MPNs. The tissue bank was interrogated for MPN patients with peripheral blood samples banked 1-6 months after yearly trivalent/quadrivalent influenza vaccination. A total of 13 MPN patients were included, with a median age of 70 (32-86). Five patients had MF, 3 patients had PV, 4 patients had ET, and 1 patient had pre-fibrotic MF. Five patients were on treatment with ruxolitinib, 4 patients were on hydroxyurea (HU), and 4 patients were without treatment. Peripheral blood mononuclear cells (PBMCs) from 11 healthy donors 3-6 months post-vaccination, with a median age of 50 (28-56), were sourced commercially as controls.Cryopreserved samples were thawed and PBMC samples divided equally prior to incubation for 18 hours with peptides derived from Influenza A or sham. Subsequently samples were labeled with a 41-antibody panel and analyzed by mass cytometry. Manual gating together with FlowSOM clustering followed by EdgeR using T-test and FDR to correct for multiple comparisons were used to identify differentially abundant immune cell clusters between cohorts and treatment conditions.Without stimulation, MPN patients were decreased in B cell and memory CD4+ T cell populations as compared to healthy donors (p<0.05), in agreement with a previous report. MPN patients also exhibited an increase in a subset of mature B cells (p<0.05) and lineage negative CD123+ cells (p<0.05) as compared to controls. Stimulation included in this study aimed to expand on these distinctions and identified that baseline differences were retained with additional increases in CD4+ and CD8+ T cell responses in healthy donors as compared to MPN patients. Conversely, stimulation increased the frequency of inflammatory monocytic cells in MPN patients compared to healthy controls (p<0.05).In healthy donors stimulation induced several alterations in, most notably an increase in CD4+ effector memory cells (p<0.03), as compared to matched unstimulated controls. In contrast, comparison of pre- and post-stimulation within the MPN cohort revealed no significant differences in immune cell populations apart from a decrease in naïve CD4+ T cells (p<0.05). Patients receiving HU were enriched for naïve CD4+ and effector CD8+ T cells as compared to patients receiving ruxolitinib (p<0.05); however, these differences were diminished following stimulation. Within MPN patients, pre-stimulation samples in MF patients were characterized by increased abundance of activated monocyte/macrophage clusters and a lineage-negative CD123+ population; there were no significant differences in post-stimulation samples between MF and ET/PV/pre-fibrotic MF patients.We evaluated immunologic responses to influenza vaccination, with and without peptide stimulation, in MPN patients and compared to healthy controls. Overall, MPN patients demonstrated less robust B- and T-cell responses and a muted response to stimulation as compared to healthy controls, which may indicate reduced cellular responses following influenza vaccination. Ongoing analysis will interrogate specific immune populations and subsets in detail to refine current observations and will evaluate associations between immunologic cell clusters with serologic responses and additional patient characteristics. The results of our study highlight important alterations in the immune response to influenza vaccination and muted response to stimulation in MPN patients and will inform a future prospective study of vaccine responsiveness and immune dysfunction in patients with MPNs. [Display omitted] DisclosuresReeves: PR Fludigm: Honoraria; Immunoscape: Consultancy. Hobbs: Merck: Research Funding; Incyte Corporation: Research Funding; AbbVie.: Consultancy; Novartis: Consultancy; Celgene/Bristol Myers Squibb: Consultancy; Constellation Pharmaceuticals: Consultancy, Research Funding; Bayer: Research Funding.

Gut microbiota in Parkinson\u2019s disease patients: hospital-based study

BackgroundParkinson’s disease (PD) is one of the most common neurodegenerative diseases. There is accumulating evidence that link gut microbiota to symptomatology and pathophysiology of PD. The aim of this study was to describe the pattern of gut microbiota and its association with PD and identify the effect of environmental factors on gut microbiota. This case–control study included 46 patients diagnosed as Parkinson’s disease (PD) and 31 healthy volunteers age and sex matched. Detailed history including age of onset, duration of disease, environmental risk factors, diet data, treatment, Unified Parkinson’s Disease Rating Scale (UPDRS), and gastrointestinal tract (GIT) domain of Non‐Motor Symptoms Scale (NMSS) were assessed. After extraction of bacterial DNA from the fecal samples, bacterial abundance was quantified by qPCR using 16S rRNA group-specific primers.ResultsSignificant high abundance of Clostridium cluster IV, Akkermansia, Bifidobacterium, and lactic acid bacteria were found in the PD group compared with the control group (P < 0.001, 0.04, 0.02 and < 0.001, respectively), while Firmicutes were significantly less abundant in the PD group (P < 0.001) compared with the control group. The naive PD patients had significant abundance of Bifidobacterium, and lactic acid compared with control group. Interestingly, Akkermansia was more abundant in treated than untreated patients. There were significant associations between pesticide exposure and Bifidobacterium (P = 0.002), while no significant correlations between different gut microbiota and demographic, environment data, different rating scores or dominant type of PD. There was a significant negative correlation between the Bifidobacterium with the duration of illness (P = 0.012). ConclusionThe present study highlighted a significant connection between PD and levels of certain types of gut microbiota, in support of a possible link between gut microbiota and a neurodegenerative cascade of PD.

Effect of thermophilic bacterium HB27 manganese superoxide dismutase in a rat model of chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS).

We investigated the therapeutic effects of superoxide dismutase (SOD) from thermophilic bacterium HB27 on chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) and its underlying mechanisms. A Sprague–Dawley rat model of CP/CPPS was prepared and then administered saline or Thermus thermophilic (Tt)-SOD intragastrically for 4 weeks. Prostate inflammation and fibrosis were analyzed by hematoxylin and eosin staining, and Masson staining. Alanine transaminase (ALT), aspartate transaminase (AST), serum creatinine (CR), and blood urea nitrogen (BUN) levels were assayed for all animals. Enzyme-linked immunosorbent assays (ELISA) were performed to analyze serum cytokine concentrations and tissue levels of malondialdehyde, nitric oxide, SOD, catalase, and glutathione peroxidase. Reactive oxygen species levels were detected using dichlorofluorescein diacetate. The messenger ribonucleic acid (mRNA) expression of tissue cytokines was analyzed by reverse transcription polymerase chain reaction (RT-PCR), and infiltrating inflammatory cells were examined using immunohistochemistry. Nuclear factor-κB (NF-κB) P65, P38, and inhibitor of nuclear factor-κBα (I-κBα) protein levels were determined using western blot. Tt-SOD significantly improved histopathological changes in CP/CPPS, reduced inflammatory cell infiltration and fibrosis, increased pain threshold, and reduced the prostate index. Tt-SOD treatment showed no significant effect on ALT, AST, CR, or BUN levels. Furthermore, Tt-SOD reduced inflammatory cytokine expression in prostate tissue and increased antioxidant capacity. This anti-inflammatory activity correlated with decreases in the abundance of cluster of differentiation 3 (CD3), cluster of differentiation 45 (CD45), and macrophage inflammatory protein 1α (MIP1α) cells. Tt-SOD alleviated inflammation and oxidative stress by reducing NF-κB P65 and P38 protein levels and increasing I-κBα protein levels. These findings support Tt-SOD as a potential drug for CP/CPPS.

Acute titanium dioxide nanoparticles exposure impaired spatial cognitive performance through neurotoxic and oxidative mechanisms in Wistar rats

Context Titanium dioxide nanoparticles (TiO2-NPs) are used in many commercial products. However, their effects on human and animal organism remained to be clarified. Objective The present study aimed to investigate the effects of TiO2-NPs on the behavioural performance, monoamine neurotransmitters and oxidative stress in the rat brain. Material and methods Rats were injected intravenously with a single dose of TiO2-NPs (20 mg/kg body weight) and were subjected to cognitive and emotional tests using Morris water maze and elevated plus maze. Results Cognitive capacity as well as the emotional reactivity were significantly disrupted, in TiO2-NPs-administered rats compared to control group. These behavioural effects were correlated with changes in brain neurotransmitter contents reflected by a significant increase in dopamine and a decrease in serotonin levels. TiO2-NPs also induced oxidative stress in the brain manifested by increased levels of H2O2 and malondialdehyde, associated with antioxidant enzymes activities disturbance, in particular, superoxide dismutase and catalase activities. Moreover, TiO2-NPs administration caused histological damages in the brain tissue with abundant lymphocytic clusters, capillary dilations, vascular congestion and oedema. Conclusions Acute intravenous injection of TiO2-NPs impaired behaviour performances through brain biochemical and structural changes and precautions should be taken to their usage in food additive and medical applications.

Co-varying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomics.

As single-cell datasets grow in sample size, there is a critical need to characterize cell states that vary across samples and associate with sample attributes like clinical phenotypes. Current statistical approaches typically map cells to clusters then assess differences in cluster abundance. We present covarying neighborhood analysis (CNA), an unbiased method to identify associated cell populations with greater flexibility than cluster-based approaches. CNA characterizes dominant axes of variation across samples by identifying groups of small regions in transcriptional space—termed neighborhoods—that covary in abundance across samples, suggesting shared function or regulation. CNA performs statistical testing for associations between any sample-level attribute and the abundances of these covarying neighborhood groups. Simulations show that CNA enables more sensitive and accurate identification of disease-associated cell states than a cluster-based approach. When applied to published datasets, CNA captures a Notch activation signature in rheumatoid arthritis, identifies monocyte populations expanded in sepsis, and identifies a novel T-cell population associated with progression to active tuberculosis.

Lamellar Hole-associated Epiretinal Proliferation in choroideremia: a case report

BackgroundTo report a clinical case of a patient affected with choroideremia (CHM) who underwent macular surgery for a macular hole (MH) with Lamellar Hole-associated Epiretinal Proliferation (LHEP).Case presentationWe have described a 48-year-old male patient affected with CHM who developed MH with LHEP over a 7-year follow-up. The patient was referred to the Regional Center for Hereditary Retinal Degenerations of the Eye Clinic in Florence (Italy) in April 2012. The patient underwent vitrectomy and Inner Limiting Membrane (ILM) and LHEP peeling with fluid-air exchange. Ultra-structural examination of the excised epiretinal proliferation, carried out using electron microscopy, showed dense amorphous material, mainly composed of abundant clusters of fibrous collagens resembling compact fibrous long spacing collagen (FLSC), embedded in native vitreous collagen (NVC) and type IV collagen. No cells were detected in any of the specimens collected. At the 3rd-week postoperative follow-up the macular hole was closed.ConclusionMacular hole with LHEP can be detected in CHM patients; in our patient the macular hole showed tractional and degenerative features, with good anatomical results after macular surgery.

Constraint-based modeling of yeast mitochondria reveals the dynamics of protein import and iron-sulfur cluster biogenesis

SummaryMitochondria are a hallmark of eukaryal cells and play an important role in cellular metabolism. There is a vast amount of knowledge available on mitochondrial metabolism and essential mitochondrial functions, such as protein import and iron-sulfur cluster biosynthesis, including multiple studies on the mitochondrial proteome. Therefore, there is a need for in silico approaches to facilitate the analysis of these data. Here, we present a detailed model of mitochondrial metabolism Saccharomyces cerevisiae, including protein import, iron-sulfur cluster biosynthesis, and a description of the coupling between charge translocation processes and ATP synthesis. Model analysis implied a dual dependence of absolute levels of proteins in protein import, iron-sulfur cluster biogenesis and cluster abundance on growth rate and respiratory activity. The model is instrumental in studying dynamics and perturbations in these processes and given the high conservation of mitochondrial metabolism in humans, it can provide insight into their role in human disease.

Effects of Zinc Source and Enzyme Addition on the Fecal Microbiota of Dogs.

Supplemental zinc from organic sources has been suggested to be more bioavailable than inorganic ones for dog foods. However, the bioavailability of zinc might be affected by dietary constituents such as phytates. The present study aimed to evaluate the effects of two zinc sources (zinc sulfate and zinc proteinate) and the addition of a multi-enzymatic complex from the solid-state fermentation of Aspergillus niger on end-products of fecal fermentation and fecal microbiota of adult Beagles fed a high-phytate diet. The experimental design consisted of three 4 × 4 Latin Squares with a 2 × 2 factorial arrangement of treatments (n = 12 Beagles), with four periods and four diets: zinc sulfate without (IZ) or with (IZ +) enzyme addition, and zinc proteinate without (OZ) or with (OZ +) enzyme addition. Enzyme addition significantly affected Faith’s phylogenetic diversity index, whereas zinc source did not affect either beta or alpha diversity measures. Linear discriminant analysis effect size detected nine taxa as markers for organic zinc, 18 for inorganic source, and none for enzyme addition. However, with the use of a negative binomial generalized linear model, further effects were observed. Organic zinc was associated with a significantly higher abundance of Firmicutes and lower Proteobacteria and Bacteroidetes, although at a genus level, the response varied. The DNA abundance of Clostridium cluster I, Clostridium cluster XIV, Campylobacter spp., Ruminococcaceae, Turicibacter, and Blautia was significantly higher in dogs fed IZ and IZ + diets. Higher abundance of genus Lactobacillus was observed in dogs fed enzyme-supplemented diets. End-products of fecal fermentation were not affected by zinc source or enzymes. An increase in some taxa of the phyla Actinobacteria and Firmicutes was observed in feces of dogs fed organic zinc with enzyme addition but not with inorganic zinc. This study fills a gap in knowledge regarding the effect of zinc source and enzyme addition on the fecal microbiota of dogs. An association of zinc bioavailability and bacteria abundance is suggested, but the implications for the host (dog) are not clear. Further studies are required to unveil the effects of the interaction between zinc sources and enzyme addition on the fecal microbial community.

Spatial Distribution of Plasmodium falciparum and Plasmodium vivax in Northern Ethiopia by Microscopic, Rapid Diagnostic Test, Laboratory Antibody, and Antigen Data.

Determining malaria transmission within regions of low, heterogenous prevalence is difficult. A variety of malaria tests exist and range from identification of diagnostic infection to testing for prior exposure. This study describes the concordance of multiple malaria tests using data from a 2015 household survey conducted in Ethiopia. Blood samples (n=2279) from 3 regions in northern Ethiopia were assessed for Plasmodium falciparum and Plasmodium vivax by means of microscopy, rapid diagnostic test, multiplex antigen assay, and multiplex assay for immunoglobulin G (IgG) antibodies. Geospatial analysis was conducted with spatial scan statistics and kernel density estimation to identify malaria hot spots by different test results. The prevalence of malaria infection was low (1.4% by rapid diagnostic test, 1.0% by microscopy, and 1.8% by laboratory antigen assay). For P. falciparum, overlapping spatial clusters for all tests and an additional 5 unique IgG clusters were identified. For P. vivax, clusters identified with bead antigen assay, microscopy, and IgG partially overlapped. Assessing the spatial distribution of malaria exposure using multiple metrics can improve the understanding of malaria transmission dynamics in a region. The relative abundance of antibody clusters indicates that in areas of low transmission, IgG antibodies are a more useful marker to assess malaria exposure.

Single-Nucleus RNA Sequencing Identifies New Classes of Proximal Tubular Epithelial Cells in Kidney Fibrosis.

Proximal tubular cells (PTCs) are the most abundant cell type in the kidney. PTCs are central to normal kidney function and to regeneration versus organ fibrosis following injury. This study used single-nucleus RNA sequencing (snRNAseq) to describe the phenotype of PTCs in renal fibrosis. Kidneys were harvested from naïve mice and from mice with renal fibrosis induced by chronic aristolochic acid administration. Nuclei were isolated using Nuclei EZ Lysis buffer. Libraries were prepared on the 10× platform, and snRNAseq was completed using the Illumina NextSeq 550 System. Genome mapping was carried out with high-performance computing. A total of 23,885 nuclei were analyzed. PTCs were found in five abundant clusters, mapping to S1, S1-S2, S2, S2-cortical S3, and medullary S3 segments. Additional cell clusters ("new PTC clusters") were at low abundance in normal kidney and in increased number in kidneys undergoing regeneration/fibrosis following injury. These clusters exhibited clear molecular phenotypes, permitting labeling as proliferating, New-PT1, New-PT2, and (present only following injury) New-PT3. Each cluster exhibited a unique gene expression signature, including multiple genes previously associated with renal injury response and fibrosis progression. Comprehensive pathway analyses revealed metabolic reprogramming, enrichment of cellular communication and cell motility, and various immune activations in new PTC clusters. In ligand-receptor analysis, new PTC clusters promoted fibrotic signaling to fibroblasts and inflammatory activation to macrophages. These data identify unrecognized PTC phenotype heterogeneity and reveal novel PTCs associated with kidney fibrosis.

Detailed Abundances of Planet-hosting Open Clusters. The Praesepe (Beehive) Cluster*

Abstract It is not yet fully understood how planet formation affects the properties of host stars, in or out of a cluster; however, abundance trends can help us understand this process. We present a detailed chemical abundance analysis of six stars in Praesepe, a planet-hosting open cluster. Pr0201 is known to host a close-in (period of 4.4 days) giant planet (mass of 0.54 M J), while the other five cluster members in our sample (Pr0133, Pr0081, Pr0208, Pr0051, and Pr0076) have no detected planets according to measurements of radial velocity. Using high-resolution echelle spectra with high signal-to-noise ratio obtained with Keck/HIRES and a novel approach to measurements of equivalent width (XSpect-EW), we derived abundances of up to 20 elements spanning a range of condensation temperatures (T C). We find a mean cluster metallicity of [Fe/H] = +0.21 ± 0.02 dex, in agreement with most previous determinations. We find most of our elements show an [X/Fe] scatter of ∼0.02–0.03 dex and conclude that our stellar sample is chemically homogeneous. The T C slope for the cluster mean abundances is consistent with zero and none of the stars in our sample exhibit individually a statistically significant T C slope. Using a planet engulfment model, we find that the planet host, Pr0201, shows no evidence of significant enrichment in its refractory elements when compared to the cluster mean that would be consistent with a planetary accretion scenario.

BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes.

ABSTRACTMicrobial gene clusters encoding the biosynthesis of primary and secondary metabolites play key roles in shaping microbial ecosystems and driving microbiome-associated phenotypes. Although effective approaches exist to evaluate the metabolic potential of such bacteria through identification of these metabolic gene clusters in their genomes, no automated pipelines exist to profile the abundance and expression levels of such gene clusters in microbiome samples to generate hypotheses about their functional roles, and to find associations with phenotypes of interest. Here, we describe BiG-MAP, a bioinformatic tool to profile abundance and expression levels of gene clusters across metagenomic and metatranscriptomic data and evaluate their differential abundance and expression under different conditions. To illustrate its usefulness, we analyzed 96 metagenomic samples from healthy and caries-associated human oral microbiome samples and identified 252 gene clusters, including unreported ones, that were significantly more abundant in either phenotype. Among them, we found the muc operon, a gene cluster known to be associated with tooth decay. Additionally, we found a putative reuterin biosynthetic gene cluster from a Streptococcus strain to be enriched but not exclusively found in healthy samples; metabolomic data from the same samples showed masses with fragmentation patterns consistent with (poly)acrolein, which is known to spontaneously form from the products of the reuterin pathway and has been previously shown to inhibit pathogenic Streptococcus mutans strains. Thus, we show how BiG-MAP can be used to generate new hypotheses on potential drivers of microbiome-associated phenotypes and prioritize the experimental characterization of relevant gene clusters that may mediate them.IMPORTANCE Microbes play an increasingly recognized role in determining host-associated phenotypes by producing small molecules that interact with other microorganisms or host cells. The production of these molecules is often encoded in syntenic genomic regions, also known as gene clusters. With the increasing numbers of (multi)omics data sets that can help in understanding complex ecosystems at a much deeper level, there is a need to create tools that can automate the process of analyzing these gene clusters across omics data sets. This report presents a new software tool called BiG-MAP, which allows assessing gene cluster abundance and expression in microbiome samples using metagenomic and metatranscriptomic data. Here, we describe the tool and its functionalities, as well as its validation using a mock community. Finally, using an oral microbiome data set, we show how it can be used to generate hypotheses regarding the functional roles of gene clusters in mediating host phenotypes.

Cluster assembly times as a cosmological test

ABSTRACT The abundance of galaxy clusters in the low-redshift Universe provides an important cosmological test, constraining a product of the initial amplitude of fluctuations and the amount by which they have grown since early times. The degeneracy of the test with respect to these two factors remains a limitation of abundance studies. Clusters will have different mean assembly times, however, depending on the relative importance of initial fluctuation amplitude and subsequent growth. Thus, structural probes of cluster age such as concentration, shape, or substructure may provide a new cosmological test that breaks the main degeneracy in number counts. We review analytical predictions for how mean assembly time should depend on cosmological parameters, and test these predictions using cosmological simulations. Given the overall sensitivity expected, we estimate the cosmological parameter constraints that could be derived from the cluster catalogues of forthcoming surveys such as Euclid, the Nancy Grace Roman Space Telescope, eROSITA, or CMB-S4. We show that by considering the structural properties of their cluster samples, such surveys could easily achieve errors of Δσ8 = 0.01 or better.

Influence of oral nutritional agents rich in soluble dietary fiber on intestinal flora of elderly men with malnutrition.

ObjectiveObserve the influence of oral nutritional agents rich in soluble dietary (enteral nutritional suspension [TPF‐DM]) on intestinal flora of elderly male subjects with malnutrition.MethodSeventy‐eight subjects with good nutrition were considered as the healthy control group. Twenty‐eight male subjects who had malnutrition and were older than 70 years were included and randomly divided into the short‐term (3 months) intervention group (n = 20) and the long‐term (12 months) group (n = 8). They were provided with enteral nutritional suspension (TPF‐DM) 500 mL/day or maximum tolerance dose, so as to observe the changes in nutrition‐related indexes and intestinal flora after the elderly take enteral nutritional suspension (TPF‐DM).Results(1) For elderly male subjects with malnutrition, their body weight, body mass index, hemoglobin, total protein, and albumin were significantly lower than the control group with favorable nutrition. (2) There were obvious differences in intestinal flora between healthy elderly male subjects and those with malnutrition. After the treatment of enteral nutritional suspension (TPF‐DM), intestinal flora of the malnourished elderly subjects showed recovery toward the healthy elderly subjects. The obvious gradient changes of the flora were mainly in the bacteroidetes, firmicutes, and proteobacteria phyla, and the relative abundance of CAG2 clusters in the malnourished group was higher than that in the healthy control group, and the relative abundance decreased after long‐term treatment, and the change approached the healthy control group. The relative abundance of CAG3 and CAG6 clusters in the malnourished group was lower than that in the healthy control group, and the relative abundance increased after long‐term treatment, and the change approached the healthy control group.ConclusionMalnutrition has obvious impact on intestinal flora of the elderly. Enteral nutritional suspension (TPF‐DM) not only prevents the further decline in the state of nutrition but also helps the recovery in intestinal flora of the elderly. Long‐term application can produce better effects.

Study of cellular heterogeneity and differential dynamics of autophagy in human embryonic kidney development by single-cell RNA sequencing

BackgroundAutophagy is believed to participate in embryonic development, but whether the expression of autophagy-associated genes undergoes changes during the development of human embryonic kidneys remains unknown.MethodsIn this work, we identified 36,151 human renal cells from embryonic kidneys of 9–18 gestational weeks in 16 major clusters by single-cell RNA sequencing (scRNA-seq), and detected 1350 autophagy-related genes in all fetal renal cells. The abundance of each cell cluster in Wilms tumor samples from scRNA-seq and GDC TARGET WT datasets was detected by CIBERSORTx. R package Monocle 3 was used to determine differentiation trajectories. Cyclone tool of R package scran was applied to calculate the cell cycle scores. R package SCENIC was used to investigate the transcriptional regulons. The FindMarkers tool from Seurat was used to calculate DEGs. GSVA was used to perform gene set enrichment analyses. CellphoneDB was utilized to analyze intercellular communication.ResultsIt was found that cells in the 13th gestational week showed the lowest transcriptional level in each cluster in all stages. Nephron progenitors could be divided into four subgroups with diverse levels of autophagy corresponding to different SIX2 expressions. SSBpod (podocyte precursors) could differentiate into four types of podocytes (Pod), and autophagy-related regulation was involved in this process. Pseudotime analysis showed that interstitial progenitor cells (IPCs) potentially possessed two primitive directions of differentiation to interstitial cells with different expressions of autophagy. It was found that NPCs, pretubular aggregates and interstitial cell clusters had high abundance in Wilms tumor as compared with para-tumor samples with active intercellular communication.ConclusionsAll these findings suggest that autophagy may be involved in the development and cellular heterogeneity of early human fetal kidneys. In addition, part of Wilms tumor cancer cells possess the characteristics of some fetal renal cell clusters.Graphical abstract

Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics

Five years of datasets from 2015 to 2019 of whole genome shotgun sequencing for cells trapped on 0.2-µm filters of seawater collected monthly from Ofunato Bay, an enclosed bay in Japan, were analysed, which included the 2015 data that we had reported previously. Nucleotide sequences were determined for extracted DNA from three locations for both the upper (1 m) and deeper (8 or 10 m) depths. The biotic communities analysed at the domain level comprised bacteria, eukaryotes, archaea and viruses. The relative abundance of bacteria was over 60% in most months for the five years. The relative abundance of the SAR86 cluster was highest in the bacterial group, followed by Candidatus Pelagibacter and Planktomarina. The relative abundance of Ca. Pelagibacter showed no relationship with environmental factors, and those of SAR86 and Planktomarina showed positive correlations with salinity and dissolved oxygen, respectively. The bacterial community diversity showed seasonal changes, with high diversity around September and low diversity around January for all five years. Nonmetric multidimensional scaling analysis also revealed that the bacterial communities in the bay were grouped in a season-dependent manner and linked with environmental variables such as seawater temperature, salinity and dissolved oxygen.

Differentially Amplified Repetitive Sequences Among Aegilops tauschii Subspecies and Genotypes.

Genomic repetitive sequences commonly show species-specific sequence type, abundance, and distribution patterns, however, their intraspecific characteristics have been poorly described. We quantified the genomic repetitive sequences and performed single nucleotide polymorphism (SNP) analysis between 29 Ae. tauschii genotypes and subspecies using publicly available raw genomic Illumina sequence reads and used fluorescence in situ hybridization (FISH) to experimentally analyze some repeats. The majority of the identified repetitive sequences had similar contents and proportions between anathera, meyeri, and strangulata subspecies. However, two Ty3/gypsy retrotransposons (CL62 and CL87) showed significantly higher abundances, and CL1, CL119, CL213, CL217 tandem repeats, and CL142 retrotransposon (Ty1/copia type) showed significantly lower abundances in subspecies strangulata compared with the subspecies anathera and meyeri. One tandem repeat and 45S ribosomal DNA (45S rDNA) abundances showed a high variation between genotypes but their abundances were not subspecies specific. Phylogenetic analysis using the repeat abundances of the aforementioned clusters placed the strangulata subsp. in a distinct clade but could not discriminate anathera and meyeri. A near complete differentiation of anathera and strangulata subspecies was observed using SNP analysis; however, var. meyeri showed higher genetic diversity. FISH using major tandem repeats couldn’t detect differences between subspecies, although (GAA)10 signal patterns generated two different karyotype groups. Taken together, the different classes of repetitive DNA sequences have differentially accumulated between strangulata and the other two subspecies of Ae. tauschii that is generally in agreement with spike morphology, implying that factors affecting repeatome evolution are variable even among highly closely related lineages.

Activation of Naringenin and Kaempferol through Pathway Refactoring in the Endophyte Phomopsis Liquidambaris.

Abundant gene clusters of natural products are observed in the endophytic fungus Phomopsis liquidambaris; however, most of them are silent. Herein, a plug-and-play DNA assembly tool has been applied for flavonoid synthesis in P. liquidambaris. A shuttle plasmid was constructed based on S. cerevisiae, E. coli, and P. liquidambaris with screening markers URA, Amp, and hygR, respectively. Each fragment or cassette was successively assembled by overlap extension PCR with at least 40-50 bp homologous arms in S. cerevisiae for generating a new vector. Seven native promoters were screened by the DNA assembly based on the fluorescence intensity of the mCherry reporter gene in P. liquidambaris, and two of them were new promoters. The key enzyme chalcone synthase was the limiting step of the pathway. The naringenin and kaempferol pathways were refactored and activated with the titers of naringenin and kaempferol of 121.53 mg/L and 75.38 mg/L in P. liquidambaris using fed-batch fermentation, respectively. This study will be efficient and helpful for the biosynthesis of secondary metabolites.

Engineering Dual Active Sites at the Interface between Nanoporous Pt and Nanosized CeO2 to Enhance Photo‐Thermocatalytic CO Oxidation

AbstractEffective catalytic oxidation of toxic emissions at low temperatures has great significance on environmental protection. Herein, a novel structure of Pt/CeO2 catalyst, composed of abundant CeO2 clusters captured by nanoporous Pt particles, is designed to enhance the photo‐thermocatalytic CO oxidation by boosting the amount of active sites. The nanosized CeO2 support is fabricated by vacuum thermal decomposition and then the Pt/CeO2 catalyst with a nanoporous structure is synthesized by a one‐pot solution reduction method in a mild condition. The synthesized catalyst exhibits great low‐temperature CO catalytic oxidation activity, and the temperature for 90% CO conversion is 154 °C, achieving comparable catalytic activity with the single‐atom Pt/CeO2 catalyst. Abundant dual active sites, in terms of active oxygen absorbed on the oxygen vacancies and spillover from ceria to Pt, and active Pt sites located near the perimeter of the Pt–CeO2 interface, are formed to improve the photo‐thermocatalytic activity for CO oxidation.