Guidelines for DC preparation and flow cytometry analysis of mouse nonlymphoid tissues.

This article is part of the Dendritic Cell Guidelines article series, which provides a collection of state-of-the-art protocols for the preparation, phenotype analysis by flow cytometry, generation, fluorescence microscopy and functional characterization of mouse and human dendritic cells (DC) from lymphoid organs and various nonlymphoid tissues. DC are sentinels of the immune system present in almost every mammalian organ. Since they represent a rare cell population, DC need to be extracted from organs with protocols that are specifically developed for each tissue. This article provides detailed protocols for the preparation of single-cell suspensions from various mouse nonlymphoid tissues, including skin, intestine, lung, kidney, mammary glands, oral mucosa and transplantable tumors. Furthermore, our guidelines include comprehensive protocols for multiplex flow cytometry analysis of DC subsets and feature top tricks for their proper discrimination from other myeloid cells. With this collection, we provide guidelines for in-depth analysis of DC subsets that will advance our understanding of their respective roles in healthy and diseased tissues. While all protocols were written by experienced scientists who routinely use them in their work, this article was also peer-reviewed by leading experts and approved by all coauthors, making it an essential resource for basic and clinical DC immunologists.

PD-1+ T lymphocyte proportions and hospitalized exacerbation of COPD: a prospective cohort study.

OBJECTIVE: To evaluate the predictive value of PD-1 expression in T lymphocytes for rehospitalization due to acute exacerbations of COPD (AECOPD) in discharged patients. METHODS: 115 participants hospitalized with COPD (average age 71.8 ± 6.0 years) were recruited at Fujian Provincial Hospital. PD1+T lymphocytes proportions (PD1+T%), baseline demographics and clinical data were recorded at hospital discharge. AECOPD re-admission were collected at 1-year follow-up. Kaplan-Meier analysis compared the time to AECOPD readmissions among groups stratified by PD1+T%. Multivariable Cox proportional hazards regression and stratified analysis determined the correlation between PD1+T%, potential confounders, and AECOPD re-admission. ROC and DCA evaluated PD1+T% in enhancing the clinical predictive values of Cox models, BODE and CODEX. RESULTS: 68 participants (59.1%) were AECOPD readmitted, those with AECOPD readmission exhibited significantly elevated baseline PD-1+CD4+T/CD4+T% and PD-1+CD8 + T/CD8 + T% compared to non-readmitted counterparts. PD1+ T lymphocyte levels statistically correlated with BODE and CODEX indices. Kaplan-Meier analysis demonstrated that those in Higher PD1+ T lymphocyte proportions had reduced time to AECOPD readmission (logRank p < 0.05). Cox analysis identified high PD1+CD4+T and PD1+CD8+T ratios as risk factors of AECOPD readmission, with hazard ratios of 1.384(95%CI [1.043-1.725]) and 1.401(95%CI [1.013-1.789]), respectively. Notably, in patients aged < 70 years and with fewer than twice AECOPD episodes in the previous year, high PD1+T lymphocyte counts significantly increased risk for AECOPD readmission(p < 0.05). The AECOPD readmission predictive model, incorporating PD1+T% exhibited superior discrimination to the Cox model, BODE index and CODEX index, AUC of ROC were 0.763(95%CI [0.633-0.893]) and 0.734(95%CI [0.570-0.899]) (DeLong's test p < 0.05).The DCA illustrates that integrating PD1+T% into models significantly enhances the utility in aiding clinical decision-making. CONCLUSION: Evaluation of PD1+ lymphocyte proportions offer a novel perspective for identifying high-risk COPD patients, potentially providing insights for COPD management. TRIAL REGISTRATION: Chinese Clinical Trial Registry (ChiCTR, URL: www.chictr.org.cn/ ), Registration number: ChiCTR2200055611 Date of Registration: 2022-01-14.

Novel 2-alkythio-4-chloro-N-[imino(heteroaryl)methyl]benzenesulfonamide Derivatives: Synthesis, Molecular Structure, Anticancer Activity and Metabolic Stability.

A series of novel 2-alkythio-4-chloro-N-[imino-(heteroaryl)methyl]benzenesulfonamide derivatives, 8-24, were synthesized in the reaction of the N-(benzenesulfonyl)cyanamide potassium salts 1-7 with the appropriate mercaptoheterocycles. All the synthesized compounds were evaluated for their anticancer activity in HeLa, HCT-116 and MCF-7 cell lines. The most promising compounds, 11-13, molecular hybrids containing benzenesulfonamide and imidazole moieties, selectively showed a high cytotoxic effect in HeLa cancer cells (IC50: 6-7 µM) and exhibited about three times less cytotoxicity against the non-tumor cell line HaCaT cells (IC50: 18-20 µM). It was found that the anti-proliferative effects of 11, 12 and 13 were associated with their ability to induce apoptosis in HeLa cells. The compounds increased the early apoptotic population of cells, elevated the percentage of cells in the sub-G1 phase of the cell cycle and induced apoptosis through caspase activation in HeLa cells. For the most active compounds, susceptibility to undergo first-phase oxidation reactions in human liver microsomes was assessed. The results of the in vitro metabolic stability experiments indicated values of the factor t½ for 11-13 in the range of 9.1-20.3 min and suggested the hypothetical oxidation of these compounds to sulfenic and subsequently sulfinic acids as metabolites.

Synthesis of 3-(2-Alkylthio-4-chloro-5-methylbenzenesulfonyl)-2-(1-phenyl-3-arylprop-2-enylideneamino)guanidine Derivatives with Pro-Apoptotic Activity against Cancer Cells.

The untypical course of reaction between chalcones and benzenesulfonylaminoguanidines led to the new 3-(2-alkylthio-4-chloro-5-methylbenzenesulfonyl)-2-(1-phenyl-3-arylprop-2-enylideneamino)guanidine derivatives 8-33. The new compounds were tested in vitro for their impact on the growth of breast cancer cells MCF-7, cervical cancer cells HeLa and colon cancer cells HCT-116 by MTT assay. The results revealed that the activity of derivatives is strongly related to the presence of hydroxy group in the benzene ring at the 3-arylpropylidene fragment. The most cytotoxic compounds 20 and 24 displayed mean IC50 values of 12.8 and 12.7 µM, respectively, against three tested cell lines and were almost 3- and 4-fold more active toward MCF-7 and HCT-116 when compared with non-malignant HaCaT cells. Furthermore, compound 24 induced apoptosis in cancer cells and caused a decrease of mitochondrial membrane potential as well as an increase of cells in sub-G1 phase in contrast to its inactive analog 31. The strongest activity against the most sensitive HCT-116 cell line was found for compound 30 (IC50 = 8 µM), which was 11-fold more effective in the growth inhibition of HCT-116 cells than those of HaCaT cells. Based on this fact, the new derivatives may be promising leading structures for the search for agents for the treatment of colon cancer.

The Effects of Photosensitizing Dyes Fagopyrin and Hypericin on Planktonic Growth and Multicellular Life in Budding Yeast.

Naphthodianthrones such as fagopyrin and hypericin found mainly in buckwheat (Fagopyrum spp.) and St. John's wort (SJW) (Hypericum perforatum L.) are natural photosensitizers inside the cell. The effect of photosensitizers was studied under dark conditions on growth, morphogenesis and induction of death in Saccharomyces cerevisiae. Fagopyrin and hypericin induced a biphasic and triphasic dose response in cellular growth, respectively, over a 10-fold concentration change. In fagopyrin-treated cells, disruptions in the normal cell cycle progression were evident by microscopy. DAPI staining revealed several cells that underwent premature mitosis without budding, a striking morphological abnormality. Flow Cytometric (FC) analysis using a concentration of 100 µM showed reduced cell viability by 41% in fagopyrin-treated cells and by 15% in hypericin-treated cells. FC revealed the development of a secondary population of G1 cells in photosensitizer-treated cultures characterized by small size and dense structures. Further, we show that fagopyrin and the closely related hypericin altered the shape and the associated fluorescence of biofilm-like structures. Colonies grown on solid medium containing photosensitizer had restricted growth, while cell-to-cell adherence within the colony was also affected. In conclusion, the photosensitizers under dark conditions affected culture growth, caused toxicity, and disrupted multicellular growth, albeit with different efficiencies.

Flow Cytometry Characterization of Pluripotent Transmembrane Glycoproteins on Resident Cervix Uteri Cells in Patients Screened for Cervical Cancer.

The aim of this study was to characterize both by flow cytometry analysis and immunohistochemistry cervix uteri cells of nulliparous women screened for cervical intraepithelial neoplasia (CIN) in comparison to a group without CIN by using mesenchymal stem cell-like and hematopoietic lineage markers. A significant expression for CD29, CD38, HLA-I, and HLA-II was correlated positively to the CIN degree and it was more relevant in patients positive for human papilloma virus (HPV). Thus, identification and detailed characterization of pluripotent resident in uteri cells could be a promising therapeutic target.

Flow cytometric analysis of the leukocyte landscape during bleomycin-induced lung injury and fibrosis in the rat.

Bleomycin-induced lung injury and fibrosis is a well-described model to investigate lung inflammatory and remodeling mechanisms. Rat models are clinically relevant and are also widely used, but rat bronchoalveolar lavage (BAL) cells are not fully characterized with flow cytometry due to the limited availability of antibodies for this species. We optimized a comprehensive time-dependent flow cytometric analysis of cells after bleomycin challenge, confirming previous studies in other species and correlating them to histological staining, cytokine profiling, and collagen accumulation analysis in rat lungs. For this purpose, we describe a novel panel of rat surface markers and a strategy to identify and follow BAL cells over time. By combining surface markers in rat alveolar cells (CD45+), granulocytes and other myeloid cells, monocytes and macrophages can be identified by the expression of CD11b/c. Moreover, different activation states of macrophages (CD163+) can be observed: steady state (CD86-MHC-IIlow), activation during inflammation (CD86+,MHC-IIhigh), activation during remodeling (CD86+MHC-IIlow), and a population of newly recruited monocytes (CD163-α-granulocyte-). Hydroxyproline measured as marker of collagen content in lung tissue showed positive correlation with the reparative phase (CD163- cells and tissue inhibitor of metalloproteinases (TIMP) and IL-10 increase). In conclusion, after a very early granulocytic recruitment, inflammation in rat lungs is observed by activated macrophages, and high release of IL-6 and fibrotic remodeling is characterized by recovery of the macrophage population together with TIMP, IL-10, and IL-18 production. Recruited monocytes and a second peak of granulocytes appear in the transitioning phase, correlating with immunostaining of arginase-1 in the tissue, revealing the importance of events leading the changes from injury to aberrant repair.

Antigen-specific CD8 T cells in cell cycle circulate in the blood after vaccination.

Although clonal expansion is a hallmark of adaptive immunity, the location(s) where antigen-responding T cells enter cell cycle and complete it have been poorly explored. This lack of knowledge stems partially from the limited experimental approaches available. By using Ki67 plus DNA staining and a novel strategy for flow cytometry analysis, we distinguished antigen-specific CD8 T cells in G0 , in G1 and in S-G2 /M phases of cell cycle after intramuscular vaccination of BALB/c mice with antigen-expressing viral vectors. Antigen-specific cells in S-G2 /M were present at early times after vaccination in lymph nodes (LNs), spleen and, surprisingly, also in the blood, which is an unexpected site for cycling of normal non-leukaemic cells. Most proliferating cells had high scatter profile and were undetected by current criteria of analysis, which under-estimated up to 6 times antigen-specific cell frequency in LNs. Our discovery of cycling antigen-specific CD8 T cells in the blood opens promising translational perspectives.

The Importance of Detail: How Differences in Ligand Structures Determine Distinct Functional Responses in Integrin αv ß3.

Ligand-based control of protein functional motions can provide novel opportunities in the study of fundamental biological mechanisms and in the development of novel therapeutics. In this work we addressed the ligand-based modulation of integrin functions. Inhibitors of integrin αv ß3 are interesting anticancer agents but their molecular mechanisms are still unclear: Peptides and peptidomimetics characterized by the Arg-Gly-Asp (RGD) or isoAsp-Gly-Arg (isoDGR) binding motifs have shown controversial agonist/antagonist effects. We have investigated the differential mechanisms of integrin activation/deactivation by three distinct ligands (cyclo-RGDf(NMe)V (Cilengitide), cyclo[DKP3-RGD], cyclo[DKP3-isoDGR]; DKP=diketopiperazine) through a comparative analysis of ligand-controlled protein internal dynamics: Although RGD facilitates the onset of dynamic states leading to activation, isoDGR induces a diffuse rigidification of the complex consistent with antagonist activities. Computational predictions have been experimentally probed by showing that the antibody AP5, which is capable of recognizing the active form of integrin, binds specifically to the RGD complexes and not to the isoDGR complex, which supports opposite functional roles of the two motifs targeting the same binding site.

Mechanism of enhancing pyrene-degradation ability of bacteria by layer-by-layer assembly bio-microcapsules materials.

The mechanism of improving pyrene (PYR)-degrading ability of bacteria CP13 in Layer-by-layer (LBL) assembly chitosan/alginate (CHI/ALG) bio-microcapsules was investigated. Flow cytometry analysis showed that LBL microcapsules could effectively slow down the increasing rate of bacterial cell membrane permeability and the decreasing rate of the membrane potential, so as to reduce the death rate and number of the cells, which could protect the degrading bacteria. The results of Fluorescence spectrum, circular dichroism (CD) spectrum and laser light scattering (LLS) analysis revealed that the other possible mechanism for LBL microcapsules to promote bacterial degradation were following: CHI could enter the secondary structure of the protein of the extracellular polymeric substances (EPS) from CP13 and combined with EPS to generate a stable ground material, which had larger molecular weight (3.76×106 g mol-1) than the original EPS (2.52×106 g mol-1). The combination of CHI and EPS resulted in the decrease of the density of EPS from 1.18 to 0.72 g L-1, suggesting that CHI can loosen the EPS configurations, improving the capture ability of bacteria for PYR as well as the mass transfer of PYR from the extracellular to intracellular, thus eventually promoting the bacteria degrade performance.

A Single Extracellular Vesicle (EV) Flow Cytometry Approach to Reveal EV Heterogeneity.

Extracellular vesicles (EVs) actively participate in intercellular communication and pathological processes. Studying the molecular signatures of EVs is key to reveal their biological functions and clinical values, which, however, is greatly hindered by their sub-100 nm dimensions, the low quantities of biomolecules each EV carries, and the large population heterogeneity. Now, single-EV flow cytometry analysis is introduced to realize single EV counting and phenotyping in a conventional flow cytometer for the first time, enabled by target-initiated engineering (TIE) of DNA nanostructures on each EV. By illuminating multiple markers on single EVs, statistically significant differences are revealed among the molecular signatures of EVs originating from several breast cancer cell lines, and the cancer cell-derived EVs among the heterogeneous EV populations are successfully recognized. Thus, our approach holds great potential for various biological and biomedical applications.

Cell cycle synchronization and analysis of apoptosis-related gene in skin fibroblasts from domestic cat (Felis silvestris catus) and kodkod (Leopardus guigna).

The kodkod population is in constant decrease and the somatic cell nuclear transfer (SCNT) might help to preserve the genetic pool of this species. The cell cycle synchronization of donor cells plays a crucial role in SCNT. The objective of this research was to evaluate two different methods for quiescence induction, serum starvation (SS) and contact inhibition (CI), both for 1, 3 and 5 days, on skin fibroblast from domestic cat and kodkod. Flow cytometry analysis revealed that in domestic cat, SS and CI, both at 3 and 5 days, increased the percentage of fibroblasts in G0/G1 compared to growing cells (GC) (p < .05). In kodkod, only SS for 3 and 5 days and CI for 1 and 3 days increased the percentage of fibroblasts in G0/G1 compared to GC (p < .05). Viability analysis by differential staining revealed that SS for 5 days decreased the proportion of live fibroblasts in domestic cat and kodkod (p < .05). Regarding gene expression analysis, in domestic cat fibroblasts, no differences were found in the BAX/BCL2 ratio in SS and CI (both at 1, 3 and 5 days) compared to GC. In kodkod fibroblasts, BAX/BCL2 ratio was increased in CI at 3 and 5 days compared to SS at 3 and 5 days (p < .05). In conclusion, in kodkod fibroblasts SS for 5 days and CI after 3 days might have a negative impact on cellular viability. According to these results, we suggest SS for 3 days for cell cycle synchronization in kodkod fibroblasts.

Antibacterial activity of a novel fatty acid (14E, 18E, 22E, 26E)-methyl nonacosa-14, 18, 22, 26 tetraenoate isolated from Amaranthus spinosus.

CONTEXT: Amaranthus spinosus Linn. (Amaranthaceae), commonly known as ''spiny pigweed'', is used in both Indian traditional system and folk medicine for treatment of infectious diseases for a long time in several traditional herbal medicinal preparations. A novel fatty acid [(14E, 18E, 22E, 26E)-methyl nonacosa-14, 18, 22, 26 tetraenoate] is the major metabolite present. OBJECTIVE: This study examines the antibacterial potential of the fatty acid isolated from the A. spinosus against some Gram-positive and Gram-negative bacteria. MATERIALS AND METHODS: Three Gram-positive and seven Gram-negative bacterial strains were used for antibacterial assay. The minimum inhibitory concentration (MIC) of the fatty acid was analysed by dilution method and the effects of the fatty acid on the bacterial membrane were studied in detail by flow cytometry analysis. RESULTS AND DISCUSSION: All the studied bacterial strains were found to be inhibited at a concentration of 100 µg/mL. Staphylococcus aureus ML-59, Bacillus lycheniformis 10341, Shigella boydii 8, Vibrio cholera 811, Vibrio cholera 854 and Vibrio alginolyteus were susceptible and sensitive to the tested fatty acid with a MIC value of 25 µg/mL. It proved a full spectrum of antibacterial activity associated with alterations in the permeability of bacterial membranes. CONCLUSION: The fatty acid from the A. spinosus possesses potent antibacterial action.

Increased CD11b(+) Gr-1(+) cell population in the placenta after infection with Toxoplasma gondii.

Toxoplasma gondii is an obligate intracellular protozoan pathogen that can cross the placenta, resulting in congenital toxoplasmosis with severe fetal brain abnormalities. The molecular mechanisms of immune responses against T. gondii infection in the placenta have largely remained unclear. An analytical method for characterizing phenotypes of immune cells in the placenta by flow cytometry was established and it was found that numbers of CD11b(+) Gr-1(+) cells in the placenta increased significantly after T. gondii infection. These results suggest that innate immune responses play an important role in immunity against T. gondii infection via the feto-maternal interface.

Ultra-structural morphology of long-term cultivated white adipose tissue-derived stem cells.

White adipose tissue was long perceived as a passive lipid storage depot but it is now considered as an active and important endocrine organ. It also harbours not only adipocytes and vascular cells but also a wide array of immunologically active cells, including macrophages and lymphocytes, which may induce obesity-related inflammation. Recently, adipose tissue has been reported as a source of adult mesenchymal stem cells with wide use in regenerative medicine and tissue engineering. Their relatively non-complicated procurement and collection (often performed as liposuction during aesthetic surgery) and grand plasticity support this idea even more. We focused our research on exploring the issues of isolation and long-term cultivation of mesenchymal stem cells obtained from adipose tissue. Ultra-structural morphology of the cells cultivated in vitro has been studied and analysed in several cultivation time periods and following serial passages--up to 30 passages. In the first passages they had ultra-structural characteristics of cells with high proteosynthetic activity. Within the cytoplasm, big number of small lipid droplets and between them, sparsely placed, small and inconspicuous, electron-dense, lamellar bodies, which resembled myelin figures were observed. The cells from the later passages contained high number of lamellar electron-dense structures, which filled out almost the entire cytoplasm. In between, mitochondria were often found. These bodies were sometimes small and resembled myelin figures, but several of them reached huge dimensions (more than 1 µm) and their lamellar structure was not distinguishable. We did not have an answer to the question about their function, but they probably represented the evidence of active metabolism of lipids present in the cytoplasm of these cells or represented residual bodies, which arise after the breakdown of cellular organelles, notably mitochondria during long-term cultivation.

Isolation and characterization of intestinal stem cells based on surface marker combinations and colony-formation assay.

BACKGROUND & AIMS: Identification of intestinal stem cells (ISCs) has relied heavily on the use of transgenic reporters in mice, but this approach is limited by mosaic expression patterns and difficult to directly apply to human tissues. We sought to identify reliable surface markers of ISCs and establish a robust functional assay to characterize ISCs from mouse and human tissues. METHODS: We used immunohistochemistry, real-time reverse-transcription polymerase chain reaction, and fluorescence-activated cell sorting (FACS) to analyze intestinal epithelial cells isolated from mouse and human intestinal tissues. We compared different combinations of surface markers among ISCs isolated based on expression of Lgr5-green fluorescent protein. We developed a culture protocol to facilitate the identification of functional ISCs from mice and then tested the assay with human intestinal crypts and putative ISCs. RESULTS: CD44(+)CD24(lo)CD166(+) cells, isolated by FACS from mouse small intestine and colon, expressed high levels of stem cell-associated genes. Transit-amplifying cells and progenitor cells were then excluded based on expression of GRP78 or c-Kit. CD44(+)CD24(lo)CD166(+) GRP78(lo/-) putative stem cells from mouse small intestine included Lgr5-GFP(hi) and Lgr5-GFP(med/lo) cells. Incubation of these cells with the GSK inhibitor CHIR99021 and the E-cadherin stabilizer Thiazovivin resulted in colony formation by 25% to 30% of single-sorted ISCs. CONCLUSIONS: We developed a culture protocol to identify putative ISCs from mouse and human tissues based on cell surface markers. CD44(+)CD24(lo)CD166(+), GRP78(lo/-), and c-Kit(-) facilitated identification of putative stem cells from the mouse small intestine and colon, respectively. CD44(+)CD24(-/lo)CD166(+) also identified putative human ISCs. These findings will facilitate functional studies of mouse and human ISCs.

Comparison of T cells mediated immunity and side effects of mRNA vaccine and conventional COVID-19 vaccines administrated in Jordan.

Various COVID-19 vaccines can affect the immune system. Discrepancies have been noted in immune system characteristics, such as T-lymphocyte levels, between vaccinated and non-vaccinated individuals. This study investigates the variations in immune responses among the four administered COVID-19 vaccines, influencing factors, and clinical outcomes in Jordan. A total of 350 adults, who were at least two doses vaccinated, were interviewed and blood samples were collected for subsequent laboratory analyses. The study involved the quantification of T-cells specifically targeting anti-SARS CoV-2 using Flow cytometry analysis. BNT162b2 (Pfizer) recipients displayed significantly higher CD3+/CD4+ T-helper cell responses (90.84%, 87.46% - 94.22%) compared to non-Pfizer-BioNTech recipients {BBIBP-CorV (Sinopharm) and Sputnik V (Gamaleya Research Institute), then ChAdOx1 nCoV-19 (AstraZeneca)} (83.62%, 77.91% - 89.33%). The CD3+/CD8+ (T cytotoxic) level was notably elevated in non-Pfizer-BioNTech recipients {Sinopharm and Sputnik V then ChAdOx1 nCoV-19 AstraZeneca (73.94%, 69.38% - 78.49%) compared to BNT162b2 (Pfizer) recipients (58.26%, 53.07% - 63.44%). The CD3+ (T-cells) level showed no significant difference between BNT162b2 recipients (73.74%) and non-Pfizer-BioNTech recipients (77.83%), with both types generating T-cells. Comparing two doses of non-Pfizer-BioNTech vaccines with the third dose of BNT162b2 recipients (Pfizer), no difference in the type of immune reaction was observed, with non-Pfizer-BioNTech recipients still stimulating endogenous pathways like cell-mediated cytotoxic effects for cells. All COVID-19 vaccines administered in Jordan were effective, with respect to the total number of T cells. Non-Pfizer-BioNTech had higher in toxic T-cells and Pfizer-BioNTech was higher in helper T-cells that stimulate plasma cells to produce antibodies.

A GC-MS-based untargeted metabolomics approach for comprehensive metabolic profiling of mycophenolate mofetil-induced toxicity in mice.

Background: Mycophenolate mofetil (MMF), the morpholinoethyl ester of mycophenolic acid, is widely used for maintenance immunosuppression in transplantation. The gastrointestinal toxicity of MMF has been widely uncovered. However, the comprehensive metabolic analysis of MMF-induced toxicity is lacking. This study is aimed to ascertain the metabolic changes after MMF administration in mice. Methods: A total of 700 mg MMF was dissolved in 7 mL dimethyl sulfoxide (DMSO), and then 0.5 mL of mixture was diluted with 4.5 mL of saline (100 mg/kg). Mice in the treatment group (n = 9) were given MMF (0.1 mL/10 g) each day via intraperitoneal injection lasting for 2 weeks, while those in the control group (n = 9) received the same amount of blank solvent (DMSO: saline = 1:9). Gas chromatography-mass spectrometry was utilized to identify the metabolic profiling in serum samples and multiple organ tissues of mice. The potential metabolites were identified using orthogonal partial least squares discrimination analysis. Meanwhile, we used the MetaboAnalyst 5.0 (http://www.metaboanalyst.ca) and Kyoto Encyclopedia of Genes and Genomes database (http://www.kegg.jp) to depict the metabolic pathways. The percentages of lymphocytes in spleens were assessed by multiparameter flow cytometry analysis. Results: Compared to the control group, we observed that MMF treatment induced differential expression of metabolites in the intestine, hippocampus, lung, liver, kidney, heart, serum, and cortex tissues. Subsequently, we demonstrated that multiple amino acids metabolism and fatty acids biosynthesis were disrupted following MMF treatment. Additionally, MMF challenge dramatically increased CD4+ T cell percentages but had no significant influences on other types of lymphocytes. Conclusion: MMF can affect the metabolism in various organs and serum in mice. These data may provide preliminary judgement for MMF-induced toxicity and understand the metabolic mechanism of MMF more comprehensively.

Co-cultivation of microalgae and bacteria for optimal bioenergy feedstock production in wastewater by using response surface methodology.

This work uses response surface methodology (RSM) to study the co-cultivation of symbiotic indigenous wastewater microalgae and bacteria under different conditions (inoculum ratio of bacteria to microalgae, CO2, light intensity, and harvest time) for optimal bioenergy feedstock production. The findings of this study demonstrate that the symbiotic microalgae-bacteria culture not only increases total microalgal biomass and lipid productivity, but also enlarges microalgal cell size and stimulates lipid accumulation. Meanwhile, inoculum ratio of bacteria to microalgae, light intensity, CO2, and harvest time significantly affect biomass and lipid productivity. CO2 concentration and harvest time have significant interactive effect on lipid productivity. The response of microalgal biomass and lipid productivity varies significantly from 2.1 × 105 to 1.9 × 107 cells/mL and 2.8 × 102 to 3.7 × 1012 Total Fluorescent Units/mL respectively. Conditions for optimum biomass and oil accumulation are 100% of inoculation ratio (bacteria/microalgae), 3.6% of CO2 (v/v), 205.8 µmol/m2/s of light intensity, and 10.6 days of harvest time. This work provides a systematic methodology with RSM to explore the benefits of symbiotic microalgae-bacteria culture, and to optimize various cultivation parameters within complex wastewater environments for practical applications of integrated wastewater-microalgae systems for cost-efficient bioenergy production.

FlowAtlas: an interactive tool for high-dimensional immunophenotyping analysis bridging FlowJo with computational tools in Julia.

As the dimensionality, throughput and complexity of cytometry data increases, so does the demand for user-friendly, interactive analysis tools that leverage high-performance machine learning frameworks. Here we introduce FlowAtlas: an interactive web application that enables dimensionality reduction of cytometry data without down-sampling and that is compatible with datasets stained with non-identical panels. FlowAtlas bridges the user-friendly environment of FlowJo and computational tools in Julia developed by the scientific machine learning community, eliminating the need for coding and bioinformatics expertise. New population discovery and detection of rare populations in FlowAtlas is intuitive and rapid. We demonstrate the capabilities of FlowAtlas using a human multi-tissue, multi-donor immune cell dataset, highlighting key immunological findings. FlowAtlas is available at https://github.com/gszep/FlowAtlas.jl.git.