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1.
J Agric Food Chem ; 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38836763

ABSTRACT

Mung bean contains up to 32.6% protein and is one of the great sources of plant-based protein. Because many allergens also function as defense-related proteins, it is important to determine their abundance levels in the high-yielding, disease-resistant cultivars. In this study, for the first time, we compared the seed proteome of high-yielding mung bean cultivars developed by a conventional breeding approach. Using a label-free quantitative proteomic platform, we successfully identified and quantified a total of 1373 proteins. Comparative analysis between the high-yielding disease-resistant cultivar (MC5) and the other three cultivars showed that a total of 69 common proteins were significantly altered in their abundances across all cultivars. Bioinformatic analysis of these altered proteins demonstrated that PDF1 (a defensin-like protein) exhibited high sequence similarity and epitope matching with the established peanut allergens, indicating a potential mung bean allergen that showed a cultivar-specific response. Conversely, known mung bean allergen proteins such as PR-2/PR-10 (Vig r 1), Vig r 2, Vig r 4, LTP1, ß-conglycinin, and glycinin G4 showed no alternation in the MC5 compared to other cultivars. Taken together, our findings suggest that the known allergen profiles may not be impacted by the conventional plant breeding method to develop improved mung bean cultivars.

2.
Food Chem ; 456: 139887, 2024 May 29.
Article in English | MEDLINE | ID: mdl-38865819

ABSTRACT

Fennel essential oil (FEO) a natural spice that has versatile biological activities. However, the direct use of FEO is limited due to its water insolubility and poor stability. Chilled pork is prone to spoilage during storage. To solve these problems, this study aimed to prepare an inclusion complex (IC) of FEO with hydroxypropyl-ß-cyclodextrin via co-precipitation and apply it to the preservation of chilled pork. Results indicated that the optimal parameters were encapsulating temperature 37 °C, wall-core ratio 14:1 g/mL, stirring speed 600 r/min, and encapsulating time 240 min, obtaining an encapsulation efficiency of 83.75%. The results of scanning electron microscopy, Fourier transform infra-red spectroscopy, and nuclear magnetic resonance demonstrated the successful preparation of IC. The release of FEO from IC was controllable through adjusting the different temperatures and relative humidities. Furthermore, IC effectively delayed the spoilage of chilled pork and extended its shelf life by 6 days at 4 °C.

3.
Cell Commun Signal ; 22(1): 249, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38693584

ABSTRACT

Copper plays vital roles in numerous cellular processes and its imbalance can lead to oxidative stress and dysfunction. Recent research has unveiled a unique form of copper-induced cell death, termed cuproptosis, which differs from known cell death mechanisms. This process involves the interaction of copper with lipoylated tricarboxylic acid cycle enzymes, causing protein aggregation and cell death. Recently, a growing number of studies have explored the link between cuproptosis and cancer development. This review comprehensively examines the systemic and cellular metabolism of copper, including tumor-related signaling pathways influenced by copper. It delves into the discovery and mechanisms of cuproptosis and its connection to various cancers. Additionally, the review suggests potential cancer treatments using copper ionophores that induce cuproptosis, in combination with small molecule drugs, for precision therapy in specific cancer types.


Subject(s)
Copper , Neoplasms , Humans , Neoplasms/metabolism , Neoplasms/drug therapy , Neoplasms/pathology , Copper/metabolism , Animals , Signal Transduction , Cell Death
4.
AMB Express ; 14(1): 35, 2024 Apr 13.
Article in English | MEDLINE | ID: mdl-38615116

ABSTRACT

Endophytic bacteria are one of the symbiotic microbial groups closely related to host algae. However, less research on the endophytic bacteria of marine algae. In this study, the endophytic bacterial community of Sargassum thunbergii was investigated using the culture method and high-throughput sequencing. Thirty-nine endophytic bacterial strains, belonging to two phyla, five genera and sixteen species, were isolated, and Firmicutes, Bacillus and Metabacillus indicus were the dominant taxa at the phylum, genus and species level, respectively. High-throughput sequencing revealed 39 phyla and 574 genera of endophytic bacteria, and the dominant phylum was Proteobacteria, while the dominant genus was Ralstonia. The results also indicated that the endophytic bacteria of S. thunbergii included various groups with nitrogen fixation, salt tolerance, pollutant degradation, and antibacterial properties but also contained some pathogenic bacteria. Additionally, the endophytic bacterial community shared a large number of groups with the epiphytic bacteria and bacteria in the surrounding seawater, but the three groups of samples could be clustered separately. In conclusion, there are a variety of functional endophytic bacteria living in S. thunbergii, and the internal condition of algae is a selective factor for the formation of endophytic bacterial communities. This study enriched the database of endophytic bacteria in marine macroalgae, paving the way for further understanding of the interrelationships between endophytic bacteria, macroalgae, and the environment.

5.
Sci Total Environ ; 927: 172273, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38583625

ABSTRACT

Firefighters are frequently exposed to a variety of chemicals formed from smoke, which pose a risk for numerous diseases, including cancer. Comparative urine proteome profiling could significantly improve our understanding of the early detection of potential cancer biomarkers. In this study, for the first time, we conducted a comparative protein profile analysis of 20 urine samples collected from ten real-life firefighters prior to and following emergency fire-induced smoke. Using a label-free quantitative proteomics platform, we identified and quantified 1325 unique protein groups, of which 45 proteins showed differential expressions in abundance in response to fire-smoke exposure (post) compared to the control (pre). Pathway analysis showed proteins associated with epithelium development (e.g., RHCG, HEG1, ADAMTSL2) and Alzheimer's disease (SORL1) were significantly increased in response to smoke exposure samples. A protein-protein-network study showed a possible link between these differentially abundant proteins and the known cancer gene (TP53). Moreover, a cross-comparison analysis revealed that seven proteins-ALDH1A1, APCS, POMC, COL2A1, RDX, DDAH2, and SDC4 overlapped with the previously published urine cancer proteome datasets, suggesting a potential cancer risk. Our findings demonstrated that the discovery proteomic platform is a promising analytical technique for identifying potential non-invasive biomarkers associated with fire-smoke exposure in firefighters that may be related to cancer.


Subject(s)
Firefighters , Occupational Exposure , Proteome , Smoke , Humans , Pilot Projects , Smoke/adverse effects , Male , Biomarkers/urine , Adult , Carcinogens , Proteomics
6.
Front Microbiol ; 15: 1334918, 2024.
Article in English | MEDLINE | ID: mdl-38559345

ABSTRACT

Endophytic bacteria have a complex coevolutionary relationship with their host macroalgae. Dioecious macroalgae are important producers in marine ecosystems, but there is still a lack of research on how sex influences their endophytic bacteria. In this study, the endophytic bacterial communities in male and female S. thunbergii and their reproductive tissues (receptacles) were compared using culture methods and high-throughput sequencing. The endophytic bacterial communities detected by the two methods were different. Among the 78 isolated strains, the dominant phylum, genus, and species were Bacillota, Alkalihalobacillus, and Alkalihalobacillus algicola, respectively, in the algal bodies, while in the receptacles, they were Bacillota, Vibrio, and Vibrio alginolyticus. However, 24 phyla and 349 genera of endophytic bacteria were identified by high-throughput sequencing, and the dominant phylum and genus were Pseudomonadota and Sva0996_ Marine_ Group, respectively, in both the algal body and the receptacles. The two methods showed similar compositions of endophytic bacterial communities between the samples of different sexes, but the relative abundances of dominant and specific taxa were different. The high-throughput sequencing results showed more clearly that the sex of the host alga had an effect on its endophyte community assembly and a greater effect on the endophytic bacterial community in the receptacles. Moreover, most specific bacteria and predicted functional genes that differed between the samples from the males and females were related to metabolism, suggesting that metabolic differences are the main causes of sex differences in the endophytic bacterial community. Our research is the first to show that host sex contributes to the composition of endophytic bacterial communities in dioecious marine macroalgae. The results enrich the database of endophytic bacteria of dioecious marine macroalgae and pave the way for better understanding the assembly mechanism of the endophytic bacterial community of algae.

7.
Adv Med Sci ; 69(1): 167-175, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38521458

ABSTRACT

PURPOSE: Psoriasis is a skin disease characterized by excessive proliferation, inflammation and oxidative stress in keratinocytes. The present study aimed to investigate the therapeutic effects of Dendrobium officinale polysaccharide (DOP) on keratinocyte psoriasis-like models. METHODS: The HaCaT keratinocyte inflammation models were induced by interleukin (IL)-22 or lipopolysaccharide (LPS), respectively, and oxidative stress damage within cells was elicited by H2O2 and treated using DOP. CCK-8 and EdU were carried out to detect cell proliferation. ELISA, qRT-PCR, and Western blot were conducted to measure the expression of pro-inflammatory cytokines IL17A, IL-23, IL1ß, tumor necrosis factor alpha (TNF-α), and IL-6. Reactive oxygen species (ROS) level in keratinocytes was detected by flow cytometry. Cell proliferation-associated proteins (PCNA, Ki67, Cyclin D1) and pathway proteins (p-AKT and AKT), and oxidative stress marker proteins (Nrf-2, CAT, SOD1) were detected by Western blot. RESULT: DOP did not affect the proliferation of normal keratinocytes, but DOP was able to inhibit the proliferative activity of IL-22-induced overproliferating keratinocytes and suppress the expression of proliferation-related factors PCNA, Ki67, and Cyclin D1 as well as the proliferation pathway p-AKT. In addition, DOP treatment was able to inhibit IL-22 and LPS-induced inflammation and H2O2-induced oxidative stress, including the expression of IL17A, IL-23, IL1ß, TNF-α, IL-6, and IL1ß, as well as the expression levels of intracellular ROS levels and cellular oxidative stress-related indicators SOD, MDA, CAT, Nrf-2 and SOD1. CONCLUSION: DOP inhibits keratinocyte hyperproliferation, inflammation and oxidative stress to improve the keratinocyte psoriasis-like state.


Subject(s)
Cell Proliferation , Dendrobium , Inflammation , Keratinocytes , Oxidative Stress , Polysaccharides , Psoriasis , Oxidative Stress/drug effects , Dendrobium/chemistry , Humans , Keratinocytes/drug effects , Keratinocytes/metabolism , Cell Proliferation/drug effects , Polysaccharides/pharmacology , Inflammation/drug therapy , Inflammation/pathology , Inflammation/metabolism , Psoriasis/drug therapy , Psoriasis/pathology , Psoriasis/metabolism , Reactive Oxygen Species/metabolism , Cytokines/metabolism
8.
Life Sci ; 344: 122556, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38471620

ABSTRACT

Engineering a patient's own T cells to accurately identify and eliminate cancer cells has effectively cured individuals afflicted with previously incurable hematologic cancers. These findings have stimulated research into employing chimeric antigen receptor (CAR) T therapy across various areas within the field of oncology. However, evidence from both clinical and preclinical investigations emphasize the broader potential of CAR T therapy, extending beyond oncology to address autoimmune disorders, persistent infections, cardiac fibrosis, age-related ailments and other conditions. Concurrently, the advent of novel technologies and platforms presents additional avenues for utilizing CAR T therapy in non-cancerous contexts. This review provides an overview of the rationale behind CAR T therapy, delineates ongoing challenges in its application to cancer treatment, summarizes recent findings in non-cancerous diseases, and engages in discourse regarding emerging technologies that bear relevance. The review delves into prospective applications of this therapeutic approach across a diverse range of scenarios. Lastly, the review underscores concerns related to precision and safety, while also outlining the envisioned trajectory for extending CAR T therapy beyond cancer treatment.


Subject(s)
Hematologic Neoplasms , Neoplasms , Receptors, Chimeric Antigen , Humans , Receptors, Chimeric Antigen/therapeutic use , Neoplasms/therapy , Immunotherapy, Adoptive , T-Lymphocytes , Hematologic Neoplasms/therapy
9.
Phys Chem Chem Phys ; 26(14): 10494-10505, 2024 Apr 03.
Article in English | MEDLINE | ID: mdl-38517057

ABSTRACT

Hexagonal boron nitride possesses a unique layered structure, high specific surface area and similar electronic properties as graphene, which makes it not only a promising catalyst support, but also a highly effective metal-free catalyst in the booming field of green chemistry. Reactions involving small molecules (e.g., oxygen, low carbon alkanes, nitrogen and carbon dioxide) have always been a hot topic in catalytic research, especially associated with the adsorption and activation regime of different forms of small molecules on catalysts. In this review, we have investigated the adsorption of different small molecules and the relevant activation mechanisms of four typical chemical bonds (OO, C-H, NN, CO) on hexagonal boron nitride. Recent progress on approaches adopted to enhance the activation capacity such as doping, defect engineering and heterostructuring are summarized, highlighting the potential applications of nonmetallic hexagonal boron nitride catalysts in various reactions. This comprehensive investigation offers a reference point for the enhanced mechanistic understanding and future design of effective and sustainable catalytic systems based on boron nitride.

10.
ACS Nano ; 18(12): 9128-9136, 2024 Mar 26.
Article in English | MEDLINE | ID: mdl-38492230

ABSTRACT

The growth of all-inorganic perovskite single-crystal microstructures on substrates is a promising approach for constructing photonic and electronic microdevices. However, current preparation methods typically involve direct control of ions or atoms, which often depends on specific lattice-matched substrates for epitaxial growth and other stringent conditions that limit the mild preparation and flexibility of device integration. Herein, we present the on-substrate fabrication of CsPbBr3 single-crystal microstructures obtained via a nanoparticle self-assembly assisted low-temperature sintering (NSALS) method. Sintering guided by self-assembled atomically oriented superlattice embryos facilitated the formation of single-crystal microstructures under mild conditions without substrate dependence. The as-prepared on-substrate microstructures exhibited a consistent out-of-plane orientation with a carrier lifetime of up to 82.7 ns. Photodetectors fabricated by using these microstructures exhibited an excellent photoresponse of 9.15 A/W, and the dynamic optical response had a relative standard deviation as low as 0.1831%. The discrete photosensor microarray chip with 174000 pixels in a 100 mm2 area showed a response difference of less than 6%. This method of nanoscale particle-controlled single crystal growth on a substrate offers a perspective for mild-condition preparation and in situ repair of crystals of various types. This advancement can propel the flexible integration and widespread application of perovskite devices.

11.
Skin Res Technol ; 30(1): e13543, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38186063

ABSTRACT

BACKGROUND: Rosacea, a common chronic inflammatory skin disease worldwide, is currently incurable with complex pathogenesis. Dendrobium polysaccharide (DOP) may exert therapeutic effects on rosacea via acting on the NF-κB-related inflammatory and oxidative processes. MATERIALS AND METHODS: In this study, an LL-37-induced rosacea-like mouse model was established. HE staining was used to assess the skin lesions, erythema severity scores, pathological symptoms, and inflammatory cell numbers of mice in each group. The inflammation level was quantitatively analyzed using enzyme-linked immunosorbent assay (ELISA) and reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR). The expression levels of TLR4 and p-NF-κB were finally detected. RESULTS: DOP improved skin pathological symptoms of rosacea mice. DOP also alleviated the inflammation of rosacea mice. Moreover, the TLR4/NF-κB pathway was observed to be inhibited in the skin of mice after DOP application. These findings evidenced the anti-inflammatory effects of DOP on the LL-37-induced rosacea mouse model. DOP could inhibit NF-κB activation, suppress neutrophil infiltration, and reduce pro-inflammatory cytokines production, which may be the reason for DOP protecting against rosacea. CONCLUSION: This study may propose an active candidate with great potential for rosacea drug development and lay a solid experimental foundation for promoting DOP application in rosacea therapy.


Subject(s)
Dendrobium , Rosacea , Animals , Mice , NF-kappa B , Toll-Like Receptor 4 , Rosacea/chemically induced , Rosacea/drug therapy , Disease Models, Animal , Inflammation , Polysaccharides/pharmacology , Polysaccharides/therapeutic use
12.
Int J Biol Macromol ; 259(Pt 1): 129103, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38181907

ABSTRACT

Wearable electronic skin has gained increasing popularity due to its remarkable properties of high flexibility, sensitivity, and lightweight, making it an ideal choice for detecting human physiological activity. In this study, we successfully prepared e-skin using regenerated chitin (RCH) and sulfonated carbon nanotubes (SCNTs). The e-skin demonstrated brilliant mechanical and sensing properties, exhibiting a sensitivity of 1.75 kPa-1 within the 0-5 kPa range and a fast response-recovery time of <10 ms. Furthermore, it displayed an ultra-low detection limit of 1.39 Pa (5 mg), exceptional stability (up to 11,000 cycles), and a remarkable mechanical strength, reaching up to 50 MPa. Moreover, the e-skin was fabricated through a simple and economical approach. With the popularity of micro sensing devices, the e-skin holds tremendous potential for various applications, including wearable electronic devices, health and sports monitoring, artificial intelligence and other fields.


Subject(s)
Nanotubes, Carbon , Wearable Electronic Devices , Humans , Artificial Intelligence , Chitin , Skin
13.
Biomed Chromatogr ; 38(3): e5795, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38071756

ABSTRACT

Following the highly successful Chinese American Society for Mass Spectrometry (CASMS) conferences in the previous 2 years, the 3rd CASMS Conference was held virtually on August 28-31, 2023, using the Gather.Town platform to bring together scientists in the MS field. The conference offered a 4-day agenda with a scientific program consisting of two plenary lectures, and 14 parallel symposia in which a total of 70 speakers presented technological innovations and their applications in proteomics and biological MS and metabo-lipidomics and pharmaceutical MS. In addition, 16 invited speakers/panelists presented at two research-focused and three career development workshops. Moreover, 86 posters, 12 lightning talks, 3 sponsored workshops, and 11 exhibitions were presented, from which 9 poster awards and 2 lightning talk awards were selected. Furthermore, the conference featured four young investigator awardees to highlight early-career achievements in MS from our society. The conference provided a unique scientific platform for young scientists (i.e. graduate students, postdocs, and junior faculty/investigators) to present their research, meet with prominent scientists, learn about career development, and job opportunities (http://casms.org).


Subject(s)
Mass Spectrometry , Lipidomics , Pharmaceutical Preparations , Proteomics , Congresses as Topic
14.
Anal Chem ; 95(51): 18871-18879, 2023 12 26.
Article in English | MEDLINE | ID: mdl-38092461

ABSTRACT

Nitric oxide (NO) is a small molecule that plays important roles in biological systems and human diseases. The abundance of intracellular NO is tightly related to numerous biological processes. Due to cell heterogeneity, the intracellular NO amounts significantly vary from cell to cell, and therefore, any meaningful studies need to be conducted at the single-cell level. However, measuring NO in single cells is very challenging, primarily due to the extremely small size of single cells and reactive nature of NO. In the current studies, the quantitative reaction between NO and amlodipine, a compound containing the Hantzsch ester group, was performed in live cells. The product dehydro amlodipine was then detected by the Single-probe single-cell mass spectrometry technique to quantify NO in single cells. The experimental results indicated heterogeneous distributions of intracellular NO amounts in single cells with the existence of subpopulations.


Subject(s)
Amlodipine , Nitric Oxide , Humans , Nitric Oxide/analysis , Mass Spectrometry/methods
15.
J Med Virol ; 95(12): e29318, 2023 12.
Article in English | MEDLINE | ID: mdl-38112106

ABSTRACT

To examine the effectiveness of azvudine and nirmatrelvir-ritonavir in treating hospitalized patients with moderate-to-severe COVID-19. We emulated a target trial with a multicenter retrospective cohort of hospitalized adults with moderate-to-severe COVID-19 without contraindications for azvudine or nirmatrelvir-ritonavir between December 01, 2022 and January 19, 2023 (during the Omicron BA.5.2 variant wave). Exposures included treatment with azvudine or nirmatrelvir-ritonavir for 5 days versus no antiviral treatment during hospitalization. Primary composite outcome (all-cause death and initiation of invasive mechanical ventilation), and their separate events were evaluated. Of the 1154 patients, 27.2% were severe cases. In the intent-to-treat analyses, azvudine reduced all-cause death (Hazard ratio [HR]: 0.31; 95% CI: 0.12-0.78), and its composite with invasive mechanical ventilation (HR: 0.47; 95% CI: 0.24-0.92). Nirmatrelvir-ritonavir reduced invasive mechanical ventilation (HR: 0.42; 95% CI: 0.17-1.05), and its composite with all-cause death (HR: 0.38; 95% CI: 0.18-0.81). The study did not identify credible subgroup effects. The per-protocol analyses and all sensitivity analyses confirmed the robustness of the findings. Both azvudine and nirmatrelvir-ritonavir improved the prognosis of hospitalized adults with moderate-to-severe COVID-19.


Subject(s)
Antiviral Agents , COVID-19 Drug Treatment , COVID-19 , Ritonavir , Adult , Humans , Antiviral Agents/therapeutic use , Retrospective Studies , Ritonavir/therapeutic use
16.
Nat Commun ; 14(1): 6395, 2023 Oct 13.
Article in English | MEDLINE | ID: mdl-37833262

ABSTRACT

Artificial intelligence (AI) has been widely applied in drug discovery with a major task as molecular property prediction. Despite booming techniques in molecular representation learning, key elements underlying molecular property prediction remain largely unexplored, which impedes further advancements in this field. Herein, we conduct an extensive evaluation of representative models using various representations on the MoleculeNet datasets, a suite of opioids-related datasets and two additional activity datasets from the literature. To investigate the predictive power in low-data and high-data space, a series of descriptors datasets of varying sizes are also assembled to evaluate the models. In total, we have trained 62,820 models, including 50,220 models on fixed representations, 4200 models on SMILES sequences and 8400 models on molecular graphs. Based on extensive experimentation and rigorous comparison, we show that representation learning models exhibit limited performance in molecular property prediction in most datasets. Besides, multiple key elements underlying molecular property prediction can affect the evaluation results. Furthermore, we show that activity cliffs can significantly impact model prediction. Finally, we explore into potential causes why representation learning models can fail and show that dataset size is essential for representation learning models to excel.

17.
Mol Phys ; 121(9-10)2023.
Article in English | MEDLINE | ID: mdl-37638114

ABSTRACT

We propose a simple procedure for visualizing the electron density changes (EDC) during a chemical reaction, which is based on a mapping of rectangular grid points for a stationary structure into (distorted) positions around atoms of another stationary structure. Specifically, during a small step along the minimum energy pathway (MEP), the displacement of each grid point is obtained as a linear combination of the motion of all atoms, with the contribution from each atom scaled by the corresponding Hirshfeld weight. For several reactions (identity SN2, Claisen rearrangement, Diels-Alder reaction, [3+2] cycloaddition, and phenylethyl mercaptan attack on pericosine A), our EDC plots showed an expected reduction of electron densities around severed bonds (or those with the bond-order lowered), with the opposite observed for newly-formed or enhanced chemical bonds. The EDC plots were also shown for copper triflate catalyzed N2O fragmentation, where the N-O bond weakening initially occurred on a singlet surface, but continued on a triplet surface after reaching the minimum-energy crossing point (MECP) between the two potential energy surfaces.

18.
Microorganisms ; 11(8)2023 Aug 06.
Article in English | MEDLINE | ID: mdl-37630579

ABSTRACT

Sulfate-reducing bacteria (SRB) are an important group of microorganisms that cause microbial corrosion. In this study, culturable SRB were isolated and identified from the inner rust layer of three kinds of steel and from sediments, and a comparison of amino acid sequences encoding related enzymes in the sulfate reduction pathway between anaerobic and facultative anaerobic SRB strains was carried out. The main results are as follows. (1) Seventy-seven strains were isolated, belonging to five genera and seven species, with the majority being Desulfovibrio marinisediminis. For the first time, Holodesulfovibrio spirochaetisodalis and Acinetobacter bereziniae were separated from the inner rust layer of metal, and sulfate reduction by A. bereziniae, Virgibacillus dokdonensis, and Virgibacillus chiguensis, etc., was also demonstrated for the first time. (2) Three strains of strictly anaerobic bacteria and four strains of facultative anaerobic bacteria were screened from seven bacterial strains. (3) Most of the anaerobic SRB only contained enzymes for the dissimilatory sulfate reduction pathway, while those of facultative anaerobic bacteria capable of producing hydrogen sulfide included two possible ways: containing the related enzymes from the dissimilatory pathway only, or containing enzymes from both dissimilatory and assimilation pathways. This study newly discovered that some bacterial genera exhibit sulfate reduction ability and found that there are differences in the distribution of enzymes related to the sulfate reduction pathway between anaerobic and facultative anaerobic SRB type trains, providing a basis for the development and utilization of sulfate-reducing bacterial resources and furthering our understanding of the metabolic mechanisms of SRB.

19.
Proteomics ; 23(20): e2300150, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37199141

ABSTRACT

Blood serum is arguably the most analyzed biofluid for disease prediction and diagnosis. Herein, we benchmarked five different serum abundant protein depletion (SAPD) kits with regard to the identification of disease-specific biomarkers in human serum using bottom-up proteomics. As expected, the IgG removal efficiency among the SAPD kits is highly variable, ranging from 70% to 93%. A pairwise comparison of database search results showed a 10%-19% variation in protein identification among the kits. Immunocapturing-based SAPD kits against IgG and albumin outperformed the others in the removal of these two abundant proteins. Conversely, non-antibody-based methods (i.e., kits using ion exchange resins) and kits leveraging a multi-antibody approach were proven to be less efficient in depleting IgG/albumin from samples but led to the highest number of identified peptides. Notably, our results indicate that different cancer biomarkers could be enriched up to 10% depending on the utilized SAPD kit compared with the undepleted sample. Additionally, functional analysis of the bottom-up proteomic results revealed that different SAPD kits enrich distinct disease- and pathway-specific protein sets. Overall, our study emphasizes that a careful selection of the appropriate commercial SAPD kit is crucial for the analysis of disease biomarkers in serum by shotgun proteomics.

20.
Anal Chem ; 95(18): 7127-7133, 2023 05 09.
Article in English | MEDLINE | ID: mdl-37115510

ABSTRACT

Mass spectrometry (MS) has become an indispensable tool for metabolomics studies. However, due to the lack of applicable experimental platforms, suitable algorithm, software, and quantitative analyses of cell heterogeneity and subpopulations, investigating global metabolomics profiling at the single cell level remains challenging. We combined the Single-probe single cell MS (SCMS) experimental technique with a bioinformatics software package, SinCHet-MS (Single Cell Heterogeneity for Mass Spectrometry), to characterize changes of tumor heterogeneity, quantify cell subpopulations, and prioritize the metabolite biomarkers of each subpopulation. As proof of principle studies, two melanoma cancer cell lines, the primary (WM115; with a lower drug resistance) and the metastatic (WM266-4; with a higher drug resistance), were used as models. Our results indicate that after the treatment of the anticancer drug vemurafenib, a new subpopulation emerged in WM115 cells, while the proportion of the existing subpopulations was changed in the WM266-4 cells. In addition, metabolites for each subpopulation can be prioritized. Combining the SCMS experimental technique with a bioinformatics tool, our label-free approach can be applied to quantitatively study cell heterogeneity, prioritize markers for further investigation, and improve the understanding of cell metabolism in human diseases and response to therapy.


Subject(s)
Antineoplastic Agents , Melanoma , Humans , Metabolomics/methods , Mass Spectrometry/methods , Algorithms , Melanoma/drug therapy , Melanoma/pathology
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