keyword
https://read.qxmd.com/read/38547507/phylogeny-and-expansion-of-serine-threonine-kinases-in-phagocytotic-bacteria-in-the-phylum-planctomycetota
#1
JOURNAL ARTICLE
Anna Odelgard, Emil Hägglund, Lionel Guy, Siv G E Andersson
The recently isolated bacterium "Candidatus Uabimicrobium amorphum" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that "Ca. Uabimicrobium amorphum" represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in "Ca...
March 28, 2024: Genome Biology and Evolution
https://read.qxmd.com/read/38547315/one-shot-single-cell-proteome-and-metabolome-analysis-strategy-for-the-same-single-cell
#2
JOURNAL ARTICLE
Jie Wu, Qin-Qin Xu, Yi-Rong Jiang, Jian-Bo Chen, Wei-Xin Ying, Qian-Xi Fan, Hui-Feng Wang, Yu Wang, Shao-Wen Shi, Jian-Zhang Pan, Qun Fang
Characterizing the profiles of proteome and metabolome at the single-cell level is of great significance in single-cell multiomic studies. Herein, we proposed a novel strategy called one-shot single-cell proteome and metabolome analysis (scPMA) to acquire the proteome and metabolome information in a single-cell individual in one injection of LC-MS/MS analysis. Based on the scPMA strategy, a total workflow was developed to achieve the single-cell capture, nanoliter-scale sample pretreatment, one-shot LC injection and separation of the enzyme-digested peptides and metabolites, and dual-zone MS/MS detection for proteome and metabolome profiling...
March 28, 2024: Analytical Chemistry
https://read.qxmd.com/read/38547124/retraction-blood-biomarker-discovery-for-autism-spectrum-disorder-a-proteomic-analysis
#3
(no author information available yet)
No abstract text is available yet for this article.
2024: PloS One
https://read.qxmd.com/read/38546974/multiomics-plasma-effects-of-switching-from-triple-antiretroviral-regimens-to-dolutegravir-plus-lamivudine
#4
JOURNAL ARTICLE
Elisa de Lazzari, Eugenia B Negredo, Pere Domingo, Juan M Tiraboschi, Esteve Ribera, Nadia Abdulghani, Verònica Alba, Salvador Fernández-Arroyo, Consuelo Viladés, Joaquim Peraire, Jose M Gatell, Jose L Blanco, Francesc Vidal, Anna Rull, Esteban Martinez
INTRODUCTION: The DOLAM trial revealed that switching from triple antiretroviral therapy (three-drug regimen; 3DR) to dolutegravir plus lamivudine (two-drug regimen; 2DR) was virologically non-inferior to continuing 3DR after 48 weeks of follow-up. Weight increased with 2DR relative to 3DR but it did not impact on metabolic parameters. METHODS: Multiomics plasma profile was performed to gain further insight into whether this therapy switch might affect specific biological pathways...
March 28, 2024: Journal of Antimicrobial Chemotherapy
https://read.qxmd.com/read/38546438/metabolites-healthy-lifestyle-and-polygenic-risk-score-associated-with-upper-gastrointestinal-cancer-findings-from-the-uk-biobank-study
#5
JOURNAL ARTICLE
Shuting Li, Jiajing Che, Bingbing Gu, Yunfei Li, Xinyue Han, Tiantian Sun, Keyu Pan, Jiali Lv, Shuai Zhang, Cheng Wang, Tao Zhang, Jialin Wang, Fuzhong Xue
Previous metabolomics studies have highlighted the predictive value of metabolites on upper gastrointestinal (UGI) cancer, while most of them ignored the potential effects of lifestyle and genetic risk on plasma metabolites. This study aimed to evaluate the role of lifestyle and genetic risk in the metabolic mechanism of UGI cancer. Differential metabolites of UGI cancer were identified using partial least-squares discriminant analysis and the Wilcoxon test. Then, we calculated the healthy lifestyle index (HLI) score and polygenic risk score (PRS) and divided them into three groups, respectively...
March 28, 2024: Journal of Proteome Research
https://read.qxmd.com/read/38546334/large-scale-plasma-proteomics-in-the-uk-biobank-modestly-improves-prediction-of-major-cardiovascular-events-in-a-population-without-previous-cardiovascular-disease
#6
JOURNAL ARTICLE
Patrick Royer, Elias Björnson, Martin Adiels, Rebecca Josefson, Eva Hagberg, Anders Gummesson, Göran Bergström
AIMS: Improved identification of individuals at high risk of developing cardiovascular disease would enable targeted interventions and potentially lead to reductions in mortality and morbidity. Our aim was to determine whether use of large-scale proteomics improves prediction of cardiovascular events beyond traditional risk factors (TRFs). METHODS: Using proximity extension assays, 2919 plasma proteins were measured in 38 380 participants of the UK Biobank. Both data- and literature-based feature selection and trained models using extreme gradient boosting machine learning were used to predict risk of major cardiovascular events (MACE: fatal and non-fatal myocardial infarction, stroke and coronary artery revascularisation) during a 10-year follow-up...
March 28, 2024: European Journal of Preventive Cardiology
https://read.qxmd.com/read/38545981/-analysis-of-signal-peptides-and-secreted-proteins-in-the-whole-proteome-of-pichia-pastoris
#7
JOURNAL ARTICLE
Lingxuan Zhu, Xin Cui, Shantong Hu, Shihui Wang, Guimin Zhang
The signal peptide is a key factor that affects the efficiency of protein secretion in Pichia pastoris . Currently, the most used signal peptide is the α-mating factor (MFα) pre-pro leader from Saccharomyces cerevisiae . This exogenous signal peptide has been successfully utilized to express and secret many heterologous proteins. However, MFα is not suitable for the secretory expression of all heterologous proteins. Many typical signal peptides are present in the secretory proteins of P . pastoris , which provides more options besides MFα...
March 25, 2024: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://read.qxmd.com/read/38545623/identifying-ferroptosis-inducers-hdac-and-rtk-inhibitor-sensitivity-in-melanoma-subtypes-through-unbiased-drug-target-prediction
#8
Indira Pla, Botond L Szabolcs, Petra Nikolett Péter, Zsuzsanna Ujfaludi, Yonghyo Kim, Peter Horvatovich, Aniel Sanchez, Krzysztof Pawlowski, Elisabet Wieslander, Jéssica Guedes, Dorottya Mp Pál, Anna A Ascsillán, Lazaro Hiram Betancourt, István Balázs Németh, Jeovanis Gil, Natália Pinto de Almeida, Beáta Szeitz, Leticia Szadai, Viktória Doma, Nicole Woldmar, Áron Bartha, Zoltan Pahi, Tibor Pankotai, Balázs Győrffy, A Marcell Szasz, Gilberto Domont, Fábio Nogueira, Ho Jeong Kwon, Roger Appelqvist, Sarolta Kárpáti, David Fenyö, Johan Malm, György Marko-Varga, Lajos V Kemény
UNLABELLED: The utilization of PD1 and CTLA4 inhibitors has revolutionized the treatment of malignant melanoma (MM). However, resistance to targeted and immune-checkpoint-based therapies still poses a significant problem. Here we mine large scale MM proteogenomic data integrating it with MM cell line dependency screen, and drug sensitivity data to identify druggable targets and forecast treatment efficacy and resistance. Leveraging protein profiles from established MM subtypes and molecular structures of 82 cancer treatment drugs, we identified nine candidate hub proteins, mTOR, FYN, PIK3CB, EGFR, MAPK3, MAP4K1, MAP2K1, SRC and AKT1, across five distinct MM subtypes...
February 12, 2024: bioRxiv
https://read.qxmd.com/read/38545622/hybrid-immunity-to-sars-cov-2-arises-from-serological-recall-of-igg-antibodies-distinctly-imprinted-by-infection-or-vaccination
#9
William N Voss, Michael A Mallory, Patrick O Byrne, Jeffrey M Marchioni, Sean A Knudson, John M Powers, Sarah R Leist, Bernadeta Dadonaite, Douglas R Townsend, Jessica Kain, Yimin Huang, Ed Satterwhite, Izabella N Castillo, Melissa Mattocks, Chelsea Paresi, Jennifer E Munt, Trevor Scobey, Allison Seeger, Lakshmanane Premkumar, Jesse D Bloom, George Georgiou, Jason S McLellan, Ralph S Baric, Jason J Lavinder, Gregory C Ippolito
UNLABELLED: We used plasma IgG proteomics to study the molecular composition and temporal durability of polyclonal IgG antibodies triggered by ancestral SARS-CoV-2 infection, vaccination, or their combination ("hybrid immunity"). Infection, whether primary or post-vaccination, mainly triggered an anti-spike antibody response to the S2 domain, while vaccination predominantly induced anti-RBD antibodies. Immunological imprinting persisted after a secondary (hybrid) exposure, with >60% of the ensuing serological response originating from the initial antibodies generated during the first exposure...
January 23, 2024: bioRxiv
https://read.qxmd.com/read/38545550/the-protective-effect-of-traditional-chinese-medicine-jinteng-qingbi-granules-on-rats-with-rheumatoid-arthritis
#10
JOURNAL ARTICLE
Yingying Wan, Wenting Sun, Jiaxi Yang, Haonan Wang, Wenqian Wang, Wanting Ye, Guoliang Cheng, Bing Li, Jianxun Ren, Qiuai Kou
Introduction: Jinteng Qingbi granules (JTQBG), a traditional Chinese medicine formulation, are widely used for the treatment of rheumatoid arthritis (RA) due to their satisfactory therapeutic efficacy. However, the underlying mechanism of action remains unclear. This study aims to investigate the protective effects of JTQBG against RA and elucidates its potential molecular mechanisms. Methods: A collagen-induced arthritis (CIA) rat model was utilized, and JTQBG (1.25, 2.5, 5 g/kg/day) or methotrexate (MTX, 1 mg/kg/week) was orally administered...
2024: Frontiers in Pharmacology
https://read.qxmd.com/read/38545378/rhein-against-staphylococcus-xylosus-by-interfering-with-respiratory-metabolism-and-inducing-oxidative-stress
#11
JOURNAL ARTICLE
Yuyang Li, Weiwei Chen, Jinxin Ma, Guoying Huang, Guangquan Li, Qiumei He, Xiangyu Kong, Ling Tang, Jinqing Chen, Wenyou Ding, Zhongbin Zhang, Wenya Ding
Currently, dairy mastitis caused by Staphylococcus xylosus poses a serious challenge for dairy farming. In this study, we explored the role and mechanism of rhein against S. xylosus with the hope of providing new research ideas to solve mastitis in dairy cows and ensure the source safety of dairy products. Through in vitro antimicrobial studies, we found that the minimum inhibitory concentration (MIC) of rhein was 64 μg/mL, and it significantly interfered with the formation of S. xylosus biofilm at sub-MIC...
2024: Current research in food science
https://read.qxmd.com/read/38545252/proteome-wide-assessment-of-human-interactome-as-a-source-of-capturing-domain-motif-and-domain-domain-interactions
#12
JOURNAL ARTICLE
Sobia Idrees, Keshav Raj Paudel
Protein-protein interactions (PPIs) play a crucial role in various biological processes by establishing domain-motif (DMI) and domain-domain interactions (DDIs). While the existence of real DMIs/DDIs is generally assumed, it is rarely tested; therefore, this study extensively compared high-throughput methods and public PPI repositories as sources for DMI and DDI prediction based on the assumption that the human interactome provides sufficient data for the reliable identification of DMIs and DDIs. Different datasets from leading high-throughput methods (Yeast two-hybrid [Y2H], Affinity Purification coupled Mass Spectrometry [AP-MS], and Co-fractionation-coupled Mass Spectrometry) were assessed for their ability to capture DMIs and DDIs using known DMI/DDI information...
March 2024: Journal of Cell Communication and Signaling
https://read.qxmd.com/read/38545181/integrated-genomic-and-proteomic-analyses-identify-pygl-as-a-novel-experimental-therapeutic-target-for-clear-cell-renal-cell-carcinoma
#13
JOURNAL ARTICLE
Mingyong Li, Guoqiang Zhu, Yiqi Liu, Xuefeng Li, Yuxia Zhou, Cheng Li, Minglei Wang, Jin Zhang, Zhenping Wang, Shuangfeng Tan, Wenqi Chen, Hu Zhang
Sunitinib, the first-line targeted therapy for metastatic clear cell renal cell carcinoma (ccRCC), faces a significant challenge as most patients develop acquired resistance. Integrated genomic and proteomic analyses identified PYGL as a novel therapeutic target for ccRCC. PYGL knockdown inhibited cell proliferation, cloning capacity, migration, invasion, and tumorigenesis in ccRCC cell lines. PYGL expression was increased in sunitinib-resistant ccRCC cell lines, and CP-91149 targeting the PYGL could restore drug sensitivity in these cell lines...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38544831/corrigendum-glioblastoma-survival-is-associated-with-distinct-proteomic-alteration-signatures-post-chemoirradiation-in-a-large-scale-proteomic-panel
#14
Andra Valentina Krauze, Michael Sierk, Trinh Nguyen, Qingrong Chen, Chunhua Yan, Ying Hu, William Jiang, Erdal Tasci, Theresa Cooley Zgela, Mary Sproull, Megan Mackey, Uma Shankavaram, Daoud Meerzaman, Kevin Camphausen
[This corrects the article DOI: 10.3389/fonc.2023.1127645.].
2024: Frontiers in Oncology
https://read.qxmd.com/read/38544816/multiplexing-of-tmt-labeling-reveals-folate-deficient-diet-specific-proteome-changes-in-ntds
#15
JOURNAL ARTICLE
Pei Pei, Jinying Shen, Xuejia He, Yubing Zeng, Ting Zhang, Shan Wang
Introduction: In the early stage of embryonic development, the neural tube (NT) cannot be closed properly due to some complex factors, including environmental factors, genetic factors, and the relationship between various factors, leading to the occurrence of neural tube defects (NTDs). Methods: In this study, we induced a mouse model of NTDs by feeding mice with a low-folate diet and intraperitoneally injecting them with 1.5 mg/kg methotrexate on E7.5. Fetal mice were achieved at E13.5, and we extracted proteins from brain tissues with trypsin digestion...
2024: Frontiers in Cell and Developmental Biology
https://read.qxmd.com/read/38543937/cell-mediated-proteomics-and-serological-and-mucosal-humoral-immune-responses-after-seasonal-influenza-immunization-characterization-of-serological-responders-and-non-responders
#16
JOURNAL ARTICLE
Hanna Carlsson, Lars Brudin, Lena Serrander, Jorma Hinkula, Ivar Tjernberg
Immunization against influenza through vaccination is the most effective method with which to prevent infection. To assess protection after immunization, analysing humoral response with a hemagglutinin inhibition assay is the gold standard, but cell-mediated immune response has been shown to better correlate with protection in the elderly. Our aim was to explore the influenza-specific cell-mediated and mucosal humoral responses in serologically defined responders and non-responders. We analysed sera for total immunoglobulins (Ig) A, G, and M and nasal swab samples for influenza-specific IgA...
March 14, 2024: Vaccines
https://read.qxmd.com/read/38543773/label-free-quantitative-analysis-of-pig-liver-proteome-after-hepatitis-e-virus-infection
#17
JOURNAL ARTICLE
Camillo Martino, Alessio Di Luca, Francesca Bennato, Andrea Ianni, Fabrizio Passamonti, Elisa Rampacci, Michael Henry, Paula Meleady, Giuseppe Martino
Hepatitis E represents an emerging zoonotic disease caused by the Hepatitis E virus (HEV), for which the main route of transmission is foodborne. In particular, infection in humans has been associated with the consumption of contaminated undercooked meat of pig origin. The aim of this study was to apply comparative proteomics to determine if porcine liver protein profiles could be used to distinguish between pigs seropositive and seronegative for HEV. Preliminarily, an ELISA was used to evaluate the presence of anti-HEV antibodies in the blood serum of 136 animals sent to slaughter...
March 6, 2024: Viruses
https://read.qxmd.com/read/38543727/proteomic-and-lipidomic-profiling-of-calves-experimentally-co-infected-with-influenza-d-virus-and-mycoplasma-bovis-insights-into-the-host-pathogen-interactions
#18
JOURNAL ARTICLE
Ignacio Alvarez, Mariette Ducatez, Yongzhi Guo, Adrien Lion, Anna Widgren, Marc Dubourdeau, Vincent Baillif, Laure Saias, Siamak Zohari, Jonas Bergquist, Gilles Meyer, Jean-Francois Valarcher, Sara Hägglund
The role of Influenza D virus (IDV) in bovine respiratory disease remains unclear. An in vivo experiment resulted in increased clinical signs, lesions, and pathogen replication in calves co-infected with IDV and Mycoplasma bovis ( M . bovis ), compared to single-infected calves. The present study aimed to elucidate the host-pathogen interactions and profile the kinetics of lipid mediators in the airways of these calves. Bronchoalveolar lavage (BAL) samples collected at 2 days post-infection (dpi) were used for proteomic analyses by liquid chromatography-tandem mass spectrometry (LC-MS/MS)...
February 27, 2024: Viruses
https://read.qxmd.com/read/38543672/dynamic-protein-phosphorylation-in-streptococcus-pyogenes-during-growth-stationary-phase-and-starvation
#19
JOURNAL ARTICLE
Stefan Mikkat, Michael Kreutzer, Nadja Patenge
Phosphorylation of proteins at serine, threonine, and tyrosine residues plays an important role in physiological processes of bacteria, such as cell cycle, metabolism, virulence, dormancy, and stationary phase functions. Little is known about the targets and dynamics of protein phosphorylation in Streptococcus pyogenes , which possesses a single known transmembrane serine/threonine kinase belonging to the class of PASTA kinases. A proteomics and phosphoproteomics workflow was performed with S. pyogenes serotype M49 under different growth conditions, stationary phase, and starvation...
March 20, 2024: Microorganisms
https://read.qxmd.com/read/38543504/sars-cov-2-infection-and-anemia-a-focus-on-rbc-deformability-and-membrane-proteomics-integrated-observational-prospective-study
#20
JOURNAL ARTICLE
Angelo D'Alessandro, Elena Krisnevskaya, Valentina Leguizamon, Ines Hernández, Carolina de la Torre, Joan-Josep Bech, Josep-Tomàs Navarro, Joan-Lluis Vives-Corrons
INTRODUCTION: The multifaceted impact of COVID-19 extends beyond the respiratory system, encompassing intricate interactions with various physiological systems. This study elucidates the potential association between SARS-CoV-2 infection and anemia, with a particular emphasis on the deformability of red blood cells (RBCs), stability of hemoglobin, enzymatic activities, and proteomic profiles. METHODS: The study encompasses a cohort of 74 individuals, including individuals positive for COVID-19, a control group, and patients with other viral infections to discern the specific effects attributable to COVID-19...
February 23, 2024: Microorganisms
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