scholarly journals An Update of the Virion Proteome of Kaposi Sarcoma-Associated Herpesvirus

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1382
Author(s):  
Ramina Nabiee ◽  
Basir Syed ◽  
Jesus Ramirez Castano ◽  
Rukhsana Lalani ◽  
Jennifer E. Totonchy
Keyword(s):  
Mass Spectrometry ◽  
Kaposi Sarcoma ◽  
Protein Composition ◽  
Viral Proteins ◽  
Novel Proteins ◽  
Flight Mass Spectrometry ◽  
Associated Proteins ◽  
Cellular Components ◽  
First Time ◽  
Insight Into

The virion proteins of Kaposi sarcoma-associated herpesvirus (KSHV) were initially characterized in 2005 in two separate studies that combined the detection of 24 viral proteins and a few cellular components via LC-MS/MS or MALDI-TOF. Despite considerable advances in the sensitivity and specificity of mass spectrometry instrumentation in recent years, leading to significantly higher yields in detections, the KSHV virion proteome has not been revisited. In this study, we have re-examined the protein composition of purified KSHV virions via ultra-high resolution Qq time-of-flight mass spectrometry (UHR-QqTOF). Our results confirm the detection of all previously reported virion proteins, in addition to 17 other viral proteins, some of which have been characterized as virion-associated using other methods, and 10 novel proteins identified as virion-associated for the first time in this study. These results add KSHV ORF9, ORF23, ORF35, ORF48, ORF58, ORF72/vCyclin, K3, K9/vIRF1, K10/vIRF4, and K10.5/vIRF3 to the list of KSHV proteins that can be incorporated into virions. The addition of these proteins to the KSHV virion proteome provides novel and important insight into early events in KSHV infection mediated by virion-associated proteins. Data are available via ProteomeXchange with identifier PXD022626.

scholarly journals Salmonella Typhi and Salmonella Paratyphi A elaborate distinct systemic metabolite signatures during enteric fever

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Elin Näsström ◽  
Nga Tran Vu Thieu ◽  
Sabina Dongol ◽  
Abhilasha Karkey ◽  
Phat Voong Vinh ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Gas Chromatography ◽  
Bacterial Infections ◽  
Enteric Fever ◽  
Salmonella Typhi ◽  
Two Dimensional ◽  
Flight Mass Spectrometry ◽  
Metabolite Profiles ◽  
Diagnostic Approaches ◽  
First Time

The host–pathogen interactions induced by Salmonella Typhi and Salmonella Paratyphi A during enteric fever are poorly understood. This knowledge gap, and the human restricted nature of these bacteria, limit our understanding of the disease and impede the development of new diagnostic approaches. To investigate metabolite signals associated with enteric fever we performed two dimensional gas chromatography with time-of-flight mass spectrometry (GCxGC/TOFMS) on plasma from patients with S. Typhi and S. Paratyphi A infections and asymptomatic controls, identifying 695 individual metabolite peaks. Applying supervised pattern recognition, we found highly significant and reproducible metabolite profiles separating S. Typhi cases, S. Paratyphi A cases, and controls, calculating that a combination of six metabolites could accurately define the etiological agent. For the first time we show that reproducible and serovar specific systemic biomarkers can be detected during enteric fever. Our work defines several biologically plausible metabolites that can be used to detect enteric fever, and unlocks the potential of this method in diagnosing other systemic bacterial infections.

scholarly journals Microscopic Mass Spectrometry Imaging Reveals the Distribution of Phytochemicals in the Dried Root of Isatis tinctoria

2021 ◽  
Vol 12 ◽  
Author(s):  
Li-Xing Nie ◽  
Jing Dong ◽  
Lie-Yan Huang ◽  
Xiu-Yu Qian ◽  
Chao-Jie Lian ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Imaging ◽  
Viral Infections ◽  
Ion Trap ◽  
Partial Least Square ◽  
Least Square ◽  
Isatis Tinctoria ◽  
Chinese Medicines ◽  
Flight Mass Spectrometry ◽  
First Time

The dried root of Isatis tinctoria L. (Brassicaceae) is one of the most popular traditional Chinese medicines with well-recognized prevention and treatment effects against viral infections. Above 300 components have been isolated from this herb, but their spatial distribution in the root tissue remains unknown. In recent years, mass spectrometry imaging (MSI) has become a booming technology for capturing the spatial accumulation and localization of molecules in fresh plants, animal, or human tissues. However, few studies were conducted on the dried herbal materials due to the obstacles in cryosectioning. In this study, distribution of phytochemicals in the dried root of Isatis tinctoria was revealed by microscopic mass spectrometry imaging, with application of atmospheric pressure–matrix-assisted laser desorption/ionization (AP-MALDI) and ion trap–time-of-flight mass spectrometry (IT-TOF/MS). After optimization of the slice preparation and matrix application, 118 ions were identified without extraction and isolation, and the locations of some metabolites in the dried root of Isatis tinctoria were comprehensively visualized for the first time. Combining with partial least square (PLS) regression, samples collected from four habitats were differentiated unambiguously based on their mass spectrometry imaging.

AN ANALYSIS OF THE THZ FREQUENCY SIGNATURES IN THE CELLULAR COMPONENTS OF BIOLOGICAL AGENTS

2007 ◽  
Vol 17 (02) ◽  
pp. 225-237 ◽  
Author(s):  
ALEXEI BYKHOVSKI ◽  
TATIANA GLOBUS ◽  
TATYANA KHROMOVA ◽  
BORIS GELMONT ◽  
DWIGHT WOOLARD
Keyword(s):  
Molecular Structure ◽  
Structural Similarity ◽  
Md Simulations ◽  
Detection Capability ◽  
Dna Structures ◽  
E Coli ◽  
Cellular Components ◽  
First Time ◽  
Insight Into ◽  
Specific Contribution

The development of an effective biological (bio) agent detection capability based upon terahertz (THz) frequency absorption spectra will require insight into how the constituent cellular components contribute to the overall THz signature. In this work, the specific contribution of ribonucleic acid (RNA) to THz spectra is analyzed in detail. Previously, it has only been possible to simulate partial fragments of the RNA (or DNA) structures due to the excessive computational demands. For the first time, the molecular structure of the entire transfer RNA (tRNA) molecule of E. coli was simulated and the associated THz signature was derived theoretically. The tRNA that binds amino acid tyrosine (tRNAtyr) was studied. Here, the molecular structure was optimized using the potential energy minimization and molecular dynamical (MD) simulations. Solvation effects (water molecules) were also included explicitly in the MD simulations. To verify that realistic molecular signatures were simulated, a parallel experimental study of tRNAs of E. coli was also conducted. Two very similar molecules, valine and tyrosine tRNA were investigated experimentally. Samples were prepared in the form of water solutions with the concentrations in the range 0.01-1 mg/ml. A strong correlation of the measured THz signatures associated with valine tRNA and tyrosine tRNA was observed. These findings are consistent with the structural similarity of the two tRNAs. The calculated THz signature of the tyrosine tRNA of E. coli reproduces many features of our measured spectra, and, therefore, provides valuable new insights into bio-agent detection.

scholarly journals Rapid Screening and Structural Characterization of Antioxidants from the Extract ofSelaginella doederleiniiHieron with DPPH-UPLC-Q-TOF/MS Method

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Gang Wang ◽  
Shun Yao ◽  
Xiu-Xiu Zhang ◽  
Hang Song
Keyword(s):  
Mass Spectrometry ◽  
High Performance ◽  
Radical Scavenging ◽  
Free Radical Scavenging ◽  
Rapid Screening ◽  
Flight Mass Spectrometry ◽  
First Time ◽  
Strong Capacity ◽  
Tof Ms

2,2-Diphenyl-1-picrylhydrazyl-ultra-high performance liquid chromatography-Q-time-of-flight mass spectrometry (DPPH-UPLC-Q-TOF/MS), as a rapid and efficient means, now was used for the first time to screen antioxidants fromSelaginella doederleinii. The nine biflavone compounds were screened as potential antioxidants. The biflavones were structurally identified and divided into the three types, that is, amentoflavone-type, robustaflavone-type, and hinokiflavone-type biflavonoids. Among the compounds bilobetin (3) and putraflavone (8) were found fromSelaginella doederleiniifor the first time and others including amentoflavone (1), robustaflavone (2), 4′-methoxy robustaflavone (4), podocarpusflavone A (5), hinokiflavone (6), ginkgetin (7), and heveaflavone (9) were identified previously in the plant. Moreover, nine biflavones possessed a good antioxidant activity via their DPPH free radical scavenging. It demonstrates that DPPH-UPLC-Q-TOF/MS exhibits strong capacity in separation and identification for small molecule. The method is suitable for rapid screening of antioxidants without the need for complicated systems and additional instruments.

scholarly journals A molecular war: convergent and ontogenetic evidence for adaptive host manipulation in related parasites infecting divergent hosts

2019 ◽  
Vol 286 (1915) ◽  
pp. 20191827 ◽  
Author(s):  
Ryan Herbison ◽  
Steven Evans ◽  
Jean-François Doherty ◽  
Michael Algie ◽  
Torsten Kleffmann ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Host Response ◽  
Behavioural Change ◽  
General Function ◽  
Host Manipulation ◽  
Forficula Auricularia ◽  
Associated Proteins ◽  
Mechanistic Basis ◽  
Hyperactive Behaviour ◽  
Insight Into

Mermithids (phylum Nematoda) and hairworms (phylum Nematomorpha) somehow drive their arthropod hosts into water, which is essential for the worms' survival after egression. The mechanisms behind this behavioural change have been investigated in hairworms, but not in mermithids. Establishing a similar mechanistic basis for host behavioural change between these two distantly related parasitic groups would provide strong convergent evidence for adaptive manipulation and insight into how these parasites modify and/or create behaviour. Here, we search for this convergence, and also contrast changes in physiology between hosts infected with immature and mature mermithids to provide the first ontogenetic evidence for adaptive manipulation by disentangling host response and pathology from the parasite's apparent manipulative effects. We used SWATH-mass spectrometry on brains of Forficula auricularia (earwig) and Bellorchestia quoyana (sandhopper), infected with the mermithids Mermis nigrescens and Thaumamermis zealandica , respectively, at both immature and mature stages of infection, to quantify proteomic changes resulting from mermithid infection. Across both hosts (and hairworm-infected hosts, from earlier studies), the general function of dysregulated proteins was conserved. Proteins involved in energy generation/mobilization were dysregulated, corroborating reports of erratic/hyperactive behaviour in infected hosts. Dysregulated proteins involved in axon/dendrite and synapse modulation were also common to all hosts, suggesting neuronal manipulation is involved in inducing positive hydrotaxis. Furthermore, downregulation of CamKII and associated proteins suggest manipulation of memory also contributes to the behavioural shift.

scholarly journals Metabolomics study of fibroblasts damaged by UVB and BaP

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiaoyu Yang ◽  
Jiateng Wang ◽  
Hecong Wang ◽  
Xueying Li ◽  
Congfen He ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Ultra Performance Liquid Chromatography ◽  
Glutathione Metabolism ◽  
Metabolic Profiles ◽  
Skin Cells ◽  
Flight Mass Spectrometry ◽  
Metabolomics Study ◽  
Underlying Mechanisms ◽  
Guanidinosuccinic Acid ◽  
Insight Into

AbstractWe have recently shown that both UVB and BaP can induce the production of ROS, apoptosis and even cancer. However, the differences in the metabolic profiles of skin damaged by UVB, BaP or UVB combined with BaP have not been studied. Therefore, we examined the metabolic changes in the human foreskin fibroblast injured by UVB or BaP or the combination of the two, using ultra performance liquid chromatography (UPLC) coupled with quadrupole time-of-flight mass spectrometry (qTOF-MS). 24 metabolites were altered in the UVB damage group, 25 in the BaP damage group, and 33 in the UVB combined with BaP group. These alterations indicated that the metabolic mechanisms of HFF-1 cells treated with UVB or BaP are related to multiple main metabolites including glycerophosphocholine (PC), lactosylceramide (LacCer), guanidinosuccinic acid (GSA), glutathione(GSH), and lysophosphatidylcholine (LysoPC) and the main mechanisms involved glycerophospholipid and glutathione metabolism. Thus, our report provided useful insight into the underlying mechanisms of UVB and BaP damage to skin cells.

scholarly journals Characterization and identification of the major flavonoids in Phyllostachys edulis leaf extract by UPLC–QTOF–MS/MS

2020 ◽  
Vol 32 (4) ◽  
pp. 228-237 ◽  
Author(s):  
S.-Y. Shao ◽  
Y. Ting ◽  
J. Wang ◽  
J. Sun ◽  
X.-F. Guo
Keyword(s):  
Mass Spectrometry ◽  
Leaf Extract ◽  
Ultra Performance Liquid Chromatography ◽  
Rapid Identification ◽  
Phyllostachys Edulis ◽  
Practical Applications ◽  
Mass Spectral ◽  
Flight Mass Spectrometry ◽  
Product Ions ◽  
First Time

Phyllostachys edulis (PES), the most important bamboo species in China, is widely distributed in East Asia. Flavonoids, which are important bioactive natural compounds, often have similar structures, making their structural elucidation difficult. The aim of this study was to represent valuable, reliable mass spectral data for the identification of flavonoids in plant leaves. Ultra-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UPLC–Q-TOF-MS/MS) method was established for characterization and identification of the major flavonoids in PES leaf extract. A total of 13 flavonoids were simultaneously characterized, and their proposed characteristic product ions and fragmentation pathways were investigated. Thirteen compounds were separated on an Agilent Zorbax RRHD SB-C18 column (150 mm × 2.1 mm, 1.8 μm). On the basis of comparing with the 4 reference standards and the literature data, the other 9 flavonoids were identified by tandem mass spectrometry (MS/MS). Eight compounds (compounds 1, 4, 5, 8, 9, 10, 11, and 12) were found in PES leaves for the first time. An efficient UPLC–QTOF-MS/MS method was successfully applied for the structural identification of flavonoids in PES leaves. These results have practical applications for the rapid identification and structural characterization of these compounds in crude bioactive extracts or mixtures.

scholarly journals Effect of Acidic pH on Expression of Surface-Associated Proteins of Streptococcus oralis

2003 ◽  
Vol 69 (9) ◽  
pp. 5290-5296 ◽  
Author(s):  
Joanna C. Wilkins ◽  
David Beighton ◽  
Karen A. Homer
Keyword(s):  
Mass Spectrometry ◽  
Phosphoglycerate Kinase ◽  
Protein Translation ◽  
Culture Conditions ◽  
Oral Streptococci ◽  
Ribosome Recycling Factor ◽  
Two Dimensional Gel Electrophoresis ◽  
Flight Mass Spectrometry ◽  
Streptococcus Oralis ◽  
Associated Proteins

ABSTRACT Streptococcus oralis, a member of the mitis group of oral streptococci, is implicated in the pathogenesis of infective endocarditis and is the predominant aciduric non-mutans-group streptococcus in dental plaque. We undertook to identify the most abundant surface-associated proteins of S. oralis and to investigate changes in protein expression when the organism was grown under acidic culture conditions. Surface-associated proteins were extracted from cells grown in batch culture, separated by two-dimensional gel electrophoresis, excised, digested with trypsin, and analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry and liquid chromatography-tandem mass spectrometry. Putative functions were assigned by homology to a translated genomic database of Streptococcus pneumoniae. A total of 27 proteins were identified; these included a lipoprotein, a ribosome recycling factor, and the glycolytic enzymes phosphoglycerate kinase, fructose bisphosphate aldolase, glyceraldehyde-3-phosphate dehydrogenase, and enolase. The most abundant protein, phosphocarrier protein HPr, was present as three isoforms. Neither lactate dehydrogenase nor pyruvate oxidase, dominant intracellular proteins, were present among the proteins on the gels, demonstrating that proteins in the surface-associated pool did not arise as a result of cell lysis. Eleven of the proteins identified were differentially expressed when cells were grown at pH 5.2 versus pH 7.0, and these included superoxide dismutase, a homologue of dipeptidase V from Lactococcus lactis, and the protein translation elongation factors G, Tu, and Ts. This study has extended the range of streptococcal proteins known to be expressed at the cell surface. Further investigations are required to ascertain their functions at this extracellular location and determine how their expression is influenced by other environmental conditions.

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