32 results on '"Stoychev, S."'
Search Results
2. Dimethylformamide is a novel nitrilase inducer in Rhodococcus rhodochrous
- Author
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Chhiba-Govindjee, V. P., Mathiba, K., van der Westhuyzen, C. W., Steenkamp, P., Rashamuse, J. K., Stoychev, S., Bode, M. L., and Brady, D.
- Published
- 2018
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3. EE245 Impact of Modelling the Inclusion of Productivity Losses in Economic Analyses of Vaccines for Clostridioides Difficile Infections and Respiratory Syncytial Virus
- Author
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Mewes, JC, primary, Neri, M, additional, Albuquerque de Almeida, F, additional, Stoychev, S, additional, Minarovic, N, additional, Charos, A, additional, Shea, KM, additional, and Steuten, L, additional
- Published
- 2022
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4. EE52 Defining and Measuring Health System Pressure: A Conceptual Framework and Application to RSV and C. Difficile Infections
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Neri, M, primary, Brassel, S, additional, Schirrmacher, H, additional, Steuten, L, additional, Shea, KM, additional, Stoychev, S, additional, Albuquerque de Almeida, F, additional, Charos, A, additional, Ben Mehidi, I, additional, and Schley, K, additional
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- 2022
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5. Crack-tip stresses and their effect on stress intensity factor for crack propagation
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Stoychev, S. and Kujawski, D.
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- 2008
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6. Proteogenomic analysis demonstrates novel potential targets of pancreatic ductal adenocarcinoma in African patients
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Nweke, E.E., primary, Naicker, P., additional, Aaron, S., additional, Stoychev, S., additional, Devar, J., additional, Tabb, D., additional, Omoshoro-Jones, J., additional, Smith, M., additional, and Candy, G., additional
- Published
- 2021
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7. Differential inhibition of adenylylated and deadenylylated forms of M. tuberculosis glutamine synthetase as a drug discovery platform
- Author
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Theron, A., primary, Roth, R. L., additional, Hoppe, H., additional, Parkinson, C., additional, van der Westhuyzen, C. W., additional, Stoychev, S., additional, Wiid, I., additional, Pietersen, R. D., additional, Baker, B., additional, and Kenyon, C. P., additional
- Published
- 2017
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8. COMPARATIVE STUDY ON FATTENING AND MEAT QUALITY OF FINE WOOL AND CROSSBRED LAMBS
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Petev, M., Stoychev, S., Stankov, I., and Sivkova, K.
- Subjects
body weight ,feed conversion ratio ,animal diseases ,meat yield traits ,average daily gain ,meat chemical composition - Abstract
Experiment was carried out to characterize fattening and meat quality of lambs from two fine wool breeds - Caucasian, and North Caucasian, and one crossbred breed - South Bulgarian Corriedale. The results from the research showed that over a 60-day intensive fattening period the average daily gain was 205g for the North Caucasian and 220g for lambs of the South Bulgarian Corriedale breed. The average daily gain of lambs of the South Bulgarian Corriedale breed was higher than that of the Caucasian by about 5% and that of the North Caucasian by 6.8%. Consumption of net energy (feed units) per kilogram gain for South Bulgarian Corriedale lambs was 7.4% lower than that for the North Caucasian and 3.2% lower than that of the Caucasian breed. Lambs of the South Bulgarian Corriedale breed showed the best meat production traits and protein contents in the meat.
- Published
- 2004
9. Interatomic Coulombic decay of NeAr dimers following Auger decay
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Ouchi, T, primary, Sakai, K, additional, Fukuzawa, H, additional, Liu, X-J, additional, Ueda, K, additional, Higuchi, I, additional, Tamenori, Y, additional, Iwayama, H, additional, Nagaya, K, additional, Yao, M, additional, Saito, N, additional, Zhang, D, additional, Ding, D, additional, Schöffler, M, additional, Mazza, T, additional, Chiang, Y-C, additional, Stoychev, S D, additional, Demekhin, Ph V, additional, Kuleff, A I, additional, and Cederbaum, L S, additional
- Published
- 2012
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10. Interatomic Coulombic decay and electron-transfer-mediated decay following triple ionization in Ne2, NeAr, and Ar2
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Sakai, K, primary, Ouchi, T, additional, Fukuzawa, H, additional, Ueda, K, additional, Higuchi, I, additional, Tamenori, Y, additional, Schöffler, M, additional, Mazza, T, additional, Nagaya, K, additional, Yao, M, additional, Stoychev, S, additional, Kuleff, A I, additional, and Saito, N, additional
- Published
- 2012
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11. Effects of spectrum modification on fatigue crack growth
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KUJAWSKI, D., primary and STOYCHEV, S., additional
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- 2010
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12. Methods for crack opening load and crack tip shielding determination: a review.
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Stoychev, S. and Kujawski, D.
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- *
STRAINS & stresses (Mechanics) , *STATISTICAL correlation , *GROWTH rate , *LEGAL compliance - Abstract
In this paper a review of the literature on crack closure/opening load and crack tip shielding effects determination methods is presented. Commonly used ‘subjective’ (visual) and ‘non-subjective’ approaches have been included. Procedures associated with the determination of an effective crack driving force for both Elber type and that of partial (or incremental) crack closure models have been covered. Comparison among different methods of analyses based on compliance and fatigue crack growth rate measurements is discussed together with their implications and difficulties in fatigue crack growth correlations. [ABSTRACT FROM AUTHOR]
- Published
- 2003
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13. High throughput proteome and phosphorpoteome sample processing coupled to fast gradient DIA
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Stoychev, S., Bekker-Jensen, D., Martinez Del Val, A., Steigerwald, S., Batth, T., Gerber, I., Jordaan, J., Jesper Olsen, Chien, A., Knudtson, K., and Martin, R.
- Subjects
Poster Abstracts - Abstract
This work focusses on the application of high throughput workflows for proteome and phosphoproteome profiling followed by fast gradient liquid chromatography (LC) coupled to data-independent acquisition (DIA) mass spectrometry analysis. Automation of sample preparation increased throughput and reproducibility covering all steps from protein extract to mass spectrometry analysis allowing for parallel processing of up-to 96 samples in less than 6 hours (excluding digest time). We show the adaptation of the sample preparation methods including protein capture, clean-up, and on-bead digestion as well as phosphopeptide enrichment for use in a magnetic handling stations (Thermo Scientific King Fisher Flex) allowing for semi-automated sample processing. The methods are readily transferable to a range of liquid handling robots with magnetic handling stations (capabilities). Efficient protein isolation from wide range of tissues was achieved using 5% SDS followed by aggregation-based protein capture method (PAC) on MagReSyn® Amine magnetic microparticles allowing for efficient contaminant removal and on-bead digestion. For phosphoproteome profiling the PAC-generated peptides were further processed using MagReSyn® Ti-IMAC HP magnetic microparticles. All steps except for plate aliquoting and desalting were performed using a magnetic handling station that allowed for automated processing of up-to 96 samples in parallel. 500 ng peptides or enriched phosphopeptides were loaded directly on Evotips and further analysed using 21-minute gradients on Evosep LC coupled to Orbitrap Exploris equipped with FAIMS source allowing for up-to 60 samples per day to be analysed. Over 8,000 proteins and 22,000 unique phospho-peptides were quantified across the 12 tissues in a total mass spectrometry time of 28 hours.
14. Proteomic profiling of Nguni cattle liver tissue using gel and Gel-Free approaches: methodology development and potential applications
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Buthelezi, Sindisiwe, Blackburn, Jonathan, Mancama, D, and Stoychev, S
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Medical Biochemistry - Abstract
Includes abstract., Includes bibliographical references., In South Africa, resource-poor farmers mainly depend on livestock farming for their livelihoods, with cattle production being the most important livestock sector. As a consequence of natural selection in stressful conditions, Nguni cattle have been reported to be metabolically superior to other cattle breeds under unfavourable conditions. Using proteomics, with mass spectrometry at the core of the analysis, the objective of this study was to establish a reliable set of methods for the protein profiling of Nguni cattle livers. To achieve this several alternative technologies were employed and their outcomes compared namely, two-dimensional electrophoresis, fractionation by solution phase iso-electric focusing-reversed phase chromatography (IEF-RP), offline strong cation exchange- low pH reversed phase chromatography (SCX-RP) and offline high pH reverse phase-low pH reverse phase chromatography (RP-RP). All solution based methods were coupled to a tandem mass spectrometer. Protein identification was performed using the ParagonTMAlgorithm of Protein Pilot v4.0 as well as PEAKS v6. The IEF-RP and RP-RP methods achieved similar results in terms of number of proteins identified. In addition, proteins that play a role in the urea cycle (which is believed to contribute to the Nguni cattle’s enhanced metabolic ability) were all identified with both techniques. The RP-RP method was selected as the most appropriate method for future research linked to this work and will be used in the next phase of this project, on the basis that it is easier to automate compared to the IEF-RP method. It will be used beyond the scope of this work to compare levels of expression and modification of the liver proteins and their isoforms in Nguni and Hereford cattle grown under adverse environmental conditions, in order to identify those that may contribute to enhanced liver metabolism in Nguni cattle. This will be complemented by the identification and characterisation of potential polymorphisms with in such proteins that can be used to select for this trait during breeding.
- Published
- 2013
15. Comparison of the Proteome of Huh7 Cells Transfected with Hepatitis B Virus Subgenotype A1, with or without G1862T.
- Author
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Padarath K, Deroubaix A, Naicker P, Stoychev S, and Kramvis A
- Abstract
HBeAg is a non-structural, secreted protein of hepatitis B virus (HBV). Its p25 precursor is post-translationally modified in the endoplasmic reticulum. The G1862T precore mutation leads to the accumulation of P25 in the endoplasmic reticulum and activation of unfolded protein response. Using mass spectrometry, comparative proteome profiling of Huh-7 cells transfected with wildtype (WT) or G1862T revealed significantly differentially expressed proteins resulting in 12 dysregulated pathways unique to WT-transfected cells and 7 shared between cells transfected with either WT or G1862T. Except for the p38 MAPK signalling pathway, WT showed a higher number of DEPs than G1862T-transfected cells in all remaining six shared pathways. Two signalling pathways: oxidative stress and cell cycle signalling were differentially expressed only in cells transfected with G1862T. Fifteen pathways were dysregulated in G1862T-transfected cells compared to WT. The 15 dysregulated pathways were involved in the following processes: MAPK signalling, DNA synthesis and methylation, and extracellular matrix organization. Moreover, proteins involved in DNA synthesis signalling (replication protein A (RPA) and DNA primase (PRIM2)) were significantly upregulated in G1862T compared to WT. This upregulation was confirmed by mRNA quantification of both genes and immunofluorescent confocal microscopy for RPA only. The dysregulation of the pathways involved in these processes may lead to immune evasion, persistence, and uncontrolled proliferation, which are hallmarks of cancer.
- Published
- 2024
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16. Comparative Proteomic Analysis of Huh7 Cells Transfected with Sub-Saharan African Hepatitis B Virus (Sub)genotypes Reveals Potential Oncogenic Factors.
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Padarath K, Deroubaix A, Naicker P, Stoychev S, and Kramvis A
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- Humans, Cell Line, Tumor, Signal Transduction, Africa South of the Sahara, Proteome, rhoC GTP-Binding Protein metabolism, rhoC GTP-Binding Protein genetics, Carcinoma, Hepatocellular virology, Carcinoma, Hepatocellular metabolism, Carcinoma, Hepatocellular genetics, Transfection, Liver Neoplasms virology, Liver Neoplasms metabolism, Liver Neoplasms genetics, Hepatitis B virology, Hepatitis B metabolism, Hepatitis B genetics, Hepatitis B virus genetics, Proteomics, Genotype
- Abstract
In sub-Saharan Africa (SSA), the (sub)genotypes A1, D3, and E of the hepatitis B virus (HBV) prevail. Individuals infected with subgenotype A1 have a 4.5-fold increased risk of HCC compared to those infected with other (sub)genotypes. The effect of (sub)genotypes on protein expression and host signalling has not been studied. Mass spectrometry was used to analyse the proteome of Huh7 cells transfected with replication-competent clones. Proteomic analysis revealed significantly differentially expressed proteins between SSA (sub)genotypes. Different (sub)genotypes have the propensity to dysregulate specific host signalling pathways. Subgenotype A1 resulted in dysregulation within the Ras pathway. Ras-associated protein, RhoC, was significantly upregulated in cells transfected with subgenotype A1 compared to those transfected with other (sub)genotypes, on both a proteomic (>1.5-fold) and mRNA level ( p < 0.05). Two of the main cellular signalling pathways involving RHOC, MAPK and PI3K/Akt/mTOR, regulate cell growth, motility, and survival. Downstream signalling products of these pathways have been shown to increase MMP2 and MMP9 expression. An extracellular MMP2 and MMP9 ELISA revealed a non-significant increase in MMP2 and MMP9 in the cells transfected with A1 compared to the other (sub)genotypes ( p < 0.05). The upregulated Ras-associated proteins have been implicated as oncoproteins in various cancers and could contribute to the increased hepatocarcinogenic potential of A1.
- Published
- 2024
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17. Impact of including productivity costs in economic analyses of vaccines for C. difficile infections and infant respiratory syncytial virus, in a UK setting.
- Author
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Neri M, Mewes JC, de Almeida FA, Stoychev S, Minarovic N, Charos A, Shea KM, and Steuten LMG
- Abstract
Objectives: It has been estimated that vaccines can accrue a relatively large part of their value from patient and carer productivity. Yet, productivity value is not commonly or consistently considered in health economic evaluations of vaccines in several high-income countries. To contribute to a better understanding of the potential impact of including productivity value on the expected cost-effectiveness of vaccination, we illustrate the extent to which the incremental costs would change with and without productivity value incorporated., Methods: For two vaccines currently under development, one against Cloistridioides difficile (C. difficile) infection and one against respiratory syncytial disease (RSV), we estimated their incremental costs with and without productivity value included and compared the results., Results: In this analysis, reflecting a UK context, a C. difficile vaccination programme would prevent £12.3 in productivity costs for every person vaccinated. An RSV vaccination programme would prevent £49 in productivity costs for every vaccinated person., Conclusions: Considering productivity costs in future cost-effectiveness analyses of vaccines for C. difficile and RSV will contribute to better-informed reimbursement decisions from a societal perspective., (© 2024. The Author(s).)
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- 2024
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18. Secretomics reveals hormone-therapy of breast cancer may induce survival by facilitating hypercoagulation and immunomodulation in vitro.
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Augustine TN, Buthelezi S, Pather K, Xulu KR, and Stoychev S
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- Humans, Female, Cell Communication, Signal Transduction, Immunomodulation, Hormones pharmacology, Breast Neoplasms pathology
- Abstract
Tumour cell haematogenous dissemination is predicated on molecular changes that enhance their capacity for invasion and preparation of the pre-metastatic niche. It is increasingly evident that platelets play an essential role in this transformation. The systemic nature of signalling molecules and extravascular factors that participate in mediating platelet-tumour cell interactions led to the development of an in vitro co-culture using whole blood and breast tumour cells, allowing us to decipher the impact of hormone-therapy on tumour cells and associated changes in the plasma proteome. Using mass spectrometry, we determined dysregulation of proteins associated with maintaining an invasive tumour phenotype. Tumour changes in genes associated with EMT and survival were documented. This is postulated to be induced via tumour cell interactions with the coagulatory and immune systems. Results highlight tumour cell adaptability to both treatment and blood resulting in a pro-tumorigenic response and a hypercoagulatory state. We illustrate that the breast cancer cell secretome can be altered by hormone-therapy, subject to the tumour subphenotype and linked to platelet activation. More sophisticated co-culture systems are required to recapitulate these interactions to better understand tumorigenesis. Moreover, deeper plasma profiling, using abundant protein depleted and/or vesicle enriched strategies, will likely reveal additional secretory proteins related to tumour cell-platelet interactions., (© 2024. The Author(s).)
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- 2024
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19. Experimental Ultrasound Approach for Studying Knee Intra-Articular Femur-Tibia Movements under Different Loads.
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Ivanov I, Ranchev S, and Stoychev S
- Abstract
The purpose of the present study was to develop an experimental model for the study of intra-articular knee movements depending on the function of the knee joint and involved muscle groups under isometric stretching conditions with different loads. The experimental procedure included an ultrasound examination of a knee joint after isometric stretching in healthy men ( n = 32). The changes (in millimeters) in the distances between the femur and tibia were measured using an ultrasound sonographer at three stages. The first stage was performed on ten ( n = 10) healthy men in five different sitting and upright positions. In the second and third experimental model stages, lower limbs loading was applied to 22 participants. Our hypothesis, which was confirmed, was that as a result of increased loads on the participant's back, an intra-articular decrease in the femur-tibia cartilage surface distance would be observed. The accuracy of the created experimental model was improved over its three stages from 30% to 9%. Quantitative model data can help to create a mathematical model of the mechanical effects during the deformation of knee joint bone cartilage and it can also help outline some future tasks: increasing loading weights, enlarging participant groups, performing comparisons of men and women, and performing comparisons of healthy and pathological individuals.
- Published
- 2023
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20. Assessing the dynamics and macromolecular interactions of the intrinsically disordered protein YY1.
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Donald H, Blane A, Buthelezi S, Naicker P, Stoychev S, Majakwara J, and Fanucchi S
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- YY1 Transcription Factor genetics, YY1 Transcription Factor metabolism, DNA metabolism, Gene Expression Regulation, Intrinsically Disordered Proteins genetics, Intrinsically Disordered Proteins metabolism
- Abstract
YY1 is a ubiquitously expressed, intrinsically disordered transcription factor involved in neural development. The oligomeric state of YY1 varies depending on the environment. These structural changes may alter its DNA binding ability and hence its transcriptional activity. Just as YY1's oligomeric state can impact its role in transcription, so does its interaction with other proteins such as FOXP2. The aim of this work is to study the structure and dynamics of YY1 so as to determine the influence of oligomerisation and associations with FOXP2 on its DNA binding mechanism. The results confirm that YY1 is primarily a disordered protein, but it does consist of certain specific structured regions. We observed that YY1 quaternary structure is a heterogenous mixture of oligomers, the overall size of which is dependent on ionic strength. Both YY1 oligomerisation and its dynamic behaviour are further subject to changes upon DNA binding, whereby increases in DNA concentration result in a decrease in the size of YY1 oligomers. YY1 and the FOXP2 forkhead domain were found to interact with each other both in isolation and in the presence of YY1-specific DNA. The heterogeneous, dynamic multimerisation of YY1 identified in this work is, therefore likely to be important for its ability to make heterologous associations with other proteins such as FOXP2. The interactions that YY1 makes with itself, FOXP2 and DNA form part of an intricate mechanism of transcriptional regulation by YY1, which is vital for appropriate neural development., (© 2023 The Author(s).)
- Published
- 2023
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21. Urine-HILIC: Automated Sample Preparation for Bottom-Up Urinary Proteome Profiling in Clinical Proteomics.
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Govender IS, Mokoena R, Stoychev S, and Naicker P
- Abstract
Urine provides a diverse source of information related to a patient's health status and is ideal for clinical proteomics due to its ease of collection. To date, most methods for the preparation of urine samples lack the throughput required to analyze large clinical cohorts. To this end, we developed a novel workflow, urine-HILIC (uHLC), based on an on-bead protein capture, clean-up, and digestion without the need for bottleneck processing steps such as protein precipitation or centrifugation. The workflow was applied to an acute kidney injury (AKI) pilot study. Urine from clinical samples and a pooled sample was subjected to automated sample preparation in a KingFisher™ Flex magnetic handling station using the novel approach based on MagReSyn
® HILIC microspheres. For benchmarking, the pooled sample was also prepared using a published protocol based on an on-membrane (OM) protein capture and digestion workflow. Peptides were analyzed by LCMS in data-independent acquisition (DIA) mode using a Dionex Ultimate 3000 UPLC coupled to a Sciex 5600 mass spectrometer. The data were searched in Spectronaut™ 17. Both workflows showed similar peptide and protein identifications in the pooled sample. The uHLC workflow was easier to set up and complete, having less hands-on time than the OM method, with fewer manual processing steps. Lower peptide and protein coefficient of variation was observed in the uHLC technical replicates. Following statistical analysis, candidate protein markers were filtered, at ≥8.35-fold change in abundance, ≥2 unique peptides and ≤1% false discovery rate, and revealed 121 significant, differentially abundant proteins, some of which have known associations with kidney injury. The pilot data derived using this novel workflow provide information on the urinary proteome of patients with AKI. Further exploration in a larger cohort using this novel high-throughput method is warranted.- Published
- 2023
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22. Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling.
- Author
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Koenig C, Martinez-Val A, Naicker P, Stoychev S, Jordaan J, and Olsen JV
- Subjects
- Proteomics methods, Mass Spectrometry methods, Workflow, Phosphopeptides analysis, Proteome analysis
- Abstract
Tandem mass tags data-dependent acquisition (TMT-DDA) as well as data-independent acquisition-based label-free quantification (LFQ-DIA) have become the leading workflows to achieve deep proteome and phosphoproteome profiles. We present a modular pipeline for TMT-DDA and LFQ-DIA that integrates steps to perform scalable phosphoproteome profiling, including protein lysate extraction, clean-up, digestion, phosphopeptide enrichment, and TMT-labeling. We also detail peptide and/or phosphopeptide fractionation and pre-mass spectrometry desalting and provide researchers guidance on choosing the best workflow based on sample number and input. For complete details on the use and execution of this protocol, please refer to Koenig et al.
1 and Martínez-Val et al.2 ., Competing Interests: Declaration of interests P.N., S.S., and J.J. work for ReSyn Biosciences that supplied some of the reagents for digest preparation and phosphopeptide enrichment utilized in this workflow. S.S. further works for Evosep Biosystems whose LC system is utilized as part of the LC-MS setup., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2023
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23. Local colonisations and extinctions of European birds are poorly explained by changes in climate suitability.
- Author
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Howard C, Marjakangas EL, Morán-Ordóñez A, Milanesi P, Abuladze A, Aghababyan K, Ajder V, Arkumarev V, Balmer DE, Bauer HG, Beale CM, Bino T, Boyla KA, Burfield IJ, Burke B, Caffrey B, Chodkiewicz T, Del Moral JC, Mazal VD, Fernández N, Fornasari L, Gerlach B, Godinho C, Herrando S, Ieronymidou C, Johnston A, Jovicevic M, Kalyakin M, Keller V, Knaus P, Kotrošan D, Kuzmenko T, Leitão D, Lindström Å, Maxhuni Q, Mihelič T, Mikuska T, Molina B, Nagy K, Noble D, Øien IJ, Paquet JY, Pladevall C, Portolou D, Radišić D, Rajkov S, Rajković DZ, Raudonikis L, Sattler T, Saveljić D, Shimmings P, Sjenicic J, Šťastný K, Stoychev S, Strus I, Sudfeldt C, Sultanov E, Szép T, Teufelbauer N, Uzunova D, van Turnhout CAM, Velevski M, Vikstrøm T, Vintchevski A, Voltzit O, Voříšek P, Wilk T, Zurell D, Brotons L, Lehikoinen A, and Willis SG
- Subjects
- Animals, Ecosystem, Birds, Climate Change
- Abstract
Climate change has been associated with both latitudinal and elevational shifts in species' ranges. The extent, however, to which climate change has driven recent range shifts alongside other putative drivers remains uncertain. Here, we use the changing distributions of 378 European breeding bird species over 30 years to explore the putative drivers of recent range dynamics, considering the effects of climate, land cover, other environmental variables, and species' traits on the probability of local colonisation and extinction. On average, species shifted their ranges by 2.4 km/year. These shifts, however, were significantly different from expectations due to changing climate and land cover. We found that local colonisation and extinction events were influenced primarily by initial climate conditions and by species' range traits. By contrast, changes in climate suitability over the period were less important. This highlights the limitations of using only climate and land cover when projecting future changes in species' ranges and emphasises the need for integrative, multi-predictor approaches for more robust forecasting., (© 2023. The Author(s).)
- Published
- 2023
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24. Ecological barriers mediate spatiotemporal shifts of bird communities at a continental scale.
- Author
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Marjakangas EL, Bosco L, Versluijs M, Xu Y, Santangeli A, Holopainen S, Mäkeläinen S, Herrando S, Keller V, Voříšek P, Brotons L, Johnston A, Princé K, Willis SG, Aghababyan K, Ajder V, Balmer DE, Bino T, Boyla KA, Chodkiewicz T, Del Moral JC, Mazal VD, Ferrarini A, Godinho C, Gustin M, Kalyakin M, Knaus P, Kuzmenko T, Lindström Å, Maxhuni Q, Molina B, Nagy K, Radišić D, Rajkov S, Rajković DZ, Raudoniki L, Sjeničić J, Stoychev S, Szép T, Teufelbauer N, Ursul S, van Turnhout CAM, Velevski M, Vikstrøm T, Wilk T, Voltzit O, Øien IJ, Sudfeldt C, Gerlach B, and Lehikoinen A
- Subjects
- Animals, Biodiversity, Climate Change, Forecasting, Birds physiology, Ecosystem
- Abstract
Species' range shifts and local extinctions caused by climate change lead to community composition changes. At large spatial scales, ecological barriers, such as biome boundaries, coastlines, and elevation, can influence a community's ability to shift in response to climate change. Yet, ecological barriers are rarely considered in climate change studies, potentially hindering predictions of biodiversity shifts. We used data from two consecutive European breeding bird atlases to calculate the geographic distance and direction between communities in the 1980s and their compositional best match in the 2010s and modeled their response to barriers. The ecological barriers affected both the distance and direction of bird community composition shifts, with coastlines and elevation having the strongest influence. Our results underscore the relevance of combining ecological barriers and community shift projections for identifying the forces hindering community adjustments under global change. Notably, due to (macro)ecological barriers, communities are not able to track their climatic niches, which may lead to drastic changes, and potential losses, in community compositions in the future.
- Published
- 2023
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25. SAPrIm, a semi-automated protocol for mid-throughput immunopeptidomics.
- Author
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Lim Kam Sian TCC, Goncalves G, Steele JR, Shamekhi T, Bramberger L, Jin D, Shahbazy M, Purcell AW, Ramarathinam S, Stoychev S, and Faridi P
- Subjects
- Humans, HLA Antigens, Histocompatibility Antigens Class II, Immunotherapy, Histocompatibility Antigens Class I, Peptides
- Abstract
Human leukocyte antigen (HLA) molecules play a crucial role in directing adaptive immune responses based on the nature of their peptide ligands, collectively coined the immunopeptidome. As such, the study of HLA molecules has been of major interest in the development of cancer immunotherapies such as vaccines and T-cell therapies. Hence, a comprehensive understanding and profiling of the immunopeptidome is required to foster the growth of these personalised solutions. We herein describe SAPrIm, an Immunopeptidomics tool for the Mid-Throughput era. This is a semi-automated workflow involving the KingFisher platform to isolate immunopeptidomes using anti-HLA antibodies coupled to a hyper-porous magnetic protein A microbead, a variable window data independent acquisition (DIA) method and the ability to run up to 12 samples in parallel. Using this workflow, we were able to concordantly identify and quantify ~400 - 13000 unique peptides from 5e5 - 5e7 cells, respectively. Overall, we propose that the application of this workflow will be crucial for the future of immunopeptidome profiling, especially for mid-size cohorts and comparative immunopeptidomics studies., Competing Interests: Author SS was employed by ReSyn Biosciences. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Lim Kam Sian, Goncalves, Steele, Shamekhi, Bramberger, Jin, Shahbazy, Purcell, Ramarathinam, Stoychev and Faridi.)
- Published
- 2023
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26. Diet of Eastern Imperial Eagle ( Aquilaheliaca ) in Bulgaria: composition, distribution and variation.
- Author
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Demerdzhiev D, Boev Z, Dobrev D, Terziev N, Nedyalkov N, Stoychev S, and Petrov T
- Abstract
The Eastern Imperial Eagle (EIE) is a top predator exploiting different prey in different parts of its distribution. In this study, we summarise data collected over a long period of time (for 25 consecutive years), identifying key prey species in the different regions, as well as clarifying seasonal preferences in the eagle's diet. Most studies on the EIE food composition covering different parts of the species distribution range analyse the breeding season, while data about the winter diet are scarce. To the best of our knowledge, this is the first study detailing the differences in EIE's dietary preferences between the breeding and the winter periods. We identified 4891 specimens belonging to 196 different taxa, which represents the most comprehensive study considering the diet diversity of this threatened species. Mammals represented the largest proportion of the diet, followed by birds and reptiles. Northern White-breasted Hedgehog was the most common prey, accounting for 25.7% of the total prey caught and 26.75% of the biomass. The European Souslik was the second most important prey with 14.35% participation in the eagle's diet, but with a 3.75% contribution to the biomass. As we predicted, prey composition and main prey species varied spatially and seasonally. Modelling differences in the EIE diet, we found that the "territory effect" had the strongest impact on the dietary variations. Diet diversity differed significantly between regions (F = 12.6, df = 4, p = 0.01). During the breeding season, eagles fed mainly on Hedgehogs (29.88%), Sousliks (16.85%) and Storks (7.74%), while the winter diet was predominantly small rodents (44.17%) and songbirds (13.96%). We found that top predators, such as EIE, have successfully adapted to a novel food source, which is abundant in the area. The detected flexibility in the diet of the species and its ability to switch to alternative prey, if available, when the primary prey decreased, should be considered when planning species conservation efforts. Investigating the temporal change of the main prey in the eagle's diet is also crucial for further species conservation measures., (Dimitar Demerdzhiev, Zlatozar Boev, Dobromir Dobrev, Nikolay Terziev, Nedko Nedyalkov, Stoycho Stoychev, Tseno Petrov.)
- Published
- 2022
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27. Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato).
- Author
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Tomescu MS, Sooklal SA, Ntsowe T, Naicker P, Darnhofer B, Archer R, Stoychev S, Swanevelder D, Birner-Grünberger R, and Rumbold K
- Subjects
- Flowers genetics, Gene Expression Regulation, Plant genetics, Plant Leaves genetics, Solanum tuberosum genetics, Tandem Mass Spectrometry, Hypoxis genetics, Proteome genetics, Proteomics, Transcriptome genetics
- Abstract
The corm of Hypoxis hemerocallidea, commonly known as the African potato, is used in traditional medicine to treat several medical conditions such as urinary infections, benign prostate hyperplasia, inflammatory conditions and testicular tumours. The metabolites contributing to the medicinal properties of H. hemerocallidea have been identified in several studies and, more recently, the active terpenoids of the plant were profiled. However, the biosynthetic pathways and the enzymes involved in the production of the terpene metabolites in H. hemerocallidea have not been characterised at a transcriptomic or proteomic level. In this study, total RNA extracted from the corm, leaf and flower tissues of H. hemerocallidea was sequenced on the Illumina HiSeq 2500 platform. A total of 143,549 transcripts were assembled de novo using Trinity and 107,131 transcripts were functionally annotated using the nr, GO, COG, KEGG and SWISS-PROT databases. Additionally, the proteome of the three tissues were sequenced using LC-MS/MS, revealing aspects of secondary metabolism and serving as data validation for the transcriptome. Functional annotation led to the identification of numerous terpene synthases such as nerolidol synthase, germacrene D synthase, and cycloartenol synthase amongst others. Annotations also revealed a transcript encoding the terpene synthase phytoalexin momilactone A synthase. Differential expression analysis using edgeR identified 946 transcripts differentially expressed between the three tissues and revealed that the leaf upregulates linalool synthase compared to the corm and the flower tissues. The transcriptome as well as the proteome of Hypoxis hemerocallidea presented here provide a foundation for future research., Competing Interests: The funders (Omics Center Graz, BioTechMed and ACIB GmbH) provided support in the form of salaries for authors [B.D and R.B.G]. This does not alter our adherence to PLOS ONE policies on sharing data and materials.
- Published
- 2021
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28. Health outcomes and economic burden of hospitalized COVID-19 patients in the United States.
- Author
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Di Fusco M, Shea KM, Lin J, Nguyen JL, Angulo FJ, Benigno M, Malhotra D, Emir B, Sung AH, Hammond JL, Stoychev S, and Charos A
- Subjects
- Aged, Aged, 80 and over, COVID-19 epidemiology, COVID-19 mortality, Cost of Illness, Disease Progression, Female, Hospital Mortality, Humans, Insurance Coverage economics, Intensive Care Units economics, Length of Stay economics, Male, Middle Aged, Respiration, Artificial economics, Retrospective Studies, SARS-CoV-2, United States epidemiology, COVID-19 economics, Hospital Charges statistics & numerical data, Hospitalization economics, Outcome Assessment, Health Care
- Abstract
Objective: The aims of this study were to evaluate health outcomes and the economic burden of hospitalized COVID-19 patients in the United States., Methods: Hospitalized patients with a primary or secondary discharge diagnosis code for COVID-19 (ICD-10 code U07.1) from 1 April to 31 October 2020 were identified in the Premier Healthcare COVID-19 Database. Patient demographics, hospitalization characteristics, and concomitant medical conditions were assessed. Hospital length of stay (LOS), in-hospital mortality, hospital charges, and hospital costs were evaluated overall and stratified by age groups, insurance types, and 4 COVID-19 disease progression states based on intensive care unit (ICU) and invasive mechanical ventilation (IMV) usage., Results: Of the 173,942 hospitalized COVID-19 patients, the median age was 63 years, 51.0% were male, and 48.5% were covered by Medicare. The most prevalent concomitant medical conditions were cardiovascular disease (73.5%), hypertension (64.8%), diabetes (40.7%), obesity (27.0%), and chronic kidney disease (24.2%). Approximately one-fifth (21.9%) of the hospitalized COVID-19 patients were admitted to the ICU and 16.9% received IMV; most patients (73.6%) did not require ICU admission or IMV, and 12.4% required both. The median hospital LOS was 5 days, in-hospital mortality was 13.6%, median hospital charges were $43,986, and median hospital costs were $12,046. Hospital LOS and in-hospital mortality increased with ICU and/or IMV usage and age; hospital charges and costs increased with ICU and/or IMV usage. Patients with both ICU and IMV usage had the longest median hospital LOS (15 days), highest in-hospital mortality (53.8%), and highest hospital charges ($198,394) and hospital costs ($54,402)., Limitations: This retrospective administrative database analysis relied on coding accuracy and a subset of admissions with validated/reconciled hospital costs., Conclusions: This study summarizes the severe health outcomes and substantial hospital costs of hospitalized COVID-19 patients in the US. The findings support the urgent need for rapid implementation of effective interventions, including safe and efficacious vaccines.
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- 2021
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29. SWATH-MS based proteomic profiling of pancreatic ductal adenocarcinoma tumours reveals the interplay between the extracellular matrix and related intracellular pathways.
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Nweke EE, Naicker P, Aron S, Stoychev S, Devar J, Tabb DL, Omoshoro-Jones J, Smith M, and Candy G
- Subjects
- Aged, Aged, 80 and over, Carcinoma, Pancreatic Ductal genetics, Carcinoma, Pancreatic Ductal metabolism, Carcinoma, Pancreatic Ductal surgery, Case-Control Studies, Cohort Studies, Female, Follow-Up Studies, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Gene Regulatory Networks, Humans, Male, Mass Spectrometry, Middle Aged, Pancreatic Neoplasms genetics, Pancreatic Neoplasms metabolism, Pancreatic Neoplasms surgery, Prognosis, Biomarkers, Tumor genetics, Biomarkers, Tumor metabolism, Carcinoma, Pancreatic Ductal pathology, Extracellular Matrix metabolism, Pancreatic Neoplasms pathology, Polymorphism, Single Nucleotide, Proteome analysis
- Abstract
Pancreatic cancer accounts for 2.8% of new cancer cases worldwide and is projected to become the second leading cause of cancer-related deaths by 2030. Patients of African ancestry appear to be at an increased risk for pancreatic ductal adenocarcinoma (PDAC), with more severe disease and outcomes. The purpose of this study was to map the proteomic and genomic landscape of a cohort of PDAC patients of African ancestry. Thirty tissues (15 tumours and 15 normal adjacent tissues) were obtained from consenting South African PDAC patients. Optimisation of the sample preparation method allowed for the simultaneous extraction of high-purity protein and DNA for SWATH-MS and OncoArray SNV analyses. We quantified 3402 proteins with 49 upregulated and 35 downregulated proteins at a minimum 2.1 fold change and FDR adjusted p-value (q-value) ≤ 0.01 when comparing tumour to normal adjacent tissue. Many of the upregulated proteins in the tumour samples are involved in extracellular matrix formation (ECM) and related intracellular pathways. In addition, proteins such as EMIL1, KBTB2, and ZCCHV involved in the regulation of ECM proteins were observed to be dysregulated in pancreatic tumours. Downregulation of pathways involved in oxygen and carbon dioxide transport were observed. Genotype data showed missense mutations in some upregulated proteins, such as MYPN, ESTY2 and SERPINB8. Approximately 11% of the dysregulated proteins, including ISLR, BP1, PTK7 and OLFL3, were predicted to be secretory proteins. These findings help in further elucidating the biology of PDAC and may aid in identifying future plausible markers for the disease., Competing Interests: The authors have declared that no competing interests exist.
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- 2020
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30. Biochemical Pulldown of mRNAs and Long Noncoding RNAs from Cellular Lysates Coupled with Mass Spectrometry to Identify Protein Binding Partners.
- Author
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Savulescu AF, Stoychev S, Mamputha S, and Mhlanga MM
- Abstract
RNA binding proteins (RBPs) interact with cellular mRNAs, controlling various steps throughout the lifetime of these transcripts, including transcription, cellular transport, subcellular localization, translation and degradation. In addition to binding mRNA transcripts, a growing number of RBPs are shown to bind long noncoding RNAs (lncRNAs), controlling key cellular processes, including gene expression and translation of proteins. Current methodologies aimed at identifying and characterizing protein binding partners of specific RNAs of interest typically rely on tagging of the RNA with affinity aptamers, using in vitro transcribed RNA or immobilized oligonucleotides to capture RNA-protein complexes under native conditions. These assays are coupled with mass spectrometry or Western Blot analysis to identify or/and confirm interacting proteins. Here, we describe an alternative approach to identify protein binding partners of mRNAs and large long noncoding RNAs. This approach relies on biochemical pulldown of specific target RNAs and interacting protein partners from cellular lysates coupled with mass spectrometry to identify novel interacting proteins. By using 24-48 ~20 mer biotinylated DNA probes that hybridize to the target RNA, the method ensures high specificity and minimal off target binding. This approach is reproducible and fast and serves as a base for discovery studies to identify proteins that bind to RNAs of interest., Competing Interests: Competing interestsThe authors declare no competing interests., (Copyright © 2020 The Authors; exclusive licensee Bio-protocol LLC.)
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- 2020
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31. Amide hydrogen exchange in HIV-1 subtype B and C proteases--insights into reduced drug susceptibility and dimer stability.
- Author
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Naicker P, Stoychev S, Dirr HW, and Sayed Y
- Subjects
- Amino Acid Sequence, Dimerization, HIV Protease chemistry, Microbial Sensitivity Tests, Molecular Sequence Data, Sequence Homology, Amino Acid, Amides metabolism, HIV Protease metabolism, HIV-1 enzymology
- Abstract
Since its identification, HIV has continued to have a detrimental impact on the lives of millions of people throughout the world. The protease of HIV is a major target in antiviral treatment. The South African HIV-1 subtype C (C-SA) protease displays weaker binding affinity for some clinically approved protease inhibitors in comparison with the HIV-1 subtype B protease. The heavy HIV burden in sub-Saharan Africa, where subtype C HIV-1 predominates, makes this disparity a topic of great interest. In light of this, the enzyme activity and affinity of protease inhibitors for the subtype B and C-SA proteases were determined. The relative vitality, indicating the selective advantage of polymorphisms, of the C-SA protease relative to the subtype B protease in the presence of ritonavir and darunavir was four- and tenfold greater, respectively. Dynamic differences that contribute to the reduced drug susceptibility of the C-SA protease were investigated by performing hydrogen-deuterium exchange/mass spectrometry (HDX/MS) on unbound subtype B and C-SA proteases. The reduced propensity to form the E35-R57 salt bridge, and alterations in the hydrophobic core of the C-SA protease, are proposed to affect the anchoring of the flexible flaps, resulting in an increased proportion of the fully open flap conformation. HDX/MS data suggested that the N-terminus of both proteases is less stable than the C-terminus of the proteases, thus explaining the increased efficacy of dimerization inhibitors targeted toward the C-terminus of HIV proteases. As far as we are aware, this is the first report on assessment of HIV protease dynamics using HDX/MS., (© 2014 FEBS.)
- Published
- 2014
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32. Plasmodium falciparum spermidine synthase inhibition results in unique perturbation-specific effects observed on transcript, protein and metabolite levels.
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Becker JV, Mtwisha L, Crampton BG, Stoychev S, van Brummelen AC, Reeksting S, Louw AI, Birkholtz LM, and Mancama DT
- Subjects
- Cyclohexylamines pharmacology, Gene Expression Profiling, Metabolic Networks and Pathways, Plasmodium falciparum enzymology, Polyamines metabolism, Protozoan Proteins metabolism, Gene Expression Regulation drug effects, Plasmodium falciparum drug effects, Plasmodium falciparum metabolism, Spermidine Synthase antagonists & inhibitors
- Abstract
Background: Plasmodium falciparum, the causative agent of severe human malaria, has evolved to become resistant to previously successful antimalarial chemotherapies, most notably chloroquine and the antifolates. The prevalence of resistant strains has necessitated the discovery and development of new chemical entities with novel modes-of-action. Although much effort has been invested in the creation of analogues based on existing drugs and the screening of chemical and natural compound libraries, a crucial shortcoming in current Plasmodial drug discovery efforts remains the lack of an extensive set of novel, validated drug targets. A requirement of these targets (or the pathways in which they function) is that they prove essential for parasite survival. The polyamine biosynthetic pathway, responsible for the metabolism of highly abundant amines crucial for parasite growth, proliferation and differentiation, is currently under investigation as an antimalarial target. Chemotherapeutic strategies targeting this pathway have been successfully utilized for the treatment of Trypanosomes causing West African sleeping sickness. In order to further evaluate polyamine depletion as possible antimalarial intervention, the consequences of inhibiting P. falciparum spermidine synthase (PfSpdSyn) were examined on a morphological, transcriptomic, proteomic and metabolic level., Results: Morphological analysis of P. falciparum 3D7 following application of the PfSpdSyn inhibitor cyclohexylamine confirmed that parasite development was completely arrested at the early trophozoite stage. This is in contrast to untreated parasites which progressed to late trophozoites at comparable time points. Global gene expression analyses confirmed a transcriptional arrest in the parasite. Several of the differentially expressed genes mapped to the polyamine biosynthetic and associated metabolic pathways. Differential expression of corresponding parasite proteins involved in polyamine biosynthesis was also observed. Most notably, uridine phosphorylase, adenosine deaminase, lysine decarboxylase (LDC) and S-adenosylmethionine synthetase were differentially expressed at the transcript and/or protein level. Several genes in associated metabolic pathways (purine metabolism and various methyltransferases) were also affected. The specific nature of the perturbation was additionally reflected by changes in polyamine metabolite levels., Conclusions: This study details the malaria parasite's response to PfSpdSyn inhibition on the transcriptomic, proteomic and metabolic levels. The results corroborate and significantly expand previous functional genomics studies relating to polyamine depletion in this parasite. Moreover, they confirm the role of transcriptional regulation in P. falciparum, particularly in this pathway. The findings promote this essential pathway as a target for antimalarial chemotherapeutic intervention strategies.
- Published
- 2010
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