Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative proteomics analysis of virulent and less virulent strains of Rhizoctonia solani

ABSTRACT: Comparative proteomics analysis of a virulent and a less virulent strains of Rhizoctonia solani was carried out using LC-MS/MS (Label free quantitation).

INSTRUMENT(S): Synapt MS

ORGANISM(S): Rhizoctonia Solani Ag-1

SUBMITTER: SR Prabhukarthikeyan

LAB HEAD: Prabhukarthikeyan SR

PROVIDER: PXD023430 | Pride | 2022-05-19

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	RS15_1.raw.rar	Raw
	RS15_1.xls	Xls
	RS15_1_CID.pkl	Other
	RS15_2.raw.rar	Raw
	RS15_2.xls	Xls

Items per page:

1 - 5 of 18

Publications

Comparative Proteomic Analysis of Rhizoctonia solani Isolates Identifies the Differentially Expressed Proteins with Roles in Virulence.

Prabhukarthikeyan Seenichamy Rathinam SR Parameswaran Chidambaranathan C Sawant Shraddha Bhaskar SB Naveenkumar Ramasamy R Mahanty Arabinda A Keerthana Umapathy U Yadav Manoj Kumar MK Anandan Annamalai A Panneerselvam Periyasamy P Bag Manas Kumar MK Rath Prakash Chandra PC

Journal of fungi (Basel, Switzerland) 20220405 4

Sheath blight of rice is a destructive disease that could be calamitous to rice cultivation. The significant objective of this study is to contemplate the proteomic analysis of the high virulent and less virulent isolate of Rhizoctonia solani using a quantitative LC-MS/MS-based proteomic approach to identify the differentially expressed proteins promoting higher virulence. Across several rice-growing regions in Odisha, Eastern India, 58 Rhizoctonia isolates were obtained. All the i ...[more]

PMID: 35448601

Similar Datasets

Effect of dietary replacement of fish meal with spent brewer’s waste on the muscle proteome profile of the Indian major carp Labeo rohita

Project description:The effect of dietary replacement of fish meal with spent brewer’s waste was evaluated by investigating the changes in muscle proteome profile of the Indian major carp Labeo rohita

2023-03-10 | PXD020093 | Pride

Proteomic changes in liver tissue of Rat (Rattus norvegicus) following formalin exposure

Project description:Formaldehyde (HCHO) is the simplest form of aldehyde and it is naturally present in a wide range of resources. In spite of its cosmopolitan presence, formaldehyde can have deleterious health effects at higher concentrations like leukemia. However, most of the studies carried out so far have focused on the effect of formaldehyde exposure through inhalation and not much has been studied on the its exposure through food. In this context, the present study was carried out to investigate the effect of formaldehyde exposure through drinking water on the liver proteome of rat which would not only be helpful in assessing the impact of formaldehyde on health of organisms but also would be helpful in understanding the mechanism of detoxification.

2020-01-07 | PXD010534 | Pride

Andrographis paniculata proteome

Project description:Andrographis paniculata (AP) is a medicinal herb used to treat infectious diseases. The medicinal properties are due to presence of andrographolide and other secondary metabolites synthesized via mevalonic acid (MVA) and methyl erythritol phosphate (MEP) pathways. To increase the andrographolide content plants were treated with 50µM Jasmonic acid (JA) for one week. HPLC analysis revealed that one fold increase in the andrographolide content compared to control. To study the signal mechanism underlying in the stress response, samples were subjected to Q-TOF-LC-MS/MS analysis. JA influences the expression of MVA and MEP enzymes in treated (22 enzymes) than in untreated (3 enzymes). We found total 3308 proteins in control and 3994 in elicited sample in which 1393 were commonly found in both. The differential expression revealed 621 proteins were down-regulated and 201 proteins were up regulated. The functional annotation involved 40 metabolic processes where post translational modifications was highly up regulated in treated (5.7%). The total proteome of A.paniculata was reported for the first time. The comparison of elicited and non elicited (control) samples revealed that the elicitation is an integrated process which release variety of bioactive compounds to defend itself from variety of pathogens. The Knowledge obtained from this scrutiny, JA dependent stress adaptive response is likely to have industrial and agricultural impact. It creates a hope towards future for the development of eco-friendly ways of managing pests and tapping into a largely unexplored treasure of plant-derived bioactive metabolites for human use. Particularly in this plant, it is useful for the production of medicines to cure different kinds of diseases and disorders.

2020-01-13 | PXD010674 | Pride

Cross-linked amyloidogenic proteins as potential aggregation inhibitors

Project description:Amyloidogenic proteins, characterized by their ability to form fibrillar aggregates with β sheet structure play an important role in several degenerative diseases, including Parkinson’s disease. Numerous amyloidogenic proteins, such as α synuclein, are intrinsically disordered (or contain ID regions, hence they also present as highly dynamic conformational ensembles in these regions. Aggregation is an inherent property of the polypeptide chains and under non physiological, appropriate conditions most of the proteins can aggregate and form polymers of various structures. Since amyloid fib ril s and oligomers are associated with a great variety of human diseases, inhibition of protein aggregation has great importance and it can be addressed by using small molecules, peptides or proteins. Our research aim was to study the potential application of modified forms of different amyloidogenic proteins as inhibitor molecules by introducing structural constraints in them. Under various conditions, different amyloidogenic proteins’ (α-synuclein and β2-microglobulin) monomer molecules have been cross linked intramolecularly and the heterogeneous mixtures has been fractionated by HPLC. The inhibitory potential of the isolated and effective molecules has been experimentally investigated by various methods ThT assay, TEM, CD spectroscopy). Furthermore, the locations of the crosslinks in the molecules were determined by mass spectrometry, and their structures are modeled in silico. Our results revealed that conformational constrains applied by cross linking on amyloidogenic proteins block their amyloid formation. Moreover, these molecules exhibited inhibitory effect on the aggregation of the unmodified proteins, as well.

2023-10-24 | PXD042501 | Pride

LC-MS characterization of anti-PD-L1 and CXCR4 bispecific nanobodies

Project description:Antibodies and derivative drugs targeting immune checkpoints have been approved for the treatment of several malignancies, but there are fewer responses in patients with pancreatic cancer. Here, we designed a nanobody molecule with bi-targeting on PD-L1 and CXCR4, as both targets are overexpressed in many cancer cells and play important roles in tumorigenesis. The nanobody sequences targeting PD-L1 and CXCR4 were linked by the (G4S)3 flexible peptide to construct the anti-PD-L1/CXCR4 bispecific nanobody. The bispecific nanobody was expressed in E. coli cells and purified by affinity chromatography. The purified nanobody was biochemically characterized by mass spectrometry, Western blotting and flow cytometry to confirm the molecule and its association with both PD-L1 and CXCR4. The biological function of the nanobody and its anti-tumour effects were examined.

2023-03-11 | PXD037102 | Pride

Profiling the proteome of Mycobacterium tuberculosis during dormancy and reactivation

Project description:Tuberculosis, caused by Mycobacterium tuberculosis, still remains a major global health problem. The main obstacle in eradicating this disease is the ability of this pathogen to remain dormant in macrophages, and to get reactivated later under immuno-compromised conditions. The physiology of hypoxic nonreplicating M. tuberculosis is well studied using many in vitro dormancy models. However, the physiological changes that take place during the shift from dormancy to aerobic growth (reactivation) have rarely been subjected to a detailed investigation. In this study, we developed an in vitro reactivation system by re-aerating bacteria that were made dormant employing Wayne’s dormancy model, and compared the proteome profiles of dormant and reactivated bacteria using label-free one-dimensional LC/MS/MS analysis.

2015-06-01 | PXD001158 | Pride

2DE images and LC-MS/MS of smooth and rough strains of Salmonella Gallinarum

Project description:Antigens of SG002, field isolated Salmonella Gallinarum in Korea, were tested against antiserum of SG002 and SR2-N6 (rough mutant of SG002) using 2DE western blotting. Different blots obtained were analyzed using LC-MS/MS. Outer membrane protein extracts of SR2-N6 were also tested against the antiserum of SR2-N6 using 2DE western blotting. Spots were analyzed with LC-MS/MS.

2020-10-20 | PXD022024 | Pride

Human follicular fluid neurotransmitters LC-MSMS

Project description:Pretreated human follicular fluid was prepared for targeted metabolomics experiments. For this purpose, 12-point standard calibration curves in the respective range with reference material were measured, and the limit of detection (LOD) and limit of quantification (LOQ) for each neurotransmitter under investigation were calculated. LC-MS/MS was conducted by an ultra-performance liquid chromatography method using a Waters ACQUITY UPLC BEH C18 column (2.1 mm×100 mm, 1.7 µm, Waters, USA). The Waters acquisition UPLC was coupled to an API 4000 triple quadrupole mass spectrometer (AB SCIEX, USA). The mobile phase A buffer was 10% methanol in water (containing 0.1% formic acid), and the mobile phase B buffer was 50% methanol in water (containing 0.1% formic acid). The LC gradient elution was at a flow rate of 0.3 mL/min at 0-8.0 min and 0.4 ml/min at 8.0-17.5 min, then 10%-30% B at 0-6.5 min; 30%-100% B at 6.5-7 min; 100% B at 7-14min; and 100%-10% B at 14-17.5min. The injection volume was 5 µl and the column temperature was set to 40 °C. Twenty-three metabolites (Ach: Acetylcholine chloride; Gln: Glutamine; Glu: Glutamate; His: L-Histidine; NE: norepinephrine; Tyr:Tyrosine; Trp:Tryptophan; Kyn: Kynurenine; GABA: 4-Aminobutyric acid;HisA:Histamine; PA:Picolinic acid;TyrA:Tyramine;DA:Hydroxytyramine hydrochloride; TrpA:Tryptamine;5-HT:Serotonin hydrochloride;E:Adrenaline hydrochloride;KynA:Kynurenic acid;5-HIAA:5-Hydroxyindole-3-acetic acid;DOPA:Levodopa;XA:Xanthurenic acid;VWA:Vanillymandelic Acid; 5-HTTP:5-Hydroxytryptophan;MT:Melatonine)were simultaneously reported in LC-MS/MS multiple reaction monitoring (MRM) mode. Data analysis was performed with Analyst 1.6 software.

2022-08-12 | PXD031560 | Pride

HDX-MS data of trigger factor and GAPDH binding

Project description:We present HDX-MS data of the trigger factor:GAPDH complex to define the interaction sites for GAPDH on trigger factor and the structure of GAPDH in the bound state.

2022-06-07 | PXD029364 | Pride

Pervasive cis-antisense transcription negatively regulates gene expression in E. coli K12 in response to environmental changes

Project description:cis-antisense RNAs (cis-asRNAs) in prokaryotes are more pervasive than originally thought. However, little is known about their expression patterns and functions. Here we determined transcriptomes and proteomes of E. coli at multiple time points in five culture conditions using directional RNA-seq and tandem mass spectrometry. We found that a highly varying portion (27.2%~90.8%) of transcribed genes had cis-asRNAs dependent on growth phases and culture conditions, and that almost all transcribed genes changed their cis-asRNA levels relative to the mRNA level at different growth phases and culture conditions. Intriguingly, the correlation between the protein and mRNA levels of genes is abolished the increasing cis-asRNA levels relative to the mRNA levels, suggesting that cis-asRNAs might directly or indirectly inhibit translation by forming duplexes with mRNAs. All data sets are available for data mining from a unified resource to support further biological discoveries and insights into cis-asRNA-mediated gene expressional regulation.

2022-02-28 | PXD001640 | Pride