مجال
التميز
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تميز دراسي وبحثي + جوائز تفوقية
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البحوث المنشورة
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البحث (1):
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عنوان البحث:
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Optimization of matrix assisted
desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS)for the
characterization of Bacillus and Brevibacillus species
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رابط إلى البحث:
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Click here
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تاريخ النشر:
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Accepted 19 June 2014
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موجز عن البحث:
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Over the past few decades there has been an
increased interest in using various analytical techniques for detecting and
identifying microorganisms. More recently there has been an explosion in the
application of matrix assisted laser desorption ionization time of flight
mass spectrometry (MALDI-TOF-MS) for bacterial characterization, and here we
optimize this approach in order to generate reproducible MS data from
bacteria belonging to the genera Bacillus and Brevibacillus. Unfortunately
MALDI-TOF-MS generates large amounts of data and is prone to instrumental
drift. To overcome these challenges we have developed a preprocessing
pipeline that includes baseline correction, peak alignment followed by peak
picking that in combination significantly reduces the dimensionality of the
MS spectra and corrects for instrument drift. Following this two different
prediction models were used which are based on support vector machines and
these generated satisfactory prediction accuracies of approximately 90%.
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البحث (2):
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عنوان البحث:
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Phenotypic Characterisation of Shewanella oneidensis MR-1
Exposed to X-Radiation
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رابط إلى البحث:
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Click here
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تاريخ النشر:
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22/06/2015
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موجز عن البحث:
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Biogeochemical processes mediated by Fe(III)-reducing bacteria
such as Shewanella oneidensis have the potential to influence the
post-closure evolution of a geological disposal facility for radioactive
wastes and to affect the solubility of some radionuclides. Furthermore, their
potential to reduce both Fe(III) and radionuclides can be harnessed for the
bioremediation of radionuclide-contaminated land. As some such sites are
likely to have significant radiation fluxes, there is a need to characterise
the impact of radiation stress on such microorganisms. There have, however,
been few global cell analyses on the impact of ionizing radiation on
subsurface bacteria, so here we address the metabolic response of S.
oneidensis MR-1 to acute doses of X-radiation. UV/Vis spectroscopy and CFU
counts showed that although X-radiation decreased initial viability and
extended the lag phase of batch cultures, final biomass yields remained
unchanged. FT-IR spectroscopy of whole cells indicated an increase in lipid
associated vibrations and decreases in vibrations tentatively assigned to
nucleic acids, phosphate, saccharides and amines. MALDI-TOF-MS detected an
increase in total protein expression in cultures exposed to 12 Gy. At 95 Gy,
a decrease in total protein levels was generally observed, although an
increase in a putative cold shock protein was observed, which may be related
to the radiation stress response of this organism. Multivariate statistical
analyses applied to these FT-IR and MALDI-TOF-MS spectral data suggested that
an irradiated phenotype developed throughout subsequent generations. This
study suggests that significant alteration to the metabolism of S. oneidensis
MR-1 is incurred as a result of X-irradiation and that dose dependent changes
to specific biomolecules characterise this response. Irradiated S. oneidensis
also displayed enhanced levels of poorly crystalline Fe(III) oxide reduction,
though the mechanism underpinning this phenomenon is unclear.
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البحث (3):
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عنوان البحث:
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Chicken,
beams, and Campylobacter: rapid differentiation of foodborne bacteria via
vibrational spectroscopy and MALDI-mass spectrometry
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رابط إلى البحث:
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Click here
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تاريخ النشر:
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07/01/2016
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موجز عن البحث:
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Campylobacter
species are one of the main causes of food poisoning worldwide. Despite the
availability of established culturing and molecular techniques, due to the
fastidious nature of these microorganisms, simultaneous detection and species
differentiation still remains challenging. This study focused on the
differentiation of eleven Campylobacter strains from six species, using
Fourier transform infrared (FT-IR) and Raman spectroscopies, together with
matrix-assisted laser desorption ionisation-time of flight-mass spectrometry
(MALDI-TOF-MS), as physicochemical approaches for generating biochemical
fingerprints. Cluster analysis of data from each of the three analytical
approaches provided clear differentiation of each Campylobacter species,
which was generally in agreement with a phylogenetic tree based on 16S rRNA
gene sequences. Notably, although C. fetus subspecies fetus and venerealis
are phylogenetically very closely related, using FT-IR and MALDI-TOF-MS data
these subspecies were readily differentiated based on differences in the
lipid (2920 and 2851 cm(-1)) and fingerprint regions (1500-500 cm(-1)) of the
FT-IR spectra, and the 500-2000 m/z region of the MALDI-TOF-MS data. A
finding that was further investigated with targeted lipidomics using liquid
chromatography-mass spectrometry (LC-MS). Our results demonstrate that such
metabolomics approaches combined with molecular biology techniques may
provide critical information and knowledge related to the risk factors,
virulence, and understanding of the distribution and transmission routes
associated with different strains of foodborne Campylobacter spp.
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البحث (4):
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عنوان البحث:
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Metabolic
Fingerprinting of Pseudomonas putida DOT-T1E Strains: Understanding the
Influence of Divalent Cations in Adaptation Mechanisms Following Exposure to
Toluene
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رابط إلى البحث:
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Click here
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تاريخ النشر:
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26/04/2016
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موجز عن البحث:
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Pseudomonas putida strains can adapt
and overcome the activity of toxic organic solvents by the employment of
several resistant mechanisms including efflux pumps and modification to
lipopolysaccharides (LPS) in their membranes. Divalent cations such as magnesium
and calcium play a crucial role in the development of solvent tolerance in
bacterial cells. Here, we have used Fourier transform infrared (FT-IR)
spectroscopy directly on cells (metabolic fingerprinting) to monitor
bacterial response to the absence and presence of toluene, along with the
influence of divalent cations present in the growth media. Multivariate
analysis of the data using principal component-discriminant function analysis
(PC-DFA) showed trends in scores plots, illustrating phenotypic alterations
related to the effect of Mg(2+), Ca(2+) and toluene on cultures. Inspection
of PC-DFA loadings plots revealed that several IR spectral regions including
lipids, proteins and polysaccharides contribute to the separation in PC-DFA
space, thereby indicating large phenotypic response to toluene and these
cations. Finally, the saturated fatty acid ratio from the FT-IR spectra
showed that upon toluene exposure, the saturated fatty acid ratio was
reduced, while it increased in the presence of divalent cations. This study
clearly demonstrates that the combination of metabolic fingerprinting with
appropriate chemometric analysis can result in practicable knowledge on the
responses of important environmental bacteria to external stress from
pollutants such as highly toxic organic solvents, and indicates that these
changes are manifest in the bacterial cell membrane. Finally, we demonstrate
that divalent cations improve solvent tolerance in P. putida DOT‑T1E strains.
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البحث (5):
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عنوان البحث:
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Fractional
Factorial Design of MALDI-TOF-MS Sample Preparations for the Optimized
Detection of Phospholipids and Acylglycerols
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رابط إلى البحث:
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Click here
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تاريخ النشر:
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26/05/2016
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موجز عن البحث:
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Matrix-assisted laser desorption
ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has successfully
been used for the analysis of high molecular weight compounds, such as
proteins and nucleic acids. By contrast, analysis of low molecular weight
compounds with this technique has been less successful due to interference
from matrix peaks which have a similar mass to the target analyte(s).
Recently, a variety of modified matrices and matrix additives have been used
to overcome these limitations. An increased interest in lipid analysis arose
from the feasibility of correlating these components with many diseases, e.g.
atherosclerosis and metabolic dysfunctions. Lipids have a wide range of
chemical properties making their analysis difficult with traditional methods.
MALDI-TOF-MS shows excellent potential for sensitive and rapid analysis of
lipids, and therefore this study focuses on computational-analytical
optimization of the analysis of five lipids (4 phospholipids and 1
acylglycerol) in complex mixtures using MALDI-TOF-MS with fractional
factorial design (FFD) and Pareto optimality. Five different experimental
factors were investigated using FFD which reduced the number of experiments
performed by identifying 720 key experiments from a total of 8064 possible
analyses. Factors investigated included the following: matrices, matrix
preparations, matrix additives, additive concentrations, and deposition
methods. This led to a significant reduction in time and cost of sample
analysis with near optimal conditions. We discovered that the key factors
used to produce high quality spectra were the matrix and use of appropriate
matrix additives.
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البحث (6):
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عنوان البحث:
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Metabolic
analysis of the response of Pseudomonas putida DOT-T1E strains to toluene
using Fourier transform infrared spectroscopy and gas chromatography mass
spectrometry
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رابط إلى البحث:
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Click here
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تاريخ النشر:
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21/06/2016
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موجز عن البحث:
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An
exceptionally interesting stress response of Pseudomonas putida strains to
toxic substances is the induction of efflux pumps that remove toxic chemical
substances from the bacterial cell out to the external environment. To
exploit these microorganisms to their full potential a deeper understanding of
the interactions between the bacteria and organic solvents is required. Thus,
this study focuses on investigation of metabolic changes in P. putida upon
exposure to toluene
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البحث (7):
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عنوان البحث:
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Metabolomics Analysis Reveals the Participation of Efflux Pumps
and Ornithine in the Response of Pseudomonas putida DOT-T1E Cells to
Challenge with Propranolol
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رابط إلى البحث:
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Click here
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تاريخ النشر:
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22/06/2016
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موجز عن البحث:
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Efflux
pumps are critically important membrane components that play a crucial role
in strain tolerance in Pseudomonas putida to antibiotics and aromatic
hydrocarbons that result in these toxicants being expelled from the bacteria.
Here, the effect of propranolol on P. putida was examined by sudden addition
of 0.2, 0.4 and 0.6 mg mL-1 of this β-blocker to several strains of P.
putida, including the wild type DOT-T1E and the efflux pump knockout mutants
DOT-T1E-PS28 and DOT-T1E-18. Bacterial viability measurements reveal that the
efflux pump TtgABC plays a more important role than the TtgGHI pump in strain
tolerance to propranolol. Mid-infrared (MIR) spectroscopy was then used as a
rapid, high-throughput screening tool to investigate any phenotypic changes resulting
from exposure to varying levels of propranolol. Multivariate statistical
analysis of these MIR data revealed gradient trends in resultant ordination
scores plots, which were related to the concentration of propranolol. MIR
illustrated phenotypic changes associated with the presence of this drug
within the cell that could be assigned to significant changes that occurred
within the bacterial protein components. To complement this phenotypic
fingerprinting approach metabolic profiling was performed using gas
chromatography mass spectrometry (GC-MS) to identify metabolites of interest
during the growth of bacteria following toxic perturbation with the same
concentration levels of propranolol. Metabolic profiling revealed that
ornithine, which was only produced by P. putida cells in the presence of
propranolol, presents itself as a major metabolic feature that has important
functions in propranolol stress tolerance mechanisms within this highly
significant and environmentally relevant species of bacteria.
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المؤتمرات العلمية:
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المؤتمر (1):
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عنوان المؤتمر:
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Saudi Student International Conference
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تاريخ الإنعقاد:
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1-2/02/2014
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مكان
الإنعقاد:
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Edinburgh, UK
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طبيعة المشاركة:
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Poster presentation
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عنوان المشاركة:
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Optimization of Matrix Assisted Desorption/Ionization
Time of Flight Mass Spectrometry (MALDI-TOF-MS) for Bacillus characterization
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ملخص المشاركة:
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Matrix assisted laser desorption/ionization
time of flight spectrometry MALDI-TOF-MS is a powerful, rapid and sensitive
tool used in the analysis and characterisation of protein for intact
bacteria. MALDI-TOF-MS data can be analysed using chemometrics to successfully
identify proteins observed in spectra obtained. This research project focused
on the identification of 34 bacteria strains from the Bacillus group using
MALDI-TOF-MS. The importance of studying this group of bacteria lies in its
ability to cause a variety of diseases such as anthrax and food poisoning.
This research project successfully demonstrated that reliable and accurate
identifications can be obtained at species levels of bacteria from the
Bacillus group using MALDI-TOF-MS. Sample preparation for MALDI-TOF-MS was
optimised to generate reproducible data. Using sinapinic acid (SA) as a
matrix and mixed method for sample preparation.
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المؤتمر (2):
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عنوان المؤتمر:
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The 8th Saudi Students’ Conference
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تاريخ الإنعقاد:
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31/01/2015
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مكان
الإنعقاد:
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London – UK
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طبيعة المشاركة:
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Poster Presentation
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عنوان المشاركة:
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Analysis Of a Lipid Mixture Using MALDI-TOF-MS and FFD
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ملخص المشاركة:
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An increased interest in lipid analysis arises from the ability
of correlating these components with many diseases such atherosclerosis and
metabolic dysfunctions. Lipids are known to have a wide range of chemical
properties making their analysis difficult. Tradition methods used are
labourious, time consuming and tedious. Nowadays, matrix assisted laser
desorption/ionization mass spectrometry (MALDI-TOF-MS) shows excellent,
powerful and rapid analysis in the field of lipidomics. In this research
study a five different lipids were mixed together at the same concentration,
followed by analysis using MALDI-TOF-MS. Moreover, different factors were
investigated. Fractional factorial design of experiments was used to reduce
the number of experiments from 7920 to 720. A combination of MALDI data and
chemometrics are needed to achieve robust results.
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المؤتمر (3):
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عنوان المؤتمر:
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Metabolic Profiling Forum
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تاريخ الإنعقاد:
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07/12/2015
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مكان
الإنعقاد:
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Cambridge – UK
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طبيعة المشاركة:
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Poster
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عنوان المشاركة:
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·
Optimization of Experimental Conditions for
the Detection of Lipid Mixtures using MALDI-TOF-MS and FFD
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ملخص المشاركة:
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An
increased interest in lipid analysis arises from the ability to correlate
these components with many diseases such atherosclerosis and metabolic
dysfunctions. Lipids are known to have a wide range of chemical properties
making their analysis difficult. Traditional methods used are laborious, time
consuming and tedious. Nowadays, matrix assisted laser desorption/ionization
mass spectrometry (MALDI-TOF-MS) shows excellent, powerful and rapid analysis
in the field of lipidomics. In this research study, five different lipids
were mixed together at the same concentration, followed by analysis using
MALDI-TOF-MS. Moreover, five different factors were investigated including:
matrices, matrix preparations, matrix additives, matrix additive
concentrations and deposition methods. Fractional factorial design (FFD) of
experiments was used to reduce the number of experiments from 7920 to 720. A
combination of MALDI data and chemometrics achieved robust results and helped
for rapid study design.
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جوائز التكريم:
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الجائزة (1):
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مسمى الجائزة:
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Certificate
of Participation & Prize Winner
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الجهة المانحة:
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Metabolic
Profiling Forum director
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تاريخ منح الجائزة:
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07/12/2015
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مجال التكريم:
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Prize
Winner for the poster entitled: “Optimization of Experimental Conditions for
the Detection of Lipid Mixtures using MALDI-TOF-MS and FFD” presented in the Metabolic Profiling
Forum
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الجائزة (2):
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مسمى الجائزة:
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First
prize for the presentation – PhD final year talks-
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الجهة المانحة:
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Manchester University. Institute of
Biotechnology School of Chemistry
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تاريخ منح الجائزة:
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05/06/2015
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مجال التكريم:
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The
student has been awarded first prize for her presentation at the PhD final
year talks in the School of Chemistry.
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الرابط:
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http://www.biospec.net/prize-for-najla/
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