11 research outputs found
New Interface for Purification of Proteins: One-Dimensional TiO<sub>2</sub> Nanotubes Decorated by Fe<sub>3</sub>O<sub>4</sub> Nanoparticles
In this work, a high
surface area interface, based on anodic one-dimensional (1D) TiO<sub>2</sub> nanotubes homogeneously decorated by Fe<sub>3</sub>O<sub>4</sub> nanoparticles (TiO<sub>2</sub>NTs@Fe<sub>3</sub>O<sub>4</sub>NPs) is reported for the first time for an unprecedented purification
of His-tagged recombinant proteins. Excellent purification results
were achieved from the model protein mixture, as well as from the
whole cell lysate (with His-tagged ubiquitin). Compared to a conventional
immobilized-metal affinity chromatography (IMAC) system, specific
isolation of selected His-tagged proteins on behalf of other proteins
was significantly enhanced on TiO<sub>2</sub>NTs@Fe<sub>3</sub>O<sub>4</sub>NPs interface under optimized binding and elution conditions.
The combination of specific isolation properties, magnetic features,
biocompatibility, and ease of preparation of this material consisting
of two basic metal oxides makes it a suitable candidate for future
purification of recombinant proteins in biotechnology. The principally
new material bears a large potential to open new pathways for discoveries
in nanobiotechnology and nanomedicine
Application of SILAC Labeling to Primary Bone Marrow-Derived Dendritic Cells Reveals Extensive GM-CSF-Dependent Arginine Metabolism
Although dendritic cells (DCs) control
the priming of the adaptive
immunity response, a comprehensive description of their behavior at
the protein level is missing. The introduction of the quantitative
proteomic technique of metabolic labeling (SILAC) into the field of
DC research would therefore be highly beneficial. To achieve this,
we applied SILAC labeling to primary bone marow-derived DCs (BMDCs).
These cells combine both biological relevance and experimental feasibility,
as their in vitro generation permits the use of <sup>13</sup>C/<sup>15</sup>N-labeled amino acids. Interestingly, BMDCs appear to exhibit
a very active arginine metabolism. Using standard cultivation conditions,
∼20% of all protein-incorporated proline was a byproduct of
heavy arginine degradation. In addition, the dissipation of <sup>15</sup>N from labeled arginine to the whole proteome was observed. The latter
decreased the mass accuracy in MS and affected the natural isotopic
distribution of peptides. SILAC-connected metabolic issues were shown
to be enhanced by GM-CSF, which is used for the differentiation of
DC progenitors. Modifications of the cultivation procedure suppressed
the arginine-related effects, yielding cells with a proteome labeling
efficiency of ≥90%. Importantly, BMDCs generated according
to the new cultivation protocol preserved their resemblance to inflammatory
DCs in vivo, as evidenced by their response to LPS treatment
Phlomis crinita
An example of bacterium, which undergoes a complex development,
is the genus of <i>Streptomyces</i> whose importance lies
in their wide capacity to produce secondary metabolites, including
antibiotics. In this work, a proteomic approach was applied to the
systems study of germination as a transition from dormancy to the
metabolically active stage. The protein expression levels were examined
throughout the germination time course, the kinetics of the accumulated
and newly synthesized proteins were clustered, and proteins detected
in each group were identified. Altogether, 104 2DE gel images at 13
time points, from dormant state until 5.5 h of growth, were analyzed.
The mass spectrometry identified proteins were separated into functional
groups and their potential roles during germination were further assessed.
The results showed that the full competence of spores to effectively
undergo active metabolism is derived from the sporulation step, which
facilitates the rapid initiation of global protein expression during
the first 10 min of cultivation. Within the first hour, the majority
of proteins were synthesized. From this stage, the full capability
of regulatory mechanisms to respond to environmental cues is presumed.
The obtained results might also provide a data source for further
investigations of the process of germination
Systems Insight into the Spore Germination of <i>Streptomyces coelicolor</i>
An example of bacterium, which undergoes a complex development,
is the genus of <i>Streptomyces</i> whose importance lies
in their wide capacity to produce secondary metabolites, including
antibiotics. In this work, a proteomic approach was applied to the
systems study of germination as a transition from dormancy to the
metabolically active stage. The protein expression levels were examined
throughout the germination time course, the kinetics of the accumulated
and newly synthesized proteins were clustered, and proteins detected
in each group were identified. Altogether, 104 2DE gel images at 13
time points, from dormant state until 5.5 h of growth, were analyzed.
The mass spectrometry identified proteins were separated into functional
groups and their potential roles during germination were further assessed.
The results showed that the full competence of spores to effectively
undergo active metabolism is derived from the sporulation step, which
facilitates the rapid initiation of global protein expression during
the first 10 min of cultivation. Within the first hour, the majority
of proteins were synthesized. From this stage, the full capability
of regulatory mechanisms to respond to environmental cues is presumed.
The obtained results might also provide a data source for further
investigations of the process of germination
Systems Insight into the Spore Germination of <i>Streptomyces coelicolor</i>
An example of bacterium, which undergoes a complex development,
is the genus of <i>Streptomyces</i> whose importance lies
in their wide capacity to produce secondary metabolites, including
antibiotics. In this work, a proteomic approach was applied to the
systems study of germination as a transition from dormancy to the
metabolically active stage. The protein expression levels were examined
throughout the germination time course, the kinetics of the accumulated
and newly synthesized proteins were clustered, and proteins detected
in each group were identified. Altogether, 104 2DE gel images at 13
time points, from dormant state until 5.5 h of growth, were analyzed.
The mass spectrometry identified proteins were separated into functional
groups and their potential roles during germination were further assessed.
The results showed that the full competence of spores to effectively
undergo active metabolism is derived from the sporulation step, which
facilitates the rapid initiation of global protein expression during
the first 10 min of cultivation. Within the first hour, the majority
of proteins were synthesized. From this stage, the full capability
of regulatory mechanisms to respond to environmental cues is presumed.
The obtained results might also provide a data source for further
investigations of the process of germination
Systems Insight into the Spore Germination of <i>Streptomyces coelicolor</i>
An example of bacterium, which undergoes a complex development,
is the genus of <i>Streptomyces</i> whose importance lies
in their wide capacity to produce secondary metabolites, including
antibiotics. In this work, a proteomic approach was applied to the
systems study of germination as a transition from dormancy to the
metabolically active stage. The protein expression levels were examined
throughout the germination time course, the kinetics of the accumulated
and newly synthesized proteins were clustered, and proteins detected
in each group were identified. Altogether, 104 2DE gel images at 13
time points, from dormant state until 5.5 h of growth, were analyzed.
The mass spectrometry identified proteins were separated into functional
groups and their potential roles during germination were further assessed.
The results showed that the full competence of spores to effectively
undergo active metabolism is derived from the sporulation step, which
facilitates the rapid initiation of global protein expression during
the first 10 min of cultivation. Within the first hour, the majority
of proteins were synthesized. From this stage, the full capability
of regulatory mechanisms to respond to environmental cues is presumed.
The obtained results might also provide a data source for further
investigations of the process of germination
Proteomic Profiling of Dilated Cardiomyopathy Plasma Samples Searching for Biomarkers with Potential to Predict the Outcome of Therapy
Determination of the prognosis and treatment outcomes
of dilated
cardiomyopathy is a serious problem due to the lack of valid specific
protein markers. Using in-depth proteome discovery analysis, we compared
49 plasma samples from patients suffering from dilated cardiomyopathy
with plasma samples from their healthy counterparts. In total, we
identified 97 proteins exhibiting statistically significant dysregulation
in diseased plasma samples. The functional enrichment analysis of
differentially expressed proteins uncovered dysregulation in biological
processes like inflammatory response, wound healing, complement cascade,
blood coagulation, and lipid metabolism in dilated cardiomyopathy
patients. The same proteome approach was employed in order to find
protein markers whose expression differs between the patients well-responding
to therapy and nonresponders. In this case, 45 plasma proteins revealed
statistically significant different expression between these two groups.
Of them, fructose-1,6-bisphosphate aldolase seems to be a promising
biomarker candidate because it accumulates in plasma samples obtained
from patients with insufficient treatment response and with worse
or fatal outcome. Data are available via ProteomeXchange with the
identifier PXD046288
Proteomic Profiling of Dilated Cardiomyopathy Plasma Samples Searching for Biomarkers with Potential to Predict the Outcome of Therapy
Determination of the prognosis and treatment outcomes
of dilated
cardiomyopathy is a serious problem due to the lack of valid specific
protein markers. Using in-depth proteome discovery analysis, we compared
49 plasma samples from patients suffering from dilated cardiomyopathy
with plasma samples from their healthy counterparts. In total, we
identified 97 proteins exhibiting statistically significant dysregulation
in diseased plasma samples. The functional enrichment analysis of
differentially expressed proteins uncovered dysregulation in biological
processes like inflammatory response, wound healing, complement cascade,
blood coagulation, and lipid metabolism in dilated cardiomyopathy
patients. The same proteome approach was employed in order to find
protein markers whose expression differs between the patients well-responding
to therapy and nonresponders. In this case, 45 plasma proteins revealed
statistically significant different expression between these two groups.
Of them, fructose-1,6-bisphosphate aldolase seems to be a promising
biomarker candidate because it accumulates in plasma samples obtained
from patients with insufficient treatment response and with worse
or fatal outcome. Data are available via ProteomeXchange with the
identifier PXD046288
Proteomic Profiling of Dilated Cardiomyopathy Plasma Samples Searching for Biomarkers with Potential to Predict the Outcome of Therapy
Determination of the prognosis and treatment outcomes
of dilated
cardiomyopathy is a serious problem due to the lack of valid specific
protein markers. Using in-depth proteome discovery analysis, we compared
49 plasma samples from patients suffering from dilated cardiomyopathy
with plasma samples from their healthy counterparts. In total, we
identified 97 proteins exhibiting statistically significant dysregulation
in diseased plasma samples. The functional enrichment analysis of
differentially expressed proteins uncovered dysregulation in biological
processes like inflammatory response, wound healing, complement cascade,
blood coagulation, and lipid metabolism in dilated cardiomyopathy
patients. The same proteome approach was employed in order to find
protein markers whose expression differs between the patients well-responding
to therapy and nonresponders. In this case, 45 plasma proteins revealed
statistically significant different expression between these two groups.
Of them, fructose-1,6-bisphosphate aldolase seems to be a promising
biomarker candidate because it accumulates in plasma samples obtained
from patients with insufficient treatment response and with worse
or fatal outcome. Data are available via ProteomeXchange with the
identifier PXD046288
Proteomic Profiling of Dilated Cardiomyopathy Plasma Samples Searching for Biomarkers with Potential to Predict the Outcome of Therapy
Determination of the prognosis and treatment outcomes
of dilated
cardiomyopathy is a serious problem due to the lack of valid specific
protein markers. Using in-depth proteome discovery analysis, we compared
49 plasma samples from patients suffering from dilated cardiomyopathy
with plasma samples from their healthy counterparts. In total, we
identified 97 proteins exhibiting statistically significant dysregulation
in diseased plasma samples. The functional enrichment analysis of
differentially expressed proteins uncovered dysregulation in biological
processes like inflammatory response, wound healing, complement cascade,
blood coagulation, and lipid metabolism in dilated cardiomyopathy
patients. The same proteome approach was employed in order to find
protein markers whose expression differs between the patients well-responding
to therapy and nonresponders. In this case, 45 plasma proteins revealed
statistically significant different expression between these two groups.
Of them, fructose-1,6-bisphosphate aldolase seems to be a promising
biomarker candidate because it accumulates in plasma samples obtained
from patients with insufficient treatment response and with worse
or fatal outcome. Data are available via ProteomeXchange with the
identifier PXD046288