Abstract: The worldwide prevalence of H3N2 influenza virus
and its increasing resistance to the existing drugs necessitates for the
development of an improved/better targeting anti-influenza drug.
H3N2 influenza neuraminidase is one of the two membrane-bound
proteins belonging to group-2 neuraminidases. It acts as key player
involved in viral pathogenicity and hence, is an important target of
anti-influenza drugs. Oseltamivir is one of the potent drugs targeting
this neuraminidase. In the present work, we have taken subtype N2
neuraminidase as the receptor and probable analogs of oseltamivir as
drug molecules to study the protein-drug interaction in anticipation of
finding efficient modified candidate compound. Oseltamivir analogs
were made by modifying the functional groups using Marvin Sketch
software and were docked using Schrodinger-s Glide. Oseltamivir
analog 10 was detected to have significant energy value (16% less
compared to Oseltamivir) and could be the probable lead molecule. It
infers that some of the modified compounds can interact in a novel
manner with increased hydrogen bonding at the active site of
neuraminidase and it might be better than the original drug. Further
work can be carried out such as enzymatic inhibition studies;
synthesis and crystallizing the drug-target complex to analyze the
interactions biologically.
Abstract: The present study has been conducted to characterize
the prophenoloxidase (PPO) system of the desert locust, Schistocerca
gregaria following injection of Bacillus thuringiensis kurstaki (Bt).
The bulk of PPO system was associated with haemocytes and a little
amount was found in plasma. This system was activated by different
activators such as laminarin, lipopolysaccharide (LPS) and trypsin
suggesting that the stimulatory mechanism may involve an enzyme
cascade of one or more associated molecules. These activators did
not activate all the molecules of the cascade. Presence of
phenoloxidase activity (PO) coincides with the appearance of protein
band with molecular weight (MW) 70.154 KD (Kilo Dalton).
Abstract: Recent studies demonstrated that high-fat diet increases oxidative stress in plasma and in a variety of tissues. Many researchers have been looking for natural products, which can reverse the effect of high fat diet. Recently, buckwheat is becoming common ingredient in functional food because of it properties. In study on buckwheat, it is known that, this plant plays roles as anti-oxidative, anti-inflammatory and anti-hypertensive. Nevertheless still little is known about buckwheat groats. The aim of this study was to investigate the effects of addition of buckwheat groats to the fat diet (30% lard), on some antioxidant and oxidant stress parameters in plasma and selected tissues in Wistar rats. The experiment was carried out with three months old male Wistar rats ca. 250g of body weight fed for 5 weeks with either a high-fat (30% of lard) diet or control diet, with or without addition of buckwheat groats. In plasma biochemistry and the activities of the antioxidant enzymes were measured selected tissues: glutathione peroxidase (GPX), catalase (CAT) and the levels of total and reduced glutathione (GSH), free thiol groups (pSH), antioxidant potential of plasma (FRAP) and oxidant stress indices - proteins carbonyl groups (CO) and malonyldialdehyde concentration (MDA). Activity of catalase (CAT) in plasma of rats was significantly increased in buckwheat groats groups and activity of GPx3 in plasma of rats was decreased in buckwheat groups as compared to control group. The reduced glutathione (GSH) in plasma of rats was significantly increased and protein CO was significantly decreased in buckwheat groups as compared to controls. The lowered concentration of GSH was found in serum of rats fed buckwheat groats addition but it accompanied in 7-fold increase in reduced-to-oxidized glutatione ratio, significant increase in HDL and decrease in nonHDL concentration. Conclusions: Buckwheat groats indicate a beneficial effect in inhibiting protein and lipid peroxidation in rats and improved lipid profile. These results suggest that buckwheat groats exert a significant antioxidant potential and may be used as normal food constituent to ameliorate the oxidant-induced damage in organism.
Abstract: Tumor cells have an invasive and metastatic phenotype
that is the main cause of death for cancer patients. Tumor
establishment and penetration consists of a series of complex
processes involving multiple changes in gene expression. In this study,
intraperitoneal administration of a high concentration of ascorbic acid
inhibited tumor establishment and decreased tumor mass in BALB/C
mice implanted with S-180 sarcoma cancer cells. To identify proteins
involved in the ascorbic acid-mediated inhibition of tumor
progression, changes in the tumor proteome associated with ascorbic
acid treatment of BALB/C mice implanted with S-180 were
investigated using two-dimensional gel electrophoresis and mass
spectrometry. Twenty protein spots were identified whose expression
was different between control and ascorbic acid treatment groups.
Abstract: Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.
Abstract: This research studied the simulation of increased
ambient ozone to estimate nutrient content and genetic changes in
two Thai soybean cultivars (Chiang Mai 60 and Srisumrong 1).
Ozone stress conditions affected proteins and lipids. It was found
that proteins decreased, but lipids increased. Srisumrong 1 cultivars
were more sensitive to ozone stress than Chiang Mai 60 cultivars.
The effect of ozone stress conditions on plant phenotype and
genotype was analyzed using the AFLP technique for the 2 Thai
soybean cultivars (Chiang Mai 60 and Srisumrong 1).
Abstract: There is strong evidence that water channel proteins
'aquaporins (AQPs)' are central components in plant-water relations
as well as a number of other physiological parameters. We had
previously reported the isolation of 24 plasma membrane intrinsic
protein (PIP) type AQPs. However, the gene numbers in rice and the
polyploid nature of bread wheat indicated a high probability of
further genes in the latter. The present work focused on identification
of further AQP isoforms in bread wheat. With the use of altered
primer design, we identified five genes homologous, designated
PIP1;5b, PIP2;9b, TaPIP2;2, TaPIP2;2a, TaPIP2;2b. Sequence
alignments indicate PIP1;5b, PIP2;9b are likely to be homeologues of
two previously reported genes while the other three are new genes
and could be homeologs of each other. The results indicate further
AQP diversity in wheat and the sequence data will enable physical
mapping of these genes to identify their genomes as well as genetic to
determine their association with any quantitative trait loci (QTLs)
associated with plant-water relation such as salinity or drought
tolerance.
Abstract: Protein subchloroplast locations are correlated with its
functions. In contrast to the large amount of available protein
sequences, the information of their locations and functions is less
known. The experiment works for identification of protein locations
and functions are costly and time consuming. The accurate prediction
of protein subchloroplast locations can accelerate the study of
functions of proteins in chloroplast. This study proposes a Random
Forest based method, ChloroRF, to predict protein subchloroplast
locations using interpretable physicochemical properties. In addition
to high prediction accuracy, the ChloroRF is able to select important
physicochemical properties. The important physicochemical
properties are also analyzed to provide insights into the underlying
mechanism.
Abstract: Nonspecific protein adsorption generally occurs on
any solid surfaces and usually has adverse consequences. Adsorption
of proteins onto a solid surface is believed to be the initial and
controlling step in biofouling. Surfaces modified with end-tethered
poly(ethylene glycol) (PEG) have been shown to be protein-resistant
to some degree. In this study, the adsorption of β-casein and
lysozyme was performed on 6 different types of surfaces where PEG
was tethered onto stainless steel by polyethylene imine (PEI) through
either OH or NHS end groups. Protein adsorption was also performed
on the bare stainless steel surface as a control. The adsorption was
conducted at 23 °C and pH 7.2. In situ QCM-D was used to
determine PEG adsorption kinetics, plateau PEG chain densities,
protein adsorption kinetics and plateau protein adsorbed quantities.
PEG grafting density was the highest for a NHS coupled chain,
around 0.5 chains / nm2. Interestingly, lysozyme which has smaller
size than β-casein, appeared to adsorb much less mass than that of β-
casein. Overall, the surface with high PEG grafting density exhibited
a good protein rejection.
Abstract: The Egyptian Bacillus thuringiensis isolate (M5) produce crystal proteins that is toxic against insects was irradiated with UV light to induce mutants. Upon testing 10 of the resulting mutants for their toxicity against cotton leafworm larvae, the three mutants 62, 64 and 85 proved to be the most toxic ones. Upon testing these mutants along with their parental isolate by SDS-PAGE analysis of spores-crystals proteins as well as vegetative cells proteins, new induced bands appeared in the three mutants by UV radiation and also they showed disappearance of some other bands as compared with the wild type isolate. Multiplex PCR technique, with five sets of specific primers, was used to detect the three types of cryI genes cryIAa, cryIAb and cryIAc. Results showed that these three genes exist, as distinctive bands, in the wild type isolate (M5) as well as in mutants 62 and 85, while the mutant 64 had two distinctive bands of cryIAb and cryIAc genes, and a faint band of cryI Aa gene. Finally, these results revealed that mutant 62 is considered as the promising mutant since it is UV resistant, highly toxic against Spodoptera littoralis and active against a wide range of Lepidopteran insects.
Abstract: The prediction of transmembrane helical segments
(TMHs) in membrane proteins is an important field in the
bioinformatics research. In this paper, a method based on discrete
wavelet transform (DWT) has been developed to predict the number
and location of TMHs in membrane proteins. PDB coded as 1F88 was
chosen as an example to describe the prediction of the number and
location of TMHs in membrane proteins by using this method. One
group of test data sets that contain total 19 protein sequences was
utilized to access the effect of this method. Compared with the
prediction results of DAS, PRED-TMR2, SOSUI, HMMTOP2.0 and
TMHMM2.0, the obtained results indicate that the presented method
has higher prediction accuracy.
Abstract: The whole-cell protein-profiling technique was
evaluated for studying differences in banding pattern of three
different species of Cyanobacteria i.e. Anabaena fertilissima,
Aulosira fertilissima and Westiellopsis prolifica under the influence
of four different pesticides-2,4-D (Ethyl Ester of 2,4-Dichloro
Phenoxy Acetic Acid), Pencycuron (N-[(4-chlorophenyl)methyl]-Ncyclopentyl-
N'–phenylurea), Endosulfan (6,7,8,9,10,10hexachloro-
1,5,5a,6,9,9a-hexahydro-6,9-methano-2,4,3-benzodioxathiepine-3-
oxide) and Tebuconazole (1-(4-Chlorophenyl)-4,4-dimethyl-3-(1,2,4-
triazol-1-ylmethyl)pentan-3-ol). Whole-cell extracts were obtained by
sonication treatment (Sonifier cell disruptor -Branson Digital Sonifier
S-450D, USA) and were analyzed by sodium dodecyl sulfate
polyacrylamide gel electrophoresis (SDS-PAGE). SDS-PAGE
analyses of the total protein profile of Anabaena fertilissima,
Aulosira fertilissima and Westiellopsis prolifica showed a linear
decrease in the protein content with increasing pesticide stress when
administered to different concentrations of 2, 4-D, Pencycuron,
Endosulfan and Tebuconazole. The results indicate that different
stressors exert specific effects on cyanobacterial protein synthesis.
Abstract: Atherosclerosis was identified as a chronic inflammatory process resulting from interactions between plasma lipoproteins, cellular components (monocyte, macrophages, T lymphocytes, endothelial cells and smooth muscle cells) and the extracellular matrix of the arterial wall. Several types of genes were known to express during formation of atherosclerosis. This study is carried out to identify unknown differentially expressed gene (DEG) in atherogenesis. Rabbit’s aorta tissues were stained by H&E for histomorphology. GeneFishing™ PCR analysis was performed from total RNA extracted from the aorta tissues. The DNA fragment from DEG was cloned, sequenced and validated by Real-time PCR. Histomorphology showed intimal thickening in the aorta. DEG detected from ACP-41 was identified as cathepsin B gene and showed upregulation at week-8 and week-12 of atherogenesis. Therefore, ACP-based GeneFishing™ PCR facilitated identification of cathepsin B gene which was differentially expressed during development of atherosclerosis.
Abstract: The influence of flakes from biologically activated
hull-less barley grain and malt extract on chemical composition of
yoghurt was studied.
Pasteurized milk, freeze-dried yoghurt culture YF-L811 (Chr.
Hansen, Denmark), flakes from biologically activated hull-less
barley grain (Latvia) and malt extract (Ilgezeem, Latvia) were used
for experiments. Yoghurt samples with and without flakes from
biologically activated hull-less barley grain and malt extract were
analyzed for content of total solids, total proteins, fats, amino acids
and riboflavin.
The addition of flakes from biologically activated hull-less barley
grain and malt extract allowed increase of nutritional value of
yoghurt samples. There was obtained the increase of total proteins
(p>0.05) and the decrease of fat (p>0.05). The presence of flakes
from biologically activated hull-less barley grain and malt extract in
yoghurt samples provided significant increase of amino acids amount
(p
Abstract: This paper describes a novel approach for deriving
modules from protein-protein interaction networks, which combines
functional information with topological properties of the network.
This approach is based on weighted clustering coefficient, which
uses weights representing the functional similarities between the
proteins. These weights are calculated according to the semantic
similarity between the proteins, which is based on their Gene
Ontology terms. We recently proposed an algorithm for identification
of functional modules, called SWEMODE (Semantic WEights for
MODule Elucidation), that identifies dense sub-graphs containing
functionally similar proteins. The rational underlying this approach is
that each module can be reduced to a set of triangles (protein triplets
connected to each other). Here, we propose considering semantic
similarity weights of all triangle-forming edges between proteins. We
also apply varying semantic similarity thresholds between
neighbours of each node that are not neighbours to each other (and
hereby do not form a triangle), to derive new potential triangles to
include in module-defining procedure. The results show an
improvement of pure topological approach, in terms of number of
predicted modules that match known complexes.
Abstract: We report a novel fusion tag for expressing
recombinant proteins in E. coli. The fusion tag is the C-terminus part
of the human GMCSF gene comprising 45 amino acids, which aid in
over expression of otherwise non expressible genes. Expression of
hIFN a2b with this fusion tag also escapes the requirement of rare
codons for expression. This is also a first report of a small fusion tag
of human origin having affinity to heparin sepharose column
facilitating the purification of fusion protein.
Abstract: The prediction of transmembrane helical segments
(TMHs) in membrane proteins is an important field in the
bioinformatics research. In this paper, a new method based on discrete
wavelet transform (DWT) has been developed to predict the number
and location of TMHs in membrane proteins. PDB coded as 1KQG
was chosen as an example to describe the prediction of the number and
location of TMHs in membrane proteins by using this method. To
access the effect of the method, 80 proteins with known 3D-structure
from Mptopo database are chosen at random as the test objects
(including 325 TMHs), 308 of which can be predicted accurately, the
average predicted accuracy is 96.3%. In addition, the above 80
membrane proteins are divided into 13 groups according to their
function and type. In particular, the results of the prediction of TMHs
of the 13 groups are satisfying.
Abstract: Complex assemblies of interacting proteins carry out
most of the interesting jobs in a cell, such as metabolism, DNA
synthesis, mitosis and cell division. These physiological properties
play out as a subtle molecular dance, choreographed by underlying
regulatory networks that control the activities of cyclin-dependent
kinases (CDK). The network can be modeled by a set of nonlinear
differential equations and its behavior predicted by numerical
simulation. In this paper, an innovative approach has been proposed
that uses genetic algorithms to mine a set of behavior data output by
a biological system in order to determine the kinetic parameters of
the system. In our approach, the machine learning method is
integrated with the framework of existent biological information in a
wiring diagram so that its findings are expressed in a form of system
dynamic behavior. By numerical simulations it has been illustrated
that the model is consistent with experiments and successfully shown
that such application of genetic algorithms will highly improve the
performance of mathematical model of the cell division cycle to
simulate such a complicated bio-system.
Abstract: In vitro gastro-duodenal digestion model was used to investigate the changes of emulsions under digestion conditions. Oil in water emulsions stabilized by whey proteins (2%) and stabilized by whey proteins (2%) with addition of carboxymethyl cellulose (0.75%) as gelling agent of continuous phase were prepared at pH7. Both emulsions were destabilized under gastric conditions; however the protective role of carboxymethyl cellulose was indicated by recording delay of fat digestibility of this emulsion. In the presence of carboxymethyl cellulose whey proteins on the interfacial surface of droplets were more resistant to gastric degradation causing limited hydrolysis of fat due to the poor acceptability of lipids for the enzymes. Studies of emulsions using in vivo model supported results from in vitro studies. Lower content of triglycerides in blood serum and higher amount of fecal fat of rats were determined when rats were fed by diet containing emulsion made with whey proteins and carboxymethyl cellulose.
Abstract: The classification of the protein structure is commonly
not performed for the whole protein but for structural domains, i.e.,
compact functional units preserved during evolution. Hence, a first
step to a protein structure classification is the separation of the
protein into its domains. We approach the problem of protein domain
identification by proposing a novel graph theoretical algorithm. We
represent the protein structure as an undirected, unweighted and
unlabeled graph which nodes correspond the secondary structure
elements of the protein. This graph is call the protein graph. The
domains are then identified as partitions of the graph corresponding
to vertices sets obtained by the maximization of an objective function,
which mutually maximizes the cycle distributions found in the
partitions of the graph. Our algorithm does not utilize any other kind
of information besides the cycle-distribution to find the partitions. If
a partition is found, the algorithm is iteratively applied to each of
the resulting subgraphs. As stop criterion, we calculate numerically
a significance level which indicates the stability of the predicted
partition against a random rewiring of the protein graph. Hence,
our algorithm terminates automatically its iterative application. We
present results for one and two domain proteins and compare our
results with the manually assigned domains by the SCOP database
and differences are discussed.