Abstract: Globin superfamily proteins including myoglobin and
hemoglobin, have welcome new members recently, namely,
cytoglobin, neuroglobin and globin X, though their physiological
functions are still to be addressed. Fish are the excellent models for the
study of these globins, but their characteristics have not yet been
discussed to date. In the present study, attempts have been made to
characterize their structural uniqueness by making use of proteomics
approach. This is the first comparative study on the characterization of
globin superfamily proteins from fish.
Abstract: The paper is included within the framework of a
complex research program, which was initiated from the hypothesis
arguing on the existence of a correlation between pineal indolic and
peptide hormones and the somatic development rhythm, including
thus the epithalamium-epiphysis complex involvement. At birds,
pineal gland contains a circadian oscillator, playing a main role in the
temporal organization of the cerebral functions. The secretion of
pineal indolic hormones is characterized by a high endogenous
rhythmic alternation, modulated by the light/darkness (L/D)
succession and by temperature as well. The research has been carried
out using 100 chicken broilers - “Ross" commercial hybrid,
randomly allocated in two experimental batches: Lc batch, reared
under a 12L/12D lighting schedule and Lexp batch, which was photic
pinealectomised through continuous exposition to light (150 lux, 24
hours, 56 days). Chemical and physical features of the meat issued
from breast fillet and thighs muscles have been studied, determining
the dry matter, proteins, fat, collagen, salt content and pH value, as
well. Besides the variations of meat chemical composition in relation
with lighting schedule, other parameters have been studied: live
weight dynamics, feed intake and somatic development degree. The
achieved results became significant since chickens have 7 days of
age, some variations of the studied parameters being registered,
revealing that the pineal gland physiologic activity, in relation with
the lighting schedule, could be interpreted through the monitoring of
the somatic development technological parameters, usually studied
within the chicken broilers rearing aviculture practice.
Abstract: Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.
Abstract: Cluster analysis divides data into groups that are
meaningful, useful, or both. Analysis of biological data is creating a
new generation of epidemiologic, prognostic, diagnostic and
treatment modalities. Clustering of protein sequences is one of the
current research topics in the field of computer science. Linear
relation is valuable in rule discovery for a given data, such as if value
X goes up 1, value Y will go down 3", etc. The classical linear
regression models the linear relation of two sequences perfectly.
However, if we need to cluster a large repository of protein sequences
into groups where sequences have strong linear relationship with
each other, it is prohibitively expensive to compare sequences one by
one. In this paper, we propose a new technique named General
Regression Model Technique Clustering Algorithm (GRMTCA) to
benignly handle the problem of linear sequences clustering. GRMT
gives a measure, GR*, to tell the degree of linearity of multiple
sequences without having to compare each pair of them.
Abstract: Mushrooms are a group of fleshy macroscopic fungi.
They have been valued throughout the world as both edible and
medicine. They are highly nutritious with good amount of quality
proteins, vitamins and minerals. An edible mushroom, Calocybe
indica was selected to validate its nutritional and medicinal
properties. Since tissue damage in hyperglycemia has been related to
oxidative stress, we evaluated the enzymatic and non-enzymatic
antioxidant status in the serum, liver and kidney since they are the
target organs in diabetic complications. From the results, increased
oxidative stress and decreased antioxidants might be related to the
causation of diabetes mellitus. The treatment in the diabetic rats with
the Calocybe indica showed an increase in the antioxidant system
and decrease in the production of free radicals. The mushrooms
which contain antioxidant phytochemicals has potential free radical
scavenging capacity and hence can induce the antioxidant system in
the body significantly reduces the generated free radicals thereby
maintaining the normal levels of the antioxidants
Abstract: Supplementation of palm vitamin E has been reported
to prevent loss of bone density in ovariectomised female rats. The
mechanism by which palm vitamin E exerts these effects is still
unknown. We hypothesized that palm vitamin E may act by
preventing the protein expression changes. Two dimensional poly
acyrilamide gel electrophoresis (2-D PAGE) and PD Quest software
genomic solutions Investigator (proteomics) was used to analyze the
differential protein expression profile in femoral and humeri bones
harvested from three groups of rats; sham-operated rats (SO),
ovariectomised rats (Ovx) and ovariectomised rats supplemented for
2 months with palm vitamin E. The results showed that there were
over 300 valued spot on each of the groups PVE and OVX as
compared to about 200 in SO. Comparison between the differential
protein expression between OVX and PVE groups showed that ten
spots were down –regulated in OVX but up-regulated in PVE. The
ten differential spots were separately named P1-P10. The
identification and understanding of the pathway of the differential
protein expression among the groups is ongoing and may account for
the molecular mechanism through which palm vitamin E exert its
anti-osteoporotic effect.
Abstract: Acute disseminated encephalomyelitis (ADEM) has
been reported to develop after a hymenoptera sting, but its
pathogenesis is not known in detail. Myelin basic protein (MBP)-
specific T cells have been detected in the blood of patients with
ADEM, and a proportion of these patients develop multiple sclerosis
(MS). In an attempt to understand the mechanisms underlying
ADEM, molecular mimicry between hymenoptera venom peptides
and the human immunodominant MBP peptide was scrutinized,
based on the sequence and structural similarities, whether it was the
root of the disease. The results suggest that the three wasp venom
peptides have low sequence homology with the human
immunodominant MBP residues 85-99. Structural similarity analysis
among the three venom peptides and the MS-related HLA-DR2b
(DRA, DRB1*1501)-associated immunodominant MHC
binding/TCR contact residues 88-93, VVHFFK showed that
hyaluronidase residues 7-12, phospholipase A1 residues 98-103, and
antigen 5 residues 109-114 showed a high degree of similarity
83.3%, 100%, and 83.3% respectively. In conclusion, some wasp
venom peptides, particularly phospholipase A1, may potentially act
as the molecular motifs of the human 3HLA-DR2b-associated
immunodominant MBP88-93, and possibly present a mechanism for
induction of wasp sting-associated ADEM.
Abstract: In the present research, two nutraceuticals made from
red grape and walnut that showed previously to improve kidney
dysfunction were incorporated separately into functional foods' bread
made from barley and rice bran. The functional foods were evaluated
in rats in which chronic renal failure was induced through feeding
diet rich in adenine and phosphate (APD). The evaluation based on
assessing kidney function, oxidative stress, inflammatory biomarkers
and body weight gain. Results showed induction of chronic kidney
failure reflected in significant increase in plasma urea, creatinine,
malondialdehyde, tumor necrosis factor- α and low density
lipoprotein cholesterol along with significant reduction of plasma
albumin, and total antioxidant and creatinine clearance and body
weight gain on feeding APD compared to control healthy group.
Feeding the functional foods produced amelioration in the different
biochemical parameters and body weight gain indicating
improvement in kidney function.
Abstract: The study of proteomics reached unexpected levels of
interest, as a direct consequence of its discovered influence over some
complex biological phenomena, such as problematic diseases like
cancer. This paper presents the latest authors- achievements regarding
the analysis of the networks of proteins (interactome networks), by
computing more efficiently the betweenness centrality measure. The
paper introduces the concept of betweenness centrality, and then
describes how betweenness computation can help the interactome net-
work analysis. Current sequential implementations for the between-
ness computation do not perform satisfactory in terms of execution
times. The paper-s main contribution is centered towards introducing
a speedup technique for the betweenness computation, based on
modified shortest path algorithms for sparse graphs. Three optimized
generic algorithms for betweenness computation are described and
implemented, and their performance tested against real biological
data, which is part of the IntAct dataset.
Abstract: UK breweries generate extensive by products in the
form of spent grain, slurry and yeast. Much of the spent grain is
produced by large breweries and processed in bulk for animal feed.
Spent brewery grains contain up to 20% protein dry weight and up to
60% fiber and are useful additions to animal feed. Bulk processing is
economic and allows spent grain to be sold so providing an income
to the brewery. A proportion of spent grain, however, is produced by
small local breweries and is more variably distributed to farms or
other users using intermittent collection methods. Such use is much
less economic and may incur losses if not carefully assessed for
transport costs. This study reports an economic returns of using wet
brewery spent grain (WBSG) in animal feed using the Co-product
Optimizer Decision Evaluator model (Cattle CODE) developed by
the University of Nebraska to predict performance and economic
returns when byproducts are fed to finishing cattle. The results
indicated that distance from brewery to farm had a significantly
greater effect on the economics of use of small brewery spent grain
and that alternative uses than cattle feed may be important to
develop.
Abstract: Effect of oral administration of “Gadagi" tea on liver
function was assessed on 50 healthy male albino rats which were
grouped and administered with different doses(mg/kg) i.e low dose
(380mg/kg, 415mg/kg, 365mg/kg, 315mg/kg for “sak", “sada" and
“magani" respectively), standard dose ( 760mg/kg, 830mg/kg,
730mg/kg for “sak-, “sada" and “magani" respectively) and high dose
(1500mg/kg, 1700mg/kg and 1460mg/kg for “sak--,"sada" and
“magani" groups respectively) for a period of four weeks. Animals
that were not administered with the tea constituted the control group.
At the end of fourth week, the animals were sacrificed and their
serum alanine aminotransferase (ALT), aspartate aminotransferase
(AST), alkaline phosphatase (ALP), total protein (TP), albumin
(ALB), and globulins (GLO) were determined. Mean serum ALT and
ALP activities were significantly higher (P
Abstract: COPD is characterized by loss of elastic fibers from
small airways and alveolar walls, with the decrease in elastin
increasing with disease severity. It is unclear why there is a lack of
repair of elastic fibers. We have examined fibroblasts cultured from
lung tissue from normal and COPD subjects to determine if the
secretory profile explains lack of tissue repair. In this study,
fibroblasts were cultured from lung parenchyma of bronchial
carcinoma patients with varying degrees of COPD; controls
(non-COPD, n=5), mild COPD (GOLD 1, n=5) and moderate-severe
COPD (GOLD 2-3, n=12). Measurements were made of proliferation,
senescence-associated beta-galactosidase-1, mRNA expression of
IL-6, IL-8, MMP-1, tropoelastin and versican, and protein levels for
IL-6, IL-8, PGE2, tropoelastin, insoluble elastin, and versican. It was
found that GOLD 2-3 fibroblasts proliferated more slowly (p
Abstract: Oxidative stress is considered to be the cause for onset
and the progression of type 2 diabetes mellitus (T2DM) and
complications including neuropathy. It is a deleterious process that
can be an important mediator of damage to cell structures: protein,
lipids and DNA. Data suggest that in patients with diabetes and
diabetic neuropathy DNA repair is impaired, which prevents effective
removal of lesions. Objective: The aim of our study was to evaluate
the association of the hOGG1 (326 Ser/Cys) and XRCC1 (194
Arg/Trp, 399 Arg/Gln) gene polymorphisms whose protein is
involved in the BER pathway with DNA repair efficiency in patients
with diabetes type 2 and diabetic neuropathy compared to the healthy
subjects. Genotypes were determined by PCR-RFLP analysis in 385
subjects, including 117 with type 2 diabetes, 56 with diabetic
neuropathy and 212 with normal glucose metabolism. The
polymorphisms studied include codon 326 of hOGG1 and 194, 399
of XRCC1 in the base excision repair (BER) genes. Comet assay was
carried out using peripheral blood lymphocytes from the patients and
controls. This test enabled the evaluation of DNA damage in cells
exposed to hydrogen peroxide alone and in the combination with the
endonuclease III (Nth). The results of the analysis of polymorphism
were statistically examination by calculating the odds ratio (OR) and
their 95% confidence intervals (95% CI) using the ¤ç2-tests. Our data
indicate that patients with diabetes mellitus type 2 (including those
with neuropathy) had higher frequencies of the XRCC1 399Arg/Gln
polymorphism in homozygote (GG) (OR: 1.85 [95% CI: 1.07-3.22],
P=0.3) and also increased frequency of 399Gln (G) allele (OR: 1.38
[95% CI: 1.03-1.83], P=0.3). No relation to other polymorphisms
with increased risk of diabetes or diabetic neuropathy. In T2DM
patients complicated by neuropathy, there was less efficient repair of
oxidative DNA damage induced by hydrogen peroxide in both the
presence and absence of the Nth enzyme. The results of our study
suggest that the XRCC1 399 Arg/Gln polymorphism is a significant
risk factor of T2DM in Polish population. Obtained data suggest a
decreased efficiency of DNA repair in cells from patients with
diabetes and neuropathy may be associated with oxidative stress.
Additionally, patients with neuropathy are characterized by even
greater sensitivity to oxidative damage than patients with diabetes,
which suggests participation of free radicals in the pathogenesis of
neuropathy.
Abstract: Yeast cells live in a constantly changing environment that requires the continuous adaptation of their genomic program in order to sustain their homeostasis, survive and proliferate. Due to the advancement of high throughput technologies, there is currently a large amount of data such as gene expression, gene deletion and protein-protein interactions for S. Cerevisiae under various environmental conditions. Mining these datasets requires efficient computational methods capable of integrating different types of data, identifying inter-relations between different components and inferring functional groups or 'modules' that shape intracellular processes. This study uses computational methods to delineate some of the mechanisms used by yeast cells to respond to environmental changes. The GRAM algorithm is first used to integrate gene expression data and ChIP-chip data in order to find modules of coexpressed and co-regulated genes as well as the transcription factors (TFs) that regulate these modules. Since transcription factors are themselves transcriptionally regulated, a three-layer regulatory cascade consisting of the TF-regulators, the TFs and the regulated modules is subsequently considered. This three-layer cascade is then modeled quantitatively using artificial neural networks (ANNs) where the input layer corresponds to the expression of the up-stream transcription factors (TF-regulators) and the output layer corresponds to the expression of genes within each module. This work shows that (a) the expression of at least 33 genes over time and for different stress conditions is well predicted by the expression of the top layer transcription factors, including cases in which the effect of up-stream regulators is shifted in time and (b) identifies at least 6 novel regulatory interactions that were not previously associated with stress-induced changes in gene expression. These findings suggest that the combination of gene expression and protein-DNA interaction data with artificial neural networks can successfully model biological pathways and capture quantitative dependencies between distant regulators and downstream genes.
Abstract: Alpfa-fetoprotein and its fragments may be an important vehicle for targeted delivery of radionuclides to the tumor. We investigated the effect of conditions on the labeling of biologically active synthetic peptide based on the (F-afp) with technetium-99m. The influence of the nature of the buffer solution, pH, concentration of reductant, concentration of the peptide and the reaction temperature on the yield of labeling was examined. As a result, the following optimal conditions for labeling of (F-afp) are found: pH 8.5 (phosphate and bicarbonate buffers) and pH from 1.7 to 7.0 (citrate buffer). The reaction proceeds with sufficient yield at room temperature for 30 min at the concentration of SnCl2 and (Fafp) (F-afp) is to be less than 10 mkg/ml and 25 mkg/ml, respectively. Investigations of the test drug accumulation in the tumor cells of human breast cancer were carried out. Results can be assumed that the in vivo study of the (F-afp) in experimental tumor lesions will show concentrations sufficient for imaging these lesions by SPECT.
Abstract: Shadoo protein (Sho) was described in 2003 as the newest member of Prion protein superfamily [1]. Sho has similar structural motifs like prion protein (PrP) that is known for its central role in transmissible spongiform enchephalopathies. Although a great number of functions have been proposed, the exact physiological function of PrP is not known yet. Investigation of the function and localization of Sho may help us to understand the function of the Prion protein superfamily. Analyzing the subcellular localization of YFP-tagged forms of Sho, we detected the protein in the plasma membrane and in the nucleus of various cell lines. To reveal the localization of the endogenous protein we generated antibodies against Shadoo as well as employed commercially available anti-Shadoo antibodies: i) EG62 anti-mouse Shadoo antibody generated by Eurogentec Ltd.; ii) S-12 anti-human Shadoo antibody by Santa Cruz Biotechnology Inc.; iii) R-12 anti-mouse Shadoo antibody by Santa Cruz Biotechnology Inc.; iv) SPRN antibody against human Shadoo by Abgent Inc. We carried out immunocytochemistry on non-transfected HeLa, Zpl 2-1, Zw 3-5, GT1-1, GT1-7 and SHSY5Y cells as well as on YFP-Sho, Sho-YFP, and YFP-GPI transfected HeLa cells. Their specificity (in antibody-peptide competition assay) and co-localization (with the YFP signal) were assessed.
Abstract: This study proposes a basic molecular formula for all
proteins. A total of 10,739 proteins belonging to 9 different protein
groups classified on the basis of their functions were selected
randomly. They included enzymes, storage proteins, hormones,
signalling proteins, structural proteins, transport proteins,
immunoglobulins or antibodies, motor proteins and receptor proteins.
After obtaining the protein molecular formula using the ProtParam
tool, the H/C, N/C, O/C, and S/C ratios were determined for each
randomly selected sample. In this case, H, N, O, and S coefficients
were specified per carbon atom. Surprisingly, the results
demonstrated that H, N, O, and S coefficients for all 10,739 proteins
are similar and highly correlated. This study demonstrates that
despite differences in the structure and function, all known proteins
have a similar basic molecular formula CnH1.58 ± 0.015nN0.28 ± 0.005nO0.30
± 0.007nS0.01 ± 0.002n. The total correlation between all coefficients was
found to be 0.9999.
Abstract: The main aim is to perform mutational analysis of CTLA4 gene Exon 1 in SLE patients. A total of 61 SLE patients fulfilling “American College of Rheumatology (ACR) criteria" and 61 controls were enrolled in this study. The region of CTLA4 gene exon 1 was amplified by using Step-down PCR technique. Extracted DNA of band 354 bp was sequenced to analyze mutations in the exon-1 of CTLA-4 gene. Further, protein sequences were identified from nucleotide sequences of CTLA4 Exon 1 by using Expasy software and through Blast P software it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. No variations were found after patients sequences were compared with that of the control sequence. Furthermore it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. Thus CTLA4 gene may not be responsible for an autoimmune disease SLE.
Abstract: The study of proteomics reached unexpected levels of
interest, as a direct consequence of its discovered influence over
some complex biological phenomena, such as problematic diseases
like cancer. This paper presents a new technique that allows for an
accurate analysis of the human interactome network. It is basically
a two-step analysis process that involves, at first, the detection of
each protein-s absolute importance through the betweenness centrality
computation. Then, the second step determines the functionallyrelated
communities of proteins. For this purpose, we use a community
detection technique that is based on the edge betweenness
calculation. The new technique was thoroughly tested on real biological
data and the results prove some interesting properties of those proteins that are involved in the carcinogenesis process. Apart from its
experimental usefulness, the novel technique is also computationally
effective in terms of execution times. Based on the analysis- results, some topological features of cancer mutated proteins are presented
and a possible optimization solution for cancer drugs design is suggested.
Abstract: A computational platform is presented in this
contribution. It has been designed as a virtual laboratory to be used
for exploring optimization algorithms in biological problems. This
platform is built on a blackboard-based agent architecture. As a test
case, the version of the platform presented here is devoted to the
study of protein folding, initially with a bead-like description of the
chain and with the widely used model of hydrophobic and polar
residues (HP model). Some details of the platform design are
presented along with its capabilities and also are revised some
explorations of the protein folding problems with different types of
discrete space. It is also shown the capability of the platform to
incorporate specific tools for the structural analysis of the runs in
order to understand and improve the optimization process.
Accordingly, the results obtained demonstrate that the ensemble of
computational tools into a single platform is worthwhile by itself,
since experiments developed on it can be designed to fulfill different
levels of information in a self-consistent fashion. By now, it is being
explored how an experiment design can be useful to create a
computational agent to be included within the platform. These
inclusions of designed agents –or software pieces– are useful for the
better accomplishment of the tasks to be developed by the platform.
Clearly, while the number of agents increases the new version of the
virtual laboratory thus enhances in robustness and functionality.