Abstract: Amyloid aggregation of polypeptides is related to a
growing number of pathologic states known as amyloid disorders. In
recent years, blocking or reversing amyloid aggregation via the use of
small compounds are considered as two useful approaches in
hampering the development of these diseases. In this research, we
have compared the ability of several manganese-salen derivatives, as
synthetic compounds, and apigenin, as a natural flavonoid, to inhibit
of hen egg-white lysozyme (HEWL) aggregation, as an in vitro
model system.
Different spectroscopic analyses such as Thioflavin T (ThT) and
Anilinonaphthalene-8-sulfonic acid (ANS) fluorescence, Congo red
(CR) absorbance along with transmission electron microscopy were
used in this work to monitor the HEWL aggregation kinetic and
inhibition. Our results demonstrated that both type of compounds
were capable to prevent the formation of lysozyme amyloid
aggregation in vitro. In addition, our data indicated that synthetic
compounds had higher activity to inhibit of the β-sheet structures
relative to natural compound. Regarding the higher antioxidant
activities of the salen derivatives, it can be concluded that in addition
to aromatic rings of each of the compounds, the potent antioxidant
properties of salen derivatives contributes to lower lysozyme fibril
accumulation.
Abstract: Soy protein is a common ingredient added to processed meats to enhance its functional characteristics. In our study, soybean products (fermented soy Natto and protein hydrolysate) containing hydrolyzed peptides and amino acids, with or without ascorbic acid were added to burger in order to improve its quality characteristics. Results showed that soy additives significantly increased moisture and protein content and reduced (P < 0.05) fat values. Ash content did not affect with Natto additive. Color tools, lightness and yellowness were higher (P
Abstract: Soybean Natto powder was added to the burger in order to enhance the oxidative stability as well as decreases the microbial spoilage. The soybean bioactives compound (soybean Natto) as antioxidant and antimicrobial were added at level of 1, 2 and 3%. Chemical analysis and physical properties were affected by soybean Natto addition. All the tested soybean Natto additives showed strong antioxidant properties. The microbiological indicators were significantly (P < 0.05) affected by the addition of the soybean Natto. Decreasing trends of different extent were also observed in samples of the treatments for total viable counts, Coliform, Staphylococcus aureus, yeast and molds. Storage period was significantly (P < 0.05) affected on microbial counts in all samples Staphylococcus aureus were the most sensitive microbe followed by Coliform group of the sample containing soybean Natto. Sensory attributes were also performed, added soybean Natto exhibits beany flavor which was clear about samples of 3% soybean Natto.
Abstract: Using an enzyme of known specificity the hydrolysis of protein was carried out in a controlled manner. The aim was to obtain oligopeptides being the so-called active peptides or their direct precursors. An original way of expression of the protein hydrolysis kinetics was introduced. Peptide bonds contained in the protein were recognized as a diverse-quality substrate for hydrolysis by the applied protease. This assumption was positively verified taking as an example the hydrolysis of albumin by thermolysin. Peptide linkages for this system should be divided into at least four groups. One of them is a group of bonds non-hydrolyzable by this enzyme. These that are broken are hydrolyzed at a rate that differs even by tens of thousands of times. Designated kinetic constants were k'F = 10991.4 L/g.h, k'M = 14.83L/g.h, k'S about 10-1 L/g.h for fast, medium and slow bonds, respectively. Moreover, a procedure for unfolding of the protein, conducive to the improved susceptibility to enzymatic hydrolysis (approximately three-fold increase in the rate) was proposed.
Abstract: MicroRNAs (miRNAs), a class of approximately 22 nucleotide long non coding RNAs which play critical role in different biological processes. The mature microRNA is usually 19–27 nucleotides long and is derived from a bigger precursor that folds into a flawed stem-loop structure. Mature micro RNAs are involved in many cellular processes that encompass development, proliferation, stress response, apoptosis, and fat metabolism by gene regulation. Resent finding reveals that certain viruses encode their own miRNA that processed by cellular RNAi machinery. In recent research indicate that cellular microRNA can target the genetic material of invading viruses. Cellular microRNA can be used in the virus life cycle; either to up regulate or down regulate viral gene expression Computational tools use in miRNA target prediction has been changing drastically in recent years. Many of the methods have been made available on the web and can be used by experimental researcher and scientist without expert knowledge of bioinformatics. With the development and ease of use of genomic technologies and computational tools in the field of microRNA biology has superior tremendously over the previous decade. This review attempts to give an overview over the genome wide approaches that have allow for the discovery of new miRNAs and development of new miRNA target prediction tools and databases.
Abstract: A simple, rapid and non-invasive electromagnetic sensor (C-FAST device) was- patented; for diagnosis of HCV RNA. Aim: To test the validity of the device compared to standard HCV PCR. Subjects and Methods: The first phase was done as pilot in Egypt on 79 participants; the second phase was done in five centers: one center from Egypt, two centers from Pakistan and two centers from India (800, 92 and 113 subjects respectively). The third phase was done nationally as multicenter study on (1600) participants for ensuring its representativeness. Results: When compared to PCR technique, C-FAST device revealed sensitivity 95% to 100%, specificity 95.5% to 100%, PPV 89.5% to 100%, NPV 95% to 100% and positive likelihood ratios 21.8% to 38.5%. Conclusion: It is practical evidence that HCV nucleotides emit electromagnetic signals that can be used for its identification. As compared to PCR, C-FAST is an accurate, valid and non-invasive device.
Abstract: Sea level rise threatens to increase the impact of future
storms and hurricanes on coastal communities. Accurate sea level
change prediction and supplement is an important task in determining
constructions and human activities in coastal and oceanic areas. In
this study, support vector machines (SVM) is proposed to predict
daily tidal levels along the Jeddah Coast, Saudi Arabia. The optimal
parameter values of kernel function are determined using a genetic
algorithm. The SVM results are compared with the field data and
with back propagation (BP). Among the models, the SVM is superior
to BPNN and has better generalization performance.
Abstract: Protein hydrolysates prepared from a number of medicinal plants are promising sources of various bioactive peptides. In this work, proteins from dried whole plant of Euphorbia hirta Linn. were extracted and digested with pepsin for 12h. The hydrolysates of lesser than 3 KDa were fractionated by a cut-off membrane. The peptide hydrolysate was then purified by an anion-exchange chromatography on DEAE-Sephacel™ column and reverse-phase chromatography on Sep-pak C18 column, respectively. The cytotoxic effect of each peptide fraction against a gastric carcinoma cell line (KATO-III, ATCC No. HTB103) was investigated using colorimetric MTT viability assay. A human liver cell line (Chang Liver, CLS No. 300139) was used as a control normal cell line. Two purified peptide peaks, peak l and peak ll at 100µg peptides mL-1 affected cell viability of the gastric cancer cell lines to 63.85±4.94 and 66.92±6.46%, respectively. Our result showed for the first time that the peptide fractions derived from protein hydrolysate of Euphorbia hirta Linn. have anti-gastric cancer activity, which offers a potential novel and natural anti-gastric cancer remedy.
Abstract: Mammalian genomes contain large number of
retroelements (SINEs, LINEs and LTRs) which could affect
expression of protein coding genes through associated transcription
factor binding sites (TFBS). Activity of the retroelement-associated
TFBS in many genes is confirmed experimentally but their global
functional impact remains unclear. Human SINEs (Alu repeats) and
mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich
gene rich genome segments consistent with the view that they
can contribute to regulation of gene expression. We have shown
earlier that Alu are involved in formation of cis-regulatory modules
(clusters of TFBS) in human promoters, and other authors reported
that Alu located near promoter CpG islands have an increased
frequency of CpG dinucleotides suggesting that these Alu are
undermethylated. Human Alu and mouse B1/B2 elements have an
internal bipartite promoter for RNA polymerase III containing
conserved sequence motif called B-box which can bind basal
transcription complex TFIIIC. It has been recently shown that TFIIIC
binding to B-box leads to formation of a boundary which limits
spread of repressive chromatin modifications in S. pombe. SINEassociated
B-boxes may have similar function but conservation of
TFIIIC binding sites in SINEs located near mammalian promoters
has not been studied earlier. Here we analysed abundance and
distribution of retroelements (SINEs, LINEs and LTRs) in annotated
sequences of the Database of mammalian transcription start sites
(DBTSS). Fractions of SINEs in human and mouse promoters are
slightly lower than in all genome but >40% of human and mouse
promoters contain Alu or B1/B2 elements within -1000 to +200 bp
interval relative to transcription start site (TSS). Most of these SINEs
is associated with distal segments of promoters (-1000 to -200 bp
relative to TSS) indicating that their insertion at distances >200 bp
upstream of TSS is tolerated during evolution. Distribution of SINEs
in promoters correlates negatively with the distribution of CpG
sequences. Using analysis of abundance of 12-mer motifs from the
B1 and Alu consensus sequences in genome and DBTSS it has been
confirmed that some subsegments of Alu and B1 elements are poorly
conserved which depends in part on the presence of CpG
dinucleotides. One of these CpG-containing subsegments in B1
elements overlaps with SINE-associated B-box and it shows better
conservation in DBTSS compared to genomic sequences. It has been
also studied conservation in DBTSS and genome of the B-box
containing segments of old (AluJ, AluS) and young (AluY) Alu
repeats and found that CpG sequence of the B-box of old Alu is
better conserved in DBTSS than in genome. This indicates that Bbox-
associated CpGs in promoters are better protected from
methylation and mutation than B-box-associated CpGs in genomic
SINEs. These results are consistent with the view that potential
TFIIIC binding motifs in SINEs associated with human and mouse
promoters may be functionally important. These motifs may protect
promoters from repressive histone modifications which spread from
adjacent sequences. This can potentially explain well known
clustering of SINEs in GC-rich gene rich genome compartments and
existence of unmethylated CpG islands.
Abstract: Deoxyribonucleic Acid or DNA computing has
emerged as an interdisciplinary field that draws together chemistry,
molecular biology, computer science and mathematics. Thus, in this
paper, the possibility of DNA-based computing to solve an absolute
1-center problem by molecular manipulations is presented. This is
truly the first attempt to solve such a problem by DNA-based
computing approach. Since, part of the procedures involve with
shortest path computation, research works on DNA computing for
shortest path Traveling Salesman Problem, in short, TSP are reviewed.
These approaches are studied and only the appropriate one is adapted
in designing the computation procedures. This DNA-based
computation is designed in such a way that every path is encoded by
oligonucleotides and the path-s length is directly proportional to the
length of oligonucleotides. Using these properties, gel electrophoresis
is performed in order to separate the respective DNA molecules
according to their length. One expectation arise from this paper is that
it is possible to verify the instance absolute 1-center problem using
DNA computing by laboratory experiments.
Abstract: The aim of the study was to determine how different
ripening processes (traditional vs. industrial) influenced the
proteolysis in traditional Serbian dry-fermented sausage Petrovská
klobása. The obtained results indicated more intensive pH decline
(0.7 units after 9 days) in industrially ripened products (I), what had a
positive impact on drying process and proteolytic changes in these
samples. Thus, moisture content in I sausages was lower at each
sampling time, amounting 24.7% at the end of production period
(90 days). Likewise, the process of proteolysis was more pronounced
in I samples, resulting in higher contents of non-protein nitrogen
(NPN) and free amino acids nitrogen (FAAN), as well as in faster
and more intensive degradation of myosin (≈220 kDa), actin (≈45
kDa) and other polypeptides during processing. Consequently, the
appearance and accumulation of several protein fragments were
registered.
Abstract: Recent research has shown that milk proteins can
yield bioactive peptides with opioid, mineral binding,
cytomodulatory, antihypertensive, immunostimulating, antimicrobial
and antioxidative activity in the human body. Bioactive peptides are
encrypted in milk proteins and are only released by enzymatic
hydrolysis in vivo during gastrointestinal digestion, food processing
or by microbial enzymes in fermented products. At present
significant research is being undertaken on the health effects of
bioactive peptides. A variety of naturally formed bioactive peptides
have been found in fermented dairy products, such as yoghurt, sour
milk and cheese. In particular, antihypertensive peptides have been
identified in fermented milks, whey and ripened cheese. Some of
these peptides have been commercialized in the form of fermented
milks. Bioactive peptides have the potential to be used in the
formulation of health-enhancing nutraceuticals, and as potent drugs
with well defined pharmacological effects.
Abstract: The Deoxyribonucleic Acid (DNA) which is a doublestranded helix of nucleotides consists of: Adenine (A), Cytosine (C), Guanine (G) and Thymine (T). In this work, we convert this genetic code into an equivalent digital signal representation. Applying a wavelet transform, such as Haar wavelet, we will be able to extract details that are not so clear in the original genetic code. We compare between different organisms using the results of the Haar wavelet Transform. This is achieved by using the trend part of the signal since the trend part bears the most energy of the digital signal representation. Consequently, we will be able to quantitatively reconstruct different biological families.
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: In order to characterize the soy protein hydrolysate obtained in this study, gel chromatography on Sephadex G-25 was used to perform the separation of the peptide mixture and electrophoresis in SDS-polyacrylamide gel has been employed. Protein hydrolysate gave high antioxidant activities, but didn't give any antimicrobial activities. The antioxidant activities of protein hydrolysate was in the same trend of peptide content which gave high antioxidant activities and high peptide content between fractions 15 to 50. With increasing peptide concentrations, the scavenging effect on DPPH radical increased until about 70%, thereafter reaching a plateau. In compare to different concentrations of BHA, which exhibited higher activity (90%), soybean protein hydrolysate exhibited high antioxidant activities (70%) at a concentration of 1.45 mg/ml at fraction 25. Electrophoresis analysis indicated that, low- MW hydrolysate fractions (F1) appeared, on average, to have higher DPPH scavenging activities than high-MW fractions. These results revealed that soybean peptides probably contain substances that were proton donors and could react with free radicals to convert them to stable diamagnetic molecules.
Abstract: Dried soy protein hydrolysate powder was added to
the burger in order to enhance the oxidative stability as well as
decreases the microbial spoilage. The soybean bioactive compounds
(soy protein hydrolysate) as antioxidant and antimicrobial were added
at level of 1, 2 and 3 %.Chemical analysis and physical properties
were affected by protein hydrolysate addition. The TBA values were
significantly affected (P < 0.05) by the storage period and the level of
soy protein hydrolysate. All the tested soybean protein hydrolysate
additives showed strong antioxidant properties. Samples of soybean
protein hydrolysate showed the lowest (P < 0.05) TBA values at each
time of storage.
The counts of all determined microbiological indicators were
significantly (P < 0.05) affected by the addition of the soybean
protein hydrolysate. Decreasing trends of different extent were also
observed in samples of the treatments for total viable counts,
Coliform, Staphylococcus aureus, yeast and molds. Storage period
was being significantly (P < 0.05) affected on microbial counts in all
samples Staphylococcus aureus were the most sensitive microbe
followed by Coliform group of the sample containing protein
hydrolysate, while molds and yeast count showed a decreasing trend
but not significant (P < 0.05) until the end of the storage period
compared with control sample. Sensory attributes were also
performed, added protein hydrolysate exhibits beany flavor which
was clear about samples of 3% protein hydrolysate.
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: Radiolabeled cyclic RGD peptides targeting integrin αvβ3 are reported as promising agents for the early diagnosis of metastatic tumors. With an aim to improve tumor uptake and retention of the peptide, cyclic RGD peptide dimer E[c (RGDfK)] 2 (E = Glutamic acid, f = phenyl alanine, K = lysine) coupled to the bifunctional chelator DOTA was custom synthesized and radiolabelled with 68Ga. Radiolabelling of cyclic RGD peptide dimer with 68Ga was carried out using HEPES buffer and biological evaluation of the complex was done in nude mice bearing HT29 tumors.
Abstract: The phylogenetic analysis using the most conservative
portions of 18S rRNA gene revealed the phylogenetic relationship
among the two populations where DNA divergence showed that the
nucleotides diversity value were -0.00838 for the Tanjung Dawai,
Kedah and -0.00708 for the Cherating, Pahang populations
respectively. The net nucleotide divergence among populations (Da)
was -0.0073 indicating a low polymorphism among the populations
studied. Total number of mutations in the Tanjung Dawai, Kedah
samples was higher than Cherating, Pahang samples, which are 73 and
59 respectively while shared mutations across the populations were 8,
and reveal the evolutionary in the genome of Malaysian T. gigas. The
tree topology of both populations inferred using Neigbour-joining
method by comparing 1791 bp of partial 18S rRNA sequence revealed
that T. gigas haplotypes were clustered into seven clades, suggesting
that they are genetically diverse among populations which derived
from a common ancestor.
Abstract: Tandem mass spectrometry (MS/MS) is the engine
driving high-throughput protein identification. Protein mixtures possibly
representing thousands of proteins from multiple species are
treated with proteolytic enzymes, cutting the proteins into smaller
peptides that are then analyzed generating MS/MS spectra. The
task of determining the identity of the peptide from its spectrum
is currently the weak point in the process. Current approaches to de
novo sequencing are able to compute candidate peptides efficiently.
The problem lies in the limitations of current scoring functions. In this
paper we introduce the concept of proteome signature. By examining
proteins and compiling proteome signatures (amino acid usage) it is
possible to characterize likely combinations of amino acids and better
distinguish between candidate peptides. Our results strongly support
the hypothesis that a scoring function that considers amino acid usage
patterns is better able to distinguish between candidate peptides. This
in turn leads to higher accuracy in peptide prediction.