Abstract: The Kinetics formation of labile Complex
Ag (I) tetra (p-carboxyphenyl) porphyrin, was investigated at 25oC
and I=0.1M (NaNO3). By spectrophotometric titration, the
composition ratio of the complex was established to be 2:1
(Ag : H2TCPP). The equilibrium constant, K, was found to be
log 10-6.53. Binding of the first Ag (I) was found to be rate
determining step with rate constant, k1= 4.67×102 . A plausible
mechanism is discussed. We discus theoretically why Ag(I)2TCPP is
unstable.
Abstract: The purpose of research was to know the role of
immunogenic protein of 49 kDa from V.alginolyticus which capable
to initiate molecule expression of MHC Class II in receptor of
Cromileptes altivelis. The method used was in vivo experimental
research through testing of immunogenic protein 49 kDa from
V.alginolyticus at Cromileptes altivelis (size of 250 - 300 grams)
using 3 times booster by injecting an immunogenic protein in a
intramuscular manner. Response of expressed MHC molecule was
shown using immunocytochemistry method and SEM. Results
indicated that adhesin V.alginolyticus 49 kDa which have
immunogenic character could trigger expression of MHC class II on
receptor of grouper and has been proven by staining using
immunocytochemistry and SEM with labeling using antibody anti
MHC (anti mouse). This visible expression based on binding between
epitopes antigen and antibody anti MHC in the receptor. Using
immunocytochemistry, intracellular response of MHC to in vivo
induction of immunogenic adhesin from V.alginolyticus was shown.
Abstract: This paper proposes new algorithms for the computeraided
design and manufacture (CAD/CAM) of 3D woven multi-layer
textile structures. Existing commercial CAD/CAM systems are often
restricted to the design and manufacture of 2D weaves. Those
CAD/CAM systems that do support the design and manufacture of
3D multi-layer weaves are often limited to manual editing of design
paper grids on the computer display and weave retrieval from stored
archives. This complex design activity is time-consuming, tedious
and error-prone and requires considerable experience and skill of a
technical weaver. Recent research reported in the literature has
addressed some of the shortcomings of commercial 3D multi-layer
weave CAD/CAM systems. However, earlier research results have
shown the need for further work on weave specification, weave
generation, yarn path editing and layer binding. Analysis of 3D
multi-layer weaves in this research has led to the design and
development of efficient and robust algorithms for the CAD/CAM of
3D woven multi-layer textile structures. The resulting algorithmically
generated weave designs can be used as a basis for lifting plans that
can be loaded onto looms equipped with electronic shedding
mechanisms for the CAM of 3D woven multi-layer textile structures.
Abstract: A newly designed gas-distributor for granulation of powdery materials in equilibrated fluidized bed and a system for collecting the granules prepared are suggested. The aim of these designs is to solve the problems arising by the granulation of powdery materials in fluidized bed devices. The gasdistributor and the collection system proved to be reliable at operation; they reduce the size of still zones, effectively disperse the binding solution in the bed and ensure the collection of granules of given diameter
Abstract: Tumour suppressors are key participants in the
prevention of cancer. Regulation of their expression through
miRNAs is important for comprehensive translation inhibition of
tumour suppressors and elucidation of carcinogenesis mechanisms.
We studies the possibility of 1521 miRNAs to bind with 873 mRNAs
of human tumour suppressors using RNAHybrid 2.1 and ERNAhybrid
programmes. Only 978 miRNAs were found to be
translational regulators of 812 mRNAs, and 61 mRNAs did not have
any miRNA binding sites. Additionally, 45.9% of all miRNA binding
sites were located in coding sequences (CDSs), 33.8% were located
in 3' untranslated region (UTR), and 20.3% were located in the
5'UTR. MiRNAs binding with more than 50 target mRNAs and
mRNAs binding with several miRNAs were selected. Hsa-miR-5096
had 15 perfectly complementary binding sites with mRNAs of 14
tumour suppressors. These newly indentified miRNA binding sites
can be used in the development of medicines (anti-sense therapies)
for cancer treatment.
Abstract: Geometry optimizations of metal complexes of Salen(bis(Salicylidene)1,2-ethylenediamine) were carried out at HF and DFT methods employing Lanl2DZ basis set. In this work structural, energies, bond lengths and other physical properties between Mn2+,Cu2+ and Ni2+ ions coordinated by salen–type ligands are examined. All calculations were performed using Gaussian 98W program series. To investigate local aromaticities, NICS were calculated at all centers of rings. The higher the band gap indicating a higher global aromaticity. The possible binding energies have been evaluated. We have evaluated Frequencies and Zero-point energy with freq calculation. The NICS(Nucleous Independent Chemical Shift) Results show Ni(II) complexes are antiaromatic and aromaticites of Mn(II) complexes are larger than Cu(II) complexes. The energy Results show Cu(II) complexes are stability than Mn(II) and Ni(II) complexes.
Abstract: Deaminated lesions were produced via nitrosative oxidation of natural nucleobases; uracul (Ura, U) from cytosine (Cyt, C), hypoxanthine (Hyp, H) from adenine (Ade, A), and xanthine (Xan, X) and oxanine (Oxa, O) from guanine (Gua, G). Such damaged nucleobases may induce mutagenic problems, so that much attentions and efforts have been poured on the revealing of their mechanisms in vivo or in vitro. In this study, we employed these deaminated lesions as useful probes for analysis of DNA-binding/recognizing proteins or enzymes. Since the pyrimidine lesions such as Hyp, Oxa and Xan are employed as analogues of guanine, their comparative uses are informative for analyzing the role of Gua in DNA sequence in DNA-protein interaction. Several DNA oligomers containing such Hyp, Oxa or Xan substituted for Gua were designed to reveal the molecular interaction between DNA and protein. From this approach, we have got useful information to understand the molecular mechanisms of the DNA-recognizing enzymes, which have not ever been observed using conventional DNA oligomer composed of just natural nucleobases.
Abstract: Regulatory relationships of 686 intronic miRNA and 784 intergenic miRNAs with mRNAs of 51 intronic miRNA coding genes were established. Interaction features of studied miRNAs with 5'UTR, CDS and 3'UTR of mRNA of each gene were revealed. Functional regions of mRNA were shown to be significantly heterogenous according to the number of binding sites of miRNA and to the location density of these sites.
Abstract: Non-viral gene carriers composed of biodegradable
polymers or lipids have been considered as a safer alternative for gene
carriers over viral vectors. We have developed multi-functional
nano-micelles for both drug and gene delivery application.
Polyethyleneimine (PEI) was modified by grafting stearic acid (SA)
and formulated to polymeric micelles (PEI-SA) with positive surface
charge for gene and drug delivery. Our results showed that PEI-SA
micelles provided high siRNA binding efficiency. In addition, siRNA
delivered by PEI-SA carriers also demonstrated significantly high
cellular uptake even in the presence of serum proteins. The
post-transcriptional gene silencing efficiency was greatly improved by
the polyplex formulated by 10k PEI-SA/siRNA. The amphiphilic
structure of PEI-SA micelles provided advantages for multifunctional
tasks; where the hydrophilic shell modified with cationic charges can
electrostatically interact with DNA or siRNA, and the hydrophobic
core can serve as payloads for hydrophobic drugs, making it a
promising multifunctional vehicle for both genetic and chemotherapy
application.
Abstract: IETF defines mobility support in IPv6, i.e. MIPv6, to
allow nodes to remain reachable while moving around in the IPv6
internet. When a node moves and visits a foreign network, it is still
reachable through the indirect packet forwarding from its home
network. This triangular routing feature provides node mobility but
increases the communication latency between nodes. This deficiency
can be overcome by using a Binding Update (BU) scheme, which let
nodes keep up-to-date IP addresses and communicate with each other
through direct IP routing. To further protect the security of BU, a
Return Routability (RR) procedure was developed. However, it has
been found that RR procedure is vulnerable to many attacks. In this
paper, we will propose a lightweight RR procedure based on
geometric computing. In consideration of the inherent limitation of
computing resources in mobile node, the proposed scheme is
developed to minimize the cost of computations and to eliminate the
overhead of state maintenance during binding updates. Compared with
other CGA-based BU schemes, our scheme is more efficient and
doesn-t need nonce tables in nodes.
Abstract: Lectins have a good scope in current clinical
microbiology research. In the present study evaluated the
antimicrobial activities of a D-galactose binding lectin (PnL) was
purified from the annelid, Perinereis nuntia (polychaeta) by affinity
chromatography. The molecular mass of the lectin was determined to
be 32 kDa as a single polypeptide by SDS-PAGE under both reducing
and non-reducing conditions. The hemagglutinating activity of the
PnL showed against trypsinized and glutaraldehyde-fixed human
erythrocytes was specifically inhibited by D-Gal, GalNAc,
Galβ1-4Glc and Galα1-6Glc. PnL was evaluated for in vitro
antibacterial screening studies against 11 gram-positive and
gram-negative microorganisms. From the screening results, it was
revealed that PnL exhibited significant antibacterial activity against
gram-positive bacteria. Bacillus megaterium showed the highest
growth inhibition by the lectin (250 μg/disc). However, PnL did not
inhibit the growth of gram-negative bacteria such as Vibrio cholerae
and Pseudomonas sp. PnL was also examined for in vitro antifungal
activity against six fungal phytopathogens. PnL (100 μg/mL) inhibited
the mycelial growth of Alternaria alternata (24.4%). These results
indicate that future findings of lectin applications obtained from
annelids may be of importance to life sciences.
Abstract: Search for a tertiary substructure that geometrically
matches the 3D pattern of the binding site of a well-studied protein provides a solution to predict protein functions. In our previous work,
a web server has been built to predict protein-ligand binding sites
based on automatically extracted templates. However, a drawback of such templates is that the web server was prone to resulting in many
false positive matches. In this study, we present a sequence-order constraint to reduce the false positive matches of using automatically
extracted templates to predict protein-ligand binding sites. The binding site predictor comprises i) an automatically constructed template library and ii) a local structure alignment algorithm for
querying the library. The sequence-order constraint is employed to
identify the inconsistency between the local regions of the query protein and the templates. Experimental results reveal that the sequence-order constraint can largely reduce the false positive matches and is effective for template-based binding site prediction.
Abstract: Certain tRNA synthetases have developed highly accurate molecular machinery to discriminate their cognate amino acids. Those aaRSs achieve their goal via editing reaction in the Connective Polypeptide 1 (CP1). Recently mutagenesis studies have revealed the critical importance of residues in the CP1 domain for editing activity and X-ray structures have shown binding mode of noncognate amino acids in the editing domain. To pursue molecular mechanism for amino acid discrimination, molecular modeling studies were performed. Our results suggest that aaRS bind the noncognate amino acid more tightly than the cognate one. Finally, by comparing binding conformations of the amino acids in three systems, the amino acid binding mode was elucidated and a discrimination mechanism proposed. The results strongly reveal that the conserved threonines are responsible for amino acid discrimination. This is achieved through side chain interactions between T252 and T247/T248 as well as between those threonines and the incoming amino acids.
Abstract: Empirical force fields and density functional theory
(DFT) was used to study the binding energies and structures of
methylamine on the surface of activated carbons (ACs). This is a first
step in studying the adsorption of alkyl amines on the surface of
functionalized ACs. The force fields used were Dreiding (DFF),
Universal (UFF) and Compass (CFF) models. The generalized
gradient approximation with Perdew Wang 91 (PW91) functional
was used for DFT calculations. In addition to obtaining the aminecarboxylic
acid adsorption energies, the results were used to establish
reliability of the empirical models for these systems. CFF predicted a
binding energy of -9.227 (kcal/mol) which agreed with PW91 at -
13.17 (kcal/mol), compared to DFF 0 (kcal/mol) and UFF -0.72
(kcal/mol). However, the CFF binding energies for the amine to ester
and ketone disagreed with PW91 results. The structures obtained
from all models agreed with PW91 results.
Abstract: The aim of this study was to determine noise level of
six different types of machines in printing companies in Novi Sad.
The A-weighted levels on Leq, Lmax and Lmin Sound Pressure Level
(SPL) in dBA were measured. It was found that the folders, offset
printing presses and binding machines are the predominant noise
sources. The noise levels produced by 12 of 38 machines exceed the
limiting threshold level of 85 dBA, tolerated by law. Since it was
determined that the average noise level for folders (87.7 dB) exceeds
the permitted value the octave analysis of noise was performed.
Abstract: Bone growth factors, such as Bone Morphogenic
Protein-2 (BMP-2) have been approved by the FDA to replace grafting for some surgical interventions, but the high dose requirement limits its use in patients. Noggin, an extracellular protein, blocks the effect of BMP-2 by binding to BMP. Preventing
the BMP-2/noggin interaction will help increase the free
concentration of BMP-2 and therefore should enhance its efficacy to
induce bone formation. The work presented here involves
computational design of novel small molecule inhibitory agents of BMP-2/noggin interaction, based on our current understanding of
BMP-2, and its known putative ligands (receptors and antagonists). A
successful acquisition of such an inhibitory agent of BMP-2/noggin interaction would allow clinicians to reduce the dose required of
BMP-2 protein in clinical applications to promote osteogenesis. The
available crystal structures of the BMPs, its receptors, and the binding partner noggin were analyzed to identify the critical residues
involved in their interaction. In presenting this study, LUDI de novo design method was utilized to perform virtual screening of a large
number of compounds from a commercially available library against the binding sites of noggin to identify the lead chemical compounds
that could potentially block BMP-noggin interaction with a high specificity.
Abstract: The present study has been taken to explore the
screening of in vitro antimicrobial activities of D-galactose-binding
sponge lectin (HOL-30). HOL-30 was purified from the marine
demosponge Halichondria okadai by affinity chromatography. The
molecular mass of the lectin was determined to be 30 kDa with a
single polypeptide by SDS-PAGE under non-reducing and reducing
conditions. HOL-30 agglutinated trypsinized and glutaraldehydefixed
rabbit and human erythrocytes with preference for type O
erythrocytes. The lectin was subjected to evaluation for inhibition of
microbial growth by the disc diffusion method against eleven human
pathogenic gram-positive and gram-negative bacteria. The lectin
exhibited strong antibacterial activity against gram-positive bacteria,
such as Bacillus megaterium and Bacillus subtilis. However, it did
not affect against gram-negative bacteria such as Salmonella typhi
and Escherichia coli. The largest zone of inhibition was recorded of
Bacillus megaterium (12 in diameter) and Bacillus subtilis (10 mm in
diameter) at a concentration of the lectin (250 μg/disc). On the other
hand, the antifungal activity of the lectin was investigated against six
phytopathogenic fungi based on food poisoning technique. The lectin
has shown maximum inhibition (22.83%) of mycelial growth of
Botrydiplodia theobromae at a concentration of 100 μg/mL media.
These findings indicate that the lectin may be of importance to
clinical microbiology and have therapeutic applications.
Abstract: Hierarchical Mobile IPv6 (HMIPv6) was designed to
support IP micro-mobility management in the Next Generation
Networks (NGN) framework. The main design behind this protocol is
the usage of Mobility Anchor Point (MAP) located at any level router
of network to support hierarchical mobility management. However,
the distance MAP selection in HMIPv6 causes MAP overloaded and
increase frequent binding update as the network grows. Therefore, to
address the issue in designing MAP selection scheme, we propose a
dynamic load control mechanism integrates with a speed detection
mechanism (DMS-DLC). From the experimental results we obtain
that the proposed scheme gives better distribution in MAP load and
increase handover speed.
Abstract: Calcium is a vital second messenger used in signal transduction. Calcium controls secretion, cell movement, muscular contraction, cell differentiation, ciliary beating and so on. Two theories have been used to simplify the system of reaction-diffusion equations of calcium into a single equation. One is excess buffer approximation (EBA) which assumes that mobile buffer is present in excess and cannot be saturated. The other is rapid buffer approximation (RBA), which assumes that calcium binding to buffer is rapid compared to calcium diffusion rate. In the present work, attempt has been made to develop a model for calcium diffusion under excess buffer approximation in neuron cells. This model incorporates the effect of [Na+] influx on [Ca2+] diffusion,variable calcium and sodium sources, sodium-calcium exchange protein, Sarcolemmal Calcium ATPase pump, sodium and calcium channels. The proposed mathematical model leads to a system of partial differential equations which have been solved numerically using Forward Time Centered Space (FTCS) approach. The numerical results have been used to study the relationships among different types of parameters such as buffer concentration, association rate, calcium permeability.
Abstract: Chitosan is a biopolymer composed of glucosamine
and N-acetyl glucosamine. Solubility and viscosity pose problems in
some applications. These problems can be overcome with unique
modifications. In this study, firstly, chitosan was modified by caffeic
acid and thioglycolic acid, separately. Then, growing effects of these
modified polymers was observed in U937 cell line. Caffeic acid is a
phenolic compound and its modifications act carcinogenic inhibitors
in drugs. Thiolated chitosans are commonly being used for drugdelivery
systems in various routes, because of enhancing
mucoadhesiveness property. U937 cell line was used model cell for
leukaemia. Modifications were achieved by 1 – 15 % binding range.
Increasing binding ratios showed higher radical-scavenging activity
and reducing cell growth, in compared to native chitosan. Caffeic
acid modifications showed higher radical-scavenging activity than
thiolated chitosans at the same concentrations. Caffeic acid and
thioglycolic acid modifications inhibited growth of U937, effectively.