Abstract: Biological data has several characteristics that strongly differentiate it from typical business data. It is much more complex, usually large in size, and continuously changes. Until recently business data has been the main target for discovering trends, patterns or future expectations. However, with the recent rise in biotechnology, the powerful technology that was used for analyzing business data is now being applied to biological data. With the advanced technology at hand, the main trend in biological research is rapidly changing from structural DNA analysis to understanding cellular functions of the DNA sequences. DNA chips are now being used to perform experiments and DNA analysis processes are being used by researchers. Clustering is one of the important processes used for grouping together similar entities. There are many clustering algorithms such as hierarchical clustering, self-organizing maps, K-means clustering and so on. In this paper, we propose a clustering algorithm that imitates the ecosystem taking into account the features of biological data. We implemented the system using an Ant-Colony clustering algorithm. The system decides the number of clusters automatically. The system processes the input biological data, runs the Ant-Colony algorithm, draws the Topic Map, assigns clusters to the genes and displays the output. We tested the algorithm with a test data of 100 to1000 genes and 24 samples and show promising results for applying this algorithm to clustering DNA chip data.
Abstract: Austenite and Martensite indicate the phases of solids undergoing phase transformation which we usually associate with materials and not with living organisms. This article provides an overview of bacterial proteins and structures that are undergoing phase transformation and suggests its probable effect on mechanical behavior. The context is mainly within the role of phase transformations occurring in the flagellum of bacteria. The current knowledge of molecular mechanism leading to phase variation in living organisms is reviewed. Since in bacteria, each flagellum is driven by a separate motor, similarity to a Differential drive in case of four-wheeled vehicles is suggested. It also suggests the application of the mechanism in which bacteria changes its direction of movement to facilitate single point turning of a multi-wheeled vehicle. Finally, examples are presented to illustrate that the motion due to phase transformation of flagella in bacteria can start a whole new research on motion mechanisms.
Abstract: Reverse engineering of full-genomic interaction networks based on compendia of expression data has been successfully applied for a number of model organisms. This study adapts these approaches for an important non-model organism: The major human fungal pathogen Candida albicans. During the infection process, the pathogen can adapt to a wide range of environmental niches and reversibly changes its growth form. Given the importance of these processes, it is important to know how they are regulated. This study presents a reverse engineering strategy able to infer fullgenomic interaction networks for C. albicans based on a linear regression, utilizing the sparseness criterion (LASSO). To overcome the limited amount of expression data and small number of known interactions, we utilize different prior-knowledge sources guiding the network inference to a knowledge driven solution. Since, no database of known interactions for C. albicans exists, we use a textmining system which utilizes full-text research papers to identify known regulatory interactions. By comparing with these known regulatory interactions, we find an optimal value for global modelling parameters weighting the influence of the sparseness criterion and the prior-knowledge. Furthermore, we show that soft integration of prior-knowledge additionally improves the performance. Finally, we compare the performance of our approach to state of the art network inference approaches.
Abstract: Carbonic anhydrases (CAs) has been focused as
biological catalysis for CO2 sequestration process because it can
catalyze the conversion of CO2 to bicarbonate. Here, codon-optimized
sequence of α type-CA cloned from Duneliala species. (DsCAopt) was
constructed, expressed, and characterized. The expression level in E.
coli BL21(DE3) was better for codon-optimized DsCAopt than intact
sequence of DsCAopt. DsCAopt enzyme shows high-stability at pH
7.6/10.0. In final, we demonstrated that in the Ca2+ solution, DsCAopt
enzyme can catalyze well the conversion of CO2 to CaCO3, as the
calcite form.
Abstract: The enzyme alkaline protease production was determined under
solid state fermentation using the soil bacteria Serratia marcescens
sp7. The maximum production was obtained from wheat bran
medium than ground nut shell and chemically defined medium. The
physiological fermentation factors such as pH of the medium (pH 8),
Temperature (40oC) and incubation time (48 hrs) played a vital role
in alkaline protease production in all the above. 100Mm NaCl has
given better resolution during elution of the enzymes. The enzyme
production was found to be associated with growth of the bacterial
culture.
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.
Abstract: The importance for manipulating an incorporated
scaffold and directing cell behaviors is well appreciated for tissue
engineering. Here, we developed newly nano-topographic oxidized
silicon nanosponges capable of being various chemical modifications
to provide much insight into the fundamental biology of how cells
interact with their surrounding environment in vitro. A wet etching
technique is exerted to allow us fabricated the silicon nanosponges in a
high-throughput manner. Furthermore, various organo-silane
chemicals enabled self-assembled on the surfaces by vapor deposition.
We have found that Chinese hamster ovary (CHO) cells displayed
certain distinguishable morphogenesis, adherent responses, and
biochemical properties while cultured on these chemical modified
nano-topographic structures in compared with the planar oxidized
silicon counterparts, indicating that cell behaviors can be influenced
by certain physical characteristic derived from nano-topography in
addition to the hydrophobicity of contact surfaces crucial for cell
adhesion and spreading. Of particular, there were predominant
nano-actin punches and slender protrusions formed while cells were
cultured on the nano-topographic structures. This study shed potential
applications of these nano-topographic biomaterials for controlling
cell development in tissue engineering or basic cell biology research.
Abstract: Liposomal magnetofection is a simple, highly efficient
technology for cell transfection, demonstrating better outcome than a
number of other common gene delivery methods. However,
aggregate complexes distribution over the cell surface is non-uniform
due to the gradient of the permanent magnetic field. The aim of this
study was to estimate the efficiency of liposomal magnetofection for
prostate carcinoma PC3 cell line using newly designed device,
“DynaFECTOR", ensuring magnetofection in a dynamic gradient
magnetic field. Liposomal magnetofection in a dynamic gradient
magnetic field demonstrated the highest transfection efficiency for
PC3 cells – it increased for 21% in comparison with liposomal
magnetofection and for 42% in comparison with lipofection alone.
The optimal incubation time under dynamic magnetic field for PC3
cell line was 5 minutes and the optimal rotation frequency of
magnets – 5 rpm. The new approach also revealed lower cytotoxic
effect to cells than liposomal magnetofection.
Abstract: Vernonia divergens Benth., commonly known as
“Insulin Plant” (Fam: Asteraceae) is a potent sugar killer. Locally the
leaves of the plant, boiled in water are successfully administered to a
large number of diabetic patients. The present study evaluates the
putative anti-diabetic ingredients, isolated from the in vivo and in
vitro grown plantlets of V. divergens for their antimicrobial and
anticancer activities. Sterilized explants of nodal segments were
cultured on MS (Musashige and Skoog, 1962) medium in presence of
different combinations of hormones. Multiple shoots along with
bunch of roots were regenerated at 1mg l-1 BAP and 0.5 mg l-1 NAA.
Micro-plantlets were separated and sub-cultured on the double
strength (2X) of the above combination of hormones leading to
increased length of roots and shoots. These plantlets were
successfully transferred to soil and survived well in nature. The
ethanol extract of plantlets from both in vivo & in vitro sources were
prepared in soxhlet extractor and then concentrated to dryness under
reduced pressure in rotary evaporator. Thus obtainedconcentrated
extracts showed significant inhibitory activity against gram
negative bacteria like Escherichia coli and Pseudomonas
aeruginosa but no inhibition was found against gram positive
bacteria. Further, these ethanol extracts were screened for in vitro
percentage cytotoxicity at different time periods (24 h, 48 h and 72 h)
of different dilutions. The in vivo plant extract inhibited the growth of
EAC mouse cell lines in the range of 65, 66, 78, and 88% at 100, 50,
25 & 12.5μg mL-1 but at 72 h of treatment. In case of the extract of in
vitro origin, the inhibition was found against EAC cell lines even at
48h. During spectrophotometric scanning, the extracts exhibited
different maxima (ʎ) - four peaks in in vitro extracts as against single
in in vivo preparation suggesting the possible change in the nature of
ingredients during micropropagation through tissue culture
techniques.
Abstract: The effects of divers carbon substrates were
investigated for the tabtoxin production of an isolated pathogenic
Pseudomonas syringae pv. tabaci, the causal agent of wildfire of
tobacco and are discussed in relation to the bacterium growth. The
isolated organism was grown in batch culture on Woolley's
medium (28°C, 200 rpm, during 5 days). The growth has been
measured by the optical density (OD) at 620 nm and the tabtoxin
production quantified by Escherichia coli (K-12) bioassay
technique. The growth and the tabtoxin production were both
influenced by the substrates (sugars, amino acids, organic acids)
used, each, as a sole carbon source and as a supplement for the
same amino acids. The most significant quantities of tabtoxin were
obtained in presence of some amino acids used as sole carbon
source and/or as supplement.
Abstract: Protein residue contact map is a compact
representation of secondary structure of protein. Due to the
information hold in the contact map, attentions from researchers in
related field were drawn and plenty of works have been done
throughout the past decade. Artificial intelligence approaches have
been widely adapted in related works such as neural networks,
genetic programming, and Hidden Markov model as well as support
vector machine. However, the performance of the prediction was not
generalized which probably depends on the data used to train and
generate the prediction model. This situation shown the importance
of the features or information used in affecting the prediction
performance. In this research, support vector machine was used to
predict protein residue contact map on different combination of
features in order to show and analyze the effectiveness of the
features.
Abstract: Microbial oil was produced by soil isolated
oleaginous yeast YU5/2 in flask-batch fermentation. The yeast was
identified by molecular genetics technique based on sequence
analysis of the variable D1/D2 domain of the large subunit (26S)
ribosomal DNA and it was identified as Torulaspora globosa. T.
globosa YU5/2 supported maximum values of 0.520 g/L/d, 0.472 g
lipid/g cells, 4.16 g/L, and 0.156 g/L/d for volumetric lipid
production rate, and specific yield of lipid, lipid concentration, and
specific rate of lipid production respectively, when culture was
performed in nitrogen-limiting medium supplemented with 80g/L
glucose. Among the carbon sources tested, maximum cell yield
coefficient (YX/S, g/L), maximum specific yield of lipid (YP/X, g
lipid/g cells) and volumetric lipid production rate (QP, g/L/d) were
found of 0.728, 0.237, and 0.619, respectively, using sweet potato
tubers hydrolysates as carbon source.
Abstract: Bacterial magnetic nanoparticles have great useful potential in biotechnological and biomedical applications. In this study, a liquid growth medium was modified for cultivation a fastidious magnetotactic bacterium that has been isolated from Anzali
lagoon, Iran in our previous research. These modifications include
change in vitamin, mineral, carbon sources and etcetera. In our
experience, the serum bottles and designed air-tight laboratory bottles
were used to create microaerobic conditions in order to development
of a method for scale-up experiment. This information may serve as a
guide to green chemistry based biological protocols for the synthesis
of magnetic nanoparticles with control over the chemical
composition, morphology and size.
Abstract: 16-Mercaptohexadecanoic acid (MHDA) and tripeptide glutathione conjugated with gold nanoparticles (Au-NPs) are characterized by Fourier Transform InfaRared (FTIR) spectroscopy combined with Surface-enhanced Raman scattering (SERS) spectroscopy. Surface Plasmon Resonance (SPR) technique based on FTIR spectroscopy has become an important tool in biophysics, which is perspective for the study of organic compounds. FTIR-spectra of MHDA shows the line at 2500 cm-1 attributed to thiol group which is modified by presence of Au-NPs, suggesting the formation of bond between thiol group and gold. We also can observe the peaks originate from characteristic chemical group. A Raman spectrum of the same sample is also promising. Our preliminary experiments confirm that SERS-effect takes place for MHDA connected with Au-NPs and enable us to detected small number (less than 106 cm-2) of MHDA molecules. Combination of spectroscopy methods: FTIR and SERS – enable to study optical properties of Au- NPs and immobilized bio-molecules in context of a bio-nano-sensors.
Abstract: The aim of this study was to estimate the frequency of
EBV infection in Hodgkin's lymphoma (HL) and non-Hodgkin's
lymphoma (NHL) occurring in Jordanian patients. A total of 55
patients with lymphoma were examined in this study. Of 55 patients,
30 and 25 were diagnosed as HL and NHL, respectively. The four
HL subtypes were observed with the majority of the cases exhibited
the mixed cellularity (MC) subtype followed by the nodular sclerosis
(NS). The high grade was found to be the commonest subtype of
NHL in our sample, followed by the low grade. The presence of EBV
virus was detected by immunostating for expression of latent
membrane protein-1 (LMP-1). The frequency of LMP-1 expression
occurred more frequent in patients with HL (60.0%) than in patients
with NHL (32.0%). The frequency of LMP-1 expression was also
higher in patients with MC subtype (61.11%) than those patients with
NS (28.57%). No age or gender difference in occurrence of EBV
infection was observed among patient with HL. By contrast, the
prevalence of EBV infection in NHL patients aged below 50 was
lower (16.66%) than in NHL patients aged 50 or above (46.15%). In
addition, EBV infection was more frequent in females with NHL
(38.46%) than in male with NHL (25%). In NHL cases, the
frequency of EBV infection in intermediate grade (60.0%) was high
when compared with frequency of low (25%) or high grades (25%).
In conclusion, analysis of LMP-1 expression indicates an important
role for this viral oncogene in the pathogenesis of EBV-associated
malignant lymphomas. These data also support the previous findings
that people with EBV may develop lymphoma and that efforts to
maintain low lymphoma should be considered for people with EBV
infection.
Abstract: The soil ecology of the organic and mineral soil layers
of laurel-leaved and Cryptomeria japonica forest in the Kasuga-yama
Hill Primeval Forest (Nara, Japan) was assessed. The number of
bacteria obtained by the dilution plate count method was less than
0.05% of those counted by the direct microscopic count. We therefore
found that forest soil contains large numbers of non-culturable
bacteria compared with agricultural soils. The numbers of bacteria and
fungi obtained by both the dilution plate count and the direct
microscopic count were larger in the deeper horizons (F and H) of the
organic layer than in the mineral soil layer. This suggests that active
microbial metabolism takes place in the organic layer. The numbers of
bacteria and the length of fungal hyphae obtained by the direct count
method were greater in the H horizon than in the F horizon. The direct
microscopic count revealed numerous non-culturable bacteria and
fungi in the soil. The ratio of fungal to bacterial biomass was lower in
the laurel-leaved forest soil. The fungal biomass was therefore
relatively low in the laurel-leaved forest soil due to differences in
forest vegetation.
Abstract: The characterization of κ-carrageenan could provide a
better understanding of its functions in biological, medical and
industrial applications. Chemical and physical analyses of
carrageenan from seaweeds, Euchema cottonii L., were done to offer
information on its properties and the effects of Co-60 γ-irradiation on
its thermochemical characteristics. The structural and morphological
characteristics of κ-carrageenan were determined using scanning
electron microscopy (SEM) while the composition, molecular weight
and thermal properties were determined using attenuated total
reflectance Fourier transform infrared spectroscopy (ATR-FTIR), gel
permeation chromatography (GPC), thermal gravimetric analysis
(TGA) and differential scanning calorimetry (DSC). Further chemical
analysis was done using hydrogen-1 nuclear magnetic resonance (1H
NMR) and functional characteristics in terms of biocompatibility
were evaluated using cytotoxicity test.
Abstract: fibers of pure cellulose can be made from some bacteria such as acetobacter xylinum. Bacterial cellulose fibers are very pure, tens of nm across and about 0.5 micron long. The fibers are very stiff and, although nobody seems to have measured the strength of individual fibers. Their stiffness up to 70 GPa. Fundamental strengths should be at least greater than those of the best commercial polymers, but best bulk strength seems to about the same as that of steel. They can potentially be produced in industrial quantities at greatly lowered cost and water content, and with triple the yield, by a new process. This article presents a critical review of the available information on the bacterial cellulose as a biological nonwoven fabric with special emphasis on its fermentative production and applications. Characteristics of bacterial cellulose biofabric with respect to its structure and physicochemical properties are discussed. Current and potential applications of bacterial cellulose in textile, nonwoven cloth, paper, films synthetic fiber coating, food, pharmaceutical and other industries are also presented.
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: Hair is a non homogenous complex material which
can be associated with a polymer. It is made up 95% of Keratin.
Hair has a great social significance for human beings. In the High
Middle Ages, for example, long hairs have been reserved for kings
and nobles.
Most common interest in hair is focused on hair growth, hair types
and hair care, but hair is also an important biomaterial which can
vary depending on ethnic origin or on age, hair colour for example
can be a sign of ethnic ancestry or age (dark hair for Asiatic, blond
hair for Caucasian and white hair for old people in general).
In this context, different approaches have been conducted to
determine the differences in mechanical properties and characterize
the fracture topography at the surface of hair depending on its type
and its age.
A tensile testing machine was especially designed to achieve
tensile tests on hair. This device is composed of a microdisplacement
system and a force sensor whose peak load is limited to
3N. The curves and the values extracted from each experiment, allow
us to compare the evolution of the mechanical properties from one
hair to another.
Observations with a Scanning Electron Microscope (SEM) and
with an interferometer were made on different hairs. Thus, it is
possible to access the cuticle state and the fracture topography for
each category.