• Bioinformatics and Biosystems
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• v.1 no.1
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• pp.46-50
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• 2006

According to the advancement of experimental techniques in molecular biology, genomic and protein sequence databases are increasing in size exponentially, and mean sequence lengths are also increasing. Because the sizes of these databases become larger, it is difficult to search similar sequences in biological databases with significant homologies to a query sequence. In this paper, we present the N-gram indexing method to retrieve similar sequences fast, precisely and comparably. This method regards a protein sequence as a text written in language of 20 amino acid codes, adapts N-gram tokens of fixed-length as its indexing scheme for sequence strings. After such tokens are indexed for all the sequences in the database, sequences can be searched with information retrieval algorithms. Using this new method, we have developed a protein sequence search system named as ProSeS (PROtein Sequence Search). ProSeS is a protein sequence analysis system which provides overall analysis results such as similar sequences with significant homologies, predicted subcellular locations of the query sequence, and major keywords extracted from annotations of similar sequences. We show experimentally that the N-gram indexing approach saves the retrieval time significantly, and that it is as accurate as current popular search tool BLAST.

• Journal of Microbiology and Biotechnology
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• v.4 no.4
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• pp.256-263
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• 1994

The aceB gene, encoding for malate synthase, one of the key enzymes of glyoxylate bypass, was isolated from a pMT1-based Corynebacterium glutamicum gene library via complementation of an Escherichia coli aceB mutant on an acetate minimal medium. The aceB gene was closely linked to aceA, separated by 598 base pairs, and transcribed in divergent direction. The aceB expressed a protein product of Mr 83, 000 in Corynebacterium glutamicum which was unusually large compared with those of other malate synthases. A DNA-sequence analysis of the cloned DNA identified an open-reading frame of 2, 217 base pairs which encodes a protein with the molecular weight of 82, 311 comprising 739 aminoo acids. The putative protein product showed only limited amino acid-sequence homology to its counteliparts in other organisms. The N-terminal region of the protein, which shows no apparent homology with the known sequences of other malate synthases, appeared to be responsible for the protein s unusually large size. A potential calciumbinding domain of EF-hand structure found among eukaryotes was detected in the N-terminal region of the deduced protein.

• Journal of Microbiology and Biotechnology
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• v.8 no.4
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• pp.333-340
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• 1998

Streptomyces griseus trypsin (SGT) is an extracellular proteinase produced by S. griseus. The sprT gene, which encodes premature SGT protein, was cloned into the plasmid pWHM3, a Streptomyces-E. coli shuttle vector. When the recombinant plasmid was introduced into Streptomyces lividans TK24, two proteins with molecular weights of 28 kDa and 42 kDa were detected. The 28-kDa protein was a SGT protein while the larger 42-kDa protein is thought to have been a premature form of the SGT protein. The SGT protein was purified to homogeneity via ammonium sulfate fractionation and many column chromatographies, including CM -sepharose chromatography, Mono-S chromatography, and Superose-12 chromatography, from the culture broth of S. lividans TK24 harboring the sprT gene. The N-terminal amino acid sequence, isoelectric points, and stabilities at various conditions of the SGT proteins purified from the Pronase and transformant were almost identical. The amount of the expressed SGT in S. lividans TK 24 was determined to be 5 times more than that of S. griseus based on the enzymatic activity against artificial substrate.

• BMB Reports
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• v.38 no.5
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• pp.591-594
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• 2005

One of the small proteins from Helicobacter pylori, HP1242, was investigated by the solution nuclear magnetic resonance (NMR) spectroscopy. HP1242 is known as a 76-residue conserved hypothetical protein and its function cannot be identified based on sequence homology. Here, the results of the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments of the HP1242 are reported using double- and triple-resonance techniques. About 95% of all of the $^1HN$, $^{15}N$, $^{13}CO$, $^{13}C{\alpha}$, and $^{13}C{\beta}$ resonances that cover 75 non- Proline residues of the 76 residues are clarified through sequential- and specific- assignments. In addition, three helical regions were clearly identified on the basis of the resonance assignments.

• Korean journal of food and cookery science
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• v.10 no.2
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• pp.146-150
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• 1994

The addition of nonfish protein significantly reduced the strength of nonfish protein-incorporated surimi gel in terms of cohesiveness, rigidity and shear force. The sensory textural properties of fiberi-3ed surimi gel product was characterized as the reduction in intensity of undesirable rubberiness, chewiness and firmness, thus increasing the desirability in over all texture. Gel strength of both cohesiveness and rigidity of nonfish protein was inversely correlated with those of nonfish protein-incorporated surimi gel. The variation of texture-modifying properties of nonfish protein in surimi gel was attributed to the differences in thermal hydration and gelation properties of nonfish protein.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.4
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• pp.537-542
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• 2002

A study was conducted to evaluate the nutritive potential value of different aquatic plants: duckweed (Lemna trisulaca), duckweed (Lemna perpusila), azolla (Azolla pinnata) and water-hyacinth (Eichhornia crassipes) from Bangladesh. A wide variability in protein, mineral composition, gas production, microbial protein synthesis, rumen degradable nitrogen and in situ dry matter and crude protein degradability were recorded among species. Crude protein content ranged from 139 to 330 g/kg dry matter (DM). All species were relatively high in Ca, P, Na, content and very rich in K, Fe, Mg, Mn, Cu and Zn concentration. The rate of gas production was highest in azolla and lowest in water-hyacinth. A similar trend was observed with in situ DM degradability. Crude protein degradability was highest in duckweed. Microbial protein formation at 24 h incubation ranged from 38.6-47.2 mg and in vitro rumen degradable nitrogen between 31.5 and 48.4%. Based on the present findings it is concluded that aquatic species have potential as supplementary diet to livestock.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.10
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• pp.1439-1444
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• 2002

An objective of this study was to determine the effects of increasing contents of rumen undegradable protein (RUP) from formalin treated soy bean (FSBM) on rumen functions. Four rumen canulated non-lactating cows were randomly allocated to total mixed rations (TMR) containing different proportions of soy bean meal (SBM) and FSBM. Of rumen fermentation characteristics, concentrations of ruminal fluid ammonia and molar proportions of isoacids decreased with increasing contents of RUP in diets (p<0.01). The animals on TMR containing only SBM gained less weight and had smaller rumen volume than those on TMR containing RUP from FSBM (p<0.05). Organic matter and neutral detergent fiber digestibility in sacco were not different (p>0.05). The density of protozoa particularly small Entodinium sp. in ruminal fluid was higher in animal fed TMR containing SBM:FSBM (34:66) and FSBM than those fed TMR containing SBM:FSBM (66:34) and SBM (p<0.01). Total viable count, and net microbial protein synthesis as indicated by purine derivatives in urine increased with increasing contents of RUP from FSBM (p<0.01). It can be concluded that a reduction in net microbial protein synthesis in the rumen with increasing contents of RUP in the diet can be due to the reduction of preformed protein available for microbial growth as well as an increased turnover rate of microbial cells by predatory activity of protozoa.

• Asian-Australasian Journal of Animal Sciences
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• v.13 no.4
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• pp.490-496
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• 2000

In vivo digestibility, nitrogen retention and microbial protein yield from diets of 100% ammonia treated rice straw (ARS) ($D_1$); 65% untreated rice straw (URS)+30% rice bran (RB)+5% SBM ($D_2$) and 85% ARS+15% RB ($D_3$) were determined using three Japanese Corriedale wethers in a $3{\times}3$ Latin Square Design. Results showed that DM consumption and organic matter digestibility were highest in $D_3$; but did not promote high protein digestibility, which RB+SBM had effected in URS based-diet. Dry matter intake and OM digestibility were the same for $D_1$ and $D_3$. Solubility of fiber bonds was increased by ammoniation, resulting in higher NDF digestibility. Nitrogen retention and microbial protein yield of rice bran supplemented groups was higher than ARS, but supplementation did not significantly increase efficiency of microbial protein synthesis from ARS which did occur when RB+SBM was added to untreated straw. The quality of ammoniated rice straw could be improved through RB supplementation because of its positive effects on DM digestibility, nitrogen retention and microbial protein yield. However, the addition of RB+SBM to URS resulted to more efficient N utilization.

• Journal of Sensor Science and Technology
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• v.13 no.2
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• pp.90-95
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• 2004

Protein and gene detection have been growing importance in medical diagnostics. Field effect transistor (FET) - type biosensors have many advantages such as miniaturization, standardization, and mass-production. In this work, we have fabricated metal-oxide-semiconductor (MOS) FET that operates as molecular recognitions based electronic sensor. Measurements were taken with the devices under phosphate buffered saline solution. The drain current ($I_{D}$) was decreased after forming self-assembled mono-layers (SAMs) used to capture the protein, which resulted from the negative charges of SAMs, and increased after forming protein by 11.5% at $V_{G}$ = 0 V due to the positive charges of protein.

• Proceedings of the KIEE Conference
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• 2008.07a
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• pp.1466-1467
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• 2008

We describe here a novel micro total analysis system for the purification and identification of the affinity-captured proteins. Also we demonstrated the mass analysis of the Carcinoembrionic antigen (CEA) and Alpha femtoprotein which were chosen as the target cancer marker. For MALDI-TOF analyses, the proteins should to be separated from a protein mixture and be concentrated when needed. This procedure usually takes a long time even before protease-digested samples are to be obtained from them. Here, we describe integrated and efficient micro chip for protein purification and digestion for MALDI-TOF analyses. At first, disease protein is purified by passing the micro chamber from a protein mixture or human whole serum and released from the micro affinity beads by thermal heating. Purified protein is then transfer to the hole for trypsin digestion. The final sample is analyzed by MALDI-TOF. All the processes could be finished successfully within one hour, which renders MALDI-TOF analyses of a target protein quite simple.