Biomedical subjects

Shir-Ly Huang

Publications and source records attributed to Shir-Ly Huang.

10 recordsLinked to original sources

PubMed2006

Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures.

Recent investigations on the stability of proteins have demonstrated various structural factors, but few have considered sequence factors such as protein motifs. These motifs represent highly conserved regions and describe critical regions that may only exist on proteins that remain functional at high temperatures. This investigation presents a method for identifying and comparing corresponding mesophilic and thermophilic sequence motifs between protein families. Discriminative motifs that are conserved only in the mesophilic or thermophilic subfamily are identified. Analysis of the results shows that, although the subfamilies of most protein families share similar motifs, some discriminative motifs are present in particular thermophilic/mesophilic subfamilies. The thermophilic discriminative motifs are conserved only in thermophilic organisms, revealing that physiochemical principles support thermostability.

Amino Acid Motifs↗

PubMed2006

Growth factors, kinetics and biodegradation mechanism associated with Pseudomonas nitroreducens TX1 grown on octylphenol polyethoxylates.

The growth properties and biodegradation mechanism of a Gram-negative bacterium, Pseudomonas nitroreducens TX1 that was able to grow on branched octylphenol polyethoxylates (OPEO(n), average n=9.5) as the sole carbon source over a wide concentration range (1-100,000 mgl(-1)) were studied. Analysis of growth factors indicated the highest specific growth rate (micro) of 0.53 h(-1) was obtained at an initial concentration of 5,000 mgl(-1) OPEO(n). An optimal C/N ratio of 12 was obtained for (NH(4))(2)SO(4) as the nitrogen source in a cultivated medium at pH 7. The kinetic analysis demonstrated that bacterial growth and OPEO(n) degradation followed the Monod equation and were based on a substrate concentration inhibition model and pseudo-first-order reaction, respectively. The substrate inhibition coefficient was over 18,000 mgl(-1) and this indicates that the strain has an ability to sustain growth at high concentrations of OPEO(n) and use it as the sole carbon source under such a stress condition. Furthermore, LC-MS analysis showed that the biodegradation mechanism of dodecyl octaethoxylate (AEO8) by P. nitroreducens TX1 was the sequential cleavage of the ethoxylate chain.

Cell Proliferation↗

PubMed2005

Biodegradation of octylphenol polyethoxylate surfactant Triton X-100 by selected microorganisms.

Octylphenol polyethoxylate (OPEO(n)) surfactants are used in numerous commercial and industrial products. Large amounts of such surfactants and their various residual biodegradation by-products are ultimately released into the environment. OPEO(n) biodegradation was performed in this study using pure cultures of Pseudomonas species and strains under different environmental conditions. Environmental factors including the pH, nitrogen sources, and growth kinetics of the cells were investigated. The intermediates of Triton X-100 biotransformation were detected by high performance liquid chromatography-mass spectrophotograph (HPLC-MS). We found the highest specific growth rate (mu) was 0.56 h(-1) and this was achieved by strain E with an initial concentration of Triton X-100 of 5000 mg L(-1). A pH level of 7 was most favorable for cell growth for all five strains. The highest specific growth rate was achieved using (NH(4))(2)SO(4) as the sole nitrogen source for strain E. Strain A showed an enhancement of growth when between 0.2 and 1.4 mg L(-1) of H(2)O(2) was added. Detection of intermediates was possible after four days of transformation and the octylphenol triethoxylate (OPEO(3)) peak was predominant, while the high molecular weight peaks had all disappeared. The kinetic analysis demonstrated that the greatest maximum specific growth rate (mu(max)) and the greatest saturation constant (K(s)) of 0.83 h(-1) and 5.24 mg L(-1), respectively, were obtained for strain E in 5000 mg L(-1) Triton X-100. The higher K(i) revealed that strain A was resistant to higher Triton X-100 concentrations.

Base Sequence↗

PubMed2005

Microcalorimetric studies of the effects on the interactions of human recombinant interferon-alpha2a.

The applicability of the physical stability of protein solution monitored by isothermal titration calorimetry (ITC) was evaluated. The second virial coefficient, b2, derived from the dilution enthalpies of protein solution measured by ITC under various experimental conditions was studied. The protein applied in this work is human recombinant interferon-alpha2a (hrIFN-alpha2a), which is a commercial drug applied for the treatment of virus-infected diseases. The results obtained were used to predict the possibility of hrIFN-alpha2a aggregation, and the prediction can be further confirmed by size-exclusion chromatography (SEC). Various factors affecting the stability of protein solution were investigated, for example, temperature, salts, surfactants, and mechanical stress. Specifically, the results show that the dilution enthalpy of hrIFN-alpha2a increased with increasing temperature and NaCl concentration, while b2 decreased, indicating that the attraction between hrIFN-alpha2a molecules was enhanced under these conditions. On studying the effect of mechanical stress, the data obtained reveals that the introduction of centrifugal or vortex force strengthened the attractive forces between hrIFN-alpha2a molecules. These implications were supported by SEC data, demonstrating that the amount of aggregated hrIFN-alpha2a was increased. As a consequence, the methodologies presented in this investigation offer a possibility of monitoring the physical stability of protein solution at various stages of recovery, purification as well as the development of appropriate drug storage formulations.

Calorimetry↗

PubMed2004

Identifying transcriptional regulatory sites in the human genome using an integrated system.

This work develops an integrated system which, after a set of genes are inputted, is able to predict transcriptional regulatory sites and to detect the co-occurrence of these regulatory sites. The system integrates several site detection methods such as known site matching, over-presented oligonucleotide detection and DNA motif discovery programs. User profiles and history pages enable users to trace the sequence analyses of these transcriptional regulatory sites. Two groups of co-regulated genes were used to test the proposed system. The results predicted by the proposed system consist of known site homologs and putative regulatory sites. By comparing these sites with previously published results, the proposed system is able to help biologists identify possible candidates for the regulatory sites from groups of co-regulated genes. The integrated system is now available at http://rgsminer. csie.ncu.edu.tw/.

Databases, Nucleic Acid↗

PubMed2004

PGTdb: a database providing growth temperatures of prokaryotes.

UNLABELLED: Included in Prokaryotic Growth Temperature database (PGTdb) are a total of 1334 temperature data from 1072 prokaryotic organisms, Bacteria and Archaea: PGTdb integrates microbial growth temperature data from literature survey with their nucleotide/protein sequence and protein structure data from related databases. A direct correlation is observed between the average growth temperature of an organism and the melting temperature of proteins from the organism. Therefore, this database is useful not only for microbiologists to obtain cultivation condition, but also for biochemists and structure biologists to study the correlation between protein sequences/structures and their thermostability. In addition, the taxonomy and ribosomal RNA sequence(s) of an organism are linked through NCBI Taxonomy and the Ribosomal RNA Operon Copy Number Database umdb, respectively. PGTdb is the only integrated database on the Internet to provide the growth temperature data of the prokaryotes and the combined information of their nucleotide/protein sequences, protein structures, taxonomy and phylogeny. AVAILABILITY: http://pgtdb.csie.ncu.edu.tw

Archaea↗

PubMed2004

A probabilistic method to correlate ion pairs with protein thermostability.

Recent developments in research on the stability of proteins - specifically, comparisons of the ion pairs of homologous structures - show that ion pairs potentially contribute to the thermostability of proteins. This study proposes a probabilistic Bayesian statistical method to efficiently predict the thermostability of proteins based on the properties of ion pairs. The experimental results suggest that the numbers, types and bond lengths of ion pairs can be used to predict with high accuracy (up to 80%) the thermostability of functionally similar proteins. The predictions have high precision (99%), especially for hyperthermophilic proteins. Results for proteins with differing functions also indicate that the number of ion pairs is related to the thermostability of proteins, and that predictions of thermostability can also be made for proteins with different functions.

Algorithms↗

PubMed2003

Computing motif correlations in proteins.

Protein motifs, which are specific regions and conserved regions, are found by comparing multiple protein sequences. These conserved regions in general play an important role in protein functions and protein folds, for example, for their binding properties or enzymatic activities. The aim here is to find the existence correlations of protein motifs. The knowledge of protein motif/domain sharing should be important in shedding new light on the biologic functions of proteins and offering a basis in analyzing the evolution in the human genome or other genomes. The protein sequences used here are obtained from the PIR-NREF database and the protein motifs are retrieved from the PROSITE database. We apply data mining approach to discover the occurrence correlations of motif in protein sequences. The correlation of motifs mined can be used in evolution analyses and protein structure prediction. We discuss the latter, i.e., protein structure prediction in this study. The correlations mined are stored and maintained in a database system. The database is now available at http://bioinfo.csie.ncu.edu.tw/ProMotif/.

Algorithms↗

PubMed2002

The repetitive sequence database and mining putative regulatory elements in gene promoter regions.

At least 43% of the human genome is occupied by repetitive elements. Moreover, around 51% of the rice genome is occupied by repetitive elements. The analysis of repetitive elements reveals that repetitive elements in our genome may have been very important in the evolutionary genomics. The first part of this study is to describe a database of repetitive elements - RSDB. The RSDB database contains repetitive elements, which are classified into the following categories: exact, tandem, and similar. The interfaces needed to query and show the results and statistical data, such as the relationship between repetitive elements and genes, cross-references of repetitive elements among different organisms, and so on, are provided. The second part of this study then attempts to mine the putative binding site for information on how combinations of the known regulatory sites and overrepresented repetitive elements in RSDB are distributed in the promoter regions of groups of functionally related genes. The overrepresented repetitive elements appearing in the associations are possible transcription factor binding sites. Our proposed approach is applied to Saccharomyces cerevisiae and the promoter regions of Yeast ORFs. The complete contents of RSDB and partial putative binding sites are available to the public at www.rsdb.csie.ncu.edu.tw. The readers may download partial query results.

Animals↗

PubMed2002

Mining putative regulatory elements in promoter regions of Saccharomyces cerevisiae.

The availability of genome-wide gene expression data provides a unique set of genes from which we can decipher the mechanisms underlying the common transcriptional response. Transcription factors, which can bind to specific DNA sites, cooperatively regulate the transcription of genes. This study attempts to mine putative binding sites to investigate how combinations of the sites predicted from known sites and over-represented repetitive elements are distributed in the promoter regions of groups of functionally related genes. The over-represented repetitive elements appearing in the associations are possible transcription factor binding sites. The deduced association rules would facilitate to predict putative regulatory elements and to identify genes which are potentially co-regulated by the putative regulatory elements. Our proposed approach is applied to Saccharomyces cerevisiae and the promoter regions of yeast ORFs.

Base Sequence↗