Shir-Ly Huang

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

Pilot-scale ethanol production from rice straw hydrolysates using xylose-fermenting Pichia stipitis.

Ethanol was produced at pilot scale from rice straw hydrolysates using a Pichia stipitis strain previously adapted to NaOH-neutralized hydrolysates. The highest ethanol yield was 0.44 ± 0.02 g(p)/g(s) at an aeration rate of 0.05 vvm using overliming-detoxified hydrolysates. The yield with hydrolysates conditioned by ammonia and NaOH was 0.39 ± 0.01 and 0.34 ± 0.01 g(p)/g(s), respectively, were achieved at the same aeration rate. The actual ethanol yield from hydrolysate fermentation with ammonia neutralization was similar to that with overliming hydrolysate after taking into account the xylose loss resulting from these conditioning processes. Moreover, the ethanol yield from ammonia-neutralized hydrolysates could be further enhanced by increasing the initial cell density by two-fold or reducing the combined concentration of furfural and 5-hydroxymethyl furfural to 0.6g/L by reducing the severity of operational conditions in pretreatment. This study demonstrated the potential for commercial ethanol production from rice straw via xylose fermentation.

Analysis of bacterial degradation pathways for long-chain alkylphenols involving phenol hydroxylase, alkylphenol monooxygenase and catechol dioxygenase genes.

Eighteen 4-t-octylphenol-degrading bacteria were isolated and screened for the presence of degradative genes by polymerase chain reaction method using four designed primer sets. The primer sets were designed to amplify specific fragments from multicomponent phenol hydroxylase, single component monooxygenase, catechol 1,2-dioxygenase and catechol 2,3-dioxygenase genes. Seventeen of the 18 isolates exhibited the presence of a 232 bp amplicon that shared 61-92% identity to known multicomponent phenol hydroxylase gene sequences from short and/or medium-chain alkylphenol-degrading strains. Twelve of the 18 isolates were positive for a 324 bp region that exhibited 78-95% identity to the closest published catechol 1,2-dioxygenase gene sequences. The two strains, Pseudomonas putida TX2 and Pseudomonas sp. TX1, contained catechol 1,2-dioxygenase genes also have catechol 2,3-dioxygenase genes. Our result revealed that most of the isolated bacteria are able to degrade long-chain alkylphenols via multicomponent phenol hydroxylase and the ortho-cleavage pathway.

Co-metabolic degradation of trichloroethylene by Pseudomonas putida in a fibrous bed bioreactor

Co-metabolic degradation of trichloroethylene (TCE) by Pseudomonas putida F1 was investigated in a novel bioreactor with a fibrous bed. A pseudo-first-order rate constant for TCE degradation was 1.4 h−1 for 2.4 to 100 mg TCE l−1. Competitive inhibition of toluene on TCE removal could be prevented in this bioreactor. 90% TCE was removed over 4 h when 95 mg toluene l−1 was presented simultaneously.

Multiple approaches to characterize the microbial community in a thermophilic anaerobic digester running on swine manure: A case study

In this study, the first survey of microbial community in thermophilic anaerobic digester using swine manure as sole feedstock was performed by multiple approaches including denaturing gradient gel electrophoresis (DGGE), clone library and pyrosequencing techniques. The integrated analysis of 21 DGGE bands, 126 clones and 8506 pyrosequencing read sequences revealed that Clostridia from the phylum Firmicutes account for the most dominant Bacteria. In addition, our analysis also identified additional taxa that were missed by the previous researches, including members of the bacterial phyla Synergistetes, Planctomycetes, Armatimonadetes, Chloroflexi and Nitrospira which might also play a role in thermophilic anaerobic digester. Most archaeal 16S rRNA sequences could be assigned to the order Methanobacteriales instead of Methanomicrobiales comparing to previous studies. In addition, this study reported that the member of Methanothermobacter genus was firstly found in thermophilic anaerobic digester.

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.

Degradation of triclocarban by a triclosan-degrading Sphingomonas sp. strain YL-JM2C

Bacterial degradation plays a vital role in determining the environmental fate of micropollutants like triclocarban. The mechanism of triclocarban degradation by pure bacterium is not yet explored. The purpose of this study was to identify metabolic pathway that might be involved in bacterial degradation of triclocarban. Triclosan-degrading Sphingomonas sp. strain YL-JM2C was first found to degrade up to 35% of triclocarban (4 mg L(-1)) within 5 d. Gas chromatography-mass spectrometry detected 3,4-dichloroaniline, 4-chloroaniline and 4-chlorocatechol as the major metabolites of the triclocarban degradation. Furthermore, total organic carbon results confirmed that the intermediates, 3,4-dichloroaniline (4 mg L(-1)) and 4-chloroaniline (4 mg L(-1)) could be degraded up to 77% and 80% by strain YL-JM2C within 5 d.

Growth of Pseudomonas sp. TX1 on a wide range of octylphenol polyethoxylate concentrations and the formation of dicarboxylated metabolites

Pseudomonas sp. TX1, is able to use octylphenol polyethoxylates (OPEO(n), or Triton X-100; average n = 9.5) as a sole carbon source. It can grow on 0.05-20% of OPEO(n) with a specific growth rate of 0.34-0.44 h(-1). High-performance liquid chromatography-mass spectrometer analysis of OPEO(n) degraded metabolites revealed that strain TX1 was able to shorten the ethoxylate chain and produce octylphenol (OP). Furthermore, formation of the short carboxylate metabolites, such as carboxyoctylphenol polyethoxylates (COPEO(n), n = 2, 3) and carboxyoctylphenol polyethoxycarboxylates (COPEC(n), n = 2, 3) began at the log stage, while octylphenol polyethoxycarboxylates (OPEC(n), n = 1-3) was formed at the stationary phase. All the short-ethoxylated metabolites, OPEO(n), OPEC(n), COPEO(n), and COPEC(n), accumulated when the cells were in the stationary phase. This study is the first to demonstrate the formation of COPEO(n) and COPEC(n) from OPEO(n) by an aerobic bacterium.

Microcalorimetric studies of the effects on the interactions of human recombinant interferon-α2a

Abstract The applicability of the physical stability of protein solution monitored by isothermal titration calorimetry (ITC) was evaluated. The second virial coefficient, b 2, 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-α2a (hrIFN-α2a), which is a commercial drug applied for the treatment of virus-infected diseases. The results obtained were used to predict the possibility of hrIFN-α2a 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-α2a increased with increasing temperature and NaCl concentration, while b 2 decreased, indicating that the attraction between hrIFN-α2a 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-α2a molecules. These implications were supported by SEC data, demonstrating that the amount of aggregated hrIFN-α2a 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.

Catabolism of 4-alkylphenols by Acinetobacter sp. OP5: genetic organization of the oph gene cluster and characterization of alkylcatechol 2, 3-dioxygenase.

In this study, a specific PCR primer set was successfully designed for alkylcatechol 2, 3-dioxygenase genes and applied to detect the presence of this biomarker in 4-t-octylphenol-degrading Acinetobacter sp. strain OP5. A gene cluster (ophRBA1A2A3A4A5A6CEH) encoding multicomponent phenol hydroxylase and alkylcatechol 2, 3-dioxygenase was then cloned from this strain and showed the highest homology to those involved in the published medium-chain alkylphenol gene clusters. The pure enzyme of recombinant cell harboring ophB showed meta-cleavage activities for 4-methylcatechol (1,435%), 4-ethylcatechol (982%), catechol (100%), 4-t-butylcatechol (16.6%), and 4-t-octylcatechol (3.2%). The results suggest that the developed molecular technique is useful and easy in detection of medium/long-chain alkylphenol degradation gene cluster. In addition, it also provides a better understanding of the distribution of biodegradative genes and pathway for estrogenic-active long-chain alkylphenols in bacteria.