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Lactose metabolism is a changeable phenotype in strains of Lactobacillus casei. In this study, we found that L. casei ATOC 27139 was unable to utilize lactose. However, when exposed to lactose as the sole carbon source, spontaneous [Lac.sup.+] clones could be obtained. A gene cluster (lacTEGF--galKETRM) involved in the metabolism of lactose and galactose in L. casei ATCC 27139 ([Lac.sup.-]) and its [Lac.sup.+] revertant (designated strain R1) was sequenced and characterized. We found that only one nucleotide, located in the lacTEGF promoter (lacTp), of the two lac--gal gene clusters was different. The protein sequence identity between the lac--gal gene cluster and those reported previously for some L. casei ([Lac.sup.+]) strains was high; namely, 96-100 % identity was found and no premature stop codon was identified. A single point mutation located within the lacTp promoter region was also detected for each of the 41 other independently isolated [Lac.sup.+] revertants of L. casei ATCC 27139. The revertants could be divided into six classes based on the positions of the point mutations detected. Primer extension experiments conducted on transcription from lacTp revealed that the lacTp promoter of these six classes of [Lac.sup.+] revertants was functional, while that of L. casei ATCC 27139 was not. Northern blotting experiments further confirmed that the lacTEGF operon of strain R1 was induced by lactose but suppressed by glucose, whereas no blotting signal was ever detected for L. casei ATCC 27139. These results suggest that a single point mutation in the lacTp promoter was able to restore the transcription of a fully functional lacTEGF operon and cause a phenotype switch from [Lac.sup.-] to [Lac.sup.+] for L. casei ATCC 27139.

An insertion sequence, ISLC3, of 1351 bp has been isolated from Lactobacillus casei. Formation of IS circles containing a 3 bp spacer (complete junction) or deletion of 25 bp at the left inverted repeat (IRL) between the abutted IS ends of the ISLC3 junction region (deleted junction) was also discovered in the lactobacilli and Escherichia coli system studied. We found that the promoter formed by the complete junction Pjun was more active than that formed by the 25 bp deleted junction [P.sub.djun] or the indigenous promoter [P.sub.IRL]. The corresponding transcription start sites for both promoter [P.sub.jun] and [P.sub.IRL] as well as [P.sub.djun] were subsequently determined using a primer extension assay. The activity of transposase OrfAB of ISLC3 was also assayed using an in vitro system. It was found that this transposase preferred to cleave a single DNA strand at the IRR over the IRL end in the transposition process, suggesting that attack of one end by the other was oriented from IRR to IRL.

Abstract Background The protein structures of the disease-associated proteins are important for proceeding with the structure-based drug design to against a particular disease. Up until now, proteins structures are usually searched through a PDB id or some sequence information. However, in the HDAPD database presented here the protein structure of a disease-associated protein can be directly searched through the associated disease name keyed in. Description The search in HDAPD can be easily initiated by keying some key words of a disease, protein name, protein type, or PDB id. The protein sequence can be presented in FASTA format and directly copied for a BLAST search. HDAPD is also interfaced with Jmol so that users can observe and operate a protein structure with Jmol. The gene ontological data such as cellular components, molecular functions, and biological processes are provided once a hyperlink to Gene Ontology (GO) is clicked. Further, HDAPD provides a link to the KEGG map such that where the protein is placed and its relationship with other proteins in a metabolic pathway can be found from the map. The latest literatures namely titles, journals, authors, and abstracts searched from PubMed for the protein are also presented as a length controllable list. Conclusions Since the HDAPD data content can be routinely updated through a PHP-MySQL web page built, the new database presented is useful for searching the structures for some disease-associated proteins that may play important roles in the disease developing process for performing the structure-based drug design to against the diseases.

Abstract Background The number of sequences compiled in many genome projects is growing exponentially, but most of them have not been characterized experimentally. An automatic annotation scheme must be in an urgent need to reduce the gap between the amount of new sequences produced and reliable functional annotation. This work proposes rules for automatically classifying the fungus genes. The approach involves elucidating the enzyme classifying rule that is hidden in UniProt protein knowledgebase and then applying it for classification. The association algorithm, Apriori, is utilized to mine the relationship between the enzyme class and significant InterPro entries. The candidate rules are evaluated for their classificatory capacity. Results There were five datasets collected from the Swiss-Prot for establishing the annotation rules. These were treated as the training sets. The TrEMBL entries were treated as the testing set. A correct enzyme classification rate of 70% was obtained for the prokaryote datasets and a similar rate of about 80% was obtained for the eukaryote datasets. The fungus training dataset which lacks an enzyme class description was also used to evaluate the fungus candidate rules. A total of 88 out of 5085 test entries were matched with the fungus rule set. These were otherwise poorly annotated using their functional descriptions. Conclusion The feasibility of using the method presented here to classify enzyme classes based on the enzyme domain rules is evident. The rules may be also employed by the protein annotators in manual annotation or implemented in an automatic annotation flowchart.

Polymer solution dynamics may be inferred from light scattering spectra of dissolved optical probe particles. We compare a variety of probes in solutions of several polymers. In the ‘‘overlapping’’ concentration/molecular weight regime, the Stokes–Einstein equation fails by up to a factor of 2, while the probe diffusion coefficient D follows a scaling law D/D0=exp(-aMγcνRδ) (c, M, and R are the polymer concentration, molecular weight, and the probe radius, respectively). Experimentally, γ=0.8±0.1, ν=0.6–1.0, and δ=-0.1 to 0, contrary to the theoretical predictions γ=0 and δ=1. With very high molecular-weight polymers, we observe a further ‘‘entangled’’ regime, characterized by huge (104) failures of the Stokes–Einstein equation and the appearance of ‘‘fast’’ modes in the scattering spectrum. [ABSTRACT FROM AUTHOR]