A variety of yeast species are known to host systems of cytoplasmic linear dsDNA molecules that establish replication and transcription independent of the nucleus via self-encoded enzymes that are phylogenetically related to those encoded by true infective viruses. Such yeast virus-like elements (VLE) fall into two categories: autonomous VLEs encode all the essential functions for their inheritance, and additional, dependent VLEs, which may encode a toxin-antitoxin system, generally referred to as killer toxin and immunity. In the two cases studied in depth, killer toxin action relies on chitin binding and hydrophobic domains, together allowing a separate toxic subunit to sneak into the target cell. Mechanistically, the latter sabotages codon-anticodon interaction by endonucleolytic cleavage of specific tRNAs 3' of the wobble nucleotide. This primary action provokes a number of downstream effects, including DNA damage accumulation, which contribute to the cell-killing efficiency and highlight the importance of proper transcript decoding capacity for other cellular processes than translation itself. Since wobble uridine modifications are crucial for efficient anticodon nuclease (ACNase) action of yeast killer toxins, the latter are valuable tools for the characterization of a surprisingly complex network regulating the addition of wobble base modifications in tRNA.

This study aims to obtain lactic acid bacteria (LAB) which have probiotic properties and inhibitory effects against pathogens. Peda fish fermented in 20% salt solution used as samples. Antimicrobial properties of LAB isolates against gram-positive and gram-negative pathogens (Salmonella typhi BPE 127.1.MC, Salmonella typhi BPE 122.4.CCA, Salmonella typhi NCTC 786, Salmonella typhimurium FNCC 0050, Pseudomonas putida FNCC 0071, Bacillus subtilis ATCC 6633 and Staphylococcus aureus ATCC 25923) were tested using agar well diffusion method. To exclude acid production, the cell-free culture supernatant (CFCS) solution was neutralized using 1 N NaOH before antimicrobial activity was tested. Likewise with bacteriocin tests, CFCS solutions that have been neutralized, were treated first by heating at 100ºC for 10 minutes in order to enzyme inactivation. A total of 26 out of 50 LAB isolates showed clear zones in the MRS-CaCO3 agar medium, gram positive, and negative catalase as the main characteristics of LAB. Sixteen of the 26 LAB isolates were known to be tolerant to pH 2 and 1% of bile salts. In addition, 92.3% of LAB isolates (15 of 16 LAB isolates) were homofermentative. The antimicrobial test results found that two of 26 LAB isolates (i.e. LAB Pr.3.4L and Pi.5.8 isolates) were shown to have very strong inhibitory effects against gram-positive pathogens S. aureus ATCC 25923 compared to S. typhi BPE 122.4.CCA. Thus the two strains of LAB are indicated as bacteriocin-producing probiotic strains, and need to be pursued further for identification and optimization of production.

Debaryomyces hansenii is a halotolerant yeast species that has been shown to carry various nuclear genes of plasmid or viral origin (NUPAVs). However, a recent ancestor of such NUPAVs has not been identified. Here we determined for the first time the molecular structure of an entire cytoplasmic linear plasmid, pDH1A, indigenous to this species. The element is related to non-autonomous killer plasmids from Kluyveromyces lactis and Pichia acaciae and carries a B-type DNA polymerase as well as remnants of a killer toxin system, a secreted chitin-binding protein. Other essential toxin subunits or an immunity function, however, appear to be lost, while two additional small open reading frames are present. Transcripts for all four genes located on pDH1A could be verified by RT-PCR. Interestingly, all genes from pDH1A could be identified as ancestors of NUPAVs located at different chromosomes within the nucleus of D. hansenii, suggesting repeated nuclear capture of fragments originating from pDH1A. The sequence of pDH1A has been deposited in the GenBank data library, Accession No. JN624283.

Study on molecular characteristics of Salmonella from clinical isolates was done in order to find out its relationship, especially those isolated from Indonesia. Partial sequence of genes belonging to QRDR region, i.e. gyrA, gyrB, parC, and parE were employed. Specific primer pairs covering those genes are used to amplify the bacterial DNA obtained. The amplicons were then analyzed by means of sequencing, and the sequences are analysed bioinformatically to find out similarities and build phylogenetic trees. By comparing all of the phylogenetic tree from QRDR region, this study revealed gyrA as the most suitable gene for rapidly identify member of salmonellae as it gives better separation of samples being analysed. However, the use of parC is recommended as it gives a consistent and reliable value to separate member of Salmonella and other Enterobacter. Further studies are under way to include member of this group, like E. coli, and the use of full sequence of QRDR genes region to verify this report.