Colony size optimisation in colony-based laser imaging for microbial source tracking.

The colony-based laser scatter imaging provides a convincing solution to microbial source tracking. The optical scattering patterns of bacterial colonies are tightly correlated to the corresponding growth patterns. This relationship is manifested as the development of optical scattering patterns with the increment of colony size. An investigation was conducted into this relationship and the optimal range of colony size for improving the accuracy of microbial source tracking technique. All the bacterial samples from five host species were cultivated under the same conditions. The optical scattering patterns were recorded for the average colony diameter from 0.1 mm to 1.5 mm, using a bench top laser imaging system. Gabor wavelet was utilised to encode image signatures. Fuzzy-C-means was employed to cluster the colony patterns from the same host species. The experimental results demonstrate that the optimal range of the colony diameters is 0.8-1.0 mm. The corresponding identification rate of microbial source tracking is >80%.

Algorithms for modeling structural changes in human chromosomes.

Human cytogenetics is the study of chromosomes (typically at mitotic metaphase). The study of chromosomes has recently become integrated with molecular biology and genomics. Thus, it is an important part of genetics education. However, it is time consuming to train students and clinical technologists to recognize patterns of G-banded human chromosomes because of the dynamic nature of G-band resolutions in different metaphase spreads. Moreover, there are limited resources to obtain the images of abnormal chromosomes. We present in this paper an advanced version of computer based interactive tutorial program capable of simulating chromosome abnormalities, altering chromosome shapes, and manipulating G-band resolutions for human cytogenetic seduction. By simulating chromosomes using digital image processing and pattern recognition, the versatile software, together with various strategies such as website links and dialogs, will provide students with a virtual learning environment for self-practicing and testing, thus transforming the traditionally dry and ineffective approach into an exciting and efficient learning process.

Laser imaging for rapid Microbial Source Tracking.

DNA fingerprinting, PCR and other genomic technologies have recently been used to determine sources of fecal bacteria in waterways. Here, we report on the development of a simple and automated optical method for potential use in Microbial Source Tracking (MST) of E. coli. The method employs laser imaging of bacterial colonies and high-resolution optical scattering image analysis for information extraction and classification. Cross validation is used to statistically evaluate the robustness of the classifiers. The entire image analysis procedure can be fully automated, making this a potentially useful tool for future MST studies.

Interactive computer program for learning genetic principles of segregation and independent assortment through meiosis.

Teaching fundamental principles of genetics such as segregation and independent assortment of genes could be challenging for high school and college biology instructors. Students without thorough knowledge in meiosis often end up of frustration and failure in genetics courses. Although all textbooks and laboratory manuals have excellent graphic demonstrations and photographs of meiotic process, students may not always master the concept due to the lack of hands-on exercise. In response to the need for an effective lab exercise to understand the segregation of allelic genes and the independent assortment of the unlinked genes, we developed an interactive program for students to manually manipulate chromosome models and visualize each major step of meiosis so that these two genetic principles can be thoroughly understood.

Stable transcriptional status in the apoptotic erythroid genome.

When a cell is destined for apoptosis, will its genome reprogram its transcriptional machinery to overcome the life-threatening challenge? To address this issue, we performed a genome-wide transcriptome analysis in EPO (erythropoietin) deprivation-induced apoptotic erythroid cells using the SAGE method. The results show that the transcript contents for the majority of the genes remain unchanged in the apoptotic cells, including the apoptotic genes and the heat shock genes. Of the small number of genes with an altered expression, they are mainly associated with cellular structure. Our study reveals that there is no genetic reprogramming for the transcriptional machinery in the apoptotic genome. Apoptosis, as defined by programmed cell death, is not a crisis but a peaceful physiological process.

Seasonal persistence and population characteristics of Escherichia coli and enterococci in deep backshore sand of two freshwater beaches.

We studied the shoreward and seasonal distribution of E. coil and enterococci in sand (at the water table) at two southern Lake Michigan beaches-Dunbar and West Beach (in Indiana). Deep, backshore sand (approximately 20 m inland) was regularly sampled for 15 months during 2002-2003. E. coli counts were not significantly different in samples taken at 5-m intervals from 0-40 m inland (P = 0.25). Neither E. coli nor enterococci mean counts showed any correlation or differences between the two beaches studied. In laboratory experiments, E. coli readily grew in sand supplemented with lake plankton, suggesting that in situ E. coil growth may occur when temperature and natural organic sources are adequate. Of the 114 sand enterococci isolates tested, positive species identification was obtained for only 52 (46%), with E. faecium representing the most dominant species (92%). Genetic characterization by ribotyping revealed no distinct genotypic pattern (s) for E. coli, suggesting that the sand population was rather a mixture of numerous strains (genotypes). These findings indicate that E. coli and enterococci can occur and persist for extended periods in backshore sand at the groundwater table. Although this study was limited to two beaches of southern Lake Michigan, similar findings can be expected at other temperate freshwater beaches. The long-term persistence of these bacteria, perhaps independent of pollution events, complicates their use as indicator organisms. Further, backshore sand at the water table may act as a reservoir for these bacteria and potentially for human pathogens.

2.45 GHz radiofrequency fields alter gene expression in cultured human cells.

The biological effect of radiofrequency (RF) fields remains controversial. We address this issue by examining whether RF fields can cause changes in gene expression. We used the pulsed RF fields at a frequency of 2.45 GHz that is commonly used in telecommunication to expose cultured human HL-60 cells. We used the serial analysis of gene expression (SAGE) method to measure the RF effect on gene expression at the genome level. We observed that 221 genes altered their expression after a 2-h exposure. The number of affected genes increased to 759 after a 6-h exposure. Functional classification of the affected genes reveals that apoptosis-related genes were among the upregulated ones and the cell cycle genes among the downregulated ones. We observed no significant increase in the expression of heat shock genes. These results indicate that the RF fields at 2.45 GHz can alter gene expression in cultured human cells through non-thermal mechanism.