A simplified strategy for the identification of Gram negative fermenting rods using a desk-top computer

A total of 845 strains of Gram negative, fermenting rods isolated from humans were routinely identified using a desk-top computer. A reduced matrix of 54 taxa x 29 tests was used for a multistep procedure. By an average number of 24 tests, 97–5% of strains reached an identification score of P < 0.9.     

Development of a computer identification system for coliform strains

A computer identification system, previously described, was tested on 279 β-galactosidase-positive enterobacteria isolated from clinical material, and the results compared with API and Micro ID methods. The system was also applied to the identification of 564 strains isolated from drinking water samples. Faecal coliform species and also some new groups and species of aquatic and telluric origin characterized by numerical analysis and DNA-DNA hybridization procedures could be identified. The performance of the computer identification system with bacterial isolates from food and water is discussed.     

根瘤菌可溶性蛋白和酯酶的电泳图谱分析

我们分析行了二十株根瘤菌可溶性蛋白和酯酶的电泳图谱。菌株中14株分离自野大豆的快生型大豆根瘤菌和3株慢生型大豆根瘤菌;另外3株根瘤菌分别分离于苜蓿、豌豆和三叶草。根据它们电泳谱带的Rf值,计算了各根瘤菌可溶性蛋白图谱间的相似性系数。快生型大豆根瘤菌的电泳图谱均不同于慢生型大豆根瘤菌和其他根瘤菌。鉴于各菌株有其独特图谱,以此作为根瘤菌分类和鉴定的依据,是较可靠的方法。     

The Use of Supercomputers and Microcomputers in Computational Chemistry — Job Turnaround Time as a Criterion for the Choice of System

Abstract

The performance of a supercomputer installation (Cray-IS with Amdahl front-end) is compared with a ‘desk-top’ computer (IBM PC-AT with 80287 Numeric Data Processor) using both execution time and total job turnaround time for a set of benchmark programs which includes a Monte Carlo simulation. The effect of compiler efficiency and optimisation for system-specific hardware on execution time are discusssed. We propose the use of ‘turn-around time’ as a criterion for computer system performance, and show that judged by this criterion, ‘desk-top’ computing can provide a significant fraction of the power of a networked supercomputer installation.     

A method of DNA histogram analysis by computer and its evaluation by simultaneous combination with 3H-thymidine autoradiography

A method for determining the fractions of cells in the G1, S, and G2 + M phases of the cell life cycle, by quantifying DNA histograms derived from static fluorescence cytophotometry, was evaluated by simultaneous combination with 3H-thymidine autoradiography. DNA histograms were obtained by cytofluorometry on the Feulgen-stained autoradiographs of HeLa cells, and mouse and rat hepatocytes, after DNA labelling with 3H-thymidine. The synthetic histogram determined by "sum of discrete normal curves" technique was fitted to the experimental data according to a weighted least-squares method by a desk-top computer (HP 85F). The mean relative percent deviations of estimated cell cycle phase fractions from the actual phase fractions determined directly on an autoradiograph was 6.6 +/- 3.3%.     

Peculiarities of Alteromonas macleodii strains reflects their deep/surface habitation rather than geographical distribution

The phenotypic, chemotaxonomic and genetic peculiarities of 5 deep strains of Alteromonas macleodii (isolated from Adriatic and Ionian Sea water from a depth of 1,000-3,500 m) and 5 strains of the same species isolated from the surface layer of Aegean, Andaman, Black Sea and Atlantic Ocean water near the British shore have been studied. Electron microscopy has shown that the deep strains' cells were, on average, two times longer (2.1±0.2×0.7±0.1 μm) than the surface strains' (1.1±0.1×0.6±0.1 μm). Using fatty acid analysis (particularly the mono-unsaturated C16:1 and C18:1 fatty acids contents) the deep and surface isolates were clearly separated into two clusters. Distinctions between them were also found in different lectin binding capacity, which is probably determined by the structure of their extracellular polysaccharide matrix. Analysis of the results of PCR with primers to repeated nucleotide sequences revealed a higher level of genetic polymorphism in surface strains in comparison with the deep isolates. This division was confirmed by the cluster analysis method though it was not as clear as in the fatty acids analysis. The described peculiarities are probably reflective of specific conditions in which A. macleodii strains live on the surface or in the depth of the world's oceans.     

An inexpensive,accurate method for measuring leaf area and defoliation through digital image analysis

We report a protocol using a common desk-top scanner and public domain software for measuring existing leaf area and leaf area removed as a result of herbivory. We compared the accuracy and precision of this method to that of a standard leaf area meter. Both methods were used to measure metal disks of a known area, the area of soybean (Glycine max L.) leaves, and the area removed by simulating leaf feeding with a hole-punch. We varied the amount of injury across a low, medium, and high degree of simulated feeding. The mean area of 10 cm2 and 50 cm2 metal disks was more accurately estimated with the leaf area meter than the desk-top scanner. Leaf area estimates from both methods were highly correlated. The desk-top scanner accurately estimated the leaf area removed from the low, medium, or high degree of simulated leaf feeding. However, the leaf area meter overestimated low levels of simulated feeding injury. Though measuring a leaf's surface area with a desk-top scanner requires two steps (creating a digital image file and calculating the area represented by that image), the overall time required to measure leaf injury is shorter than with a leaf area meter. This relatively simple and inexpensive method of estimating leaf area and feeding damage has advantages in certain experimental situations where a prefeeding measurement of the leaf is impossible or undesirable, or when small amounts of feeding occur.     

Cryptococcus neoformans population includes hybrid strains homozygous at mating-type locus

Recent attempts to characterise the hybrid strains of Cryptococcus neoformans have led to the identification of a cryptic population of hybrid strains ('H strains') with double DNA content but only a single mating-type allele. To verify a set of hypotheses concerning their origin, we investigated 14 previously isolated H strains and ten F1-progeny strains arising from H99 and JEC20 mating. The double DNA content was tested by flow cytometry; the presence of only one mating type was tested by amplifying 12 mating-type-specific genes and one gene unlinked with the mating-type locus (URA5). Analysis of the F1 progeny identified two H strains, and electrophoretic karyotyping confirmed the occurrence of genetic recombination. The simultaneous presence of the homozygous and heterozygous loci, and the fact that all of the F1-progeny strains presented a recombinant karyotype, suggest that the H strains originated from the post-meiotic random fusion of two of the four recombinant nuclei. Further studies are required to elucidate the role of the homozygous mating-type loci in the virulence of C. neoformans.     

A desk-top computer coupled fermentation system for the study of microbial processes: Description and some applications

The configuration and hardware components of a desk-top computer coupled system for bench-top bioreactors are described. Examples of on-line acquisition of several directly accessible environmental process parameters and computations of directly inaccessible state variables are presented. The system described offers great advantages in experiments for establishing sophisticated control algorithms and for studying the physiological behaviour of microbial populations.     

Comparable studies of immunostimulating activities in vitro among Mycobacterium bovis bacillus Calmette–Guérin (BCG) substrains

During the serial passage of Mycobacterium bovis bacillus Calmette–Guérin (BCG) in different countries after initial seed distribution from the Pasteur Institute, specific insertions and deletions in the genome among BCG substrains were observed and speculated to result in differences in immunological activities. 'Early-shared strains' of BCG (Russia, Moreau, Japan, Sweden, Birkhaug), distributed by the Pasteur Institute, which conserve three types of mycolate (α, methoxy, keto) in cell wall, exhibited stronger activities of induction of nitric oxide, interleukin-1β (IL-1β), IL-6, IL-8, IL-12 and tumor necrosis factor (TNF)-α, from human epithelial cell line A549, human myelomonocytic cell line THP-1 and mouse bone marrow cells in the presence of interferon-γ (IFN-γ) than did 'late-shared strains' of BCG (Danish, Glaxo, Mexico, Tice, Connaught, Montreal, Phipps, Australia, Pasteur). The stronger induction of IL-12 and TNF-α in the presence of IFN-γ was also observed by trehalose 6,6'-dimycolate (TDM) extracted from BCG-Japan than by TDM from BCG-Connaught, which lacks the methoxymycolate residue. These results suggest that 'early-shared strains' are more potent immunostimulating agents than 'late-shared strains', which could be attributed partially to methoxymycolate. Our study provides the basic information for immunological characterization of various BCG strains and may contribute to a re-evaluation of them as a reference strain for vaccination against tuberculosis.     

Use of numerical profiles for studying bacterial diversity

A total of 308 bacteria were isolated from oil-storage tanks. Of these 20% were unidentifiable, even at the generic level. A numerical scoring method differentiated between the isolates and was used to estimate the diversity of the bacterial communities in the tanks over a period of 11 months. Although the scoring method suggested a higher diversity than did conventional identification, there was some consistency in the results produced by the two approaches. It is suggested that a scoring method based on only nine tests could be useful for estimating and comparing bacterial diversity in other habitats.     

Evaluation of colony-forming ability experiments using normal and DNA repair-deficient human fibroblast strains and an automatic colony counter

An automated procedure for evaluation of colony-forming ability experiments has been developed using normal and xeroderma pigmentosum fibroblast strains. Technically this consists of an image analyzer equipped with a contrast-intensifying video camera, monitor, and a desk-top computer. Complex structures composed of overlapping colonies could be reduced to the constituent single colonies by special correction programs. Eighteen experiments were evaluated, and the D0 values for colony-forming ability were determined. A systematic but correctable deviation between visual and automated counting was found. The source of this deviation is described and a solution for correction is provided. The automatic procedure reduced the evaluating time by a factor of five to ten.     

The Education and Training of Biology Teachers

A technique for the numerical identification of bacteria using normalized likelihoods calculated from a probabilistic database is described, and the principles of the technique are explained. A simple computer program, which can be used to perform the calculations and identifications on a microcomputer in undergraduate classes, is presented. The program is annotated so that the steps in the calculation can be linked to the equivalent steps in the program to assist in teaching the principles of programming. Specimen results from the program, and examples of how they should be interpreted and explained, are given. It is expected that the program will be of use to teachers of undergraduates to teach the principles of numerical identification and an important use of computers in biology.     

Carbohydrate assimilation by clinical and environmental Rhodotorula glutinis strains

This study was carried to determine the carbohydrate assimilation patterns of Rhodotorula strains isolated from clinical and environmental specimens. We have tested the commercial system ID 32C (bioMerieux, France) on 80 different strains of Rhodotorula glutinis: 47 strains from clinical samples and 33 strains from environmental samples. The assimilation percentages obtained in our study for galactose, cellobiose, gluconate and sorbose were lower than those showed in the identification table of the method. However, the assimilation percentages for mannitol and esculin were higher. According to our results, we conclude that the numerical profiles and the identification software of the commercial system present limitations for the characterization of some R. glutinis strains.     

Evaluation and Reliability of a Simplified Method for Identification of Food-Borne Yeasts

A simplified identification key described by Deak and Beuchat (T. Deak and L. R. Beuchat, J. Food Prot. 50:243-264, 1987) and the computer method of Barnett et al. (J. A. Barnett, R. W. Payne, and D. Yarrow, Yeast Identification Program, 1985) were used to identify 12 reference strains and 382 yeasts isolated from cultured milk products. Because the simplified key failed to account for species variability with regard to physiological, morphological, and sexual reproduction characteristics, poor agreement of the identification results was obtained. A reevaluation of the basic theoretical assumptions of the simplified key only confirmed the practical results and indicates that this identification method is unsatisfactory     

CLASSIFY: A group teaching exercise in microbial identification and numerical taxonomy using a Commodore 64 microcomputer

An exercise designed to teach the basic principles of numerical taxonomy is described. The exercise utilizes a computer program, CLASSIFY, written in BASIC for the Commodore 64 microcomputer, which will accept student data obtained from the identification of bacteria, calculate the similarity coefficients, and perform Single Linkage Cluster Analysis. Bacterial identification can be achieved using live cultures and rapid identification kits, or, alternatively, via the bacterial culture simulation program, BUG SIMULATOR, which would be useful for data generation by students inexperienced in handling microbes (e.g. secondary school students).     

元阳梯田地方水稻品种根部内生菌及根际微生物的分离与鉴定

采用组织分离法和土壤稀释涂板法,对元阳哈尼梯田2个地方品种‘月亮谷’和‘红脚老粳’的根部内生细菌及根际土壤细菌进行了分离,研究元阳梯田传统水稻品种特殊的内生菌组成.结果表明: 试验共得到399个菌株.经形态特征及生理生化鉴定,月亮谷根部和其根际土壤分别分离到8和5个属,其中5个属是共有的;红脚老粳的根部和其根际土壤中分别分离到10和7个属,其中6个属是共有的.经分子生物学鉴定,月亮谷根部分离到11个种和5个属,根际土壤分离到8个种和4个属,其中5个种和4个属是共有的;红脚老粳根部分离到9个种和5个属,根际土壤分离到10个种和3个属,其中4个种和2个属是共有的.通过分子生物学鉴定,大部分菌株都可以鉴定到种,而通过形态及生理生化特性只能初步鉴定到属,但两种方法在属层次上的鉴定结果基本一致.元阳地方水稻根部内生细菌及根际土壤细菌具有一定的种属同源性与特异性.     

Computer Program Designed to Follow Fluctuations in Microbial Populations and Its Application in a Study of Chesapeake Bay Microflora

A computer program has been developed which performs cluster analysis of microorganisms using methods of numerical taxonomy. The program is designed to group related strains, identify the groups by reference to known strains, and calculate a hypothetical median organism (HMO) for each group. The HMO serves to condense taxonomic information and provides a tag for each strain cluster. Every strain in a group is compared with the HMO established for that group. A representative strain for the group is obtained by selection of the strain showing highest similarity to the HMO. New data sets can be compared with data sets of previous analyses. Hence, the occurrence of the same taxonomic groups within separate data sets can be determined. Quantitative or qualitative differences in distribution of taxonomic groups within or between data sets can be measured. The output from the computer is a graphical display, using an on-line plotter; thus, the investigator is provided with visual comparison of data sets. Results obtained from a study applying the computer program in an analysis of taxonomic data obtained for 43 bacterial strains isolated from Chesapeake Bay indicate the usefulness of this method of taxonomic analysis in microbial ecology.     

Production of a Pyrrole Antibiotic by a Marine Bacterium

Evidence is presented for the isolation and identification of bacteria able to synthesize an unusual antibiotic containing five bromine atoms per molecule. The identification and taxonomic position of these bacteria was made by use of a computer in conjunction with traditional methods. These microorganisms and closely related strains have been isolated on various occasions from tropical water in the vicinity of Puerto Rico. One bacterium, a pseudomonad, has been given the name Pseudomonas bromoutilis because of its distinctive capability. The antibiotic has been extracted, purified, and obtained in crystal form, and its structure has been determined. Although clinical tests of its properties were not encouraging, it may be of significant value and interest from an ecological standpoint.