Identification of signature and primers specific to genus <Emphasis Type="Italic">Pseudomonas</Emphasis> using mismatched patterns of 16S rDNA sequences

Background

Pseudomonas, a soil bacterium, has been observed as a dominant genus that survives in different habitats with wide hostile conditions. We had a basic assumption that the species level variation in 16S rDNA sequences of a bacterial genus is mainly due to substitutions rather than insertion or deletion of bases. Keeping this in view, the aim was to identify a region of 16S rDNA sequence and within that focus on substitution prone stretches indicating species level variation and to derive patterns from these stretches that are specific to the genus.

Results

Repeating elements that are highly conserved across different species of Pseudomonas were considered as guiding markers to locate a region within the 16S gene. Four repeating patterns showing more than 80% consistency across fifty different species of Pseudomonas were identified. The sub-sequences between the repeating patterns yielded a continuous region of 495 bases. The sub-sequences after alignment and using Shanon's entropy measure yielded a consensus pattern. A stretch of 24 base positions in this region, showing maximum variations across the sampled sequences was focused for possible genus specific patterns. Nine patterns in this stretch showed nearly 70% specificity to the target genus. These patterns were further used to obtain a signature that is highly specific to Pseudomonas. The signature region was used to design PCR primers, which yielded a PCR product of 150 bp whose specificity was validated through a sample experiment.

Conclusions

The developed approach was successfully applied to genus Pseudomonas. It could be tried in other bacterial genera to obtain respective signature patterns and thereby PCR primers, for their rapid tracking in the environmental samples.

     

Revision of the coral genus Acropora (Scleractinia: Astrocoeniina: Acroporidae) in Indonesia

The coral genus Acropora is reviewed from Indonesia for the first time, following detailed collections made at 131 sites and additional material collected from approximately 40 sites throughout the archipelago during the period 1993–6. Eighty-three species are recorded, four of these ( Acropora halmaherae, A. awi, A. plumosa and A. simplex ) new to science, six first described in 1994 and six in 1997. Records are compared with specimen-based records from localities worldwide. The species of Acrokora occurring in Indonesian waters include five recorded only from the Indian Ocean and Indonesia, seven recorded only from the Pacific Ocean, South China Sea and Indonesia, and a further 10 species apparently endemic to Indonesia, as well as widespread Indo-Pacific species. Two species ( A. jacquelineae Wallace, 1994 and A. batunai Wallace, 1996) are recorded only from north central Indonesia and Papua New Guinea, and two species ( A. russelli Wallace, 1994 and A. turaki Wallace, 1994) only from north central Indonesia and north western Australia. The findings contribute to a new view of the corals of the Indo-Pacific 'centre of diversity' as a composite fauna with origins in a number of events in space and time.     

Physiological and Anatomical Effects of Growth Temperature on Phaseolus vulgaris L. Cultivars

Two Phaseolus vulgaris L. cultivars were grown at 20/15, 25/20,and 30/25 °C day/night temperatures in growth chambers witha 16 h thermoperiod corresponding to the photoperiod. When thefirst trifoliolate leaf was fully expanded rates of CO₂ exchange(CER) were measured at 27 °C and saturating light usinginfrared gas analysis. Stomatal (r_s) and mesophyll resistances,CO₂ compensation points, activities of the enzymes ribulosebisphosphate carboxylase (RuBPCase), glycolate oxidase (GAO),malate dehydrogenase (MDH), and fructose-1, 6 diphosphate (FDP),chlorophyll content, Hill activities, and leaf anatomy at boththe light and electron microscope level were also investigatedin these leaves. Rates of CO₂ exchange in the light, transpiration rate, andchlorophyll content increased with increasing growth temperaturewhile leaf thickness, specific leaf weight, RuBPCase activity,compensation point, and stomatal resistance decreased. Mesophyllresistance also decreased when calculated assuming zero chloroplastCO₂ concentration (rm, o), but not when calculated assuminga chloroplast CO₂ concentration equal to the CO₂ compensationconcentration (rm, g). Average leaf size was maximal in 25/20°C plants while dark respiration, MDH activity, stomataldensity, and starch were minimal. The activities of GAO andFDP and Hill activity were not affected by temperature pretreatment.     

A Newly Revised Classification of the Protozoa*

SYNOPSIS The subkingdom Protozoa now includes over 65,000 named species, of which over half are fossil and ～ 10,000 are parasitic. Among living species, this includes ～ 250 parasitic and 11,300 free-living sarcodines (of which ～ 4,600 are foraminiferids); 1.800 parasitic and 5,100 free-living flagellates: ～ 5,600 parasitic “Sporozoa” (including Apicomplexa, Microspora, Myxospora, and Aseetospora); and ～ 2,500 parasitic and 4,700 free-living ciliates. There are undoubtedly thousands more still unmamed. Seven phyla of PROTOZOA are accepted in this classification—SARCOMASTIGOPHORA. LABYRINTHOMORPHA, APICOMPLEXA, MICROSPORA, ASCETOSPORA, MYXOSPORA, and CILIOPHORA. Diagnoses are given for these and for all higher taxa through suborders, and representative genera of each are named. the present scheme is a considerable revision of the Society's 1964 classification, which was prepared at a time when perhaps 48,000 species had been named. It has been necessitated by the acquisition of a great deal of new taxonomic information, much of it through electron microscopy. It is hoped that the present classification incorporates most of the major changes that will be made for some time. and that it will be used for many years by both protozoologists and non-protozoologists.