PCR-based assay for detection of four coral pathogens

Several microorganisms have been identified as pathogenic agents responsible for various outbreaks of coral disease. Little has been learned about the exclusivity of a pathogen to given disease signs. Most pathogens have only been implicated within a subset of corals, leaving gaps in our knowledge of the host range and geographic extent of a given pathogen. PCR-based assays provide a rapid and inexpensive route for detection of pathogens. Pathogen-specific 16S rDNA primer sets were designed to target four identified coral pathogens: Aurantimonas coralicida, Serratia marcescens, Vibrio shilonii, and Vibrio coralliilyticus. Assays detected the presence of targets at concentrations of less than one cell per microliter. The assay was applied to 142 coral samples from the Florida Keys, Puerto Rico, and U.S. Virgin Islands as an in situ specificity test. Assays displayed a high-level of specificity, seemingly limited only by the resolution of the 16S rDNA.

Fish recolonization in temperate Australian rockpools: a quantitative experimental approach

Understanding recolonization processes of intertidal fish assemblages is integral for predicting the consequences of significant natural or anthropogenic impacts on the intertidal zone. Recolonization of experimentally defaunated intertidal rockpools by fishes at Bass Point, New South Wales (NSW), Australia, was assessed quantitatively by using one long-term and two short-term studies. Rockpools of similar size and position at four sites within the intertidal zone were repeatedly defaunated of their fish fauna after one week, one month, and three months during two shortterm studies in spring and autumn (5 months each), and every six months for the long-term study (12 months). Fish assemblages were highly resilient to experimental perturbations—recolonizing to initial fish assemblage structure within 1−3 months. This recolonization was primarily due to subadults (30−40 mm TL) and adults (>40 mm TL) moving in from adjacent rockpools and presumably to abundant species competing for access to vacant habitat. The main recolonizers were those species found in highest numbers in initial samples, such as Bathygobius cocosensis, Enneapterygius rufopileus, and Girella elevata. Defaunation did not affect the size composition of fishes, except during autumn and winter when juveniles (<30 mm TL) recruited to rockpools. It appears that Bass Point rockpool fish assemblages are largely controlled by postrecruitment density-dependent mechanisms that indicate that recolonization may be driven by deterministic mechanisms.

Quantitative determination of the timing of otolith ring formation from marginal increments in four marine teleost species from northwestern Australia

The sectioned otoliths of four fish species from a tropical demersal trawl fishery in Western Australia revealed a series of alternating trans-lucent and opaque zones in reflected light. The translucent zones, referred to as growth rings, were counted to determine fish ages. The width of the opaque zone on the periphery of the otolith section as a proportion of the width of the previous opaque zone (index of completion) was used to determine the periodicity of growth-ring formation. This article describes a method for modeling changes in the index of ring completion over time, from which a parameter for the most probable time of growth-ring formation (with confidence intervals) can be determined. The parameter estimate for the timing of new growth-ring formation for Lethrinus sp. 3 was from mid July to mid September, for Lutjanus vitta from early July to the end of August, for Nemipterus furcosus from mid July to late September, and for Lutjanus sebae from mid July to mid November. The confidence intervals for the timing of formation of growth rings was variable between species, being smallest for L. vitta, and variable between fish of the same species with different numbers of growth rings. The stock assessments of these commercially important species relies on aging information for all the age classes used in the assessment. This study demonstrated that growth rings on sectioned otoliths were laid down annually, irrespective of the number of growth rings, and also demonstrated that the timing of ring formation for these tropical species can be determined quantitatively (with confidence intervals.

Quantitative and qualitative studies on the bacterial flora of fresh sardines

Plate counts at R T and 8 C on the skin with muscle and the gut contents of absolutely fresh sardines (Sardinella longiceps) caught off Cochin showed a seasonal variation when sampling was done over a period of 12 months. The counts of the gut contents ran parallel with those of the skin with muscle, but at a higher level of magnitude. Qualitatively, the analysis of 360 strains of bacteria isolated from the skin with muscle and 100 strains from the guts during a year's study revealed a very high preponderance of Gram negative rods, mainly of Achromobacter, Vibrio, and Pseudomonas groups. The percentage of Gram positive organism was very low or nil at times in the ocean fresh sardines.

Quantitative survey of Sargassum along the south-west coast of Ceylon

Sargassum is a brown seaweed from which alginic acid is extracted. A survey was carried out off the south-west coast of Ceylon in December 1963 and January 1964 with the view to determining the quantity of Sargassum available.

Quantitative and qualitative assessment of plankton: some ecological aspect and water quality parameters of the river Meghna, Bangladesh

Investigation on the seasonal distribution and abundance of various major taxa of phyto and zooplankton and the corresponding physico-chemical characteristics were carried out in four selected stations between the latitude 22°35.494N N-23°23.987 N and longitude 90°35.793 E- 90°49.061 E of the Meghna river system, Bangladesh. Drop count method was followed for the qualitative and quantitative analysis of both phyto- and zooplankton. A total of 41 phytoplankton genera belonging to 17 families and 13 zooplankton genera belonging to 11 families were recorded. Zooplankton growth cycle was noticeably less (3.0%) than the phytoplankton abundance almost throughout the study period. Quantity of plankton registered to increase chronologically from the upper to lower stretches of the river. During summer investigation the load of phytoplankton was recorded maximum (11,300-51,850 No/1). Ratio-wise quantitative difference between zoo- and phytoplankton in composition of the total standing crop fluctuated between 1.0:5.5 and 1:1037. Among the phytoplanktonic groups, Chlorophyceae was found to be dominating (95.0%) in all sampling stations. Protococcus, a single genus of Chlorophyceae played a unique role during summer, contributing the highest density of about 74.0%. The pattern of qualitative and quantitative difference of plankton standing crop in different sampling sites can be attributed to the existing physico-chemical characteristics, mainly water temperature, pH and hardness.

Extraction, PCR amplification, and sequencing of mitochondrial DNA from scent mark and feces in the giant panda

To expand the feasibility of applying simple, efficient, non-invasive DNA preparation methods using samples that can be obtained from giant pandas living in the wild, we investigated the use of scent markings and fecal samples. Giant panda-specific oligonucleotide primers were used to amplify a portion of the mitochondrial DNA control region as well as a portion of the mitochondrial DNA cytochrome b gene and tRNA(Thr) gene region. A 196 base pair (bp) fragment in the control region and a 449 bp fragment in the cytochrome b gene and tRNA(Thr) gene were successfully amplified. Sequencing of polymerase chain reaction (PCR) products demonstrated that the two fragments are giant panda sequences. Furthermore, under simulated field conditions we found that DNA can be extracted from fecal samples aged as long as 3 months. Our results suggest that the scent mark and fecal samples are simple, efficient, and easily prepared DNA sources. (C) 1998 Wiley-Liss, Inc.

Characterization of Sarcocystis species in domestic animals using a PCR-RFLP analysis of variation in the 18S rRNA gene: a cost-effective and simple technique for routine species identification

Thirteen restriction endonucleases were used to investigate nucleotide sequence variation in the 18S rRNA DNA of 88 individuals from ten Sarcocystis taxa collected as cysts from their intermediate hosts, swine, cattle and water buffalo. A DNA sequence of

A PCR-based RFLP analysis of Sarcocystis cruzi (Protozoa : Sarcocystidae) in Yunnan province, PR china, reveals the water buffalo (Bubalus bubalis) as a natural intermediate host

A polymerase chain reaction-based restriction fragment length polymorphism (RFLP) approach is used to examine Sarcocystis cruzi-like taxa from the atypical intermediate host, water buffalo, in Yunnan, People's Republic of China. The loci examined lie with

The bacteriology of oil sardine (Sardinella longiceps) and mackerel (Rastrelliger kanagurta) caught from tropical waters off Cochin. 1 - Quantitative aspects

The total aerobic viable plate counts (TPCs) of skin, gills and intestine of newly caught oil sardine (Sardinella longiceps) and Indian mackerel ( Rastrelliger kanagurta) at four different temperatures, namely 36 ± 1°C, 28 ± 2°C (RT), 8 ± 1°C and 1 ±1°C, are reported. The total plate count at RT of the skin of oil sardine and Indian mackerel were in the range of l0 super(3) to 10 super(7) and 10 super(4) to 10 super(6) per cm², that of gills in the range of 10 super(5) to 10 super(9) and 10 super(4) to 10 super(8) per g and that intestine in the range of 10 super(5) to 10 sueper(9) and 10 super(5) to 10 super(8) per g respectively. The TPCs were markedly affected by the incubation temperature. Incubation at 28 ± 2°C gave the highest count; at 36 ± 1°C and 8 ± 1°C, the counts decreased by nearly 1-2 log cycles from that at RT. Incubation at 1 ± 1°C registered the lowest count. The peak values for bacterial counts of these fishes occurred at different periods of the year.