The diversity of extradiol dioxygenase (edo) genes in cresol degrading rhodococci from a creosote-contaminated site that express a wide range of degradative abilities.

Analysis of the bacterial population of soil surface samples from a creosote-contaminated site showed that up to 50% of the culturable micro-organisms detected were able to utilise a mixture of cresols. From fifty different microbial isolates fourteen that could utilise more than one cresol isomer were selected and identified by 16S rRNA analysis. Eight isolates were Rhodococcus strains and six were Pseudomonas strains. In general, the Rhodococcus strains exhibited a broader growth substrate range than the Pseudomonas strains. The distribution of various extradiol dioxygenase (edo) genes, previously associated with aromatic compound degradation in rhodococci, was determined for the Rhodococcus strains by PCR detection and Southern-blot hybridization. One strain, Rhodococcus sp. I1 exhibited the broadest growth substrate range and possessed five different edo genes. Gene disruption experiments indicated that two genes (edoC and edoD) were associated with isopropylbenzene and naphthalene catabolism respectively. The other Rhodococcus strains also possessed some of the edo genes and one (edoB) was present in all of the Rhodococcus strains analysed. None of the rhodococcal edo genes analysed were present in the Pseudomonas strains isolated from the site. It was concluded that individual strains of Rhodococcus possess a wide degradative ability and may be very important in the degradation of complex mixtures of substrates found in creosote.

The Diversity of Type Ia Supernovae: Evidence for Systematics?

The photometric and spectroscopic properties of 26 well-observed Type Ia Supernovae (SNe Ia) were analyzed with the aim of exploring SN Ia diversity. The sample includes (Branch) normal SNe, as well as extreme events such as SN 1991T and SN 1991bg, while the truly peculiar SNe Ia, SN 2000cx and SN 2002cx, are not included in our sample. A statistical treatment reveals the existence of three different groups. The first group (FAINT) consists of faint SNe Ia similar to SN 1991bg, with low expansion velocities and rapid evolution of Si II velocity. A second group consists of normal SNe Ia, also with high temporal velocity gradient (HVG), but with brighter mean absolute magnitude =-19.3 and higher expansion velocities than the FAINT SNe. The third group includes both normal and SN 1991T-like SNe Ia: these SNe populate a narrow strip in the Si II velocity evolution plot, with a low-velocity gradient (LVG), but have absolute magnitudes similar to HVGs. While the FAINT and HVG SNe Ia together seem to define a relation between R(Si II) and ���m15(B), the LVG SNe either do not conform to that relation or define a new, looser one. The R(Si II) premaximum evolution of HVGs is strikingly different from that of LVGs. We discuss the impact of this evidence on the understanding of SN Ia diversity, in terms of explosion mechanisms, degree of ejecta mixing, and ejecta-circumstellar material interaction.

Levels and distribution of genetic diversity of coconut (Cocos nucifera L., var. Typica form typica) from Sri Lanka assessed by microsatellite markers

The coconut variety Typica, form typica, commonly known as Sri Lanka tall coconuts is the most widely exploited and grown variety in Sri Lanka. Under the coconut bio-diversity conservation programme, several Typica populations have been collected by island-wide surveys and planted ex situ. Thirty-three coconut populations were subjected to microsatellite assay with eight coconut-specific microsatellite primer pairs in order to study the levels and distribution of genetic variation of the collected materials for formulating future collection strategies and selecting parents for the breeding programme. A total of 56 alleles were detected ranging from 3 to 10 alleles per primer pair with an average of 7 alleles per locus. Overall a very high level of genetic diversity was detected (0.999) for all the populations studied ranging from 0.526 for population Debarayaya to 0.683 for population Dickwella. Only four introduced coconut populations, i.e. Clovis, Margeret, Dickwella, Mirishena and an embryo-cultured population were clearly separated from the resulting dendrogram. A very high level of within population variation (99%) accounted for native populations suggests a common history and a restricted genetic base for native Sri Lankan tall coconuts. Categorization of alleles into different classes according to their frequency and distribution confirmed the results of the dedrogram and concluded the adequacy of single large collection from the entire target area to represent the total genetic diversity in Sri Lanka. This study discusses useful information regarding conservation and breeding of coconut in Sri Lanka.

Understanding genetic diversity of the liver fluke Fasciola hepatica

Economical breeding is important to obtain maximum gain from the breeding in the animal sector. The economic loss has to be eliminated or should be minimized. The liver fluke, Fasciola hepatica, present mostly in sheep and dairy cattle affect the yield of animals and even cause their death. To eliminate or minimize the impact of these parasites on the animals, it is important to understand the genetic diversity of the liver fluke populations and the relationship between parasite and host at regional bases. This research was carried out to determine diversity by sequence analysis of the mitochondrial ND1 gene and ribosomal ITS1 region.

Comparison of techniques to examine the diversity of fungi in adult patients with cystic fibrosis

This study compares conventional and molecular techniques for the detection of fungi in 77 adult cystic fibrosis (CF) patients. Three different methods were investigated, i.e., (1) conventional microbiological culture (including yeasts and filamentous fungi), (2) mycological culture with CF-derived fungal specific culture media, and (3) Non-culture and direct DNA extraction from patient sputa. Fungi isolated from environmental air samples of the CF unit were compared to fungi in sputa from CF patients. Fungi (n = 107) were detected in 14/77(18%) of patients by method 1, in 60/77 (78%) of patients by method 2 and with method 3, in 77/77(100%) of the patients. The majority of yeasts isolated were Candida albicans and C. dubliniensis. Exophiala (Wangiella) dermatitidis, Scedosporiumapiospermum, Penicillium spp., Aspergillus fumigatus, and Aspergillus versicolor were also identified by sequence analysis of the rDNA short internal transcribed spacer (ITS2) region. Conventional laboratory analysis failed to detect fungi in 63 patients mainly due to overgrowth by Gram-negative organisms. Mycological culture with antibiotics dramatically increased the number of fungi that could be detected. Molecular techniques detected fungi such as Saccharomyces cerevisiae, Malassezia spp., Fuscoporia ferrea, Fusarium culmorum, Acremonium strictum, Thanatephorus cucumeris and Cladosporium spp. which were not found with other methods. This study demonstrates that several potentially important fungi may not be detected if mycological culture methods alone are used. A polyphasic approach employing both enhanced mycological culture with molecular detection will help determine the presence of fungi in the sputa of patients with CF and their healthcare environment.

Molecular diversity of the HLA-C gene identified in a Caucasian population

A DNA typing procedure, based on a two stage polymerase chain reaction-sequence-specific oligonucleotide probe (PCR-SSOP) typing strategy, has been developed and applied to DNA from 1000 healthy individuals from the Northern Ireland region. The two-stage procedure involves human leukocyte antigen (HLA-C) identification through the use of a medium resolution PCR-SSOP system, followed by four secondary group specific PCR-SSOP systems, to enable allele resolution. The PCR-SSOP systems were designed for the identification of HLA-Cw alleles with possible discrimination within exons 2 and 3 of the HLA-C gene, i.e., HLA-Cw*01-Cw*16. PCR-SSP tests were designed for the resolution of HLA-Cw*17 and -Cw*18 alleles. The systems can also be used independently of each other if selective allele resolution is required. HLA-Cw allele frequencies occuring within the Northern Ireland population have been compiled, along with estimations of HLA-B/Cw haplotype frequencies. (C) American Society for Histocompatibility and Immunogenetics, 2002. Published by Elsevier Science Inc.

Genetic diversity of liver flukes (Fasciola hepatica) from Eastern Europe.

The genetic diversity of liver fluke populations in three different countries from Eastern Europe (Greece, Bulgaria, and Poland) in comparison with available data from other countries was determined. Specifically, SNPs from regions of two nuclear genes, 28S rDNA, ß-tubulin 3 and an informative region of the mitochondrial genome were examined. Two major lineages for the 28S rDNA gene based on the highly polymorphic 105th nucleotide position were found. These lineages were widely and almost equally spread not only through the countries studied but also in other investigated geographical areas. Two basic lineages and additional haplotypes were defined for the mtDNA gene region, consisting of the cytochrome c oxidase subunit III gene, transfer RNA histidine gene and cytochome b gene. The basic lineages were observed within Greek, Bulgarian, and Polish Fasciola hepatica populations but the distribution of additional haplotypes differed between the populations from the three countries. For the ß-tubulin 3 gene multiple polymorphic sites were revealed but no explicit clades. The SNPs were spread unequally in all studied geographical regions with an evident distinction between the Greek and Polish specimens. Additional genotypes for the 28S rDNA region as well as haplotypes of the mtDNA region that were typical for the Greek or Polish populations were observed. Significant polymorphisms for ß-tubulin 3 gene were displayed with decreasing percentage of presence within populations from Greece to Poland. There was an amino acid substitution in ß-tubulin 3 protein found only among Polish specimens. It is hypothesized that genotypic differences between Greek, Bulgarian, and Polish liver fluke populations are due to territorial division and genetic drift in past epochs.

SN 2004aw: confirming diversity of Type Ic supernovae

Optical and near-infrared (near-IR) observations of the Type Ic supernova (SN Ic) 2004aw are presented, obtained from -3 to +413 d with respect to the B-band maximum. The photometric evolution is characterized by a comparatively slow post-maximum decline of the light curves. The peaks in redder bands are significantly delayed relative to the bluer bands, the I-band maximum occurring 8.4 d later than that in B. With an absolute peak magnitude of -18.02 in the V band the SN can be considered fairly bright, but not exceptional. This also holds for the U through I bolometric light curve, where SN 2004aw has a position intermediate between SNe 2002ap and 1998bw. Spectroscopically SN 2004aw provides a link between a normal SN Ic like SN 1994I and the group of broad-lined SNe Ic. The spectral evolution is rather slow, with a spectrum at day +64 being still predominantly photospheric. The shape of the nebular [O-I] lambda lambda 6300, 6364 line indicates a highly aspherical explosion. Helium cannot be unambiguously identified in the spectra, even in the near-IR. Using an analytical description of the light-curve peak we find that the total mass of the ejecta in SN 2004aw is 3.5-8.0 M-circle dot, significantly larger than that in SN 1994I, although not as large as in SN 1998bw. The same model suggests that about 0.3 M-circle dot of Ni-56 has been synthesized in the explosion. No connection to a GRB can be firmly established.

Population dynamics of the liver fluke, Fasciola hepatica: the effect of time and spatial separation on the genetic diversity of fluke populations in the Netherlands

An evaluation of the genetic diversity within Fasciola hepatica (liver fluke) may provide an insight into its potential to respond to environmental changes, such as anthelmintic use or climate change. In this study, we determined the mitochondrial DNA haplotypes of >400 flukes from 29 individual cattle, from 2 farms in the Netherlands, as an exemplar of fasciolosis in a European context. Analysis of this dataset has provided us with a measure of the genetic variation within infrapopulations (individual hosts) and the diversity between infrapopulations within a herd of cattle. Temporal sampling from one farm allowed for the measurement of the stability of genetic variation at a single location, whilst the comparison between the two farms provided information on the variation in relation to distance and previous anthelmintic regimes. We showed that the liver fluke population in this region is predominantly linked to 2 distinct clades. Individual infrapopulations contain a leptokurtic distribution of genetically diverse flukes. The haplotypes present on a farm have been shown to change significantly over a relatively short time-period.