Intraspecific nuclear DNA variation in Drosophila

We have summarized and analyzed all available nuclear DNA sequence polymorphism studies for three species of Drosophila, D. melanogaster (24 loci), D. simulans (12 loci), and D. pseudoobscura (5 loci). Our major findings are: (1) The average nucleotide heterozygosity ranges from about 0.4% to 2% depending upon species and function of the region, i.e., coding or noncoding. (2) Compared to D. simulans and D. pseudoobscura (which are about equally variable), D. melanogaster displays a low degree of DNA polymorphism. (3) Noncoding introns and 3' and 5' flanking DNA shows less polymorphism than silent sites within coding DNA. (4) X-linked genes are less variable than autosomal genes. (5) Transition (Ts) and transversion (Tv) polymorphisms are about equally frequent in non-coding DNA and at fourfold degenerate sites in coding DNA while Ts polymorphisms outnumber Tv polymorphisms by about 2:1 in total coding DNA. The increased Ts polymorphism in coding regions is likely due to the structure of the genetic code: silent changes are more often Ts's than are replacement substitutions. (6) The proportion of replacement polymorphisms is significantly higher in D. melanogaster than in D. simulans. (7) The level of variation in coding DNA and the adjacent noncoding DNA is significantly correlated indicating regional effects, most notably recombination. (8) Surprisingly, the level of polymorphism at silent coding sites in D. melanogaster is positively correlated with degree of codon usage bias. (9) Three proposed tests of the neutral theory of DNA polymorphisms have been performed on the data: Tajima's test, the HKA test, and the McDonald-Kreitman test. About half of the loci fail to conform to the expectations of neutral theory by one of the tests. We conclude that many variables are affecting levels of DNA polymorphism in Drosophila, from properties of nucleotides to population history and, perhaps, mating structure. No simple, all encompassing explanation satisfactorily accounts for the data.      

A molecular phylogeny for the Drosophila melanogaster subgroup and the problem of polymorphism data

Drosophila melanogaster belongs to a closely related group of eight species collectively known as the melanogaster subgroup; all are native to sub-Saharan Africa and islands off the east coast of Africa. The phylogenetic relationships of most species in this subgroup have been well documented; however, the three most closely related species, D. simulans, D. sechellia, and D. mauritiana, have remained problematic from a phylogenetic standpoint as no data set has unambiguously resolved them. We present new DNA sequence data on the nullo and Serendipity-alpha genes and combine them with all available nuclear DNA sequence data; the total data encompass 12 genes and the ITS of rDNA. A methodological problem arose because nine of the genes had information on intraspecific polymorphisms in at least one species. We explored the effect of inclusion/exclusion of polymorphic sites and found that it had very little effect on phylogenetic inferences, due largely to the fact that 82% of polymorphisms are autapomorphies (unique to one species). We have also reanalyzed our previous DNA-DNA hybridization data with a bootstrap procedure. The combined sequence data set and the DNA-DNA hybridization data strongly support the sister status of the two island species, D. sechellia and D. mauritiana. This at least partially resolves what had been a paradox of parallel evolution in these two species.      

Heavy Metal Contamination in Urban Surface Soil of Klang District (Malaysia)

This study aimed to determine bioavailability of heavy metal concentrations (Al, Fe, Zn, Cu, Co, Cd, Pb and Cr) in 76 urban surface soil samples of Klang district (Malaysia). This study also aimed to determine health risks posed by bioavailability of heavy metals in urban soil on adults and children. For bioavailability of heavy metal concentrations, a physiologically bioavailability extraction test in vitro digestion model was used. Mean values of bioavailability heavy metal concentrations for this study were found to be the highest in Al (25.44 mg/kg) and lowest in Cr (0.10 mg/kg). Results of Spearman correlation coefficient (r) values showed significant correlations were observed for Al-Fe (r = 0.681), Cd-Co (r = 0.495), Cu-Zn (r = 0.232), Fe-Pb (r = 0.260), Fe-Zn (r = 0.239). For cluster analysis, output showed that these heavy metals could be classified into four clusters: Cluster 1 consisted of Cd, Cr, Co, and Pb; Cluster 2 consisted of Zn and Cu; Cluster 3 consisted of Fe; and Cluster 4 consisted of Al. For Clusters 1 and 2, anthropogenic sources were believed to be the sources, while for Clusters 3 and 4 the heavy metals originated from natural sources. Health risks were determined in adults and children through health risk assessment. For adults, Hazard Quotient (HQ) value was <1, indicating no non-carcinogenic risk, while for children, the HQ value was >1, indicating a non-carcinogenic risk. Meanwhile, for carcinogenic risk, heavy metal contamination in the Klang district might not pose a carcinogenic risk to adults while it may pose a carcinogenic risk to children because TR values in this study were >1.0E-04 for children. Output has identified the general health risk in the Klang district. Moreover, this study's findings will contribute to fill in the gap of knowledge on heavy metals' impacts on human health and urban development in the Klang District.     

Spatial Assessment of Heavy Metals in Surface Soil from Klang District (Malaysia): An Example from a Tropical Environment

Heavy metals (Al, Cd, Co, Cr, Cu, Fe, Pb, Zn) in surface soil of Klang district were determined and multivariate analysis was used to understand their potential sources. The total and bioavailability of concentrations were used in identifying the potential risks to the ecology and human health. The means for the total heavy metal concentrations were found to be in the order of Fe > Al > Zn > Pb > Cu > Cr > Co > Cd, while the means for the bioavailability concentrations were found to be in the order of Al > Fe > Zn > Cu > Co > Cd > Pb > Cr. Principal Component Analysis showed Principal Component 1 as being of natural origin whereas Principal Components 2, 3, and 4 were associated with mixed anthropogenic sources, such as traffic and industrial emissions, organic matter, and granulometric fractions. Potential ecological risk assessment indicated an overall low ecological risk. Spatial assessment of non-carcinogenic risks showed that the Hazard Index values were more than one in Johan Setia, due to biomass burning of peat swamps exploited for agricultural development. While for spatial assessment of carcinogenic risks, the Lifetime Cancer Risk values were in the limit (1 × 10^?5), indicating low cancer inducing risks. Nevertheless, with intense development pressure in the Klang district could overlap pollution inputs in the future.     

Influence of the cystic fibrosis transmembrane conductance regulator on expression of lipid metabolism-related genes in dendritic cells

Background

Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Infections of the respiratory tract are a hallmark in CF. The host immune responses in CF are not adequate to eradicate pathogens, such as P. aeruginosa. Dendritic cells (DC) are crucial in initiation and regulation of immune responses. Changes in DC function could contribute to abnormal immune responses on multiple levels. The role of DC in CF lung disease remains unknown.

Methods

This study investigated the expression of CFTR gene in bone marrow-derived DC. We compared the differentiation and maturation profile of DC from CF and wild type (WT) mice. We analyzed the gene expression levels in DC from naive CF and WT mice or following P. aeruginosa infection.

Results

CFTR is expressed in DC with lower level compared to lung tissue. DC from CF mice showed a delayed in the early phase of differentiation. Gene expression analysis in DC generated from naive CF and WT mice revealed decreased expression of Caveolin-1 (Cav1), a membrane lipid raft protein, in the CF DC compared to WT DC. Consistently, protein and activity levels of the sterol regulatory element binding protein (SREBP), a negative regulator of Cav1 expression, were increased in CF DC. Following exposure to P. aeruginosa, expression of 3β-hydroxysterol-Δ7 reductase (Dhcr7) and stearoyl-CoA desaturase 2 (Scd2), two enzymes involved in the lipid metabolism that are also regulated by SREBP, was less decreased in the CF DC compared to WT DC.

Conclusion

These results suggest that CFTR dysfunction in DC affects factors involved in membrane structure and lipid-metabolism, which may contribute to the abnormal inflammatory and immune response characteristic of CF.     

Responses of elongation growth rate,turgor pressure and cell wall extensibility of stem cells of Impatiens balsamina to lead,cadmium and zinc

Elongation growth rate of stem cells of Impatiens balsamina was inhibited by the heavy metals Pb²⁺, Cd²⁺ and Zn²⁺ due to their suppression on cell wall extensibility. Effective turgor was also inhibited by Pb²⁺ and Cd²⁺ but it played a secondary role in reducing the stem cell elongation growth rate. The major rate-limiting factor for cell elongation growth was the cell wall extensibility. Furthermore, Cd²⁺ was found to be more toxic than Pb²⁺, while Pb²⁺ was more toxic than Zn²⁺.