Analysis of the microbial community in moderately acidic drainage from the Yanahara pyrite mine in Japan

Acid rock drainage (ARD) originating from the Yasumi-ishi tunnel near the main tunnel of the Yanahara mine in Japan was characterized to be moderately acidic (pH 4.1) and contained iron at a low concentration (51?mg/L). The composition of the microbial community was determined by sequence analysis of 16S rRNA genes using PCR and denaturing gradient gel electrophoresis. The analysis of the obtained sequences showed their similarity to clones recently detected in other moderately acidic mine drainages. Uncultured bacteria related to Ferrovum- and Gallionella-like clones were dominant in the microbial community. Analyses using specific primers for acidophilic iron- or sulfur-oxidizing bacteria, Acidithiobacillus ferrooxidans, Leptospirillum spp., Acidithiobacillus caldus, Acidithiobacillus thiooxidans, and Sulfobacillus spp. revealed the absence of these bacteria in the microbial community in ARD from the Yasumi-ishi tunnel. Clones affiliated with a member of the order Thermoplasmatales were detected as the dominant archaea in the ARD microbial population.     

Isolation and characterization of BADH2 gene from in vitro propagated <Emphasis Type="Italic">Pandanus amaryllifolius</Emphasis> Roxb

The 2-acetyl-1-pyrroline (2AP) induced ‘basmati rice’ aroma is plausibly the highest among the plant kingdom in Pandanus amaryllifolius Roxb. The defective/truncated allelic forms of betaine aldehyde dehydrogenase (BADH2) gene is the major contributing factor behind the accumulation of this fragrance. The present study reports the isolation and characterization of the full-length BADH2 gene from P. amaryllifolius Roxb. The in silico analysis involving homology modelling and docking studies revealed the deficiency in catalytic efficiency of Pandanus BADH2 towards its substrate γ-aminobutyraldehyde (GAB-ald) as compared to the functional BADH2 gene of rice. We have also studied the tissue-specific expression of the BADH2 gene in different plant parts of in vivo donor and in vitro propagated P. amaryllifolius Roxb. In addition to the leaves, we are reporting histochemical localization of 2AP for the first time in the roots of P. amaryllifolius.     

Effect of Onosma echioides on DMBA/croton oil mediated carcinogenic response, hyperproliferation and oxidative damage in murine skin

The current study unveils the effect of O. echioides extract on two-stage skin carcinogenesis and on tumor promoter induced markers and oxidative stress in Swiss mice. Treatment of dorsal shaven cutaneous portions of the mice with single topical application of benzoyl peroxide (BPO) followed by exposure to ultraviolet B (UVB) radiation induced significant oxidative stress and elevated the marker parameters of tumor promotion. Similar effects were observed with 12-O-tetradecanoyl phorbol-13-acetate (TPA) treatment. Pretreatment of O. echioides extract (5 mg & 10 mg/Kg b.wt) in both the studies with BPO+UVB and TPA restored the levels of reduced glutathione (GSH) and cellular protective enzymes (p < 0.05). Concomitantly, malondialdehyde (MDA) formation and hydrogen peroxide (H2O2) content were also reduced significantly (p < 0.05) at both the doses. The promotion parameters tested (ornithine decarboxylase activity and DNA synthesis) were also significantly suppressed (p < 0.05). Thereafter, we proceeded with studies on mouse skin carcinogenesis. After ten days of 7,12-dimethylbenz(a)anthracene (DMBA) treatment, twice-weekly applications of croton oil for 20 weeks resulted in 100% incidence of tumors in the animals. However, O. echioides showed reduction in the number of tumors/ mouse and percentage of tumor bearing mice at the end of the study. The study was further histologically confirmed. The protective activity of the plant might be due to the two major constituents (alkannins and shikonins) present in the plant. O. echioides is thus, proposed to be helpful in prevention of experimental skin carcinogenesis.     

Lipoxygenase inhibition by novel fatty acid ester from Annona squamosa seeds

Studies on the seeds of Annona squamosa yielded a novel lipoxygenase inhibitor fatty acid ester, (+) - annonlipoxy (1). Compound 1 was screened for its enzyme inhibitory activity against lipoxygenase (E.C.1.14.18.1), exhibiting activity with IC(50) 69.05 +/- 5.06 microm. Baicalein (IC(50) 22.6 +/- 0.5 microm) was used as a positive control. Crude extracts of Annona squamosa fruit pulp and seeds were screened for its enzyme inhibitory activity against lipoxygenase and acetylcholinesterase. The crude ethanolic extract of fruit pulp and seeds of Annona squamosa also exhibited lipoxygenase activity with 22.2 and 26.7% inhibition, while the pet.ether extract of seeds of A. squamosa exhibited 52.7% inhibition at a concentration of 40 microg/200 ml. The crude ethanolic extract of seeds of Annona squamosa was also bioassayed for acetylcholinesterase inhibition and it was found inactive.     

Agonist and antagonist activities of ligands derived from naltrexone and oxymorphone.

The pharmacological profile of naltrindole (NTI) and three of its analogues, N-methyl-NTI (N-Me-NTI), oxymorphindole (OMI) and naltriben (NTB) were studied in antinociceptive assays. The compounds were found to have agonist activities that appear to be mediated mainly by kappa opioid receptors because norbinaltorphimine (nor-BNI), the selective kappa opioid receptor antagonist inhibited their effects significantly. All of the compounds, behaved as antagonists at doses that were lower than those that produced agonist effects and they possessed a profile that was very selective for inhibiting the antinociceptive activities of delta opioid receptor agonists. Differential antagonism by NTB of the activities of DSLET and DPDPE was demonstrated.     

Population genetic structure of Bactrocera dorsalis based on cox1 sequences from Bangladesh and neighboring countries

Oriental fruit fly, Bactrocera dorsalis (Hendel), is a destructive and highly polyphagous invasive fruit fly species of numerous fruit crops in global agriculture. Population genetic structure of this species from five different locations of Bangladesh was examined with other samples (collected from GenBank) from 15 sites of neighboring Asian countries. A fragment of 770 bp mitochondrial DNA cox1 was used to investigate the genetic diversity and the relationship between genetic patterns and geographical distribution of B. dorsalis. A total of 232 variable sites (33.23% of the 698 bp aligned consensus sequences) and 419 unique haplotypes were identified from 710 individuals. Indices of genetic diversity suggested that without exclusion from geographical areas, B. dorsalis retained a relatively high degree of genetic diversity. A demographic assessment [Tajimas’ D test, Fu’s Fs test and sum of square deviation (SSD values)] revealed that both current and historical variables performed a significant role in deciding the weak genetic structure with some exceptions. In Bangladesh, high levels of genetic diversity with a weak genetic structure indicated that the severity of this pest might increase in the future. Proper management techniques should be taken to overcome the future severity of this kind of destructive insect.     

Irxl1 mutant mice show reduced tendon differentiation and no patterning defects in musculoskeletal system development

Irxl1 (Iroquois-related homeobox like-1) is a newly identified three amino-acid loop extension (TALE) homeobox gene, which is expressed in various mesoderm-derived tissues, particularly in the progenitors of the musculoskeletal system. To analyze the roles of Irxl1 during embryonic development, we generated mice carrying a null allele of Irxl1. Mice homozygous for the targeted allele were viable, fertile, and showed reduced tendon differentiation. Skeletal morphology and skeletal muscle weight in Irxl1-knockout mice appeared normal. Expression patterns of several marker genes for cartilage, tendon, and muscle progenitors in homozygous mutant embryos were unchanged. These results suggest that Irxl1 is required for the tendon differentiation but dispensable for the patterning of the musculoskeletal system in development.     

The PE-PPE domain in mycobacterium reveals a serine α/β hydrolase fold and function: an in-silico analysis

The PE and PPE proteins first reported in the genome sequence of Mycobacterium tuberculosis strain H37Rv are now identified in all mycobacterial species. The PE-PPE domain (Pfam ID: PF08237) is a 225 amino acid residue conserved region located towards the C-terminus of some PE and PPE proteins and hypothetical proteins. Our in-silico sequence analysis revealed that this domain is present in all Mycobacteria, some Rhodococcus and Nocardia farcinica genomes. This domain comprises a pentapeptide sequence motif GxSxG/S at the N-terminus and conserved amino acid residues Ser, Asp and His that constitute a catalytic triad characteristic of lipase, esterase and cutinase activity. The fold prediction and comparative modeling of the 3-D structure of the PE-PPE domain revealed a "serine α/β hydrolase" structure with a central β-sheet flanked by α-helices on either side. The structure comprises a lid insertion with a closed structure conformation and has a solvent inaccessible active site. The oxyanion hole that stabilizes the negative charge on the tetrahedral intermediate has been identified. Our findings add to the growing list of serine hydrolases in mycobacterium, which are essential for the maintenance of their impermeable cell wall and virulence. These results provide the directions for the design of experiments to establish the function of PE and PPE proteins.     

Identification and Validation of a Putative Polycomb Responsive Element in the Human Genome

Epigenetic cellular memory mechanisms that involve polycomb and trithorax group of proteins are well conserved across metazoans. The cis-acting elements interacting with these proteins, however, are poorly understood in mammals. In a directed search we identified a potential polycomb responsive element with 25 repeats of YY1 binding motifthatwe designate PRE-PIK3C2B as it occurs in the first intron of human PIK3C2B gene. It down regulates reporter gene expression in HEK cells and the repression is dependent on polycomb group of proteins (PcG). We demonstrate that PRE-PIK3C2B interacts directly with YY1 in vitro and recruits PRC2 complex in vivo. The localization of PcG proteins including YY1 to PRE-PIK3C2B in HEK cells is decreased on knock-down of either YY1 or SUZ12. Endogenous PRE-PIK3C2B shows bivalent marking having H3K27me3 and H3K4me3 for repressed and active state respectively. In transgenic Drosophila, PRE-PIK3C2B down regulates mini-white expression, exhibits variegation and pairing sensitive silencing (PSS), which has not been previously demonstrated for mammalian PRE. Taken together, our results strongly suggest that PRE-PIK3C2B functions as a site of interaction for polycomb proteins.     

Attenuation of oxidative stress, inflammation and early markers of tumor promotion by caffeic acid in Fe-NTA exposed kidneys of Wistar rats

Iron nitrilotriacetate (Fe-NTA), a chief environmental pollutant, is known for its extensive toxic manifestations on renal system. In the present study, caffeic acid, one of the most frequently occurring phenolic acids in fruits, grains, and dietary supplements was evaluated for its shielding effect against the Fe-NTA-induced oxidative, inflammatory, and pathological damage in kidney. Fe-NTA was administered (9 mg Fe/kg body weight) intraperitoneally to the Wistar male rats on 20th day while caffeic acid was administered orally (20 and 40 mg/kg body weight) before administration of Fe-NTA. The intraperitoneal administration of Fe-NTA-enhanced lipid peroxidation, xanthine oxidase, and hydrogen peroxide generation with reduction in renal glutathione content, antioxidant enzymes, viz., catalase, glutathione peroxidase, and glutathione reductase. A sharp elevation in the levels of myloperoxidase, blood urea nitrogen (BUN), and serum creatinine has also been observed. Tumor promotion markers viz., ornithine decarboxylase (ODC) and [(3)H] thymidine incorporation into renal DNA were also significantly increased. Treatment of rats orally with caffeic acid (20 and 40 mg/kg body weight) resulted in a significant decrease in xanthine oxidase (P < 0.001), lipid peroxidation (P < 0.001), γ-glutamyl transpeptidase (P < 0.01), and H(2)O(2) (P < 0.01). There was significant recovery of renal glutathione content (P < 0.001) and antioxidant enzymes (P < 0.001). There was also a reversal in the enhancement of renal ODC activity, DNA synthesis, BUN, and serum creatinine (P < 0.001). All these changes were supported by histological observations. The results indicate that caffeic acid may be beneficial in ameliorating the Fe-NTA-induced oxidative damage and tumor promotion in the kidney of rats.