Microbial populations in acid mineral bioleaching systems of Tong Shankou Copper Mine, China

AIMS

To understand the composition and structure of microbial communities in different acid mineral bioleaching systems, and to present a more complete picture of microbially mediated acid mine drainage production.

METHODS AND RESULTS

In Tong Shankou Copper Mine, China, two samples (named K1 and K2) from two different sites with bioleaching were studied. A bacterial 16S rDNA library and an archaeal 16S rDNA library of the sample from each site were constructed by 16S rDNA polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP) and sequencing. A total of 18 bacterial representative sequences and 12 archaeal representative sequences were obtained. Phylogenetic analysis indicated that 77.09% of the total bacterial clones were affiliated with Proteobacteria, and 21.22% of the total bacterial clones were closely related to Nitrospira. The rest of the bacterial clones were related to Firmicutes (1.68%). Sequences affiliated with the archaea of the Thermoplasma and Ferroplasma lineages were detected abundantly in the two samples. Unexpectedly, sequences affiliated with Sulfolobales and Methanothermus genera were also detected.

CONCLUSIONS

The molecular studies appear to be consistent with the environmental conditions existing at the sites, which coincides with previous studies. High concentrations of some elements (such as copper, iron and sulfur) seemed to be the key factors resulting in the diverse distribution of typical iron-oxidizing bacteria such as Leptospirillum species and Acidithiobacillus ferrooxidans.

SIGNIFICANCE AND IMPACT OF THE STUDY

Research on micro-organisms present in bioleaching systems especially archaea is not abundant. The acidophiles in the two bioleaching sites obtained from Tong Shankou Copper Mine, China, have not been reported until now. These results may expand our knowledge of the microbial diversity in the acid mineral bioleaching systems.

Novel ordering of an S = 1/2 quasi-1d Ising-like antiferromagnet in magnetic field

High-field specific heat measurements on BaCo(2)V(2)O(8), which is a good realization of an S=1/2 quasi-one-dimensional (1D) Ising-like antifferomagnet, have been performed in magnetic fields up to 12 T along the chain and at temperature down to 200 mK. We have found a new magnetic ordered state in the field-induced phase above H(c) approximately 3.9 T. We suggest that a novel type of the incommensurate order, which is caused by the quantum effect inherent in the S=1/2 quasi-1D Ising-like antiferromagnet, appears in the field-induced phase.

Relationship between TFAM Gene Polymorphisms and Endurance Capacity in Response to Training

The aim of this study was to explore whether polymorphisms in mitochondrial transcription factor A ( TFAM) gene are associated with endurance capacity in a pretraining state (baseline) and/or in response to a supervised 18-wk endurance training (changes) in 102 young Chinese males (nonathletes). Phenotypes measured were running economy (RE) and V(.)O (2max). Genomic DNA was extracted from white blood cells and the genotypes were analyzed by PCR-RFLP in single nucleotide polymorphisms (SNP) rs1937, rs2306604 and rs1049432. Genotype distributions were in Hardy-Weinberg equilibrium at three loci (p > 0.05). When the three polymorphisms were considered together, three haplotypes were estimated, i.e., G (rs1937)-A (rs2306604)-G (rs1049432) (49 %), G (rs1937)-G (rs2306604)-G (rs1049432) (33 %) and C (rs1937)-G (rs2306604)-T (rs1049432) (18 %). SNPrs1937 and rs1049432 achieved near complete linkage disequilibrium (LD) (D' = 1 and r (2) = 0.903). We found no significant differences in baseline levels of V(.)O (2max) and RE between TFAM genotypes or haplotypes. Similarly, we found no differences for the training-induced changes of both variables. It was concluded that the three polymorphisms in TFAM gene rs1937, rs2306604 and rs1049432 do not predict endurance capacity/trainability, at least in Chinese males.

VEGF receptor inhibition slows the progression of polycystic kidney disease

Although the receptors for vascular endothelial growth factor (VEGF) exert their effects on vasculogenesis and angiogenesis through receptors located on endothelial cells, recent studies have shown that these receptors are also present on renal tubular epithelial cells. We investigated the role of VEGF on increased tubule cell proliferation in the Han:SPRD heterozygous (Cy/+) rat model of polycystic kidney disease. The levels of VEGF in the kidneys and the serum, and the expression of the two receptors on tubules were increased in Cy/+ rats. These rats were given ribozymes that specifically inhibited VEGFR1 and VEGFR2 mRNA expression. Tubule cell proliferation within the cysts was significantly decreased in the ribozyme-treated animals leading to decreased cystogenesis, blunted renal enlargement, and prevented the loss of renal function. Our studies show that inhibition of VEGF function may be an important therapeutic option to delay the progression of polycystic kidney disease.

NRF2 Genotype Improves Endurance Capacity in Response to Training

The aim of this work was to examine the association between the polymorphisms in nuclear respiratory factor (NRF2) gene and endurance capacity measured prior to and after an 18-wk endurance training program in young Chinese men. The phenotypes measured were running economy (RE) and VO(2max). The RE was determined by measuring submaximal VO(2) for 5 min at a constant running speed of 12 km x h (-1) and VO(2max) was measured during an incremental test to volitional exhaustion. Genomic DNA was extracted from white cells of peripheral blood and the genotypes were examined in SNPrs12594956, rs8031031 and rs7181866 by PCR-RFLP. Genotype distributions were in Hardy-Weinberg equilibrium at three loci, and linkage disequilibrium was observed (LD D' = 1 and r (2) = 0.903) between rs8031031 and rs7181866. The VO(2max) was associated with rs12594956 at baseline while the training response of VO(2) at RE, was associated with rs12594956, rs8031031 and rs7181866. When the three SNPs were considered together, those carrying the ATG haplotype had 57.5 % higher training response in VO(2) at RE (p = 0.006) than non-carriers. In conclusion, polymorphisms in NRF2 gene may explain some of the between-person variance in endurance capacity.

Field-induced order-disorder transition in antiferromagnetic BaCo(2)V(2)O(8) driven by a softening of spinon excitation

High field magnetization and ESR measurements on the quasi-one-dimensional (1D) antiferromagnet BaCo(2)V(2)O(8) have been performed in magnetic fields up to 50 T along the chain. The experimental results are explained well in terms of a 1D S=1/2 antiferromagnetic XXZ model in longitudinal fields. We show that the quantum phase transition from the Néel ordered phase to the spin liquid one in the model is responsible for a peculiar order to disorder transition in BaCo(2)V(2)O(8).

Prolonged survival in patients with persistently elevated tumor markers after chemotherapy for nonseminomatous germ cell cancer

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Background: Persistently elevated levels of either AFP or HCG or both after chemotherapy are thought to represent residual viable disease while the normalization of tumor markers predicts favorable outcomes. This study was to evaluate the clinical implication of tumor marker normalization for disseminated nonseminomatous germ cell tumors (GCTs). Methods: This was a retrospective data analysis from two prospective randomized trials (ECOG E4887 and E3887). In E4887, 178 patients with minimal- or moderate-stage disease (Indiana stage) were randomized to receive three cycles of cisplatin plus etoposide with/without bleomycin. In E3887, 304 patients with advanced disseminated GCTs were randomized to receive four cycles of bleomycin, etoposide and cisplatin versus the combination of etoposide, ifosfamide and cisplatin. AFP and HCG were assessed at baseline and after each cycle of chemotherapy. Tumor marker normalization was defined as AFP or HCG normalized after completing chemotherapy. OS and PFS curves were estimated by the Kaplan-Meier method. Multivariate and univariate models, stratified on International Germ Cell Consensus Classification (IGCCCG), were used to assess the impact of marker normalization for patients with abnormal markers at study entry. Results: Median follow-up is 14.8 years. About 40% to 60% of Patients with persistently elevated AFP or HCG after chemotherapy have prolonged PFS and/or OS. In IGCCCG poor risk patients, 35% to 55% of them with persistently elevated AFP or HCG after chemotherapy have prolonged PFS and/or OS. There is a statistically significant difference in OS associated with AFP normalization in both multivariate (p=0.008, HR=0.51 with 95% CI=0.31–0.84) and univariate analysis (p=0.0008, HR=0.43 with 95% CI=0.26–0.71). However, there was no statistically significant difference in OS associated with normalization of HCG in both multivariate analysis (p=0.52, HR=0.84 with 95% CI=0.50–1.41) and univariate analysis (p=0.29, HR=0.76 with 95% CI=0.46–1.26). Conclusions: Patients with persistently elevated AFP or HCG after chemotherapy may still have prolonged PFS and/or OS. Normalization of AFP but not HCG is associated with better OS in patients with disseminated nonseminomatous GCTs.

No significant financial relationships to disclose.

Is there an association between PPARGC1A genotypes and endurance capacity in Chinese men?

Our purpose was to determine the possible association between genotypes of three polymorphisms (Gly482Ser, Thr394Thr and A2962G) of the peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PPARGC1A) gene, on one hand, and both the pre- (baseline) and post-training levels of maximal (i.e., maximal oxygen uptake [VO2max]) and submaximal human endurance capacity (i.e., running economy [RE]). We studied 102 young males (physically active, non-athletes; age: 19+/-1 yrs) from Northern China (of Han origin) who underwent a 18-week endurance training (running) program and were tested on a treadmill (for VO2max and RE determination) before and after training. None of the VO2max and RE related traits were associated with the Gly482Ser and Thr394Thr polymorphisms at baseline or after training. The A2962G polymorphism was however associated with VO2max at baseline, as carriers of the G allele (AG+GG genotypes; n=49) had higher levels of VO2max than the AA group (n=53) (58.2+/-4.3 vs 56.3+/-3.9 mL/kg/min; P=0.017). Our results do not support previous data on Caucasians showing an association between the Gly482Ser variant and VO2max but suggest the potential role of another polymorphism (A2962G) to explain individual VO2max differences in Chinese men.

Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion

Desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells transitioned from the exponential to the stationary phase during electron donor depletion. In addition to temporal transcriptomics, total protein, carbohydrate, lactate, acetate, and sulfate levels were measured. The microarray data were examined for statistically significant expression changes, hierarchical cluster analysis, and promoter element prediction and were validated by quantitative PCR. As the cells transitioned from the exponential phase to the stationary phase, a majority of the down-expressed genes were involved in translation and transcription, and this trend continued at the remaining times. There were general increases in relative expression for intracellular trafficking and secretion, ion transport, and coenzyme metabolism as the cells entered the stationary phase. As expected, the DNA replication machinery was down-expressed, and the expression of genes involved in DNA repair increased during the stationary phase. Genes involved in amino acid acquisition, carbohydrate metabolism, energy production, and cell envelope biogenesis did not exhibit uniform transcriptional responses. Interestingly, most phage-related genes were up-expressed at the onset of the stationary phase. This result suggested that nutrient depletion may affect community dynamics and DNA transfer mechanisms of sulfate-reducing bacteria via the phage cycle. The putative feoAB system (in addition to other presumptive iron metabolism genes) was significantly up-expressed, and this suggested the possible importance of Fe2+ acquisition under metal-reducing conditions. The expression of a large subset of carbohydrate-related genes was altered, and the total cellular carbohydrate levels declined during the growth phase transition. Interestingly, the D. vulgaris genome does not contain a putative rpoS gene, a common attribute of the delta-Proteobacteria genomes sequenced to date, and the transcription profiles of other putative rpo genes were not significantly altered. Our results indicated that in addition to expected changes (e.g., energy conversion, protein turnover, translation, transcription, and DNA replication and repair), genes related to phage, stress response, carbohydrate flux, the outer envelope, and iron homeostasis played important roles as D. vulgaris cells experienced electron donor depletion.

Potent antitumor efficacy of XAF1 delivered by conditionally replicative adenovirus vector via caspase-independent apoptosis

XAF1 is a newly identified tumor-suppressor gene that can antagonize XIAP and sensitize cells to other cell death triggers. In this study, we utilized ZD55, a conditionally replicative adenovirus (CRAd) similar to ONYX-015 as the vector to transfer XAF1 into the tumor cells to evaluate its antitumor efficacy in vitro and in vivo. Potent and specific cytopathic effect (CPE) was observed upon infection with ZD55-XAF1 in tumor cell lines. Importantly, ZD55-XAF1 exhibited a superior suppression of tumor growth in an animal model of colorectal carcinoma in nude mice compared with Ad-XAF1 (E1-deleted replication-defective viral) and ONYX-015. Complete eradication of the established tumors was observed in four of eight mice. Our data also showed that infection with ZD55-XAF1 resulted in caspase-independent apoptosis. Although caspase-3, poly(ADP-ribose) polymerase were mildly activated in response to ZD55-XAF1 infection, pretreatment with pan-caspase inhibitor hardly influence its apoptosis-inducing activity. In summary, our study strongly suggested that ZD55-XAF1 could serve as an effective gene-virotherapy strategy and has highly potential against human cancers.

Polymorphisms in the HBB gene relate to individual cardiorespiratory adaptation in response to endurance training

OBJECTIVE

The crucial role of haemoglobin in endurance performance has been well documented. We examined whether polymorphisms in the HBB gene modified aerobic capacity.

METHODS

102 recruits were trained by running 5000 m three times per week for 18 weeks. Exercise intensity progressively increased from an initial heart rate corresponding to 95% of the individual baseline ventilatory threshold during the first 10 weeks to 105% during the last 8 weeks. The phenotypes measured were running economy and VO(2)max. Running economy was determined by measuring submaximal VO(2) for 5 min at a constant running speed of 12 km.h(-1) and VO(2)max was obtained during an incremental test to exhaustion. Genomic DNA was extracted from white cells of peripheral blood and the -551C/T, intron2,+16C/G and +340 A/T genotypes were examined relative to the TAA site variants by PCR-RFLP.

RESULTS

Genotype distributions were in Hardy-Weinberg equilibrium at three loci. None of the running economy and VO(2)max-related traits were associated with the three polymorphisms or haplotypes at baseline, while the training response of running economy was associated with -551C/T and intron2,+16C/G polymorphisms. Subjects homozygous for intron2,+16C/C or -551C/C had decreased oxygen cost of running compared to the other individuals.

DISCUSSION

It was concluded that the -551C/C or intron2,+16C/C genotype might explain part of the individual variation in the cardiorespiratory adaptation to endurance training.

Microarray applications in microbial ecology research

Microarray technology has the unparalleled potential to simultaneously determine the dynamics and/or activities of most, if not all, of the microbial populations in complex environments such as soils and sediments. Researchers have developed several types of arrays that characterize the microbial populations in these samples based on their phylogenetic relatedness or functional genomic content. Several recent studies have used these microarrays to investigate ecological issues; however, most have only analyzed a limited number of samples with relatively few experiments utilizing the full high-throughput potential of microarray analysis. This is due in part to the unique analytical challenges that these samples present with regard to sensitivity, specificity, quantitation, and data analysis. This review discusses specific applications of microarrays to microbial ecology research along with some of the latest studies addressing the difficulties encountered during analysis of complex microbial communities within environmental samples. With continued development, microarray technology may ultimately achieve its potential for comprehensive, high-throughput characterization of microbial populations in near real time.

Spectroscopic Performance of Thick HgI2 Detectors

This paper presents the spectroscopic performance of two newly developed pixelated HgI₂ detectors. These detectors are 1 × 1 × 0.814 cm³ and 1 × 1 × 1.016 cm³ in size. Each detector has four closely packed 1 × mm² anode pixels at the center of one of the 1 × 1 cm² surfaces. These anode pixels are surrounded by a large anode. All results presented here are based on events from a sub-volume underneath the anode pixels. In these detectors, signals were read out by a discrete electronics based on multiple A-250 pre-amplifiers and a digital oscilloscope for sampling pulse waveforms. Depth sensing technique was used to correct the depth-dependent variation in photopeak amplitude. Main results presented are: (1) energy resolutions of 0.85 ~ 1.3% have been achieved on these detectors; (2) the electron mobility-lifetime product was measured to be ~1 × 10^-2 cm²/V and the measured electron lifetime was ~200 μs and (3) variation in electron drifting properties under different anode pixels were observed. Significant non-uniformity in internal electric field strength was also experimentally demonstrated.

Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough

Desulfovibrio vulgaris Hildenborough belongs to a class of sulfate-reducing bacteria (SRB) and is found ubiquitously in nature. Given the importance of SRB-mediated reduction for bioremediation of metal ion contaminants, ongoing research on D. vulgaris has been in the direction of elucidating regulatory mechanisms for this organism under a variety of stress conditions. This work presents a global view of this organism's response to elevated growth temperature using whole-cell transcriptomics and proteomics tools. Transcriptional response (1.7-fold change or greater; Z >/= 1.5) ranged from 1,135 genes at 15 min to 1,463 genes at 120 min for a temperature up-shift of 13 degrees C from a growth temperature of 37 degrees C for this organism and suggested both direct and indirect modes of heat sensing. Clusters of orthologous group categories that were significantly affected included posttranslational modifications; protein turnover and chaperones (up-regulated); energy production and conversion (down-regulated), nucleotide transport, metabolism (down-regulated), and translation; ribosomal structure; and biogenesis (down-regulated). Analysis of the genome sequence revealed the presence of features of both negative and positive regulation which included the CIRCE element and promoter sequences corresponding to the alternate sigma factors sigma(32) and sigma(54). While mechanisms of heat shock control for some genes appeared to coincide with those established for Escherichia coli and Bacillus subtilis, the presence of unique control schemes for several other genes was also evident. Analysis of protein expression levels using differential in-gel electrophoresis suggested good agreement with transcriptional profiles of several heat shock proteins, including DnaK (DVU0811), HtpG (DVU2643), HtrA (DVU1468), and AhpC (DVU2247). The proteomics study also suggested the possibility of posttranslational modifications in the chaperones DnaK, AhpC, GroES (DVU1977), and GroEL (DVU1976) and also several periplasmic ABC transporters.