Agricultural phosphorus flow and its environmental impacts in China

The transfer of nutrients from agricultural land to waters attracts the attention of policy makers as well as scientists as it plays an increasingly significant role in affecting the water environment. It is therefore essential to first understand the nutrient flow in agricultural systems and then correspondingly formulate a series of cost-effective policies and best management practices (BMPs). On the basis of an emission inventory analysis (EIA) and a nutrient full balance (NFB) calculation, this paper presents a partial substance flow analysis (SFA) method, as well as an Agricultural Phosphorus Flow Analysis (AgiPhosFA) model, to describe the phosphorus (P) flow in the agricultural systems in China and assess the impact of human activities on waters driven by agriculture and rural life. It is estimated that average P input and output were 28.9 kg ha(-1) a(-1) and 14.2 kg ha(-1) a(-1) respectively in China in 2004, while the total P utilization efficiency (Plant uptake P/P input) in agriculture was 45.7% leading to an average P surplus of 14.7 kg ha(-1) a(-1). Excessive P application through mineral fertilizer in the arable farming system has led to the accumulation of soil P and constituted a risk to the recipient water quality, whereas the grassland grazing system is confronted with a severe P deficit problem which has resulted in widespread grass degradation. Therefore it may be an efficient way to mitigate the problems simultaneously by regulating and balancing the P flows between the two systems. Uncertainties of the method and model are also discussed in terms of model conceptualization, data and parameters, and spatial and temporal variability.

Drug-metabolising enzyme polymorphisms and predisposition to anti-tuberculosis drug-induced liver injury: a meta-analysis

BACKGROUND

Although some case-control studies have investigated the association between drug-metabolising enzyme (DME) gene polymorphisms and susceptibility to anti-tuberculosis drug-induced liver injury (ATLI), their results are conflicting, mainly due to limited power.

OBJECTIVE

To review the literature systematically, by means of a meta-analytical review, to evaluate the putative association and provide a quantitative summary estimate on the association with ATLI.

DESIGN

We searched the databases of MEDLINE, PubMed, EMBASE and CBMdisc from 1966 to May 2007 using 'DME', 'hepatotoxicity', 'genetic polymorphism', 'genetic susceptibility' in combination with 'antitubercular agents', performed a manual search of citations from relevant original studies and review articles, and corresponded with authors.

RESULTS

Nine eligible articles were included in this meta-analysis, including five on N-acetyltransferase 2 (NAT2), four on cytochrome P450 2E1 (CYP2E1) and two on glutathione S-transferase (GST) studies, separately. The overall ORs of ATLI risk associated with NAT2 homozygous variant genotype (mt/mt), CYP2E1 homozygous wild genotype (*1A/*1A), GSTM1 homozygous null genotype (null/null) and GSTT1 homozygous null genotype (null/null) were respectively 1.93 (95%CI 0.81-4.62), 2.22 (95%CI 1.06-4.66), 2.62 (95%CI 1.45-4.75) and 1.18 (95%CI 0.61-2.29). In addition, the OR for Asian ATLI associated with the NAT2 homozygous variant (mt/mt) and the combined genotype (w/w + w/mt) was 2.52 (95%CI 1.49-4.26).

CONCLUSIONS

NAT2 mt/mt, CYP2E1*1A/*1A and GSTM1 null/null were observed to increase the risk of ATLI in tuberculosis patients. Our results support the hypothesis that NAT2 mt, CYP2E1*1A and GSTM1 null have a modest effect on genetic susceptibility to ATLI, but no significant evidence for GSTT1 null/null.

Expression of SRG3, a chromatin-remodelling factor, in the mouse oocyte and early preimplantation embryos

SRG3 (Smarcc1) is a core subunit of the SWI/SNF complex. In the absence of SRG3, embryonic development ceases during peri-implantation stages, indicating that SRG3, as well as the chromatin-remodelling process, plays an essential role in early mouse development. To gain a better understanding of chromatin remodelling during the early stages of development, we examined SRG3 expression during oogenesis and preimplantation stages using immunofluorescence and western blot assays. SRG3 was detected in nuclei of oocytes during growth and maturation. Following fertilization, SRG3 was detected in pronuclei shortly after their formation. Nuclear concentrations of SRG3 increased in a time-dependent fashion and were found to be greater in the male pronucleus than in the female pronucleus. The increase in nuclear SRG3 was partially inhibited by a protein synthesis inhibitor, but not by a transcriptional inhibitor. Expression of SRG3 is accompanied by expression of Brg1 and Ini1, two other core subunits of the SWI/SNF complex. The expression of these three remodelling factors parallels that of SP1 and TBP, both spatially and temporally, in the mouse embryo, suggesting a role for remodelling factors in chromatin structure and function during early development.

Reduced meiotic recombination on the XY bivalent is correlated with an increased incidence of sex chromosome aneuploidy in men with non-obstructive azoospermia

Both aberrant meiotic recombination and an increased frequency of sperm aneuploidy have been observed in infertile men. However, this association has not been demonstrated within individual men. The purpose of this study was to determine the association between the frequency of recombination observed in pachytene spermatocytes and the frequency of aneuploidy in sperm from the same infertile men. Testicular tissue from seven men with non-obstructive azoospermia (NOA) and six men undergoing vasectomy reversal (controls) underwent meiotic analysis. Recombination sites were recorded for individual chromosomes. Testicular and ejaculated sperm from NOA patients and controls, respectively, were tested for aneuploidy frequencies for chromosomes 9, 21, X and Y. There was a significant increase in the frequency of pachytene cells with at least one achiasmate bivalent in infertile men (12.4%) compared with controls (4.2%, P = 0.02). Infertile men also had a significantly higher frequency of sperm disomy than controls for chromosomes 21 (1.0% versus 0.24%, P = 0.001), XX (0.16% versus 0.03%, P = 0.004) and YY (0.12% versus 0.03%, P = 0.04). There was a significant correlation between meiotic cells with zero MLH1 foci in the sex body and total sex chromosome disomy (XX + YY + XY) in sperm from men with NOA (r = 0.79, P = 0.036).

Adenosine promotes IL-6 release in airway epithelia

In the airway epithelia, extracellular adenosine modulates a number of biological processes. However, little is known about adenosine's role in the inflammatory responses of airway epithelial cells. Recent studies suggest that the chronic elevation of extracellular adenosine in mice leads to pulmonary inflammation and fibrosis. Yet, the underlying molecular mechanism has not been well understood and little attention has been paid to the role of airway epithelia in adenosine-triggered inflammation. In the present work, we examined the role of adenosine in releasing IL-6 from airway epithelia. In Calu-3 human airway epithelial cells, apical but not basolateral adenosine elicited robust, apically polarized release of IL-6, along with proinflammatory IL-8. Both protein kinase A and protein kinase C mediated the adenosine-induced IL-6 release, at least partly via phosphorylation of CREB. Protein kinase C appeared to phosphorylate CREB through activating ERK. In addition, A2A but not A2B adenosine receptors were specifically required for the adenosine-induced IL-6 release. Furthermore, in rat bronchoalveolar lavage fluid, adenosine triggered the release of IL-6 as well as proinflammatory IL-1beta. Adenosine also mediated the release of a considerable portion of the LPS-induced IL-6 in rat bronchoalveolar lavage fluid. Our findings provide a possible molecular link between extracellular adenosine elevation and lung inflammation and fibrosis.

A novel lipopeptide produced by a Pacific Ocean deep-sea bacterium, Rhodococcus sp. TW53

AIMS

Our goal was to find a novel, biosurfactant-producing bacterium from Pacific Ocean deep-sea sediments.

METHODS AND RESULTS

An oil-degrading biosurfactant-producing bacterium TW53 was obtained from deep-sea sediment, and was identified through 16S rDNA analysis as belonging to the genus Rhodococcus. It lowered the surface tension of its culture to 34.4 mN m(-1). Thin layer chromatography (TLC) showed that the crude biosurfactants of TW53 were composed of lipopeptides and free fatty acids (FA). The lipopeptides were purified with column chromatography and then hydrolysed with 6 mol l(-1) HCl. Gas chromatography-mass spectrometry analysis showed that the hydrolyte in the hydrophobic fraction contained five kinds of FA with chain lengths of C(14)-C(19), and C(16)H(32)O(2) was a major component making up 59.18% of the total. However, 3-hydroxyl FA was not found, although it is usually found in lipopeptides. Silica gel TLC revealed that the hydrolyte in the hydrophilic fraction was composed of five kinds of amino acids; consistently, ESI-Q-TOF-MS analysis confirmed the composition results and provided their sequence tentatively as Ala-Ile-Asp-Met-Pro. Furthermore, the yield and CMC (critical micelle concentrations) of purified lipopeptides were examined. The purified product reduced the surface tension of water to 30.7 mN m(-1) with a CMC value of 23.7 mg l(-1). These results suggest that Rhodococcus sp. TW53 produces a novel lipopeptide that we have named rhodofactin.

CONCLUSION

The deep-sea isolate Rhodococcus sp. TW53 was the first reported lipopeptide-producing bacterium of this genus. The lipopeptides had novel chemical compositions.

SIGNIFICANCE AND IMPACT OF THE STUDY

Rhodococcus sp. TW53 has potential in the exploration of new biosurfactants and could be used in bioremediation of marine oil pollution.

Managing the performance risk of conventional waterworks in compliance with the natural organic matter regulation

In order to understand the dual impact of both deteriorating water resources and stringent water quality regulations on the performance of conventional waterworks on a nationwide level, a methodology of a risk-based screening analysis is developed and further applied to evaluate the natural organic matter (NOM) regulation in the new standards for drinking water quality. Due to the large number of drinking water sources and conventional waterworks, as well as the lack of detailed field observations in China, such an analysis is wholly based on a validated conceptual model. The performance risk of conventional waterworks in compliance with the new regulation is estimated within the framework of risk assessment through Monte Carlo simulation to account for the uncertainties associated with model parameters, source water quality and operation conditions across different waterworks. A screening analysis is simultaneously performed using a task-based Hornberger-Spear-Young algorithm to identify the critical operation parameters that determine the performance risk, based on which potential strategies to manage the performance risk are proposed and evaluated. The effects of the model parameter uncertainties on the simulation results are also discussed.

Discontinuities and unsynapsed regions in meiotic chromosomes have a trans effect on meiotic recombination of some chromosomes in human males

During meiosis, homologous chromosome pairing and synapsis are essential for subsequent meiotic recombination (crossing-over). Discontinuous regions (gaps) and unsynapsed regions (splits) were most frequently observed in the heterochromatic regions of bivalent synaptonemal complex (SC) 9, and we have previously demonstrated that gaps and splits significantly altered the distribution of MLH1 recombination foci on SC 9. Here, immunofluorescence techniques (using antibodies against SC proteins and the crossover-associated MLH1 protein) were combined with a centromere-specific fluorescence in situ hybridization technique that allows identification of every individual chromosome. The effect of gaps/splits on meiotic recombination patterns in autosomes other than chromosome 9 during the pachytene stage of meiotic prophase was then examined in 6,026 bivalents from 262 pachytene cells from three human males. In 64 analyzed cells with a gapped SC 9, the frequency of MLH1 foci in SCs 5 and 10 and in SC arms 10q, 11p and 16q was decreased compared to 168 analyzed cells with a normally-synapsed SC 9 (controls). In 24 analyzed cells with splits in SC 9, there was a significant reduction in MLH1 focus frequency for SC 5q and the whole SC5 bivalent. The positioning of MLH1 foci on other SCs in cells with gapped/split SC 9 was not altered. These studies suggest that gaps and splits not only have a cis effect, but may also have a trans effect on meiotic recombination in humans.

Using skimmed milk agar to functionally screen a gut metagenomic library for proteases may lead to false positives

AIMS

Functional screens using skimmed-milk agar to obtain protease activity is a common approach. The aim of this study was to determine the efficacy of this screen to obtain protease activity from a metagenomic library.

METHODS AND RESULTS

A distal gut metagenomic library was functionally screened using a skimmed-milk agar. The functional screen provided 231 clones generating the characteristic clear halo indicative of protease production. Clone analysis revealed that they were not protease-positive, but expressed glycosidic hydrolases and produced acid, which was responsible for the clear halos.

CONCLUSIONS

The current skimmed-milk agar method to obtain proteases is not sufficiently robust to provide a definitive screen. Other- non-protease activities will also give the same clear halo and these would be interpreted as protease positive clones without further analysis. Hence a more robust buffered medium or a specific protein should be used.

SIGNIFICANCE AND IMPACT OF THE STUDY

Functional screens are a powerful approach to obtaining enzymes from large metagenomic libraries and proteases are a particularly interesting target. The skimmed-milk agar is not sufficiently robust to ensure that only proteases are isolated and in order to save time and money this study has shown that better designed media can aid in the process.

High-pressure polymorphic transformation of rutile to alpha-PbO2-type TiO2 at {011}R twin boundaries

The presence of nano-scale lamellae of the alpha-PbO2-type polymorph of TiO2 sandwiched between twinned rutile inclusions in jadeite has been confirmed by electron diffraction and high-resolution transmission electron microscopy, backed up by image simulation techniques, from ultrahigh-pressure jadeite quartzite at Shuanghe in the Dabie Mountains, China. The crystal structure is orthorhombic with lattice parameters a=4.58 A, b=5.42 A, c=5.02 A and space group Pbcn. A three-dimensional structural model has been constructed for the rutile to alpha-PbO2-type TiO2 phase transformation based on high-resolution electron microscopic images. Computer image simulation and structural model analysis reveal that rutile {011}R twin interface is a basic structural unit of alpha-PbO2-type TiO2. Nucleation of alpha-PbO2-type TiO2 lamellae 1-2 nm thick is caused by the displacement of one half of the titanium cations within the {011}R twin slab. This displacement reduces the Ti-O-Ti distance and is favored by high pressure.

Measurement of endogenous and exogenous triacylglycerol kinetics in the fed and fasted states

Emerging evidence has shown that an abnormal postprandial accumulation of dietary fat is atherogenic. However, there is a lack of data describing the mechanisms for accumulation of triacylglycerol (TAG) in the postprandial period. There is therefore a need to establish a specific measure of the kinetics of endogenous and exogenous TAG in the postprandial period.

Occurrence of Potato Cyst Nematode, Globodera rostochiensis, on Potato in the Saint-Amable Region, Quebec, Canada

Potato (Solanum tuberosum L. subsp. tuberosum) is one of the most important food crops in Canada. Potato cyst nematodes, Globodera rostochiensis (Wollenweber, 1923) Skarbilovich, 1959 and Globodera pallida (Stone, 1973) Behrens, 1975, are considered the most economically important nematode pests of potatoes worldwide and are the subject of strict quarantine regulations in many countries including Canada. In Canada, G. rostochiensis was found in the Saanich Peninsula of Vancouver Island, British Columbia and both G. rostochiensis and G. pallida are present on the island of Newfoundland (3). During August of 2006, soil and roots of potato plants collected from a 19.2-ha field in the Saint-Amable region, Quebec, were submitted to the Nematology Laboratory, Canadian Food Inspection Agency, Ottawa. Golden, spherical-shaped cysts were found associated with the roots and were also extracted from the soil. The nematodes recovered were identified by morphological and morphometric analysis and DNA analysis. Measurements and morphological observation of 60 second-stage juveniles were as follows: body length = 427.4 ± 22.0 (395 to 495) μm; stylet length = 21.3 ± 1.2 (18 to 23) μm; distance from stylet base to dorsal esophageal gland opening = 5.5 ± 0.9 (3.5 to 7.0) μm; tail length = 46.7 ± 3.7 (36 to 58) μm; hyaline tail terminus = 21.1 ± 3.1 (13 to 27) μm; and the shape of stylet basal knobs varied from rounded to lateral flattened. Observations for 35 mature cysts were: number of cuticular ridges between anus and vulval fenestra = 21 ± 6 (12 to 31); fenestral length = 18.4 ± 3.6 (11 to 30) μm; distance from anus to the edge of fenestra = 81.1 ± 30.4 (29 to 165) μm; Granek's ratio = 4.4 ± 1.6 (1.8 to 6.0), with parallel wavy cuticular ridges between anus and vulval fenestra. These observations conformed to the published description of G. rostochiensis (2). Additionally, the identification was supported by the PCR-restriction fragment length polymorphism pattern of the ITS-1 region amplified using primers 18S (5'-TTGATTACGTCCCTGCCCTTT-3') and rDNA1.58S (5'-ACGAGCCGAGTGATCCACCG-3') and digested with BstU I and a PCR product specific for G. rostochiensis (1). Sequence of a 1,190-bp PCR fragment of ribosomal DNA amplified using primers rDNA1 (5'-TTGATTACGTCCCTGCCCTTT-3') and rDNA2 (5'- TTTCACTCGCCGTTACTAAGG-3') showed 99.0 to 100% identity with published DNA sequences of the same genomic region for G. rostochiensis (4). The sequence is available from the authors upon request. The origin of the introduction of G. rostochiensis into Saint-Amable is unknown. An intensive soil survey is underway to define the infested area, and strict quarantine measures have been taken to prevent further spread of G. rostochiensis. To our knowledge, this is the first evidence of the occurrence of G. rostochiensis in Quebec, Canada. References: (1) A. Fullaondo et al. Nematology 1:157, 1999. (2) A. M. Golden et al. Proc. Helminthol. Soc. Wash. 39:64, 1972. (3) A. R. Stone et al. Plant Dis. Rep. 61:590, 1977. (4) S. A. Subbotin et al. Nematology 2:591, 2000.

Ecological genomics of marine Roseobacters

Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir-related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.

Clinical and molecular survey in 124 Chinese patients with Leigh or Leigh-like syndrome

Leigh syndrome is the most common mitochondrial disorder in children characterized by necrotic lesions in the central nervous system. Both mitochondrial DNA (mtDNA) and nuclear DNA defects in the mitochondrial respiratory chain can lead to this disease. To characterize the clinical and genetic traits of Leigh or Leigh-like syndrome patients in China, 124 unrelated cases were collected between 1992 and 2005. Seventy-seven cases (62.1%) met the typical criteria of Leigh syndrome, including symmetrical bilateral abnormal signals in the basal ganglia, thalamus and brain stem, etc. Other cases (37.9%) belonged to Leigh-like syndrome with atypical clinical or radiological manifestations. Late-onset patients accounted for 20.2%, which is more than previously reported. Movement disorder was the most common symptoms in our patients. Thirty-two patients (25.8%) were confirmed to carry mutant genes. Among them, six cases (4.8%) have been demonstrated to have point mutations in mitochondrial DNA. Two separate patients were detected to have mutations on A8344G and A3243G. The T8993G point mutation was identified in one patient and T8993C in one other patient. SURF1 mutations associated with cytochrome-c oxidase deficiency were identified in 25 patients (20.2%). Four unreported variations have been identified in SURF1 gene from three patients. G604C was found in 22 patients. Only one patient had C214T mutation in the pyruvate dehydrogenase E1alpha subunit gene. In the remaining 92 patients (74.2%), a specific molecular dysfunction or underlying metabolic abnormality could not be identified.

Integrated risk assessment and screening analysis of drinking water safety of a conventional water supply system

Management of drinking water safety is changing towards an integrated risk assessment and risk management approach that includes all processes in a water supply system from catchment to consumers. However, given the large number of water supply systems in China and the cost of implementing such a risk assessment procedure, there is a necessity to first conduct a strategic screening analysis at a national level. An integrated methodology of risk assessment and screening analysis is thus proposed to evaluate drinking water safety of a conventional water supply system. The violation probability, indicating drinking water safety, is estimated at different locations of a water supply system in terms of permanganate index, ammonia nitrogen, turbidity, residual chlorine and trihalomethanes. Critical parameters with respect to drinking water safety are then identified, based on which an index system is developed to prioritize conventional water supply systems in implementing a detailed risk assessment procedure. The evaluation results are represented as graphic check matrices for the concerned hazards in drinking water, from which the vulnerability of a conventional water supply system is characterized.