Standard reference materials for chemical and biological studies of complex environmental samples.

Standard Reference Materials (SRMs) from the National Institute of Standards and Technology (NIST) are often used in methods development and interlaboratory comparison studies since they are homogeneous and readily available to the scientific community. SRM 1649 (urban dust/organics), SRM 1650 (diesel particulate matter), and SRM 1597 (complex mixture of polycyclic aromatic hydrocarbons from coal tar) are three environmental samples which have been used by the scientific community for these purposes. These SRMs were originally developed to assist laboratories in validating analytical procedures for the determination of polycyclic organic compounds in complex mixtures. In addition, these SRMs have been valuable for the comparison of methodologies for bacterial bioassays and the development of bioassay-directed fractionation and bioassay-directed chemical analysis techniques. Most recently these SRMs were chosen for use as test samples in a collaborative study coordinated by the World Health Organization--International Programme on Chemical Safety. This paper provides a summary of much of the work to date (published and unpublished) on the chemical and biological characterization of these three SRMs. Information regarding the availability of other NIST SRMs that might be useful for these types of studies are provided also.     

Variation among species in proteomic sulphur content is related to environmental conditions

The elemental composition of proteins influences the quantities of different elements required by organisms. Here, we considered variation in the sulphur content of whole proteomes among 19 Archaea, 122 Eubacteria and 10 eukaryotes whose genomes have been fully sequenced. We found that different species vary greatly in the sulphur content of their proteins, and that average sulphur content of proteomes and genome base composition are related. Forces contributing to variation in proteomic sulphur content appear to operate quite uniformly across the proteins of different species. In particular, the sulphur content of orthologous proteins was frequently correlated with mean proteomic sulphur contents. Among prokaryotes, proteomic sulphur content tended to be greater in anaerobes, relative to non-anaerobes. Thermophiles tended to have lower proteomic sulphur content than non-thermophiles, consistent with the thermolability of cysteine and methionine residues. This work suggests that persistent environmental growth conditions can influence the evolution of elemental composition of whole proteomes in a manner that may have important implications for the amount of sulphur used by living organisms to build proteins. It extends previous studies that demonstrated links between transient changes in environmental conditions and the elemental composition of subsets of proteins expressed under these conditions.     

Magnesium and sulphur in the calcite shells of two brachiopods, Terebratulina retusa and Novocrania anomala

This study determines the distribution of magnesium and sulphur in the shells of two species of brachiopod from the same environment to highlight environmental and biological influences on shell composition. In Terebratulina retusa there are differences in magnesium concentration between the primary layer and the outer and inner regions of the secondary layer. In contrast, Novocrania anomala has a shell composed of high magnesium calcite and there is no significant difference in magnesium concentration between the primary and the secondary shell layers. Sulphur provides an indication of the distribution of sulphated organic matrix within the shells of T. retusa and N. anomala . In T. retusa the distribution of magnesium and sulphur correlates across the shell; however, there is no evidence for a relationship between magnesium and sulphur distribution in N. anomala . The relationship between magnesium and sulphur in T. retusa indicates that a proportion of the magnesium content of the shell is associated with the sulphated fraction of the organic matrix. In these two species of brachiopod, from the same environment, magnesium and organic concentration and distribution are very different, emphasizing the importance of fully understanding the factors that control biomineral composition before the application of these biominerals to environmental studies.     

Enzymatic sulphur oxygenation reactions

Sulphur is a key constituent in a wide variety of biologically important compounds, ranging from amino acids and coenzymes to antibiotics and pesticides. In analogy with the more widely studied metabolism of aromatic or aliphatic hydrocarbons and amines, the intial step in metabolism of sulphur compounds is commonly oxygenation on sulphur. While sulphur oxygenation in vivo has been known for many years, it is only within the past decade that many of the enzymes responsible have been identified, and molecularlevel details have become available. This review focuses on the molecular aspects of enzymatic sulphur oxygenation, and considers mono and dioxygenases active on inorganic sulphur, organic thiols, thioethers, thioesters and thiones. Information from very diverse areas of the literature is brought together, and the implications of sulphur oxygenation reactions to drug design, as well as to environmental and toxicological areas, are mentioned.     

Micronised and non-micronised sulphur applications control peach scab equally well with negligible differences in fruit quality

In a 2-year study, micronised (finely ground) and non-micronised sulphur spray programmes were investigated for peach scab control and influence on peach fruit quality variables including fruit colouration, soluble solids content and flesh firmness. Both sulphur programmes, applied six or 11 times at 15 kg ha⁻¹, controlled scab equally well in both years on cultivars (cvs) Contender and Cresthaven. Six applications of a half dosage of both micronised and non-micronised sulphur programmes were significantly less effective ( P  < 0.05) compared with all other programmes when scab incidence was >90% on cv. Contender. None of the sulphur programmes influenced significantly ( P  < 0.05) colouration and flesh firmness of harvested fruits compared with the industry standard (a chlorothalonil–captan programme). Only soluble solids concentrations showed significant differences among fungicide programmes ( P  < 0.05), but these differences were not consistent with either particle sizes of sulphur fungicide or reduced application fungicide programmes. In conclusion, our study showed that (a) micronised sulphur did not control peach scab more effectively compared to non-micronised sulphur; (b) six applications of sulphur were sufficient to control peach scab when disease pressure was low to medium; and (c) neither six nor 11 applications of sulphur-based products applied at 15 kg ha⁻¹ had commercially relevant negative impacts on important peach fruit quality variables.     

Biogeochemical cycling of sulphur in karst and transfer into speleothem archives at Grotta di Ernesto, Italy

Trace amounts of sulphur in speleothems suggest that stalagmites may act as archives of sulphur deposition, thereby recording aspects of atmospheric variability in sulphur content. Accurate interpretation of this novel sulphur archive depends upon understanding how biogeochemical cycling in the soil and epikarst above the cave may modify the precursor atmospheric values of sulphur concentration and isotopic composition prior to incorporation into the speleothem record. Dual isotope analysis of δ³⁴S-SO₄ and δ¹⁸O-SO₄ is used to trace biogeochemical transformations of atmospheric sulphur through the cave system at Grotta di Ernesto in the Italian Alps and builds towards a framework for interpretation of speleothem sulphur archives which depends on overlying ecosystem dynamics and karst hydrological properties. A three component model of atmospheric sulphate signal modification is proposed to be driven by (1). vegetation and soil cycling, (2). the degree of groundwater mixing in the karst aquifer; and (3). redox status. The relative influence of each process is specific to individual drip flow sites and associated stalagmites, rendering each sulphur archive a unique signal of environmental conditions. Under conditions found in the soil and epikarst above Grotta di Ernesto, the dual isotope signatures of sulphate sulphur and oxygen incorporated into speleothem carbonate, closely reflect past conditions of industrial sulphur loading to the atmosphere and the extent of signal modification through biogeochemical cycling and aquifer mixing.     

Overview, conclusions, and recommendations of the IPCS collaborative study on complex mixtures.

The International Programme on Chemical Safety (IPCS) sponsored an international collaborative study to examine the variability associated with the extraction and bioassay of standard reference materials (SRMs) that are complex environmental mixtures provided by the U.S. National Institute of Standards and Technology (NIST). The study was also intended to evaluate the feasibility of establishing bioassay reference values and ranges for the SRMs. Twenty laboratories from North America, Europe, and Japan participated in the study. As part of the mandatory core protocol, each laboratory extracted the organic material from two particulate samples and bioassayed these extracts. A coal tar polycyclic aromatic hydrocarbon (PAH) solution and two mutagenic control compounds were also subjected to bioassay without prior extraction by the participating laboratories. The bioassay used was the Salmonella/microsomal plate incorporation assay. For the optional portion of the study, a laboratory was free to use the SRMs for any type of exploratory research. The primary purpose of the required portion of the study was to estimate the intra- and inter-laboratory variability in mutagenic potencies of the test materials and to determine whether or not the NIST mixtures could be used as reference materials by others performing the Salmonella assay. Repeatability (intra-laboratory variance) of the bioassay results ranged from 16% to 88% depending on the SRM and the bioassay conditions (tester strain and metabolic activation), whereas reproducibility (inter-laboratory variance) ranged from 33% to 152%. Between-laboratory variability was the main source of variation accounting for approximately 55-95% of the total variation for the three environmental samples. Variation in the mutagenic potency of the control compounds was comparable, with the exception of 1-nitropyrene for which the reproducibility ranged from 127% to 132%. In summary, NIST SRMs provided useful materials for an international inter-laboratory study of complex mixtures. By establishing both intra- and inter-laboratory variance for the mutagenicity results for these materials, the usefulness of these SRMs as reference materials for the Salmonella bioassay was established, critical procedures within the bioassay protocol were identified, and recommendations for future efforts were delineated.     

Environmental metabolomics: a SWOT analysis (strengths, weaknesses, opportunities, and threats)

Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively explored. This review will use a SWOT analysis model to discuss some of the strengths, weaknesses, opportunities, and threats that are apparent to an investigator venturing into this relatively new field. SWOT has been used extensively in business settings to uncover new outlooks and identify problems that would impede progress. The field of environmental metabolomics provides great opportunities for discovery, and this is recognized by a high level of interest in potential applications. However, understanding the biological consequence of environmental exposures can be confounded by inter- and intra-individual differences. Metabolomic profiles can yield a plethora of data, the interpretation of which is complex and still being evaluated and researched. The development of the field will depend on the availability of technologies for data handling and that permit ready access metabolomic databases. Understanding the relevance of metabolomic endpoints to organism health vs adaptation vs variation is an important step in understanding what constitutes a substantive environmental threat. Metabolomic applications in reproductive research are discussed. Overall, the development of a comprehensive mechanistic-based interpretation of metabolomic changes offers the possibility of providing information that will significantly contribute to the protection of human health and the environment.     

The distribution and activity of sulphate reducing bacteria in estuarine and coastal marine sediments

Sulphate-reducing bacteria (SRB) play a vital role both the carbon and sulphur cycles and thus are extremely important components of the global microbial community. However, it is clear that the ecology, the distribution and activity of different SRB groups is poorly understood. Probing of rRNA suggests that different sediments have distinctly different patterns of SRB with complex factors controlling the activity of these organisms. The linking of community structure and function using sediment slurry microcosms suggests that certain groups of SRB, e.g., Desulfobacter and Desulfobulbus, can be linked to the use of specific substrates in situ. However, it is still unclear what environmental substrates are utilised by the majority of known SRBs. The work to date has greatly enhanced our understanding of the ecology of these organisms and is beginning to suggest patterns in their distribution and activity that may be relevant to understanding microbial ecology in general. This revised version was published online in August 2006 with corrections to the Cover Date.     

Predictive current control of a switched reluctance machine in the direct-drive manipulator of cloud robotics

Cloud robotics has undergone rapid development. As an important candidate for direct-drive manipulator, switched reluctance machines (SRMs) face significant challenge in terms of control used in cloud robotics because of latency and package losses in network communication. In this paper, predictive current control of SRMs is extended to use in controller upon cloud in the face of latency and package losses. The starting point of predictive model is modified to eliminate errors caused by latency in sensor-controller communication, and the execution of control command sequence is dynamically regulated according to the arrival time of the following sequence to adapt for latency and package losses in controller-actuator communication. The proposed control method is evaluated in a 1.5 kW SRM test platform and comparison with a conventional control method is performed; the results show that the proposed control method has better tracking performance in face of time delay and package losses in transmission.     

Mobilization of sulphur in soybean cotyledons during germination

Soybean seeds ( Glycine max L. cv , Stephens) contain a large amount of sulphur (ca 40 μ mol seed⁻¹), mostly in the insoluble fraction in the cotyledons. During germination in nutrient solution lacking sulphur the amount of insoluble sulphur decreases to very low levels. This is accompanied by a transitory increase in the pool of soluble sulphur which then declines. All of the sulphur lost from the cotyledons is quantitatively recovered in the seedling. In the short term, the root and the stem are the most important sinks for sulphur from the cotyledons but as growth proceeds the shoot becomes the dominant sink for remobilized sulphur. Within the shoot most of the sulphur is recovered in leaves L1 and L2. The growth of L3 and, to a lesser extent, L2, was retarded due to sulphur insufficiency. The cotyledons of plants treated with 20 μ M sulphate also exhibited mobilization of sulphur from the insoluble fraction except that the maximum rate of loss of sulphur occurred somewhat later. Plants grown with sulphate exhibited a net gain of sulphur and did not exhibit sulphur insufficiency. In these plants, endogenous sulphur from the cotyledons was directed into L1–L3 and this sulphur remained within these leaves for the duration of the experiment. The delivery of exogenous sulphur (supplied as [³⁵S]sulphate via the roots) to the leaves increased with leaf number. In leaves L1–L3, the level of exogenous sulphur in any one leaf declined with time, indicating that this sulphur was remobilized and did not mix with the sulphur derived from the cotyledons. It was concluded that the cotyledons are an important source of sulphur to support early plant growth and development of soybean.     

Microbial community and network differently reshaped by crushed straw or biochar incorporation and associated with nitrogen fertilizer level

Straw returning has been demonstrated as a beneficial approach for the utilization of renewable biomass source, which contributes to reducing environmental pollution and strengthening the sustainability of agriculture. However, information on how microorganisms respond to different straw return modes (SRMs) at varying nitrogen fertilizer levels (NFLs) in the black soil is still limited. The community composition, network pattern, and modular function of bacteria and fungi are investigated under three SRMs, including straw removal (CK), crushed straw incorporation (SD), and biochar incorporation (BC) at three NFLs (0, 144, and 240 kg N ha⁻¹, respectively) mainly using Illumina MiSeq technique based on a long-term maize field experiment. Results showed that bacterial richness, diversity, and fungal richness decreased with NFL reduction. However, these decreases can be compensated by SD and BC, demonstrating superiority for BC at reduced NFLs. SD and BC differed in their effects on the bacterial and fungal abundances (showing increments only in SD) and fungal Shannon diversity (remaining stable only in BC irrespective of NFLs). Microbial communities were substantially affected by SRMs and interacted with NFLs, which were driven by soil NH₄⁺-N, available potassium, total nitrogen, and pH. In addition, SD induced a network characterized by its highly complex (average degree 10.259 vs. 3.364) and stable structure (average clustering coefficient 0.503 vs. 0.239), Ascomycota as predominating keystone taxa, and abundant N-cycling related bacteria, while BC formed a network comprising a superior modular structure (modularity 2.599 vs. 0.912), dominant symbiotic fungi, and soil bulk density as specific shaping factor, indicating that network pattern, keystone taxa, modular function, and determining factors shifted between SD and BC co-occurrence networks. These results deepen insights into the response divergence of bacteria and fungi to SRMs and NFLs, providing a scientific basis for selecting the suitable strategy for sustainable straw utilization in the black soil area.     

Strengthening desert plant biotechnology research in the United Arab Emirates: a viewpoint

The biotechnology of desert plants is a vast subject. The main applications in this broad field of study comprises of plant tissue culture, genetic engineering, molecular markers and others. Biotechnology applications have the potential to address biodiversity conservation as well as agricultural, medicinal, and environmental issues. There is a need to increase our knowledge of the genetic diversity through the use of molecular genetics and biotechnological approaches in desert plants in the Arabian Gulf region including those in the United Arab Emirates (UAE). This article provides a prospective research for the study of UAE desert plant diversity through DNA fingerprinting as well as understanding the mechanisms of both abiotic stress resistance (including salinity, drought and heat stresses) and biotic stress resistance (including disease and insect resistance). Special attention is given to the desert halophytes and their utilization to alleviate the salinity stress, which is one of the major challenges in agriculture. In addition, symbioses with microorganisms are thought to be hypothesized as important components of desert plant survival under stressful environmental conditions. Thus, factors shaping the diversity and functionality of plant microbiomes in desert ecosystems are also emphasized in this article. It is important to establish a critical mass for biotechnology research and applications while strengthening the channels for collaboration among research/academic institutions in the area of desert plant biotechnology.     

Importance of the functional state of alveolar macrophages of the lungs for hygienic evaluation of protective reactions and cell damage due to atmospheric pollution

Total number of cells, their viability and ability to adhesion were examined in surface alveolar macrophages isolated from rat livers after exposure to sulphur dioxide during 2, 4 and 6 weeks (0.05, 0.5, 1.0 and 5.0 mg/m3); to nitrogen oxide during 5, 8 and 15 hours, 28 and 56 days (19 mg/m3) and to carbon monoxide during 2, 28 and 56 days (0.01% or 10 MAC). In the experiment with exposure to sulphur dioxide, the activity of enzymes of varying localization in the macrophages - soluble in the cytoplasm (lactate dehydrogenase) and connected with subcellular structures - lysosomes (beta-galactosidase, beta-glucosidase and acid phosphatase) was tested by means of biochemical methods in parallel with cytological examinations. Low concentrations of various chemical contaminants of the atmospheric air (sulphur dioxide, nitrogen oxides, carbon monoxide) have an unfavourable biological effect on rats, manifest in the impairment of local immunity, i.e., decreased number of alveolar macrophages, disturbance of their viability and reduced ability of the macrophages to adhesion. At the same time, sulphur dioxide induces enzyme disorganization in lactate dehydrogenase and in a number of lysosomal enzymes of the macrophages. These results serve as a basis for the recommendation of cytobiochemical methods of elaborating methodological approaches to the regulation of environmental factors. Alveolar macrophages as a constituent part of the mononuclear phagocytic system ensuring local non-specific and specific resistance of the organism form one of the most important cellular mechanisms of protection of the organism against the harmful effect of environmental factors including chemical contaminants of the atmospheric air (1, 2).(ABSTRACT TRUNCATED AT 250 WORDS)     

Dietary supplement Standard Reference Materials

A new category of Standard Reference Materials (SRMs) based on dietary supplements is under development by the National Institute of Standards and Technology (NIST), with certified values for organic constituents and selected trace elements. These materials are provided primarily for use in method development and as control materials. The SRMs will assist manufacturers of dietary supplements in characterizing raw materials for potency, authenticity, and contamination or adulteration. In addition, the SRMs will assist in assessment of consistency and quality in finished products. The goal of this ongoing effort is to provide tools to the dietary supplement industry and measurement communities that will lead to improved quality of dietary supplements, and ultimately reduce public health risks that could potentially be associated with these products.     

Sulphur isotopes and the search for life: strategies for identifying sulphur metabolisms in the rock record and beyond

The search for life can only be as successful as our understanding of the tools we use to search for it. Here we present new sulphur isotope data (32S, 33S, 34S, 36S) from a variety of modern marine environments and use these observations, along with previously published work, to contribute to this search. Specifically, we use these new data to gain a sense of life's influences on the sulphur isotope record and to distinguish these biologically influenced signatures from their non-biological counterparts. This treatment extends sulphur isotope analyses beyond traditional (34S/32S) measures and employs trace isotope relationships (33S/32S, 36S/32S), as the inclusion of these isotopes provides unique information about biology and its role in the sulphur cycle through time. In the current study we compare and contrast isotope effects produced by sulphur-utilizing microorganisms (experimental), modern and ancient sedimentary records (observational) and non-biological reactions (theoretical). With our collective search for life now extending to neighbouring planets, we present this study as a first step towards more fully understanding the capability of the sulphur isotope system as a viable tool for life detection, both on Earth and beyond.     

荧光原位杂交技术(FISH)及其在环境微生物学中的应用

微生物对整个生态系统具有重要的影响,了解和检测微生物的种类具有十分重要的意义。但是传统的培养方法又不能满足科学研究的需要,荧光原位杂交技术（FISH）就是近年发展起来的一种快速准确检测微生物的方法,作者较全面地介绍了FISH技术的优点、微生物的分离和固定方法,以及原位杂交过程,同时对FISH技术在环境微生物学中的应用及其前景作了展望。     

Design and implementation of a collaborative study of the mutagenicity of complex mixtures in Salmonella typhimurium.

In 1987, the International Programme on Chemical Safety (IPCS) in collaboration with the U.S. Environmental Protection Agency (U.S. EPA) and the U.S. National Institute of Standards and Technology (U.S. NIST) initiated an international collaborative study of the mutagenicity of complex environmental mixtures in the Ames Salmonella typhimurium mutation assay. The objectives of this study were: (1) to estimate the inter- and intra-laboratory variability associated with the extraction of mixtures for bioassay, (2) to estimate the inter- and intra-laboratory variability associated with the Salmonella typhimurium bioassay when applied to complex mixtures, and (3) to determine whether standard reference complex mixtures would be useful in mutagenicity studies and to evaluate whether reference or certified mutagenicity values determined from this collaborative study should be reported. The complex mixtures used in this study were selected from standard reference materials (SRMs) which had previously been issued by the U.S. NIST as SRM 1597 (coal tar), SRM 1649 (diesel particulate matter) and SRM 1650 (urban air particulate matter) with certified values for polycyclic aromatic hydrocarbons. These SRM complex mixtures are available to scientists as reference standards for analytical chemistry research and are under consideration as SRMs for mutagenicity studies of complex environmental mixtures. This paper briefly describes the final study design, protocol, selection of the complex mixtures, and implementation of this international study.     

Phospholipid fatty acid profiling of microbial communities–a review of interpretations and recent applications

Profiling of microbial communities in environmental samples often utilizes phospholipid fatty acid (PLFA) analysis. This method has been used for more than 35 years and is still popular as a means to characterize microbial communities in a diverse range of environmental matrices. This review examines the various recent applications of PLFA analysis in environmental studies with specific reference to the interpretation of the PLFA results. It is evident that interpretations of PLFA results do not always correlate between different investigations. These discrepancies in interpretation and their subsequent applications to environmental studies are discussed. However, in spite of limitations to the manner in which PLFA data are applied, the approach remains one with great potential for improving our understanding of the relationship between microbial populations and the environment. This review highlights the caveats and provides suggestions towards the practicable application of PLFA data interpretation.