The Phytomanagement of Trace Elements in Soil

Trace elements (TEs) occur at low concentrations (<1000 mg kg ^?1) in organisms, yet they have a large biological effect, both as essential nutrients and environmental contaminants. Phytomanagement describes the manipulation of soil-plant systems to affect the fluxes of TEs in the environment with the goal of remediating contaminated soils, recovering valuable metals, or increasing micronutrient concentrations in crops. Phytomanagement includes all biological, chemical, and physical technologies employed on a vegetated site. Successful phytomanagement should either cost less than other remediation or fortification technologies, or be a profitable operation, by producing valuable plant biomass products. This may include bioenergy or timber production on contaminated land, a practice that does not reduce food production. We review the components of phytomanagement and the underlying biogeochemical processes, with a view to elucidating situations where this technology may be successfully applied and identifying future research needs. Many full-scale operations have proved the efficacy of plants to reduce contaminant mobility in soils (phytostabilization), particularly when used in combination with other technologies. As a stand-alone technology, the oft-touted use of plants to extract TEs from contaminated soils (phytoextraction) or low-grade ore bodies (phytomining) is unsuitable for most, if not all, sites due to low-extraction rates and problems caused by site heterogeneity, the limited rooting depth of plants and the presence of contaminant mixtures. Unsubstantiated claims about phytoextraction have tarnished the reputation of all “phyto” technologies. Nevertheless, phytoextraction, as part of a larger environmental toolkit, has a role in phytomanagement. The growth, or lack thereof, of profitable companies that provide phytomanagement will indicate its value. A critical knowledge gap in phytomanagement is the integration of the processes that affect plant–TE interactions and the biophysical processes affecting TE fluxes in the root zone, especially the effect of roots on contaminant fluxes.     

Diazotrophy in Alluvial Meadows of Subarctic River Systems

There is currently limited understanding of the contribution of biological N₂ fixation (diazotrophy) to the N budget of large river systems. This natural source of N in boreal river systems may partially explain the sustained productivity of river floodplains in Northern Europe where winter fodder was harvested for centuries without fertilizer amendments. In much of the world, anthropogenic pollution and river regulation have nearly eliminated opportunities to study natural processes that shaped early nutrient dynamics of large river systems; however, pristine conditions in northern Fennoscandia allow for the retrospective evaluation of key biochemical processes of historical significance. We investigated biological N₂ fixation (diazotrophy) as a potential source of nitrogen fertility at 71 independent floodplain sites along 10 rivers and conducted seasonal and intensive analyses at a subset of these sites. Biological N₂ fixation occurred in all floodplains, averaged 24.5 kg N ha⁻¹ yr⁻¹ and was down regulated from over 60 kg N ha⁻¹ yr⁻¹ to 0 kg N ha⁻¹ yr⁻¹ by river N pollution. A diversity of N₂-fixing cyanobacteria was found to colonize surface detritus in the floodplains. The data provide evidence for N₂ fixation to be a fundamental source of new N that may have sustained fertility at alluvial sites along subarctic rivers. Such data may have implications for the interpretation of ancient agricultural development and the design of contemporary low-input agroecosystems.     

Winery wastewater treatment: a critical overview of advanced biological processes

Wine production is one of the leading sectors of the food processing industry. The wine industry produces a large amount of wastewater characterized by a high strength in terms of organic pollution and large variability throughout the year. Most of the organic matter is soluble and easily biodegradable. On the other hand, nitrogen and phosphorous are lacking. The aerobic and anaerobic processes are largely applied for winery wastewater treatment because they can quickly react to changes in the organic loading. This review analyzes e applied biological systems, considering both aerobic and anaerobic processes, and different reactor configurations. The performances of different biological processes are evaluated in terms of operational conditions (organic loading rate and hydraulic retention time). Aerobic processes can guarantee chemical oxygen demand removal up to 98% for organic loading rates of some 1-2?kg of chemical oxygen demand m^?3d^?1 but requires good aeration systems to supply the required process oxygen. The management cost of these processes could be high considering the power density in the range 60-70?W m^?3_reactor and that nutrients should be added to support biomass growth. On the other hand, anaerobic processes are able to face high organic loads with low running costs, but COD removal is generally limited to 90%. Combination of the two treatment systems (anaerobic followed by aerobic) could reduce management costs and meet high discharge standards.     

Psychological Processes Mediate the Impact of Familial Risk,Social Circumstances and Life Events on Mental Health

Background

Despite widespread acceptance of the ‘biopsychosocial model’, the aetiology of mental health problems has provoked debate amongst researchers and practitioners for decades. The role of psychological factors in the development of mental health problems remains particularly contentious, and to date there has not been a large enough dataset to conduct the necessary multivariate analysis of whether psychological factors influence, or are influenced by, mental health. This study reports on the first empirical, multivariate, test of the relationships between the key elements of the biospychosocial model of mental ill-health.

Methods and Findings

Participants were 32,827 (age 18–85 years) self-selected respondents from the general population who completed an open-access online battery of questionnaires hosted by the BBC. An initial confirmatory factor analysis was performed to assess the adequacy of the proposed factor structure and the relationships between latent and measured variables. The predictive path model was then tested whereby the latent variables of psychological processes were positioned as mediating between the causal latent variables (biological, social and circumstantial) and the outcome latent variables of mental health problems and well-being. This revealed an excellent fit to the data, S-B χ² (3199, N = 23,397) = 126654·8, p<·001; RCFI = ·97; RMSEA = ·04 (·038–·039). As hypothesised, a family history of mental health difficulties, social deprivation, and traumatic or abusive life-experiences all strongly predicted higher levels of anxiety and depression. However, these relationships were strongly mediated by psychological processes; specifically lack of adaptive coping, rumination and self-blame.

Conclusion

These results support a significant revision of the biopsychosocial model, as psychological processes determine the causal impact of biological, social, and circumstantial risk factors on mental health. This has clear implications for policy, education and clinical practice as psychological processes such as rumination and self-blame are amenable to evidence-based psychological therapies.     

Scaling analysis of coral reef systems: an approach to problems of scale

Dimensional analysis and scaling are related, semi-formal procedures for capturing the essential process(es) controlling the behaviour of a complex system, and for describing the functional relationships between them. The techniques involve the parameterization of natural processes, the identification of the temporal and spatial scales of variation of processes, and the evaluation of potential interactions between processes referenced to those scales using non-dimensional (scaled) parameters. Scaling approaches are increasingly being applied to a broad range of marine ecological problems, with the aims of assessing the relative importance of physical and biological parameters in controlling variation in process rates, and placing limits on the ability of one process to affect another. The value of the approach to coral reef research lies in the conceptualization of relationships between discipline-specific processes, and the evaluation of scale-dependent processes across the large range of spatial and temporal scales which pertain to coral reefs. Characteristic scales of physical, geological and biological processes exhibit different patterns of distribution along the temporal dimension. Scaling arguments based on examples from reef systems indicate that a large group of biological and biogeochemical processes are strongly influenced by hydrodynamic processe occuring at similar time scales within the range from about on hour to one year. We argue that scaling approaches to process-related problems are pre-requisite to interdisciplinary research on coral reefs.     

Dielectric Spectroscopy and Membrane Organisation

The possible bases for field-mediated effects on cellular processes are reflected in the passive electrical properties of biological systems. The historical, present and prospective utility of dielectric spectroscopy in assessing the static and dynamic organisation of biological membranes is reviewed within this context. The basis for the view that the static capacitance of bioraembranes is as great as 1 fiF/cm² is doubted; contributions from the (partially restricted) motions of membrane components, and of double-layer ions, probably contribute to this apparent value in bioraembrane vesicle suspensions. The importance of improving our knowledge of the static electrical capacitance of energy coupling membranes is stressed. Theoretical and experimental procedures for assessing the contribution of rotational and translational motions of membrane components, and of double-layer/membrane interactions, to dielectric spectra in the approximate frequency range 10 to 10⁷ Hz are described. Finally, three outstanding and generally unsolved problems requiring further work are detailed.     

Removing Hexazinone from Groundwater with Microbial Bioreactors

Hexazinone, a triazine herbicide that is often detected as a ground and surface water contaminant, inhibits electron transport in photosynthetic organisms and is toxic to primary producers that serve as the base of the food chain. This laboratory study evaluated the ability of two types of microbial reactors, i.e., a vegetable oil-based nitrogen-limiting biobarrier and an aerobic slow sand filter, as methods for removing hexazinone from simulated groundwater. The N-limiting biobarriers degraded hexazinone, but did so with a 52 week incubation period and a removal efficiency that varied greatly among replicates, with one biobarrier showing a removal efficiency of ~95% and the other an efficiency of ~50%. More consistent degradation was obtained with the aerobic sand biobarriers. Four aerobic biobarriers were evaluated and all behaved in a similar manner degrading hexazinone with removal efficiencies of ~97%; challenging two of the aerobic biobarriers with large amounts of influent hexazinone showed that these barriers are capable of efficiently remediating large amounts (>100 mg L⁻¹) of hexazinone at high efficiency. The remediation process was due to biological degradation rather than abiotic processes. The long lag phase observed in both types of reactors suggests that an acclimation process, where microorganisms capable of degrading hexazinone increased in numbers, was required. Also, the isolation of bacteria that show a positive growth response to the presence of hexazinone in their growth media suggests biological degradation.     

Lanosterol Analogs: Dual-Action Inhibitors of Cholesterol Biosynthesis

Abstract

Deoxyribonucleic acid is one of the most interesting and also the most complex of all biological macromolecules. Paradoxically, this complexity arises from the simplicity of its basic subunit structure. A large eukaryotic chromosome probably contains a single chain of DNA with a molecular weight in excess of 10¹¹ daltons and is composed of a linear permutation of the four basic deoxyribonucleotides. Until recently, this fact posed considerable problems for the biochemist interested in isolating specific fragments of chromosomes as the methods available were nonspecific in nature. This is no longer so; the discovery of site specific endodeoxyribonucleases (restriction endo-nucleases) has opened new routes to the analysis of DNA structure and function and promises a revolution in molecular biology. A new field of genetic engineering is already being pioneered, and significant advances in many areas have been facilitated by the availability of these enzymes.     

Online nonlinear sequential Bayesian estimation of a biological wastewater treatment process

Online estimation of unknown state variables is a key component in the accurate modelling of biological wastewater treatment processes due to a lack of reliable online measurement systems. The extended Kalman filter (EKF) algorithm has been widely applied for wastewater treatment processes. However, the series approximations in the EKF algorithm are not valid, because biological wastewater treatment processes are highly nonlinear with a time-varying characteristic. This work proposes an alternative online estimation approach using the sequential Monte Carlo (SMC) methods for recursive online state estimation of a biological sequencing batch reactor for wastewater treatment. SMC is an algorithm that makes it possible to recursively construct the posterior probability density of the state variables, with respect to all available measurements, through a random exploration of the states by entities called ‘particle’. In this work, the simplified and modified Activated Sludge Model No. 3 with nonlinear biological kinetic models is used as a process model and formulated in a dynamic state-space model applied to the SMC method. The performance of the SMC method for online state estimation applied to a biological sequencing batch reactor with online and offline measured data is encouraging. The results indicate that the SMC method could emerge as a powerful tool for solving online state and parameter estimation problems without any model linearization or restrictive assumptions pertaining to the type of nonlinear models for biological wastewater treatment processes.     

Soil structural aspects of decomposition of organic matter by micro-organisms

Soil architecture is the dominant control over microbially mediated decomposition processes in terrestrial ecosystems. Organic matter is physically protected in soil so that large amounts of well-decomposable compounds can be found in the vicinity of largely starving microbial populations. Among the mechanisms proposed to explain the phenomena of physical protection in soil are adsorption of organics on inorganic clay surfaces and entrapment of materials in aggregates or in places inaccessible to microbes. Indirect evidence for the existence of physical protection in soil is provided by the occurrence of a burst of microbial activity and related increased decomposition rates following disruption of soil structures, either by natural processes such as the remoistening of a dried soil or by human activities such as ploughing. In contrast, soil compaction has only little effect on the transformation of ¹⁴C-glucose. Another mechanism of control by soil structure and texture on decomposition in terrestrial ecosystems is through their impact on microbial turnover processes. The microbial population is not only the main biological agent of decomposition in soil, it is also an important, albeit small, pool through which most of the organic matter in soil passes. Estimates on the relative importance of different mechanisms controlling decomposition in soil could be derived from results of combined tracer and modelling studies. However, suitable methodology to quantify the relation between soil structure and biological processes as a function of different types and conditions of soils is still lacking.     

Knowing What Counts: Unbiased Stereology in the Non-human Primate Brain

The non-human primate is an important translational species for understanding the normal function and disease processes of the human brain. Unbiased stereology, the method accepted as state-of-the-art for quantification of biological objects in tissue sections², generates reliable structural data for biological features in the mammalian brain³. The key components of the approach are unbiased (systematic-random) sampling of anatomically defined structures (reference spaces), combined with quantification of cell numbers and size, fiber and capillary lengths, surface areas, regional volumes and spatial distributions of biological objects within the reference space⁴. Among the advantages of these stereological approaches over previous methods is the avoidance of all known sources of systematic (non-random) error arising from faulty assumptions and non-verifiable models. This study documents a biological application of computerized stereology to estimate the total neuronal population in the frontal cortex of the vervet monkey brain (Chlorocebus aethiops sabeus), with assistance from two commercially available stereology programs, BioQuant Life Sciences and Stereologer (Figure 1). In addition to contrast and comparison of results from both the BioQuant and Stereologer systems, this study provides a detailed protocol for the Stereologer system.Open in a separate windowClick here to view.^{(58M, flv)}     

Endothelialized Microfluidics for Studying Microvascular Interactions in Hematologic Diseases

Advances in microfabrication techniques have enabled the production of inexpensive and reproducible microfluidic systems for conducting biological and biochemical experiments at the micro- and nanoscales ^1,2. In addition, microfluidics have also been specifically used to quantitatively analyze hematologic and microvascular processes, because of their ability to easily control the dynamic fluidic environment and biological conditions^3-6. As such, researchers have more recently used microfluidic systems to study blood cell deformability, blood cell aggregation, microvascular blood flow, and blood cell-endothelial cell interactions^6-13.However, these microfluidic systems either did not include cultured endothelial cells or were larger than the sizescale relevant to microvascular pathologic processes. A microfluidic platform with cultured endothelial cells that accurately recapitulates the cellular, physical, and hemodynamic environment of the microcirculation is needed to further our understanding of the underlying biophysical pathophysiology of hematologic diseases that involve the microvasculature.Here, we report a method to create an "endothelialized" in vitro model of the microvasculature, using a simple, single mask microfabrication process in conjunction with standard endothelial cell culture techniques, to study pathologic biophysical microvascular interactions that occur in hematologic disease. This "microvasculature-on-a-chip" provides the researcher with a robust assay that tightly controls biological as well as biophysical conditions and is operated using a standard syringe pump and brightfield/fluorescence microscopy. Parameters such as microcirculatory hemodynamic conditions, endothelial cell type, blood cell type(s) and concentration(s), drug/inhibitory concentration etc., can all be easily controlled. As such, our microsystem provides a method to quantitatively investigate disease processes in which microvascular flow is impaired due to alterations in cell adhesion, aggregation, and deformability, a capability unavailable with existing assays.     

Different target specificities of haptoglobin and hemopexin define a sequential protection system against vascular hemoglobin toxicity

Free hemoglobin (Hb) triggered vascular damage occurs in many hemolytic diseases, such as sickle cell disease, with an unmet need for specific therapeutic interventions. Based on clinical observations the Hb and heme scavenger proteins haptoglobin (Hp) and hemopexin (Hx) have been characterized as a sequential defense system with Hp as the primary protector and Hx as a backup when all Hp is depleted during more severe intravascular hemolysis. In this study we present a mechanistic rationale for this paradigm based on a combined biochemical and cell biological approach directed at understanding the unique roles of Hp and Hx in Hb detoxification. Using a novel in vitro model of Hb triggered endothelial damage, which recapitulates the well-characterized pathophysiologic sequence of oxyHb(Fe²⁺) transformation to ferric Hb(Fe³⁺), free heme transfer from ferric Hb(Fe³⁺) to lipoprotein and subsequent oxidative reactions in the lipophilic phase. The accumulation of toxic lipid peroxidation products liberated during oxidation reactions ultimately lead to endothelial damage characterized by a specific gene expression pattern with reduced cellular ATP and monolayer disintegration. Quantitative analysis of key chemical and biological parameters allowed us to precisely define the mechanisms and concentrations required for Hp and Hx to prevent this toxicity. In the case of Hp we defined an exponential relationship between Hp availability relative to oxyHb(Fe²⁺) and related protective activity. This exponential relationship demonstrates that large Hp quantities are required to prevent Hb toxicity. In contrast, the linear relationship between Hx concentration and protection defines a highly efficient backup scavenger system during conditions of large excess of free oxyHb(Fe²⁺) that occurs when all Hp is consumed. The diverse protective function of Hp and Hx in this model can be explained by the different target specificities of the two proteins.     

Microbial Consumption of Atmospheric Isoprene in a Temperate Forest Soil

Isoprene (2-methyl-1,3 butadiene) is a low-molecular-weight hydrocarbon emitted in large quantities to the atmosphere by vegetation and plays a large role in regulating atmospheric chemistry. Until now, the atmosphere has been considered the only significant sink for isoprene. However, in this study we performed both in situ and in vitro experiments with soil from a temperate forest near Ithaca, N.Y., that indicate that the soil provides a sink for atmospheric isoprene and that the consumption of isoprene is carried out by microorganisms. Consumption occurred rapidly in field chambers (672.60 ± 30.12 to 2,718.36 ± 86.40 pmol gdw⁻¹ day⁻¹) (gdw is grams [dry weight] of soil; values are means ± standard deviations). Subsequent laboratory experiments confirmed that isoprene loss was due to biological processes: consumption was stopped by autoclaving the soil; consumption rates increased with repeated exposure to isoprene; and consumption showed a temperature response consistent with biological activity (with an optimum temperature of 30°C). Isoprene consumption was diminished under low oxygen conditions (120 ± 7.44 versus 528.36 ± 7.68 pmol gdw⁻¹ day⁻¹ under ambient O₂ concentrations) and showed a strong relationship with soil moisture. Isoprene-degrading microorganisms were isolated from the site, and abundance was calculated as 5.8 × 10⁵ ± 3.2 × 10⁵ cells gdw⁻¹. Our results indicate that soil may provide a significant biological sink for atmospheric isoprene.     

Characterizing Intrinsic Bioremediation in a Petroleum Hydrocarbon-Contaminated Aquifer by Combined Chemical,Isotopic, and Biological Analyses

Chemical, isotopic, and biological parameters were evaluated over a 1-year period to characterize microbial processes associated with intrinsic bioremediation in a petroleum hydrocarbon-contaminated aquifer located in Studen, Switzerland. Chemical parameters measured included oxidants such as O₂, NO₃ ^?, and SO₄ ^2?, reduced species such as Fe²⁺ and CH₄, and dissolved inorganic carbon (DIC). Stable carbon isotope analyses of DIC were used to differentiate between different processes that contribute to DIC production. Microbial populations were identified by sequence analysis of archaeal 16S rDNA and in situ hybridization using a general DNA binding dye (DAPI) and specific probes targeting the domain Archaea (Arch915) and Bacteria (Eub338), as well as the species Methanosaeta concilii (Rotcl1) and Methanospirillum sp. (Rotcl2). Groundwater exhibited reduced conditions and elevated concentrations of DIC within the contaminated zone. Spatially distinct values of δ¹³C ranging from ?16.5l%c to ?4.44%o were found, indicating the presence of different ongoing microbial processes. Detected microbial populations (% of DAPI-stained cells) within the contaminated zone belonged to Archaea (9±2% to 31±13%) and Bacteria (13±3% to 32±13%). In wells with methanogenic activity, Methanosaeta concilii accounted for up to 26% of all DAPI-detected microorganisms. These results demonstrate that this novel combination of chemical, isotopic, and biological analysis provides valuable insights that can be used for the characterization of microbial processes in contaminated aquifers.     

Furin as proprotein convertase and its role in normal and pathological biological processes

Furin belongs to intracellular serine Ca²⁺-dependent endopeptidases of the subtilisin family, also known as proprotein convertases (PC). Human furin is synthesized as a zymogen with a molecular weight of 104 kDа, which is then autocatalytically activated in two stages. This process occurs during zymogen migration from the endoplasmic reticulum to the Golgi apparatus, where a large part of furin is accumulated. The molecular weight of the active furin is 98 kDа. Furin is the enzyme with narrow substrate specificity: it hydrolyzes peptide bonds at the site of paired basic amino acids and is active in a wide range of pH (5.0–8.0). The main biological function of furin as PC consists in activation of functionally important protein precursors. This is accompanied by initiation of cascades of reactions, which lead to appearance of biologically active molecules involved in realization of specific biological functions both in normal and in some pathological processes. The list of furin substrates includes biologically important proteins such as enzymes, hormones, growth/differentiation, receptors, adhesion proteins, plasma proteins. Furin plays an important role in the development of such processes as proliferation, invasion, cell migration, survival, maintenance of homeostasis, embryogenesis, as well as the development of a number of pathologies, including cardiovascular, cancer, and neurodegenerative diseases. Furin and furin-like proprotein convertases are key factors in the realization of the regulatory functions of proteolytic enzymes; the latter is currently considered as the most important function (compared with well recognized protease function in degradation of proteins).     

Environmental factors which influence the sink of silica in the limnetic system of the large monomictic Lake Biwa and its watershed in Japan

Dissolved silica (DSi) and its associated biological and physicochemical factors were measured in Lake Biwa, Japan and its watershed from 2002 to 2003 in order to clarify seasonal variations in the magnitude of the sink of silica and the factors that influence it within the limnetic system. Consequently, it is concluded that Lake Biwa is a noticeable body of water where a massive sink of silica is caused. Calculated silica sedimentation in Lake Biwa was 2.0 × 10⁷ kg Si year⁻¹ (7.1 × 10⁸ mol Si year⁻¹) which is equivalent to about 80% of the annual inflow discharge of DSi to Lake Biwa. The magnitude of the sink varies seasonally by increasing in the winter holomictic stirring period, since it is greatly affected by the species composition of phytoplankton, the load of phosphorus and the condition of stratification. It seems reasonable to suppose that the DSi in Lake Biwa is removed mainly by biological processes, i.e., the assimilation of DSi by large centric diatoms and its accumulation in their frustules. Such silica sinks occur naturally in deeper stagnant waters, providing extended water residence time and supplying a certain amount of nutrients. These findings indicate that an increase in nutrient loads and abundance of stagnant water due to the construction of large dams lead to an expansion in the magnitude of the silica sink in a limnetic system.