DStat: A Versatile,Open-Source Potentiostat for Electroanalysis and Integration

Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as “black boxes,” giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat), an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat’s voltammetric measurements are much more sensitive than those of “CheapStat” (a popular open-source potentiostat described previously), and are comparable to those of a compact commercial “black box” potentiostat. Likewise, in head-to-head tests, DStat’s potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the “open source” movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools.     

Kinetic assay for the determination of the oxidative stress biomarker, advanced oxidation protein products (AOPP) in the human blood plasma

A number of human diseases and pathological conditions were found to be associated with increased oxidative stress. In the literature several techniques are available for the assessment of oxidative stress, but most of them are not applicable for a routine medical laboratory due to the complex methodology and/or financial reasons. We report here on a simple, inexpensive, kinetic assay for the determination of the oxidative stress biomarker, advanced oxidation protein products (AOPP) in the human blood plasma. METHODS: This study involved 70 patients (47M/23F; mean age: 64.6 y; range: 16-85) admitted to our Department with a wide range of cardiovascular and peripheral vascular diseases. Three critically ill patients were assigned for monitoring purposes. Plasma AOPP were simultaneously determined using an end-point assay as reference method and by a kinetic method developed in our laboratory. Plasma fibrinogen concentration was measured according to the Clauss method. RESULTS: There was a highly significant correlation (r2 = 0.588; p < 0.0001) between AOPP concentration (reference method) and AOPP reactivity (kinetic method). Both AOPP concentration and AOPP reactivity also significantly correlated with plasma fibrinogen concentration (r2 = 0.780; p < 0.0001; r2 = 0.564; p < 0.0001). The three representative cases presented appear to support the relevance of our novel method in the monitoring of critically ill patients. CONCLUSIONS: This simple and inexpensive kinetic assay can be widely used in any routine laboratory interested in oxidative stress research. It is especially recommended for monitoring critically ill or other patients.     

Public Internet‐connected cameras used as a cross‐continental ground‐based plant phenology monitoring system

Plant phenology is highly sensitive to changes in environmental conditions and can vary widely across landscapes. Current observation methods are either manual for small‐scale, high precision measurements or by satellite remote sensing for large‐scale, low spatial resolution measurement. The development of inexpensive approaches is necessary to advance large scale, high precision phenology monitoring. The use of publicly available, Internet‐connected cameras, often associated with airports, national parks, and roadway conditions, for detecting and monitoring plant phenology at a continental scale can augment existing ground and satellite‐based methodologies. We collected twice‐daily images from over 1100 georeferenced public cameras across North America from February 2008 to 2009. Using a test subset of these cameras, we compared modeled spring ‘green‐up’ with that from co‐occurring remote sensing products. Although varying image exposure and color correction introduced noise to camera measurements, we were able to correlate spring green‐up across North America with visual validation from images and detect a latitudinal trend. Public cameras had an equivalent or higher ability to detect spring compared with satellite‐based data for corresponding locations, with fewer numbers of poor quality days, shorter continuous bad data days, and significantly lower errors of spring estimates. Manual image segmentation into deciduous, evergreen, and understory vegetation allowed detection of spring and fall onset for multiple vegetation types. Additional advantages of a public camera‐based monitoring system include frequent image capture (subdaily) and the potential to detect quantitative responses to environmental changes in organisms, species, and communities. Public cameras represent a relatively untapped and freely available resource for supporting large‐scale ecological and environmental monitoring.     

Changes in bird populations as criteria of environmental changes

Järvinen, O. and Väisänen, R. A. 1979. Changes in bird populations as criteria of environmental changes. – Holarct. Ecol. 2: 75-80.
Birds are a powerful tool of environmental monitoring, on account of their ecological diversity. Because of this, bird populations seem best suited for monitoring biological, possibly non-linear effects of specified environmental changes, such as habitat modification, and for "general monitoring" aimed at detecting unexpected environmental changes as they occur. Because many population changes have multiple causes, monitoring specific environmental changes is most rewarding if birds are grouped by e.g. habitat, major strategy (e.g. resident vs. migrant species), or feeding guild. A blueprint for a Nordic monitoring system based on breeding land birds is presented. Local trends may be atypical, and representative coverage of the major habitats in large areas should thus be ensured. As annual population fluctuations usually give little information in environmental monitoring, long-term projects are necessary. The line transect method seems applicable to many monitoring purposes, as it is rapid, inexpensive, relatively accurate, and suitable for sampling the northern terrestrial biota of the Holarctic region, probably including the temperate deciduous forests.     

Mandatory " enriched" housing of laboratory animals: the need for evidence-based evaluation

Environmental enrichment for laboratory animals has come to be viewed as a potential method for improving animal well-being in addition to its original sense as a paradigm for learning how experience molds the brain. It is suggested that the term housing supplementation better describes the wide range of alterations to laboratory animal housing that has been proposed or investigated. Changes in the environments of animals have important effects on brain structure, physiology, and behavior--including recovery from illness and injury--and on which genes are expressed in various organs. Studies are reviewed that show how the brain and other organs respond to environmental change. These data warrant caution that minor cage supplementation intended for improvement of animal well-being may alter important aspects of an animal's physiology and development in a manner not easily predicted from available research. Thus, various forms of housing supplementation, although utilized or even preferred by the animals, may not enhance laboratory animal well-being and may be detrimental to the research for which the laboratory animals are used.     

Digital image processing for rapid analysis of differentially expressed transcripts on high-density cDNA arrays.

Usage of filter arrays is becoming increasingly attractive for many research laboratories involved in determination of gene-expression profiles. However, analysis of numerous spots, representing genes or partial gene sequences (ESTs), is still tedious work involving the ordered analysis of vast amounts of numerical tabular data. We present a rapid and efficient method for the visual identification of differentially expressed targets on high-density cDNA filter arrays using standard laboratory equipment and standard software, which is available for free. The method we introduce provides an inexpensive alternative, and no changes in the experimental set up are required. Our results were verified by densitometric analyses performed with an established system.     

A micro flow injection electrochemical biosensor for organophosphorus pesticides

We describe a disposable, amperometric micro flow injection electrochemical biosensor that can be applied to the identification and quantification of highly toxic organophosphorus (OP) compounds in the environment, on the spot and in a short time. The system traces very small quantities of OP by monitoring the enzymatic reaction of acetylcholine esterase (AChE) and its inhibition. The sensor is sensitive, rapid, small, inexpensive, disposable and can be operated by non-professional technicians. The electrochemical cell consists of screen-printed electrodes covered with an enzymatic membrane and placed in a home-made flow cell. The electrodes are connected to a computer-controlled potentiostat. We quantitatively detected the OP compound, dimethyl 2,2-dichlorovinyl phosphate (DDVP), by monitoring the OP induced decrease in enzymatic degradation of the substrate, acetylthiocholine chloride (ATCh), to thiocholine and acetic acid. Thiocholine reacts with hexacyanoferrate ion in the working solution and the reduction of [Fe(CN)6](-3) to [Fe(CN)6](-4) and its subsequent reoxidization by the electrode generates very sharp, rapid and reproducible electric signals. The ability to detect low quantities is extremely important when dealing with hazardous environmental pollutants.     

A methodology for screening haemolymph of intertidal mussels, Mytilus edulis, using FT-IR spectroscopy as a tool for environmental assesment

Developing effective, rapid and inexpensive methods for monitoring and conserving aquatic resources is an important issue for environmental managers. This study focuses on Mytilus edulis, a keystone species of many coastal marine communities, which is frequently used as a biomonitor for a range of pollutants. Recent advances in post-genomic technologies have provided new methods of biochemical screening, and Fourier transform-infrared spectroscopy (FT-IR) is one such method that could enable bioindicator species to be used for environmental assessment. This paper develops a methodology to apply the FT-IR approach to marine intertidal M. edulis and addresses three methodological issues: First, the optimum physical location for biofluid sampling is examined (i.e. laboratory versus field). Secondly, the effects of transportation of frozen biofluid sampling from either the field-site or laboratory to the analytical facility are considered. Finally, the effect of repeated FT-IR measurements on collected M. edulis haemolymph samples is examined. From these results we suggest sampling haemolymph from M. edulis at the top of the shore prior to immediate snap-freezing in liquid nitrogen. Sample transportation can occur on ice for up to eight hours before storage at −80 °C. FT-IR measurements should occur within three months of collection and samples should not be used or thawed more than twice. We show how this method can be used to differentiate successfully between four different estuarine environments. Ultimately, through addressing these methodological questions, we provide a protocol to allow efficient sampling and FT-IR measurement of M. edulis as collected from the intertidal areas of rocky and muddy shores. We conclude that due to current monitoring needs presented by the European Water Framework Directive such an approach could prove to be an invaluable future tool for assessing coastal water quality.     

Online and in situ monitoring of environmental pollutants: electrochemical biosensing of cadmium

Online sensitive monitoring of gene expression is essential for understanding microbial life and microbial communities, especially under stress-inducing conditions, such as the presence of environmental pollutants. We describe here a novel use of promoter-based electrochemical biosensing for online and in situ monitoring of gene expression in response to pollutants. As a model system, we used a cadmium-responsive promoter from Escherichia coli fused to a promoterless lacZ gene, which was monitored using an electrochemical assay of β-galactosidase activity. This whole-cell biosensor could detect, within minutes, nanomolar concentrations of cadmium in water, sea water and soil samples, and it can be used for continuous online and in situ monitoring.     

Species-specific peptide ligands for the detection of Bacillus anthracis spores

Currently available detectors for spores of Bacillus anthracis, the causative agent of anthrax, are inadequate for frontline use and general monitoring. There is a critical need for simple, rugged, and inexpensive detectors capable of accurate and direct identification of B. anthracis spores. Necessary components in such detectors are stable ligands that bind tightly and specifically to target spores. By screening a phage display peptide library, we identified a family of peptides, with the consensus sequence TYPXPXR, that bind selectively to B. anthracis spores. We extended this work by identifying a peptide variant, ATYPLPIR, with enhanced ability to bind to B. anthracis spores and an additional peptide, SLLPGLP, that preferentially binds to spores of species phylogenetically similar to, but distinct from, B. anthracis. These two peptides were used in tandem in simple assays to rapidly and unambiguously identify B. anthracis spores. We envision that these peptides can be used as sensors in economical and portable B. anthracis spore detectors that are essentially free of false-positive signals due to other environmental Bacillus spores.     

Boots on the ground: in defense of low-tech,inexpensive, and robust survey methods for Africa’s under-funded protected areas

Protected area managers need reliable information to detect spatial and temporal trends of the species they intend to protect. This information is crucial for population monitoring, understanding ecological processes, and evaluating the effectiveness of management and conservation policies. In under-funded protected areas, managers often prioritize ungulates and carnivores for monitoring given their socio-economic value and sensitivity to human disturbance. Aircraft-based surveys are typically utilized for monitoring ungulates because they can cover large areas regardless of the terrain, but such work is expensive and subject to bias. Recently, unmanned aerial vehicles have shown great promise for ungulate monitoring, but these technologies are not yet widely available and are subject to many of the same analytical challenges associated with traditional aircraft-based surveys. Here, we explore use of inexpensive and robust distance sampling methods in Kafue National Park (KNP) (22,400 km²), carried out by government-employed game scouts. Ground-based surveys spanning 101, 5-km transects resulted in 369 ungulate group detections from 20 species. Using generalized linear models and distance sampling, we determined the environmental and anthropogenic variables influencing ungulate species richness, density, and distribution. Species richness was positively associated with permanent water and percent cover of closed woodland vegetation. Distance to permanent water had the strongest overall effect on ungulate densities, but the magnitude and direction of this effect varied by species. This ground-based approach provided a more cost-effective, unbiased, and repeatable method than aerial surveys in KNP, and could be widely implemented by local personnel across under-funded protected areas in Africa.     

Computer-based image analysis for the automated counting and morphological description of microalgae in culture

A largely unexplored area is the application of digital image processing to counting and sizing of microalgal cells from culture. Commercial systems are available, but have not been tested, nor necessarily optimized for high speed counting and sizing of phytoplankton. The present work describes the design, construction, specifications and comparative performance of an inexpensive system optimized for counting and sizing microalgal cells. This system has been tested with cells of the picoplankton to nanoplankton size ranges (1–20 μm). The hardware was a widely available standard microcomputer, an inexpensive video camera and monitor, and a video digitization board (frame grabber). A modifiable menu-driven program (PHYCOUNT) was written and provisions made to make this program available to other workers. The program is constructed such that it can be adapted to a variety of hardware setups Video digitization boards). Comparison of growth curves for microagae revealed there were no significant differences in division rate and cell yield as assessed by the image analysis method compared to manual counts with a hemacytometer. Several hundred cells were counted routinely within 10–15 s, far exceeding the counting rate achieved by hand tally. A variable transect feature allowed sampling every nth pixel and provided a substantial increase in execution speed. More than 1000 counts can be done per day. A protocol for the use of 96-well plates of polyvinyl chloride as counting chambers contributed to the processing of large numbers of samples rapidly. Other routines developed provided subtended area, defined the coordinates of cell perimeter, and derived cell length and width. The calculation of the latter two parameters was usually done off-line as data output is in standard numerical form accessible by other programs. Experience with daily use of the PHYCOUNT program and imaging hardware reveal that the system is reliable for cell counting and sizing. The presence of bacteria in the algal cultures does not affect cell counting or sizing.     

A novel approach to controlling dissolved oxygen levels in laboratory experiments

Hypoxia is a widespread environmental stressor that affects marine, estuarine and freshwater systems worldwide. Investigating the effects of hypoxia on aquatic animals in the natural environment is difficult and expensive. Laboratory experiments provide an alternative that allows manipulation of environmental variables and simulation of altered conditions that are expected in the future. However, controlling dissolved oxygen (DO) levels precisely in laboratory test situations is challenging and generally costly and time intensive. In this paper, we describe a novel chamber design that is capable of maintaining low DO levels precisely for a period of at least 4 days with minimal re-adjustment and nitrogen gas requirement. The system is simple, inexpensive and easy to use, and offers the additional benefit of being portable. The utility of this design is demonstrated with an experiment to test the effects of hypoxia and high salinity on hatch rates and yolk-sac larvae survival in the estuarine fish black bream Acanthopagrus butcheri (Munro, 1949). The results show that early life-stage black bream are sensitive to hypoxia and increased salinity, indicating that deterioration in estuarine environmental conditions may have negative effects on spawning success and recruitment to fish populations. This new laboratory technique will be useful for testing future scenarios for the estuaries of southern Australia as predicted by climate change models. Other potential applications and modifications for further development of this new technique are discussed.     

Modifications to husbandry and housing conditions of laboratory rodents for improved well-being

For a change to be considered enriching, the change must enhance animal welfare and improve biological functioning of the animals. A review of the literature shows that a consensus on the definition of changes constituting "environmental enrichment" has yet to be reached. For this reason, the results of studies on the effects of rodent enrichment are inconsistent. In many cases, changes have not been shown to be real improvements. However, enrichment is increasingly appreciated as a way to improve the well-being of rodents, providing them with opportunities for species-specific behaviors that might be available to them in the wild. Frequently defined as "change to the environment," enrichment can be as complex as devices (frequently termed "toys") or as simple as the provision of tissues from which mice readily construct nests. Nest making is a learned behavior in rats, and laboratory rats do show preferences for chewable objects in their environment. Rather than attempting a comprehensive review of the entire literature on environmental enrichment and its effects on rodent physiology and behavior, this paper focuses on husbandry and housing alterations that may improve the welfare of laboratory rodents. The effects of beneficial changes in housing and husbandry on rodent well-being and on experimental variability--and thus cost--are discussed. Areas that require more research are suggested. Also suggested are possible inexpensive and effective enrichment schemes for laboratory mice that might include reducing the cage floor space per mouse combined with providing nesting material.     

Tetrazolium reduction as an indicator of environmental stress in lichens and isolated bionts

A rapid and inexpensive quantitative method was developed for evaluating the physiological condition of intact lichens and cultured symbionts. Formation of the colored product triphenyl formazan (TPF), which is produced after reduction of triphenyltetrazolium chloride (TTC), was used as an indication of dehydrogenase activity. Low pH, exposure to copper, supplemental UV and temperature extremes significantly reduced the capacity of cultured lichens and bionts to produce formazan, suggesting each of these treatments may produce physiological damage. It is projected that this method may also be suitable for monitoring impact of various environmental stresses on field-collected lichens.     

In-lab three-dimensional printing: An inexpensive tool for experimentation and visualization for the field of organogenesis

The development of the microscope in 1590 by Zacharias Janssenby and Hans Lippershey gave the world a new way of visualizing details of morphogenesis and development. More recent improvements in this technology including confocal microscopy, scanning electron microscopy (SEM) and optical projection tomography (OPT) have enhanced the quality of the resultant image. These technologies also allow a representation to be made of a developing tissue's three-dimensional (3-D) form. With all these techniques however, the image is delivered on a flat two-dimensional (2-D) screen. 3-D printing represents an exciting potential to reproduce the image not simply on a flat screen, but in a physical, palpable three-dimensional structure. Here we explore the scope that this holds for exploring and interacting with the structure of a developing organ in an entirely novel way. As well as being useful for visualization, 3-D printers are capable of rapidly and cost-effectively producing custom-made structures for use within the laboratory. We here describe the advantages of producing hardware for a tissue culture system using an inexpensive in-lab printer.     

A "signal-on" electrochemical aptasensor for simultaneous detection of two tumor markers

In this paper, we report a "signal-on" electrochemical aptasensor for simultaneous determination of two tumor markers MUC1 and VEGF(165), by using a ferrocene-labeled aptamer-complementary DNA (cDNA) as probe. Since the cDNA immobilized on an electrode surface can hybridize with both MUC1 aptamer and VEGF(165) aptamer to form a long double strand with ferrocene far away from the electrode surface, the probe cannot give electrochemical signal. Nevertheless, the presence of the two tumor markers will inhibit the hybridization of cDNA with the aptamers, thus the distance between ferrocene and the electrode is changed, and a "signal-on" electrochemical method to detect two tumor markers is developed. Experimental results show that the electrochemical signal increases with the addition of either tumor markers, but the biggest electrochemical signal can only be obtained when both tumor markers are present. Therefore, the proposed electrochemical aptasensor can not only detect the two markers but also distinguish their co-existence. It may also display high selectivity and sensitivity towards the detection of the tumor markers, so it might have potential clinical application in the future.     

Targeted and Highly Multiplexed Detection of Microorganisms by Employing an Ensemble of Molecular Probes

The vast majority of microscopic life on earth consists of microbes that do not grow in laboratory culture. To profile the microbial diversity in environmental and clinical samples, we have devised and employed molecular probe technology, which detects and identifies bacteria that do and do not grow in culture. The only requirement is a short sequence of contiguous bases (currently 60 bases) unique to the genome of the organism of interest. The procedure is relatively fast, inexpensive, customizable, robust, and culture independent and uses commercially available reagents and instruments. In this communication, we report improving the specificity of the molecular probes substantially and increasing the complexity of the molecular probe set by over an order of magnitude (>1,200 probes) and introduce a new final readout method based upon Illumina sequencing. In addition, we employed molecular probes to identify the bacteria from vaginal swabs and demonstrate how a deliberate selection of molecular probes can identify less abundant bacteria even in the presence of much more abundant species.     

Potential use of an arthropod database to support the non-target risk assessment and monitoring of transgenic plants

Worldwide, plants obtained through genetic modification are subject to a risk analysis and regulatory approval before they can enter the market. An area of concern addressed in environmental risk assessments is the potential of genetically modified (GM) plants to adversely affect non-target arthropods and the valued ecosystem services they provide. Environmental risk assessments are conducted case-by-case for each GM plant taking into account the plant species, its trait(s), the receiving environments into which the GM plant is to be released and its intended uses, and the combination of these characteristics. To facilitate the non-target risk assessment of GM plants, information on arthropods found in relevant agro-ecosystems in Europe has been compiled in a publicly available database of bio-ecological information during a project commissioned by the European Food Safety Authority (EFSA). Using different hypothetical GM maize case studies, we demonstrate how the information contained in the database can assist in identifying valued species that may be at risk and in selecting suitable species for laboratory testing, higher-tier studies, as well as post-market environmental monitoring.