Smartphones in ecology and evolution: a guide for the app‐rehensive

Smartphones and their apps (application software) are now used by millions of people worldwide and represent a powerful combination of sensors, information transfer, and computing power that deserves better exploitation by ecological and evolutionary researchers. We outline the development process for research apps, provide contrasting case studies for two new research apps, and scan the research horizon to suggest how apps can contribute to the rapid collection, interpretation, and dissemination of data in ecology and evolutionary biology. We emphasize that the usefulness of an app relies heavily on the development process, recommend that app developers are engaged with the process at the earliest possible stage, and commend efforts to create open‐source software scaffolds on which customized apps can be built by nonexperts. We conclude that smartphones and their apps could replace many traditional handheld sensors, calculators, and data storage devices in ecological and evolutionary research. We identify their potential use in the high‐throughput collection, analysis, and storage of complex ecological information.     

Sensor heavy metal from natural resources for a green environment: A review relation between synthesis method and luminescence properties of carbon dots

Carbon dots (CDs) are 10-nm nanomaterial classes as excellent candidates in various applications: physics, biology, chemistry, and food science due to high stable biocompatibility and high surface expansive. CDs produced from natural materials have received wide attention due to their unique benefits, easy availabilities, sufficient costs, and harmless to the ecosystem. The various properties of CDs can be obtained from various synthesis methods: hydrothermal, microwave-assisted, and pyrolysis. The CDs have shown enormous potential in metal particle detection, colorimetric sensors, electrochemical sensors, and pesticide sensors. This review provides systematic information on a synthesis method based on natural resources and the application to the environmental sensors for supporting the clean environment. We hope this review will be useful as a reference source in providing the guidance or roadmap for new researchers to develop new strategies in increasing luminescence properties CDs for multi detection of heavy metals in the environment.     

Development and validation of a timed urinary collection system for use in the cat

The aim of the study was to develop and validate a feline urinary collection system for accurate 24 h urine output measurement and glomerular filtration rate (GFR) evaluation. We hypothesized that precise identification of urination time improves the accuracy of the collection system. In a group of nine cats, urinary volume and micturition times were repeatedly recorded for up to 48 h using purpose-built collection trays containing a temperature data logger. Collection time was determined both with and without using the data loggers on 22 occasions and agreement between estimated 24 h urine outputs obtained with the two calculation methods was evaluated. GFR was repeatedly measured by endogenous urinary creatinine clearance on three occasions. Twenty-four-hour urine output was measured in 98.5% of the attempted collections (300 cat-sampling days). Sensitivity and specificity of the detection system were 97.8% and 100%, respectively. Mean 24 h urine output was 12.4 ± 4.94 mL/kg/day and mean intra-cat between-days coefficient of variation (CV) was 16.6 ± 5.6% when data loggers were used. The absolute relative volume error between the two calculation methods ranged from 0% to 131%. Median absolute relative [interquartile range] error was 9.1% [3.25-19.8]. Bias was -1.3% and lower and upper limits of agreement were -39.7% and 35.2%, respectively. Mean estimated GFR was lower than previously reported with comparable urinary clearance methods (1.92 ± 0.37 mL/min/kg) and mean within-cat CV was 12 ± 6.9%. The system was simple in design, readily affordable, allowed normal micturition behaviour and reduced intra-animal variability in 24 h feline urine collection.     

Initiating dialogue between scientists and managers of biological invasions

We describe an initiative to improve the flow of information between researchers and managers as part of two international scientific symposia on biological invasions held in South Africa in 2008 and 2009. Formal workshops and information sessions for land managers were run during the symposia. At the end of each symposium, the managers ran dedicated question-and-answer sessions on the research they felt was needed to improve their work. We discuss the potential of such interventions to increase interaction and awareness between researchers and managers of biological invasions. The symposia certainly provided the managers with opportunities to think about broader issues and develop contacts, but problems with terminology use and the lack of solutions specific to their context tempered the value of their experience. Conversely, researchers at times under-estimated the managers perceived relevance of their presentations to management. The structured and facilitated attendance of managers of invasive plants at international conferences on invasion biology is one mechanism for at least narrowing “the gap” between science and management.     

Kilogrid: a novel experimental environment for the Kilobot robot

We present the Kilogrid, an open-source virtualization environment and data logging manager for the Kilobot robot, Kilobot for short. The Kilogrid has been designed to extend the sensory-motor abilities of the Kilobot, to simplify the task of collecting data during experiments, and to provide researchers with a tool to fine-control the experimental setup and its parameters. Based on the design of the Kilobot and compatible with existing hardware, the Kilogrid is a modular system composed of a grid of computing nodes, or modules that provides a bidirectional communication channel between the Kilobots and a remote workstation. In this paper, we describe the hardware and software architecture of the Kilogrid system as well as its functioning to accompany its release as a new open hardware tool for the swarm robotics community. We demonstrate the capabilities of the Kilogrid using a 200-module Kilogrid, swarms of up to 100 Kilobots, and four different case studies: exploration and obstacle avoidance, site selection based on multiple gradients, plant watering, and pheromone-based foraging. Through this set of case studies, we show how the Kilogrid allows the experimenter to virtualize sensors and actuators not available to the Kilobot and to automatize the collection of data essential for the analysis of the experiments.     

Insect eggs at a transition between diffusion and reaction limitation: temperature, oxygen, and water. art.woods@mso.umt.edu

In diverse animal taxa, eggs and embryos are incapable of transporting oxygen by convection. In such cases, internal oxygen distributions are determined jointly by rates of oxygen consumption and diffusive transport. Here we develop a mathematical model of oxygen consumption and transport in insect eggs, with the goal of understanding-for eggs in variable-temperature environments-the interactive effects of the two processes on development. We fit the model to previously published data on development time of eggs of a sphingid moth, Manduca sexta. The fitted coefficients suggest that eggs develop at a transition point between reaction- and diffusion-limitation. We test then this conclusion with independent data on development times of eggs distributed across a set of temperatures generated by a thermal gradient bar. Finally, we develop an extension of the model that considers tradeoffs between oxygen transfer to eggs versus water loss from them. The model results provide both a rationale for why development is often mass-transfer limited and a set of new predictions about oxygen-water tradeoffs.     

Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria

Marine bacterial diversity is immense and believed to be driven in part by trade-offs in metabolic strategies. Here we consider heterotrophs that rely on organic carbon as an energy source and present a molecular-level model of cell metabolism that explains the dichotomy between copiotrophs—which dominate in carbon-rich environments—and oligotrophs—which dominate in carbon-poor environments—as the consequence of trade-offs between nutrient transport systems. While prototypical copiotrophs, like Vibrios, possess numerous phosphotransferase systems (PTS), prototypical oligotrophs, such as SAR11, lack PTS and rely on ATP-binding cassette (ABC) transporters, which use binding proteins. We develop models of both transport systems and use them in proteome allocation problems to predict the optimal nutrient uptake and metabolic strategy as a function of carbon availability. We derive a Michaelis–Menten approximation of ABC transport, analytically demonstrating how the half-saturation concentration is a function of binding protein abundance. We predict that oligotrophs can attain nanomolar half-saturation concentrations using binding proteins with only micromolar dissociation constants and while closely matching transport and metabolic capacities. However, our model predicts that this requires large periplasms and that the slow diffusion of the binding proteins limits uptake. Thus, binding proteins are critical for oligotrophic survival yet severely constrain growth rates. We propose that this trade-off fundamentally shaped the divergent evolution of oligotrophs and copiotrophs.     

Experimental and theoretical evidence for convective nutrient transport in an immobilized cell support.

Even though immobilized-cell reactors possess several engineering advantages over free-cell reactors, their full potential has not been realized because mass transfer often limits the rate of nutrient supply and product removal from immobilized cell supports. We studied the interaction between mass transfer and reaction kinetics in the anaerobic conversion of glucose to CO2 and ethanol by yeast immobilized in a porous rotating disk on the agitator shaft of a conventional CSTR. A Sherwood number correlation was used to show that external mass-transfer resistances were negligible under typical operating conditions. The modulus of Weisz based on observable reaction parameters was used to gauge the importance of pore diffusion limitations. Under conditions for which significant pore diffusion effects and hence low effectiveness factors (eta = ca. 0.1) would be predicted, the observed reaction rates were much higher than expected (eta = ca. 1), suggesting that pore diffusion limitations were at least partially relieved by convective transport of glucose into the support. Two possible mechanisms of convective transport are discussed. We hypothesize that gas evolution was responsible for the convective enhancement of glucose supply.     

Odorant binding protein based biomimetic sensors for detection of alcohols associated with Salmonella contamination in packaged beef

Detection of food-borne bacteria present in the food products is critical to prevent the spread of infectious diseases. Intelligent quality sensors are being developed for detecting bacterial pathogens such as Salmonella in beef. One of our research thrusts was to develop novel sensing materials sensitive to specific indicator alcohols at low concentrations. Present work focuses on developing olfactory sensors mimicking insect odorant binding protein to detect alcohols in low concentrations at room temperature. A quartz crystal microbalance (QCM) based sensor in conjunction with synthetic peptide was developed to detect volatile organic compounds indicative to Salmonella contamination in packaged beef. The peptide sequence used as sensing materials was derived from the amino acids sequence of Drosophila odorant binding protein, LUSH. The sensors were used to detect alcohols: 3-methyl-1-butanol and 1-hexanol. The sensors were sensitive to alcohols with estimated lower detection limits of <5 ppm. Thus, the LUSH-derived QCM sensors exhibited potential to detect alcohols at low ppm concentrations.     

Bacterial chemotaxis to saccharides is governed by a trade-off between sensing and uptake

To swim up gradients of nutrients, E. coli senses nutrient concentrations within its periplasm. For small nutrient molecules, periplasmic concentrations typically match extracellular concentrations. However, this is not necessarily the case for saccharides, such as maltose, which are transported into the periplasm via a specific porin. Previous observations have shown that, under various conditions, E. coli limits maltoporin abundance so that, for extracellular micromolar concentrations of maltose, there are predicted to be only nanomolar concentrations of free maltose in the periplasm. Thus, in the micromolar regime, the total uptake of maltose from the external environment into the cytoplasm is limited not by the abundance of cytoplasmic transport proteins but by the abundance of maltoporins. Here, we present results from experiments and modeling suggesting that this porin-limited transport enables E. coli to sense micromolar gradients of maltose despite having a high-affinity ABC transport system that is saturated at these micromolar levels. We used microfluidic assays to study chemotaxis of E. coli in various gradients of maltose and methyl-aspartate and leveraged our experimental observations to develop a mechanistic transport-and-sensing chemotaxis model. Incorporating this model into agent-based simulations, we discover a trade-off between uptake and sensing: although high-affinity transport enables higher uptake rates at low nutrient concentrations, it severely limits the range of dynamic sensing. We thus propose that E. coli may limit periplasmic uptake to increase its chemotactic sensitivity, enabling it to use maltose as an environmental cue.     

Charge transport in DNA

The base pair stack within double helical DNA provides an effective medium for charge transport. The DNA pi-stack mediates oxidative DNA damage over long molecular distances in a reaction that is exquisitely sensitive to the sequence-dependent conformation and dynamics of DNA. A mixture of tunneling and hopping mechanisms have been proposed to account for this long-range chemistry, which is gated by dynamical variations within the stack. Electrochemical sensors have also been developed, based upon the sensitivity of DNA charge transport to base pair stacking, and these sensors provide a completely new approach to diagnosing single base mismatches in DNA and monitoring protein-DNA interactions electrically. DNA charge transport, furthermore, may play a role within the cell and, indeed, oxidative damage to DNA from a distance has been demonstrated in the cell nucleus. As a result, the biological consequences of and opportunities for DNA-mediated charge transport now require consideration.     

Efficient scheduling of team truck drivers in the European Union

This paper studies the problem of scheduling working hours of team drivers in European road freight transport where a sequence of ?? locations must be visited within given time windows. Since April 2007 working hours of truck drivers in the European Union must comply with regulation (EC) No 561/2006. These regulations impose standard limits on the daily driving times of truck drivers and extended daily limits that may only be used twice a week for each driver. We present a depth-first-breadth-second search method which can find a feasible schedule complying with standard daily driving time limits in O(??²) time, if such a schedule exists. Furthermore, we show that this method can also be used to find schedules complying with regulation (EC) No 561/2006 if daily driving times may exceed the standard limit.     

Evaluation of blood collection tubes using selected reaction monitoring MS: Implications for proteomic biomarker studies

An emphasis of current proteomic research is the validation of plasma protein biomarkers. The process of blood collection itself is critical to the accuracy and reproducibility of quantitative biomarker assays. We have developed selected reaction monitoring (SRM) assays to analyse thirteen abundant plasma proteins and evaluated the impact of three different blood collection tubes on the levels of these proteins. We also assessed the implications of the time taken to analyse plasma samples by evaluating the recovery of these proteins. We showed that SRM detects minor differences in the levels of some proteins which can be attributed to collection tube type. The average recovery for 12 of 18 assays was higher for proteins that were collected in tubes containing protease inhibitors compared to conventional collection tubes. For five of the assays, the differential recovery was statistically significant. Delaying MS analysis of a freeze‐thawed sample for 1 hour showed greatly reduced recovery of these analytes; however differences attributed to tube type were only evident at the baseline timepoint. Finally, we assessed the natural variation of circulating levels of these proteins in a cohort of seven healthy individuals. This study provides useful information for researchers contemplating blood collection for undertaking protein biomarker studies.     

Genetically encoded fluorescent sensors for intracellular NADH detection

We have developed genetically encoded fluorescent sensors for reduced nicotinamide adenine dinucleotide (NADH), which manifest a large change in fluorescence upon NADH binding. We demonstrate the utility of these sensors in mammalian cells by monitoring the dynamic changes in NADH levels in subcellular organelles as affected by NADH transport, glucose metabolism, electron transport chain function, and redox environment, and we demonstrate the temporal separation of changes in mitochondrial and cytosolic NADH levels with perturbation. These results support the view that cytosolic NADH is sensitive to environmental changes, while mitochondria have a strong tendency to maintain physiological NADH homeostasis. These sensors provide a very good alternative to existing techniques that measure endogenous fluorescence of intracellular NAD(P)H and, owing to their superior sensitivity and specificity, allow for the selective monitoring of total cellular and compartmental responses of this essential cofactor.     

Retrograde Axonal Transport of Phospholipid in Rat Sciatic Nerve

Abstract: Retrograde axonal transport of phospholipid was studied in rat sciatic motoneuron axons by placing collection crushes on the nerve at intervals after injection of [methyl-³H]choline into the lumbosacral spinal cord, and allowing labelled material undergoing anterograde or retrograde movement to accumulate adjacent to the collection crushes. Control experiments showed that the accumulations of label were not a result of local uptake of circulating precursor. The majority of the ³H label was associated with phosphatidylcholine. Accumulation of label at the distal collection crush, representing retrograde transport, was observed subsequent to the anterograde transport of phospholipid. In comparison with previous study on retrograde transport of protein, the following points were noted: (1) onset of retrograde transport occurred at approximately the same time after precursor injection (10–20 h) for both protein and phospholipid; (2) retrograde transport of lipids was more prolonged: maximum retrograde transport occurred later for phospholipid (30 h) than for protein (15–20 h), and declined to half-maximum between 49 and 99 h, compared to a corresponding value of 24–28 h for protein; (3) the proportion of total anterograde-transported activity subsequently undergoing retrograde transport was less in the case of phospholipid, at least over the time interval studied (up to 99 h after precursor injection). The similar times of onset of retrograde transport of phospholipid and protein support the concept of retrograde transport as a recycling mechanism returning to the cell body membrane fragments that were earlier transported into the axon. Coordinated retrograde transport of labelled protein and phospholipid components of the recycled membranes would be predicted. Differences between protein and phospholipid in the subsequent time course and amount of retrograde transport may reflect differences in axonal handling of protein and lipid. Both the more prolonged outflow of labelled lipids from cell body into axon and exchange with a distal pool of unlabelled phospholipid may account for the prolonged time course of retrograde transport of labelled lipid.     

Oxygen supply limits the heat tolerance of lizard embryos

The mechanisms that set the thermal limits to life remain uncertain. Classically, researchers thought that heating kills by disrupting the structures of proteins or membranes, but an alternative hypothesis focuses on the demand for oxygen relative to its supply. We evaluated this alternative hypothesis by comparing the lethal temperature for lizard embryos developing at oxygen concentrations of 10–30%. Embryos exposed to normoxia and hyperoxia survived to higher temperatures than those exposed to hypoxia, suggesting that oxygen limitation sets the thermal maximum. As all animals pass through an embryonic stage where respiratory and cardiovascular systems must develop, oxygen limitation may limit the thermal niches of terrestrial animals as well as aquatic ones.     

Development of a low-pressure diamond anvil cell and analytical tools to monitor microbial activities in situ under controlled P and T

We have designed a new low-pressure Diamond Anvil Cell (DAC), calibrated two novel pressure calibrants and validated the use of semi-quantitative Raman and X-ray spectroscopies to monitor the fate of microbes, their metabolism or their cellular components under controlled pressures and temperatures in the 0.1-1.4 GPa and 20-300 degrees C P,T range. The low-pressure DAC has a 250- to 600-microm-thick observation diamond window to allow for lower detection limits and improved microscopic imaging. This new design allows the determination of cellular growth parameters from automated image analysis, which can be correlated with the spectroscopic data obtained on metabolism, ensuring high quality data collection on microbial activity under pressure. The novel pressure sensors offer the ease of use of the well-known ruby scale, while being more sensitive and reacting to pressure variations instantaneously.     

Design and development of genetically encoded fluorescent sensors to monitor intracellular chemical and physical parameters

Over the past decades many researchers have made major contributions towards the development of genetically encoded (GE) fluorescent sensors derived from fluorescent proteins. GE sensors are now used to study biological phenomena by facilitating the measurement of biochemical behaviors at various scales, ranging from single molecules to single cells or even whole animals. Here, we review the historical development of GE fluorescent sensors and report on their current status. We specifically focus on the development strategies of the GE sensors used for measuring pH, ion concentrations (e.g., chloride and calcium), redox indicators, membrane potential, temperature, pressure, and molecular crowding. We demonstrate that these fluroescent protein-based sensors have a shared history of concepts and development strategies, and we highlight the most original concepts used to date. We believe that the understanding and application of these various concepts will pave the road for the development of future GE sensors and lead to new breakthroughs in bioimaging.     

Catalytic cracking of palm oil for the production of biofuels: optimization studies

Oil palm is widely grown in Malaysia. Palm oil has attracted the attention of researchers to develop an 'environmentally friendly' and high quality fuel, free of nitrogen and sulfur. In the present study, the catalytic cracking of palm oil to biofuel was studied over REY catalyst in a transport riser reactor at atmospheric pressure. The effect of reaction temperature (400-500 degrees C), catalyst/palm oil ratio (5-10) and residence time (10-30s) was studied over the yield of bio-gasoline and gas as fuel. Design of experiments was used to study the effect of operating variables over conversion of palm oil and yield of hydrocarbon fuel. The response surface methodology was used to determine the optimum value of the operating variables for maximum yield of bio-gasoline fraction in the liquid product obtained.