A New Methodology for Studying the Activity of Underground Mammals

Biology Bulletin - A new methodology for studying the activity of underground mammals with the use of a digital portable voice recorder has been elaborated. Previously, mole rats were visually...     

Validation of a New Video and Telemetry System for Remotely Monitoring Wildlife

Abstract: Current techniques for remotely monitoring wildlife lack the capability to survey a wide area or to transmit data in real time. We addressed these technology gaps by developing and testing a new video and telemetry system for remotely sampling wildlife abundance, distribution, and behavior across large open areas. The system consisted of 2 pan-tilt-zoom video cameras equipped with 20–200× lens, and an automated telemetry scanner and data logger. All components were charged by wind and solar power and located on a hilltop overlooking an open valley (23 km²) in Yellowstone National Park, USA. A satellite up-link to the internet transmitted data in real time to the University of Minnesota-St. Paul and relayed commands from undergraduate students who controlled the cameras and systematically scanned the area at 2-hour intervals 6 times/day (0800–2000 hr) 7 days/week for about 20 consecutive weeks (Dec-Jun). During each scan, students recorded presence, activity, and location of bison (Bison bison), coyote (Canis latrans), grizzly bear (Ursus arctos), red fox (Vulpes vulpes), and wolf (Canis lupus). The telemetry system continuously scanned frequencies of 100 tagged wolves, including 4 members of the one resident pack. We determined wolf presence in real time by viewing the incoming data stream, or we assessed presence later after off-loading the data logger. Matched pairs of simultaneous observations taken by remote and on-site observers during a 13-day double-sampling period were highly correlated (r = 0.71–0.94), but remote observations were biased toward larger, more visible mammals (e.g., bison) and tended to underestimate their abundance. Nevertheless, the system was deployed longer than was practical for on-site observers and was, therefore, useful for detecting long-term, fine-scale trends such as daily changes in bison numbers as a function of snow depth. (JOURNAL OF WILDLIFE MANAGEMENT 72(8):1834–1844; 2008)     

Transformation of Tobacco, Tomato, Potato, and Arabidopsis thaliana Using a Binary Ti Vector System

Using a binary tumor-inducing (Ti) plasmid vector system, several plant species were transformed with a kanamycin resistance marker (neomycin phosphotransferase gene). Four Nicotiana species, seven tomato cultivars, two potato cultivars, and Arabidopsis thaliana were transformed by the binary vector transformation method. In this method, various plant organ pieces were co-cultivated with Agrobacterium tumefaciens cells carrying the binary vector, pGA472, and a helper Ti plasmid. We have also demonstrated that a wild type Ti plasmid can be used as a helper to obtain a transformed plant.     

New Methodology for Computer-Aided Modelling of Biomolecular Structure and Dynamics 1. Non-Cyclic Structures

Abstract

A general methodology is proposed for the conformational modelling of biomolecular systems. The approach allows one: (i) to describe the system under investigation by an arbitrary set of internal variables, i.e., torsion angles, bond angles, and bond lengths; it offers a possibility to pass from the free structure to a completely fixed one with the number of variables from 3N to zero, respectively, where N is the number of atoms; (ii) to consider both, a single molecule and a complex of many molecules, (e.g., proteins, water, ligands, etc.) in terms of one universal model; (iii) to study the dynamics of the system using explicit analytical Lagrangian equations of motion, thus opening up possibilities for investigations of slow concerted motions such as domain oscillations in proteins etc.; (iv) to calculate the partial derivatives of various functions of conformation, e.g., the conformatinal energy or external constraints imposed, using a standard efficient procedure regardless of the variables and the structure of the system. The approach is meant to be used in various investigations concerning the conformations and dynamics of biomacromolecules.     

Implicit Memory in Monkeys: Development of a Delay Eyeblink Conditioning System with Parallel Electromyographic and High-Speed Video Measurements

Delay eyeblink conditioning, a cerebellum-dependent learning paradigm, has been applied to various mammalian species but not yet to monkeys. We therefore developed an accurate measuring system that we believe is the first system suitable for delay eyeblink conditioning in a monkey species (Macaca mulatta). Monkey eyeblinking was simultaneously monitored by orbicularis oculi electromyographic (OO-EMG) measurements and a high-speed camera-based tracking system built around a 1-kHz CMOS image sensor. A 1-kHz tone was the conditioned stimulus (CS), while an air puff (0.02 MPa) was the unconditioned stimulus. EMG analysis showed that the monkeys exhibited a conditioned response (CR) incidence of more than 60% of trials during the 5-day acquisition phase and an extinguished CR during the 2-day extinction phase. The camera system yielded similar results. Hence, we conclude that both methods are effective in evaluating monkey eyeblink conditioning. This system incorporating two different measuring principles enabled us to elucidate the relationship between the actual presence of eyelid closure and OO-EMG activity. An interesting finding permitted by the new system was that the monkeys frequently exhibited obvious CRs even when they produced visible facial signs of drowsiness or microsleep. Indeed, the probability of observing a CR in a given trial was not influenced by whether the monkeys closed their eyelids just before CS onset, suggesting that this memory could be expressed independently of wakefulness. This work presents a novel system for cognitive assessment in monkeys that will be useful for elucidating the neural mechanisms of implicit learning in nonhuman primates.     

Contextual and Cued Fear Conditioning Test Using a Video Analyzing System in Mice

The contextual and cued fear conditioning test is one of the behavioral tests that assesses the ability of mice to learn and remember an association between environmental cues and aversive experiences. In this test, mice are placed into a conditioning chamber and are given parings of a conditioned stimulus (an auditory cue) and an aversive unconditioned stimulus (an electric footshock). After a delay time, the mice are exposed to the same conditioning chamber and a differently shaped chamber with presentation of the auditory cue. Freezing behavior during the test is measured as an index of fear memory. To analyze the behavior automatically, we have developed a video analyzing system using the ImageFZ application software program, which is available as a free download at http://www.mouse-phenotype.org/. Here, to show the details of our protocol, we demonstrate our procedure for the contextual and cued fear conditioning test in C57BL/6J mice using the ImageFZ system. In addition, we validated our protocol and the video analyzing system performance by comparing freezing time measured by the ImageFZ system or a photobeam-based computer measurement system with that scored by a human observer. As shown in our representative results, the data obtained by ImageFZ were similar to those analyzed by a human observer, indicating that the behavioral analysis using the ImageFZ system is highly reliable. The present movie article provides detailed information regarding the test procedures and will promote understanding of the experimental situation.     

Prospective Environmental Analyses of Emerging Technology: A Critique,a Proposed Methodology,and a Case Study on Incremental Sheet Forming

Prospective environmental assessment of emerging technology is necessary in order to inform designers of beneficial changes early in a technology's development, and policy makers looking to fund projects and nudge manufacturers toward the most sustainable application of a technology. Existing analyses often have shortcomings such as failing to consider the environmental impacts in all stages of a product's life cycle; implicitly assuming that the emerging technology will be cost‐effective wherever it is technically viable; and assuming optimistic application scenarios that discontinue long‐established trends in human behavior. In this article, we propose a new approach, complementary to the prospective and anticipatory life cycle assessment literature, addressing the above concerns and attempting to make sense of the large uncertainties inherent in such analyses by using distributions to model all the inputs. The paper focuses on emerging manufacturing technologies, such as incremental sheet forming (ISF), but the issues examined are also applicable to new end‐use products, such as autonomous vehicles. This paper makes use of approaches (such as Bass modeling and product cannibalization considerations) familiar to those in the business community who anticipate market diffusion of a new technology and the effect on existing technology sales. The proposed methodology is demonstrated by estimating the potential environmental impacts in the U.S. car industry by 2030 of an emerging double‐sided ISF process. Energy and cost models of ISF and drawing are used to estimate potential mean savings of around 100 TJ_primary and 60 million U.S. dollars per year by 2030.     

New Methodology for Computer-Aided Modelling of Biomolecular Structure and Dynamics 2. Local Deformations and Cycles

Abstract

A new methodology for the conformational modelling of biomolecular systems (1) is extended to local deformations of chain molecules and to flexible molecular rings. It is shown that these two cases may be reduced to considering an equivalent molecular model with a regular tree-like topology. A simple procedure is developed to analyze any flexible rings (the five- and six-membered suguar rings of carbohydrates and nucleic acids, in particular) and local deformation regions by energy minimization. Dynamic equations are also derived for such molecular systems. As a result, a unified approach is proposed for the efficient energy minimization and simulation of dynamic behavior of multimolecular systems having any set of variable internal coordinates, local deformation regions and cycles. Advantages and domains of applicability of the approach are discussed.     

A New Isolation Method for Labyrinthulids Using a Bacterium, Psychrobacter phenylpyruvicus

A new isolation method for labyrinthulids, marine microbes with spindle-shaped vegetative cells and gliding movement, is presented. The method for isolating labyrinthulids has been found to be more difficult and less reproducible than that for thraustochytrids, classified in the same order. So far serum seawater agar fortified with antibiotics has been proposed to be the best for isolation of labyrinthulids. The method presented here involves placing plant samples on an agar medium on which a marine bacterium, Psychrobacter phenylpyruvicus, has been grown. The new method, which utilizes fallen mangrove leaves as source material, was more than twice as effective as isolation agar medium without the bacterium. The increased effectiveness appears to derive partly from the bacterial colonies' delaying extension of fungal mycelium. The bacterium was more effective for the isolation of labyrinthulids than either the bacterium Shewanella sp. or the yeast Rhodotorula rubra.     

PVv3, a New Shuttle Vector for Gene Expression in Vibrio vulnificus

An efficient electroporation procedure for Vibrio vulnificus was designed using the new cloning vector pVv3 (3,107 bp). Transformation efficiencies up to 2 × 10⁶ transformants per μg DNA were achieved. The vector stably replicated in both V. vulnificus and Escherichia coli and was also successfully introduced into Vibrio parahaemolyticus and Vibrio cholerae. To demonstrate the suitability of the vector for molecular cloning, the green fluorescent protein (GFP) gene and the vvhBA hemolysin operon were inserted into the vector and functionally expressed in Vibrio and E. coli.     

A New Color Image Encryption Scheme Using CML and a Fractional-Order Chaotic System

The chaos-based image cryptosystems have been widely investigated in recent years to provide real-time encryption and transmission. In this paper, a novel color image encryption algorithm by using coupled-map lattices (CML) and a fractional-order chaotic system is proposed to enhance the security and robustness of the encryption algorithms with a permutation-diffusion structure. To make the encryption procedure more confusing and complex, an image division-shuffling process is put forward, where the plain-image is first divided into four sub-images, and then the position of the pixels in the whole image is shuffled. In order to generate initial conditions and parameters of two chaotic systems, a 280-bit long external secret key is employed. The key space analysis, various statistical analysis, information entropy analysis, differential analysis and key sensitivity analysis are introduced to test the security of the new image encryption algorithm. The cryptosystem speed is analyzed and tested as well. Experimental results confirm that, in comparison to other image encryption schemes, the new algorithm has higher security and is fast for practical image encryption. Moreover, an extensive tolerance analysis of some common image processing operations such as noise adding, cropping, JPEG compression, rotation, brightening and darkening, has been performed on the proposed image encryption technique. Corresponding results reveal that the proposed image encryption method has good robustness against some image processing operations and geometric attacks.     

A New Vector for Identification of Prokaryotes and Their Variable-Size Genomes

A large number of prokaryotes have been produced, so how to provide a means to describe and distinguish them accurately is becoming a key issue of prokaryotic taxonomy. We proposed an efficient algorithm to filter out most genome fragments that are horizontally transferred, and extracted a new genome vector (GV). To highlight the power of GV, we applied it to identify prokaryotes and their variable-size genome fragments. The result indicated that the new vector as species tags can accurately identify genome fragments as short as 3,000 bp at species level.     

A New Procedure for Quantitative Measurements of Virus Particles in Crude Preparations

A new method is described for the quantitative measurement of virus concentration in crude preparations by density gradient centrifugation and electron microscopy. The centrifugation is carried out in a specially designed centrifuge tube which permits separation and sedimentation of virus particles at different levels according to their sedimentation velocity. The gradient of a mixture of heavy and normal water (D(2)O-H(2)O) is designed to sediment the virus particles with constant velocity so that the optimal time of centrifugation can easily be calculated. The virus particles are collected on carbon-coated nickel grids floating on mercury at the bottom of the centrifuge tube and are counted by means of electron microscopy. The efficiency of the method is demonstrated with a crude plant extract of tobacco mosaic virus.     

A Model for Representing the Dynamics of a System of Synfire Chains

Competitive synchronization among synfire chains may model the dynamics of binding and compositionality. Typically, such models require simulations of hundreds of thousands of neurons. Here we show that the behavior of such large systems can be numerically analyzed by representing the neuronal activity in a synfire chain as a wave. The position and velocity of waves are the only parameters needed to represent the neural activity within a synfire chain. With this wave model we describe how waves are generated, decay, interact within a single chain and among chains. The behavior of the wave model is compared to the behavior of detailed simulations of synfire chains with no qualitative difference. We show that interacting waves tend to become locked to each other (wave synchronization). Finally we prove that: (1) Within a system of many synfire chains with symmetric interchain connections, as long as waves do not fade away or become fully synchronized, the total synchrony among waves can only increase (or stay constant), but never decrease. (2) A wave that increases its speed during the synchronization process becomes more stable.     

Self-Associated Submicron IgG1 Particles for Pulmonary Delivery: Effects of Non-ionic Surfactants on Size, Shape, Stability, and Aerosol Performance

The ability to produce submicron particles of monoclonal antibodies of different sizes and shapes would enhance their application to pulmonary delivery. Although non-ionic surfactants are widely used as stabilizers in protein formulations, we hypothesized that non-ionic surfactants will affect the shape and size of submicron IgG particles manufactured through precipitation. Submicron particles of IgG1 were produced by a precipitation process which explores the fact that proteins have minimum solubility but maximum precipitation at the isoelectric point. Non-ionic surfactants were used for size and shape control, and as stabilizing agents. Aerosol performance of the antibody nanoparticles was assessed using Andersen Cascade Impactor. Spinhaler® and Handihaler® were used as model DPI devices. SEM micrographs revealed that the shape of the submicron particles was altered by varying the type of surfactant added to the precipitating medium. Particle size as measured by dynamic light scattering was also varied based on the type and concentration of the surfactant. The surfactants were able to stabilize the IgG during the precipitation process. Polyhedral, sponge-like, and spherical nanoparticles demonstrated improved aerosolization properties compared to irregularly shaped (>20 μm) unprocessed particles. Stable antibody submicron particles of different shapes and sizes were prepared. Careful control of the shape of such particles is critical to ensuring optimized lung delivery by dry powder inhalation.     

A New Method of Defense Response Analysis Using a Transient Expression System in Rice Protoplasts

We established a new plant defense response assay using a transient expression system in rice protoplasts. The assay system sensitively detected defense induction by flagellin, which had previously been assigned to a specific elicitor. Our assay system provides a rapid and efficient way to dissect rice defense mechanisms.     

A Helper-Independent Adenovirus Vector with E1, E3, and Fiber Deleted: Structure and Infectivity of Fiberless Particles

The adenovirus (Ad) fiber protein largely determines viral tropism through interaction with specific cell surface receptors. This molecule may also be involved in virion assembly or maturation, as some previously characterized fiber mutants were defective for processing of viral structural proteins. We previously described packaging cell lines that express Ad type 5 (Ad5) fiber and can complement the temperature-sensitive Ad fiber mutant H5ts142. We have now used these packaging cells to construct a new adenoviral vector (Ad5.βgal.ΔF) with E1, E3, and L5 (fiber) deleted and analyzed the fiber null phenotype. Ad5.βgal.ΔF growth was completely helper independent, and fiberless particles were produced by a single final round of growth in 293 cells. Cryoelectron microscopic studies and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis showed that the structure and composition of these particles was nearly identical to those of first-generation Ad vectors. As expected, fiberless particles had reduced infectivity on epithelial cells, but they retained the ability to infect monocytic cells via an integrin-dependent pathway. These studies provide a novel approach to developing retargeted Ad gene therapy vectors.