Comparative surface accessibility of a pore-lining threonine residue (T6') in the glycine and GABA(A) receptors

The substituted cysteine accessibility method was used to probe the surface exposure of a pore-lining threonine residue (T6’) common to both the glycine receptor (GlyR) and GABAA receptor (GABAAR) chloride channels. This residue lies close to the channel activation gate, the ionic selectivity filter and the main pore blocker binding site. Recent studies have suggested that the GlyRs and GABAARs have divergent open state pore structures at the 6’ position. When both the human a1T6’C homomeric GlyR and the rat a1T6’Cb1T6’C heteromeric GABAAR were expressed in HEK293 cells, their 6’ residue surface accessibilities differed significantly in the closed state. However, when a soluble cysteine-modifying compound was applied in the presence of saturating agonist concentrations, both receptors were locked into the open state. This action was not induced by oxidising agents in either receptor. These results provide evidence for a conserved pore opening mechanism in anion-selective members of the ligand-gated ion channel family. The results also indicate that the GABAAR pore structure at the 6’ level may vary between different expression systems.

Synthesis of optically complex core-shell colloidal suspensions: Pathways to multiplexed biological screening

The ability to generate enormous random libraries of DNA probes via split-and-mix synthesis on solid supports is an important biotechnological application of colloids that has not been fully utilized to date. To discriminate between colloid-based DNA probes each colloidal particle must be 'encoded' so it is distinguishable from all other particles. To this end, we have used novel particle synthesis strategies to produce large numbers of optically encoded particle suitable for DNA library synthesis. Multifluorescent particles with unique and reproducible optical signatures (i.e., fluorescence and light-scattering attributes) suitable for high-throughput flow cytometry have been produced. In the spectroscopic study presented here, we investigated the optical characteristics of multi-fluorescent particles that were synthesized by coating silica 'core' particles with up to six different fluorescent dye shells alternated with non-fluorescent silica 'spacer' shells. It was observed that the diameter of the particles increased by up to 20% as a result of the addition of twelve concentric shells and that there was a significant reduction in fluorescence emission intensities from inner shells as an increasing number of shells were deposited.

Orientation of biological cells using plane-polarized gaussian beam optical tweezers

Optical tweezers are widely used for the manipulation of cells and their internal structures. However, the degree of manipulation possible is limited by poor control over the orientation of the trapped cells. We show that it is possible to controllably align or rotate disc-shaped cells-chloroplasts of Spinacia oleracea-in a plane-polarized Gaussian beam trap, using optical torques resulting predominantly from circular polarization induced in the transmitted beam by the non-spherical shape of the cells.

Biological polarized light reflectors in stomatopod crustaceans

Body parts that can reflect highly polarized light have been found in several species of stomatopod crustaceans (mantis shrimps). These polarized light reflectors can be grossly divided into two major types. The first type, usually red or pink in color to the human visual system, is located within an animal’s cuticle. Reflectors of the second type, showing iridescent blue, are located beneath the exoskeleton and thus are unaffected by the molt cycle. We used reflection spectropolarimetry and transmission electron microscopy (TEM) to study the reflective properties and the structures that reflect highly polarized light in stomatopods. For the first type of reflector, the degree of polarization usually changes dramatically, from less than 20% to over 70%, with a change in viewing angle. TEM examination indicates that the polarization reflection is generated by multilayer thin-film interference. The second type of reflector, the blue colored ones, reflects highly polarized light to all viewing angles. However, these reflectors show a slight chromatic change with different viewing angles. TEM sections have revealed that streams of oval-shaped vesicles might be responsible for the production of the polarized light reflection. In all the reflectors we have examined so far, the reflected light is always maximally polarized at around 500 nm, which is close to the wavelength best transmitted by sea water. This suggests that the polarized light reflectors found in stomatopods are well adapted to the underwater environment. We also found that most reflectors produce polarized light with a horizontal e-vector. How these polarized light reflectors are used in stomatopod signaling remains unknown.

A first-principles density-functional calculation of the electronic and vibrational structure of the key melanin monomers

We report first-principles density-functional calculations for hydroquinone (HQ), indolequinone (IQ), and semiquinone (SQ). These molecules are believed to be the basic building blocks of the eumelanins, a class of biomacromolecules with important biological functions (including photoprotection) and with the potential for certain bioengineering applications. We have used the difference of self-consistent fields method to study the energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital, HL. We show that HL is similar in IQ and SQ, but approximately twice as large in HQ. This may have important implications for our understanding of the observed broadband optical absorption of the eumelanins. The possibility of using this difference in HL to molecularly engineer the electronic properties of eumelanins is discussed. We calculate the infrared and Raman spectra of the three redox forms from first principles. Each of the molecules have significantly different infrared and Raman signatures, and so these spectra could be used in situ to nondestructively identify the monomeric content of macromolecules. It is hoped that this may be a helpful analytical tool in determining the structure of eumelanin macromolecules and hence in helping to determine the structure-property-function relationships that control the behavior of the eumelanins.

Fundamental Skills in Physics: Embedded Learning

Student attitudes towards a subject affect their learning. For students in physics service courses, relevance is emphasised by vocational applications. A similar strategy is being used for students who aspire to continued study of physics, in an introduction to fundamental skills in experimental physics – the concepts, computational tools and practical skills involved in appropriately obtaining and interpreting measurement data. An educational module is being developed that aims to enhance the student experience by embedding learning of these skills in the practicing physicist’s activity of doing an experiment (gravity estimation using a rolling pendulum). The group concentrates on particular skills prompted by challenges such as: • How can we get an answer to our question? • How good is our answer? • How can it be improved? This explicitly provides students the opportunity to consider and construct their own ideas. It gives them time to discuss, digest and practise without undue stress, thereby assisting them to internalise core skills. Design of the learning activity is approached in an iterative manner, via theoretical and practical considerations, with input from a range of teaching staff, and subject to trials of prototypes.

Detailed Measurements during a Transient Front in a Small Subtropical Estuary

High-resolution measurements of velocity and physio-chemistry were conducted before, during and after the passage of a transient front in a small subtropical system about 2.1 km upstream of the river mouth. Detailed acoustic Doppler velocimetry measurements, conducted continuously at 25 Hz, showed the existence of transverse turbulent shear between 300 s prior to the front passage and 1300 s after. This was associated with an increased level of suspended sediment concentration fluctuations, some transverse shear next to the bed and some surface temperature anomaly.

Morphological and biological notes on Polymorphus (Profilicollis) sphaerocephalus and Corynosoma stanleyi (Polymorphidae : Acanthocephala)

Polymorphus (Profilicollis) sphaerocephalus (Bremser in Rudolphi, 1819) Van Cleave, 1947 (Polymorphidae) cystacanths were recovered from 5 species of grapsid crabs (Paragrapsus gaimardii (Milne Edwards, 1837), Paragrapsus laevis (Dana, 1852), Paragrapsus quadridentatus (Milne Edwards, 1837), Brachynotus spinosus (Milne Edwards, 1853), and Cyclograpsus granulosus (Milne Edwards, 1853)) and 1 species of portunid crab (Nectocarcinus integrifrons (Linnaeus, 1766)) from intertidal zones in southern temperate waters of Australia. Cystacanths of Corynosoma stanleyi Smales, 1986 (Polymorphidae) were also recovered from P. gaimardii, P. quadridentatus, and C. granulosus. Polymorphus (P.) sphaerocephalus was the most prevalent (100%) in C. granulosus at Flinders I. and C. stanleyi was most prevalent (59.1%) in C. granulosus at Dunally Channel, Tasmania.

Determination of chemical shielding tensor of an indole carbon and application of tryptophan orientation of a membrane peptide

Using tryptophan C-13-enriched at the C-4 (C epsilon(3)) of the indole, the orientation of the C epsilon(3) chemical shift tensor relative to the C epsilon(3)-H dipolar axis was determined from the C-13 chemical shift/C-13-H-1 dipolar 2D NMR powder pattern. The principal values obtained were 208, 137 and 15 ppm with sigma(33) perpendicular to the indole plane, and sigma(11) (least shielded direction) 5 degrees off the C epsilon(3)-H bond toward C xi(3). The side off the C epsilon(3)-H bond was determined by comparing the reduced chemical shift anisotropies obtained by solid-state NMR and from molecular dynamics calculations of [4-C-13] tryptophans in gramicidin A aligned in phospholipid membranes. (C) 1999 Elsevier Science B.V. All rights reserved.

Optimizing electrode sites for segmental bioimpedance measurements

Recent advances in the application of bioelectrical impedance analysis (BIA) have indicated that a more accurate approach to the estimation of total body water is to consider the impedance of the various body segments rather than simply that of the whole body. The segmental approach necessitates defining and locating the physical demarcation between both the trunk and leg and the trunk and arm. Despite the use of anatomical markers, these points of demarcation are difficult to locate with precision between subjects. There are also technical problems associated with the regional dispersion of the current distribution from one segment (cylinder) to another of different cross-sectional area. The concept of equipotentials in line with the proximal aspects of the upper land lower) limbs along the contralateral limbs was investigated and, in particular, the utility of this concept in the measurement of segmental bioimpedance. The variation of measured segmental impedance using electrode sites along these equipotentials was less than 2.0% for all of the commonly used impedance parameters. This variation is approximately equal to that expected from biological variation over the measurement time. It is recommended that the electrode sites, for the measurement of segmental bioelectrical impedance in humans, described herein are adopted in accordance with the proposals of the NM Technology Assessment Conference Statement.

Knowledge discovery and data mining in biological databases

The new technologies for Knowledge Discovery from Databases (KDD) and data mining promise to bring new insights into a voluminous growing amount of biological data. KDD technology is complementary to laboratory experimentation and helps speed up biological research. This article contains an introduction to KDD, a review of data mining tools, and their biological applications. We discuss the domain concepts related to biological data and databases, as well as current KDD and data mining developments in biology.

The role of disulfide-linked dimerization in interleukin-3 receptor signaling and biological activity

Cysteine residues 86 and 91 of the beta subunit of the human interleukin (hIL)-3 receptor (h beta c) participate in disulfide-linked receptor subunit heterodimerization. This linkage is essential for receptor tyrosine phosphorylation, since the Cys-86 --> Ala (Mc4) and Cys-91 --> Ala (Mc5) mutations abolished both events. Here, we used these mutants to examine whether disulfide-linked receptor dimerization affects the biological and biochemical activities of the IL-3 receptor. Murine T cells expressing hIL-3R alpha and Mc4 or Mc5 did not proliferate in hIL-3, whereas cells expressing wild-type h beta c exhibited rapid proliferation. However, a small subpopulation of cells expressing each mutant could be selected for growth in IL-3, and these proliferated similarly to cells expressing wild-type h beta c, despite failing to undergo IL-3-stimulated h beta e tyrosine phosphorylation. The Mc4 and Mc5 mutations substantially reduced, but did not abrogate, IL-3-mediated anti-apoptotic activity in the unselected populations. Moreover, the mutations abolished IL-3-induced JAK2, STAT, and AKT activation in the unselected cells, whereas activation of these molecules in IL-3-selected cells was normal. In contrast, Mc4 and Mc5 showed a limited effect on activation of Erk1 and -2 in unselected cells. These data suggest that whereas disulfide-mediated cross-linking and h beta c tyrosine phosphorylation are normally important for receptor activation, alternative mechanisms can bypass these requirements.

Optimal release strategies for biological control agents: an application of stochastic dynamic programming to population management

1. Establishing biological control agents in the field is a major step in any classical biocontrol programme, yet there are few general guidelines to help the practitioner decide what factors might enhance the establishment of such agents. 2. A stochastic dynamic programming (SDP) approach, linked to a metapopulation model, was used to find optimal release strategies (number and size of releases), given constraints on time and the number of biocontrol agents available. By modelling within a decision-making framework we derived rules of thumb that will enable biocontrol workers to choose between management options, depending on the current state of the system. 3. When there are few well-established sites, making a few large releases is the optimal strategy. For other states of the system, the optimal strategy ranges from a few large releases, through a mixed strategy (a variety of release sizes), to many small releases, as the probability of establishment of smaller inocula increases. 4. Given that the probability of establishment is rarely a known entity, we also strongly recommend a mixed strategy in the early stages of a release programme, to accelerate learning and improve the chances of finding the optimal approach.