Multiple Surface Reactions in Arrays with Applications to Optical Biosensors

We analyze surface-volume reactions in the context of optical biosensors with arrays of reacting zones. For arrays having zones with the same rate constants, we consider a two-dimensional reacting zone boundary definition and quantify ligand depletion with the effective Damköhler number. We use asymptotics to obtain ligand depletion results for the one-dimensional case, and also compute results for the circular reacting zone case. For arrays having zones with different rate constants, depletion effects cannot be expressed as the product of time-dependent and space-dependent terms, and we propose two effective rate constant equations for this case.     

Cross‐decades stability of an avian hybrid zone

Hybrid zones are particularly valuable for understanding the evolution of partial reproductive isolation between differentiated populations. An increasing number of hybrid zones have been inferred to move over time, but in most such cases zone movement has not been tested with long‐term genomic data. The hybrid zone between Townsend's Warblers (Setophaga townsendi) and Hermit Warblers (S. occidentalis) in the Washington Cascades was previously inferred to be moving from northern S. townsendi southwards towards S. occidentalis, based on plumage and behavioural patterns as well as a 2000‐km genetic wake of hermit mitochondrial DNA (mtDNA) in coastal Townsend's Warblers. We directly tested whether hybrid zone position has changed over 2–3 decades by tracking plumage, mtDNA and nuclear genomic variation across the hybrid zone over two sampling periods (1987–94 and 2015–16). Surprisingly, there was no significant movement in genomic or plumage cline centres between the two time periods. Plumage cline widths were narrower than expected by neutral diffusion, consistent with a ‘tension zone’ model, in which selection against hybrids is balanced by movement of parental forms into the zone. Our results indicate that this hybrid zone is either stable in its location or moving at a rate that is not detectable over 2–3 decades. Despite considerable gene flow, the stable clines in multiple phenotypic and genotypic characters over decades suggest evolutionary stability of this young pair of sister species, allowing divergence to continue. We propose a novel biogeographic scenario to explain these patterns: rather than the hybrid zone having moved thousands of kilometres to its current position, inland Townsend's met coastal Hermit Warbler populations along a broad front of the British Columbia and Alaska coast and hybridization led to replacement of the Hermit Warbler plumage with Townsend's Warbler plumage patterns along this coastline. Hence, hybrid zones along British Columbia and Alaska moved only a short distance from the inland to the coast, whereas the Hermit Warbler phenotype appears stable in Washington and further south. This case provides an example of the complex biogeographic processes that have led to the distribution of current phenotypes within and among closely related species.     

AN ASSESSMENT OF THE POTENTIAL IMPACT OF ALIEN INVASIVE VEGETATION ON THE GEOMORPHOLOGY OF RIVER CHANNELS IN SOUTH AFRICA

Summary

Invasion of the riparian zone by alien vegetation is recognised as a serious problem in many areas of South Africa. Vegetation is a dynamic component of river channels. It is an important control variable affecting channel form whereas the flow and sediment regime influences vegetation growth. Wherever alien vegetation invades the riparian zone it can be expected that there will be some impact on the physical structure of the riparian habitat. This paper reviews the effect of riparian vegetation on channel processes and channel form and discusses the implications of the invasion of riparian zones by alien vegetation. Woody species in particular are seen as having a significant potential for inducing channel modification, whilst their removal could lead to significant channel instability and mobilisation of sediment. The need for further research into the impact of alien vegetation on the geomorphology of South African river channels is stressed.     

An Exclusion Zone for Ca2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse

The spatial arrangement of Ca²⁺ channels and vesicles remains unknown for most CNS synapses, despite of the crucial importance of this geometrical parameter for the Ca²⁺ control of transmitter release. At a large model synapse, the calyx of Held, transmitter release is controlled by several Ca²⁺ channels in a "domain overlap" mode, at least in young animals. To study the geometrical constraints of Ca²⁺ channel placement in domain overlap control of release, we used stochastic MCell modelling, at active zones for which the position of docked vesicles was derived from electron microscopy (EM). We found that random placement of Ca²⁺ channels was unable to produce high slope values between release and presynaptic Ca²⁺ entry, a hallmark of domain overlap, and yielded excessively large release probabilities. The simple assumption that Ca²⁺ channels can be located anywhere at active zones, except below a critical distance of ~ 30 nm away from docked vesicles ("exclusion zone"), rescued high slope values and low release probabilities. Alternatively, high slope values can also be obtained by placing all Ca²⁺ channels into a single supercluster, which however results in significantly higher heterogeneity of release probabilities. We also show experimentally that high slope values, and the sensitivity to the slow Ca²⁺ chelator EGTA-AM, are maintained with developmental maturation of the calyx synapse. Taken together, domain overlap control of release represents a highly organized active zone architecture in which Ca²⁺ channels must obey a certain distance to docked vesicles. Furthermore, domain overlap can be employed by near-mature, fast-releasing synapses.     

Study of cycle of cell wall assembly in Streptococcus faecalis by three-dimensional reconstructions of thin sections of cells.

A new ultrastructural method was used to study rounds of envelope synthesis that occur in Streptococcus faecalis in "growth zones" found between pairs of naturally occurring surface markers. The technique consists of producing three-dimensional reconstructions of these growth zones from the mathematical rotation, about a central axis, of measurements taken from central, longitudinal thin sections of cells. A cycle of exponential-phase envelope growth was then simulated by arranging a series of these reconstructions in increasing order of the amount of peripheral wall surface area or the amount of cell volume that each was calculated to contain. Using this simulated cycle of growth, the geometry of a single growth zone during a round of synthesis was studied. Based on this analysis, a model was developed for the assembly of the cell wall of S. faecalis. The model states that new cell wall surface is synthesized by the regulated flow of essentially two channels of cell wall precursors into a single growth zone. One channel of precursors would be involved in the assembly of a bilayered cross wall that would proceed at a fairly constant rate until the cross wall closes. The second channel of precursors would be involved in the separation of the bilayered cross wall into two segments of peripheral wall. These precursors would intercalate into and thicken the separating layers of the cross wall. The flow of precursors through this channel would be progressively reduced through a cycle. These decreases, when coupled with internal hydrostatic pressure, apparently would result in the enlarging peripheral wall becoming increasingly more curved and would also promote cell division by reducing the total amount of cell wall that must be assembled in order for septation to occur.     

The Crow Corvus corone hybrid zone in southern Denmark and northern Germany

In hybrid zones genetically differentiated populations meet and interbreed. As they result from ongoing divergence and potential speciation, such zones provide opportunities to study how different factors affect this process. One well-known avian hybrid zone is that between the Hooded Crow Corvus corone cornix and Carrion Crow C. c. corone , which extends throughout much of Europe. We compare the current position and width of the zone in southern Denmark and northern Germany with that described in detail by Meise in 1928. A GPS technique was used to determine the geographical position of more than 1000 Crows in established pairs in which all individuals were classified as either Carrion, Hooded or hybrid phenotype. The data show that the Carrion Crow has expanded northwards and that this is most pronounced at the eastern side of the study area. Here the hybrid zone has moved around 19 km. However, the width of the zone seems to have remained stable over time. Possible reasons for why the zone may have moved are discussed.     

Aquatic vegetation and hydrology of a braided river floodplain

The response of aquatic vegetation to the complex hydrology of a river floodplain was investigated on a stretch of former braided channels of the Rhône River near Lyon, France, which is fed by three different water inputs: underground water, surface flow from a small tributary and river overflow during spates. Water temperature, pH, conductivity, alkalinity, sulfate, nitrate, and phosphate content were measured monthly at seven sampling stations. Principal Component Analysis (PCA) of these data revealed two gradients: a gradient of spatial heterogeneity and a gradient of temporal fluctuations. A PCA of samples based on substrate grain size, flow velocity, channel width and depth, height and shade of bank vegetation suggested the division of the braided system into four zones. Along these former channels, the vegetation varies from communities with Potamogeton coloratus of nutrient-poor water, to meso-eutraphent communities with Callitriche platycarpa, Elodea canadensis, and Ranunculus trichophyllus. Correspondence Analysis (CA) of the floristic data revealed four zones. Regarding the habitat parameters investigated, one zone is assumed to be linked to the instability and the nutrient inputs of a former channel (running water from the tributary and flood disturbances), while another is linked to the stability and nutrient-poor conditions of the other former channel (supplied by underground water). The other two zones are considered as ecotones, each of them occurring in a former channel, upstream of the confluences. The location as well as the floristic and functional differences between these two ecotones are discussed.     

Gene‐flow across the European crow hybrid zone – a spatial simulation

In hybrid zones populations that are otherwise allopatric meet and produce hybrids. One of the most well‐known hybrid zones occurs throughout much of Europe between the hooded and carrion crows. Even though these species (or subspecies) of crows look very different, genetic differentiation is weak, and introgression seems to be common. In a spatial simulation that was based on empirically estimated values, we investigated how introgressing alleles that would confer some fitness advantage would flow across the zone. The advantage was assumed to be some unknown factor that enhanced survival for carriers relative to non‐carriers. We varied the yearly survival advantage between 0 to 10% and recorded how this would affect zone shape and position. In the simulation we cycled ‘yearly’ events such as reproduction, mortality and juvenile dispersal. We started the simulation by equipping all individuals of one crow type outside the zone with a homozygotic set of the beneficial allele. At all levels of advantage the allele first rapidly became fixed in the donator crow type, then transgressed into the receiving type more slowly and finally became fixed in all individuals. The time until fixation varied from around 176 yr for a 10% advantage to around 20 000 yr for 0% advantage. An exciting discovery was that the position of the zone would move during the introgression but then stop. The reason is that the beneficial allele would be common in the donating type but not in the receiving type during the introgression event. At large the crow hybrid zone appears to have been stable for a long time but there have been small recent northward movements of carrion crows in both Scotland and Denmark. We suggest that introgression by itself is a factor that should be considered as an explanation for why hybrid zones move temporarily.     

The anatomy of a ‘suture zone’ in Amazonian butterflies: a coalescent‐based test for vicariant geographic divergence and speciation

Attempts by biogeographers to understand biotic diversification in the Amazon have often employed contemporary species distribution patterns to support particular theories, such as Pleistocene rainforest refugia, rather than to test among alternative hypotheses. Suture zones, narrow regions where multiple contact zones and hybrid zones between taxa cluster, have been seen as evidence for past expansion of whole biotas that have undergone allopatric divergence in vicariant refuges. We used coalescent analysis of mutilocus sequence data to examine population split times in 22 pairs of geminate taxa in ithomiine and heliconiine butterflies. We test a hypothesis of simultaneous divergence across a suture zone in NE Peru. Our results reveal a scattered time course of diversification in this suture zone, rather than a tight cluster of split times. Additionally, we find rapid diversification within some lineages such as Melinaea contrasting with older divergence within lineages such as the Oleriina (Hyposcada and Oleria). These results strongly reject simple vicariance as a cause of the suture zone. At the same time, observed lineage effects are incompatible with a series of geographically coincident vicariant events which should affect all lineages similarly. Our results suggest that Pleistocene climatic forcing cannot readily explain this Peruvian suture zone. Lineage‐specific biological traits, such as characteristic distances of gene flow or varying rates of parapatric divergence, may be of greater importance.     

Juvenile growth of a macrohabitat generalist tied to hydrological character of large‐river system

相似文献   

Is dispersal guided by the environment? A comparison of interspecific gene flow estimates among differentiated regions of a newt hybrid zone

How frequently genes pass through a hybrid zone may be influenced by the environment. Accordingly, in long hybrid zones that span more than one environmental setting, different patterns may emerge. The varied conditions allow testing of hypotheses on dispersal as a function of the environment. We reconstruct the amount and direction of gene flow across a heterogeneous hybrid zone of two species of marbled newts (Triturus marmoratus and Triturus pygmaeus), in four widely separated areas of the Iberian Peninsula from one mitochondrial and three nuclear genes. The main variables associated with the position of the contact zone are precipitation, rivers, altitude and relief. In some sections of the contact zone, however, its position is not correlated with any environmental factor and is instead determined by the shortest geographical distance between fixed positions at either side (mountains in the East and river in the West). In areas where the position of the zone is stable, gene flow was bidirectional. External data show that T. pygmaeus has superseded T. marmoratus over a large area and here gene flow was unidirectional. The prediction that a major river would reduce gene flow was not confirmed.     

Cascade stacking and cascade electrofocusing: their interconversion and fundamental unity.

The composition of a stack [an isotachophoresis (ITP) system] containing multiple trailing buffer constituents (“cascade stack”) was computed using a modification of the program of Routs. On electrophoresis, such a buffer mixture gave rise to multiple moving boundaries in which either buffer constituents or proteins could be stacked. Buffer zones within the stack served as “spacers.” The cascade stack exhibits a pH gradient, sharp zone boundaries, and constant zone width irrespective of the duration of electrophoresis, just as in the case of a stack comprising a single leading and trailing constituent. The pH gradient, sharp zone boundaries, and the sequential order of protein zones were maintained when the cascade stack was transposed between strongly acidic and basic electrolytes. Such a transposed isotachophoretic gel functioned as an electrofocusing system, indistinguishable from electrofocusing gels made in either buffers (buffer electrofocusing, or BEF) or Ampholine (isoelectric focusing, or IF). In the converse experiment, a cascade electrofocusing gel, formed in the same buffer mixture used to form a cascade stack, was subjected to electrofocusing until the steady-state was attained and then it was transposed between the appropriate upper and lower buffers of the corresponding cascade stacking system. Such transposition gave rise to moving zones with the typically sharp boundaries of a stack, a transient state pH gradient, and an order of protein zones within the cascade stack identical to the cascade electrofocusing system. These studies indicate the essential physical-chemical identity between these two types of electrophoretic systems and indicate the need for continued development of a unified theory for isoelectric focusing and steady-state stacking (isotachophoresis).     

Stability criterion for controlling standing in able-bodied subjects

A new stability criterion that can be used to assess the standing condition of a subject from center of pressure (CoP) measurements is presented. This criterion can be applied, for example, to control a standing prosthesis, which should allow a paraplegic subject to stand up, sit down and stand safely without using hands for support. Experiments conducted with able-bodied subjects enabled us to establish a relationship between its stability and the subject's CoP position. Four CoP stability zones were identified: high preference, low preference, undesirable and unstable zones. The high preference zone is defined as the area where the CoP is found 99% of the time during quiet standing. The area where the CoP is found during the remaining 1% of the time is called the low preference zone. The undesirable zone is defined as the CoP area where the subject is forced to change posture in order to maintain balance, and the unstable zone is defined as the CoP area in which the subject is forced to step forward, backward or sideways to maintain stability. A general model of the proposed four stability zones was derived, which can be used to compute stability zones a priori for any subject and thus allows one to assess the subject's stability condition from the CoP measurements.     

Modulation of a gated ion channel admittance in lipid bilayer membranes.

A future class of amperometric biosensors may utilize gated ion channels such as acetylcholine and glutamate receptors as chemical detection components. In this study, bilayer lipid membranes containing voltage-dependent anion channels (VDAC) were used to model an ion-channel-based biosensor which could continuously monitor AC amperometric changes resulting from induced changes in channel conductance. The in-phase and quadrature components of the induced alternating membrane current were monitored as a function of the applied DC offset voltage which was superimposed on the sinusoidal test voltage. The accuracy and sensitivity of the AC-measured VDAC response was dependent on the magnitude of the AC test voltage relative to the DC offset necessary for channel closure. The VDAC channel appears to be a suitable model protein for AC impedance-based biosensor fabrication.     

Probabilistic secretion of quanta and the synaptosecretosome hypothesis: evoked release at active zones of varicosities, boutons, and endplates.

A quantum of transmitter may be released upon the arrival of a nerve impulse if the influx of calcium ions through a nearby voltage-dependent calcium channel is sufficient to activate the vesicle-associated calcium sensor protein that triggers exocytosis. A synaptic vesicle, together with its calcium sensor protein, is often found complexed with the calcium channel in active zones to form what will be called a "synaptosecretosome." In the present work, a stochastic analysis is given of the conditions under which a quantum is released from the synaptosecretosome by a nerve impulse. The theoretical treatment considers the rise of calcium at the synaptosecretosome after the stochastic opening of a calcium channel at some time during the impulse, followed by the stochastic binding of calcium to the vesicle-associated protein and the probability of this leading to exocytosis. This allows determination of the probabilities that an impulse will release 0, 1, 2,... quanta from an active zone, whether this is in a varicosity, a bouton, or a motor endplate. A number of experimental observations of the release of transmitter at the active zones of sympathetic varicosities and boutons as well as somatic motor endplates are described by this analysis. These include the likelihood of the secretion of only one quantum at an active zone of endplates and of more than one quantum at an active zone of a sympathetic varicosity. The fourth-power relationship between the probability of transmitter release at the active zones of sympathetic varicosities and motor endplates and the external calcium concentration is also explained by this approach. So, too, is the fact that the time course of the increased rate of quantal secretion from a somatic active zone after an impulse is invariant with changes in the amount of calcium that enters through its calcium channel, whether due to changes consequent on the actions of autoreceptor agents such as adenosine or to facilitation. The increased probability of quantal release that occurs during F1 facilitation at the active zones of motor endplates and sympathetic boutons is predicted by the residual binding of calcium to a high-affinity site on the vesicle-associated protein. The concept of the stochastic operation of a synaptosecretosome can accommodate most phenomena involving the release of transmitter quanta at these synapses.     

Oceanic and temperate rainforest climates and their epiphyte indicators in Britain

A biogeographic zone with high oceanicity is a well described feature of the European Atlantic region. This oceanic zone intersects with a zone of European temperate rainforest that has received increasing conservation recognition. Although having a degree of spatial overlap, the terminology applied to these different zones is not synonymous. Temperate rainforest is one example of an oceanic system, alongside others such as blanket bog or liverwort heath. Conversely, oceanic systems provide one type of climatic setting suitable to the development of temperate rainforest, alongside other and contrasting landscapes such as the orographic climate of continental mountains. Zones of high oceanicity and temperate rainforest are both strongly represented in the British Isles, and this study examines the degree of spatial overlap in Britain for standard definitions of each. Lichen epiphyte indicators associated with zones of oceanic woodland or temperate rainforest were quantified, and subsequently tested for conservation priority Atlantic oakwoods (Annex 1 Habitat Code 91A0: old sessile oak woods with Ilex and Blechnum in the British Isles). Discrepancies between oceanic woodland and temperate rainforest led to slightly different sets of indicator species that could be applied in biodiversity and habitat quality assessments. The definition of oceanic systems appeared to include warmer and lowland situations for example in coastal Wales and south-west England. In contrast, temperate rainforest extended to cooler upland areas in north-eastern Scotland. The species indicators for oceanic and temperate rainforest were nevertheless effective in identifying sites with different conservation priorities, such as for protection or restoration.     

Combinatorial augmentation for a multi-pathogen biosensor: signal analysis and design

Recent advances in combinatorial chemistries have revolutionized approaches to drug candidate synthesis and screening. Combinatorial approaches are also beginning to be used to increase the performance of diagnostic devices for both clinical and field uses. The use of combinatorial technologies is motivated by a general desire to detect as many different pathogens using the smallest, most inexpensive and fastest system possible. We examine the potential for rational design approaches to enhance the performance and miniaturization of biosensors. We describe novel combinatorial biosensor systems, in addition to mathematical frameworks for their optimization and performance prediction. The biosensors are assumed to be composed of multiple detection channels with the following characteristics. Each channel has a single output and can be dynamically set to respond to some or all of a set of pathogens. Regardless of the number of pathogens detected, however, there is a single numerical output from a channel. We evaluate the amount of ambiguity of positive signals produced as a result of increasing both the number of channels and the number of pathogens detected per channel and the effect this ambiguity has on system performance. We further discuss strategies for disambiguating positive signals. Finally we cite specific biosensor configurations that exploit the findings above and compare them to “brute force” approaches. Overall we suggest the approach we refer to as “n-squared” to simultaneously optimize device cost, speed and reagent usage.     

Microfluidic-integrated biosensors: Prospects for point-of-care diagnostics

There is a growing demand to integrate biosensors with microfluidics to provide miniaturized platforms with many favorable properties, such as reduced sample volume, decreased processing time, low cost analysis and low reagent consumption. These microfluidics-integrated biosensors would also have numerous advantages such as laminar flow, minimal handling of hazardous materials, multiple sample detection in parallel, portability and versatility in design. Microfluidics involves the science and technology of manipulation of fluids at the micro- to nano-liter level. It is predicted that combining biosensors with microfluidic chips will yield enhanced analytical capability, and widen the possibilities for applications in clinical diagnostics. The recent developments in microfluidics have helped researchers working in industries and educational institutes to adopt some of these platforms for point-of-care (POC) diagnostics. This review focuses on the latest advancements in the fields of microfluidic biosensing technologies, and on the challenges and possible solutions for translation of this technology for POC diagnostic applications. We also discuss the fabrication techniques required for developing microfluidic-integrated biosensors, recently reported biomarkers, and the prospects of POC diagnostics in the medical industry.     

Patterns of hydrological exchange and nutrient transformation in the hyporheic zone of a gravel-bottom stream: examining terrestrial—aquatic linkages

• 1 The terrestrial-aquatic interface beneath a riparian corridor was investigated as a region of hydrological and biological control of nutrient flux. Subsurface flow paths were defined from the channel toward the riparian zone and also from the riparian zone toward the channel using tracer-injection studies. Solute transport had a rapid channel component (m min^?1) and a slow hyporheic flow component (mh^?1, m day^?1). Subsurface flow beneath the riparian zone approximated a straight path entering at meanders but could also cross beneath the stream, possibly using relic channels.
• 2 Dissolved oxygen (DO) concentration in the hyporheic zone ranged from <1.0 to 9.5mgl^?1 due to permeability variations in bankside sediments. DO concentration was related to the proportion of stream water in the lateral hyporheic zone, indicating that the channel water was the DO source.
• 3 The magnitude and riming of lateral water exchange was linked to previously published studies of nitrification and denitrificarion. Both nitrification potential and channel exchange decreased with distance from the channel and were absent at sites lacking effective exchange, due to low DO. Field amendment of ammonium to an aerobic flow path indicated nitrification potential under natural hydrological conditions. Denitrification potential was inversely related to channel exchange and was insignificant in channel sediments. Field amendment of acetylene plus nitrate to a flow path with low DO and minimal channel exchange indicated denitrificarion of amended nitrate.
• 4 Comparison of hydraulic head to distribution of the biologically important solutes DO, ammonium, and nitrate was useful for interpreting previous findings and conceptualizing the riparian zone as a functioning ecotone between terrestrial and aquatic systems.

     

Flow injection analysis and in-line biosensors for bioprocess control: a comparison.

Miniaturization will unify the different approaches chosen for the application of biosensors in bioprocess control. The most versatile system, which in our opinion is flow injection analysis will be the method of choice for the introduction of biosensors in bioprocess control. A lot of experience will be gained for the future development of miniaturized total chemical analysis systems.