Mind the gap: scale‐dependent and dispersal‐mediated response to forest fragmentation

Species richness of habitat fragments is affected by spatial isolation. However, the scale of this phenomenon, and its interactions with the species’ seed dispersal potential has remained underexplored. By integrating seed trap and species distribution data, Koh et al., in this issue of the Journal of Vegetation Science, make a compelling case for scale‐dependent species’ responses to forest fragmentation.     

Circadian performance rhythms: some practical and theoretical implications

Safety and productivity are low at night and this would appear to be because we are a diurnal species. This is reflected not only in our habitual sleep time, but also in our endogenous body clocks that, together with exogenous influences, such as the patterning of meals and activity, result in predictable circadian (24 h) rhythms in our physiological processes. Our performance capabilities also vary over the course of our waking period, with task demands affecting both the precise trend over the day, and the rate at which it adjusts to the changes in sleep timing occasioned by shift work. Studies designed to examine the reasons for this have shown that memory loaded performance may have a quite separate endogenous component to that responsible for more simple performance, suggesting that these two types of performance cannot be causally related. Furthermore, it would appear that the exogenous component of circadian rhythms may also differ across measures, and our attempts to model these endogenous and exogenous components have led us to re-examine the evidence on adjustment to night work. Our findings suggest that shiftworkers merely 'stay up late' on the night shift, rather than adjust to it, and that this is responsible for the reduced safety at night. It would seem that in situations where safety is paramount, the only solution to these problems is the creation of a nocturnal sub-society that not only always works at night but also remains on a nocturnal routine on rest days.     

Epidemiology of a tick‐borne viral infection: theoretical insights and practical implications for public health

The morbidity of tick‐borne encephalitis (TBE) varies yearly by as much as 10‐fold among the people of Western Siberia. This long‐term variation is dependent on many factors such as the density of the tick populations, the prevalence of TBE virus (TBEV) among sub‐adult ticks, the yearly virulence of the TBEV, and prophylactic measures. Here we highlight the role of small mammal hosts in the circulation of TBEV through the ecosystem. Refining classical models of non‐viremic horizontal transmission, we emphasize the recently understood fact that the physiological and immunological status of the small mammal hosts affects the tick and virus‐host interactions. In addition to its theoretical interest, our approach may lead to some practical improvements in the precision of epidemiological forecasts and perhaps in forestalling the severity of outbreaks of TBE, or, at least, in forewarning medical authorities and the general public of impending TBE outbreaks.     

A common fragile site at Xq27: theoretical and practical implications.

The fragile site at Xq27 (FRAXA) is associated with a common form of X-linked mental retardation (Martin-Bell syndrome). It is induced in culture by conditions of thymidylate stress and is generally considered a rare fragile site found only in association with an X-linked form of mental retardation. Using a somatic cell hybrid system, we previously demonstrated that fragile-X expression can be induced by thymidylate stress in normal X chromosomes at low levels (4%-5%). In the present report, significantly higher levels of fragile-X expression (6%-28%) have been induced in lymphocytes or lymphoblasts of all seven control males using high doses of aphidicolin (1.5 microM). Similar high levels of expression (10%-12%) were observed in both of two normal male chimpanzees (Pan troglodytes). These data demonstrate that Xq27 contains a common fragile site (FRAXD) that is ancestral to the divergence of man and the chimpanzee. Presence of a common and a rare fragile site in the same metaphase chromosome band does not prove that they are identical and may, in fact, represent two unrelated fragile sites. However, the possibility exists that the common fragile site at Xq27 may be the substrate for unequal recombination events that produces the rare fragile site associated with Martin-Bell syndrome. In addition, presence of a common fragile site at Xq27 may explain the occasional observation of low-frequency fragile-X expression in normal control individuals. Caution is therefore warranted in the interpretation of low-level fragile-X expression in diagnostic and prenatal diagnostic settings.     

Animal space use: distinguishing a two‐level superposition of scale‐specific walks from scale‐free Lévy walk

How to differentiate between scale‐free space use like Lévy walk and a two‐level scale‐specific process like composite random walk (mixture of intra‐ and inter‐patch habitat movement) is surrounded by controversy. Composite random walk may under some parameter conditions appear Lévy walk‐like from the perspective of the path’s distribution of step lengths due to superabundance of very long steps relative to the expectation from a classic (single‐level) random walk. However, a more explicit focus on the qualitative differences between studying movement at a high resolution mechanistic (behavioral) level and the more coarse‐grained statistical mechanical level may contribute to resolving both this and other issues related to scaling complexity. Specifically, a re‐sampling of a composite random walk at larger time lags than the micro‐level unit time step for the simulation makes a Lévy‐look‐alike step length distribution re‐shaping towards a Brownian motion‐like pattern. Conversely, a true Levy walk maintains its scaling characteristics upon re‐sampling. This result illustrates how a confusing pattern at the mechanistic level may be resolved by changing observational scale from the micro level to the coarser statistical mechanical meso‐ or macro‐scale. The instability of the composite random walk pattern under rescaling is a consequence of influence of the central limit theorem. I propose that a coarse‐graining test – studying simulated animal paths at a coarsened temporal scale by re‐sampling a series – should be routinely performed prior to comparing theoretical results with those patterns generated from GPS data describing animal movement paths. Fixes from terrestrial mammals are often collected at hourly intervals or larger, and such a priori coarse‐grained series may thus comply better with the statistical mechanical meso‐ or macro‐level of analysis than the behavioral mechanics observed at finer resolutions typically in the range of seconds and minutes. If fixes of real animals are collected at this high frequency, coarse graining both the simulated and real series is advised in order to bring the analysis into a temporal scale domain where analytical methods from statistical mechanics can be applied.     

Invertebrate availability and vegetation characteristics explain use of nonnesting cover types by mature‐forest songbirds during the postfledging period

ABSTRACT Some species of mature‐forest‐nesting songbirds use regenerating clearcuts and forested wetlands during the postfledging period (between nesting and migration). Relatively dense vegetation structure and abundant food resources in non‐mature‐forest cover types have been hypothesized to explain this phenomenon. We examined the relative importance of vegetation structure and invertebrate availability on use of nonnesting cover types by adult and hatch‐year Ovenbirds (Seiurus aurocapilla) and American Redstarts (Setophaga ruticilla) during the postfledging period of 2009 in northern Minnesota. We used mist nets to sample bird use of forested wetlands and regenerating clearcuts of three age groups: 1–6, 7–12, and 16–19 yr after harvest. We modeled captures of birds using vegetation characteristics and invertebrate availability sampled around nets as explanatory variables. For all birds studied, captures were best explained by food availability and secondarily by vegetation characteristics including litter depth and woody debris for Ovenbirds and canopy height for American Redstarts. Shrub‐level invertebrate availability received a cumulative weight of 0.74–0.99 in Akaike's information criterion corrected ranked models for adult and hatch‐year birds of both species. Vegetation density and variation in vegetation density explained almost no variation in captures of either species. We conclude that both invertebrate availability and some vegetation characteristics influence use of nonnesting cover types by Ovenbirds and American Redstarts during the postfledging period, but that invertebrate availability is generally the stronger predictor of that use.     

A greenhouse gas indicator for bioenergy: some theoretical issues with practical implications

Background, aim, and scope  The expectations with respect to biomass as a resource for sustainable energy are sky-high. Many industrialized countries have adopted ambitious policy targets and have introduced financial measures to stimulate the production or use of bioenergy. Meanwhile, the side-effects and associated risks have been pointed out as well. To be able to make a well-informed decision, the Dutch government has expressed the intention to include sustainability criteria into relevant policy instruments. Main features  Among other criteria, it has been proposed to calculate a so-called life-cycle-based greenhouse gas (GHG) indicator, which expresses the reduction of GHG emissions of a bio-based fuel chain in comparison with a fossil-based fuel chain. Life-cycle-based biofuel studies persistently have problems with the handling of biogenic carbon balances and with the treatment of coproducts and recycling. In life-cycle assessments (LCAs) of agricultural products, a distinction between “negative” and “positive” emissions may be relevant. In particular, carbon dioxide, as a naturally occurring compound or an anthropogenic emission, takes part in the so-called geochemical carbon cycle. The most appropriate way to treat carbon cycles is to view them as genuine cycles and, thus, at the systems level, subtract the fixation of CO₂ during tree growth from the CO₂ emitted during waste treatment of discarded wood and to quantify the CH₄ emitted. In solving the multifunctionality problem, two steps may be distinguished. The first concerns the modeling of the product system studied in the inventory analysis. In this step, system boundaries are set, processes are described, and process flows are quantified. Multifunctionality problems can be identified and the model of the product system is drafted. The second step concerns solving the remaining multifunctionality problems. For this step, various ways of solving the multifunctionality problem have been proposed and applied, on the basis of mass, energy, economic value, avoided burdens, etc. As the GHG indicator may constitute the basis for granting subsidies to stimulate the use of bioenergy, for example, and as the method for the GHG indicator provides no guidelines on the handling of biogenic CO₂ and guidelines for solving multifunctionality problems such as with coproducts and recycling that leave room for various choices, this study analyzed whether the current GHG indicator provides results that are a robust basis for granting such subsidies. Results  For the robustness check, a hypothetical case study on wood residue-based electricity was set up in order to illustrate what the effects of different solutions and choices for the two steps mentioned may be. The case dealt with the production of wood pellets (residues of the wood industry) that are cofired in a coal-fired power plant. The functional unit is 1 kWh of electricity. Three possibilities for the places of the multifunctional process, two possibilities for whether or not to include biogenic CO₂, and four possibilities for the allocation method were distinguished and calculated. Varying the options for these three choices in this way appears to have a huge effect on the GHG indicator, while no clear pattern seems to emerge. Discussion  The results found for this hypothetical case indicate that there are several methodological choices that have not sufficiently been fixed by the presently available standards and guidelines for LCA and GHG assessment of bioenergy systems. In particular, we have focused on issues related to biogenic CO₂ and allocation, two issues that play a prominent role in the assessment of bioenergy systems. Moreover, we have demonstrated with a small hypothetical case study that these are not only issues that might theoretically show up, but that they play a decisive role in practice. Conclusions  The present (Dutch) GHG indicator lacks robustness, which will raise problems for providing a sound basis for granting subsidies. This situation can, however, be improved by reducing the freedom of choices for the handling of biogenic CO₂ and allocation to an absolute minimum. Recommendations and perspectives  Even then, however, differences could appear due to different definitions, data sources, and method interpretations. It thus appears that two kinds of guidance are needed: (1) the LCA methodology itself should be expanded with guidelines for those issues that follow from science, logic, or consensus; (2) in the policy regulation that demands LCA to be the basis of the decision, additional guidelines should be specified that perhaps do not (yet) have the status of being scientifically proven or generally agreed upon, but that serve as a set of temporary extra guidelines.

Species‐specific and temporal scale‐dependent responses of birds to drought

Global climate change is increasing the frequency and intensity of weather extremes, including severe droughts in many regions. Drought can impact organisms by inhibiting reproduction, reducing survival and abundance, and forcing range shifts. For birds, considering temporal scale by averaging drought‐related variables over different time lengths (i.e., temporal grains) captures different hydrologic attributes which may uniquely influence food supplies, vegetation greenness/structure, and other factors affecting populations. However, studies examining drought impacts on birds often assess a single temporal grain without considering that different species have different life histories that likely determine the temporal grain of their drought response. Furthermore, while drought is known to influence bird abundance and drive between‐year range shifts, less understood is whether it causes within‐range changes in species distributions. Our objectives were to (a) determine which temporal grain of drought (if any) is most related to bird presence/absence and whether this response is species specific; and (b) assess whether drought alters bird distributions by quantifying probability of local colonization and extinction as a function of drought intensity. We used North American Breeding Bird Survey data collected over 16 years, generalized linear mixed models, and dynamic occupancy models to meet these objectives. Different bird species responded to drought at different temporal grains, with most showing the strongest signal at annual or near‐annual grains. For all drought‐responsive species, increased drought intensity at any temporal grain always correlated with decreased occupancy. Additionally, colonization/extinction analyses indicated that one species, the dickcissel (Spiza americana), is more likely to colonize novel areas within the southern/core portion of its range during drought. Considering drought at different temporal grains, along with hydrologic attributes captured by each grain, may better reveal mechanisms behind drought impacts on birds and other organisms, and therefore improve understanding of how global climate change impacts species and the landscapes they inhabit.     

Carnoy fixation: practical and theoretical considerations

Summary The Carnoy-fixation, paraffin-embedding procedure was modified to minimize shrinkage and to suit the schedule of general histology laboratories. Blocks of tissues were fixed in Carnoy's fluid overnight, transferred to absolute alcohol in the morning and washed in three changes of alcohol for a total of 6–8 hours. Tissues were then left in methyl benzoate overnight, transferred to an Autotechnicon in the morning, cleared in xylene and xylene-paraffin 1 hour each and infiltrated in 2–3 changes of paraffin for a total of 4–5 hours. This procedure has worked well in our hands for nine years.A review of the chemical literature showed that the components of Carnoy's fluid-ethanol, chloroform and acetic acid-can interact by hydrogen bond formation with each other and with various groups in tissues. These association compounds apparently stabilize tissue structures and prevent or minimize shrinkage. Ethanol alone causes collapse of protein structures; exposure must be limited to eight hours or less. Addition of water to an ethanol-acetic acid solution causes considerable swelling of proteins and subsequent shrinkage in absolute alcohol; hence, the ratio fixative: tissue should be not less than 201. In our experience, Carnoy's fluid is the fixative of choice for studies of fibrous proteins and associated carbohydrates by histochemical and special staining technics.     

Rate-of-dialysis technique: theoretical and practical aspects

In the rate-of-dialysis technique, chemical equilibrium exists throughout the experiment between the contents of the two halves of a dialysis cell. Initially, however, a trace amount of labeled dialysand is present in one of the half-cells, and the dialysis of that is followed as a function of time. The method is able to reveal whether a compound is stable under the conditions used or whether it is affected, for example, by aggregation, precipitation, oxidation, or hydrolysis. The rate constants for six inorganic ions and 22 organic molecules were determined, and no simple relations were found between rate constants and functions of molar masses. However, in two homologous series of compounds, a linear relationship between rate constant and molar mass was found, allowing for a preliminary identification of an unknown substance. Whether the presence of a macromolecule results in binding of the dialysand is easily tested for because in that case its rate constant is sharply diminished. High-affinity binding was studied using octanoate and laurate as ligands and human serum albumin as binding protein. The primary binding constants determined were similar to those obtained by equilibrium dialysis. However, the rate-of-dialysis technique is much faster, and its results are less scattered. The technique is well suited for binding studies performed with high protein concentrations because it is not affected by any osmosis or Donnan effects.     

Clocks for the city: circadian differences between forest and city songbirds

To keep pace with progressing urbanization organisms must cope with extensive habitat change. Anthropogenic light and noise have modified differences between day and night, and may thereby interfere with circadian clocks. Urbanized species, such as birds, are known to advance their activity to early morning and night hours. We hypothesized that such modified activity patterns are reflected by properties of the endogenous circadian clock. Using automatic radio-telemetry, we tested this idea by comparing activity patterns of free-living forest and city European blackbirds (Turdus merula). We then recaptured the same individuals and recorded their activity under constant conditions. City birds started their activity earlier and had faster but less robust circadian oscillation of locomotor activity than forest conspecifics. Circadian period length predicted start of activity in the field, and this relationship was mainly explained by fast-paced and early-rising city birds. Although based on only two populations, our findings point to links between city life, chronotype and circadian phenotype in songbirds, and potentially in other organisms that colonize urban habitats, and highlight that urban environments can significantly modify biologically important rhythms in wild organisms.     

High seed dispersal rates in faunally intact tropical rain forest: theoretical and conservation implications

Dispersal limitation may promote high tree-species diversity in rain forest by slowing local competitive exclusion, but evidence is scarce. By comparing the species lists of tree plots with those of nested seedling plots in rain forest at Gunung Palung, we found that the proportion of local seedlings arising from active dispersal events (via wind or animals, but not simply dropped from parent trees) was high: 68% of species and 46% of the individual seedlings. Local seedling species richness was not limited by the local richness of adults. Using these data, a spatially explicit simulation model indicated that dispersal limitation may not contribute substantially to the maintenance of tree diversity in this forest. We predict that the loss of animal seed dispersers would reduce local species richness of seedlings by 60%. While this reduction could possibly increase the influence of dispersal limitation, it would interfere with other mechanisms maintaining diversity.     

Testosterone and year‐round territoriality in tropical and non‐tropical songbirds

Past studies have suggested a fundamental difference in testosterone concentrations between tropical and northern latitude male birds, with the convention being that males in the tropics express much lower levels of testosterone. However, recent comparative studies have shown that tropical males with a short and synchronous breeding season (i.e. a breeding season typical of northern species) express maximum testosterone levels similar to those of northern latitude birds. Here, we ask the converse: do northern latitude songbirds that express a defining life‐history characteristic typical of the tropics, i.e. year‐round territoriality, have an annual testosterone profile similar to that of tropical songbirds? For the few year‐round territorial species for which data are available, we found that seasonal testosterone profiles and seasonal maxima in plasma testosterone were similar between males of tropical and non‐tropical species. For example, males of both groups expressed seasonal maxima during the period when females were fertile, and testosterone levels at this time were similar. In contrast, this and other studies show that species with seasonal territories typically express maximum testosterone levels earlier in the breeding cycle, when territories are first being established. Taken together, we suggest that specific life‐history traits may play a more important role in determining testosterone profiles of tropical and non‐tropical birds than breeding latitude and encourage further studies to allow for more formal comparisons.     

Production and scale‐up of a monoclonal antibody against 17‐hydroxyprogesterone

The hybridoma 192 was used to produce a monoclonal antibody (MAb) against 17‐hydroxyprogesterone (17‐OHP), for possible use in screening for congenital adrenal hyperplasia (CAH). The factors influencing the MAb production were screened and optimized in a 2 L stirred bioreactor. The production was then scaled up to a 20 L bioreactor. All of the screened factors (aeration rate, stirring speed, dissolved oxygen concentration, pH, and temperature) were found to significantly affect production. Optimization using the response surface methodology identified the following optimal production conditions: 36.8°C, pH 7.4, stirring speed of 100 rpm, 30% dissolved oxygen concentration, and an aeration rate of 0.09 vvm. Under these conditions, the maximum viable cell density achieved was 1.34 ± 0.21 × 10⁶ cells mL^?1 and the specific growth rate was 0.036 ± 0.004 h^?1. The maximum MAb titer was 11.94 ± 4.81 μg mL^?1 with an average specific MAb production rate of 0.273 ± 0.135 pg cell^?1 h^?1. A constant impeller tip speed criterion was used for the scale‐up. The specific growth rate (0.040 h^?1) and the maximum viable cell density (1.89 × 10⁶ cells mL^?1) at the larger scale were better than the values achieved at the small scale, but the MAb titer in the 20 L bioreactor was 18% lower than in the smaller bioreactor. A change in the culture environment from the static conditions of a T‐flask to the stirred bioreactor culture did not affect the specificity of the MAb toward its antigen (17‐OHP) and did not compromise the structural integrity of the MAb. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2013     

Mimic of a large‐scale diafiltration process by using ultra scale‐down rotating disc filter

Ultra scale‐down (USD) approach is a powerful tool to predict large‐scale process performance by using very small amounts of material. In this article, we present a method to mimic flux and transmission performance in a labscale crossflow operation by an USD rotating disc filter (RDF). The Pellicon 2 labscale system used for evaluation of the mimic can readily be related to small pilot and industrial scale. Adopted from the pulsed sample injection technique by Ghosh and Cui (J Membr Sci. 2000;175:5‐84), the RDF has been modified by building in inserts to allow the flexibility of the chamber volume, so that only 1.5 mL of processing material is required for each diafiltration experiment. The reported method enjoys the simplicity of dead‐end mode operation with accurate control of operation conditions that can mimic well the crossflow operation in large scale. Wall shear rate correlations have been established for both the labscale cassette and the USD device, and a mimic has been developed by operating both scales under conditions with equivalent averaged shear rates. The studies using E. coli lysate show that the flux vs. transmembrane pressure profile follows a first‐order model, and the transmission of antibody fragment (Fab′) is independent of transmembrane pressure. Predicted flux and transmission data agreed well with the experimental results of a labscale diafiltration where the cassette resistance was considered. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Non‐lethal foraging by bell miners on a herbivorous insect: Potential implications for forest health

Tree health is often negatively linked with the localized abundance of parasitic invertebrates. One group, the sap‐sucking psyllid insects (Homoptera: Psyllidae) are well known for their negative impact upon vegetation, an impact that often culminates in the defoliation and even death of hosts. In Australia, psyllid‐infested forest in poor health is also frequently occupied by a native honeyeater, the bell miner (Manorina melanophrys; Meliphagidae), so much so that the phenomenon has been dubbed ‘bell miner‐associated dieback’ (BMAD). Bell miners are thought to be the causative agent behind BMAD, in part because the species may selectively forage only upon the outer covering (lerp) exuded by psyllid nymphs, leaving the insect underneath to continue parasitizing hosts. As bell miners also aggressively exclude all other avian psyllid predators from occupied areas, these behavioural traits may favour increases in psyllid populations. We examined bell miner foraging behaviour to determine if non‐lethal foraging upon psyllid nymphs occurred more often than in a congener, the noisy miner (M. melanocephala; Meliphagidae). This was indeed the case, with bell miners significantly more likely to remove only the lerp covering during feeding, leaving the insect intact underneath. This arose from bell miners using their tongue to pry off the lerp cases, whereas noisy miners used their mandibles to snap at both the lerp and insect underneath. Furthermore, psyllids left behind following a bell miner foraging event were significantly more likely to be viable and regrow a lerp covering than those exposed by noisy miners. Together, this behaviour supports the theory that non‐lethal foraging behaviour of bell miners may contribute to high psyllid abundance, consistent with the mechanisms by which BMAD is thought to develop.