The normalised difference vegetation index obtained from agrometeorological standard radiation sensors: a comparison with ground-based multiband spectroradiometer measurements during the phenological development of an oat canopy

Following the methodology of K. F. Huemmrich and colleagues [Huemmrich et al. (1999) J Geophys Res 104:27,935–27,944], agrometeorological standard radiation sensors, i.e. two photosynthetically active radiation sensors and an albedometer, were used to measure the broadband visible and optical–infrared reflectance of an oat plot during its whole growth period. From these reflectance data – recorded as 15-min averages and pooled to daily means – the seasonal cycle of the normalised difference vegetation index (NDVI) was calculated. In addition, a ground-based multi-channel spectroradiometer was used as a reference to estimate narrowband “green” and “red” NDVIs at weekly intervals near noon. The narrowband “green” NDVI was shown to be consistent with the simultaneous broadband 15-min NDVI. This shows that the configuration of agrometeorological radiation sensors is suitable to adequately track phenological crop dynamics.

Individual variability of behavioural responses by Wandering Albatrosses (Diomedea exulans) to human disturbance

Sub-Antarctic Marion Island has had a permanent research station for 50 years and the islands Wandering Albatrosses have been intensively studied for 20 years. The reactions of breeding birds to approaches by a human on foot were recorded. Three response variables were calculated: intensity of vocal reaction (IVR), intensity of non-vocal reaction (INR) and overall response index (ORI). At 5 m from the nest, twice as many birds stood and/or vocalised as at 15 m. Nearest neighbour distance, age and gender did not explain individual variability of responses. Study colony birds had higher IVR scores than non-study colony birds; birds at colonies closest to the station had the highest ORI scores. A better breeding record was associated with lower IVR and ORI scores, but a causative relationship remains to be demonstrated. A minimum viewing distance of 25 m is recommended for breeding Wandering Albatrosses.

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Leitlinien zur molekulargenetischen Diagnostik: Fragiles-X und Fragiles-X assoziiertes Tremor/Ataxie Syndrom

Ohne Zusammenfassung

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Changes in Pyrenean woodlands as a result of the intensity of human exploitation: 2,000 years of metallurgy in Vallferrera, northeast Iberian Peninsula

This research is based on the discovery of a large number of charcoal kiln sites and abandoned iron mines in Vallferrera (Axial Pyrenees, northeastern Spain). The study reveals that this region has been affected by the metal mining and smelting industry for at least 2,000 years, with maximum intensity in the eighteenth and nineteenth centuries, followed by abandonment of the activity. The region’s woodland dendrochronology and historical records indicate that exploitation of wood charcoal for metalworking affected the past vegetation in the area and impeded the development of mature woodland. Our findings suggest that the greatest changes in vegetation and landscape history occurred at times of particular specialization in socioeconomic activities.

Adaptationism and the adaptive landscape

Debates over adaptationism can be clarified and partially resolved by careful consideration of the ‘grain’ at which evolutionary processes are described. The framework of ‘adaptive landscapes’ can be used to illustrate and facilitate this investigation. We argue that natural selection may have special status at an intermediate grain of analysis of evolutionary processes. The cases of sickle-cell disease and genomic imprinting are used as case studies.

Metabolic activity interferometer: description and calibration of an interferometric method to measure growth of mycobacteria

An interferometer that measures the refractive index changes due to bacterial metabolism is described. The apparatus permits simultaneous and real time measurement of bacterial growth in several samples of slowly growing mycobacteria. The error sources are discussed and the sensitivity of the apparatus is tested. For the species Mycobacterium bovis BCG and M. smegmatis, a relation between refractive index change and bacterial concentration is determined experimentally and the time constant of bacterial growth is measured.

Is it a revolution?

Jablonka and Lamb's claim that evolutionary biology is undergoing a ‘revolution’ is queried. But the very concept of revolutionary change has uncertain application to a field organized in the manner of contemporary biology. The explanatory primacy of sequence properties is also discussed.

Hennigian Phylogenetic Systematics and the ‘Groundplan’ vs. ‘Post-Groundplan’ Approaches: A Reply to Kukalová-Peck

The recent contribution by Jarmila Kukalová-Peck on Hennigian phylogenetics and hexapod limb evolution is critically evaluated.

Prospects for the eradication of rats from a large inhabited island: community based ecosystem studies on Great Barrier Island, New Zealand

Great Barrier Island (c. 27,400 ha) is the largest off-shore Island in New Zealand. Some of the most serious introduced mammalian pests of New Zealand are absent, but feral cats and rodents are present. Community based trusts are spear-heading ecological studies to support conservation and a pest eradication programme. Rodent numbers are greatest in late summer/autumn and lowest in winter/early spring. Maximum abundances were recorded in riparian and coastal vegetation, and in mature forest. Monitoring shows that trapping alone is not able to reduce rat numbers sufficiently for safety in avian re-introductions. A combination of trapping and strategically pulsed toxin baits, however, achieved low levels of rats. Ecosystem recovery is demonstrated by increases in key tree seedlings, large invertebrates and lizards in managed compared to unmanaged areas, and by the survivorship of translocated robins (Petroica longipes). The Great Barrier Island Charitable Trust is communicating these benefits, and associated risks, to the Island community, with a view to promoting pest eradication as a key component in an ecology-based economy, centred on eco-tourism.

Laying the foundations for a bio-economy

Biological technologies are becoming an important part of the economy. Biotechnology already contributes at least 1% of US GDP, with revenues growing as much as 20% annually. The introduction of composable biological parts will enable an engineering discipline similar to the ones that resulted in modern aviation and information technology. As the sophistication of biological engineering increases, it will provide new goods and services at lower costs and higher efficiencies. Broad access to foundational engineering technologies is seen by some as a threat to physical and economic security. However, regulation of access will serve to suppress the innovation required to produce new vaccines and other countermeasures as well as limiting general economic growth.

Intelligent design and mathematical statistics: a troubled alliance

The explanatory filter is a proposed method to detect design in nature with the aim of refuting Darwinian evolution. The explanatory filter borrows its logical structure from the theory of statistical hypothesis testing but we argue that, when viewed within this context, the filter runs into serious trouble in any interesting biological application. Although the explanatory filter has been extensively criticized from many angles, we present the first rigorous criticism based on the theory of mathematical statistics.

Corpus Interruptus: Biotech Drugs, Insurance Providers and the Treatment of Breast Cancer

In researching the biomedically-engineered drug Neulasta (filgrastim), a breast cancer patient becomes aware of the extent to which knowledge about the development and marketing of drugs influences her decisions with regard to treatment. Time spent on understanding the commercial interests of insurers and pharmaceutical companies initially thwarts but ultimately aids the healing process. This first-person narrative calls for physicians to recognize that the alignment of commercial interests transgresses the patient’s humanity.

Rattus exulans and the catastrophic disappearance of Hawai’i’s native lowland forest

Paleoenvironmental and archaeological investigations from the ’Ewa Plain of O’ahu provide insight into the problem of understanding lowland native forest loss in Hawai’i. Data from pollen analysis of a pond core record, avian paleontology, and archeology, document a precipitous decline of the native forest starting before Polynesian settlement on the ’Ewa Plain but after Polynesian colonization of O’ahu. It is hypothesized that rats, introduced by Polynesian colonizers, increased exponentially in the absence of significant predators or competitors, feeding on a largely endemic vegetation that had evolved in the absence of mammalian predators. Rats radiated ahead of human colonizers on O’ahu, eating their way through the vegetation, perhaps before the colonizers had encountered much of the pristine lowland forest into which the rats had radiated. This hypothesis is supported by several observations, including the almost complete absence of extinct or extirpated avian faunal remains in archaeological deposits, the present distribution of endemic vegetation in Hawai’i, rat ecology, population biology, and other evidence.

The connectionist framework for gene regulation

I show that gene regulation networks are qualitatively consistent and therefore sufficiently similar to linearly seperable connectionist networks to warrant that the connectionist framework be applied to gene regulation. On this view, natural selection designs gene regulation networks to overcome the difficulty of development. I offer some general lessons about their evolvability that can be learned by examining the generic features of connectionist networks.

The return of reciprocity: a psychological approach to the evolution of cooperation

Recent developments in evolutionary game theory argue the superiority of punishment over reciprocity as accounts of large-scale human cooperation. I introduce a distinction between a behavioral and a psychological perspective on reciprocity and punishment to question this view. I examine a narrow and a wide version of a psychological mechanism for reciprocity and conclude that a narrow version is clearly distinguishable from punishment, but inadequate for humans; whereas a wide version is applicable to humans but indistinguishable from punishment. The mechanism for reciprocity in humans emerges as a meta-norm that governs both retaliation and punishment. I make predictions open to empirical investigation to confirm or disconfirm this view.

Olfactory system gamma oscillations: the physiological dissection of a cognitive neural system

Oscillatory phenomena have been a focus of dynamical systems research since the time of the classical studies on the pendulum by Galileo. Fast cortical oscillations also have a long and storied history in neurophysiology, and olfactory oscillations have led the way with a depth of explanation not present in the literature of most other cortical systems. From the earliest studies of odor-evoked oscillations by Adrian, many reports have focused on mechanisms and functional associations of these oscillations, in particular for the so-called gamma oscillations. As a result, much information is now available regarding the biophysical mechanisms that underlie the oscillations in the mammalian olfactory system. Recent studies have expanded on these and addressed functionality directly in mammals and in the analogous insect system. Sub-bands within the rodent gamma oscillatory band associated with specific behavioral and cognitive states have also been identified. All this makes oscillatory neuronal networks a unique interdisciplinary platform from which to study neurocognitive and dynamical phenomena in intact, freely behaving animals. We present here a summary of what has been learned about the functional role and mechanisms of gamma oscillations in the olfactory system as a guide for similar studies in other cortical systems.

One oxidant,many pathways: a theoretical perspective of monooxygenation mechanisms by cytochrome P450 enzymes

Density functional theoretical studies of monooxygenation reactivity of the high-valent oxoiron(IV) porphyrin cation-radical compound of cytochrome P450, the so-called Compound I, and of its precursor, the ferric(III)-hydroperoxide species, are described. The degeneracy of the spin states of Compound I, its electron deficiency, and dense orbital manifold lead to two-state and multi-state reactivity scenarios and may thereby create reactivity patterns as though belonging to two or more different oxidants. Most of the controversies in the experimental data are reconciled using Compound I as the sole competent oxidant. Theory finds ferric(III)-hydroperoxide to be a very sluggish oxidant, noncompetitive with Compound I. If and when Compound I is absent, P450 oxidation will logically proceed by another form, but this has to be more reactive than ferric(III)-hydroperoxide. Theoretical studies are conducted to pinpoint such an oxidant for P450.

Biosemiotic Questions

This paper examines the biosemiotic approach to the study of life processes by fashioning a series of questions that any worthwhile semiotic study of life should ask. These questions can be understood simultaneously as: (1) questions that distinguish a semiotic biology from a non-semiotic (i.e., reductionist–physicalist) one; (2) questions that any student in biosemiotics should ask when doing a case study; and (3) still currently unanswered questions of biosemiotics. In addition, some examples of previously undertaken biosemiotic case studies are examined so as to suggest a broad picture of how such a biosemiotic approach to biology might be done.

A finite volume method for stochastic integrate-and-fire models

The stochastic integrate and fire neuron is one of the most commonly used stochastic models in neuroscience. Although some cases are analytically tractable, a full analysis typically calls for numerical simulations. We present a fast and accurate finite volume method to approximate the solution of the associated Fokker-Planck equation. The discretization of the boundary conditions offers a particular challenge, as standard operator splitting approaches cannot be applied without modification. We demonstrate the method using stationary and time dependent inputs, and compare them with Monte Carlo simulations. Such simulations are relatively easy to implement, but can suffer from convergence difficulties and long run times. In comparison, our method offers improved accuracy, and decreases computation times by several orders of magnitude. The method can easily be extended to two and three dimensional Fokker-Planck equations.