Gene gain and gene loss in streptococcus: is it driven by habitat?

Bacterial genomes can evolve either by gene gain, gene loss, mutating existing genes, and/or by duplication of existing genes. Recent studies have clearly demonstrated that the acquisition of new genes by lateral gene transfer (LGT) is a predominant force in bacterial evolution. To better understand the significance of LGT, we employed a comparative genomics approach to model species-specific and intraspecies gene insertions/deletions (ins/del among 12 sequenced streptococcal genomes using a maximum likelihood method. This study indicates that the rate of gene ins/del is higher on the external branches and varies dramatically for each species. We have analyzed here some of the experimentally characterized species-specific genes that have been acquired by LGT and conclude that at least a portion of these genes have a role in adaptation.     

How is the balance between protein synthesis and degradation achieved?

Unlike most substances that cells manufacture, proteins are not produced and broken down by a common series of chemical reactions, but by completely different (independent and disconnected) mechanisms that possess no intrinsic means of making the rates of the two processes equal and attaining steady state concentrations. Balance between them is achieved extrinsically and is often imagined today to be the result of the actions of chemical feedback agents. But however instantiated, chemical feedback or any similar mechanism can only rectify induced imbalances in a system previously balanced by other means. Those "other means" necessarily involve reversible mass action or equilibrium-based interactions between native and altered forms of protein molecules somewhere in time and space between their synthesis and degradation.     

Avian thyroid development in chemically contaminated environments: is there evidence of alterations in thyroid function and development?

Poor reproductive success, developmental abnormalities, and behavioral alterations in fish-eating birds in some Great Lakes areas have led to more than 35 years of toxicological studies and residue monitoring of herring gull (Larus argentatus) populations. Polyhalogenated aromatic hydrocarbons (PHAHs), especially polychlorinated biphenyls (PCBs), are widespread contaminants in the Great Lakes ecosystem. The introduction of regulations and elimination of point sources since the 1970s have resulted in decreased PHAHs in fish-eating bird eggs and tissues. PCB exposure is associated with thyroid disruption (hypothyroidism) in mammals, but much less is known of PCB effects on avian thyroid function. Our 1998-2000 studies of herring gulls from the Great Lakes show that both pipping embryos and prefledglings from highly contaminated sites have marked depletion of thyroid gland hormone stores compared with similarly aged gulls at the reference sites. However, organismal hypothyroidism was not apparent in many embryo and chick collections where severe depletion of thyroid gland hormone was observed. Adults, sampled at two high PCB sites and a low PCB site in the Great Lakes and the maritime reference colony in 2001, showed no differences in organismal thyroid status across sites, but gulls from the high sites had enlarged thyroid glands and depressed thyroid gland hormone stores. Here we discuss the evidence that ecological exposure to PHAHs are responsible for thyroid deficiencies in gulls and that during development these deficiencies lead to developmental abnormalities in young gulls from highly contaminated Great Lakes sites.     

Social rank,feeding and winter weight loss in red deer: any evidence of interference competition?

During winter at northern latitudes, large herbivores often exploit patches of concentrated, relatively high quality forage, which may lead to interference competition. The factors affecting success in contests and subsequent dominance rank, such as age and body weight, remain key issues in ungulate behavioural ecology. Maternal effects on offspring body weight are well known, but few studies have investigated if mothers social rank influence offspring rank. Moreover, no study has related dominance rank in ungulates to weight loss during winter. Outcomes of social interactions (n=7,609), feeding time and spatial position in red deer (Cervus elaphus) hinds and calves, and weight loss of calves, were registered from 1981 to 1996 at six winter-feeding sites within the county of Sør-Trøndelag in Norway. The level of aggressiveness was higher among calves than among adult hinds, and the factors determining the outcome of contests also differed. The initiator won the majority of interactions (more than 90% in both hinds and calves). Social rank was related to both age and body weight in adult hinds, and related to body weight and mother rank in calves. The relationship between feeding time and rank was non-linear. Feeding time was correlated with rank only among high ranked hinds, while there was no such relationship among low ranked hinds or calves. There was no correlation between winter weight loss and social rank in calves. Our study therefore underlines that, although frequent aggression is observed at artificial feeding sites of northern herbivores, this is not necessarily sufficient to give rise to interference competition.     

Insect herbivory and ontogeny: How do growth and development influence feeding behaviour,morphology and host use?

Herbivorous insects exploit many different plants and plant parts and often adopt different feeding strategies throughout their life cycle. The conceptual framework for investigating insect–plant interactions relies heavily on explanations invoking plant chemistry, neglecting a suite of competing and interacting pressures that may also limit herbivory. In the present paper, the methods by which ontogeny, feeding strategies and morphological characters inhibit herbivory by mandibulate holometabolous insects are examined. The emphasis on mechanical disruption of plant cells in the insect digestive strategy changes the relative importance of plant ‘defences’, increasing the importance of leaf structure in inhibiting herbivory. Coupled with the implications of substantial morphological and behavioural changes in ontogeny, herbivores adopt a range of approaches to herbivory that are independent of plant chemistry alone. Many insect herbivores exhibit substantial ontogenetic character displacement in mandibular morphology. This is tightly correlated with changes in feeding strategy, with changes to the cutting edges of mandibles increasing the efficiency of feeding. The changes in feeding strategy are also characterized by changes in feeding behaviour, with many larvae feeding gregariously in early instars. Non‐nutritive hypotheses considering the importance of natural enemies, shelter‐building and thermoregulation may also be invoked to explain the ontogenetic consequences of changes to feeding behaviour. There is a need to integrate these factors into a framework considering the gamut of potential explanations of insect herbivory, recognizing that ontogenetic constraints are not only viable explanations but a logical starting point. The interrelations between ontogeny, size, morphology and behaviour highlight the complexity of insect–plant relationships. Given the many methods used by insect herbivores to overcome the challenges of consuming foliage, the need for species‐specific and stage‐ specific research investigating ontogeny and host use by insect herbivores is critical for developing general theories of insect–plant interactions.     

How useful is PCR in the diagnosis of malaria?

Polymerase chain reaction (PCR) assays are the most sensitive and specific method to detect malaria parasites, and have acknowledged value in research settings. However, the time lag between sample collection, transportation and processing, and dissemination of results back to the physician limits the usefulness of PCR in routine clinical practice. Furthermore, in most areas with malaria transmission, factors such as limited financial resources, persistent subclinical parasitaemia, inadequate laboratory infrastructures in the poorer, remote rural areas preclude PCR as a diagnostic method. Even in affluent, non-endemic countries, PCR is not a suitable method for routine use. Nonetheless, PCR could be clinically useful in selected situations.     

How dim is dim? Precision of the celestial compass in moonlight and sunlight

Prominent in the sky, but not visible to humans, is a pattern of polarized skylight formed around both the Sun and the Moon. Dung beetles are, at present, the only animal group known to use the much dimmer polarization pattern formed around the Moon as a compass cue for maintaining travel direction. However, the Moon is not visible every night and the intensity of the celestial polarization pattern gradually declines as the Moon wanes. Therefore, for nocturnal orientation on all moonlit nights, the absolute sensitivity of the dung beetle's polarization detector may limit the precision of this behaviour. To test this, we studied the straight-line foraging behaviour of the nocturnal ball-rolling dung beetle Scarabaeus satyrus to establish when the Moon is too dim--and the polarization pattern too weak--to provide a reliable cue for orientation. Our results show that celestial orientation is as accurate during crescent Moon as it is during full Moon. Moreover, this orientation accuracy is equal to that measured for diurnal species that orient under the 100 million times brighter polarization pattern formed around the Sun. This indicates that, in nocturnal species, the sensitivity of the optical polarization compass can be greatly increased without any loss of precision.     

How does pattern of feeding and rate of nutrient delivery influence conditioned food preferences?

Ruminant herbivores have been shown to learn about food properties by associating food flavours with the food’s post-ingestive consequences. Previous experimentation supporting the conditioned food aversion/preference hypothesis has generally employed very simple diet learning tasks which do not effectively represent the wide range of foods selected within single bouts typical of wild, free-ranging ruminant herbivores. We tested the ability of a ruminant herbivore to associate a food with artificially administered nutrient rewards in a designed experiment where we altered the temporal pattern of encounter with the food as well as the nature (fast or slow reward) of the post-ingestive outcome. Twenty-four goats were offered branches of Sitka spruce (SS) and Norway spruce (NS) for 4 h per day on two days per week for five weeks. The pattern of feeding varied with treatment such that the species on offer changed every hour (short) or every 2 h (long). The energy treatment altered the reward delivered during Sitka consumption so that animals were dosed either with predominantly sugar (rapidly fermented), predominantly starch (slower fermentation rate), or with water (placebo). Preference was measured on the day following each learning day. We expected that goats would find it easier to associate SS with post-ingestive rewards when the duration of encounter was longest, and that associations would be stronger with the most rapidly digested post-ingestive reward. In the event, goats did not alter their consumption of SS in response to the treatments. Our results suggest that at the scale of temporal resolution of encounters with different plant species (1–2 h), and at the different rates of experiencing post-ingestive consequences tested in this experiment, ruminants do not appear to discriminate the nutritive properties of foods predominantly through a post-ingestive feedback mechanism. They must, instead, use a range of cues—including post-ingestive consequences—to assess food properties. An erratum to this article can be found at     

A loss of heterozygosity,a loss in competition? The effects of inbreeding,pre‐ and postnatal conditions on nestling development

The early developmental trajectory is affected by genetic and environmental factors that co‐depend and interact often in a complex way. In order to distinguish their respective roles, we used canaries (Serinus canaria) of different genetic backgrounds (inbred and outbred birds). An artificial size hierarchy was created to provoke within‐nest competition, manipulating postnatal conditions. To this end, inbred birds were weight‐matched with outbred birds into duos, and each nest contained one duo of size‐advantaged, and one duo of size‐disadvantaged inbred and outbred nestlings. Prenatal (maternal) effects were taken into account also, enabling us to study the separate as well as the interactive effects of inbreeding, pre‐ and postnatal conditions on nestling development. We find that postnatal conditions were the most important determinant of early growth, with size‐advantaged nestlings growing faster and obtaining larger size/body mass at fledging in comparison with size‐disadvantaged nestlings. Prenatal conditions were important too, with birds that hatched from eggs that were laid late in the laying order obtaining a larger size at fledging than those hatched from early laid eggs. Inbreeding inhibited growth, but surprisingly this did not depend on (dis)advantageous pre‐ or postnatal conditions. Our findings imply that inbred individuals lose when they are in direct competition with same‐sized outbred individuals regardless of the rearing conditions, and we thus propose that reduced competitiveness is one of the driving forces of inbreeding depression.     

How strong is the mutagenicity of recombination in mammals?

It is commonly believed that a high recombination rate such as that in a pseudoautosomal region (PAR) greatly increases the mutation rate because a 170-fold increase was estimated for the mouse PAR region. However, sequencing PAR and non-PAR introns of the Fxy gene in four Mus taxa, we found an increase of only twofold to fivefold. Furthermore, analyses of sequence data from human and orangutan PAR and X-linked regions and from autosomal regions showed a weak effect of recombination on mutation rate (a slope of less than 0.2% per cM/Mb), although a much stronger effect on GC content (1% to 2% per cM/Mb). Because typical recombination rates in mammals are much lower than those in PARs, the mutagenicity of recombination is weak or, at best, moderate, although its effect on GC% is much stronger. In addition, contrary to a previous study, we found no Fxy duplicate in Mus spretus.     

What is the role of cell division in leaf development?

An idea underlying a great deal of research and discussion in plant cell and developmental biology is that the spatial regulation of cell division plays a key role in plant development. In this article, the role of cell division in two aspects of leaf development is analysed: morphogenesis (leaf initiation, growth, and the generation of leaf shape) and histogenesis (the differentiation of leaf cells to form the various cell types that make up a functional leaf). The point of view that emerges from this analysis is that the rate and pattern of cell division is important for leaf development, but does not dictate leaf size, shape, or cell fate.     

Can we detect the development of baroreflex sensitivity in humans between 11 and 20 years of age?

The aim of the study was to determine changes of baroreflex sensitivity in humans between 11 and 20 years of age. Continuous 5 min blood pressure recordings using a Finapres were taken in 415 healthy subjects while in a sitting, resting position (breathing at a frequency of 0.33 Hz). Beat-by-beat values of interbeat intervals (IBI) or heart rate, and systolic and diastolic blood pressures were measured. Baroreflex sensitivity in ms/mmHg (BRS) and in mHz/mmHg (BRSf) was determined at an average frequency of 0.1 Hz by spectral analysis. BRS did not correlate with age, but BRSf significantly decreased with age (p < 0.001). BRS correlated with mean IBI (p < 0.001) in all subjects and also in the particular subgroups, but BRSf was IBI-independent. Results of multiregression equations were BRS = 1.37 - 0.56 x age (years) + 0.02 x IBI (ms) (p < 0.001 for BRS vs. age and for BRS vs. IBI); BRSf = 34.74 - 0.97 x age (years) - 0.001 x IBI (ms) (p < 0.001 only for BRS vs. age), where age was measured in years and IBI was measured in ms. The limits of BRS were estimated for the total group: 5th percentile, 3.9; 50th percentile, 9.1; and 95th percentile, 18.7 ms/mmHg; and limits for BRSf were 5th percentile, 8.5; 50th percentile, 16.4; and 95th percentile, 33.6 mHz/mmHg. We conclude that IBI-dependent BRS was unchanged in the particular age groups, but the standardization of BRS on IBI decreased with age. BRSf was IBI-independent and better reflected the development of the BRS.     

How useful is DNA extracted from the legs of archived insects for microsatellite-based population genetic analyses?

DNA obtained from museum specimens provides a historical perspective on levels of genetic diversity. Archived samples are irreplaceable so it is desirable that only parts of the specimens are used, which constrains the amount of DNA obtained from small taxa. However, at present there are no quantitative data on yields of DNA from such samples. In this paper we determine the amount of DNA that may be extracted from the legs of museum-archived specimens of the damselfly Coenagrion mercuriale (Charpentier) and the suitability of this DNA for PCR-amplification of nuclear genetic loci (microsatellites). We find that (i) the yield of DNA correlates with the genotyping success rate and (ii) the amount of DNA obtained from the legs decreases with time since sample collection until 1954, before which no DNA could be detected (although DNA may be present in very low quantities). This cut-off point for successful DNA extraction corresponds with the date until reliable genotypes could be obtained by routine PCR. Thus, air-dried insect legs more than 50 years old appear to have limited usefulness for studies that seek to amplify many nuclear loci without the use of other techniques that may be used to increase the possible low-quantities of template DNA present.     

Glycosylation of the sodium channel β4 subunit is developmentally regulated and involves in neuritic degeneration

Aberrant protein glycosylation plays major roles in neurodegenerative diseases, including Parkinson's disease (PD). Glycoproteomics showed that the glycosylation of sodium channel β4 was significantly increased in human brain tissue. β4-specific antibodies reacted in immunoblot assays with the 35- and 38-kDa bands from the membrane fractions isolated from neonatal PD transgenic mice but only with the 35-kDa band of the neonatal wild-type mice. The size of the 38-kDa immunoreactive protein is in close agreement with previously reported, suggesting heavy glycosylation of this protein in adult wild-type and neonatal PD transgenic brain tissues. However, the neonatal wild-type mice membrane fractions only contained the 35-kDa immunoreactive protein, and the additional 38-kDa band was not shown until postnatal day 7. Enzymatic deglycosylation of the membrane preparations only converted the 38-kDa band into a faster migrating protein, which was consistent with heavy glycosylation of this protein. The glycosylated state of β4 was developmentally regulated and was altered in disease state. Neurite outgrowth assay demonstrated that overexpression of deglycosylated mutant β4-MUT accelerated neurite extension and increased the number of filopodia-like protrusions, when compared with β4-WT and the vector. These results suggest that extensive glycosylation of β4 subunit play roles in morphological changes, and the altered glycosylation may be involved in the pathogenesis of PD.