Quasispecies and recombination

Recombination is introduced into Eigen's theory of quasispecies evolution. Comparing numerical simulations of the rate equations in the non-recombining and recombining cases show that recombination has a strong effect on the error threshold and, for a wide range of mutation rates, gives rise to two stable fixed points in the dynamics. This bi-stability results in the existence of two error thresholds. However, we prove that, for low mutation rates the bi-stability breaks down and the unique equilibrium distribution is concentrated around the sequence with highest fitness.     

Competitive exclusion and limiting similarity: a unified theory

Robustness of coexistence against changes of parameters is investigated in a model-independent manner by analyzing the feedback loop of population regulation. We define coexistence as a fixed point of the community dynamics with no population having zero size. It is demonstrated that the parameter range allowing coexistence shrinks and disappears when the Jacobian of the dynamics decreases to zero. A general notion of regulating factors/variables is introduced. For each population, its impact and sensitivity niches are defined as the differential impact on, and the differential sensitivity towards, the regulating variables, respectively. Either the similarity of the impact niches or the similarity of the sensitivity niches results in a small Jacobian and in a reduced likelihood of coexistence. For the case of a resource continuum, this result reduces to the usual "limited niche overlap" picture for both kinds of niche. As an extension of these ideas to the coexistence of infinitely many species, we demonstrate that Roughgarden's example for coexistence of a continuum of populations is structurally unstable.     

Rapid PCR amplification of DNA utilizing Coriolis effects

A novel polymerase chain reaction (PCR) method is presented that utilizes Coriolis and centrifugal effects, produced by rotation of the sample disc, in order to increase internal circulatory rates, and with them temperature homogenization and mixing speeds. A proof of concept has been presented by testing a rapid 45-cycle PCR DNA amplification protocol. During the repeated heating and cooling that constitutes a PCR process, the 100 μL samples were rotated at a speed equivalent to an effective acceleration of gravity of 7,000 g. A cycle time of 20.5 s gave a total process time of 15 min to complete the 45 cycles. A theoretical and numerical analysis of the resulting flow, which describes the increased mixing and temperature homogenization, is presented. The device gives excellent reaction speed efficiency, which is beneficial for rapid PCR.     

A genetic component of resistance to fungal infection in frog embryos

The embryo has traditionally been considered to completely rely upon parental strategies to prevent threats to survival posed by predators and pathogens, such as fungi. However, recent evidence suggests that embryos may have hitherto neglected abilities to counter pathogens. Using artificial fertilization, we show that among-family variation in the number of Saprolegnia-infected eggs and embryos in the moor frog, Rana arvalis, cannot be explained by maternal effects. However, analysed as a within-females effect, sire identity had an effect on the degree of infection. Furthermore, relatively more eggs and embryos were infected when eggs were fertilized by sperm from the same, compared with a different, population. These effects were independent of variation in fertilization success. Thus, there is likely to be a significant genetic component in embryonic resistance to fungal infection in frog embryos. Early developmental stages may show more diverse defences against pathogens than has previously been acknowledged.     

S-Sulfo-Cysteine is an Endogenous Amino Acid in Neonatal Rat Brain but an Unlikely Mediator of Cysteine Neurotoxicity

S-sulfo-cysteine (SSC) is an agonist of glutamate receptors which could be involved in cysteine-induced neurotoxicity. Here we analyzed SSC by HPLC and demonstrated that the concentration of SSC in cortex of cysteine-injected rats increased to 1.4 μM, about four times the value of control rats. The neurotoxic effect of SSC was evaluated in slice cultures of rat hippocampus and compared to NMDA and cysteine. The neurotoxicity threshold of SSC was well above the tissue concentration. Our results show that SSC increases in neonatal rat brain after cysteine injection but reaches a tissue concentration far below concentrations that induce neurotoxicity in vitro. Thus, even if all the tissue SSC after cysteine injection was extracellular it would be below the threshold for toxicity, indicating that SSC is not a main excitotoxin involved in cysteine toxicity. Special issue article in honor of Dr. Frode Fonnum. Part of this work has been submitted as an abstract and presented as a poster to the 7th Biennial Meeting of the Asian Pacific Society for Neurochemistry (APSN) 2–5 July 2006.     

Ablation of collagen IX and COMP disrupts epiphyseal cartilage architecture.

Chondrodysplasias are a genetically heterogeneous group of skeletal disorders. Mutations in genes coding for cartilage oligomeric matrix protein (COMP), collagen IX and matrilin-3 have been described to cause the autosomal dominantly inherited form of multiple epiphyseal dysplasia (MED). Even though there is clear evidence that these cartilage matrix proteins interact with each other, their exact functions in matrix organisation and bone development still need to be elucidated. We generated a mouse model lacking both collagen IX and COMP to study the potential complementary role of these proteins in skeletal development. Mice deficient in both proteins exhibit shortened and widened long bones as well as an altered bone structure. They display severe growth plate abnormalities with large hypocellular areas in the central parts of the tibia. In addition, chondrocytes in the proliferative and hypertrophic zones do not show their typical columnar arrangement. These phenotypical traits were not observed in mice deficient only in COMP, while mice lacking only collagen IX showed similar growth plate disturbances and shorter and wider tibiae. The contribution of COMP to the phenotype of mice deficient in both collagen IX and COMP appears minor, even though clear differences in the deposition of matrilin-3 were detected.     

Histidine-rich glycoprotein protects from systemic Candida infection

Fungi, such as Candida spp., are commonly found on the skin and at mucosal surfaces. Yet, they rarely cause invasive infections in immunocompetent individuals, an observation reflecting the ability of our innate immune system to control potentially invasive microbes found at biological boundaries. Antimicrobial proteins and peptides are becoming increasingly recognized as important effectors of innate immunity. This is illustrated further by the present investigation, demonstrating a novel antifungal role of histidine-rich glycoprotein (HRG), an abundant and multimodular plasma protein. HRG bound to Candida cells, and induced breaks in the cell walls of the organisms. Correspondingly, HRG preferentially lysed ergosterol-containing liposomes but not cholesterol-containing ones, indicating a specificity for fungal versus other types of eukaryotic membranes. Both antifungal and membrane-rupturing activities of HRG were enhanced at low pH, and mapped to the histidine-rich region of the protein. Ex vivo, HRG-containing plasma as well as fibrin clots exerted antifungal effects. In vivo, Hrg(-/-) mice were susceptible to infection by C. albicans, in contrast to wild-type mice, which were highly resistant to infection. The results demonstrate a key and previously unknown antifungal role of HRG in innate immunity.     

A major QTL and an SSR marker associated with glycoalkaloid content in potato tubers from <Emphasis Type="Italic">Solanum tuberosum </Emphasis>× <Emphasis Type="Italic">S. sparsipilum</Emphasis> located on chromosome I

New potato (Solanum tuberosum) varieties are required to contain low levels of the toxic glycoalkaloids and a potential approach to obtain this is through marker-assisted selection (MAS). Before applying MAS it is necessary to map quantitative trait loci (QTLs) for glycoalkaloid content in potato tubers and identify markers that link tightly to this trait. In this study, tubers of a dihaploid BC(1) population, originating from a cross between 90-HAF-01 (S. tuberosum(1)) and 90-HAG-15 (S. tuberosum(2) x S. sparsipilum), were evaluated for content of alpha-solanine and alpha-chaconine (total glycoalkaloid, TGA) after field trials. In addition, tubers were assayed for TGA content after exposure to light. A detailed analysis of segregation patterns indicated that a major QTL is responsible for the TGA content in tubers of this potato population. One highly significant QTL was mapped to chromosome I of the HAG and the HAF parent. Quantitative trait loci for glycoalkaloid production in foliage of different Solanum species have previously been mapped to this chromosome. In the present research, QTLs for alpha-solanine and alpha-chaconine content were mapped to the same location as for TGA content. Similar results were observed for tubers exposed to light. The simple sequence repeat marker STM5136 was closely linked to the identified QTL.     

Correlation of the rat behavior after immobilization with structural reorganization in the motor cortex

Behavioral changes and accompanying morphological neuron-glia reorganization in the rat brain were compared after emotional stress. Wistar rats (n = 20) were stressed by the interrupted immobilization, which was carried out during one week 7-8 h daily. Behavioral immobilization of rats was accompanied by an increase in horizontal and vertical locomotors activity and in duration of the III and IV phases of grooming ("comfortable" grooming) in the "open field" test. The morphometric studies showed a statistically significant increase in the density of hypoxic neurons in the right neocortex of the experimental animals as compared with control. Hypoxic changes in neurons were of functional character. Experimental rats can be considered as a model of redistribution of functional brain activity with preferential intensification of the left brain hemisphere.