Amplification of KIT, PDGFRA, VEGFR2, and EGFR in gliomas

Receptor tyrosine kinase aberrations are implicated in the genesis of gliomas. We investigated expression and amplification of KIT, PDGFRA, VEGFR2, and EGFR in 87 gliomas consisting of astrocytomas, anaplastic astrocytomas, oligodendrogliomas, or oligoastrocytomas in tumor samples collected at the time of the diagnosis and in samples of the same tumors at tumor recurrence. Gene amplifications were investigated using either chromogenic in situ hybridization or fluorescence in situ hybridization, and protein expression using immunohistochemistry. In samples collected at glioma diagnosis, KIT and PDGFRA amplifications were more frequent in anaplastic astrocytomas than in astrocytomas, oligodendrogliomas, and oligoastrocytomas [28% versus 5% (P = 0.012) and 33% versus 2% (P = 0.0008), respectively]. VEGFR2 amplifications occurred in 6% to 17% of the gliomas at diagnosis, and EGFR amplifications in 0% to 12%. Amplified KIT was more frequently present in recurrent gliomas than in newly diagnosed gliomas (P = 0.0066). KIT amplification was associated with KIT protein expression and with presence of PDGFRA and EGFR amplifications both at the time of the first glioma diagnosis and at tumor recurrence, and with VEGFR2 amplification at tumor recurrence. Three (4%) primary gliomas and 10 (14%) recurrent gliomas that were evaluable for coamplification of KIT, PDGFRA, and VEGFR2 showed amplification of at least two of these genes; the amplicon contained amplified KIT in all 13 cases. In conclusion, besides glioblastoma, amplified KIT, PDGFRA, and VEGFR may also occur in lower-grade gliomas and in their recurrent tumors. It is currently not known whether specific tyrosine kinase inhibitors are effective in the treatment of such gliomas.     

Winter-time ecology in the Bothnian Bay, Baltic Sea: nutrients and algae in fast ice

Landfast ice algal communities were studied in the strongly riverine-influenced northernmost part of the Baltic Sea, the Bothnian Bay, during the winter-spring transition of 2004. The under-ice river plume, detected by its low salinity and elevated nutrient concentrations, was observed only at the station closest to the river mouth. The bottommost ice layer at this station was formed from the plume water (brine volume 0.71%). This was reflected by the low flagellate-dominated (93%) algal biomass in the bottom layer, which was one-fifth of the diatom-dominated (74%) surface-layer biomass of 88 μg C l⁻¹. Our results indicate that habitable space plays a controlling role for ice algae in the Bothnian Bay fast ice. Similarly to the water column in the Bothnian Bay, average dissolved inorganic N:P-ratios in the ice were high, varying between 12 and 265. The integrated chlorophyll a (0.1–2.2 mg m⁻²) and algal biomass in the ice (1–31 mg C m⁻²) correlated significantly (Spearman ρ = 0.79), with the highest values being measured close to the river mouth in March and during the melt season in April. Flagellates <20 μm generally dominated in both the ice and water columns in February–March. In April the main ice-algal biomass was composed of Melosira arctica and unidentified pennate diatoms, while in the water column Achnanthes taeniata, Scrippsiella hangoei and flagellates dominated. The photosynthetic efficiency (0.003–0.013 (μg C [μg chl a ⁻¹] h⁻¹)(μE m⁻²s⁻¹)⁻¹) and maximum capacity (0.18–1.11 μg C [μg chl a ⁻¹] h⁻¹) could not always be linked to the algal composition, but in the case of a clear diatom dominance, pennate species showed to be more dark-adapted than centric diatoms.     

A Battery of Cell- and Structure-specific Markers for the Adult Porcine Retina

The pig is becoming an increasingly used non-primate model in experimental studies of human retinal diseases and disorders. The anatomy, size, and vasculature of the porcine eye and retina closely resemble their human counterparts, which allows for application of standard instrumentation and diagnostics used in the clinic. Despite many reports that demonstrate immunohistochemistry as a useful method for exploring neuropathological changes in the mammalian central nervous system, including the pig, the porcine retina has been sparsely described. Hence, to facilitate further immunohistochemical analysis of the porcine retina, we report on the successful use of a battery of antibodies for staining of paraformaldehyde-fixed cryosectioned retina. The following antibodies were evaluated for neuronal cells and structures: recoverin (cones and rods), Rho4D2 (rods), transducin-γ (cones), ROM-1 (photoreceptor outer segments), calbindin (horizontal cells), PKC-α (bipolar cells), parvalbumin (amacrine and displaced amacrine cells), and NeuN (ganglion cells and displaced amacrines). For detecting synaptic connections in fiber layers, we used an antibody against synaptobrevin. For detecting retinal pigment epithelium, we studied antibodies against cytokeratin and RPE65, respectively. The glial cell markers used were bFGF (Müller cells and displaced amacrine cells), GFAP (Müller cells and astrocytes), and vimentin (Müller cells). Each staining effect was evaluated with regard to its specificity, sensitivity, and reproducibility in the identification of individual cells, specific cell structures, and fiber layers, respectively. The markers parvalbumin and ROM-1 were tested here for the first time for the porcine retina. All antibodies tested resulted in specific staining of high quality. In conclusion, all immunohistochemical protocols presented here will be applicable in fixed, cryosectioned pig retina. (J Histochem Cytochem 58:377–389, 2010)     

The solution structure of the invasive tip complex from Afa/Dr fibrils

Afa/Dr family of adhesins are produced by pathogenic Escherichia coli strains that are especially prevalent in chronic diarrhoeal and recurrent urinary tract infections. Most notably, they are found in up to 50% of cystitis cases in children and 30% of pyelonephritis in pregnant women. Afa/Dr adhesins are capped surface fibrils that mediate recognition of the host and subsequent bacterial internalization. Using the newly solved three-dimensional structure of the minimal invasive complex (AfaDE) combined with biochemical and cellular assays, we reveal the architecture of the fibrillar cap and identify a novel mode of synergistic integrin recognition.     

Observations on thermoregulatory ontogeny of mink (Mustela vison)

(1) We measured cooling rate for neonatal mink during a 10min coldroom (3.9 degrees C) exposure and subsequent warming rate during a 20min incubator (37.2 degrees C) exposure, the behaviour of the kits and the changes in their pelage between 1 and 46d of age, in an attempt to monitor the ontogeny of their thermoregulatory capacity. (2) Body weight of the 1d old kits averaged only 12.8+/-2.3g (n=4), but they gained weight rapidly reaching 226.1+/-28.3g (males, n=4) and 207.6+/-16.1g (females, n=4) at 30-31d of age, and 562.3+/-43.2g (males, n=3) and 435.7+/-35.5g (females, n=4) at 45-46d of age. (3) Body cooling rate (C(rate) ( degrees C/min); n=80) was affected by the age (between 1 and 31d), BW, initial rectal temperature (T(r0)), and sex of the kits, in addition to their body posture (P(cold), 1=extended, 2=curled-up) during coldroom exposure. C(rate) ( degrees C/min)=-0.34-0.02age-0.002BW+0.05T(r0)-0.06sex-0.20P(cold) (R(2)=0.75). (4) Body warming rate (W(rate) ( degrees C/min); n=80) was influenced by the age(2) and rectal temperature of the kit after the coldroom exposure (T(r10)). W(rate)( degrees C/min)=1.24+0.0002age(2)-0.04T(r10) (R(2)=0.76). (5) Kit fur fibre length increased from 5.45+/-0.63mm (males, n=2) and 6.20+/-0.20mm (females, n=3) at 22-23d of age to 9.43+/-1.44mm (males, n=4) and 8.70+/-1.89mm (females, n=4) at 30-31d of age, and to 12.93+/-0.47mm (males, n=3) and 11.38+/-0.41mm (females, n=4) at 45-46d of age, the growth averaging about 0.26mm per day. (6) Under normal circumstances newborn mink kits are hypothermic.Their thermoregulation develops only gradually and is dependent on increase in body mass, insulation and behavioural thermoregulation. Their strategy of survival is based on the ability to withstand hypothermia and on the nutrition and warmth provided by the dam.     

No effects of short-term GSM mobile phone radiation on cerebral blood flow measured using positron emission tomography

The present study investigated the effects of 902.4 MHz Global System for Mobile Communications (GSM) mobile phone radiation on cerebral blood flow using positron emission tomography (PET) with the ¹⁵O‐water tracer. Fifteen young, healthy, right‐handed male subjects were exposed to phone radiation from three different locations (left ear, right ear, forehead) and to sham exposure to test for possible exposure effects on brain regions close to the exposure source. Whole‐brain [¹⁵O]H₂O–PET images were acquired 12 times, 3 for each condition, in a counterbalanced order. Subjects were exposed for 5 min in each scan while performing a simple visual vigilance task. Temperature was also measured in the head region (forehead, eyes, cheeks, ear canals) during exposure. The exposure induced a slight temperature rise in the ear canals but did not affect brain hemodynamics and task performance. The results provided no evidence for acute effects of short‐term mobile phone radiation on cerebral blood flow. Bioelectromagnetics 33:247–256, 2012. © 2011 Wiley Periodicals, Inc.     

Net atmospheric impacts of forest bioenergy production and utilization in Finnish boreal conditions

The net CO₂ exchange of forests was investigated to study net atmospheric impact of forest bioenergy production (BP) and utilization in Finnish boreal conditions. Net CO₂ exchange was simulated with a life cycle assessment tool over a 90‐year period and over the whole Finland based on National Forest Inventory data. The difference in the net exchanges between the traditional timber production (TP) and BP regime was considered the net atmospheric impact of forest bioenergy utilization. According to the results, forests became net sources of CO₂ after about 20 years of simulation, and the net exchange was higher in the BP regime than in the TP regime until the middle of the simulation period. From 2040 onwards, the net exchange started to decrease in both regimes and became higher in the TP regime, excluding the last decade of the simulation. The shift of forests to becoming a CO₂ source reflected the decrease in CO₂ sequestration due to the increasing share of recently harvested and seedling stands that are acting as sources of CO₂, and an increase of emissions from degradation of wood products. When expressed in terms of radiative forcing, the net atmospheric impact was on average 19% less for bioenergy compared with that for coal energy over the whole simulation period. The results show the importance of time dependence when considering dynamic forest ecosystems in BP and climate change mitigation. Furthermore, the results emphasize the dualistic role and possibilities of forest management in controlling the build and release of carbon into and from the stocks and in controlling the rate of the build speed, i.e. growth. This information is needed in identifying the capability and possibilities of ecosystems to produce biomass for energy, alongside other products and ecosystem services (e.g. pulp wood and timber), and simultaneously to mitigate climate change.     

Improved classification of Alzheimer's disease data via removal of nuisance variability

Diagnosis of Alzheimer's disease is based on the results of neuropsychological tests and available supporting biomarkers such as the results of imaging studies. The results of the tests and the values of biomarkers are dependent on the nuisance features, such as age and gender. In order to improve diagnostic power, the effects of the nuisance features have to be removed from the data. In this paper, four types of interactions between classification features and nuisance features were identified. Three methods were tested to remove these interactions from the classification data. In stratified analysis, a homogeneous subgroup was generated from a training set. Data correction method utilized linear regression model to remove the effects of nuisance features from data. The third method was a combination of these two methods. The methods were tested using all the baseline data from the Alzheimer's Disease Neuroimaging Initiative database in two classification studies: classifying control subjects from Alzheimer's disease patients and discriminating stable and progressive mild cognitive impairment subjects. The results show that both stratified analysis and data correction are able to statistically significantly improve the classification accuracy of several neuropsychological tests and imaging biomarkers. The improvements were especially large for the classification of stable and progressive mild cognitive impairment subjects, where the best improvements observed were 6% units. The data correction method gave better results for imaging biomarkers, whereas stratified analysis worked well with the neuropsychological tests. In conclusion, the study shows that the excess variability caused by nuisance features should be removed from the data to improve the classification accuracy, and therefore, the reliability of diagnosis making.     

Do allopatric male Calopteryx virgo damselflies learn species recognition?

There is a growing amount of empirical evidence that premating reproductive isolation of two closely related species can be reinforced by natural selection arising from avoidance of maladaptive hybridization. However, as an alternative for this popular reinforcement theory, it has been suggested that learning to prefer conspecifics or to discriminate heterospecifics could cause a similar pattern of reinforced premating isolation, but this possibility is much less studied. Here, we report results of a field experiment in which we examined (i) whether allopatric Calopteryx virgo damselfly males that have not encountered heterospecific females of the congener C. splendens initially show discrimination, and (ii) whether C. virgo males learn to discriminate heterospecifics or learn to associate with conspecifics during repeated experimental presentation of females. Our experiment revealed that there was a statistically nonsignificant tendency for C. virgo males to show initial discrimination against heterospecific females but because we did not use sexually naïve individuals in our experiment, we were not able to separate the effect of innate or associative learning. More importantly, however, our study revealed that species discrimination might be further strengthened by learning, especially so that C. virgo males increase their association with conspecific females during repeated presentation trials. The role of learning to discriminate C. splendens females was less clear. We conclude that learning might play a role in species recognition also when individuals are not naïve but have already encountered potential conspecific mates.     

Genetics of microenvironmental sensitivity of body weight in rainbow trout (Oncorhynchus mykiss) selected for improved growth

Microenvironmental sensitivity of a genotype refers to the ability to buffer against non-specific environmental factors, and it can be quantified by the amount of residual variation in a trait expressed by the genotype's offspring within a (macro)environment. Due to the high degree of polymorphism in behavioral, growth and life-history traits, both farmed and wild salmonids are highly susceptible to microenvironmental variation, yet the heritable basis of this characteristic remains unknown. We estimated the genetic (co)variance of body weight and its residual variation in 2-year-old rainbow trout (Oncorhynchus mykiss) using a multigenerational data of 45,900 individuals from the Finnish national breeding programme. We also tested whether or not microenvironmental sensitivity has been changed as a correlated genetic response when genetic improvement for growth has been practiced over five generations. The animal model analysis revealed the presence of genetic heterogeneity both in body weight and its residual variation. Heritability of residual variation was remarkably lower (0.02) than that for body weight (0.35). However, genetic coefficient of variation was notable in both body weight (14%) and its residual variation (37%), suggesting a substantial potential for selection responses in both traits. Furthermore, a significant negative genetic correlation (-0.16) was found between body weight and its residual variation, i.e., rapidly growing genotypes are also more tolerant to perturbations in microenvironment. The genetic trends showed that fish growth was successfully increased by selective breeding (an average of 6% per generation), whereas no genetic change occurred in residual variation during the same period. The results imply that genetic improvement for body weight does not cause a concomitant increase in microenvironmental sensitivity. For commercial production, however, there may be high potential to simultaneously improve weight gain and increase its uniformity if both criteria are included in a selection index.