Discovering isochores by least-squares optimal segmentation

The isochore structure of a genome is observable by variation in the G+C (guanine and cytosine) content within and between the chromosomes. Describing the isochore structure of vertebrate genomes is a challenging task, and many computational methods have been developed and applied to it. Here we apply a well-known least-squares optimal segmentation algorithm to isochore discovery. The algorithm finds the best division of the sequence into k pieces, such that the segments are internally as homogeneous as possible. We show how this simple segmentation method can be applied to isochore discovery using as input the G+C content of sliding windows on the sequence. To evaluate the performance of this segmentation technique on isochore detection, we present results from segmenting previously studied isochore regions of the human genome. Detailed results on the MHC locus, on parts of chromosomes 21 and 22, and on a 100 Mb region from chromosome 1 are similar to previously suggested isochore structures. We also give results on segmenting all 22 autosomal human chromosomes. An advantage of this technique is that oversegmentation of G+C rich regions can generally be avoided. This is because the technique concentrates on greater global, instead of smaller local, differences in the sequence composition. The effect is further emphasized by a log-transformation of the data that lowers the high variance that is observed in G+C rich regions. We conclude that the least-squares optimal segmentation method is computationally efficient and yields results close to previous biologically motivated isochore structures.     

Rapid screening for soil ecotoxicity with a battery of luminescent bacteria tests

A bacterial test battery, involving i) Microtox, an aquatic test, ii) the Flash assay, a soil-suspension test (with Vibrio fischeri as the test organism), and iii) the Metal Detector assay, a semi-specific aquatic test for heavy metals (with recombinant luminescent Escherichia coli), was used in a combined toxicological and chemical hazard assessment of Estonian soils sampled from a former Soviet military airfield (13 samples) and from traffic-influenced roadsides (5 samples). The soils showed slightly elevated levels of total petroleum hydrocarbons (TPH), but not of heavy metals. In most of the samples, the levels of TPH did not exceed the Estonian permitted limit values set for residential areas. Toxicity testing was performed on both fresh and dried soils, after aqueous extraction for 1 hour and 24 hours. The toxicity results obtained with the Microtox test did not significantly differ in all of the sample treatment schemes; however, it appeared that the drying and sieving of the soils increased the bioavailability of toxicants, probably due to an enlarged reactive soil surface area. According to chemical analysis of the soils and the data from the Microtox test and the Metal Detector assay (performed on aqueous elutriates of the soils), these soils would not be considered to be hazardous. In contrast, the Flash assay performed on soil-water suspensions of dried soils, showed that most of the soils were toxic and thus probably contained undetermined particle-bound bioavailable toxicants. The photobacterial toxicity test (the Flash assay) can be recommended for the rapid screening of soils, as it is sensitive, cheap and inexpensive, and provides valuable information on particle-bound bioavailable toxicants, useful for complementing a chemical analysis and for assessing the risks originating from polluted soils.     

Morphological and molecular characterisation of Paranoplocephala buryatiensis n. sp. and P. longivaginata Chechulin & Gulyaev, 1998 (Cestoda: Anoplocephalidae) in voles of the genus Clethrionomys

A new species, Paranoplocephala buryatiensis n. sp. (Cestoda:Anoplocephalidae), is described from the grey-sided vole Clethrionomys rufocanus (Sundevall) in the Republic of Buryatia (Russian Federation) and compared with P. longivaginata Chechulin & Gulyaev, 1998, a parasite of the red vole C. rutilus (Pallas) in the same region. P. buryatiensis n. sp. and P. longivaginata both have an exceptionally long vagina and cirrus, unique features among known species of Paranoplocephala Lühe, 1910. The new species differs from P. longivaginata primarily by its wider and more robust body, lower length/width ratio of mature proglottides, tendency of testes to occur in two separate groups, seminal receptacle of a different shape and the position of the cirrus-sac with respect to the ventral longitudinal osmoregulatory canal. The cytochrome oxidase subunit I (COI) sequence data support the independent status of these species, and show that they form a monophyletic assemblage within Paranoplocephala (sensu lato). Assuming cospeciation, an indirect calibration using host speciation dates estimated a rate of mtDNA substitution of 1.0–1.7% pairwise (0.5–0.85% per lineage) sequence divergence per million years. A faunistic review of Paranoplocephala species in C. rufocanus and C. rutilus in the Holarctic region is presented.     

Effect of liver fat on insulin clearance

A fatty liver is associated with fasting hyperinsulinemia, which could reflect either impaired insulin clearance or hepatic insulin action. We determined the effect of liver fat on insulin clearance and hepatic insulin sensitivity in 80 nondiabetic subjects [age 43 +/- 1 yr, body mass index (BMI) 26.3 +/- 0.5 kg/m(2)]. Insulin clearance and hepatic insulin resistance were measured by the euglycemic hyperinsulinemic (insulin infusion rate 0.3 mU.kg(-1).min(-1) for 240 min) clamp technique combined with the infusion of [3-(3)H]glucose and liver fat by proton magnetic resonance spectroscopy. During hyperinsulinemia, both serum insulin concentrations and increments above basal remained approximately 40% higher (P < 0.0001) in the high (15.0 +/- 1.5%) compared with the low (1.8 +/- 0.2%) liver fat group, independent of age, sex, and BMI. Insulin clearance (ml.kg fat free mass(-1).min(-1)) was inversely related to liver fat content (r = -0.52, P < 0.0001), independent of age, sex, and BMI (r = -0.37, P = 0.001). The variation in insulin clearance due to that in liver fat (range 0-41%) explained on the average 27% of the variation in fasting serum (fS)-insulin concentrations. The contribution of impaired insulin clearance to fS-insulin concentrations increased as a function of liver fat. This implies that indirect indexes of insulin sensitivity, such as homeostatic model assessment, overestimate insulin resistance in subjects with high liver fat content. Liver fat content correlated significantly with fS-insulin concentrations adjusted for insulin clearance (r = 0.43, P < 0.0001) and with directly measured hepatic insulin sensitivity (r = -0.40, P = 0.0002). We conclude that increased liver fat is associated with both impaired insulin clearance and hepatic insulin resistance. Hepatic insulin sensitivity associates with liver fat content, independent of insulin clearance.     

Willow bud and shoot foraging by ptarmigan in relation to snow level in NW Finnish Lapland

Willow buds and twigs compose the main part of the willow ptarmigan’s (Lagopus lagopus) diet during winter. This study evaluated how position of willow ramets in relation to snow level affects the browsing of willow ptarmigan in NW Finland. Ramet position in relation to snow level affected the browsing intensity of willow ptarmigan: 5% of shoots were cut and more than 8% of buds were eaten by willow ptarmigan when ramet was staked at the maximum snow level, whereas ramets bent down were unbrowsed and browsing of ramets staked upright was negligible. Browsing significantly decreased the number of vegetative buds and catkins. The results show that snow level and ramet characteristics are important determinants of willow ptarmigan foraging.     

Diversity of Manota Williston (Diptera,Mycetophilidae) in Ulu Temburong National Park,Brunei

A total of 15 species of Manota Williston, 1896 are recorded from Brunei, based on the investigations in 2013-2014. Thirteen species are recorded from Ulu Temburong National Park and three species from the Universiti Brunei Darussalam Campus in Tungku. Six species are described as new to science: Manota belalongensis sp. n., M. kaspraki sp. n., M. macrothrix sp. n., M. megachaeta sp. n. and M. pileata sp. n. from Ulu Temburong, and M. ricina sp. n. from Tungku. New records of the following species are given: Manota bifida Hippa & Papp, M. bruneiensis Hippa & Ševčík, M. hyboloma Hippa & Ševčík, M. oligochaeta Hippa, M. pappi Hippa, M. perangulata Hippa & Ševčík, M. pollex Hippa, M. procera Hippa and M. simplex Hippa.     

Does the introduced signal crayfish occupy an equivalent trophic niche to the lost native noble crayfish in boreal lakes?

The introduced North-American signal crayfish (Pacifastacus leniusculus) has become widespread throughout Europe where it has often replaced the native noble crayfish (Astacus astacus). The impact of this replacement on ecosystem processes in boreal lakes is still largely unknown. We compared the trophic niches of these two crayfish species in 16 small to medium sized boreal lakes in southern Finland; eight lakes with noble crayfish and eight lakes where the native crayfish populations had been lost and replaced by signal crayfish. We analysed carbon and nitrogen stable isotopes from samples of the crayfish and their putative food sources, and used stable isotope models to compare trophic niche widths of the two species of crayfish and to quantify the food sources used by them. At species level the signal crayfish exhibited a substantially larger trophic niche than that of the noble crayfish, but within-lake populations of the species did not differ in their niche widths. The isotopic niches of the two species strongly overlapped, and while the estimated proportions of food resources (profundal and littoral macroinvertebrates, terrestrial leaf detritus and macrophytes) used by crayfish varied considerably among individual populations, they did not differ consistently between the species. Our results suggest that, contrary to often expressed concerns, replacement of lost noble crayfish populations by the signal crayfish may not greatly alter the littoral food web structure in boreal lakes.     

Hydroclimate Variations in Central and Monsoonal Asia over the Past 700 Years

Hydroclimate variations since 1300 in central and monsoonal Asia and their interplay on interannual and interdecadal timescales are investigated using the tree-ring based Palmer Drought Severity Index (PDSI) reconstructions. Both the interannual and interdecadal variations in both regions are closely to the Pacific Decadal Oscillation (PDO). On interannual timescale, the most robust correlations are observed between PDO and hydroclimate in central Asia. Interannual hydroclimate variations in central Asia are more significant during the warm periods with high solar irradiance, which is likely due to the enhanced variability of the eastern tropical Pacific Ocean, the high-frequency component of PDO, during the warm periods. We observe that the periods with significant interdecadal hydroclimate changes in central Asia often correspond to periods without significant interdecadal variability in monsoonal Asia, particularly before the 19^th century. The PDO-hydroclimate relationships appear to be bridged by the atmospheric circulation between central North Pacific Ocean and Tibetan Plateau, a key area of PDO. While, in some periods the atmospheric circulation between central North Pacific Ocean and monsoonal Asia may lead to significant interdecadal hydroclimate variations in monsoonal Asia.     

Experimental Infection of Voles with Francisella tularensis Indicates Their Amplification Role in Tularemia Outbreaks

Tularemia outbreaks in humans have been linked to fluctuations in rodent population density, but the mode of bacterial maintenance in nature is unclear. Here we report on an experiment to investigate the pathogenesis of Francisella tularensis infection in wild rodents, and thereby assess their potential to spread the bacterium. We infected 20 field voles (Microtus agrestis) and 12 bank voles (Myodes glareolus) with a strain of F. tularensis ssp. holarctica isolated from a human patient. Upon euthanasia or death, voles were necropsied and specimens collected for histological assessment and identification of bacteria by immunohistology and PCR. Bacterial excretion and a rapid lethal clinical course with pathological changes consistent with bacteremia and tissue necrosis were observed in infected animals. The results support a role for voles as an amplification host of F. tularensis, as excreta and, in particular, carcasses with high bacterial burden could serve as a source for environmental contamination.     

Acute Brain Trauma in Mice Followed By Longitudinal Two-photon Imaging

Although acute brain trauma often results from head damage in different accidents and affects a substantial fraction of the population, there is no effective treatment for it yet. Limitations of currently used animal models impede understanding of the pathology mechanism. Multiphoton microscopy allows studying cells and tissues within intact animal brains longitudinally under physiological and pathological conditions. Here, we describe two models of acute brain injury studied by means of two-photon imaging of brain cell behavior under posttraumatic conditions. A selected brain region is injured with a sharp needle to produce a trauma of a controlled width and depth in the brain parenchyma. Our method uses stereotaxic prick with a syringe needle, which can be combined with simultaneous drug application. We propose that this method can be used as an advanced tool to study cellular mechanisms of pathophysiological consequences of acute trauma in mammalian brain in vivo. In this video, we combine acute brain injury with two preparations: cranial window and skull thinning. We also discuss advantages and limitations of both preparations for multisession imaging of brain regeneration after trauma.