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.     

Associations of Physical Activity and Sedentary Behavior with Academic Skills – A Follow-Up Study among Primary School Children

Background

There are no prospective studies that would have compared the relationships of different types of physical activity (PA) and sedentary behavior (SB) with academic skills among children. We therefore investigated the associations of different types of PA and SB with reading and arithmetic skills in a follow-up study among children.

Methods

The participants were 186 children (107 boys, 79 girls, 6–8 yr) who were followed-up in Grades 1–3. PA and SB were assessed using a questionnaire in Grade 1. Reading fluency, reading comprehension and arithmetic skills were assessed using standardized tests at the end of Grades 1–3.

Results

Among all children more recess PA and more time spent in SB related to academic skills were associated with a better reading fluency across Grades 1–3. In boys, higher levels of total PA, physically active school transportation and more time spent in SB related to academic skills were associated with a better reading fluency across the Grades 1–3. Among girls, higher levels of total PA were related to worse arithmetic skills across Grades 1–3. Moreover, total PA was directly associated with reading fluency and arithmetic skills in Grades 1–3 among girls whose parents had a university degree, whereas these relationships were inverse in girls of less educated parents.

Conclusions

Total PA, physically active school transportation and SB related to academic skills may be beneficial for the development of reading skills in boys, whereas factors that are independent of PA or SB may be more important for academic skills in girls.

Trial Registration

ClinicalTrials.gov: {"type":"clinical-trial","attrs":{"text":"NCT01803776","term_id":"NCT01803776"}}NCT01803776     

An EF-hands protein, centrin-1, is an EGTA-sensitive SUMO-interacting protein in mouse testis

A multifunctional calcium‐binding protein, centrin‐1, is specifically expressed in male germ cells, certain neurons and ciliated cells. We identified centrin‐1 as a protein interacting with SUMO‐2/3 using yeast two‐hybrid screening of a mouse testicular cDNA library. In bead halo assays, the interaction between centrin‐1 and SUMO‐2/3 was reduced in the presence of EGTA and facilitated by the addition of CaCl_2. immunostaining of seminiferous tubules in 35‐day‐old mouse testes revealed that cells in the layer containing spermatogonia showed colocalization of SUMO‐2/3 with centrin‐1 in cytoplasmic spots. Identification of centrin‐1 as the EGTA‐sensitive SUMO‐2/3‐interacting protein indicates the possible role of calcium in modulating the centrin‐1–SUMO‐2/3 interaction and suggests the importance of this interaction in mouse testis. Copyright © 2010 John Wiley & Sons, Ltd.     

Ash in composting of source-separated catering waste

Our earlier experiments in small composters (220 l) indicated the favourable effect of ash from co-incineration of sorted dry waste on the composting of catering waste. The aim of this new study was to clarify further, at a scale of 10 m3, the feasibility of using similar ash as an additive in composting. Source-separated catering waste was mixed with bulking agent (peat and wood chips) and fuel ash from a small (4 MW) district heating power plant. Three compost mixes (CM) were obtained: CM I with 0%, CM II with 10% and CM III with 20 wt.% of fuel ash. These three different mixes were composted in a 10-m3 drum composter as three parallel experiments for 2 weeks each, from January to April 2000. After drum composting, masses were placed according to mixing proportions in separate curing piles. The catering waste fed to the drum was cold, sometimes icy. Even then the temperature rapidly increased to over 50 degrees C. In CM III, the temperature rose as high as 80 degrees C, and after the first week of composting the temperature was about 20 degrees C higher in the CMs II and III than in the CM I. It also improved the oxygen concentrations at the feeding end of the drum and obviously prevented the formation of H2S. No odour problems arose during the composting. Addition of ash increased the heavy metal contents of the composting masses, but the compost was suitable for cultivation or green area construction. Ash clearly decreased the loss of total nitrogen in a time span of 2 years. The lower amounts of nitrogen mean that the amounts applied per hectare can be greater than for normal composts. Measured by mineralization, the breaking down of the organic matter was more rapid in the CM III than in the CM I. Humic acid increased steadily during first 12 months composting, from the initial 39 mg/g organic matter to 115 and 137 mg/g in CMs II and III. Measured by temperature, mineralization and humification the addition of ash appeared to boost the composting. Ash had also other beneficial effects on composting it improved the availability of oxygen in compost mass during the drum composting phase and reduced the formation of odorous gases, especially H2S.     

Development of chloroplast structure and photosynthetic competence in dark-adapted moss protonemata after exposure to light

Summary Sporelings and protonemata ofCeratodon purpureus were grown in darkness for one to two months. On their exposure to light, starch was observed after 30 minutes but only minor changes occurred in the chloroplast structure during the first hours. After one day in light, the chloroplasts had a structure similar to that of the chloroplasts of light-grown material. The dark-grown material evolved oxygen and assimilated CO₂ readily after exposure to light. Nevertheless, maximization of the photosynthetic rate was not achieved until the second day in light, coinciding with the development of light-type chloroplasts. The ultrastructural localization of photosystems I and II revealed much higher activity of PS I in dark-adapted material than in material grown in light, whereas the activity of PS II appeared to be greater in light-grown material.     

The role of metal ions in the activation of arginase.

The role of metal ions as activators of arginase hydrolyzing arginine were studied. The metal ion is assumed to form a complex with arginine and to promote the enzymatic reaction. The activating ability of the metal ion appears to be governed by the chelating ability and/or the coordination numbers which determine whether the metal ion combines with the enzyme or the substrate (or both substrate and enzyme) and factors which influence the configuration of the resulting complexes.