T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.

Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse.

Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.

Cost-Efficiency of Birch Sprinkling in Kraft Pulping

Työn tavoitteena oli selvittää koivun kasteluvarastoinnin kannattavuus selluteollisuudessa. Lisäksi tutkittiin, kuinka kastelu vaikuttaa puuaineeseen varastoinnin aikana ja kuinka koivun kasteluvarastointi vaikuttaa puun kuorintaan ja haketukseen, keitettävyyteen, vaalenevuuteen sekä sellun laatuun. Enocellin puukentälle rakennettiin kasteluvarasto, jossa varastoitiin 40,000 m3sob koivua. Kastelu oli päällä huhtikuusta lokakuuhun asti. Kastelun vaikutusta puuaineen muutoksiin arvioitiin lahotutkimusten avulla. Tehdaskoeajoissa verrattiin tuoretta, kasteluvarastoitua ja kuivavarastoitua koivua. Puuaines säilyi lähes muuttumattomana yhden kesän kasteluvarastoinnissa. Kastellulla koivulla terveen puun osuus oli yli 85 % kesän lopussa, kun se oli alle 20 % kuivavarastoidulla koivulla. Kuorinnan puuhäviö laskee selvästi kastelukoivulla ja myös hakkeen laatu oli parempaa kuin kuivavarastoidulla koivulla. Kastelukoivulla hakkeen kuoripitoisuus oli vain 0.13 %. Kuoren kuiva-aine oli 12 prosenttiyksikköä alhaisempi kuin kuivalla koivulla, mutta kuoren lämpöarvossa ero oli vain 1 €/ADt. Varastointimenetelmällä ei ollut vaikutusta hakkeen keitettävyyteen, mutta tuoreella puulla keitettävyys oli parempi kuin varastoidulla puulla. Sellun asetoniuutepitoisuus oli samalla tasolla tuoreella ja kastellulla puulla. Kuivalla syyspuulla uutetaso oli korkeampi, vaikka hartsisaippuan annostusta nostettiin 10 kg/ADt. Betulinolitaso oli kastellulla puulla erittäin alhainen puun hyvän kuoriutuvuuden vuoksi. Kastellun ja tuoreen puun vaalenevuus oli parempi kuin kuivalla puulla. Aktiivikloorin kulutus oli 3 – 4 kg/ADt alhaisempi kuin kuivalla syyspuulla. Puun varastoinnilla ei ollut vaikutusta sellun laatuun. Koivun kasteluvarastoinnin kannattavuus on erittäin hyvä. Tuotantokustannukset määritettiin tuoreelle, kastellulle, kierrätetylle sekä kuivalle koivulle. Kasteluvarastointi laskee tuotantokustannuksia noin 10 €/ADt verrattuna kierrätettyyn koivuun. Kuivavarastoidun puun käyttö nostaa tuotantokustannuksia noin 5 €/ADt verrattuna kastelukoivuun. Kierrätetyn ja kuivavarastoidun puun kustannusero johtuu kierrätyskustannuksista. Kasteluvarastolle, jota käytettiin kesällä 2004, takaisinmaksuaika on vain 0.4 vuotta. Jos tavoiteltu takaisinmaksuaika olisi kaksi vuotta, niin perusinvestointi 80,000 m3sob varastolle voisi maksaa noin 370 k€.

Genetic variation in the European hake, Merluccius merluccius. Description of protein loci and genetic divergence between Atlantic and Mediterranean populations = Anàlisi de la variabilitat genètica en el lluç europeu, Merluccius merluccius. Descripció dels loci electroforètics i divergència genètica entre les poblacions atlàntica i mediterrània

We examined the genetic population structure of the european hake (Merluccius merluccius) using electrophoretically detectable population markers in 35 protein loci. Samples were collected from 7 locations in the Atlantic Ocean and Mediterranean Sea. Six loci were polymorphic using the 0.05 criterion of polymorphism. Sample heterozigosities ranged from 0.052 to 0.072 and averaged 0.0625. In this study, significant allele frequency differences were detected between Atlantic and Mediterranean populations in three polymorphic loci: GAPDH-1*, GPI-2* and SOD-1*. Two major genetic groups were considered: a North-Atlantic stock and the Mediterranean stock. The Nei genetic distance, D, (based on 33 loci) between samples from these two groups ranged from 0.002 to 0.006. Genetic differenciation between these areas appears to reflect the barrier effect of Strait of Gibraltar. On average over loci, 96.92 % of the total gene diversity was contained within samples, 0.23 % expressed differences among locations within areas, and 2.64 % differences between regions. A review of morphological variation together with the genetic data presented here suggest that the populations of hake from these areas are subdivided into two different stocks: the North-Atlantic stock and the Mediterranean stock. The most conservative approach to the management of these stocks is to consider the Atlantic and Mediterranean stocks independently from oneanother

The efficiency of indicator groups for the conservation of amphibians in the Brazilian Atlantic Forest

The adequate selection of indicator groups of biodiversity is an important aspect of the systematic conservation planning. However, these assessments differ in the spatial scale, in the methods used and in the groups considered to accomplish this task, which generally produces contradictory results. The quantification of the spatial congruence between species richness and complementarity among different taxonomic groups is a fundamental step to identify potential indicator groups. Using a constructive approach, the main purposes of this study were to evaluate the performance and efficiency of eight potential indicator groups representing amphibian diversity in the Brazilian Atlantic Forest. Data on the geographic range of amphibian species that occur in the Brazilian Atlantic Forest was overlapped to the full geographic extent of the biome, which was divided into a regular equal-area grid. Optimization routines based on the concept of complementarily were applied to verify the performance of each indicator group selected in relation to the representativeness of the amphibians in the Brazilian Atlantic Forest as a whole, which were solved by the algorithm"simulated annealing", through the use of the software MARXAN. Some indicator groups were substantially more effective than others in regards to the representation of the taxonomic groups assessed, which was confirmed by the high significance of data (F = 312.76; p < 0.01). Leiuperidae was considered as the best indicator group among the families analyzed, as it showed a good performance, representing 71% of amphibian species in the Brazilian Atlantic Forest (i.e. 290 species), which may be associated with the diffuse geographic distribution of its species. This study promotes understanding of how the diversity standards of amphibians can be informative for systematic conservation planning on a regional scale.

Mechanisms of protein homeostasis in health, aging and disease.

When emerging from the ribosomes, new polypeptides need to fold properly, eventually translocate, and then assemble into stable, yet functionally flexible complexes. During their lifetime, native proteins are often exposed to stresses that can partially unfold and convert them into stably misfolded and aggregated species, which can in turn cause cellular damage and propagate to other cells. In animal cells, especially in aged neurons, toxic aggregates may accumulate, induce cell death and lead to tissue degeneration via different mechanisms, such as apoptosis as in Parkinson's and Alzheimer's diseases and aging in general. The main cellular mechanisms effectively controlling protein homeostasis in youth and healthy adulthood are: (1) the molecular chaperones, acting as aggregate unfolding and refolding enzymes, (2) the chaperone-gated proteases, acting as aggregate unfolding and degrading enzymes, (3) the aggresomes, acting as aggregate compacting machineries, and (4) the autophagosomes, acting as aggregate degrading organelles. For unclear reasons, these cellular defences become gradually incapacitated with age, leading to the onset of degenerative diseases. Understanding these mechanisms and the reasons for their incapacitation in late adulthood is key to the design of new therapies against the progression of aging, degenerative diseases and cancers.

Design and production of protein nanostructures for biomolecular detection

Particulate nanostructures are increasingly used for analytical purposes. Such particles are often generated by chemical synthesis from non-renewable raw materials. Generation of uniform nanoscale particles is challenging and particle surfaces must be modified to make the particles biocompatible and water-soluble. Usually nanoparticles are functionalized with binding molecules (e.g., antibodies or their fragments) and a label substance (if needed). Overall, producing nanoparticles for use in bioaffinity assays is a multistep process requiring several manufacturing and purification steps. This study describes a biological method of generating functionalized protein-based nanoparticles with specific binding activity on the particle surface and label activity inside the particles. Traditional chemical bioconjugation of the particle and specific binding molecules is replaced with genetic fusion of the binding molecule gene and particle backbone gene. The entity of the particle shell and binding moieties are synthesized from generic raw materials by bacteria, and fermentation is combined with a simple purification method based on inclusion bodies. The label activity is introduced during the purification. The process results in particles that are ready-to-use as reagents in bioaffinity. Apoferritin was used as particle body and the system was demonstrated using three different binding moieties: a small protein, a peptide and a single chain Fv antibody fragment that represents a complex protein including disulfide bridge.If needed, Eu3+ was used as label substance. The results showed that production system resulted in pure protein preparations, and the particles were of homogeneous size when visualized with transmission electron microscopy. Passively introduced label was stably associated with the particles, and binding molecules genetically fused to the particle specifically bound target molecules. Functionality of the particles in bioaffinity assays were successfully demonstrated with two types of assays; as labels and in particle-enhanced agglutination assay. This biological production procedure features many advantages that make the process especially suited for applications that have frequent and recurring requirements for homogeneous functional particles. The production process of ready, functional and watersoluble particles follows principles of “green chemistry”, is upscalable, fast and cost-effective.

Improving the efficiency of PV low-power processing circuits by selecting an optimal inductor current of the DC/DC converter

In the context of autonomous sensors powered by small-size photovoltaic (PV) panels, this work analyses how the efficiency of DC/DC-converter-based power processing circuits can be improved by an appropriate selection of the inductor current that transfers the energy from the PV panel to a storage unit. Each component of power losses (fixed, conduction and switching losses) involved in the DC/DC converter specifically depends on the average inductor current so that there is an optimal value of this current that causes minimal losses and, hence, maximum efficiency. Such an idea has been tested experimentally using two commercial DC/DC converters whose average inductor current is adjustable. Experimental results show that the efficiency can be improved up to 12% by selecting an optimal value of that current, which is around 300-350 mA for such DC/DC converters.

Fate of peat utilization

Peat is an organic substance with the maintenance of a mineral part, what shows it as interesting object for studying. Both organic and mineral parts of peat find application in various fields of activity of the people. Antibacterial properties of peat are known since an antiquity. Today people have expanded a spectrum of application of peat to use of by-products of its processing for reception of rather ecologically harmless fuel. The master theses are focused on peat, as on ambiguous raw materials for processing and fuel manufacture. The purpose of theses to show how much widely applied peat, technologies on its processing and its influence on environment at all stages of its working out.

Mineral and vitamin content of beef, chicken, and turkey hydrolysates mineral and vitamin content of protein hydrolysates

The purpose of this study was to assess the concentration of vitamins and minerals in meat protein hydrolysates. Calcium, phosphorus and iron were analyzed by inductively coupled-plasma atomic emission spectrophotometry; vitamin C was analyzed by the reduction of cupric ions and vitamins B1 and B2 by fluorescence. Regarding minerals, the beef hydrolysate (BH) had more iron than the turkey hydrolysate (TH) and the chicken hydrolysate (CH); TH had a little more phosphorus. BH had the largest amount of vitamin C, and similar amounts of vitamins B1 and B2. The amount of these nutrients found in the hydrolysates suggests that it is possible to use them to enrich special dietary formulations.

High encapsulation efficiency of sodium alendronate in eudragit S100/HPMC blend microparticles

The hydrophilic drug sodium alendronate was encapsulated in blended microparticles of Eudragit® S100 and Methocel® F4M or Methocel® K100LV. Both formulations prepared by spray-drying showed spherical collapsed shape and smooth surface, encapsulation efficiencies of 85 and 82% and mean diameters of 11.7 and 8.4 µm, respectively. At pH 1.2, in vitro dissolution studies showed good gastro-resistance for both formulations. At pH 6.8, the sodium alendronate release from the microparticles was delayed and was controlled by Fickian diffusion. In conclusion, the prepared microparticles showed high encapsulation efficiency of sodium alendronate presenting gastro-resistance and sustained release suitable for its oral administration.

Efficiency of the ISM Code in Finnish Shipping Companies

Due to increasing waterborne transportation in the Gulf of Finland, the risk of a hazardous accident increases and therefore manifold preventive actions are needed. As a main legislative authority in the maritime community, The International Maritime Organization (IMO) has set down plenary laws and recommendations which are e.g., utilised in the safe operations in ships and pollution prevention. One of these compulsory requirements, the ISM Code, requires proactive attitude both from the top management and operational workers in the shipping companies. In this study, a crosssectional approach was taken to analyse whether the ISM Code has actively enhanced maritime safety in the Gulf of Finland. The analysis included; 1) performance of the ISM Code in Finnish shipping companies, 2) statistical measurements of maritime safety, 3) influence of corporate top management to the safety culture and 4) comparing safety management practices in shipping companies and port operations of Finnish maritime and port authorities. The main results found were that maritime safety culture has developed in the right direction after the launch of the ISM Code in the 1990´s. However, this study does not exclusively prove that the improvements are the consequence of the ISM Code. Accident prone ships can be recognized due to their behaviour and there is a lesson to learn from the safety culture of some high standard safety disciplines such as, air traffic. In addition, the reporting of accidents and nearmisses should be more widely used in shipping industry. In conclusion, there is still much to be improved in the maritime safety culture of the Finnish Shipping industry, e.g., a “no blame culture” needs to be adopted.

Efficiency of phylloplane bacteria in controlling aerial tomato diseases under field conditions

The capacity of two bacteria isolated from the tomato phylloplane to control late blight (Phytophthora infestans) was investigated in the field, and compared against the effectiveness of spraying with the fungicide chlorothalonil (1.5 g a.i. L-1) or water (control). A 55% reduction in late blight intensity was observed in the leaves of the middle of the plant and 62% in those of the upper leaves when using the antagonist UFV-STB 6 (Novosphingobium capsulatum) as compared to the control. Isolate UFV-IEA 6 (Bacillus cereus) was able to reduce disease intensity by 55%, but only in the upper leaves of the tomato plants. Treatment with isolate UFV-STB 6 also led to a significant reduction in the percentage of fruits with late blight symptoms. The results demonstrate the potential of these two bacteria in controlling this disease.