From RNA-seq reads to differential expression results

Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.     

Effects of aluminum on nucleoli in root tip cells and selected physiological and biochemical characters in <Emphasis Type="Italic">Allium cepa</Emphasis> var. <Emphasis Type="Italic">agrogarum</Emphasis>L

Background  

Increased Al concentration causes reduction of mitotic activity, induction of nucleolar alteration, increase of the production of ROS and alteration of several antioxidant enzyme activities in plant cells. Allium cepa is an excellent plant and a useful biomarker for environmental monitoring. Limited information is available about the effects of Al on nucleoli, antioxidant enzyme system, contents of MDA and soluble protein in A. cepa. Therefore, we carried out the investigation in order to better understand the effects of Al on the growth, nucleoli in root tip cells and selected physiological and biochemical characters.     

Effect of culture conditions on the biomass determination by ergosterol of <Emphasis Type="Italic">Lentinus crinitus</Emphasis> and <Emphasis Type="Italic">Psilocybe castanella</Emphasis>

Estimating fungal growth is important in processes of soil bioremediation. It has been demonstrated that ergosterol is a good indicator of fungal biomass in solid substrata. In the present study were evaluated the effects upon the ergosterol rate of Lentinus crinitus Berk. and Psilocybe castanella Peck through the culture conditions of these fungi, which are evaluated for the bioremediation of soils contaminated by organochlorates. A good correlation between fungal biomass and ergosterol was observed for both species. The culture conditions did not influence the ergosterol rate of L. crinitus. Yet the ergosterol rate of P. castanella was influenced from 35 days of culture and when grown in the presence of 15.00 g hexachlorobenzene l⁻¹ of culture medium. So it is possible to estimate growth of both species using ergosterol as indicator in processes of soil bioremediation since the influences observed in the ergosterol rate of P. castanella are considered.     

Healing in the Sámi North

There is a special emphasis today on integrating traditional healing within health services. However, most areas in which there is a system of traditional healing have undergone colonization and a number of pressures suppressing tradition for hundreds of years. The question arises as to how one can understand today’s tradition in light of earlier traditions. This article is based on material collected in Sámi areas of Finnmark and Nord-Troms Norway; it compares local healing traditions with what is known of earlier shamanic traditions in the area. The study is based on 27 interviews among healers and their patients. The findings suggest that although local healing traditions among the Sámi in northern Norway have undergone major transformations during the last several hundred years, they may be considered an extension of a long-standing tradition with deep roots in the region. Of special interest are also the new forms tradition may take in today’s changing global society.     

Lessons from practice: assessing early progress and success in river rehabilitation

This article comprises a literature analysis of 41 river rehabilitation projects to assess the short-term (5 years) ability of indicator groups to demonstrate progress towards river rehabilitation goals. Positive indications were compared to land-use, river size, rehabilitation intervention and time. A questionnaire was developed to investigate river manager’s interpretation of rehabilitation success and to assess their level of adherence to recommendations in the literature with regard to rehabilitation assessment on a conceptual level. A total of 54 responses were received from respondents based in Germany, The Netherlands and the United Kingdom. The results indicate that macroinvertebrate indicators, while widely used in assessing river rehabilitation efforts, exhibited a lower frequency of positive responses than most other indicator types in the short term. Conversely, terrestrial floodplain indicators exhibited the most frequent level of positive response for all ecological type indicators leading to recommendations for further investigations into their use for short-term monitoring. Assessment procedures recommended in literature are largely followed, illustrating the advances that have been made with regard to assessment planning. Indicator responses are influenced by scale factors, for example, land-use and river size, that are often not considered by rehabilitation managers. While an emphasis is placed on ecological, hydrological and morphological indicators in monitoring schemes, the socioeconomic perspective (emphasized in the literature as forming an integral part of the river system) is neglected.     

Phase Separation Behavior of Caseins in Milk Containing Flaxseed Gum and κ-Carrageenan: A Light-Scattering and Ultrasonic Spectroscopy Study

The physico-chemical properties of skim milk containing κ-carrageenan (in the concentration range 0–0.06% w/v), flaxseed gum (in the concentration range 0–0.40% w/v), or a mixture of both polysaccharides were studied using dynamic light scattering, under diluted conditions, as well as in situ, undiluted, using diffusing wave spectroscopy (DWS) and ultrasonic spectroscopy. Flaxseed gum causes phase separation in milk mixtures, because of thermodynamic incompatibility between the casein micelles and the polysaccharide chains. Confocal microscopy and ultrasonic spectroscopy showed that while the addition of 0.01% κ-carrageenan was not sufficient to hinder phase separation, when 0.03% was added, the helix–helix interactions between κ-carrageenan molecules were sufficient to form a network and stabilize the system. DWS clearly demonstrated that clusters of casein micelles still form even at very low concentrations of polysaccharides (below the visible phase separation threshold) and that κ-carrageenan hinders visible phase separation by decreasing the mobility of the casein micelles.     

Phenetic diversity in the <Emphasis Type="Italic">Fritillaria camschatcensis</Emphasis> population grown on the Sapporo campus of Hokkaido University

Triploid Fritillaria camschatcensis (L.) Ker-Gawler (2n = 3x = 36) is a wild species growing in the low-lying areas of Hokkaido Island, Japan, including the Sapporo campus of Hokkaido University. Many F. camschatcensis plants grew on the campus about a century ago, but we seldom find the plants nowadays and so a project to restore this species is being planned. Because preservation of genetic diversity and composition in populations has become a major target of conservation, this study compared variation in the F. camschatcensis population on the Sapporo campus with that in two other populations in Hokkaido. Phenetic variation assessed by 57 randomly amplified polymorphic DNA markers showed that the three populations were significantly distinct from each other; analysis of molecular variance showed 64.3% of variation (P < 0.001) existed among the three populations. Comparison of phenetic diversity on the Sapporo campus population with that in the two other populations showed that the Sapporo campus population contained large genetic variation despite reduced plant numbers. These results indicate that multiplying F. camschatcensis individuals on the Sapporo campus is adequate to restore the Sapporo campus population because this population contains enough genetic diversity, and that transplanting from other populations should be avoided so as not to introduce different genotypes into the campus. These results will be used to design the restoration strategy.     

Development and Characterization of Enteric-Coated Immediate-Release Pellets of Aceclofenac by Extrusion/Spheronization Technique Using κ-Carrageenan as a Pelletizing Agent

In the present study, an attempt was made to prepare immediate-release enteric-coated pellets of aceclofenac, a poorly soluble nonsteroidal anti-inflammatory drug that has a gastrointestinal intolerance as its serious side effect. Formulation of enteric-coated pellets with improved solubility of aceclofenac could address both of these problems. To achieve these goals, pellets were prepared by extrusion–spheronization method using pelletizing agents that can contribute to the faster disintegration and thereby improve the solubility of the drug. Different disintegrants like β-cyclodextrin, kollidon CL, Ac-Di-Sol, and sodium starch glycolate were tried in order to further improve disintegration time. The pellets were characterized for drug content, particle size distribution, flow properties, infrared spectroscopy, surface morphology, disintegration rate, and dissolution profile. The formulations, which showed best disintegration and dissolution profiles, were coated with Eudragit L100-55, an enteric-coated polymer which does not dissolve at gastric pH but dissolves at intestinal pH, releasing the drug immediately in the dissolution medium. The optimized enteric-coated formulation containing 20% κ-carrageenan, lactose, and sodium starch glycolate as a disintegrant did inhibit the release of the drug for 2 h in 0.1 N HCl, whereas 87% of the drug was released within 45 min. The improvement was substantial when it was compared with solubility of pure drug under the same conditions. Thus, dissolution profiles suggested that combination of κ-carrageenan and sodium starch glycolate resulted into fast-disintegrating, immediate-release pellets, overcoming the bioavailability problem of the poorly soluble drug, aceclofenac, and enteric coating of these pellets avoids the exposure of aceclofenac to ulcer-prone areas of the gastrointestinal tract.     

Observation of brown-throated three-toed sloths: mating behaviour and the simultaneous nurturing of two young

Bradypus variegatus is a member of the Order Pilosa, Family Bradypodidae, and is distributed in many subtropical and tropical countries in South and Central America. However, studies on this species in the wild are relatively limited and many aspects of its reproductive behaviour are unknown or unclear. The current report presents new observations of the reproductive behaviour of B. variegatus in its natural environment. These include details of both a male–female copulation and the simultaneous nurturing of two young sloths.