THERPA: A small molecule database related to prion protein regulation and prion diseases progression

Prion diseases are fatal neurodegenerative disorders that affect humans and animals. Although various small molecules have been evaluated for application in the treatment of prion diseases, none have been shown to be efficacious. Expanding our knowledge of these molecules is important for understanding of the complex mechanisms of prion diseases. To improve access to the scattered information on small molecules related to prion diseases, we built a database of therapeutic molecules associated with prion diseases (THERPA, therpa.pythonanywhere.com). THERPA includes 119 small molecules and their 283 relationships with prion diseases. THERPA is an interactive visual database and useful for improving search efficiency which can help researchers identify intrinsic small molecules that can be used for developing therapeutics for prion diseases.     

The African savannah elephant population in Kidepo Valley National Park, Uganda: changes in size and structure from 1967 to 2000

The age and sex structure of the elephant population in Kidepo Valley National Park were studied using recognition files. Moreover, population trends were reviewed using past studies. From 1967 to 2000, the elephant population varied between 200 and 500 individuals. Of the minimum number of 374 elephants found to use the Park, 352 were individually identified. Seventy‐nine per cent of these were recorded in 29 families ranging from three to 22 animals with a mean group size of ten. Young animals dominated the population (45% aged 0–9.9 years), while 11% were 10–14.9 years of age and only 18% over 25 years of age. Overall, males constituted 45% of the population, but only 32% of the individuals in the 10–14.9‐year age class were males. Individuals ≥15 years of age displayed a skewed sex ratio of 1 : 1.4 in favour of females. The extent of skew was greatest among mature animals (≥25 years of age), which had four times as many females as males. The skewed age structure in the year 2000 caused by poaching and drought, led to a significant difference between the age distribution in 1970 and 2000. Recent counts suggest that the Kidepo elephant population may be increasing.     

Recent advances in ecological stoichiometry: insights for population and community ecology

Conventional theories of population and community dynamics are based on a single currency such as number of individuals, biomass, carbon or energy. However, organisms are constructed of multiple elements and often require them (in particular carbon, phosphorus and nitrogen) in different ratios than provided by their resources; this mismatch may constrain the net transfer of energy and elements through trophic levels. Ecological stoichiometry, the study of the balance of elements in ecological processes, offers a framework for exploring ecological effects of such constraints. We review recent theoretical and empirical studies that have considered how stoichiometry may affect population and community dynamics. These studies show that stoichiometric constraints can affect several properties of populations (e.g. stability, oscillations, consumer extinction) and communities (e.g. coexistence of competitors, competitive interactions between different guilds). We highlight gaps in general knowledge and focus on areas of population and community ecology where incorporation of stoichiometric constraints may be particularly fruitful, such as studies of demographic bottlenecks, spatial processes, and multi-species interactions. Finally, we suggest promising directions for new research by recommending potential study systems (terrestrial insects, detritivory-based webs, soil communities) to improve our understanding of populations and communities. Our conclusion is that a better integration of stoichiometric principles and other theoretical approaches in ecology may allow for a richer understanding of both population and community structure and dynamics.     

Diversity of the bacterial community in Myanmar traditional salted fish <Emphasis Type="Italic">yegyo ngapi</Emphasis>

The distribution and characterization of bacteria including lactic acid bacteria (LAB) in the traditional and popular salted fish yegyo ngapi in Myanmar were studied to clarify the contribution of these bacteria to the curing and ripening of this product. Samples of yegyo ngapi purchased from a market in Yangon were used. Most of the isolates obtained using de Man, Rogosa and Sharpe medium containing 10 % NaCl were identified as coccoid LAB on the basis of their basic phenotypic characteristics. From the results of 16S rRNA gene sequencing and PCR-restriction fragment length polymorphism analysis of this gene, most of the isolates were identified as the halophilic LAB Tetragenococcus muriaticus. Analyses of the 16S rRNA gene based on the clone library using DNA extracted from salted fish products were also performed. The results of these molecular-analysis-based techniques showed that spore-forming and non-spore-forming anaerobic bacteria including the genera Clostridium and Halanaerobium in addition to T. muriaticus were also frequently found in bacterial communities. These findings suggest that the anaerobic condition during curing and ripening resulted in bacterial communities composed of strictly anaerobic bacteria and halophilic LAB, and that these bacteria might also contribute to the manufacturing processes of this product. In addition, DNA sequences similar to that of Clostridium botulinum were found in the clone library analysis. Therefore, despite no reports of botulism poisoning from the region where the samples were taken, closer surveillance should be carried out from the viewpoint of food safety.     

A contribution to the history of Rumex alpinus in the Italian central Alps. A palaeobotanical study from Val Febbraro, Valle Spluga

The archaeological site of Lavazzé at 2108 m a.s.l., and the summer farming site of Borghetto Sotto at 1897 m a.s.l., have been studied using pollen analysis. The pollen diagrams reflect human disturbance from the Bronze and Neolithic ages respectively. The name Lavazzé is also used as a local name for Rumex alpinus. At both sites, significant values of R. alpinus, up to about 10% of total terrestrial pollen, have been recorded, from about 2400 b.p. (ca 360 cal b.c.) onwards, although Lavazzé is above the present-day known local limit for R. alpinus. Written sources document local growth and cultivation of the species at 1300 m. It was used for various purposes in the past, and the high values are interpreted as reflecting former intensive local growth. Local cultivation at higher altitudes should not be excluded. Use of R. alpinus is known as far north as Scotland and Finland, and the species ought to be regarded as an apophyte and/or a naturalised crop.     

Relationships between stretch-shortening cycle performance and maximum muscle strength

This study aimed to examine the relationships between muscle power output using the stretch-shortening cycle (SSC) and maximum strength, as measured by the 1 RM (1 repetition maximum) test and the isokinetic dynamometer under elbow flexion. Sixteen trained, young adult males pulled a constant load of 40% MVC (maximum voluntary elbow flexion contraction) by ballistic elbow flexion under the following two preliminary conditions: 1) the static relaxed muscle state (SR condition) and 2) using the SSC (SSC condition). Muscle power was determined from the product of the pulling velocity and load mass by a power measurement instrument with a rotary encoder. The 1 RM bench press (1RM BP) and isokinetic maximum strength under elbow flexion with the Cybex-325 were measured as indicators of dynamic maximum strength. 1) The early power output exerted under the SSC condition showed a significant and high correlation with the 1 RM BP (r = 0.83), but only moderate correlation with the isokinetic muscle strength (r = 0.50-0.67). 2) The contribution of the 1 RM BP to the early muscle contraction velocity exerted under the SSC condition was large. These results suggested that muscle power exerted using the SSC shows a stronger relationship with maximum muscle strength measured by a 1 RM test rather than isokinetic maximum strength.     

Site-specific chlorophyll reference conditions for lakes in Northern and Western Europe

The Water Framework Directive (WFD) requires EU Member States to assess the “ecological status” of surface waters. As a component of ecological status, many European countries are developing a classification scheme for chlorophyll concentrations as a measure of phytoplankton biomass. The chlorophyll classification must be based on the degree of divergence of a water body from an appropriate baseline or ‘reference condition’. This article describes the development of a series of regression models for predicting reference chlorophyll concentrations on a site-specific basis. For model development, a large dataset of European lakes considered to be in reference condition, 466 lakes in total, was assembled. Data were included from 12 European countries, but lakes from Northern and Western Europe dominated and made up 92% of all reference lakes. Data have been collated on chlorophyll concentration, altitude, mean depth, alkalinity, humic type, surface area and geographical region. Regression models were developed for estimating site-specific reference chlorophyll concentrations from significant predictor ‘typology’ variables. Reference chlorophyll concentrations were found to vary along a number of environmental gradients. Concentrations increased with colour and alkalinity and decreased with lake depth and altitude. Forward selection was used to identify independent explanatory variables in regression models for predicting site-specific reference chlorophyll concentrations. Depth was selected as an explanatory variable in all models. Alkalinity was included in models for low colour and humic lakes and altitude was included in models for low colour and very humic lakes. Uncertainty in the models was quite high and arises from errors in the data used to develop the models (including natural temporal and spatial variability in data) and also from additional explanatory variables not considered in the models, particularly nutrient concentrations, retention time and grazing. Despite these uncertainties, site-specific reference conditions are still recommended in preference to type-specific reference conditions, as they use the individual characteristics of a site known to influence phytoplankton biomass, rather than adopt standards set to generally represent a large population of lakes of a particular type. For this reason, site-specific reference conditions should result in reduced error in ecological status classifications, particularly for lakes close to typology boundaries.     

The invertebrate fauna of High Arctic seabird nests: the microarthropod community inhabiting nests on Spitsbergen,Svalbard

The invertebrate fauna of the nests of three seabird species, black-legged kittiwakes (Rissa tridactyla), common eider (Somateria mollissima) and glaucous gull (Larus hyperboreus), were sampled in Kongsfjorden, Spitsbergen, Svalbard. The invertebrate community was species poor, consisting predominantly of the flea, Mioctenopsylla arctica arctica (Insecta: Siphonaptera), but with six species of oribatid mite (Acari: Oribatida), Diapterobates notatus, Oribatula tibialis, Ameronothrus lineatus, Hermannia reticulata, Trichoribates trimaculatus and Ceratoppia bipilis, plus an occasional mesostigmatid mite. No Collembola or ticks (Acari: Ixodidae) were observed. With the exception of M. arctica arctica, the fauna of seabird nests consisted of opportunistic microarthropod species rather than specialised nest-dwelling or bird parasitic species. Species diversity of soil oribatid mites was greater in nests of the common eider than compared to nests of the black-legged kittiwake, which may be related to the ground nesting behaviour of the common eiders. No rare or unusual microarthropod species for Svalbard were found in the seabird nests. The contentions that nests may facilitate microarthropod colonisation of High Arctic regions via bird phoresy by providing a high-quality habitat at the point of arrival, or that there might be a specialised microarthropod fauna exploiting this habitat, were not supported in this study. These are amongst the first data on the microarthropod community of seabird nests in the High Arctic.