Long-term change of the littoral Cladocera in the Tatra Mountain lakes through a major acidification event

In our study, we focused on littoral Cladocera living and feeding in shallow shore parts of 46 mountain lakes in the Tatra Mountains (Slovakia and Poland). The studied lakes underwent a major acidification event in the 1980s and are now in the process of recovery. Lakes were divided into three categories based on their sensitivity to acidification: 5 extremely sensitive (ES), 11 acid sensitive (AS), and 30 non-sensitive (NS) lakes. In our study, we included historical data from the literature, and data from sediment core and littoral samples, which together represent the evolution of the littoral communities from a pre-industrial period up to the present. In total, 11 littoral species were found belonging to three cladoceran families. Most of the species were members of the family Chydoridae: Alona affinis, A. quadrangularis, A. rectangula, A. guttata, Acroperus harpae, Alonella excisa, A. nana, Chydorus sphaericus, and Eurycercus lamellatus. One species belonged to each family Daphniidae (Ceriodaphnia quadrangula) and Polyphemidae (Polyphemus pediculus). The most numerous littoral taxa were Alona affinis, Acroperus harpae, and Chydorus sphaericus. All species reacted to decreased pH levels during peak acidification in the 1980s by disappearing from most of the lakes of all categories; the only persisting species was Chydorus sphaericus. Most species returned to the lakes when pH started to increase in the 1990s, although their return was noticeably slower in AS lakes. Alona quadrangularis decreased its distribution range over the studied period; Polyphemus pediculus was mostly detected in the 1910s only. The number of species was highest in all lake categories when dwarf pine was present in the lake catchment. On the whole, the littoral community was richest in NS lakes.     

Protein reutilisation in corms of Colchicum autumnale

Colchicum autumnale L. is a monocotyledonous geophyte with hysteranthous leaves, i.e. flowering and leaf growth occur in different time periods. Because after the starch, the second prominent storage compound of corm is represented by proteins, we were interested in nitrogen remobilisation during the annual life cycle of C. autumnale. In this context the content of soluble and insoluble proteins were measured in parallel with determination of some exo-and endopeptidase activities. Our results indicate that the continual proteolysis occurs in both mother and new daughter corms during the whole life-cycle of the plant. L-Ala-aminopeptidase and trypsin-like endopeptidase were the most active peptidases in both mother and daughter corms. As the protein level of mother corm did not change significantly during the development of the future above-ground part under the soil surface (the first, autumnal developmental stage), the developmental profile of nitrate reductase activity was estimated followed by evaluation of total nitrogen and amino acid contents. Significant activity of root nitrate reductase was detected in the roots only in the second, vernal stage. Our results showed that the stored proteins constituted a relevant nitrogen source partly required by the growth processes of the late autumnal stage, but mainly by the intensive growth of leaves and reproductive structures during the second, photosynthetically active stage of the life-cycle.     

Chemical composition of the Tatra Mountain lakes: Response to acidification

Data from two surveys of the Tatra Mountain lakes (Slovakia and Poland) performed in the autumns of 1984 (53 lakes) and 1993 or 1994 (92 lakes) were used to estimate spatial variability in water chemistry in this lake district during the period of maximum European acid deposition. The ionic content of the lakes was generally low, with conductivity (at 20°C) ranging from 1.1 to 4.7 mS m^?1 and 23% of the lakes had a depleted carbonate buffering system. Major factors governing differences in lake-water chemistry were bedrock composition and amount of soil and vegetation in their catchment areas. Compared to lakes in the predominantly granitic central part of the Tatra Mountains, lakes in the West Tatra Mountains had higher concentrations of base cations and alkalinity due to the presence of metamorphic rocks in the bedrock. Concentrations of phosphorus, organic carbon, organic nitrogen, and chlorophyll-a were highest in forest lakes and decreased with decreasing density of vegetation and soil cover in the catchment areas. Concentrations of nitrate showed an opposite trend. Several exceptions to these general patterns in chemical and biological composition were due to exceptional geology or hydrology of the lake catchments.     

Seasonal dynamics of chironomids in the profundal zone of a mountain lake (L’adové pleso,the Tatra Mountains,Slovakia)

The profundal community of L’adové pleso (an oligotrophic high mountain seepage lake at an altitude of 2,057 m with a max. depth of 18 m and an ice-cover period from October–July) was studied from December 2000–October 2001. Chironomidae, the most significant part of the studied community, are represented by four taxa and dominated by Micropsectra radialis Goetghebuer, 1939 and Pseudodiamesa nivosa (Goethgebuer, 1928). These two species showed a 1-year life cycle. The total densities of chironomids varied from 0 to 5,927 ind. m^?2; no chironomids, or very low densities, were found during the winter/spring period, probably due to low oxygen concentrations in the medial part of the lake. These low oxygen concentrations probably caused the relocation of larvae from the medial part of the sedimentary area at the same time.     

GC content dependency of open reading frame prediction via stop codon frequencies

A frequently used approach for detecting potential coding regions is to search for stop codons. In the standard genetic code 3 out of 64 trinucleotides are stop codons. Hence, in random or non-coding DNA one can expect every 21st trinucleotide to have the same sequence as a stop codon. In contrast, the open reading frames (ORFs) of most protein-coding genes are considerably longer. Thus, the stop codon frequency in coding sequences deviates from the background frequency of the corresponding trinucleotides. This has been utilized for gene prediction, in particular, in detecting protein-coding ORFs. Traditional methods based on stop codon frequency are based on the assumption that the GC content is about 50%. However, many genomes show significant deviations from that value. With the presented method we can describe the effects of GC content on the selection of appropriate length thresholds of potentially coding ORFs. Conversely, for a given length threshold, we can calculate the probability of observing it in a random sequence. Thus, we can derive the maximum GC content for which ORF length is practicable as a feature for gene prediction methods and the resulting false positive rates. A rough estimate for an upper limit is a GC content of 80%. This estimate can be made more precise by including further parameters and by taking into account start codons as well. We demonstrate the feasibility of this method by applying it to the genomes of the bacteria Rickettsia prowazekii, Escherichia coli and Caulobacter crescentus, exemplifying the effect of GC content variations according to our predictions. We have adapted the method for predicting coding ORFs by stop codon frequency to the case of GC contents different from 50%. Usually, several methods for gene finding need to be combined. Thus, our results concern a specific part within a package of methods. Interestingly, for genomes with low GC content such as that of R. prowazekii, the presented method provides remarkably good results even when applied alone.     

2-Styrylindolium based fluorescent probes visualize neurofibrillary tangles in Alzheimer’s disease

We evaluated 2-styrylindolium derivatives (6–11) as novel and selective probes for neurofibrillary tangles (NFTs) on brain sections of AD patients. The staining experiments indicated that these compounds may bind selectively to NFTs in the presence of ß-amyloid (Aß) plaques. Cell free binding assays confirmed that 2-[2-[4-(1-pyrrolidinyl)phenyl]ethenyl]-1,3,3-trimethyl-3H-indolium iodide (9) and 2-[2-[4-(diethylamino)phenyl]ethenyl]-1-butyl-3,3-dimethyl-3H-indolium iodide (11) display excellent affinities to Tau-aggregates (IC₅₀ values of 5.1 and 1.4 nM, respectively) in the displacement of Thiazin Red R. These probes have good solubility in distilled water and low or no cytotoxicity in zebrafish embryo and liver hepatocellular carcinoma cell assays.