A Reexamination of Correlations of Amino Acids with Particular Secondary Structures

Using the data from Protein Data Bank the correlations of primary and secondary structures of proteins were analyzed. The correlation values of the amino acids and the eight secondary structure types were calculated, where the position of the amino acid and the position in sequence with the particular secondary structure differ at most 25. The diagrams describing these results indicate that correlations are significant at distances between −9 and 10. The results show that the substituents on Cβ or Cγ atoms of amino acid play major role in their preference for particular secondary structure at the same position in the sequence, while the polarity of amino acid has significant influence on α-helices and strands at some distance in the sequence. The diagrams corresponding to polar amino acids are noticeably asymmetric. The diagrams point out the exchangeability of residues in the proteins; the amino acids with similar diagrams have similar local folding requirements. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Occurrence and chemical diversity of the genus Bryoria in the Sučí Potok Valley, Veporské Vrchy Mountains (Central Slovakia)

Four species of the genus, Bryoria were found in the Sučí Potok Valley: B. capilaris (Ach.) Brodo & D. Hawksw., B. fuscescens (Gyeln.) Brodo & D. Hawksw., B. implexa (Hoffm.) Brodo & D. Hawksw., B. nadvornikiana (Gyeln.) Brodo & D. Hawksw. The most common species in the valley was B. implexa. Four chemotypes of this lichen were recognized.     

Cranial ontogenetic variability,sex ratio and age structure of the Red fox

Describing the sex ratio, age structure of the population and ontogenetic variability of Red fox, Vulpes vulpes (Canidae, Carnivora) skull parameters, this study is based on 416 male and 289 female skulls collected in the Czech Republic. The skulls analysed came from feral individuals, that were shot by hunters. The male to female ratio was 1:0.69 regarding the whole population. Individuals younger than one year prevailed in the population (54% males, 48% females were in their first year of life). Four growth patterns of skull dimensions were described. The first group included mainly skull length dimensions (e.g. condylobasal length). They grew rapidly until the sixth month of life, becoming stabilised afterwards. The second group comprised parameters that were stable throughout the life (e.g. cheek tooth rows). Measurements representing the third growth pattern showed continual growth (mainly width dimensions, e.g. zygomatic breadth). Conversely, smaller dimensions of postorbital breadth were observed after the sixth month of life. Postorbital breadth represented the fourth growth pattern. It was concluded, that male and female Red foxes had similar ontogenetic skull development, even though there were some differences, e.g. in jugular breadth, which increased after the age of six months in males unlike in females.     

Optimized syntheses of Fmoc azido amino acids for the preparation of azidopeptides

The rise of CuI‐catalyzed click chemistry has initiated an increased demand for azido and alkyne derivatives of amino acid as precursors for the synthesis of clicked peptides. However, the use of azido and alkyne amino acids in peptide chemistry is complicated by their high cost. For this reason, we investigated the possibility of the in‐house preparation of a set of five Fmoc azido amino acids: β‐azido l ‐alanine and d ‐alanine, γ‐azido l ‐homoalanine, δ‐azido l ‐ornithine and ω‐azido l ‐lysine. We investigated several reaction pathways described in the literature, suggested several improvements and proposed several alternative routes for the synthesis of these compounds in high purity. Here, we demonstrate that multigram quantities of these Fmoc azido amino acids can be prepared within a week or two and at user‐friendly costs. We also incorporated these azido amino acids into several model tripeptides, and we observed the formation of a new elimination product of the azido moiety upon conditions of prolonged couplings with 2‐(1H‐benzotriazol‐1‐yl)‐1,1,3,3‐tetramethyluronium hexafluorophosphate/DIPEA. We hope that our detailed synthetic protocols will inspire some peptide chemists to prepare these Fmoc azido acids in their laboratories and will assist them in avoiding the too extensive costs of azidopeptide syntheses. Experimental procedures and/or analytical data for compounds 3 – 5 , 20 , 25 , 26 , 30 and 43 – 47 are provided in the supporting information. © 2017 The Authors Journal of Peptide Science published by European Peptide Society and John Wiley & Sons Ltd.     

Long-lasting Imprint of Former Glassworks on Vegetation Pattern in an Extremely Species-rich Grassland: A Battle of Species Pools on Mesic Soils

Increasing evidence suggests that past human activities have irreversibly changed soil properties and biodiversity patterns. In the White Carpathian Mts (Central-Eastern Europe), a mosaic of hyper-species-rich and species-rich patches have developed in a regularly mown dry grassland in the area of a glassworks abandoned in the eighteenth century. We tested whether and how anthropogenically changed soils affected the distribution of extraordinary species richness. Using magnetometry we detected former furnaces, workspace, waste deposit and unaffected surrounding grasslands and compared their vegetation and environmental conditions. Archaeological features, especially furnaces and waste deposits, showed a higher pH, higher soil concentrations of exchangeable phosphorus, manganese, lead and calcium, and higher productivity. Surrounding grassland showed higher iron and sodium concentrations in the soil, higher N:P ratio in the biomass and higher species richness. Moisture was uniformly lower in soils on archaeological features, where non-trivially a more ‘mesic’ vegetation in terms of European habitat classification occurred. Plant compositional variation was best explained by water-extractable phosphorus. Because nutrient-richer patches were not moister as common elsewhere, and because species richness was only poorly accounted for by productivity, the occurrence of a species-poor ‘mesic’ vegetation on archaeological features was evidently caused by a long-lasting phosphorus oversupply which favours a comparatively small species pool of rather recently arriving species. On the contrary, surrounding phosphorus-poorer grasslands still contain the ancient species pool whose extraordinary size determines the exceptional species richness of grasslands in the study region. Its maintenance or restoration demands a persistent phosphorus deficiency.     

Mechanical strain to maxillary incisors during direct laryngoscopy

Dexmedetomidine is a highly selective adrenergic receptor agonist, which has a dose-dependent sedative hypnotic effect. Furthermore, it also has pharmacological properties, and the ability to inhibit sympathetic activity and improve cardiovascular stability during an operation. However, its protective effect on patients with severe craniocerebral injury in the perioperative period remains unclear. Eighty adult male SD rats were used and divided into two groups (n = 40, each group): dexmedetomidine injury group (experimental group), and sodium chloride injury group (control group). Models of severe craniocerebral injury were established in these two groups using the modified Feeney’s free-fall method. As soon as the establishment of models was succeed, rat in the experimental group received 1 μg of dexmedetomidine (0.1 ml), while each rat in the control group was given 0.1 ml of 0.9% sodium chloride. Blood was sampled from an incision at the femoral vein to detect TNF-α and IL-2 levels at 1, 12, 24,36,48 and 72 h after establishing the model in the two groups. After severe craniocerebral injury, TNF-α levels of rats were lower in every stage and at different degrees in the experimental group than in the control group (P < 0.05), while IL-2 levels were lower in the experimental group to different extents (P < 0.05). Dexmedetomidine protects the brain of rats with severe craniocerebral injury by reducing the release of inflammatory mediators.     

On the classification of normally distributed neurons: an application to human dentate nucleus

One of the major goals in cellular neurobiology is the meaningful cell classification. However, in cell classification there are many unresolved issues that need to be addressed. Neuronal classification usually starts with grouping cells into classes according to their main morphological features. If one tries to test quantitatively such a qualitative classification, a considerable overlap in cell types often appears. There is little published information on it. In order to remove the above-mentioned shortcoming, we undertook the present study with the aim to offer a novel method for solving the class overlapping problem. To illustrate our method, we analyzed a sample of 124 neurons from adult human dentate nucleus. Among them we qualitatively selected 55 neurons with small dendritic fields (the small neurons), and 69 asymmetrical neurons with large dendritic fields (the large neurons). We showed that these two samples are normally and independently distributed. By measuring the neuronal soma areas of both samples, we observed that the corresponding normal curves cut each other. We proved that the abscissa of the point of intersection of the curves could represent the boundary between the two adjacent overlapping neuronal classes, since the error done by such division is minimal. Statistical evaluation of the division was also performed.