Isolation and Characterization of a Serine Protease,Ba III-4, from Peruvian <Emphasis Type="Italic">Bothrops atrox</Emphasis> venom

A serine protease from Bothrops atrox (Peruvian specimen’s venom) was isolated in two chromatographic steps in LC molecular exclusion and reverse phase-HPLC. This protein was denominated Ba III-4 (33,080.265 Da determinated by MALDI-TOF mass spectrometry) and showed pI of 5.06, Km 0.2 × 10⁻¹ M and the V _máx 4.1 × 10⁻¹ nmoles p-NA/lt/min on the synthetic substrate BapNA. Ba III-4 also showed ability to coagulate bovine fibrinogen. The serine protease was inhibited by soyben trypsin inhibitor and DA2II, which is an anti-hemorrhagic factor isolated from the opossum specie Didelphis albiventris. The primary structure of Ba III-4 showed the presence of His(44), Asp(94) and Ser(193) residues in the corresponding positions to the catalytic triad established in the serine proteases and Ser(193) are inhibited by phenylmethylsulfonylfluoride (PMSF). Amino acid analysis showed a high content of Asp, Glu, Gly, Ser, Ala and Pro, as well as 12 half-cysteine residues. Ba III-4 contained 293 amino acid residues and the primary structure of VIGGDECDIN EHPFLAFMYY SPRYFCGMTL INQEWVLTAA HCRYFCGMTL IHLGVHRESE KANYDEVRRF PKEKYFIFCD NNFTDDEVDK DIMLIRLDKP VSNSEHIAPL SLPSNPPSVG SVCRIMGWGQ TTTSPIDVLS PDEPHCANIN LFDNTVCHTA HPQVANTRTS TDTLCAGDLQ GGRDTCNGDS GGPLICNEQL HGILSWGGDP CAQPNKPAFY TKVYYFDHPW IKSIIAGNKK TVNFTCPPLR SDAKDDSTTY INQEWDWVLT AEHCDRTHMR NSFYDYSSIN SDS. Titration experiments did not show the presence of free sulfhydryl groups after 4 h incubation, nor were differences found in relation to titration kinetics in the presence of nondenaturating buffer. The isolation of this protein, Ba III-4, is of potential interest for the understanding of the pathomechanism of the snake venom action and for the identification of new blood coagulation enzymes of natural sources.     

Le site Paléolithique supérieur de Yudinovo : résultats des recherches archéologiques des années 2004–2016

The Upper Palaeolithic site of Yudinovo is one of the reference sites, located in the Desna River Basin. Multidisciplinary field studies, organized by the Desna mission (MAE RAS) and conducted between 2004 and 2016, have changed the vision existed so far on the structure and character of the Yudinovo site as well as on the duration of its occupations. The researchers found an ancient ford used by mammoths and other big mammals to cross the river, and a water source was one of the main factors in explaining the location of the Yudinovo site. The site has been occupied in a cyclical way for stays of varied duration. It was frequented by Prehistoric Men during the different seasons, and periods of occupation were apparently of different duration. The stratigraphy of the Yudinovo site reveals two major episodes in the evolution of the site. The dating of the lower archaeological layer dates back to 15,000–13,500 BC. J.C., while the upper layer is attributed to the period of 12,500–12,000 BC. The lower layer, which was formed during the major episode of occupation of the site, is rather thin and shows the complex stratigraphic structure. Various areas of activities, evacuation structures, storage areas with mammoth bones are discovered. Some elements of the lower archaeological layer are perfectly correlated with different episodes of sporadic occupation.     

Diapause decision in the small tortoiseshell butterfly,Aglais urticae

Insects in temperate areas spend the inhospitable winter conditions in a resting stage known as diapause. In species that diapause in the larval or pupal stage, the decision whether to diapause or develop directly is customarily taken during the late instars, with long days (i.e., long light phases) and high temperatures promoting direct development. Among butterflies that overwinter as adults, data are rare and variable, but imply that the larval daylength conditions can affect the pathway decision. We studied the small tortoiseshell, Aglais urticae L. (Lepidoptera: Nymphalidae, Nymphalini), which is partially bivoltine from Central Scandinavia and southwards, and tested whether the pathway decision is taken in the larval or adult stage. We reared larvae under long‐day (L22:D2) or short‐day (L12:D12) photoperiods, and recorded the pathway taken by the eclosing adults by scoring their propensity to mate and produce eggs. We also tested whether the larval photoperiod influenced adult ability to diapause by assessing adult survival. The results clearly indicate that (1) there is no detectable effect of larval photoperiod treatment on the pathway decision taken by adults whether to enter diapause or to develop directly, (2) some individuals are obligately univoltine and insensitive to photoperiod during adulthood, whereas (3) other individuals can facultatively enter diapause or direct development, depending on the photoperiod experienced after adult eclosion.     

Modulation of K+ translocation by AKT1 and AtHAK5 in Arabidopsis plants

Root cells take up K⁺ from the soil solution, and a fraction of the absorbed K⁺ is translocated to the shoot after being loaded into xylem vessels. K⁺ uptake and translocation are spatially separated processes. K⁺ uptake occurs in the cortex and epidermis whereas K⁺ translocation starts at the stele. Both uptake and translocation processes are expected to be linked, but the connection between them is not well characterized. Here, we studied K⁺ uptake and translocation using Rb⁺ as a tracer in wild‐type Arabidopsis thaliana and in T‐DNA insertion mutants in the K⁺ uptake or translocation systems. The relative amount of translocated Rb⁺ to the shoot was positively correlated with net Rb⁺ uptake rates, and the akt1 athak5 T‐DNA mutant plants were more efficient in their allocation of Rb⁺ to shoots. Moreover, a mutation of SKOR and a reduced plant transpiration prevented the full upregulation of AtHAK5 gene expression and Rb⁺ uptake in K⁺‐starved plants. Lastly, Rb⁺ was found to be retrieved from root xylem vessels, with AKT1 playing a significant role in K⁺‐sufficient plants. Overall, our results suggest that K⁺ uptake and translocation are tightly coordinated via signals that regulate the expression of K⁺ transport systems.     

Gene co-expression network analysis for identifying genetic markers in Parkinson's disease - a three-way comparative approach

Parkinson's disease (PD) is a neurodegenerative disorder involving progressive deterioration of dopaminergic neurons. Although few genetic markers for familial PD are known, the etiology of sporadic PD remains poorly understood. Microarray data was analysed for induced pluripotent stem cells (iPSCs) derived from PD patients and mature neuronal cells (mDA) differentiated from these iPSCs. Combining expression and semantic similarity, a highly-correlated PD interactome was constructed that included interactions of established Parkinson's disease marker genes. A novel three-way comparative approach was employed, delineating topologically and functionally important genes. These genes showed involvement in pathways like Parkin-ubiquitin proteosomal system (UPS), immune associated biological processes and apoptosis. Of interest are three genes, eEF1A1, CASK, and PSMD6 that are linked to PARK2 activity in the cell and thereby form attractive candidate genes for understanding PD. Network biology approach delineated in this study can be applied to other neurodegenerative disorders for identification of important genetic regulators.     

The energetic cost of arousal from torpor in the marsupial Sminthopsis macroura : benefits of summer ambient temperature cycles

The costs of arousal from induced torpor were measured in the striped-faced dunnart (Sminthopsis macroura; ca. 25 g) under two experimental ambient temperature cycles. The sinusoidal-type temperature cycles were designed to evaluate the effects of passive, ambient temperature heating during arousal from torpor in these insectivorous marsupials. It was hypothesised that diel ambient temperature cycles may offer significant energy savings during arousal in animals that employ daily torpor in summer as a response to unpredictable food availability. The cost of arousal in animals in which passive, exogenous heating occurred was significantly lower than that in animals not exposed to an ambient temperature cycle. The total cost of all three phases of torpor (entry, maintenance and arousal) was almost halved when animals were exposed to an ambient heating cycle from 15 °C to 25 °C over a 24-h period. In all animals, irrespective of the experimental ambient temperature cycle employed, the minimum torpor body temperature was 17–18 °C. The body temperature (T_b) of animals exposed to exogenous heating increased from the torpor T_b minimum to a mean value of 22.59 °C before endogenous heat production commenced. This relatively small increase in T_b of ca. 5 °C through `free' passive heating was sufficient to account for the significant ca. three-fold decrease in the cost of arousal and may represent an important energetic aid to free-ranging animals. Accepted: 4 October 1998     

Regeneration failure of lakeshore plants under an artificially altered water regime

To reveal the effects of artificial alteration of water level regime on the regeneration of lakeshore plants from seeds, we examined the factors causing regeneration failure in Lake Kasumigaura, Japan. A survey of microtopography within and around a remnant fragment of lakeshore vegetation revealed that, over a large range, the habitat is frequently inundated in spring under the current water regime, although it was rarely inundated under past water regimes. Analysis of the patterns of seedling emergence and establishment at microsites at various elevations revealed a significant negative correlation between number of inundation days and abundance or species-richness of seedlings that emerged in the spring. Most seedling deaths occurred when the study site was inundated. We suggest that regeneration failure caused by the artificial raising of the lakes water level is one of the principal mechanisms of the recent vegetational decline in the lake.     

Efficient identification of side-chain patterns using a multidimensional index tree

Convergent evolution often produces similar functional sites in nonhomologous proteins. The identification of these sites can make it possible to infer function from structure, to pinpoint the location of a functional site, to identify enzymes with similar enzymatic mechanisms, or to discover putative functional sites. In this article, a novel method is presented that (a) queries a database of protein structures for the occurrence of a given side chain pattern and (b) identifies interesting side-chain patterns in a given structure. For efficiency and to make a robust statistical evaluation of the significance of a similarity possible, patterns of three residues (or triads) are considered. Each triad is encoded as a high-dimensional vector and stored in an SR (Sphere/Rectangle) tree, an efficient multidimensional index tree. Identifying similar triads can then be reformulated as identifying neighboring vectors. The method deals with many features that otherwise complicate the identification of meaningful patterns: shifted backbone positions, conservative substitutions, various atom label ambiguities and mirror imaged geometries. The combined treatment of these features leads to the identification of previously unidentified patterns. In particular, the identification of mirror imaged side-chain patterns is unique to the here-described method. Interesting triads in a given structure can be identified by extracting all triads and comparing them with a database of triads involved in ligand binding. The approach was tested by an all-against-all comparison of unique representatives of all SCOP superfamilies. New findings include mirror imaged metal binding and active sites, and a putative active site in bacterial luciferase.