MODBASE, a database of annotated comparative protein structure models

MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAST, IMPALA and MODELLER. MODBASE uses the MySQL relational database management system for flexible and efficient querying, and the MODVIEW Netscape plugin for viewing and manipulating multiple sequences and structures. It is updated regularly to reflect the growth of the protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different datasets. The largest dataset contains models for domains in 304 517 out of 539 171 unique protein sequences in the complete TrEMBL database (23 March 2001); only models based on significant alignments (PSI-BLAST E-value < 10^–4) and models assessed to have the correct fold are included. Other datasets include models for target selection and structure-based annotation by the New York Structural Genomics Research Consortium, models for prediction of genes in the Drosophila melanogaster genome, models for structure determination of several ribosomal particles and models calculated by the MODWEB comparative modeling web server.     

Vocal repertoire of the social Mashona mole-rat (Fukomys darlingi) and how it compares with other mole-rats

Vocalizations play a major role in communication of mammals with subterranean lifestyles since other senses are dramatically restricted in the environment of below ground burrows. In our study, we recorded vocalizations of 10 adult males and 10 adult females of a social bathyergid, the Mashona mole-rat (Fukomys darlingi) in different behavioural contexts. Vocalizations were divided into four categories according to behavioural contexts. Similar to other subterranean mammals, the range of Mashona mole-rat calls is shifted towards lower frequencies. We described 10 types of true vocal signals and 2 mechanical sounds. The vocal repertoire of the Mashona mole-rat is less rich compared to other social mole-rats, corresponding with its low mean family size. Interestingly, this species has a higher diversity in contact and distress calls, while using a relatively low number of aggressive signals.     

Presence of antibodies against Aujeszky's disease virus in wild boar (Sus scrofa) in Slovenia

Serum samples from 427 hunter-killed wild boar (Sus scrofa) from Slovenia were tested for antibodies to Aujeszky's disease virus (ADV). Samples were collected throughout Slovenia and corresponded to 6.2% of the total harvest. Antibodies against ADV were detected in 111 sera (26%) using a commercial enzyme-linked immunosorbent assay (ELISA). Antibody prevalence increased significantly with age. This report describes the first evidence of ADV infection in wild boar populations in Slovenia.     

Adiaspiromycosis in large free living carnivores

Adiaspiromycosis was identified in 6 animals in the examination of the lungs of 90 large carnivores. Emmonsia crescens (Chrysosporium parvum var. crescens) was demonstrated as the causative agent in 5 cases of disease — in the badger (Meles meles), the otter (Lutra lutra) and the fox (Vulpes vulpes). E. parva was demonstrated in the remaining case of disease in a fox. The badger is a new, up to the present unknown host of E. crescens. The sporadic occurrence of adiaspiromycosis in the fox and the otter classifies this disease among rare diseases of these animals.     

Chromosome aberrations caused by the effect of ultrasound in the meristematic cells ofvicia faba

In our present work the formation of chromosome aberrations has been studied in dependence on the tima interval between sonication and fixation of the primary root tips of Vicia faba. Maximum occurrence of aberrations was recorded immediately after sonication. The results of our experiments pointed to the fact that the frequency of the induced changes was independent on the sonic waves intensity within the range of 0-2—3-0 W/cm² and on ultrasond treatment duration within the range of 1—20 min. Studies of the distribution of chromosome abnormalities caused by ultrasound between the large and small chromosomes of theVicia faba meristematic cells in various time intervals showed that the frequency of the aberrations in both chromosome groups was proportional to its total metaphase lengths. Analysis of the type of aberrations observed in various time intervals after sonication indicated the simultaneous formation of chromosome and chromatide abnormalities.     

Herbicide Induced Oxidative Stress in Lettuce, Beans, Pea Seeds and Leaves

The effects of different paraquat, alachlor and metolachlor concentrations on superoxide dismutase (SOD), catalase (CAT), guaiacol peroxidase (GPX) activities and pigment contents in lettuce, bean and pea seeds and leaves were studied. Under paraquat (1.0 and 2.0 M) treatment declined SOD and CAT activities were observed in seeds and undetectable ativity of GPX. Germination of all investigated seeds was completely inhibited. All used concentrations of alachlor and metolachlor inhibited antioxidant enzyme activities in seeds but did not prevent germination and growth. In leaves, lower concentrations of these herbicides increased activities of antioxidant enzymes but at the highest herbicide concentrations (200 M) activities of investigated enzymes declined. The pigment contents the leaves decreased due to alachlor and metolachlor treatment in a concentration dependent manner.     

Analysis of nrDNA polymorphism in closely related diploid sexual, tetraploid sexual and polyploid agamospermous species

Nuclear sequences of ITS1-5.8S-ITS2 region of rDNA may be an important source of phylogenetically informative data provided that nrDNA is cloned and the character of sequence variation of clones is properly analyzed. nrDNA of selected Taraxacum sections was studied to show sequence variation differences among diploid sexual, tetraploid sexual and polyploid agamospermous species. We examined nucleotide characteristics, substitution pattern, secondary structure, and the phylogenetic utility of ITS1-5.8S-ITS2 from 301 clones of 32 species representing 11 sections. The most divergent sequences of ITS1&2 differed by 17.1% and in 5.8S only by 3.7%. The ITS1-5.8S-ITS2 characteristics, integrity and also stability of secondary structures confirmed that pseudogenes are not responsible for the above variation. The within-individual polymorphism of clones implies that the concerted evolution of ITS cistron of agamospermous polyploid Taraxacum is remarkably suppressed. Sequences of ITS clones proved to be a useful tool for mapping pathways of complex reticulation (polyploid hybridity) in agamospermous Taraxacum.     

Twirling Motion of Actin Filaments in Gliding Assays with Nonprocessive Myosin Motors

We present a model study of gliding assays in which actin filaments are moved by nonprocessive myosin motors. We show that even if the power stroke of the motor protein has no lateral component, the filaments will rotate around their axis while moving over the surface. Notably, the handedness of this twirling motion is opposite from that of the actin filament structure. It stems from the fact that the gliding actin filament has target zones, where its subunits point toward the surface and are therefore more accessible for myosin heads. Each myosin head has a higher binding probability before it reaches the center of the target zone than afterwards, which results in a left-handed twirling. We present a stochastic simulation and an approximative analytical solution. The calculated pitch of the twirling motion depends on the filament velocity (ATP concentration). It reaches ∼400 nm for low speeds and increases with higher speeds.     

The posibility of soil micromycetes produced the abscisic acid

The typical soil micromycetes Aspergillus niger and Cladosporium cladosporioides from the family moniliaceae were investigated with emphasis on production of ABA into the culture medium. The both fungi were cultivated in a static liquid Czapek — Dox medium and agar Czapek — Dox medium. Aspergillus niger and Cladosporium cladosporioides showed ability to produce ABA. Analytical detection of ABA from the culture medium was performed by TLC combinated with biotest and HPLC with spectroscopy.