The molecular genetic typification of planarians in the genus Bdellocephala (Dendrocoelidae, Tricladida, Turbellaria) from Lake Baikal with an assessment of their species diversity

Baikal planaria from genus Bdellocephala were typified using rDNA locus coding 5'--end domain of 18S ribosome RNA. Five colour forms of 24 possible variants that differ in diapason 0-1.3% of genotype were determined by comparative analysis of nucleotide sequences. The authors use back colour--one of the most variable and typical character in the given group--to collect material for investigation. It allows to minimize the size of investigation sample and at the same time to cover maximum variability of Bdellocephala. One of the positive result of molecular typification of colour forms was a discovery of unique individuals that belong to new species. Karyological analysis of colour forms shows variations in chromosome numbers that divide planaria into 3 groups (2n = 20, 24, 26). Comparative analysis of morphological and ecological characters and karyotypes of some forms united by the same genotype allows to distinguish them as separate species. Criteria of modern phenetic system of Baikal planaria are discussed.     

Spaceflight Effects on Cytochrome P450 Content in Mouse Liver

Hard conditions of long-term manned spaceflight can affect functions of many biological systems including a system of drug metabolism. The cytochrome P450 (CYP) superfamily plays a key role in the drug metabolism. In this study we examined the hepatic content of some P450 isoforms in mice exposed to 30 days of space flight and microgravity. The CYP content was established by the mass-spectrometric method of selected reaction monitoring (SRM). Significant changes in the CYP2C29, CYP2E1 and CYP1A2 contents were detected in mice of the flight group compared to the ground control group. Within seven days after landing and corresponding recovery period changes in the content of CYP2C29 and CYP1A2 returned to the control level, while the CYP2E1 level remained elevated. The induction of enzyme observed in the mice in the conditions of the spaceflight could lead to an accelerated biotransformation and change in efficiency of pharmacological agents, metabolizing by corresponding CYP isoforms. Such possibility of an individual pharmacological response to medication during long-term spaceflights and early period of postflight adaptation should be taken into account in space medicine.     

In vitro organotypic cultivation of adult newt and rat retinas

Adult rat and newt retinas were studied during long organotypic 3D cultivation. A high proliferation level was discovered in the region of growth by applying DNA synthesis markers and in vitro mitosis registration in newt retina. Aggregates were formed in the retina spheroid cavity because dedifferentiated cells migrated into this region. Small cell populations in nuclear layers also had dividing and migration capacity. Rosette formation has been shown in newt retina. It is a characteristic of fetal retinal development under pathological conditions. The antiGFAP antibody dye demonstrated an increase in the parent Müller cell population and generation of a small cell pool with short GFAP-extensions de novo. Recoverin expression studies detected its translocation from photoreceptor extensions to the cell bodies. Moreover, protein was presented in some cells inside the spheroid. It has been shown for the first time that cell proliferation occurred in the adult rat retinal spheroid developing in vitro; BrdU-positive cells and multiple mitoses were revealed in this fissue. However, the source of proliferation was not in the peripheral retina, and resident macrophages and glial cells located among neurons of the inner nuclear layer had the ability to divide. The antiGFAP antibody showed an increase in GFAP fibers in the rat retina as well as in the newt retina. Recoverin translocated into photoreceptor perikaryons and the outer plexiform layer in cultivated rat retina. Interestingly, some cells with probably de novo expression of recoverin were discovered in rat and newt inner retinas.     

Glutamine effect on cultured granule neuron death induced by glucose deprivation and chemical hypoxia

Using a specific fluorescent probe of mitochondrial membrane potential (tetramethylrhodamine ethyl ester), we have shown that glucose deprivation (GD) of cultured cerebellar granule neurons (CGN) for 3 h lowers mitochondrial membrane potential in these cells. Longer glucose starvation (24 h) causes CGN death that is not prevented by blockers of ionotropic glutamate receptors (MK-801 (10 μM) and NBQX (10 μM)). Glutamine or pyruvate (2 mM) maintain membrane potential of mitochondria and decrease CGN death under GD conditions. In the presence of glucose the mitochondrial respiratory chain blocker rotenone induces neuron death potentiated by glutamine. The potentiation effect is completely prevented by blockers of ionotropic glutamate receptors. These results show that glutamine under conditions of GD can be utilized by mitochondria as substrate, but at the same time, in the case of mitochondrial function deterioration, metabolism of this amino acid results in glutamate accumulation to toxic level.     

LTR retrotransposons in the <Emphasis Type="Italic">Aspergillus fumigatus</Emphasis> and <Emphasis Type="Italic">A. nidulans</Emphasis> genomes

Fungi of the genus Aspergillus can infect all tissues and organs, causing invasive mycosis (aspergillosis). This disease can be fatal, especially in immunocompromised patients. Microbiological monitoring of these infectious agents is obligatory in modern medical facilities. Mobile elements can be used as markers to identify the Aspergillus species and strains found indoors as well as to diagnose aspergillosis. Genomic sequences of two Aspergillus species, A. fumigatus and A. nidulans, were analyzed in silico in order to detect LTR retrotransposons. These species were found to considerably differ in the composition of retrotransposon families. One of the families, present in both Aspergillus species, was phylogenetically quite different from all known fungal retrotransposons. The majority of its elements were damaged copies. Nevertheless, allegedly undamaged LTR retrotransposon copies were described that contained intact ORFs and might be active.     

Homology-dependent inactivation of LTR retrotransposons in genomes of Aspergillus fumigatus and A. nidulans

Repeat-induced point mutation (RIP) is the most intriguing among the known mechanisms of repeated sequences inactivation because of its ability to produce irreversible mutation of repeated DNA. Discovered for the first time in Neurospora crassa, RIP is characterized by C:G to T:A transitions in duplicated sequences. The mechanisms and distribution of RIP are still purely investigated. Mobile elements are a common target for the processes which lead to homology-dependent silencing because of their ability to propagate themselves. We have done comparative analysis of LTR retrotransposons in genomic scale from genomes of two aspergilli fungi--Aspergillus funmigatus and A. nidulans, based on several copies we reconstructed "de-RIP" retroelements. Investigations of frequencies of CpG, CpA and TpG sites, which are potential targets for mutagenesis, showed the much lower frequencies of these sites in mobile elements in comparison with structural genes. LTR retrotransposons from A. fumigatus and A. nidulans have different ratio of types of substitutions. Our analysis indicates that two investigated fungi have or had the RIP-like processes for repeated sequences inactivation, in various modes. Whereas in A. fumigatus the context for mutagenesis consists of both CpG and CpA sites, in A. nidulans inactivation seems to proceed only on CpG dinucleotides. The present investigation gives a theoretical background for planning of experimental studying of RIP inactivation in aspergilli.     

Improving model construction of profile HMMs for remote homology detection through structural alignment

Background  

Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance.     

Post-translational environmental switch of RadA activity by extein–intein interactions in protein splicing

Post-translational control based on an environmentally sensitive intervening intein sequence is described. Inteins are invasive genetic elements that self-splice at the protein level from the flanking host protein, the exteins. Here we show in Escherichia coli and in vitro that splicing of the RadA intein located in the ATPase domain of the hyperthermophilic archaeon Pyrococcus horikoshii is strongly regulated by the native exteins, which lock the intein in an inactive state. High temperature or solution conditions can unlock the intein for full activity, as can remote extein point mutations. Notably, this splicing trap occurs through interactions between distant residues in the native exteins and the intein, in three-dimensional space. The exteins might thereby serve as an environmental sensor, releasing the intein for full activity only at optimal growth conditions for the native organism, while sparing ATP consumption under conditions of cold-shock. This partnership between the intein and its exteins, which implies coevolution of the parasitic intein and its host protein may provide a novel means of post-translational control.