Comparative Genomics of Marine Mussels (Mytilus spp.) Gender Associated mtDNA: Rapidly Evolving atp8

The unusual mode of mitochondrial DNA inheritance, with two separate: maternal (F) and paternal (M) lineages, gives unique opportunities to study the evolution of the mitochondrial genome. This system was first discovered in the marine mussels Mytilus. The three related species: Mytilus edulis, Mytilus galloprovincialis and Mytilus trossulus form a complex in which the divergence of M and F lineages pre-dates the speciation. The complete mitochondrial genomes of both lineages were known for all species except Pacific M. trossulus. Here we report, for the first time, the complete sequences of both mitochondrial genomes of Pacific M. trossulus, filling the gap. While the reported M and F genomes are highly diverged (26%), they have similar organisation. The only difference is the translocation of one tRNA gene into the long, mosaic control region of the F genome. Consistent presence of an ORF which most likely represents the atp8 gene was confirmed in both genomes. The predicted protein has characteristics expected of the functional atp8 even though the M and F versions are markedly different in length. Comparative analysis involving all three species led to the conclusion that the cause of a faster evolution of atp8 and Mytilus mtDNA in general is most likely the Compensation-Draft Feedback process coupled with relatively relaxed selection in the M lineage. Thus, we postulate that the adaptive changes may have played a role in the emergence of highly diverged, barely recognizable atp8 in Mytilus mussels.     

Quantitative analysis of mRNA expression levels and DNA methylation profiles of three neighboring genes: FUS1, NPRL2/G21 and RASSF1A in non-small cell lung cancer patients

Background

Tumor suppressor gene (TSG) inactivation plays a crucial role in carcinogenesis. FUS1, NPRL2/G21 and RASSF1A are TSGs from LUCA region at 3p21.3, a critical chromosomal region in lung cancer development. The aim of the study was to analyze and compare the expression levels of these 3 TSGs in NSCLC, as well as in macroscopically unchanged lung tissue surrounding the primary lesion, and to look for the possible epigenetic mechanism of TSG inactivation via gene promoter methylation.

Methods

Expression levels of 3 TSGs and 2 DNA methyltransferases, DNMT1 and DNMT3B, were assessed using real-time PCR method (qPCR) in 59 primary non-small cell lung tumors and the matched macroscopically unchanged lung tissue samples. Promoter methylation status of TSGs was analyzed using methylation-specific PCRs (MSP method) and Methylation Index (MI) value was calculated for each gene.

Results

The expression of all three TSGs were significantly different between NSCLC subtypes: RASSF1A and FUS1 expression levels were significantly lower in squamous cell carcinoma (SCC), and NPRL2/G21 in adenocarcinoma (AC). RASSF1A showed significantly lower expression in tumors vs macroscopically unchanged lung tissues. Methylation frequency was 38–76 %, depending on the gene. The highest MI value was found for RASSF1A (52 %) and the lowest for NPRL2/G21 (5 %). The simultaneous decreased expression and methylation of at least one RASSF1A allele was observed in 71 % tumor samples. Inverse correlation between gene expression and promoter methylation was found for FUS1 (rs = −0.41) in SCC subtype. Expression levels of DNMTs were significantly increased in 75–92 % NSCLCs and were significantly higher in tumors than in normal lung tissue. However, no correlation between mRNA expression levels of DNMTs and DNA methylation status of the studied TSGs was found.

Conclusions

The results indicate the potential role of the studied TSGs in the differentiation of NSCLC histopathological subtypes. The significant differences in RASSF1A expression levels between NSCLC and macroscopically unchanged lung tissue highlight its possible diagnostic role in lung cancer in situ recognition. High percentage of lung tumor samples with simultaneous RASSF1A decreased expression and gene promoter methylation indicates its epigenetic silencing. However, DNMT overexpression doesn’t seem to be a critical determinate of its promoter hypermethylation.     

Combined molecular and morphological data provide insights into the evolution and classification of Chilocorini ladybirds (Coleoptera: Coccinellidae)

Ladybirds of the cosmopolitan tribe Chilocorini prey mainly on coccids and include several important biocontrol agents. The phylogenetic relationships of Chilocorini are poorly known. In this paper, we provide a phylogenetic reconstruction of Chilocorini containing all 27 genera based on five molecular markers and 86 adult morphological characters. Morphological character states were mapped on the combined data tree from Bayesian inference to analyse morphological traits of each genus. Sixteen morphological characters were selected to reconstruct the ancestral states using maximum parsimony and maximum likelihood methods. Divergence times were estimated based on the relaxed molecular clock approach. Our results indicate that Chilocorini, excluding Chilocorellus Miyatake, is monophyletic and closely related to Plotinini. The crown group Chilocorini was estimated to date back to the Middle Cretaceous. Anisorcus Crotch, Egius Mulsant, Phaenochilus Weise and Simmondsius Ahmad & Ghani are synonymized here with Chilocorus Leach ( syn.n. ). The genus Chilocorellus is excluded from Chilocorini. The split of current genera was estimated to have occurred during the Middle Paleogene to Late Paleogene.     

Variability and structure of natural populations of Hordelymus europaeus (L.) Jess. ex Harz and Leymus arenarius (L.) Hochst. as revealed by morphology and DNA markers

Seven populations of Hordelymus europaeus and four populations of Leymus arenarius from Poland were subjected to examination of 36 morphological characters. This study showed that both species are relatively uniform and that morphological variation of their populations represents a continuum. Of those, three populations of either species were selected for analysis with molecular markers – RAPDs and AFLPs. These populations differed with respect of geographical location as well as syntaxa and habitat. RAPD-PCR was performed for individual plants and clearly grouped them according to the population origin. For either H. europaeus or L. arenarius - the studied populations differed in degree of their intrinsic variation while none of them as a whole was significantly different from the remaining ones. In AFLP analysis the studied populations were represented by DNA pools of several individual plants. Also this approach allowed discrimination among the population samples of both H. europaeus and L. arenarius. Both RAPDs and AFLPs were accordant in indication that H. europaeus exceeds L. arenarius with respect to variation accumulated at the DNA level. It is the sixth paper of the series: Biodiversity of wild Triticeae (Poaceae) in Poland. The first is: M. Mizianty (2005). Variability and structure of natural populations of Elymus caninus (L.) L. based on morphology. Pl. Syst. Evol. 251: 199-216. The second: M. Mizianty, and M. Szklarczyk (2005). Systematic significance of Elymus caninus morphological characters revealed by AFLP analysis. In: L. Frey (ed.) Biology of grasses. W. Szafer Institute of Botany, Polish Academy of Sciences. Kraków, pp 9–21. The third: M. Mizianty et al. (2006). Variability and structure of natural populations of Elymus caninus (L.) L. and their possible relationship with Hordelymus europaeus (L.) Jess. ex Harz revealed by AFLP analysis. Pl. Syst. Evol. 256: 193–200. The fourth: M. Mizianty (2006). Variability and structure of natural populations of Hordeum murinum L. based on morphology. Pl. Syst. Evol. 261: 139–150. The fifth: B. Paszko Variability and structure of natural populations of Brachypodium pinnatum and B. sylvaticum based on morphology. Acta Soc. Bot. Pol. (in press).     

Coexpression of vimentin and desmin in gastric leiomyomas. An immunohistochemical study in paraffin sections

The aim of the study was to evaluate the incidence of the reactions for vimentin and desmin in gastric leiomyomas routinely processed in formalin and embedded i paraffin. The material studied included four benign leiomyomas, seven malignant leiomyomas and three malignant epithelioid leiomyomas. A positive reaction to vimentin was found in 13 out 14 leiomyomas under study. The number of neoplastic cells showing vimentin expression was larger in malignant, especially epithelioid leiomyomas than in non-malignant leiomyomas. A positive reaction for desmin in neoplastic cells was found in 9 leiomyomas 64%. One non-malignant leiomyoma showed a moderate reaction. In the remaining eight cases the reaction was weak and occurred in single neoplastic cells. Coexpression of vimentin and desmin in neoplastic cells occurred in 8 out of 9 leiomyomas with a positive reaction for desmin. Coexpression of vimentin and desmin occurred also in the smooth muscle cells of blood vessels in all 14 cases. A weak reaction for desmin or its lack in the tumour cells of leiomyomas with its marked expression in the smooth muscle cells of the blood vessels and gastric wall outside the tumor points rather to a small number of desmin filaments in the neoplastic cells than to their destruction by fixation in formalin. The occurrence of the reaction to desmin only in a limited number of neoplastic cells questions the reliability of its use in the oligopiopsy material.     

Neuronal Autophagy: Self-eating or Self-cannibalism in Alzheimer’s Disease

Autophagy is a major intracellular degeneration pathway involved in the elimination and recycling of damaged organelles and long-lived proteins by lysosomes. Many of the pathological factors, which trigger neurodegenerative diseases, can perturb the autophagy activity, which is associated with misfolded protein aggregates accumulation in these disorders. Alzheimer’s disease, the first neurodegenerative disorder between dementias, is characterized by two aggregating proteins, β-amyloid peptide (plaques) and τ-protein (tangles). In Alzheimer’s disease autophagosomes dynamically form along neurites within neuronal cells and in synapses but effective clearance of these structures needs retrograde transportation towards the neuronal soma where there is a major concentration of lysosomes. Maturation of autophago-lysosomes and their retrograde trafficking are perturbed in Alzheimer’s disease, which causes a massive concentration of autophagy elements along degenerating neurites. Transportation system is disturbed along defected microtubules in Alzheimer’s disease brains. τ-protein has been found to control the stability of microtubules, however, phosphorylation of τ-protein or an increase in the total level of τ-protein can cause dysfunction of neuronal cells microtubules. Current evidence has shown that autophagy is developing in Alzheimer’s disease brains because of ineffective degradation of autophagosomes, which hold amyloid precursor protein-rich organelles and secretases important for β-amyloid peptides generation from amyloid precursor. The combination of raised autophagy induction and abnormal clearance of β-amyloid peptide-generating autophagic vacuoles creates circumstances helpful for β-amyloid peptide aggregation and accumulation in Alzheimer’s disease. However, the key role of autophagy in Alzheimer’s disease development is still under consideration today. One point of view suggests that abnormal autophagy induction causes a concentration of autophagic vacuoles rich in amyloid precursor protein, β-amyloid peptide and the elements crucial for its formation, whereas other hypothesis points to marred autophagic clearance or even decrease in autophagic effectiveness playing a role in maturation of Alzheimer’s disease. In this review we present the recent evidence linking autophagy to Alzheimer’s disease and the role of autophagic regulation in the development of full-blown Alzheimer’s disease.     

Macrozoobenthos of two Antarctic glacial coves: a comparison with non-disturbed bottom areas

There are only few studies on shallow Antarctic benthic communities associated with habitats affected by intense mineral sedimentation inflow. The analysis of macrofaunal communities associated with two shallow, isolated glacial coves was performed in Admiralty Bay (King George Island) and compared with non-disturbed sites. Multivariate analyses (hierarchical classification, nMDS) clearly separated glacial cove communities (two assemblages) from the sites situated outside both basins (two assemblages). The community influenced by the streamflow of glacial discharge of meltwater situated in the area with sandy–clay–silt sediments had a very low species richness, diversity and abundance. It was dominated by eurytopic, motile deposit feeding polychaetes such as Mesospio moorei, Tharyx cincinnatus and Leitoscoloplos kerguelensis as well as the bivalve Yoldia eightsi. The second glacial community of the area located at a grater distance from the outlet of the stream was characterized by sandy–clay–silt and clay–silt deposits and showed also a low diversity and species richness. The most abundant here were peracarid crustaceans, with the dominant opportunistic feeder Cheirimedon femoratus. Community from the non-disturbed area with silty–clay–sand, and silty–sand sediments had higher species richness and diversity. The assemblage of fauna from the sandy bottom has values of those two indexes similar to those found in the disturbed areas.