Model-based Evidence for Cyclic Phenomena in a High-Elevation,Two-Species Forest

Cyclic phenomena have been the focus of many studies in stressed conifer forests. In these systems, suppressed seedlings are released following the synchronous death of canopy trees. These cycles occur over hundreds of years, and thus studying them in the field is difficult, if not impossible in some cases. This difficulty highlights the advantages of vegetation modeling studies. We used the individual-based gap model, University of Virginia Forest Model Enhanced (UVAFME), to simulate forest dynamics over time at a high-elevation, subalpine forest (dominated by Engelmann spruce and subalpine fir) in southern Wyoming. Following model calibration, UVAFME was validated by running it up an elevation gradient to determine if it could simulate changes in species composition with elevation. UVAFME was then run exclusively at the high-elevation location for periods of 3000 years to simulate long-term forest dynamics at the site. It was found that without the intrusion of exogenous disturbances, the subalpine zone of the Rocky Mountains demonstrates cyclic phenomena, both at the plot scale and the landscape scale. By itself, Engelmann spruce demonstrates a natural periodicity of 300 years, whereas subalpine fir has a natural periodicity of 200 years. In the two-species forest, both species have a periodicity of 300 years. This output corresponds well with field data from similar high-elevation conifer sites. These results, along with other examples of cyclic phenomena in ecological systems, indicate that periodicities in ecosystems may be more common than previously thought, though they may be difficult to distinguish due to disturbances and the time- and space-scales at which they occur.     

Folate and choline metabolism gene variants in relation to ovarian cancer risk in the Polish population

Data indicates that genetic factors alone do not account for ovarian tumorigenesis, suggesting that epigenetic status additionally affects this process. Therefore, we assessed the possible contribution of polymorphic variants of genes that may affect DNA methylation to the risk of ovarian cancer incidence in the Polish population. Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890), MTHFD1 (rs2236225), MTHFR (rs1801133), MTR (rs1805087), MTRR (rs1801394) and TCN2 (rs1801198) genotypes and alleles in patients with ovarian cancer (n = 136) and controls (n = 160). Moreover, using DNA and methylation-specific PCR (MSP) we also determined the methylation of the Cadherin 13 (CDH13) promoter in cancerous tissue from these patients. We did not observe a significant association between all studied gene variants and the incidence of ovarian cancer. The lowest P _trend = 0.1226 was observed for the MTHFR Ala222Val polymorphism. Moreover, the lowest P = 0.0772 was found in the comparison of MTHFR Ala/Ala versus Val/Val and Val/Ala genotypes in patients and control groups. The multifactor dimensionality reduction analysis also did not indicate a significant interactive genetic effect on ovarian cancer incidence for all analyzed SNPs. However, we observed frequent methylation of the CDH13 promoter in approximately 21% (29/136) patients with ovarian carcinomas. Our results might suggest that the selected polymorphic gene variants may not contribute to ovarian cancer incidence.     

Long-Term Patterns in the Population Dynamics of Daphnia longispina,Leptodora kindtii and Cyanobacteria in a Shallow Reservoir: A Self-Organising Map (SOM) Approach

The recognition of long-term patterns in the seasonal dynamics of Daphnia longispina, Leptodora kindtii and cyanobacteria is dependent upon their interactions, the water temperature and the hydrological conditions, which were all investigated between 1999 and 2008 in the lowland Sulejow Reservoir. The biomass of cyanobacteria, densities of D. longispina and L. kindtii, concentration of chlorophyll a and water temperature were assessed weekly from April to October at three sampling stations along the longitudinal reservoir axis. The retention time was calculated using data on the actual water inflow and reservoir volume. A self-organising map (SOM) was used due to high interannual variability in the studied parameters and their often non-linear relationships. Classification of the SOM output neurons into three clusters that grouped the sampling terms with similar biotic states allowed identification of the crucial abiotic factors responsible for the seasonal sequence of events: cluster CL-ExSp (extreme/spring) corresponded to hydrologically unstable cold periods (mostly spring) with extreme values and highly variable abiotic factors, which made abiotic control of the biota dominant; cluster CL-StSm (stable/summer) was associated with ordinary late spring and summer and was characterised by stable non-extreme abiotic conditions, which made biotic interactions more important; and the cluster CL-ExSm (extreme/summer), was associated with late spring/summer and characterised by thermal or hydrological extremes, which weakened the role of biotic factors. The significance of the differences between the SOM sub-clusters was verified by Kruskal-Wallis and post-hoc Dunn tests. The importance of the temperature and hydrological regimes as the key plankton-regulating factors in the dam reservoir, as shown by the SOM, was confirmed by the results of canonical correlation analyses (CCA) of each cluster. The demonstrated significance of hydrology in seasonal plankton dynamics complements the widely accepted pattern proposed by the plankton succession model for lakes, the PEG (Plankton Ecology Group), and may be useful for the formulation of management decisions in dam reservoirs.     

Horizontal migration of zooplankton in a littoral zone of the lowland Sulejow Reservoir (Central Poland)

Horizontal migrations of zooplankton between macrophyte patches and open areas were investigated in the sparsely vegetated littoral zone of the Sulejow Reservoir in June-July 2000 and 2001, using one-litre plastic traps. Large-bodied zooplankton: daphnids and copepods generally swam towards the open water at dusk and towards submerged macrophytes at dawn. Small-bodied zooplankton (Bosmina sp., Chydorus sp.) did not show any pattern of horizontal movement. At the time of the research the phytoplankton community was dominated by eatable diatoms (Cyclotella sp.), whose biomass reached 14 mg l⁻¹. Thus, bottom-up forces (food scarcity) are not likely to be responsible for the observed zooplankton migrations. Analyses of fish stomach contents showed high contribution of large zooplankters to the food of juvenile roach (Rutilus rutilus) and perch (Perca fluviatilis) which densely inhabited the littoral zone of reservoir. High fish pressure in the littoral zone along with high density of the predatory cladoceran, Leptodora kindtii in the open water, suggest that top-down forces (predatory pressure) were responsible for the migration of large zooplankton. At dusk predatory pressure of fish fry exceeded that of L. kindtii, forcing endangered zooplankton to escape from macrophytes towards open water. The opposite situation occurred at dawn. The consequences of the relationships for both zooplankton and fish fry communities dynamics are discussed.

     

Copy number variations of genes involved in stress responses reflect the redox state and DNA damage in brewing yeasts

The yeast strains of the Saccharomyces sensu stricto complex involved in beer production are a heterogeneous group whose genetic and genomic features are not adequately determined. Thus, the aim of the present study was to provide a genetic characterization of selected group of commercially available brewing yeasts both ale top-fermenting and lager bottom-fermenting strains. Molecular karyotyping revealed that the diversity of chromosome patterns and four strains with the most accented genetic variabilities were selected and subjected to genome-wide array-based comparative genomic hybridization (array-CGH) analysis. The differences in the gene copy number were found in five functional gene categories: (1) maltose metabolism and transport, (2) response to toxin, (3) siderophore transport, (4) cellular aldehyde metabolic process, and (5) L-iditol 2-dehydrogenase activity (p < 0.05). In the Saflager W-34/70 strain (Fermentis) with the most affected array-CGH profile, loss of aryl-alcohol dehydrogenase (AAD) gene dosage correlated with an imbalanced redox state, oxidative DNA damage and breaks, lower levels of nucleolar proteins Nop1 and Fob1, and diminished tolerance to fermentation-associated stress stimuli compared to other strains. We suggest that compromised stress response may not only promote oxidant-based changes in the nucleolus state that may affect fermentation performance but also provide novel directions for future strain improvement.     

Spatial and temporal distribution of copepod communities in the Adriatic Sea

The distribution of planktonic copepods in the Adriatic Seahas been analyzed on the basis of 132 samples collected at 35fixed stations during 4 seasonal cruises. A total of 127 specieshave been determined and 3 characteristic copepod communitieshave been identified. The distribution of copepod species hasbeen found to reflect the dual physiognomy of the Adriatic.The shallow northern section is characterized by high densityvalues, low species diversity, and the dominance of speciesbelonging to the estuarine and coastal communities. The relativelydeep waters of the southern section are characterized by lowdensity values, high species diversity, and the presence ofmany species belonging to the upper, middle, and lower zonesof the oceanic community. Temporal variations in the horizontalspread of these 3 communities are discussed in relation to seasonalcycles in abundance, vertical migration patterns, and the currentregime in the Adriatic.     

Polymerase eta is a short-lived, proteasomally degraded protein that is temporarily stabilized following UV irradiation in Saccharomyces cerevisiae

Saccharomyces cerevisiae Rad30 is the homolog of human DNA polymerase eta whose inactivation leads to the cancer-prone syndrome xeroderma pigmentosum variant. Both human and yeast polymerase eta are responsible for error-free bypass of UV-induced cis-syn pyrimidine dimers and several other DNA lesions. Here we show, using yeast strains expressing TAP-tagged Rad30, that the level of this protein is post-translationally regulated via ubiquitination and proteasome-mediated degradation. The half-life of Rad30 is 20 min and it increases due to proteasomal defects. Mutations inactivating components of the Skp1/cullin/ F-box (SCF) ubiquitin ligase complex: Skp1 and the F-box protein Ufo1 stabilize Rad30. Our results indicate also that ultraviolet irradiation causes transient stabilization of Rad30, which leads, in turn, to temporary accumulation of this polymerase in the cell. We conclude that proteolysis plays an important role in regulating the cellular abundance of Rad30. These results are the first indication of a role for controlled proteasomal degradation in modulating cellular level of translesion DNA polymerase in eukaryotes.     

In vitro morphogenetic responses from obligatory apomictic Taraxacum belorussicum Val. N. Tikhom seedlings explants

Taraxacum belorussicum Val. N. Tikhom, a poorly known and obligatory apomictic species, is an attractive plant material for studying the embryological, genetic and molecular mechanisms of apomixis. This work aims to obtain an efficient protocol for Taraxacum belorussicum regeneration. Four types of explants (cotyledons, hypocotyls, meristems and roots) that were taken from 2-weeks-old seedlings were used for in vitro cultures, and a fast and efficient protocol of T. belorussicum regeneration was obtained. Various ½ MS-based media containing IAA (5.71 µM), TDZ (4.54 µM) and PSK (100 nM) were chosen to assess the morphogenetic abilities of selected T. belorussicum explants. Studies on the role of PSK were done in three independent experiments, where the most significant factors were always light and darkness. All explants produced callus by the third day of culture and adventitious shoots after 7 days, although in an asynchronous indirect manner, and with different intensities for all explant types. The most preferred medium culture for hypocotyl, cotyledon and meristem explants was ½ MS?+?TDZ, and ½ MS?+?IAA?+?TDZ?+?PSK for roots which were the only explant sensitive to PSK. A short darkness pretreatment (8 days) in PSK medium was found suitable to enhance organogenesis. Secondary organogenesis was observed for regenerated plants on meristem explants from the ½ MS?+?IAA?+?TDZ?+?PSK medium. A weak somatic embryogenesis was observed for hypocotyl and cotyledon explants from ½ MS?+?IAA?+?TDZ and ½ MS?+?IAA?+?TDZ?+?PSK media. Histological and scanning electron microscope images (SEM) of T. belorussicum confirmed indirect organogenesis and somatic embryogenesis. Plant material treated with aniline blue solution revealed the presence of callose in the cell walls of cotyledon and hypocotyl explants. The presence of extracellular matrix (ECM) and heterogenic structure of callus was also verified by scanning electron microscopy and light microscopy, confirming the high morphogenetic ability of T. belorussicum.

     

Prevalence of oral hairy leukoplakia and epithelial infection by Epstein-Barr virus in pregnant women and diabetes mellitus patients--cytopathologic and molecular study

Oral hairy leukoplakia (OHL) is generally reported in patients with severe immunosuppression, except for a few cases in individuals with moderate degree of immunodeficiency. It is a white lesion that appears mainly in the lateral border of the tongue, caused by Epstein-Barr virus (EBV). The nuclear changes caused by EBV (Cowdry A inclusion, ground glass and nuclear beading), observed in cytopathology, are specific and enough for the definitive diagnosis of OHL, independent of the identification of the virus. Here we investigated the prevalence of OHL and the presence of EBV-DNA in the lateral borders of the tongue from 90 pregnant women, 90 diabetes mellitus (DM) patients, 30 healthy individuals (negative group) and 30 HIV+ with OHL (positive group). Smears were analyzed by cytopathology and polymerase chain reaction (PCR). A case of subclinical OHL and candidiasis was identificated in a DM patient by cytopathologic analysis. PCR results demonstrated EBV-DNA in 65% of the pregnant women, in 35% of DM patients, and in 20% of the healthy individuals. We concluded that DM patients can develop OHL with a low prevalence. Furthermore, the prevalence of the EBV in lateral border of the tongue is larger in pregnant women than in healthy individuals.