Small scale gradient effects on isopods (Crustacea: Oniscidea) in karstic sinkholes

We studied abundance and diversity patterns of terrestrial isopod assemblages along a ‘micro-scale’ vertical gradient in sinkholes in the Aggtelek National Park, Hungary. Time restricted manual sampling yielded ten native species, including endemic and rare ones. Along the gradient we found no major differences in species richness and -composition, and abundance decreased from the bottoms to the upper zones of the sinkholes. Species specific habitat preference on a vertical gradient showed two distinct groups by indicator species analysis: occurrence of habitat “generalists” was irrespective of vertical zones while “specialists” were restricted to the bottoms of the dolines. The latter group is formed mainly by rare species. We found that both diversity and evenness of isopod assemblages were highest in the bottom zone. Our results draw the attention to the significance of such common, yet undiscovered surficial depressions that can provide shelters for rare and specialist species and can provide shelter for survival of populations under changing climatic conditions.     

Effect of KRAS mutation status on the efficiency of Avastin therapy of colorectal cancer

Anti-angiogenic therapy became a standard care of advanced colorectal cancer. Since the most frequent genetic alteration of colorectal cancer is KRAS mutation we have analyzed its effect on the efficacy of Avastin treatment. Since 2008 we have determined the KRAS status of 575 patients with colorectal carcinoma using a sensitive screening method and sequencing. In our database the frequency of KRAS mutation in colorectal cancer is 37% (codon 12: 31% followed by codon 13: 6%). We have examined the effect of KRAS status on the efficacy of Avastin treatment in 35 patients. Progression-free survival of KRAS mutant patients was highly similar to that of wild-type patients using log-rank test (9.2+/-5.5 months versus 8.7+/-5.7 months, respectively). Our data support those observations that KRAS status of colorectal cancer does not interfere with the efficacy of Avastin treatment.     

Evolution: Tracing the origins of centrioles, cilia, and flagella

Centrioles/basal bodies (CBBs) are microtubule-based cylindrical organelles that nucleate the formation of centrosomes, cilia, and flagella. CBBs, cilia, and flagella are ancestral structures; they are present in all major eukaryotic groups. Despite the conservation of their core structure, there is variability in their architecture, function, and biogenesis. Recent genomic and functional studies have provided insight into the evolution of the structure and function of these organelles.     

Comprehensive analysis of MGMT promoter methylation: correlation with MGMT expression and clinical response in GBM

O⁶-methylguanine DNA-methyltransferase (MGMT) promoter methylation has been identified as a potential prognostic marker for glioblastoma patients. The relationship between the exact site of promoter methylation and its effect on gene silencing, and the patient''s subsequent response to therapy, is still being defined. The aim of this study was to comprehensively characterize cytosine-guanine (CpG) dinucleotide methylation across the entire MGMT promoter and to correlate individual CpG site methylation patterns to mRNA expression, protein expression, and progression-free survival. To best identify the specific MGMT promoter region most predictive of gene silencing and response to therapy, we determined the methylation status of all 97 CpG sites in the MGMT promoter in tumor samples from 70 GBM patients using quantitative bisulfite sequencing. We next identified the CpG site specific and regional methylation patterns most predictive of gene silencing and improved progression-free survival. Using this data, we propose a new classification scheme utilizing methylation data from across the entire promoter and show that an analysis based on this approach, which we call 3R classification, is predictive of progression-free survival (HR  = 5.23, 95% CI [2.089–13.097], p<0.0001). To adapt this approach to the clinical setting, we used a methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) test based on the 3R classification and show that this test is both feasible in the clinical setting and predictive of progression free survival (HR  = 3.076, 95% CI [1.301–7.27], p = 0.007). We discuss the potential advantages of a test based on this promoter-wide analysis and compare it to the commonly used methylation-specific PCR test. Further prospective validation of these two methods in a large independent patient cohort will be needed to confirm the added value of promoter wide analysis of MGMT methylation in the clinical setting.     

Grazed Pannonian grassland beta-diversity changes due to C4 yellow bluestem

This study investigates how yellow bluestem affects biodiversity in a typical Pannonian grassland. Beta diversity (i.e. the finescale spatial variability of species compositions), was estimated by the realized number of species combinations sampled at various scales. Sampling was performed by a standard protocol. Presences of plant species were recorded along 52.2 m long belt transect of 1044 units of 0.05x0.05 m contiguous microquadrats. According to the results the massive presence of tested C₄ grass significantly reduced species richness of the grassland. Beta diversity assessment revealed that 90% of species combinations were lost due to yellow bluestem invasion. Fine-scale spatial pattern analyses showed complete local extinctions of other species from microsites dominated by yellow bluestem. This local extinction is enhanced by the specific clonal architecture of this species and by the accumulation of litter. Other dominant grasses had no effect on fine scale diversity, i.e. they could coexist well with other elements of the local flora. This study presents currently developed microhabitat types, forecasts and also draws attention to the danger that climate warming will probably enhance the spread of this detrimental C₄ species.     

Abundance dynamics and functional role of predaceous <Emphasis Type="Italic">Leptodora kindtii</Emphasis> in the Curonian Lagoon

The abundance and distribution of predatory cladoceran Leptodora kindtii was investigated in the estuarine lagoon (Curonian Lagoon, SE Baltic Sea). Three hydrodynamically different parts of the lagoon were selected, representing transitory oligohaline, intermediate freshwater and stagnant freshwater sites. L. kindtii was least abundant at the oligohaline site, never occurring at salinities greater than 4 psu. At the two freshwater sites, the abundance of L. kindtii varied from a low of <0.1 up to 2.2 indv. L⁻¹ during peak abundance. Two peaks of L. kindtii abundance were observed with timing differences between stations: at the stagnant site the population of L. kindtii peaked two weeks earlier relative to the more hydrodynamically active sites, likely due to a 2°C higher May temperature. The small body size of L. kindtii in the lagoon (seasonal mean 2.68±0.6 mm) shows high fish predation pressure and predicts small cladocerans, juvenile copepods and rotifers being in the preferred prey size range. The calculated L. kindtii daily consumption during the population peak was as high as 100% of the daily zooplankton production, which implies high potential of this predator to shape the grazing zooplankton community in the lagoon.     

Time-Lapse Imaging of Neuroblastoma Cells to Determine Cell Fate upon Gene Knockdown

Neuroblastoma is the most common extra-cranial solid tumor of early childhood. Standard therapies are not effective in case of poor prognosis and chemotherapy resistance. To improve drug therapy, it is imperative to discover new targets that play a substantial role in tumorigenesis of neuroblastoma. The mitotic machinery is an attractive target for therapeutic interventions and inhibitors can be developed to target mitotic entry, spindle apparatus, spindle activation checkpoint, and mitotic exit. We present an elaborate analysis pipeline to determine cancer specific therapeutic targets by first performing a focused gene expression analysis to select genes followed by a gene knockdown screening assay of live cells. We interrogated gene expression studies of neuroblastoma tumors and selected 240 genes relevant for tumorigenesis and cell cycle. With these genes we performed time-lapse screening of gene knockdowns in neuroblastoma cells. We classified cellular phenotypes and used the temporal context of the perturbation effect to determine the sequence of events, particularly the mitotic entry preceding cell death. Based upon this phenotype kinetics from the gene knockdown screening, we inferred dynamic gene functions in mitosis and cell proliferation. We identified six genes (DLGAP5, DSCC1, SMO, SNRPD1, SSBP1, and UBE2C) with a vital role in mitosis and these are promising therapeutic targets for neuroblastoma. Images and movies of every time point of all screened genes are available at https://ichip.bioquant.uni-heidelberg.de.     

Nests of Augochlora (A.) esox in Bromeliads,a Previously Unknown Site for Sweat Bees (Hymenoptera: Halictidae)

Five nests of Augochlora (Augochlora) esox (Vachal, 1911) were detected in the rosettes of bromeliads (Aechmaea nudicaulis and A. lindenii) on the island of Santa Catarina, Brazil. Two of the nests were constructed after manipulation of bromeliads as trap nests. Cells were built in the central funnel filled with moist black humus in a scattered way without a detectable pattern. One founding female and all brood stages from eggs to pupae as well as male and female imagines were found in the nests which contained between 3–16 cells each. The uppermost cells contained the youngest larvae whereas pupae and young imagines were found at the bottoms of the nests. Pollen carried by the provisioning female and present in provisions of two nests originated from 18 plant species, in particular Asteraceae and Melastomataceae. Nest architecture is compared to that of congeners, and the use of bromeliads as nest sites for bees is discussed.