Visualising chromosomal replication sites and replicons in mammalian cells

The precise regulation of DNA replication is fundamental to the preservation of intact genomes during cell proliferation. Our understanding of this process has been based traditionally on a combination of techniques including biochemistry, molecular biology and cell biology. In this report we describe how the analysis of the S phase in mammalian cells using classical cell biology techniques has contributed to our understanding of the replication process. We describe traditional and state-of-the-art protocols for imaging sites of DNA synthesis in nuclei and the organisation of active replicons along DNA, as visualised on individual DNA fibres. We evaluate how the different approaches inform our understanding of the replication process, placing particular emphasis on ways in which the higher order chromatin structures and the spatial architecture of replication sites contribute to the orderly activation of defined regions of the genome at precise times of S phase.     

Use of different areas of pen by growing rabbits depending on the elevated platforms' floor-type

The addition of platforms to rabbit cages increases their accessible area and provides rabbits greater freedom and mobility. Different types of platforms enable rabbits to situate themselves where they are most comfortable. The objective of this experiment was to analyse preference of growing rabbits between different areas of the pen depending on the elevated platforms' floor-type. Pens with a basic area of 0.84 m2 were equipped with platforms of 0.42 m2. Three types of flooring of the elevated platforms were used as treatments: deep-litter floor and an open wire-net floor (Experiment 1), and a deep-litter floor and a wire-net floor with a manure tray beneath it (Experiment 2). Growing rabbits (n = 168; 42 per treatment) between the ages of 5 and 11 weeks were studied, based on 24 h video recordings from infra-red cameras (one recording per week) applying scan sampling method with a frequency of 30 min. When the platform was deep-litter, significantly (P < 0.001) more rabbits used the area under the platform (53.7% and 54.3% in Experiments 1 and 2, respectively) than stayed on the platform (16.7% and 7.6%). In treatments of wire-net platform with and without tray beneath the platform also significantly (P < 0.001) more rabbits stayed under the platform (43.7% and 34.7%, respectively) than on the platform (19.5% and 29.9%, respectively). The differences from the expected 33.3% staying on the platform or under the platform were significant at least at the level of P < 0.05. The results show that the wire-net platform with the manure tray provides the optimal environment as it leads to the rabbits spreading themselves more evenly in the pen (i.e. the platform expands available floor area) without the risk of soiling from above, and without adverse effects on heat dissipation, and with the possibility of seeking cover when desired.     

Neuronal background of activation of estivated snails,with special attention to the monoaminergic system: a biochemical,physiological, and neuroanatomical study

Osmotic stimulation activates both estivated and inactivated specimens of Helix pomatia and increases their central arousal. High-pressure liquid chromatography has shown that, during activation, the level of both serotonin and dopamine decreases in the central nervous system (CNS) but increases in the foot and heart, organs that are involved in the eversion of the body. In isolated CNS from activated animals, the firing frequency of the heart-modulator serotonergic (RPas) neurons is significantly higher than that in the CNS of estivated or inactivated animals. These neurons innervate both the heart and the anterior aorta. In semi-intact preparations, distilled water (an osmotic stimulus) applied to the mantle collar increases their firing frequency, whereas tactile stimulation evokes their inhibition. Extracellularly applied monoamines mimic the effect of peripheral stimuli: serotonin (0.1–10 μM) increases the activity of the RPas neurons, whereas dopamine (0.1–10 μM) inhibits their activity. Tyrosine-hydroxylase immunocytochemistry and retrograde neurobiotin tracing have revealed similar bipolar receptor cells in the mantle collar and tail, organs that are exposed to environmental stimuli in estivated animals. Serotonin immunocytochemistry carried out on the same tissues does not visualize receptor cells but labels a dense network of fibers that appear to innervate neurobiotin-labeled receptor cells. The combination of neurobiotin-labeling of RPas neurons and immunolabeling suggests that RPas neurons receive direct dopaminergic inputs from receptor cells and serotonergic inputs from central serotonergic neurons, indicating that central serotonergic neurons are interconnected. Thus, the RPas neurons may belong to neuronal elements of the arousal system. This work was supported by Hungarian OTKA grants T037389, T046580, T037505, and K63451.     

Field-based artificial crossings indicate partial compatibility of reciprocal crosses between <Emphasis Type="Italic">Pinus sylvestris</Emphasis> and <Emphasis Type="Italic">Pinus mugo</Emphasis> and unexpected chloroplast DNA inheritance

Crossability relationships between Scots pine (Pinus sylvestris L.) and mountain dwarf pine (Pinus mugo Turra) was studied, using artificial pollination approach. Partial compatibility of the reciprocal crossings of these species was proved experimentally, validating the idea of a spontaneous formation of their hybrid swarms under natural conditions. The hybrids were validated using organellar DNA markers and nuclear DNA microsatellites. Based on the percentage of filled seeds, the interspecific crossings were less efficient than the intraspecific cross-pollinations of P. sylvestris and P. mugo individuals. Both species were found to intercross readily with individuals of their putative hybrid swarm, P. mugo exhibiting a higher hybridological affinity towards putatively hybrid individuals than P. sylvestris. Validation of the hybrids confirmed the paternal inheritance of chloroplast DNA (cpDNA) in the combination P. sylvestris × P. mugo only. Surprisingly, in the reciprocal crossing P. mugo × P. sylvestris, maternal inheritance of cpDNA was revealed. Obtained results offer a new insight into the direction and intensity of gene flow within the hybrid swarms of Scots pine and mountain dwarf pine.     

Challenges in the delimitation of morphologically similar species: a case study of <Emphasis Type="Italic">Tuber brumale</Emphasis> agg. (Ascomycota,Pezizales)

Tuber brumale (winter truffle) is one of the most controversial true truffles, not only in regard to its ecological and economical role but also its taxonomy. Multilocus phylogenetic analyses have revealed that specimens identified earlier as T. brumale belong to two species. These species were deemed cryptic right away, because preliminary morphological measurements did not show any phenotypical differences. In this study, we measured the morphology of 119 T. brumale agg. specimens, identified by DNA-based phylogenetic tools. We found several continuous morphological characters which show strong statistical differences between the two species, albeit not without overlap. Using a combination of these characters, we show that efficient separation of the two species is possible. We describe T. cryptobrumale sp. nov. and present the environmental demands and the potential area reconstruction of both species. We argue that non-representative sampling is a major culprit in most failures to detect both the existence of morphologically similar species and their morphological differences. Our findings illustrate the benefits of integrative taxonomy: the use of a combination of molecular, morphological and ecological tools.     

Simple Sequence Repeat and <Emphasis Type="Italic">S</Emphasis>-locus Genotyping to Explore Genetic Variability in Polyploid <Emphasis Type="Italic">Prunus spinosa</Emphasis> and <Emphasis Type="Italic">P. insititia</Emphasis>

Polyploid Prunus spinosa (2n = 4×) and P. insititia (2n = 6×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programmes. In Hungary, 17 cultivar candidates were selected from wild-growing populations including 10 P. spinosa, 4 P. insititia and three P. spinosa × P. domestica hybrids (2n = 5×). Their taxonomic classification was based on their phenotypic characteristics. Six simple sequence repeats (SSRs) and the multiallelic S-locus genotyping were used to characterize genetic variability and reliable identification of the tested accessions. A total of 98 SSR alleles were identified, which presents 19.5 average allele number per locus, and each of the 17 genotypes could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified. The complete and partial S-genotype was determined for 8 and 9 accessions, respectively. The identification of a cross-incompatible pair of cultivar candidates and several semi-compatible combinations help maximize fruit set in commercial orchards. Our results indicate that the S-allele pools of wild-growing P. spinosa and P. insititia are overlapping in Hungary. A phylogenetic and principal component analysis confirmed the high level of diversity and genetic differentiation present within the analysed genotypes and helped clarify doubtful taxonomic identities. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species. The analysed accessions represent huge genetic potential that can be exploited in commercial cultivation.     

Chromosome 9p copy number gains involving PD-L1 are associated with a specific proliferation and immune-modulating gene expression program active across major cancer types

Background

Inhibition of the PD-L1/PD-1 immune checkpoint axis represents one of the most promising approaches of immunotherapy for various cancer types. However, immune checkpoint inhibition is successful only in subpopulations of patients emphasizing the need for powerful biomarkers that adequately reflect the complex interaction between the tumor and the immune system. Recently, recurrent copy number gains (CNG) in chromosome 9p involving PD-L1 were detected in many cancer types including lung cancer, melanoma, bladder cancer, head and neck cancer, cervical cancer, soft tissue sarcoma, prostate cancer, gastric cancer, ovarian cancer, and triple-negative breast cancer.

Methods

Here, we applied functional genomics to analyze global mRNA expression changes associated with chromosome 9p gains. Using the TCGA data set, we identified a list of 75 genes that were strongly up-regulated in tumors with chromosome 9p gains across many cancer types.

Results

As expected, the gene set was enriched for chromosome 9p and in particular chromosome 9p24 (36 genes and 23 genes). Furthermore, we found enrichment of two expression programs derived from genes within and beyond 9p: one implicated in cell cycle regulation (22 genes) and the other implicated in modulation of the immune system (16 genes). Among these were specific cytokines and chemokines, e.g. CCL4, CCL8, CXCL10, CXCL11, other immunoregulatory genes such as IFN-G and IDO1 as well as highly expressed proliferation-related kinases and genes including PLK1, TTK, MELK and CDC20 that represent potential drug targets.

Conclusions

Collectively, these data shed light on mechanisms of immune escape and stimulation of proliferation in cancer with PD-L1 CNG and highlight additional vulnerabilities that may be therapeutically exploitable.

     

Development of the nitric oxide/cGMP system in the embryonic and juvenile pond snail, Lymnaea stagnalis L. A comparative in situ hybridization, histochemical and immunohistochemical study

Recent studies have indicated that nitric oxide (NO)-induced cGMP synthesis is involved in different steps of neurogenesis in invertebrates. The development of putative NO synthetising elements was described earlier in the embryonic and juvenile pond snail, Lymnaea stagnalis, applying NADPH-diaphorase histochemistry (Serf?z? et al., 1998). In the present study, we examined the distribution of NO synthase (NOS) during Lymnaea development by in situ hybridization for Lymnaea-NOS mRNA, histochemical, and immunohistochemical techniques for the NOS and NO-stimulated cGMP. Peripheral fibers projecting to the CNS and terminating in the ganglionic neuropils showed NOS immunoreactivity from 85% of embryonic development. At the same time, a fine dot-like, immunostaining indicated the presence of cGMP in the neuropil area. In the CNS, Lymnaea-NOS mRNA positive, as well as NOS and cGMP immunoreactive perikarya were detected first during postembryonic development; their number significantly increased from P3 juvenile stage. Some of the cell groups in the CNS containing NOS immunoreactive material also displayed Lymnaea-NOS mRNA hybridization signal and were cGMP-positive. However, in the subesophageal ganglia, the distribution of Lymnaea-NOS mRNA positive cell groups did not correspond to that of the NOS immunoreactive cells. Neurons revealing transient NOS and cGMP immunoreactivity, respectively, could also be detected in this part of the CNS. In most of the ganglia the number of Lymnaea-NOS mRNA containing and cGMP immunopositive neurons, respectively, exceeded that of the NOS immunoreactive cells from P4 juvenile stage. The localization of NADPH-diaphorase reaction also correlated well with that of the NOS immunoreactivity in the developing CNS. At the periphery, colocalization of Lymnaea-NOS mRNA signal, NOS and cGMP immunoreactivities were observed in the epithelial cells of the esophagus and mantle after hatching. The findings suggest the functional maturity of the NO/cGMP signal transduction pathway at both central and peripheral levels during the development of the snail, Lymnaea stagnalis. The differences in the localization of Lymnaea-NOS mRNA labeling and NOS immunoreactivity in the CNS and PNS can be explained by the existence of different NOS isoforms, posttranslational regulation of NOS, and/or some non-specific antibody labeling.