Integrated mRNA and miRNA expression profiling in blood reveals candidate biomarkers associated with endurance exercise in the horse.

The adaptive response to extreme endurance exercise might involve transcriptional and translational regulation by microRNAs (miRNAs). Therefore, the objective of the present study was to perform an integrated analysis of the blood transcriptome and miRNome (using microarrays) in the horse before and after a 160 km endurance competition. A total of 2,453 differentially expressed genes and 167 differentially expressed microRNAs were identified when comparing pre- and post-ride samples. We used a hypergeometric test and its generalization to gain a better understanding of the biological functions regulated by the differentially expressed microRNA. In particular, 44 differentially expressed microRNAs putatively regulated a total of 351 depleted differentially expressed genes involved variously in glucose metabolism, fatty acid oxidation, mitochondrion biogenesis, and immune response pathways. In an independent validation set of animals, graphical Gaussian models confirmed that miR-21-5p, miR-181b-5p and miR-505-5p are candidate regulatory molecules for the adaptation to endurance exercise in the horse. To the best of our knowledge, the present study is the first to provide a comprehensive, integrated overview of the microRNA-mRNA co-regulation networks that may have a key role in controlling post-transcriptomic regulation during endurance exercise.

Towards the identification of a tumor suppressor gene on chromosome 3p12: Physical mapping and candidate gene screening

Renal cell carcinoma (RCC) is the most common malignant tumor of the kidney. Characterization of RCC tumors indicates that the most frequent genetic event associated with the initiation of tumor formation involves a loss of heterozygosity or cytogenetic aberration on the short arm of human chromosome 3. A tumor suppressor locus Nonpapillary Renal Carcinoma-1 (NRC-1, OMIM ID 604442) has been previously mapped to a 5–7 cM region on chromosome 3p12 and shown to induce rapid tumor cell death in vivo, as demonstrated by functional complementation experiments. ^ To identify the gene that accounts for the tumor suppressor activities of NRC-1, fine-scale physical mapping was conducted with a novel real-time quantitative PCR based method developed in this study. As a result, NRC-1 was mapped within a 4.6-Mb region defined by two unique sequences within UniGene clusters Hs.41407 and Hs.371835 (78,545Kb–83,172Kb in the NCBI build 31 physical map). The involvement of a putative tumor suppressor gene Robo1/Dutt1 was excluded as a candidate for NRC-1. Furthermore, a transcript map containing eleven candidate genes was established for the 4.6-Mb region. Analyses of gene expression patterns with real-time quantitative RT-PCR assays showed that one of the eleven candidate genes in the interval (TSGc28) is down-regulated in 15 out of 20 tumor samples compared with matched normal samples. Three exons of this gene have been identified by RACE experiments, although additional exon(s) seem to exist. Further gene characterization and functional studies are required to confirm the gene as a true tumor suppressor gene. ^ To study the cellular functions of NRC-1, gene expression profiles of three tumor suppressive microcell hybrids, each containing a functional copy of NRC-1, were compared with those of the corresponding parental tumor cell lines using 16K oligonucleotide microarrays. Differentially expressed genes were identified. Analyses based on the Gene Ontology showed that introduction of NRC-1 into tumor cell lines activates genes in multiple cellular pathways, including cell cycle, signal transduction, cytokines and stress response. NRC-1 is likely to induce cell growth arrest indirectly through WEE1. ^

Involvement of histone H3 methylation in Tup1-Ssn6 repression

The Tup1-Ssn6 complex regulates the expression of diverse classes of genes in Saccharomyces cerevisiae including those regulated by mating type, DNA damage, glucose, and anaerobic stress. The complex is recruited to target genes by sequence-specific repressor proteins. Once recruited to particular promoters, it is not completely clear how it functions to block transcription. Repression probably occurs through interactions with both the basal transcriptional machinery and components of chromatin. Tup1 interactions with chromatin are strongly influenced by acetylation of histories H3 and H4. Tup1 binds to underacetylated histone tails and requires multiple histone deacetylases (HDACs) for its repressive functions. Like acetylation, histone methylation is involved in regulation of gene expression. The possible role of histone methylation in Tup1 repression is not known. Here we examined possible roles of histone methyltransferases in Tup1-Ssn6 functions. We found that like other genes, Tup1-Ssn6 target genes exhibit increases in the levels of histone H3 lysine 4 methylation upon activation. However, deletion of individual or multiple histone methyltransferases (HMTs) and other SET-domain containing genes has no apparent effect on Tup1-Ssn6 mediated repression of a number of well-defined targets. Interestingly, we discovered that Ssn6 interacts with Set2. Since deletion of SET2 does not affect Tup1-Ssn6 repression, Ssn6 may utilize Set2 in other contexts to regulate gene repression. In order examine if the two components of the Tup1-Ssn6 complex have independent functions in the cell, we identified genes differentially expressed in tup1Δ and ssn6Δ mutants using DNA microarrays. Our data indicate that ∼4% of genes in the cell are regulated by Ssn6 independently of Tup1. In addition, expression of genes regulated by Tup1-Ssn6 seems to be differently affected by deletion of Ssn6 and deletion of Tup1, which indicates that these components might have separate functions. Our data shed new light on the classical view of Tup1-Ssn6 functions, and indicate that Ssn6 might have repressive functions as well. ^

INTEGRATIVE BIOMARKER IDENTIFICATION AND CLASSIFICATION USING HIGH THROUGHPUT ASSAYS

It is well accepted that tumorigenesis is a multi-step procedure involving aberrant functioning of genes regulating cell proliferation, differentiation, apoptosis, genome stability, angiogenesis and motility. To obtain a full understanding of tumorigenesis, it is necessary to collect information on all aspects of cell activity. Recent advances in high throughput technologies allow biologists to generate massive amounts of data, more than might have been imagined decades ago. These advances have made it possible to launch comprehensive projects such as (TCGA) and (ICGC) which systematically characterize the molecular fingerprints of cancer cells using gene expression, methylation, copy number, microRNA and SNP microarrays as well as next generation sequencing assays interrogating somatic mutation, insertion, deletion, translocation and structural rearrangements. Given the massive amount of data, a major challenge is to integrate information from multiple sources and formulate testable hypotheses. This thesis focuses on developing methodologies for integrative analyses of genomic assays profiled on the same set of samples. We have developed several novel methods for integrative biomarker identification and cancer classification. We introduce a regression-based approach to identify biomarkers predictive to therapy response or survival by integrating multiple assays including gene expression, methylation and copy number data through penalized regression. To identify key cancer-specific genes accounting for multiple mechanisms of regulation, we have developed the integIRTy software that provides robust and reliable inferences about gene alteration by automatically adjusting for sample heterogeneity as well as technical artifacts using Item Response Theory. To cope with the increasing need for accurate cancer diagnosis and individualized therapy, we have developed a robust and powerful algorithm called SIBER to systematically identify bimodally expressed genes using next generation RNAseq data. We have shown that prediction models built from these bimodal genes have the same accuracy as models built from all genes. Further, prediction models with dichotomized gene expression measurements based on their bimodal shapes still perform well. The effectiveness of outcome prediction using discretized signals paves the road for more accurate and interpretable cancer classification by integrating signals from multiple sources.

Biogenic and mineral composition and foraminiferal stratigraphy of sediment cores obtained in northern Germany

The Ratekau boring ended in clays of the so-called Asterigerina-Zone; these clays have shallow-water features in the uppermost samples. The clays are overlain by deep-water clays with pteropods; this formation is split into two parts by a shallow-water deposit. The fossiliferous series ends upward in sandy deposits with shallow-water fossils. The question is raised whether the two deep-water deposits might correspond to the Lower Doberg Beds (Eochattian) and the Upper Doberg Beds (Neochattian) at the Doberg hill, closer to the rim of the basin. All fossiliferous samples from this boring are thought to be of Late Oligocene age; the boundary towards the Middle Oligocene, however, could not be ascertained. The Vaale boring ended in rather typical Septaria clay of the Middle Oligocene. This clay is capped by some metres of unfossiliferous glauconite clays, which in turn are overlain by silts and silty clays with planktonic fossils identical to those found at Dingden locality. These deposits are tentatively dated as Early Miocene. The next higher series of samples consists of sands and clays deposited in shallower waters. They contain a rich fauna of benthic molluscs, which, according to the current notion in stratigraphy, would have a Reinbek Age. In addition, they contain a set of planktonic fossils which differs from the 'Lower Miocene' assemblages. These sands and clays are overlain by a thick series of marine sands very poor in fossils. Finally, four metres of clay with foraminifera, having Younger Miocene affinities, form the top of the fossiliferous sequence. The borings at Wulksfelde and Langenhorn were not far apart and their sediments are easily correlated. Both wells start below in continental 'Lignite Sands' and contain overlying shallow water sands and clays. These yielded Hemmoor benthic mollusca, supposed to indicate Lower Miocene in the relevant literature; however, we encountered their planktonic foraminifera in the uppermost Miocene as well. The same planktonic species were found in all samples of both borings. These deposits under discussion furthermore contain a particular pteropod species. They are overlain by a thick series of gypsiferous clays, with scarce fossils. The uppermost fossiliferous clays (probably Langenfelde Age) contain another pteropod species, not met with in other samples. The discrepancies between the plankton zonation and the traditional subdivision according to benthic molluscs in the borings of Vaale, Wulksfelde and Langenhorn (and in samples from Twistringen, Dingden and Antwerp localities as well) renders the time-stratigraphic value of the denominations Reinbek and Hemmoor rather doubtful. The samples of the Westerland boring can be placed in the Gram and Sylt stages of local chronostratigraphy on the strength of the Astarte series established by HINSCH. The Gram samples contain a typical pteropod species; both groups of samples contain the same planktonic foraminifera as the borings Wulksfelde and Langenhorn. Our material did not bring the problem of the Miocene-Pliocene boundary in this region any closer to a solution. In conclusion, it can be claimed that this investigation provides strong arguments that the usual recognition of Hemmoor and Reinbek does not correspond to well-defined chronostratigraphical units. A better chronostratigraphic subdivision has to be based on the examination of many more samples, and on a better understanding of the paleoecology of the fossils involved.

Pollen and diatom analysis on varved sediments in Lake Jues (Harz Mountains, Germany)

Studies combining sedimentological and biological evidence to reconstruct Holocene climate beyond the major changes, and especially seasonality, are rare in Europe, and are nearly completely absent in Germany. The present study tries to reconstruct changes of seasonality from evidence of annual algal successions within the framework of well-established pollen zonation and 14C-AMS dates from terrestrial plants. Laminated Holocene sediments in Lake Jues (10°20.70' E, 51°39.30' N, 241 m a.s.l.), located at the SW margin of the Harz Mountains, central Germany, were studied for sediment characteristics, pollen, diatoms and coccal green algae. An age model is based on 21 calibrated AMS radiocarbon dates from terrestrial plants. The sedimentary record covers the entire Holocene period. Trophic status and circulation/stagnation patterns of the lake were inferred from algal assemblages, the subannual structure of varves and the physico-chemical properties of the sediment. During the Holocene, mixing conditions alternated between di-, oligo- and meromictic depending on length and variability of spring and fall periods, and the stability of winter and summer weather. The trophic state was controlled by nutrient input, circulation patterns and the temperature-dependent rates of organic production and mineralization. Climate shifts, mainly in phase with those recorded from other European regions, are inferred from changing limnological conditions and terrestrial vegetation. Significant changes occurred at 11,600 cal. yr. BP (Preboreal warming), between 10,600 and 10,100 cal. yr. BP (Boreal cooling), and between 8,400 and 4,550 cal. yr. BP (warm and dry interval of the Atlantic). Since 4,550 cal. yr. BP the climate became gradually cooler, wetter and more oceanic. This trend was interrupted by warmer and dryer phases between 3,440 and 2,850 cal. yr. BP and, likely, between 2,500 and 2,250 cal. yr. BP.

(Table 1) Oxygen and carbon isotope compositions of altered carbonates from DSDP Hole 6-53 from the western Pacific Ocean

In the lower part of DSDP core 53.0, partly recrystallized carbonate sediments and well recrystallized limestone breccias of Oligo-Miocene age are associated with altered volcanic flows, lithified tuffs, and tuff breccias, suggesting that carbonate alteration was the result of thermal metamorphism. However, the oxygen isotope compositions of these carbonates (-3.4 to +0.6 per mil rel. PDB) are not compatible with recrystallization and isotope exchange with sea water at high temperatures. Evaluating the effects of the composition of the water which exchanged with the carbonates and of carbonate-water isotope exchange in closed systems yields the following approximate maximum temperature of recrystallization: limestone breccias, 100°C; calcite veins rimming breccia clasts, 30°C; and unconsolidated sediments overlying the breccias, 20°C. Therefore, the volcanics at site 53.0 must have been emplaced into the primary carbonate sediments at relatively low temperatures. Subsequent carbonate alteration was probably a consequence of chemical changes in ambient pore waters resulting from the submarine weathering of volcanic material.

Downward particle fluxes at the oligotrophic and mesotrophic site of the EUMELI program

A two year record of downward particle flux was obtained with moored sediment traps at several depths of the water column in two regions characterized by different primary production levels (mesotrophic and oligotrophic) of the eastern subtropical North Atlantic Ocean in the framework of the EUMELI program. Settling particles were collected with multisample conical sediment-traps moored at 1000 and 2500 depths in the water column. Time-series samples were obtained between February 1991 and November 1992. During this time, sampling intervals varied from 8 to 10 d and were synchronized at all depths and also between the oligotrophic and mesotrophic moorings. Sediment-trap sampling procedures were consistent with JGOF and described elsewhere. The data shown here are mass, particulate organic carbon (POC), particulate inorganic carbon (PIC), coccolithophore, opal, and lithogenic downward fluxes obtained during the entire sediment-trap deployments at both sites.

Major cellular and physiological impacts of ocean acidification on a reef building coral

As atmospheric levels of CO2 increase, reef-building corals are under greater stress from both increased sea surface temperatures and declining sea water pH. To date, most studies have focused on either coral bleaching due to warming oceans or declining calcification due to decreasing oceanic carbonate ion concentrations. Here, through the use of physiology measurements and cDNA microarrays, we show that changes in pH and ocean chemistry consistent with two scenarios put forward by the Intergovernmental Panel on Climate Change (IPCC) drive major changes in gene expression, respiration, photosynthesis and symbiosis of the coral, Acropora millepora, before affects on biomineralisation are apparent at the phenotype level. Under high CO2 conditions corals at the phenotype level lost over half their Symbiodinium populations, and had a decrease in both photosynthesis and respiration. Changes in gene expression were consistent with metabolic suppression, an increase in oxidative stress, apoptosis and symbiont loss. Other expression patterns demonstrate upregulation of membrane transporters, as well as the regulation of genes involved in membrane cytoskeletal interactions and cytoskeletal remodeling. These widespread changes in gene expression emphasize the need to expand future studies of ocean acidification to include a wider spectrum of cellular processes, many of which may occur before impacts on calcification.

Geochemistry and minerals of glass shards at DSDP Leg 66 Holes

Deep Sea Drilling Project Leg 66 drilled eight sites along a transect across the Middle America Trench off Mexico, including continental (Sites 493 and 489), oceanic (Site 487), and trench (Site 486) reference sites and four sites (490, 492, 491, 488) in the trench inner wall. Because of their location - close to volcanic sources and subject to prevailing winds and marine currents (N to S, NW to SE) - analysis of airborne ashes intercalated within the sediments at these sites provides a reliable record of explosive volcanism in the area. Intense onshore volcanic activity in Mexico during the Oligo-Miocene has been well documented by the andesites and ignimbrites of the Sierra Madre Occidental and Sierra Madre del Sur and in the Plio-Quaternary by the andesites and basalts from the Trans-Mexican Neovolcanic Belt and the eastern border of Baja California.

Ecosystem regimes and responses in a coupled ancient lake system from MIS 5b to present: the diatom record of lakes Ohrid and Prespa

We reconstruct the aquatic ecosystem interactions since the last interglacial period in the oldest, most diverse, hydrologically connected European lake system, by using palaeolimnological diatom and selected geochemistry data from Lake Ohrid “DEEP site” core and equivalent data from Lake Prespa core, Co1215. Driven by climate forcing, the lakes experienced two adaptive cycles during the last 92 ka: "interglacial and interstadial" and "glacial" cycle. The short-term ecosystems reorganizations, e.g. regime shifts within these cycles substantially differ between the lakes, as evident from the inferred amplitudes of variation. The deeper Lake Ohrid shifted between ultra oligo- and oligotrophic regimes in contrast to the much shallower Lake Prespa, which shifted from a deeper, (oligo-) mesotrophic to a shallower, eutrophic lake and vice versa. Due to the high level of ecosystem stability (e.g. trophic state, lake level), Lake Ohrid appears relatively resistant to external forcing, such as climate and environmental change. Recovering in a relatively short time from major climate change, Lake Prespa is a resilient ecosystem. At the DEEP site, the decoupling between the lakes' response to climate change is marked in the prolonged and gradual changes during the MIS 5/4 and 2/1 transitions. These response differences and the lakes' different physical and chemical properties may limit the influence of Lake Prespa on Lake Ohrid. Regime shifts of Lake Ohrid due to potential hydrological change in Lake Prespa are not evident in the data presented here. Moreover, a complete collapse of the ecosystems functionality and loss of their diatom communities did not happen in either lake for the period presented in the study.