Integrating sequence information in microarray data analysis by free energy modeling

Microarray technology is a high-throughput method for genotyping and gene expression profiling. Limited sensitivity and specificity are one of the essential problems for this technology. Most of existing methods of microarray data analysis have an apparent limitation for they merely deal with the numerical part of microarray data and have made little use of gene sequence information. Because it's the gene sequences that precisely define the physical objects being measured by a microarray, it is natural to make the gene sequences an essential part of the data analysis. This dissertation focused on the development of free energy models to integrate sequence information in microarray data analysis. The models were used to characterize the mechanism of hybridization on microarrays and enhance sensitivity and specificity of microarray measurements. ^ Cross-hybridization is a major obstacle factor for the sensitivity and specificity of microarray measurements. In this dissertation, we evaluated the scope of cross-hybridization problem on short-oligo microarrays. The results showed that cross hybridization on arrays is mostly caused by oligo fragments with a run of 10 to 16 nucleotides complementary to the probes. Furthermore, a free-energy based model was proposed to quantify the amount of cross-hybridization signal on each probe. This model treats cross-hybridization as an integral effect of the interactions between a probe and various off-target oligo fragments. Using public spike-in datasets, the model showed high accuracy in predicting the cross-hybridization signals on those probes whose intended targets are absent in the sample. ^ Several prospective models were proposed to improve Positional Dependent Nearest-Neighbor (PDNN) model for better quantification of gene expression and cross-hybridization. ^ The problem addressed in this dissertation is fundamental to the microarray technology. We expect that this study will help us to understand the detailed mechanism that determines sensitivity and specificity on the microarrays. Consequently, this research will have a wide impact on how microarrays are designed and how the data are interpreted. ^

Organic compounds in sediments and pore waters of ODP Sites 117-723 and 117-724

Total organic carbon, amino compounds, and carbohydrates were measured in pore waters and sediments of Pliocene to Pleistocene age from Sites 723 and 724 (ODP Leg 117) to evaluate (1) relationships between organic matter in the sediment and in the pore water, (2) the imprint of lithological variations on the abundance and contribution of organic substances, (3) degradation of amino compounds and carbohydrates with time and/or depth, and (4) the dependence of the ammonia concentration in the pore water on the degradation of amino compounds in the sediment. Total organic carbon concentrations (TOC) of the investigated sediment samples range from 0.9% to 8.7%, and total nitrogen concentrations (TN) from 0.1% to 0.5%. Up to 4.9% of the TOC is contributed by hydrolyzable amino acids (THAA) which are present in amounts between 1.1 and 21.3 µmol/g dry sediment and decrease strongly downhole. Hydrolyzable carbohydrates (THCHO) were found in concentrations from 1.3 to 6.6 ?mol/g sediment constituting between 0.1% and 2.0% of the TOC. Differences between the distribution patterns of monomers in Sites 723 and 724 indicate higher terrigenous influence for Site 724 and, furthermore, enhanced input of organic matter that is relatively resistant to microbial degradation. Lithologically distinct facies close to the Pliocene/Pleistocene boundary yield different organic matter compositions. Laminated horizons seem to correspond with enhanced amounts of biogenic siliceous material and minor microbiological degradation. Total amounts of dissolved organic carbon (DOC) in pore waters vary between 11 and 131 mg/L. Concentrations of DOC as well as of dissolved amino compounds and carbohydrates appear to be related to microbial activity and/or associated redox zones and not so much to the abundance of organic matter in the sediments. Distributions of amino acids and monosaccharides in pore waters show a general enrichment in relatively stable components in comparison to those of the sediments. Nevertheless, the same trend appears between amino acids present in the sediments from Sites 723 and 724 as well as between amino acids in pore waters from these two sites, indicating a direct relation between the dissolved and the sedimentary organic fractions. Different ammonia concentrations in the pore waters of Sites 723 and 724 seem to be related to enhanced release of ammonia from degradation of amino compounds in Site 723.

Caracterización y cuantificación de células progenitoras endoteliales de ratas espontáneamente hipertensas alimentadas con fructosa

Objetivo: Examinar cómo se ve afecta la participación de las células progenitoras endoteliales (CPE) por la resistencia a la insulina (IR) asociada a un modelo experimental de síndrome metabólico (SM), generado por la administración crónica de fructosa a ratas espontáneamente hipertensas. Material y métodos: Ratas WKY y SHR, macho, distribuidas en 4 grupos (n=8 c/u): WKY: controles; FFR: WKY recibiendo fructosa en agua de bebida al 10 % (v/v) durante 6 semanas; SHR; FFHR: SHR recibiendo fructosa en agua de bebida al 10 % (v/v) durante 6 semanas. Al finalizar el protocolo se determinó: presión arterial sistólica, variables bioquímicas, índice HOMA, cuantificación por citometría de flujo de los niveles de CPE en sangre periférica y en médula ósea, inmunofluorescencia en cultivo celular, para identificar los marcadores CD34 y VEGFR-2, recuento de colonias de CPE y actividad de NAD(P)H-oxidasa en tejido aórtico. Resultados: Se confirmó el modelo experimental en base a las variables metabólicas analizadas. Se observó una disminución en los niveles de CPE; en sangre periférica y médula ósea, la que se hace más importante en los grupos de animales tratados con fructosa. En estos también hay menor número de colonias de CPE desarrolladas en cultivo celular y presentan un aumento en los niveles de estrés oxidativo, estimado por la actividad de NAD(P)H oxidasa. Conclusión: el SM causado por la administración crónica de fructosa en FFHR ha demostrado generar una disminución en los niveles de CPE, así como en su capacidad funcional. Los mecanismos intracelulares que producen este fenómeno podrían estar desencadenados por el grado de IR que presenta este modelo experimental.

Concentración de benciladenina, tipo y dosis de carbohidratos en el medio de cultivo para proliferación de brotes de Agave americana

Para evaluar la proliferación in vitro de brotes de Agave americana var. oaxacensis, piezas de callo con dos a tres brotes adventicios se establecieron en diversos medios de cultivo con pH 5,8 y consistencia de gel, con sales minerales MS, 100 mg L-1 myo-inositol, diversas concentraciones de benciladenina (BA) (0, 2, 4, 6, 8 y 10 mg L-1), tipo de carbohidrato (sacarosa o jarabe fructosado) y concentración de carbohidrato (20, 30, 40 g). Los cultivos se incubaron 60 días bajo luz fluorescente blanca en 16 h luz/8 h oscuridad, temperatura 20- 28°C. El experimento se estableció según un diseño completamente al azar con arreglo factorial 6x2x3. La sacarosa resultó mejor fuente de carbohidrato que el jarabe fructosado. Los explantos en el medio de cultivo sin BA y 20 g L-1 de sacarosa formaron cuatro brotes de 10,8 cm, con raíces adventicias. Al aumentar la concentración de BA y sacarosa los explantos formaron más brotes, pero en el medio con 6 mg L-1 BA y 40 g L-1 sacarosa los explantos formaron hasta 21 brotes de 6,5 cm de tamaño. La citocinina inhibió la formación de raíces.

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.

Organic compounds at DSDP Hole 90-593

Corg and Norg contents in the acid insoluble mineral fraction were studied in sediments of Site 593. Both decrease systematically from Recent to early Miocene over 425 m of carbonate facies. C/N ratios (7-11) are typically marine and indicate that residual organic matter, bound to clay minerals, was originally scavenged from the marine habitat rather than being of terrigenous origin. Variations of Corg and Norg are almost entirely controlled by rates of sedimentation, which gradually increase from Recent to early Miocene. Preliminary results of carbohydrate distribution indicate that epigenetic and diagenetic processes alter both the concentrations and the ratios of individual monomers with depth. Total carbohydrate concentrations in the samples diminish from 91 µg/g sediment at 18 m sub-bottom depth to 49 µg/g at 335 m. In contrast, sugars in the acid insoluble residue increase with depth, suggesting release of structural polysaccharides and their subsequent association with clay minerals. Ratios of arabinose to fucose, which are about 6:1 in Recent carbonaceous sediments intercepted by sediment traps, vary from 1:1 in the youngest sample to 1:2.5 in the oldest.

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.

Chemical characterization of dissolved organic compounds from coastal sea surface microlayers (Baltic Sea, Germany)

The physicochemical properties of the sea surface microlayer (SML), i.e. the boundary layer between the air and the sea, and its impact on air-sea exchange processes have been investigated for decades. However, a detailed description about these processes remains incomplete. In order to obtain a better chemical characterization of the SML, in a case study three pairs of SML and corresponding bulk water samples were taken in the southern Baltic Sea. The samples were analyzed for dissolved organic carbon and dissolved total nitrogen, as well as for several organic nitrogen containing compounds and carbohydrates, namely aliphatic amines, dissolved free amino acids, dissolved free monosaccharides, sugar alcohols, and monosaccharide anhydrates. Therefore, reasonable analytical procedures with respect to desalting and enrichment were established. All aliphatic amines and the majority of the investigated amino acids (11 out of 18) were found in the samples with average concentrations between 53 ng/l and 1574 ng/l. The concentrations of carbohydrates were slightly higher, averaging 2900 ng/l. Calculation of the enrichment factor (EF) between the sea surface microlayer and the bulk water showed that dissolved total nitrogen was more enriched (EF: 1.1 and 1.2) in the SML than dissolved organic carbon (EF: 1.0 and 1.1). The nitrogen containing organic compounds were generally found to be enriched in the SML (EF: 1.9-9.2), whereas dissolved carbohydrates were not enriched or even depleted (EF: 0.7-1.2). Although the investigated compounds contributed on average only 0.3% to the dissolved organic carbon and 0.4% to the total dissolved nitrogen fraction, these results underline the importance of single compound analysis to determine SML structure, function, and its potential for a transfer of compounds into the atmosphere.

Amino acids and carbohydrates in sediments and interstitial waters of ODP Site 112-681

Total organic carbon (TOC), dissolved organic carbon (DOC), total hydrolyzable amino acids (THAA), amino sugars (THAS), and carbohydrates (THCHO) were measured in sediments and interstitial waters from Site 681 (ODP Leg 112). TOC concentrations vary between 0.75% and 8.2% by weight of dry sediment and exhibit a general decrease with depth. DOC concentrations range from 6.1 to 49.5 mg/L, but do not correlate with TOC concentrations in the sediment. Amino compounds (AA and AS) and sugars account for 0.5% to 8% and 0.5% to 3% of TOC, respectively, while amino compounds make up between 2% and 27% of total nitrogen. Dissolved hydrolyzable amino acids (free and combined) and amino sugars were found in concentrations from 3.7 to 150 µM and from 0.1 to 3.7 µM, respectively, and together account for an average of 8.5% of DOC. Dissolved hydrolyzable carbohydrates are in the range of 6 to 49 µM. Amino acid spectra are dominated by glycine, alanine, leucine, and phenylalanine; nonproteinaceous amino acids (gamma-amino butyric acid, beta-alanine, and ornithine) are enriched in the deeper part of the section, gamma-amino butyric acid and beta-alanine are thought to be indicators of continued microbial degradation of TOC. Glycine, serine, glutamic acid, alanine, aspartic acid, and ornithine are the dominating amino compounds in the pore waters. Spectra of carbohydrates in sediments are dominated by glucose, galactose, and mannose, while dissolved sugars are dominated by glucose and fructose. In contrast to the lack of correlation between abundances of bulk TOC and DOC in corresponding interstitial waters, amino compounds and sugars do show some correlation between sediments and pore waters: A depth increase of aspartic acid, serine, glycine, and glutamic acid in the pore waters is reflected in a decrease in the sediment, while an enrichment in valine, iso-leucine, leucine, and phenylalanine in the sediment is mirrored by a decrease in the interstitial waters. The distribution of individual hexoseamines appears to be related to zones of bacterial decomposition of organic matter. Low glucoseamine to galactoseamine ratios coincide with zones of sulfate depletion in the interstitial waters.