Identification of a biomarker panel for colorectal cancer diagnosis

Background Malignancies arising in the large bowel cause the second largest number of deaths from cancer in the Western World. Despite progresses made during the last decades, colorectal cancer remains one of the most frequent and deadly neoplasias in the western countries. Methods A genomic study of human colorectal cancer has been carried out on a total of 31 tumoral samples, corresponding to different stages of the disease, and 33 non-tumoral samples. The study was carried out by hybridisation of the tumour samples against a reference pool of non-tumoral samples using Agilent Human 1A 60-mer oligo microarrays. The results obtained were validated by qRT-PCR. In the subsequent bioinformatics analysis, gene networks by means of Bayesian classifiers, variable selection and bootstrap resampling were built. The consensus among all the induced models produced a hierarchy of dependences and, thus, of variables. Results After an exhaustive process of pre-processing to ensure data quality--lost values imputation, probes quality, data smoothing and intraclass variability filtering--the final dataset comprised a total of 8, 104 probes. Next, a supervised classification approach and data analysis was carried out to obtain the most relevant genes. Two of them are directly involved in cancer progression and in particular in colorectal cancer. Finally, a supervised classifier was induced to classify new unseen samples. Conclusions We have developed a tentative model for the diagnosis of colorectal cancer based on a biomarker panel. Our results indicate that the gene profile described herein can discriminate between non-cancerous and cancerous samples with 94.45% accuracy using different supervised classifiers (AUC values in the range of 0.997 and 0.955)

The Agrobacterium vitis T-6b oncoprotein induces auxin-independent cell expansion in tobacco

Among the Agrobacterium T-DNA genes, rolB, rolC, orf13, orf8, lso, 6b and several other genes encode weakly homologous proteins with remarkable effects on plant growth. The 6b oncogene induces tumors and enations. In order to study its properties we have used transgenic tobacco plants that carry a dexamethasone-inducible 6b gene, dex-T-6b. Upon induction, dex-T-6b plants develop a large array of morphological modifications, some of which involve abnormal cell expansion. In the present investigation, dex-T-6b-induced expansion was studied in intact leaves and an in vitro leaf disc system. Although T-6b and indole-3-acetic acid (IAA) both induced expansion and were non-additive, T-6b expression did not increase IAA levels, nor did it induce an IAA-responsive gene. Fusicoccin (FC) is known to stimulate expansion by increasing cell wall plasticity. T-6b- and FC-induced expansion were additive at saturating FC concentrations, indicating that T-6b does not act by a similar mechanism to FC. T-6b expression led to higher leaf osmolality values, in contrast to FC, suggesting that the T-6b gene induces expansion by increasing osmolyte concentrations. Metabolite profiling showed that glucose and fructose played a major role in this increase. We infer that T-6b disrupts the osmoregulatory controls that govern cell expansion during development and wound healing.

Identification of a biomarker panel for colorectal cancer diagnosis

Background:Malignancies arising in the large bowel cause the second largest number of deaths from cancer in the Western World. Despite progresses made during the last decades, colorectal cancer remains one of the most frequent and deadly neoplasias in the western countries. Methods: A genomic study of human colorectal cancer has been carried out on a total of 31 tumoral samples, corresponding to different stages of the disease, and 33 non-tumoral samples. The study was carried out by hybridisation of the tumour samples against a reference pool of non-tumoral samples using Agilent Human 1A 60-mer oligo microarrays. The results obtained were validated by qRT-PCR. In the subsequent bioinformatics analysis, gene networks by means of Bayesian classifiers, variable selection and bootstrap resampling were built. The consensus among all the induced models produced a hierarchy of dependences and, thus, of variables. Results: After an exhaustive process of pre-processing to ensure data quality--lost values imputation, probes quality, data smoothing and intraclass variability filtering--the final dataset comprised a total of 8, 104 probes. Next, a supervised classification approach and data analysis was carried out to obtain the most relevant genes. Two of them are directly involved in cancer progression and in particular in colorectal cancer. Finally, a supervised classifier was induced to classify new unseen samples. Conclusions: We have developed a tentative model for the diagnosis of colorectal cancer based on a biomarker panel. Our results indicate that the gene profile described herein can discriminate between non-cancerous and cancerous samples with 94.45% accuracy using different supervised classifiers (AUC values in the range of 0.997 and 0.955).

Assessment of watercore development in apples with MRI: Effect offruit location in the canopy

tWatercore distribution inside apple fruit (block or radial), and its incidence (% of tissue) were relatedto the effect of solar radiation inside the canopy as measured by a set of low-cost irradiation sensors.221 samples were harvested in two seasons from the top and the bottom of the canopy and submittedto the non-invasive and non-destructive technique of magnetic resonance imaging (MRI) in order toobtain 20 inner tomography slices from each fruit and analyze the damaged areas using an interactive3D segmentation method. The number of fruit corresponding to each type of damage and the relevantpercentage were calculated and it was found that apples from the top of the tree were mainly of the radialtype (84%) and had more watercore (approx. 5% more) than apples from the bottom (65% radial). From theimage segmentation, the Euler number, a morphometric parameter, was extracted from the segmentedimages and related to the type of watercore symptoms. Apples with block watercore were grouped inEuler numbers between −400 and 400 with a small evolution. For apples with radial development, theEuler number was highly negative: up to −1439. Significant differences were also found regarding sugarcomposition, with higher fructose and total sugar contents in apples from the upper canopy, compared tothose in the lower canopy location. In the seasons studied (2011 and 2012), significantly higher sorbitoland lower sucrose and fructose contents were found in watercore-affected tissue compared to the healthytissue of affected apples and also compared to healthy apples.

1H HR MAS NMR metabolomic and non-destructive 2D NMR relaxometry to assess internal quality in apples.

NMR can be considered a multi-scale multidimensional technology in the sense that it provides both spatial insight at macroscopic (MRI) or microscopic level (relaxometry), together with chemical characterization (HR-MAS). In this study 296 apples (from 4 cultivars) were MRI screened (20 slices per fruit) among which 7 fruits were used for metabolomic study by 1H HR MAS in order to assess various chemical shifts: malic acid, sucrose, glucose, fructose and ethanol. On the first season, tissue samples were taken from the sound and affected apples (near the core, centre and outer part of the mesocarp) belonging to sound and affected locations, while on the second season, tissue samples were focused on the comparison between sound and affected tissue. Beside, MRI and 2D non-destructive relaxometry (on whole fruits, and localized tissue) where performed on 72 and 12 apples respectively in order to compare features at macroscopic (tissue) and microscopic (subcellular) level. HR MAS shows higher content of ?-glucose, ?-glucose, malic acid and aromatic compounds in watercore affected tissues from both seasons, while sound tissue reflects higher sucrose. Microscopic (subcellular) degradation of tissue varies according to disorder development and is in good accordance with macroscopic characterization with MRI.

Improved walnut mass micropropagation through the combined use of phloroglucinol and FeEDDHA

Despite the socioeconomic importance of walnut trees, poor rooting and recalcitrance to in vitro culture have hampered the establishment of high-yield clonal plantations. To improve walnut micropropagation, we introduced several modifications to current methods and evaluated the effects on microshoot performance and acclimatization. Nine selected genotypes (13-year-old trees) of the commercial hybrid Juglans major 209 x J. regia were cultured in vitro on DKW-C medium supplemented with 4.4 µM BA and 50 µM IBA. A protocol was developed that relies on the use of 0.40 mM phloroglucinol during shoot multiplication, 0.20 mM previous root induction, and 6.81 mg/L Fe3+ (FeEDDHA). Moreover, the addition of 83.2 µM glucose during the root expression phase significantly improved plant survival during acclimatization. Phloroglucinol promoted microshoot elongation but inhibited rooting, especially at concentrations above 0.40 mM. Replacing FeEDTA by FeEDDHA diminished chlorotic symptoms and improved rooting, with up to 90% microshoots developing viable roots. Likewise, glucose was more efficient than sucrose or fructose in promoting plant survival. At the proposed working concentrations, neither glucose nor FeEDDHA caused any noticeable deleterious effect on walnut micropropagation. Microscopic analysis revealed the physical continuity between adventitious roots and stem pericycles. Analysis of leaf genomic DNA with eight polymorphic microsatellite markers was supportive of the clonal fidelity and genetic stability of the micropropagated material. Successful clonal plantations (over 5,800 ramets) have been established by applying this protocol.

Aplicación de la celulosa bacteriana a la restauración del patrimonio bibliográfico y documental en papel

La preservación del patrimonio bibliográfico y documental en papel es uno de los mayores retos a los que se enfrentan bibliotecas y archivos de todo el mundo. La búsqueda de soluciones al problema del papel degradado ha sido abordada históricamente desde dos líneas de trabajo predominantes: la conservación de estos documentos mediante la neutralización de los ácidos presentes en ellos con agentes alcalinos, y su restauración mediante el método de laminación fundamentalmente con papel de origen vegetal. Sin embargo, no se ha explorado con éxito la posibilidad de reforzar la celulosa dañada, y el problema sigue sin encontrar una solución satisfactoria. Hasta el día de hoy, el desarrollo de tratamientos basados en biotecnología en la conservación del patrimonio documental ha sido muy escaso, aunque la capacidad de ciertas bacterias de producir celulosa lleva a plantear su uso en el campo de la conservación y restauración del papel. La celulosa bacteriana (CB) es químicamente idéntica a la celulosa vegetal, pero su organización macroscópica es diferente. Sus propiedades únicas (alto grado de cristalinidad, durabilidad, resistencia y biocompatibilidad) han hecho de este material un excelente recurso en diferentes campos. En el desarrollo de esta tesis se ha estudiado el uso de la celulosa bacteriana, de alta calidad, generada por Gluconacetobacter sucrofermentans CECT 7291, para restaurar documentos deteriorados y consolidar los que puedan estar en peligro de degradación, evitando así su destrucción y proporcionando al papel que se restaura unas buenas propiedades mecánicas, ópticas y estructurales. Se desarrollan asimismo protocolos de trabajo que permitan la aplicación de dicha celulosa. En primer lugar se seleccionó el medio de cultivo que proporcionó una celulosa adecuada para su uso en restauración. Para ello se evaluó el efecto que tienen sobre la celulosa generada las fuentes de carbono y nitrógeno del medio de cultivo, manteniendo como parámetros fijos la temperatura y el pH inicial del medio, y efectuando los ensayos en condiciones estáticas. Se evaluó, también, el efecto que tiene en la CB la adición de un 1% de etanol al medio de cultivo. Las capas de celulosa se recolectaron a cuatro tiempos distintos, caracterizando en cada uno de ellos el medio de cultivo (pH y consumo de fuente de carbono), y las capas de CB (pH, peso seco y propiedades ópticas y mecánicas). La mejor combinación de fuentes de carbono y nitrógeno resultó ser fructosa más extracto de levadura y extracto de maíz, con o sin etanol, que proporcionaban una buena relación entre la producción de celulosa y el consumo de fuente de carbono, y que generaban una capa de celulosa resistente y homogénea. La adición de etanol al medio de cultivo, si bien aumentaba la productividad, causaba un descenso apreciable de pH. Las capas de CB obtenidas con los medios de cultivo optimizados se caracterizaron en términos de sus índices de desgarro y estallido, propiedades ópticas, microscopía electrónica de barrido (SEM), difracción de rayos-X, espectroscopía infrarroja con transformada de Fourier (FTIR), grado de polimerización, ángulos de contacto estáticos y dinámicos, y porosimetría de intrusión de mercurio. Por otro lado hay que tener en cuenta que el material restaurado debe ser estable con el tiempo. Por ello esta misma caracterización se efectuó tras someter a las capas de CB a un proceso de envejecimiento acelerado. Los resultados mostraron que la CB resultante tiene un elevado índice de cristalinidad, baja porosidad interna, buenas propiedades mecánicas, y alta estabilidad en el tiempo. Para desarrollar los protocolos de trabajo que permitan la restauración con esta celulosa optimizada, se comienzó con un proceso de selección de los papeles que van a ser restaurados. Se eligieron tres tipos de papeles modelo, hechos con pasta mecánica, química y filtro (antes y después de ser sometidos a un proceso de envejecimiento acelerado), y tres libros viejos adquiridos en el mercado de segunda mano. Estos ejemplares a restaurar se caracterizaron también en términos de sus propiedades mecánicas y fisicoquímicas. El primer protocolo de restauración con CB que se evaluó fue el denominado laminación. Consiste en aplicar un material de refuerzo al documento mediante el uso de un adhesivo. Se seleccionó para ello la CB producida en el medio de cultivo optimizado con un 1% de etanol. Se aplicó un método de purificación alcalino (1 hora a 90 °C en NaOH al 1%) y como adhesivo se seleccionó almidón de trigo. El proceso de laminación se efectuó también con papel japonés (PJ), un material habitualmente utilizado en conservación, para comparar ambos materiales. Se concluyó que no hay diferencias significativas en las características estudiadas entre los dos tipos de materiales de refuerzo. Se caracterizó el material reforzado y, también, después de sufrir un proceso de envejecimiento acelerado. Los papeles laminados con CB mostraban diferencias más marcadas en las propiedades ópticas que los restaurados con PJ, con respecto a los originales. Sin embargo, el texto era más legible cuando el material de restauración era la CB. La mojabilidad disminuía con ambos tipos de refuerzo, aunque en los papeles laminados con CB de manera más marcada e independiente del material a restaurar. Esto se debe a la estructura cerrada de la CB, que también conduce a una disminución en la permeabilidad al aire. Este estudio sugiere que la CB mejora la calidad del papel deteriorado, sin alterar la información que contiene, y que esta mejora se mantiene a lo largo del tiempo. Por tanto, la CB puede ser utilizada como material de refuerzo para laminar, pudiendo ser más adecuada que el PJ para ciertos tipos de papeles. El otro método de restauración que se estudió fue la generación in situ de la CB sobre el papel a restaurar. Para ello se seleccionó el medio de cultivo sin etanol, ya que el descenso de pH que causaba su presencia podría dañar el documento a restaurar. El método de purificación elegido fue un tratamiento térmico (24 horas a 65 °C), menos agresivo para el material a restaurar que el tratamiento alcalino. Se seleccionó la aplicación del medio de cultivo con la bacteria mediante pincel sobre el material a restaurar. Una vez caracterizado el material restaurado, y éste mismo tras sufrir un proceso de envejecimiento acelerado, se concluyó que no hay modificación apreciable en ninguna característica, salvo en la permeabilidad al aire, que disminuye de manera muy evidente con la generación de CB, dando lugar a un material prácticamente impermeable al aire. En general se puede concluir que ha quedado demostrada la capacidad que tiene la celulosa generada por la bacteria Gluconacetobacter sucrofermentans CECT 7291 para ser utilizada como material de refuerzo en la restauración del patrimonio documental en papel. Asimismo se han desarrollado dos métodos de aplicación, uno ex situ y otro in situ, para efectuar esta tarea de restauración. ABSTRACT The preservation of bibliographic and documentary heritage is one of the biggest challenges that libraries and archives around the world have to face. The search for solutions to the problem of degraded paper has historically been focused from two predominants lines of work: the conservation of these documents by the neutralization of acids in them with alkaline agents, and their restoration by lining them with, basically, cellulose from vegetal sources. However, the possibility of strengthening the damaged cellulose has not been successfully explored, and the problem still persists. Until today, the development of biotechnology-based treatments in documentary heritage conservation has been scarce, although the ability of certain bacteria to produce cellulose takes to propose its use in the field of conservation and restoration of paper. The bacterial cellulose (BC) is chemically identical to the plant cellulose, but its macroscopic organization is different. Its unique properties (high degree of crystallinity, durability, strength and biocompatibility), makes it an excellent resource in different fields. The use of high-quality BC generated by Gluconacetobacter sucrofermentans CECT 7291 to restore damaged documents and to consolidate those that may be at risk of degradation, has been studied in this thesis, trying to prevent the document destruction, and to get reinforced papers with good mechanical, optical and structural properties. Protocols that allow the implementation of the BC as a reinforcing material were also developed. First of all, in order to select the culture medium that provides a cellulose suitable for its use in restoration, it has been evaluated the effect that the carbon and nitrogen sources from the culture medium have on the generated BC, keeping the temperature and the initial pH of the medium as fixed parameters, and performing the culture without shaking. The effect of the addition of 1% ethanol to the culture medium on BC properties was also evaluated. The cellulose layers were collected at four different times, characterizing in all of them the culture medium (pH and carbon source consumption), and the BC sheets (pH, dry weight and optical and mechanical properties). The best combination of carbon and nitrogen sources proved to be fructose plus yeast extract and corn steep liquor, with or without ethanol, which provided a good balance between the cellulose production and the consumption of carbon source, and generating BC sheets homogeneous and resistant. The addition of ethanol to the culture medium increased productivity but caused a noticeable decrement in pH. The BC layers generated with these optimized culture media, have been characterized in terms of tear and burst index, optical properties, scanning electron microscopy (SEM), X-ray diffraction, infrared Fourier transform spectroscopy (FTIR), polymerization degree, static and dynamic contact angles, and mercury intrusion porosimetry. Moreover it must be kept in mind that the restored materials should be stable over time. Therefore, the same characterization was performed after subjecting the layers of BC to an accelerated aging process. The results showed that the BC sheets obtained have a high crystallinity index, low internal porosity, good mechanical properties, and high stability over time. To develop working protocols to use this optimized BC in paper restoration, the first step was to select the samples to restore. Three types of model papers, made from mechanical pulp, chemical pulp and filter paper (before and after an accelerated aging process), and three old books purchased in the second hand market, were chosen. These specimens to be restored were also characterized in terms of its mechanical and physicochemical properties. The first protocol of restoration with BC to be evaluated is called linning. It consists on applying a reinforcing material to the document using an adhesive. The BC produced in the optimized culture medium with 1% ethanol was selected. An alkali purification method (1 hour at 90 °C in 1% NaOH) was applied, and wheat starch was selected as adhesive. The linning process was also carried out with Japanese paper (JP), a material commonly used in conservation, in order to compare both materials. It was concluded that there are no significant differences in the characteristics studied of the two types of reinforcing materials. The reinforced materials were characterized before and after undergoing to an accelerated aging. Papers lined with BC showed more marked differences in the optical properties that papers restored with JP. However, the text was more readable when BC was the reinforcing material. Wettability decreased with both types of reinforcement, although in the papers linned with BC it happened more marked and independently of the sample to restore. This is due to the closed structure of BC, which also leads to a decrement in air permeance. This study suggests that BC improves the deteriorated paper quality, without altering the information on it, and that this improvement is maintained over time. Therefore, the BC may be used as reinforcing material for linning, being more suitable than the JP to restore certain types of papers. The other restoration method to be evaluated was the in situ generation of BC over the paper to restore. For this purpose the culture medium without ethanol was selected, as the pH decrement caused by his presence would damage the document to restore. As purification method a heat treatment (24 hours at 65 °C) was chosen, less aggressive to the material to restore than the alkaline treatment. It was decided to apply the culture medium with the bacteria onto the material to restore with a brush. The reinforced material was characterized before and after an accelerated aging process. It was concluded that there was no substantial change in any characteristic, except for air permeance, which decreases very sharply after the generation of BC, getting a substantially air impermeable material. In general, it can be concluded that the ability of BC produced by Gluconacetobacter sucrofermentans CECT 7291 for its use as a reinforcing material in the restoration of paper documentary heritage, has been demonstrated. Also, two restoration methods, one ex situ and another in situ have been developed.

Sequence-specific polypeptoids: A diverse family of heteropolymers with stable secondary structure

We have synthesized and characterized a family of structured oligo-N-substituted-glycines (peptoids) up to 36 residues in length by using an efficient solid-phase protocol to incorporate chemically diverse side chains in a sequence-specific fashion. We investigated polypeptoids containing side chains with a chiral center adjacent to the main chain nitrogen. Some of these sequences have stable secondary structure, despite the achirality of the polymer backbone and its lack of hydrogen bond donors. In both aqueous and organic solvents, peptoid oligomers as short as five residues give rise to CD spectra that strongly resemble those of peptide α-helices. Differential scanning calorimetry and CD measurements show that polypeptoid secondary structure is highly stable and that unfolding is reversible and cooperative. Thermodynamic parameters obtained for unfolding are similar to those obtained for the α-helix to coil transitions of peptides. This class of biomimetic polymers may enable the design of self-assembling macromolecules with novel structures and functions.

The Bacillus subtilis crh gene encodes a HPr-like protein involved in carbon catabolite repression

Carbon catabolite repression (CCR) of several Bacillus subtilis catabolic genes is mediated by ATP-dependent phosphorylation of histidine-containing protein (HPr), a phosphocarrier protein of the phosphoenolpyruvate (PEP): sugar phosphotransferase system. In this study, we report the discovery of a new B. subtilis gene encoding a HPr-like protein, Crh (for catabolite repression HPr), composed of 85 amino acids. Crh exhibits 45% sequence identity with HPr, but the active site His-15 of HPr is replaced with a glutamine in Crh. Crh is therefore not phosphorylated by PEP and enzyme I, but is phosphorylated by ATP and the HPr kinase in the presence of fructose-1,6-bisphosphate. We determined Ser-46 as the site of phosphorylation in Crh by carrying out mass spectrometry with peptides obtained by tryptic digestion or CNBr cleavage. In a B. subtilis ptsH1 mutant strain, synthesis of β-xylosidase, inositol dehydrogenase, and levanase was only partially relieved from CCR. Additional disruption of the crh gene caused almost complete relief from CCR. In a ptsH1 crh1 mutant, producing HPr and Crh in which Ser-46 is replaced with a nonphosphorylatable alanyl residue, expression of β-xylosidase was also completely relieved from glucose repression. These results suggest that CCR of certain catabolic operons requires, in addition to CcpA, ATP-dependent phosphorylation of Crh, and HPr at Ser-46.

Soldier caste-specific gene expression in the mandibular glands of Hodotermopsis japonica (Isoptera: Termopsidae)

Although “polymorphic castes” in social insects are well known as one of the most important phenomena of polyphenism, few studies of caste-specific gene expressions have been performed in social insects. To identify genes specifically expressed in the soldier caste of the Japanese damp-wood termite Hodotermopsis japonica, we employed the differential-display method using oligo(dT) and arbitrary primers, compared mRNA from the heads of mature soldiers and pseudergates (worker caste), and identified a clone (PCR product) 329 bp in length termed SOL1. Northern blot analysis showed that the SOL1 mRNA is about 1.0 kb in length and is expressed specifically in mature soldiers, but not in pseudergates, even in the presoldier induction by juvenile hormone analogue, suggesting that the product is specific for terminally differentiated soldiers. By using the method of 5′- and 3′-rapid amplification of cDNA ends, we isolated the full length of SOL1 cDNA, which contained an ORF with a putative signal peptide at the N terminus. The sequence showed no significant homology with any other known protein sequences. In situ hybridization analysis showed that SOL1 is expressed specifically in the mandibular glands. These results strongly suggest that the SOL1 gene encodes a secretory protein specifically synthesized in the mandibular glands of the soldiers. Histological observations revealed that the gland actually develops during the differentiation into the soldier caste.

Structural origins of the exonuclease resistance of a zwitterionic RNA

Nuclease resistance and RNA affinity are key criteria in the search for optimal antisense nucleic acid modifications, but the origins of the various levels of resistance to nuclease degradation conferred by chemical modification of DNA and RNA are currently not understood. The 2′-O-aminopropyl (AP)-RNA modification displays the highest nuclease resistance among all phosphodiester-based analogues and its RNA binding affinity surpasses that of phosphorothioate DNA by 1°C per modified residue. We found that oligodeoxynucleotides containing AP-RNA residues at their 3′ ends competitively inhibit the degradation of single-stranded DNA by the Escherichia coli Klenow fragment (KF) 3′-5′ exonuclease and snake venom phosphodiesterase. To shed light on the origins of nuclease resistance brought about by the AP modification, we determined the crystal structure of an A-form DNA duplex with AP-RNA modifications at 1.6-Å resolution. In addition, the crystal structures of complexes between short DNA fragments carrying AP-RNA modifications and wild-type KF were determined at resolutions between 2.2 and 3.0 Å and compared with the structure of the complex between oligo(dT) and the D355A/E357A KF mutant. The structural models suggest that interference of the positively charged 2′-O-substituent with the metal ion binding site B of the exonuclease allows AP-RNA to effectively slow down degradation.