The Geometry of Normal Tissue and Cancer Gene Expression Manifolds.

A recent paper shows that in gene expression space the manifold spanned by normal tissues and the manifold spanned by the corresponding tumors are disjoint. The statement is based on a two-dimensional projection of gene expression data. In the present paper, we show that, for the multi-dimensional vectors defining the centers of cloud samples: 1. The closest tumor to a given normal tissue is the tumor developed in that tissue, 2. Two normal tissues define quasi-orthogonal directions, 3. A tumor may have a projection onto its corresponding normal tissue, but it is quasi-orthogonal to all other normal tissues, and 4. The cancer manifold is roughly obtained by translating the normal tissue manifold along an orthogonal direction defined by a global cancer progression axis. These geometrical properties add a new characterization of normal tissues and tumors and may have biological significance. Indeed, normal tissues at the vertices of a high-dimensional simplex could indicate genotype optimization for given tissue functions, and a way of avoiding errors in embryonary development. On the other hand, the cancer progression axis could define relevant pan-cancer genes and seems to be consistent with the atavistic theory of tumors.

Isolation of Lactic Acid Bacteria (LAB) from Salmonids for Potential Use as Probiotics: In Vitro Assays and Toxicity Assessment of Salmo trutta Embryonated Eggs.

This research investigates the potential of lactic acid bacteria (LAB) from freshwater salmonids as prospective probiotics for application in aquaculture. LAB and pathogenic bacteria were obtained from mucus and tissues of Oncorhynchus mykiss and Salmo trutta from fish farms in northeast Spain that had not used antibiotics for the six months preceding the study. Isolates were identified using Gram staining and sequencing of 16S rRNA and ITS-1. To assess the safety of the LAB, antibiotic susceptibility tests (ASTs) against 23 antimicrobials were performed. In vitro antagonism assays were conducted to evaluate the inhibitory effects of living LAB using the agar diffusion test method and their metabolites using the agar well diffusion method. The assays targeted six specific pathogens: Aeromonas salmonicida subsp. salmonicida, Carnobacterium maltaromaticum, Vagococcus salmoninarum, Yersinia ruckeri, Lactococcus garvieae, and the marine pathogen Vibrio jasicida. Additionally, a toxicity assay was conducted on embryonic eggs of S. trutta. The ASTs on probiotic LAB candidates revealed varied responses to antimicrobials, but no resistance to oxytetracycline or florfenicol, which are two antibiotics commonly used in aquaculture, was detected. The in vitro assays indicate that LAB exhibit antagonistic effects against pathogens, primarily when directly stimulated by their presence. In applications involving embryonic eggs or larvae, certain live strains of LAB were found to have adverse effects, with some isolates resulting in higher mortality rates compared to the control group or other isolates. Furthermore, the potential pathogenicity of certain LAB strains, typically considered safe in salmonids, warrants deeper investigation.

On the gene expression landscape of cancer.

Kauffman picture of normal and tumor states as attractors in an abstract state space is used in order to interpret gene expression data for 15 cancer localizations obtained from The Cancer Genome Atlas. A principal component analysis of this data unveils the following qualitative aspects about tumors: 1) The state of a tissue in gene expression space can be described by a few variables. In particular, there is a single variable describing the progression from a normal tissue to a tumor. 2) Each cancer localization is characterized by a gene expression profile, in which genes have specific weights in the definition of the cancer state. There are no less than 2500 differentially-expressed genes, which lead to power-like tails in the expression distribution functions. 3) Tumors in different localizations share hundreds or even thousands of differentially expressed genes. There are 6 genes common to the 15 studied tumor localizations. 4) The tumor region is a kind of attractor. Tumors in advanced stages converge to this region independently of patient age or genetic characteristics. 5) There is a landscape of cancer in gene expression space with an approximate border separating normal tissues from tumors.

Cancer Segmentation by Entropic Analysis of Ordered Gene Expression Profiles.

The availability of massive gene expression data has been challenging in terms of how to cure, process, and extract useful information. Here, we describe the use of entropic measures as discriminating criteria in cancer using the whole data set of gene expression levels. These methods were applied in classifying samples between tumor and normal type for 13 types of tumors with a high success ratio. Using gene expression, ordered by pathways, results in complexity-entropy diagrams. The map allows the clustering of the tumor and normal types samples, with a high success rate for nine of the thirteen, studied cancer types. Further analysis using information distance also shows good discriminating behavior, but, more importantly, allows for discriminating between cancer types. Together, our results allow the classification of tissues without the need to identify relevant genes or impose a particular cancer model. The used procedure can be extended to classification problems beyond the reported results.

Estimating the number of available states for normal and tumor tissues in gene expression space.

The topology of gene expression space for a set of 12 cancer types is studied by means of an entropy-like magnitude, which measures the volumes of the regions occupied by tumor and normal samples, i.e., the number of available states (genotypes) that can be classified as tumor-like or normal-like, respectively. Computations show that the number of available states is much greater for tumors than for normal tissues, suggesting the irreversibility of the progression to the tumor phase. The entropy is nearly constant for tumors, whereas it exhibits a higher variability in normal tissues, probably due to tissue differentiation. In addition, we show an interesting correlation between the fraction (tumor/normal) of available states and the overlap between the tumor and normal sample clouds, interpreted as a way of reducing the decay rate to the tumor phase in more ordered or structured tissues.

A one-dimensional parameter-free model for carcinogenesis in gene expression space.

A small portion of a tissue defines a microstate in gene expression space. Mutations, epigenetic events or external factors cause microstate displacements which are modeled by combining small independent gene expression variations and large Levy jumps, resulting from the collective variations of a set of genes. The risk of cancer in a tissue is estimated as the microstate probability to transit from the normal to the tumor region in gene expression space. The formula coming from the contribution of large Levy jumps seems to provide a qualitatively correct description of the lifetime risk of cancer in 8 tissues, and reveals an interesting connection between the risk and the way the tissue is protected against infections.

Mutations as Levy flights.

Data from a long time evolution experiment with Escherichia Coli and from a large study on copy number variations in subjects with European ancestry are analyzed in order to argue that mutations can be described as Levy flights in the mutation space. These Levy flights have at least two components: random single-base substitutions and large DNA rearrangements. From the data, we get estimations for the time rates of both events and the size distribution function of large rearrangements.

Gene expression rearrangements denoting changes in the biological state.

In many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may be the result of a selective pressure, as in the Long Term Evolution Experiment with E. Coli populations, or the progression to Alzheimer disease in aged brains, or the progression from a normal tissue to the cancer state. The first two cases seem to belong to a class of transitions, where the initial and final states are relatively close to each other, and the distribution function for the differential expressions is short ranged, with a tail of only a few dozens of strongly varying genes. In the latter case, cancer, the initial and final states are far apart and separated by a low-fitness barrier. The distribution function shows a very heavy tail, with thousands of silenced and over-expressed genes. We characterize the biological states by means of their principal component representations, and the expression distribution functions by their maximal and minimal differential expression values and the exponents of the Pareto laws describing the tails.

Summer bloom of Vulcanodinium rugosum in Cienfuegos Bay (Cuba) associated to dermatitis in swimmers.

The marine dinoflagellate Vulcanodinium rugosum produces powerful paralyzing and cytotoxic compounds named pinnatoxins (PnTX) and portimines. Even though, no related human intoxication episodes following direct exposure in seawater or the ingestion of contaminated seafood have been documented so far. This study aimed at investigating a dinoflagellate bloom linked to acute dermatitis cases in two recreational beaches in Cienfuegos Bay, Cuba. We used epidemiological and clinical data from 60 dermatitis cases consisting of individuals in close contact with the bloom. Seawater physical-chemical properties were described, and the microorganism causing the bloom was identified by means of light and scanning electron microscopy. Morphological identification was confirmed genetically by sequencing the internal transcribed spacers ITS1 and ITS2, and the 5.8S rDNA region. Toxic compounds were identified from a bloom extract using liquid chromatography (LC) coupled to high-resolution mass spectrometry (HRMS), and their concentrations were estimated based on low-resolution tandem mass spectrometry (LC-MS/MS). Sixty people who had prolonged contact with the dinoflagellate bloom suffered acute dermal irritation. Most patients (79.2%) were children and had to be treated with antibiotics; some required >5-day hospitalization. Combined morphological and genetic characters indicated V. rugosum as the causative agent of the bloom. rDNA sequences of the V. rugosum genotype found in the bloom aligned with others from Asia, including material found in the ballast tank of a ship in Florida. The predominant toxins in the bloom were portimine, PnTX-F and PnTX-E, similar to strains originating from the Pacific Ocean. This bloom was associated with unusual weather conditions such as frequent and prolonged droughts. Our findings indicate a close link between the V. rugosum bloom and a dermatitis outbreak among swimmers in Cienfuegos Bay. Phylogenetic evidence suggests a recent introduction of V. rugosum from the Pacific Ocean into Caribbean waters, possibly via ballast water.

Functional and structural analysis of maize hsp101 IRES.

Maize heat shock protein of 101 KDa (HSP101) is essential for thermotolerance induction in this plant. The mRNA encoding this protein harbors an IRES element in the 5'UTR that mediates cap-independent translation initiation. In the current work it is demonstrated that hsp101 IRES comprises the entire 5'UTR sequence (150 nts), since deletion of 17 nucleotides from the 5' end decreased translation efficiency by 87% compared to the control sequence. RNA structure analysis of maize hsp101 IRES revealed the presence of three stem-loops toward its 5' end, whereas the remainder sequence contains a great proportion of unpaired nucleotides. Furthermore, HSP90 protein was identified by mass spectrometry as the protein preferentially associated with the maize hsp101 IRES. In addition, it has been found that eIFiso4G rather than eIF4G initiation factor mediates translation of the maize hsp101 mRNA.

Scaling in the correlation energies of two-dimensional artificial atoms.

We find an unexpected scaling in the correlation energy of artificial atoms, i.e., harmonically confined two-dimensional quantum dots. The scaling relation is found through extensive numerical examinations including Hartree-Fock, variational quantum Monte Carlo, density functional, and full configuration interaction calculations. We show that the correlation energy, i.e., the true ground-state total energy minus the Hartree-Fock total energy, follows a simple function of the Coulomb energy, confinement strength and number of electrons. We find an analytic expression for this function, as well as for the correlation energy per particle and for the ratio between the correlation and total energies. Our tests for independent diffusion Monte Carlo and coupled-cluster results for quantum dots-including open-shell data-confirm the generality of the scaling obtained. As the scaling also applies well to ≳100 electrons, our results give interesting prospects for the development of correlation functionals within density functional theory.

Perioperative morbi-mortality associated with bariatric surgery: from systematic biliopancreatic diversion to a tailored laparoscopic gastric bypass or sleeve gastrectomy approach.

BACKGROUND: The effectiveness and safety of the different bariatric surgical procedures currently available depend, partly, on the characteristics of the populations under study, the technical approach, the expertise of surgical teams, and on institutional factors. To evaluate the effectiveness and safety of these procedures, we compared the surgical results for biliopancreatic diversion surgery versus laparoscopic gastric bypass and sleeve gastrectomies performed in our institution. METHODS: This was a retrospective observational study of 296 patients undergoing bariatric surgery from January 2005 through October 2010. We analyzed mortality rate, cardiocirculatory and pulmonary perioperative complications, duration of surgery, intensive care unit admissions, and length of stay. We describe the changes in the choice of the surgical procedures throughout the study period. RESULTS: We observed a rate of pulmonary complications of 2.3 % and a mortality rate 3 months after discharge of 2.36 % with sepsis secondary to anastomotic leak as the main cause of death. Biliopancreatic diversion surgery was associated with higher mortality rates (p value = 0.014) and longer hospital stay (median of 9 versus 6 days for laparoscopic gastric bypass and sleeve gastrectomy, p value <0.001). Body mass index ≥ 50 was also related to higher mortality (p value = 0.023). We confirmed a progressive increase in laparoscopic restrictive and mixed techniques in our institution (from 0 % in 2005 to 87 % of all procedures in 2010). CONCLUSIONS: Bariatric surgery in our institution has dramatically shifted from systematic biliopancreatic diversion to a tailored laparoscopic gastric bypass or sleeve gastrectomy approach, which has made it possible to reduce hospital stay and mortality rates.

MORPHOLOGICAL AND ULTRASTRUCTURAL FEATURES OF A STRAIN OF BOTRYOCOCCUS TERRIBILIS (TREBOUXIOPHYCEAE) FROM BRAZIL(1).

The genus Botryococcus comprises a group of cosmopolitan species of freshwater colonial green algae, some of which synthesize and accumulate an unusually high level (15-76%) of liquid hydrocarbons. This characteristic suggests the possibility of exploiting species from this group as renewable sources for jet fuel. An oil-rich strain of Botryococcus (Trebouxiophyceae) was isolated from a freshwater pond in the state of Bahia, Brazil, and is presently maintained under standard conditions at the Culture Collection of the Institute of Biology, Federal University of Bahia. The taxonomic classification of the species was based on light microscopy (LM); and TEM and SEM were used to better characterize its features, which have never before been described at this level. The LM characterization included the size of the colonies (35.7-157 µm) and cells (8-10 × 5-9 µm) and their connection in sub-colonies by mucilaginous strands, as well as the presence of mucilaginous processes on the periphery of some of the colonies, with most of the cells included inside the colony. Reproduction occurred through divisions into two to four autospores. These features characterized the species as Botryococcus terribilis Komárek and Marvan. The TEM study showed, in addition to the presence of starch grains, pyrenoids that are penetrated by thick thylakoids. The pyrenoid bodies appear as electron-dense protein inclusions located in the chloroplast and surrounded by a starch sheath. These structures, which contain most if not all of the Ribulose-1,5-bisphosphate carboxylase oxygenase in several algal species that have been studied closely, are newly discovered for this species.

Stationary density matrix of a pumped polariton system.

The density matrix rho of a model polariton system is obtained numerically from a master equation which takes account of pumping and losses. In the stationary limit, the coherences between eigenstates of the Hamiltonian are 3 orders of magnitude smaller than the occupations, meaning that the stationary density matrix is approximately diagonal in the energy representation. A weakly distorted grand canonical Gibbs distribution fits well the occupations.

Purification and biochemical characterization of a broad substrate specificity thermostable alkaline protease from Aspergillus nidulans.

Aspergillus nidulans PW1 produces an extracellular carboxylesterase activity that acts on several lipid esters when cultured in liquid media containing olive oil as a carbon source. The enzyme was purified by gel filtration and ion exchange chromatography. It has an apparent MW and pI of 37 kDa and 4.5, respectively. The enzyme efficiently hydrolyzed all assayed glycerides, but showed preference toward short- and medium-length chain fatty acid esters. Maximum activity was obtained at pH 8.5 at 40 degrees C. The enzyme retained activity after incubation at pHs ranging from 8 to 11 for 12 h at 37 degrees C and 6 to 8 for 24 h at 37 degrees C. It retained 80% of its activity after incubation at 30 to 70 degrees C for 30 min and lost 50% of its activity after incubation for 15 min at 80 degrees C. Noticeable activation of the enzyme is observed when Fe(2+) ion is present at a concentration of 1 mM. Inhibition of the enzyme is observed in the presence of Cu(2+), Fe(3+), Hg(2+), and Zn(2+) ions. Even though the enzyme showed strong carboxylesterase activity, the deduced N-terminal amino acid sequence of the purified protein corresponded to the protease encoded by prtA gene.

Photon emission as a source of coherent behavior of polaritons.

We show that the combined effect of photon emission and Coulomb interactions may drive an exciton-polariton system towards a dynamical coherent state, even without phonon thermalization or any other relaxation mechanism. Exact diagonalization results for a finite system (a multilevel quantum dot interacting with the lowest-energy photon mode of a microcavity) are presented in support of this statement.

Entamoeba histolytica: mechanism of decrease of virulence of axenic cultures maintained for prolonged periods.

Intraportal injection of non-virulent E. histolytica (derived from prolonged axenic culture of virulent E. histolytica) strain HM1-IMSS in normal hamsters results in no liver lesions and disappearance of the parasites 48-72 h after injection. Viability of non-virulent E. histolytica after 2 h of in vitro incubation in either fresh or decomplemented hamster serum is the same as control virulent E. histolytica (50-90%). In hamsters made leukopenic, or both leukopenic+hypocomplementemic, or hypocomplementemic+sephadex microspheres (to produce focal liver ischemia) intraportally injected non-virulent E. histolytica cause no lesions and disappear after 24 h. In addition, neither hypocomplementemia nor immunosuppression with cyclosporin A prolonged the survival of non-virulent E. histolytica. Methyl prednisolone treatment of hamsters resulted in survival of large numbers of non-virulent E. histolytica in the liver, with little inflammation and minimal tissue damage, for up to 7 days. Inflammatory cells (macrophages) would appear to be chiefly responsible for elimination of non-virulent E. histolytica. Parallel experiments with E. dispar suggest a different mechanism for its non-pathogenicity.

Leishmania lipophosphoglycan (LPG) activates NK cells through toll-like receptor-2.

Toll-like receptors (TLRs) mediate the cellular response to conserved molecular patterns shared by microorganisms. We report that TLR-2 on human NK cells is upregulated and stimulated by Leishmania major lipophosphoglycan (LPG), a phosphoglycan belonging to a family of unique Leishmania glycoconjugates. We found that purified L. major LPG upregulates both mRNA and the membrane expression of TLR-2 in NK cells. Additionally, IFN-gamma and TNF-alpha production and nuclear translocation of NF-kappaB was enhanced. The activation effect was more intense with LPG purified from infectious metacyclic parasites than from noninfectious procyclic Leishmania. Since the difference between the molecules derived from these two stages of the parasite growth cycle lies exclusively in the number of phosphosaccharide repeat domains and in the composition of glycan side chains that branch off these domains, we propose that TLR-2 possibly distinguishes between phosphorylated glycan repeats on LPG molecules. The effect of LPG on cytokine production and on membrane expression of TLR-2 could be blocked with F(ab')2 fragments of the mAb against LPG (WIC 79.3). Confocal microscopy demonstrated the co-localization of LPG and TLR-2 on the NK cell membrane. Binding of LPG to TLR-2 in NK cells was demonstrated by immunoprecipitations done with anti-TLR-2 and anti-LPG mAb followed by immunoblotting with anti-LPG and anti-TLR-2, respectively. Both antibodies recognized the immune complexes. These results suggest that NK cells are capable of recognition of, and activation by, Leishmania LPG through TLR-2, enabling them to participate autonomously in the innate immune system and thereby increasing the effective destruction of the parasite.

Efecto del extracto de nopal sobre lípidos y lipoproteínas en hipercolesterolemia moderada / The effect of prickly pear cactus extracts on lipids and lipoproteins in moderate hypercholesterolemia

Estudios epidemiológicos han encontrado asociación entre el consumo de dietas altas en fibra y la disminución en el riesgo para enfermedad car-diovascular. El extracto aislado de nopal (Opuntia fuliginosa) disminuye notablemente el colesterol de LDL en roedores alimentados con dietas altas en colesterol. Conocer la eficacia y seguridad de ese producto en humanos con hipercolestero-lemia moderada constituyó el objetivo de este estudio. El diseño fue aleatorio, doble ciego y controlado con placebo; para ello se analizaron 18 pacientes no diabéticos con colesterol total entre 200 y 300 mg/dL. Después de un periodo de dieta fase I, nueve pacientes recibieron extracto de nopal (3 g tid) y nueve, placebo. En el grupo con extracto existió tendencia a disminución en el colesterol de LDL (-8 por ciento) y triglicéridos (-10 por ciento), y aumento en el colesterol de HDL (+7 por ciento) y apolipoproteína A-I (+4 por ciento); estas diferencias no alcanzaron significado estadístico, a diferencia de las disminuciones de colesterol total (-6 por ciento, p < 0.05), apolipoproteína B (-11 por ciento, p < 0.05) y glucosa (-12 por ciento, p < 0.05). Estos resultados sugieren que la administración de 9 g/día de extracto aislado de nopal mejora el perfil lipídico de pacientes con hipercolesterolemia moderada, pero posiblemente se necesitan mayores dosis para observar un beneficio clínico.