Modelling growth dynamics and toxin production in Ostreopsis cf. ovata

The benthic dinoflagellate O. ovata represents a serious threat for human health and for the ecology of its blooming areas: thanks to its toxicity this microalga has been responsible for several cases of human intoxication and mass mortalities of benthic invertebrates. Although the large number of studies on this dinoflagellate, the mechanisms underpinning O. ovata growth and toxin production are still far to be fully understood. In this work we have enriched the dataset on this species by carrying out a new experiment on an Adriatic O. cf. ovata strain. Data from this experiment (named Beta) and from another comparable experiment previously conducted on the same strain (named Alpha), revealed some interesting aspects of this dinoflagellate: it is able to grow also in a condition of strong intracellular nutrient deficiency (C:P molar ratio > 400; C:N > 25), reaching extremely low values of chlorophyll-a to carbon ratio (0.0004). Was also found a significant inverse relationships (r > -0.7) between cellular toxin to carbon and cellular nutrient to carbon ratios of experiment Alpha. In the light of these result, we hypothesized that in O. cf. ovata nutrient-stress conditions (intended as intracellular nutrient deficiency) can cause: i) an increase in toxin production; ii) a strong decrease in chlorophyll-a synthesis; iii) a lowering of metabolism associated with the formation of a sort of resting stage. We then used a modelling approach to test and critically evaluate these hypotheses in a mechanistic way: newly developed formulation describing toxin production and fate, and ad hoc changes in the already existent formulations describing chlorophyll synthesis, rest respiration, and mortality, have been incorporated in a simplified version of the European Regional Seas Ecosystem Model (ERSEM), together with a new ad hoc parameterization. The adapted model was able to accurately reproduce many of the trends observed in the Alpha experiment, allowing us to support our hypotheses. Instead the simulations of the experiment Beta were not fully satisfying in quantitative terms. We explained this gap with the presumed different physiological behaviors between the algae of the two experiments, due to the different pre-experimental periods of acclimation: the model was not able to reproduce acclimation processes in its simulations of the experiment Beta. Thus we attempt to simulate the acclimation of the algae to nutrient-stress conditions by manual intervention on some parameters of nutrient-stress thresholds, but we received conflicting results. Further studies are required to shed light on this interesting aspect. In this work we also improve the range of applicability of a state of the art marine biogeochemical model (ERSEM) by implementing in it an ecological relevant process such as the production of toxic compounds.

Chemopreventive effects of eicosapentaenoic acid free fatty acid in a murine model of colitis-associated colorectal cancer

Inflammatory bowel diseases are associated with increased risk of developing colitis-associated colorectal cancer (CAC). Epidemiological data show that the consumption of ω-3 polyunsaturated fatty acids (ω-3 PUFAs) decreases the risk of sporadic colorectal cancer (CRC). Importantly, recent data have shown that eicosapentaenoic acid-free fatty acid (EPA-FFA) reduces polyps formation and growth in models of familial adenomatous polyposis. However, the effects of dietary EPA-FFA are unknown in CAC. We tested the effectiveness of substituting EPA-FFA, for other dietary fats, in preventing inflammation and cancer in the AOM-DSS model of CAC. The AOM-DSS protocols were designed to evaluate the effect of EPA-FFA on both initiation and promotion of carcinogenesis. We found that EPA-FFA diet strongly decreased tumor multiplicity, incidence and maximum tumor size in the promotion and initiation arms. Moreover EPA-FFA, in particular in the initiation arm, led to reduced cell proliferation and nuclear β-catenin expression, whilst it increased apoptosis. In both arms, EPA-FFA treatment led to increased membrane switch from ω-6 to ω-3 PUFAs and a concomitant reduction in PGE2 production. We observed no significant changes in intestinal inflammation between EPA-FFA treated arms and AOM-DSS controls. Importantly, we found that EPA-FFA treatment restored the loss of Notch signaling found in the AOM-DSS control, resulted in the enrichment of Lactobacillus species in the gut microbiota and led to tumor suppressor miR34-a induction. In conclusion, our data suggest that EPA-FFA is an effective chemopreventive agent in CAC.

Analysis of the pig genome for the identification of genomic regions affecting production traits

The aim of this work was to identify markers associated with production traits in the pig genome using different approaches. We focused the attention on Italian Large White pig breed using Genome Wide Association Studies (GWAS) and applying a selective genotyping approach to increase the power of the analyses. Furthermore, we searched the pig genome using Next Generation Sequencing (NSG) Ion Torrent Technology to combine selective genotyping approach and deep sequencing for SNP discovery. Other two studies were carried on with a different approach. Allele frequency changes for SNPs affecting candidate genes and at Genome Wide level were analysed to identify selection signatures driven by selection program during the last 20 years. This approach confirmed that a great number of markers may affect production traits and that they are captured by the classical selection programs. GWAS revealed 123 significant or suggestively significant SNP associated with Back Fat Thickenss and 229 associated with Average Daily Gain. 16 Copy Number Variant Regions resulted more frequent in lean or fat pigs and showed that different copies of those region could have a limited impact on fat. These often appear to be involved in food intake and behavior, beside affecting genes involved in metabolic pathways and their expression. By combining NGS sequencing with selective genotyping approach, new variants where discovered and at least 54 are worth to be analysed in association studies. The study of groups of pigs undergone to stringent selection showed that allele frequency of some loci can drastically change if they are close to traits that are interesting for selection schemes. These approaches could be, in future, integrated in genomic selection plans.

Biogas and bio-hydrogen: production and uses. A review

The first part of this essay aims at investigating the already available and promising technologies for the biogas and bio-hydrogen production from anaerobic digestion of different organic substrates. One strives to show all the peculiarities of this complicate process, such as continuity, number of stages, moisture, biomass preservation and rate of feeding. The main outcome of this part is the awareness of the huge amount of reactor configurations, each of which suitable for a few types of substrate and circumstance. Among the most remarkable results, one may consider first of all the wet continuous stirred tank reactors (CSTR), right to face the high waste production rate in urbanised and industrialised areas. Then, there is the up-flow anaerobic sludge blanket reactor (UASB), aimed at the biomass preservation in case of highly heterogeneous feedstock, which can also be treated in a wise co-digestion scheme. On the other hand, smaller and scattered rural realities can be served by either wet low-rate digesters for homogeneous agricultural by-products (e.g. fixed-dome) or the cheap dry batch reactors for lignocellulose waste and energy crops (e.g. hybrid batch-UASB). The biological and technical aspects raised during the first chapters are later supported with bibliographic research on the important and multifarious large-scale applications the products of the anaerobic digestion may have. After the upgrading techniques, particular care was devoted to their importance as biofuels, highlighting a further and more flexible solution consisting in the reforming to syngas. Then, one shows the electricity generation and the associated heat conversion, stressing on the high potential of fuel cells (FC) as electricity converters. Last but not least, both the use as vehicle fuel and the injection into the gas pipes are considered as promising applications. The consideration of the still important issues of the bio-hydrogen management (e.g. storage and delivery) may lead to the conclusion that it would be far more challenging to implement than bio-methane, which can potentially “inherit” the assets of the similar fossil natural gas. Thanks to the gathered knowledge, one devotes a chapter to the energetic and financial study of a hybrid power system supplied by biogas and made of different pieces of equipment (natural gas thermocatalitic unit, molten carbonate fuel cell and combined-cycle gas turbine structure). A parallel analysis on a bio-methane-fed CCGT system is carried out in order to compare the two solutions. Both studies show that the apparent inconvenience of the hybrid system actually emphasises the importance of extending the computations to a broader reality, i.e. the upstream processes for the biofuel production and the environmental/social drawbacks due to fossil-derived emissions. Thanks to this “boundary widening”, one can realise the hidden benefits of the hybrid over the CCGT system.

SphK1 regulates proinflammatory responses associated with endotoxin and polymicrobial sepsis

During sepsis, activation of phagocytes leads to the overproduction of proinflammatory cytokines, causing systemic inflammation. Despite substantial information regarding the underlying molecular mechanisms that lead to sepsis, several elements in the pathway remain to be elucidated. We found that the enzyme sphingosine kinase 1 (SphK1) is up-regulated in stimulated human phagocytes and in peritoneal phagocytes of patients with severe sepsis. Blockade of SphK1 inhibited phagocyte production of endotoxin-induced proinflammatory cytokines. We observed protection against sepsis in mice treated with a specific SphK1 inhibitor that was enhanced by treatment with a broad-spectrum antibiotic. These results demonstrated a critical role for SphK1 in endotoxin signaling and sepsis-induced inflammatory responses and suggest that inhibition of SphK1 is a potential therapy for septic shock.

Absence of MyD88 results in enhanced TLR3-dependent phosphorylation of IRF3 and increased IFN-(beta) and RANTES production

Toll-like receptors are a group of pattern-recognition receptors that play a crucial role in "danger" recognition and induction of the innate immune response against bacterial and viral infections. TLR3 has emerged as a key sensor of viral dsRNA, resulting in the induction of the anti-viral molecule, IFN- . Thus, a clearer understanding of the biological processes that modulate TLR3 signaling is essential. Previous studies have shown that the TLR adaptor, Mal/TIRAP, an activator of TLR4, inhibits TLR3-mediated IFN- induction through a mechanism involving IRF7. In this study, we sought to investigate whether the TLR adaptor, MyD88, an activator of all TLRs except TLR3, has the ability to modulate TLR3 signaling. Although MyD88 does not significantly affect TLR3 ligand-induced TNF- induction, MyD88 negatively regulates TLR3-, but not TLR4-, mediated IFN- and RANTES production; this process is mechanistically distinct from that employed by Mal/TIRAP. We show that MyD88 inhibits IKK -, but not TBK1-, induced activation of IRF3. In doing so, MyD88 curtails TLR3 ligand-induced IFN- induction. The present study shows that while MyD88 activates all TLRs except TLR3, MyD88 also functions as a negative regulator of TLR3. Thus, MyD88 is essential in restricting TLR3 signaling, thereby protecting the host from unwanted immunopathologies associated with the excessive production of IFN- . Our study offers a new role for MyD88 in restricting TLR3 signaling through a hitherto unknown mechanism whereby MyD88 specifically impairs IKK -mediated induction of IRF3 and concomitant IFN- and RANTES production.

Mannan-binding lectin deficiency results in unusual antibody production and excessive experimental colitis in response to mannose-expressing mild gut pathogens

In Crohn's disease (CD) the deficiency of mannan-binding lectin (MBL) is associated with an increased prevalence of anti-Saccharomyces cerevisiae antibodies (ASCA) and with complicated phenotypes of the disease. However, the role of MBL in intestinal inflammation is currently unclear. A study was undertaken to analyse local MBL expression in human intestine and the consequences of MBL deficiency in experimental colitis and yeast infection.

Numerical assessment on the effective mechanical stimuli for matrix-associated metabolism in chondrocyte-seeded constructs

The self-regeneration capacity of articular cartilage is limited, due to its avascular and aneural nature. Loaded explants and cell cultures demonstrated that chondrocyte metabolism can be regulated via physiologic loading. However, the explicit ranges of mechanical stimuli that correspond to favourable metabolic response associated with extracellular matrix (ECM) synthesis are elusive. Unsystematic protocols lacking this knowledge produce inconsistent results. This study aims to determine the intrinsic ranges of physical stimuli that increase ECM synthesis and simultaneously inhibit nitric oxide (NO) production in chondrocyte-agarose constructs, by numerically re-evaluating the experiments performed by Tsuang et al. (2008). Twelve loading patterns were simulated with poro-elastic finite element models in ABAQUS. Pressure on solid matrix, von Mises stress, maximum principle stress and pore pressure were selected as intrinsic mechanical stimuli. Their development rates and magnitudes at the steady state of cyclic loading were calculated with MATLAB at the construct level. Concurrent increase in glycosaminoglycan and collagen was observed at 2300 Pa pressure and 40 Pa/s pressure rate. Between 0-1500 Pa and 0-40 Pa/s, NO production was consistently positive with respect to controls, whereas ECM synthesis was negative in the same range. A linear correlation was found between pressure rate and NO production (R = 0.77). Stress states identified in this study are generic and could be used to develop predictive algorithms for matrix production in agarose-chondrocyte constructs of arbitrary shape, size and agarose concentration. They could also be helpful to increase the efficacy of loading protocols for avascular tissue engineering. Copyright (c) 2010 John Wiley \& Sons, Ltd.

Inflammation-associated autophagy-related programmed necrotic death of human neutrophils characterized by organelle fusion events

The most common form of neutrophil death, under both physiological and inflammatory conditions, is apoptosis. In this study, we report a novel form of programmed necrotic cell death, associated with cytoplasmic organelle fusion events, that occurs in neutrophils exposed to GM-CSF and other inflammatory cytokines upon ligation of CD44. Strikingly, this type of neutrophil death requires PI3K activation, a signaling event usually involved in cellular survival pathways. In the death pathway reported in this study, PI3K is required for the generation of reactive oxygen species, which somehow trigger the generation of large cytoplasmic vacuoles, generated by the fusion of CD44-containing endosomes with autophagosomes and secondary, but not primary, granules. Neutrophils demonstrating vacuolization undergo rapid cell death that depends on receptor-interacting protein 1 kinase activity and papain family protease(s), but not caspases, that are most likely activated and released, respectively, during or as a consequence of organelle fusion. Vacuolized neutrophils are present in infectious and autoimmune diseases under in vivo conditions. Moreover, isolated neutrophils from such patients are highly sensitive toward CD44-mediated PI3K activation, reactive oxygen species production, and cell death, suggesting that the newly described autophagy-related form of programmed neutrophil necrosis plays an important role in inflammatory responses.

Review of liver injury associated with dietary supplements

Dietary supplements (DS) are easily available and increasingly used, and adverse hepatic reactions have been reported following their intake. To critically review the literature on liver injury because of DSs, delineating patterns and mechanisms of injury and to increase the awareness towards this cause of acute and chronic liver damage. Studies and case reports on liver injury specifically because of DSs published between 1990 and 2010 were searched in the PubMed and EMBASE data bases using the terms 'dietary/nutritional supplements', 'adverse hepatic reactions', 'liver injury'; 'hepatitis', 'liver failure', 'vitamin A' and 'retinoids', and reviewed for yet unidentified publications. Significant liver injury was reported after intake of Herbalife and Hydroxycut products, tea extracts from Camellia sinensis, products containing usnic acid and high contents of vitamin A, anabolic steroids and others. No uniform pattern of hepatotoxicity has been identified and severity may range from asymptomatic elevations of serum liver enzymes to hepatic failure and death. Exact estimates on how frequent adverse hepatic reactions occur as a result of DSs cannot be provided. Liver injury from DSs mimicking other liver diseases is increasingly recognized. Measures to reduce risk include tighter regulation of their production and distribution and increased awareness of users and professionals of the potential risks.

SNPs in DNA repair genes associated to meningitis and host immune response

In vitro and in animal models, APE1, OGG1, and PARP-1 have been proposed as being involved with inflammatory response. In this work, we have investigated if the SNPs APE1 Asn148Glu, OGG1 Ser326Cys, and PARP-1 Val762Ala are associated to meningitis. The patient genotypes were investigated by PIRA-PCR or PCR-RFLP. DNA damages were detected in genomic DNA by Fpg treatment. IgG and IgA were measured from plasma and the cytokines and chemokines were measured from cerebrospinal fluid samples using Bio-Plex assays. A higher frequency (P<0.05) of APE1 Glu allele in bacterial meningitis (BM) and aseptic meningitis (AM) patients was observed. The genotypes Asn/Asn in control group and Asn/Glu in BM group was also higher. For the SNP OGG1 Ser326Cys, the genotype Cys/Cys was more frequent (P<0.05) in BM group. The frequency of PARP-1 Val/Val genotype was higher in control group (P<0.05). The occurrence of combined SNPs is significantly higher in BM patients, indicating that these SNPs may be associated to the disease. Increasing in sensitive sites to Fpg was observed in carriers of APE1 Glu allele or OGG1 Cys allele, suggesting that SNPs affect DNA repair activity. Alterations in IgG production were observed in the presence of SNPs APE1 Asn148Glu, OGG1 Ser326Cys or PARP-1 Val762Ala. Moreover, reduction in the levels of IL-6, IL-1Ra, MCP-1/CCL2 and IL-8/CXCL8 was observed in the presence of APE1 Glu allele in BM patients. In conclusion, we obtained indications of an effect of SNPs in DNA repair genes on the regulation of immune response in meningitis.

Production and characterization of a custom-made 228Th source with reduced neutron source strength for the Borexino experiment

A custom-made 228Th source of several MBq activity was produced for the Borexino experiment for studying the external background of the detector. The aim was to reduce the unwanted neutron emission produced via (alpha,n) reactions in ceramics used typically for commercial 228Th sources. For this purpose a ThCl4 solution was converted chemically into ThO2 and embedded into a gold foil. The paper describes the production and the characterization of the custom-made source by means of gamma-activity, dose rate and neutron source strength measurements. From gamma-spectroscopic measurements it was deduced that the activity transfer from the initial solution to the final source was >91% (at 68% C.L.) and the final activity was (5.41+-0.30) MBq. The dose rate was measured by two dosimeters yielding 12.1 mSv/h and 14.3 mSv/h in 1 cm distance. The neutron source strength of the 5.41 MBq 228Th source was determined as (6.59+-0.85)/sec.

Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 (PITX3) gene

Microphthalmia in sheep is an autosomal recessive inherited congenital anomaly found within the Texel breed. It is characterized by extremely small or absent eyes and affected lambs are absolutely blind. For the first time, we use a genome-wide ovine SNP array for positional cloning of a Mendelian trait in sheep. Genotyping 23 cases and 23 controls using Illumina's OvineSNP50 BeadChip allowed us to localize the causative mutation for microphthalmia to a 2.4 Mb interval on sheep chromosome 22 by association and homozygosity mapping. The PITX3 gene is located within this interval and encodes a homeodomain-containing transcription factor involved in vertebrate lens formation. An abnormal development of the lens vesicle was shown to be the primary event in ovine microphthalmia. Therefore, we considered PITX3 a positional and functional candidate gene. An ovine BAC clone was sequenced, and after full-length cDNA cloning the PITX3 gene was annotated. Here we show that the ovine microphthalmia phenotype is perfectly associated with a missense mutation (c.338G>C, p.R113P) in the evolutionary conserved homeodomain of PITX3. Selection against this candidate causative mutation can now be used to eliminate microphthalmia from Texel sheep in production systems. Furthermore, the identification of a naturally occurring PITX3 mutation offers the opportunity to use the Texel as a genetically characterized large animal model for human microphthalmia.

Aberrant low expression level of bovine beta-lactoglobulin is associated with a C to A transversion in the BLG promoter region

Beta-lactoglobulin (beta-LG) is the major whey protein in cow's milk. It is well established that the predominant 2 genetic variants, beta-LG A and B, are differentially expressed. Extensive investigation of the genetic variation in the promoter region of the BLG gene revealed the existence of specific haplotypes associated with the A and B variants, respectively. However, the genetic basis for the differential expression of BLG A and B alleles is still elusive. We have previously reported a quantitative beta-LG B variant, characterized by a very low beta-LG protein expression level. Here, we report that the corresponding BLG allele (BLG B*) shows a correspondingly low mRNA expression level. Comparative DNA sequencing of 7,670 bp of the BLG B* allele and the established BLG B allele revealed a unique difference of a C to A transversion at position 215 bp upstream of the translation initiation site (g.-215C>A). This mutation segregated perfectly with the differential phenotypic expression in a paternal half-sib family and could be confirmed in 2 independent cases. The sequence of the BLG B allele in the region of the mutation is highly conserved among 4 related ruminant species. The site of the mutation corresponds to a putative consensus-binding sequence for the transcription factors c-Rel and Elk-1 as predicted by searching the TRANSFAC database. The beta-LG B* site might be relevant in the natural production of milk of low beta-LG content.

Alcohol dehydrogenase 1C*1 allele is a genetic marker for alcohol-associated cancer in heavy drinkers

Chronic alcohol consumption is associated with an increased risk for upper aerodigestive tract cancer and hepatocellular carcinoma. Increased acetaldehyde production via alcohol dehydrogenase (ADH) has been implicated in the pathogenesis. The allele ADH1C*1 of ADH1C encodes for an enzyme with a high capacity to generate acetaldehyde. So far, the association between the ADH1C*1 allele and alcohol-related cancers among heavy drinkers is controversial. ADH1C genotypes were determined by polymerase chain reaction and restriction fragment length polymorphism in a total of 818 patients with alcohol-associated esophageal (n=123), head and neck (n=84) and hepatocellular cancer (n=86) as well as in patients with alcoholic pancreatitis (n=117), alcoholic liver cirrhosis (n=217), combined liver cirrhosis and pancreatitis (n=17) and in alcoholics without gastrointestinal organ damage (n=174). The ADH1C*1 allele and genotype ADH1C*1/1 were significantly more frequent in patients with alcohol-related cancers than that in individuals with nonmalignant alcohol-related organ damage. Using multivariate analysis, ADH1C*1 allele frequency and rate of homozygosity were significantly associated with an increased risk for alcohol-related cancers (p<0.001 in all instances). The odds ratio for genotype ADH1C*1/1 regarding the development of esophageal, hepatocellular and head and neck cancer were 2.93 (CI, 1.84-4.67), 3.56 (CI, 1.33-9.53) and 2.2 (CI, 1.11-4.36), respectively. The data identify genotype ADH1C*1/1 as an independent risk factor for the development of alcohol-associated tumors among heavy drinkers, indicating a genetic predisposition of individuals carrying this genotype.