Wine yeast selection in the Iberian Peninsula: Saccharomyces and non-Saccharomyces as drivers of innovation in Spanish and Portuguese wine industries

Yeast selection for the wine industry in Spain started in 1950 for the understanding of the microbial ecology, and for the selection of optimal strains to improve the performance of alcoholic fermentation and the overall wine quality. This process has been strongly developed over the last 30 years, firstly on Saccharomyces cerevisiae, and, lately, with intense activity on non-Saccharomyces. Several thousand yeast strains have been isolated, identified and tested to select those with better performance and/or specific technological properties. The present review proposes a global survey of this massive ex-situ preservation of eukaryotic microorganisms, a reservoir of biotechnological solutions for the wine sector, overviewing relevant screenings that led to the selection of strains from 12 genera and 22 species of oenological significance. In the first part, the attention goes to the selection programmes related to relevant wine-producing areas (i.e. Douro, Extremadura, Galicia, La Mancha and Uclés, Ribera del Duero, Rioja, Sherry area, and Valencia). In the second part, the focus shifted on specific non-Saccharomyces genera/species selected from different Spanish and Portuguese regions, exploited to enhance particular attributes of the wines. A fil rouge of the dissertation is the design of tailored biotechnological solutions for wines typical of given geographic areas.

In vivo overexpression of frataxin causes toxicity mediated by iron-sulfur cluster deficiency

Friedreich's ataxia is a rare disorder resulting from deficiency of frataxin, a mitochondrial protein implicated in the synthesis of iron-sulfur clusters. Preclinical studies in mice have shown that gene therapy is a promising approach to treat individuals with Friedreich's ataxia. However, a recent report provided evidence that AAVrh10-mediated overexpression of frataxin could lead to cardiotoxicity associated with mitochondrial dysfunction. While evaluating an AAV9-based frataxin gene therapy using a chicken β-actin promoter, we showed that toxic overexpression of frataxin could be reached in mouse liver and heart with doses between 1 × 10¹³ and 1 × 10¹⁴ vg/kg. In a mouse model of cardiac disease, these doses only corrected cardiac dysfunction partially and transiently and led to adverse findings associated with iron-sulfur cluster deficiency in liver. We demonstrated that toxicity required frataxin's primary function by using a frataxin construct bearing the N146K mutation, which impairs binding to the iron-sulfur cluster core complex. At the lowest tested dose, we observed moderate liver toxicity that was accompanied by progressive loss of transgene expression and liver regeneration. Together, our data provide insights into the toxicity of frataxin overexpression that should be considered in the development of a gene therapy approach for Friedreich's ataxia.

Biodistribution and Tolerability of AAV-PHP.B-CBh-SMN1 in Wistar Han Rats and Cynomolgus Macaques Reveal Different Toxicologic Profiles

Recombinant adeno-associated viruses (AAVs) have emerged as promising vectors for human gene therapy, but some variants have induced severe toxicity in Rhesus monkeys and piglets following high-dose intravenous (IV) administration. To characterize biodistribution, transduction, and toxicity among common preclinical species, an AAV9 neurotropic variant expressing the survival motor neuron 1 (SMN1) transgene (AAV-PHP.B-CBh-SMN1) was administered by IV bolus injection to Wistar Han rats and cynomolgus monkeys at doses of 2 × 10¹³, 5 × 10¹³, or 1 × 10¹⁴ vg/kg. A dose-dependent degeneration/necrosis of neurons without clinical manifestations occurred in dorsal root ganglia (DRGs) and sympathetic thoracic ganglia in rats, while liver injury was not observed in rats. In monkeys, one male at 5 × 10¹³ vg/kg was found dead on day 4. Clinical pathology data on days 3 and/or 4 at all doses suggested liver dysfunction and coagulation disorders, which led to study termination. Histologic evaluation of the liver in monkeys showed hepatocyte degeneration and necrosis without inflammatory cell infiltrates or intravascular thrombi, suggesting that hepatocyte injury is a direct effect of the vector following hepatocyte transduction. In situ hybridization demonstrated a dose-dependent expression of SMN1 transgene mRNA in the cytoplasm and DNA in the nucleus of periportal to panlobular hepatocytes, while quantitative polymerase chain reaction confirmed the dose-dependent presence of SMN1 transgene mRNA and DNA in monkeys. Monkeys produced a much greater amount of transgene mRNA compared with rats. In DRGs, neuronal degeneration/necrosis and accompanying findings were observed in monkeys as early as 4 days after test article administration. The present results show sensory neuron toxicity following IV delivery of AAV vectors at high doses with an early onset in Macaca fascicularis and after 1 month in rats, and suggest adding the autonomic system in the watch list for preclinical and clinical studies. Our data also suggest that the rat may be useful for evaluating the potential DRG toxicity of AAV vectors, while acute hepatic toxicity associated with coagulation disorders appears to be highly species-dependent.

Inflammatory Cell Findings in the Female Rabbit Heart and Stress-associated Exacerbation with Handling and Procedures Used in Nonclinical Studies

Despite the use of rabbits in biomedical research, including regulatory toxicology and cardiovascular studies, little data exist on heart findings in this species. This study was designed to document myocardial findings in female rabbits and the impact of study-related procedures typical for vaccine toxicology studies. One hundred and forty 6- to 8-month-old female New Zealand White rabbits were divided equally into 2 groups, high and low study procedure groups (group 1 and group 2, respectively). All animals received intramuscular (IM) injections of sterile saline every 2 weeks for 5 times and were necropsied 2 days after the final IM injection. Clinical chemistry, hematology, and urinalysis were evaluated. Blood for stress biomarkers (norepinephrine, epinephrine, cortisol, and corticosterone), C-reactive protein, cardiac troponin I, and creatine kinase were collected at time 0 (just before dose administration) and then at 4, 24, and 48 hr after dose administration in group 1 only. Hearts were assessed histologically. Focal to multifocal minimal inflammatory cell infiltrates were common (∼80%), particularly in the left ventricle and interventricular septum, and were similar to the types of infiltrates identified in other laboratory animal species. Additionally, study-related procedures elevated serum stress biomarkers and exacerbated the frequency and severity of myocardial inflammatory cell infiltrates.

Assessing the potential of the European Atlantic sturgeon Acipenser sturio to control bivalve invasions in Europe

This pilot study explored the potential of juvenile European Atlantic sturgeon Acipenser sturio to feed on two invasive bivalve species, the Asian clam Corbicula fluminea and the Eurasian zebra mussel Dreissena polymorpha. Preliminary results indicate that native A. sturio were feeding on D. polymorpha at a very limited rate and their potential to prevent the establishment of invasive bivalve species, in new and previously invaded areas, is considered limited.

Re-designing the substrate binding pocket of laccase for enhanced oxidation of sinapic acid

Iterative saturation mutagenesis was performed over six residues delimiting the substrate binding pocket of a high redox potential chimeric laccase with the aim of enhancing its activity over sinapic acid, a lignin-related phenol of industrial interest.

Abstract P2-08-02: Chronic inflammation and the development of breast cancer

Background: Recently, The Breast Cancer Working Group of the International Cancer Genome Consortium examined the patterns of somatic mutations in the cancer genomes of 21 breast cancers. They generated 5 mutations signatures. While the mechanisms responsible for most of the signatures are unknown, the pattern of one of the signatures is similar to that observed when the APOBEC family of cytidine deaminases is active.

Histologically normal tissue adjacent to a cancer provides a window into the early steps of oncogenesis. Comparison of this tissue to the cancer and to healthy, normal tissue frequently exposes a field effect/defect that changes progressively from healthy normal to adjacent normal to malignant. Comparing DNA expression in histologically normal tissue adjacent to cancer to that in normal, healthy breast tissue, we noted that the adjacent tissue is awash in inflammatory mediators. Inflammation causes genetic damage by the up-regulation of activation-induced cytidine deaminases and the production of reactive oxygen species. We hypothesize that the activation of the APOBEC family cytidine deaminases observed in a subset of the 21 breast cancers is a consequence of chronic inflammation.

Methods: RNA-Seq data from adjacent normals was downloaded from the TCGA (The Cancer Genome Atlas) data portal. The epithelia from 20 frozen tissue cores from healthy premenopausal donors to the Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center were microdissected and the RNA isolated. RNA-sequencing was carried out using the Life Technologies SOLiD Platform. RPKM gene expression values from TCGA and sequencing of the Komen normal tissues were merged, quantile normalized, and batch effect corrected. Normalization and differential gene expression was performed using Partek Genomics Suite.

Results: The expression of APOBEC3C in adjacent normal is 3.4-times that in healthy normal (p = 4.94E-03). Additionally, reactive oxygen species in the form of nitric oxide are frequently generated by inflammatory cytokine production of Nitric Oxide Synthase. Nitric oxides can act by directly oxidizing DNA or by damaging DNA repair functions. Our preliminary data reveals that the expression of Nitric Oxide Synthase 3 in adjacent normal is 4-times that in healthy normal (p = 4.55E-03).

Conclusions: In a review of inflammation-associated cancers published in Scientific American, Gary Stix remarks that “Genetic damage is the match that lights the fire of malignancy, and inflammation is the fuel that feeds the flames”. It is possible that inflammation is both the match and the fuel. The up-regulation of APOBEC in adjacent normal is likely the result of the induction of the NF-kB pathway in response to the diffusion of inflammatory mediators from the adjacent malignancy. Activated cytidine deaminases under normal, physiologic conditions contribute to the generation of antibody gene diversity in activated B lymphocytes by inducing somatic hypermutations and class switch recombination of immunoglobulin genes. However, when inappropriately expressed they produce mutagenesis. The differences in gene expression identified are some of the earliest changes in breast carcinogenesis and provide insight into the etiology of this disease and, potentially, its prevention.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-08-02.

Abstract P1-03-02: “Normal” tissue adjacent to breast cancer is not normal

Background: Gene expression data from pancreatic cancer, histologically normal tissue adjacent to the cancer and normal pancreas reveals that adjacent normal has already acquired a number of transcriptional alterations and is not, therefore, an appropriate baseline for comparison with cancers. (Gadaleta et al., 2011) The purpose of this study was to determine if this is also the case for breast cancer and, if so, to identify the differences in gene expression between adjacent normal and normal breast.

Methods: RNA-Seq data from breast cancer and adjacent normal was downloaded from the TCGA (The Cancer Genome Atlas) data portal. The epithelia from 20 frozen tissue cores from healthy premenopausal donors to the Susan G. Komen for the the Cure® Tissue Bank at the IU Simon Cancer Center were microdissected and the RNA isolated. RNA-seqeuncing was carried out using the Life Technologies SOLiD Platform. RPKM gene expression values from TCGA and sequencing of the Komen normal tissues were merged, quantile normalized, and batch effect corrected. Normalization and differential gene expression was performed using Partek Genomics Suite.

Results: Principal component analysis (PCA) reveals complete separation between adjacent normal and healthy normal breast tissue. Setting a maximum FDR (false discover rate) of 5%, 2239 genes are differentially expressed between adjacent normal and healthy normal. Ingenuity pathway analysis reveals that the Fos, Jun and TGFbeta pathways are active in the adjacent normal.

Conclusions: Tissue adjacent to a primary breast cancer is not normal when using healthy breast tissue as a comparator. As RNA-Seq data is digital, it is possible to quantify the changes in gene expression starting from healthy normal to normal adjacent to tumor to tumor. Increasing and decreasing gene expression values provide clues to the fundamental molecular changes occurring in histologically normal appearing adjacent tissue. The differences in gene expression we have identified are some of the earliest changes in breast carcinogenesis and provide insight into the etiology of this disease and, potentially, its prevention.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P1-03-02.

Amino acids and volatile compounds in wines from Cabernet Sauvignon and Tempranillo varieties subjected to malolactic fermentation in barrels

The aim of the present paper is to compare the behaviour of industrial lactic bacteria and indigenous bacteria of the cellar when malolactic fermentation was carried out in barrels. The effects of these bacteria on the concentration of metabolised amino acids during malolactic fermentation and on the composition of volatile compounds both before and after malolactic fermentation are studied. The experiment was performed with wines of the Tempranillo and Cabernet Sauvignon varieties. An analysis has been made of the easily extractable volatile compounds of the wood and the compounds from the grapes, and the action of the yeasts during the alcoholic fermentation. Acetoin and diacetyl decreased during the malolactic fermentation in barrels and the concentrations of furfural and its derivatives were up to 100 times higher in wines not subjected to malolactic fermentation. Most of the volatile phenols increased during the malolactic fermentation in wines of the Tempranillo variety, while only guaiacol ( p < 0.05) and t-isoeugenol increased in the Cabernet Sauvignon wines. The decrease in amino acids during the malolactic fermentation depends much more on the variety than on the bacterial strain which carries out the malolactic fermentation.

Abstract P6-04-01: Next-Generation Transcriptome Sequencing of the Normal Breast

Background: Our efforts to prevent and treat breast cancer are significantly impeded by a lack of knowledge of the biology and developmental genetics of the normal mammary gland. The Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center (KTB) was established expressly to address and remedy this deficiency. The KTB acquires and banks normal breast tissue, that is, breast tissue from volunteer donors with no clinical evidence of breast malignancy. This tissue is NOT from reduction mammoplasties or from histologically normal tissue adjacent to a malignancy.

The breast is one of the most complex genetic organs within the body. This is because the expression of its genes is under the control and influence of the hormonal milieu present in the circulating plasma, which changes as a function of age; for premenopausal women as a function of the menstrual cycle; and as a consequence of pregnancy. Therefore, there is unlikely to be a singular “normal” breast. We propose to produce a molecular encyclopedia of the normal breast which covers the entire spectrum of normal: puberty to menopause, low risk to high risk, nulliparous and parous.

Materials and Methods: The epithelial compartment of fresh frozen tissue from 10 premenopausal donors to the KTB, 5 women who were in the follicular phase of the menstrual cycle and 5 who were in the luteal, was isolated using laser capture microdissection. Total RNA extracted from the cells was subsequently depleted for ribosomal RNA. RNA was sequenced on an Applied Biosystems SOLiD3 sequencer using 50bp runs. Reads were mapped to the human genome. Whole blood was collected at the time of tissue donation and uniformly processed into serum. Results: RNA sequencing of the 10 samples produced 596 million reads of which 386 million (62%) mapped to the human genome. Setting the p-value at &lt;0.05 for the comparison of follicular versus luteal, there were 3395 differentially expressed RefSeq genes, 35 differentially expressed premiRNAs, 297 differentially expressed lincRNA exons and 40 differentially expressed UCRs (Ultra Conserved Regions). There were 1394 novel transcribed regions which were significantly differentially expressed. The serum estradiol at the time of donation was determined for 9 of the 10 donors. The gene expression of 901 genes was strongly correlated with serum estradiol concentration.

Proliferating Cell Nuclear Antigen (PCNA), nucleosome assembly genes and genes involved with mitosis have greater expression during the luteal phase of the menstrual cycle. Genes associated with development, e.g., NOTCH2, PAX3, DKK3 and TWIST1, are more abundantly expressed during the follicular phase. Many of the differentially expressed genes have been implicated in breast oncogenesis.

Conclusions: The Komen Tissue Bank has completed the first ever next-generation transcriptome sequencing of epithelial compartment of ten normal human breast specimens. This work has produced the most comprehensive catalog to date of the differences in the expression of protein encoding genes, pre-miRNAs, lincRNA exons, UCRs and novel transcribed regions as a function of the phase of the menstrual cycle. Additionally, this effort has identified a relatively significant number of genes whose expression is very likely under the control of estrogen.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P6-04-01.

Abstract PD01-08: Decoding the Transcriptional Landscape of Triple-Negative Breast Cancer Using Next-Generation Whole Transcriptome Sequencing

Background: Triple-negative breast cancer (TNBC) has been plagued by the absence of targeted therapies. Discovery of therapeutic targets in TNBC has in part, been hampered by an inadequate understanding of the transcriptional biology of the normal breast as an optimal comparator. Using next-generation sequencing, we embarked on a study to compare the transcriptomes of TNBC and normal breast to comprehensively identify novel targets by analyzing all full length transcripts expressed in these tissues.

Methods: Normal breast tissues from healthy pre-menopausal volunteers with no history of disease were procured from the Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center. To eliminate bias from stromal tissue, normal tissues were laser capture microdissected for ductal epithelium. cDNA libraries from 10 TNBC tumors and 10 normal breast tissues were sequenced on an Applied Biosystems (AB) SOLiD3 sequencer using 50bp fragment runs. For gene expression, mapping of reads to the genome was performed using the AB BioScope 1.2 Pipeline and outputs imported into Partek Genomics Suite for analysis. In Partek, mapped reads were cross-referenced against known genes from the UCSC database followed by statistical comparison of RPKM values for each gene between TNBC and normal. Dimensionality reduction analyses (PCA & Hierarchical clustering) and identification of Novel Transcribed Regions were also performed in Partek, whereas construction of gene networks was performed using Ingenuity Pathway Analysis. To identify gene fusions, partially mapped reads were interrogated utilizing a novel algorithm that searched for reads spanning exons from two different genes. Fusions that were supported by at least 3 reads (of which 2 had to be unique) were considered candidates and were subsequently validated. Results/Discussion: Sequencing produced 1.1 billion reads equaling 57.3GB of data of which 36.0GB (63%) mapped to the human genome. In comparing RPKM values between TNBC and Normal, we report 7140 RefSeq Genes, 22 pre-miRNAs, 109 lincRNA exons, and 15 ultraconserved regions that were differentially expressed between these tissues (FDR&lt;0.01). Biological interpretation of these results reveals upregulation of genes and miRNAs involved in DNA repair, angiogenesis, and inhibitors of Estrogen Receptor-alpha. Some previous drug targets (e.g. EGFR and c-kit) were not found to be upregulated here which may explain lack of clinical success to date. Conversely, PARP was significantly upregulated and early trial results suggest a strong signal for efficacy with inhibition of PARP. We also surveyed the genome for Novel Transcribed Regions (NTRs), defined as areas of significant transcription where no annotated gene is present. When comparing between TNBC and Normal, we report 6408 NTRs to be differentially expressed (FDR&lt;0.01). Lastly, when analyzing the dataset for gene fusions, we identified several gene fusions in the TNBC samples, though no individual fusion was present in more than one sample.

Conclusion: We report an extensive comparison of the transcriptomes of TNBC and normal ductal epithelium. We identified numerous genes previously unknown to be dysregulated in TNBC that can be utilized for therapeutic discovery.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr PD01-08.

Next-Generation Whole Transcriptome Sequencing of Triple-Negative Breast Tumors and Normal Tissues

Background: Triple-negative breast cancer predominately affects pre-menopausal women and women of African-American descent and has been plagued by the absence of targeted therapies leading to poor survival. Using a new cutting edge technology, next-generation sequencing, we embarked on a study to analyze the whole transcriptomes of triple-negative tumors and normal tissues from pre-menopausal women in order to comprehensively identify new targets by analyzing all full length transcripts expressed in these tissues. This approach is independent of pre-determined gene selection as is common with microarrays, and allows for the analysis of RNA species that have not been previously profiled in breast cancer.Methods: cDNA libraries were created from RNA isolated from 8 triple-negative tumors and 2 normal breast tissues. Triple negative tumors were procured from Origene Technologies and normal breast tissues were procured from the Susan G. Komen for the Cure tissue bank at Indiana University. Normal samples were from healthy pre-menopausal volunteers with no history of disease. In order to eliminate bias from stromal tissue, normal samples were laser capture microdissected for ductal cells and RNA extracted from the excised tissue. cDNA libraries were prepared and subsequently sequenced on an Applied Biosystems (ABI) SOLiD3 sequencer using a 50bp fragment run. Mapping of whole reads to the human genome was performed using the SOLiD Analysis Pipeline Tool software (ABI) followed by a split-read alignment in order to map reads crossing exon-exon junctions. Gene expression profiles for each sample were then created and statistically compared to identify the most differentially expressed genes. In order to analyze for fusion genes, a split-read alignment of non-mapping reads to a composite transcriptome formed from previously mapped reads (clusters) was performed.Results: Sequencing of the 10 samples produced 513 million filtered reads equaling 25.66GB of data. Mapping of the reads to the genome revealed 1.14 million transcribed regions (exons). A preliminary analysis of gene expression shows 55.2% of the transcribed loci to have significant differential expression between tumor and normal. In a further analysis for gene fusions, several candidate fusions were bioinformatically detected. These are currently being reviewed and validated.Discussion: Herein we present a preliminary analysis of the transcriptomes of triple-negative breast cancers in comparison to normal tissues. A multitude of analyses are ongoing, including but not limited to: gene fusions, differentially expressed novel genes, novel transcripts, alternative splicing, intrinsic subtyping, and presence of viral genes. In addition 2 more triple-negative tumors and 8 normal samples will also be sequenced. In the current analysis, differentially expressed non-coding RNAs was highly pervasive among the samples indicating a major role of this RNA species in tumorigenesis. In addition, triple-negative breast cancers may contain fusion genes that could be “drivers” of this malignancy. Further validation of these differentially expressed RNAs and fusion genes in a larger set of samples with subsequent functional studies is planned.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6134.

Characterization of an Atlantic salmon Salmo salar stream at the southern limit of its eastern Atlantic distribution

Ten reaches of an Atlantic stream located in north-west Spain were sampled intensively during one summer to characterize the conditions where Atlantic salmon Salmo salar have been re-introduced along the stream. Fish species richness and diversity showed a downstream increase, which was mainly attributed to the higher number of cyprinid species found in the lower reaches. Moreover, except for brown trout Salmo trutta that appeared to be the most ubiquitous species, the densities of the other species was higher in the lower than in the upper stream reaches. Redundancy analysis showed that the pattern of fish assemblages observed along the studied stream was mainly related to the expected gradient observed in the levels of dissolved oxygen, discharge and mean current speed. There was a significant differentiation between midstream and downstream reaches, both in terms of the composition of their fish assemblages and the freshwater habitat. This study emphasizes the importance of describing the variations in fish assemblages and habitat characteristics along a river to explore its relation to potential changes in the survival of fish populations. In particular, the development of habitat-fish relationships may be a useful tool for water managers to assess the effects of development and restoration projects on the habitat of S. salar.

Regulation of hdc expression and HDC activity by enological factors in lactic acid bacteria

AIMS

The aim of this work was to study the influence of enological factors on the histidine decarboxylase gene (hdc) expression and on histidine decarboxylase enzyme (HDC) activity in Lactobacillus hilgardii, Pediococcus parvulus and Oenococcus oeni.

METHODS AND RESULTS

Cell extracts and whole cells were used. Glucose, fructose, malic acid and citric acid diminished the hdc expression. Ethanol did not increase hdc expression or activity in cells, but increased HDC activity. Temperature and pH had effect on the activity of HDC but not on hdc expression. Tartaric acid and l-lactic acid, and sulphur dioxide (SO(2)) had no effect on enzyme synthesis and activity. Bacterial species differ in the relative enzymatic activity but all the factors affected similarly to L. hilgardii, P. parvulus and O. oeni.

CONCLUSIONS

The hdc gene expression was lowered by glucose, fructose, malic acid, and citric acid, whereas ethanol enhanced the HDC enzyme activity. The conditions that normally occur during malolactic fermentation and later on, could favour histamine production. SO(2) could prevent bacterial growth, but does not diminish the HDC enzyme activity.

SIGNIFICANCE AND IMPACT OF THE STUDY

Information on hdc expression and HDC activity can contribute to the prevention of histamine formation during wine production and storage.

Interlaboratory evaluation of genomic signatures for predicting carcinogenicity in the rat

The Critical Path Institute recently established the Predictive Safety Testing Consortium, a collaboration between several companies and the U.S. Food and Drug Administration, aimed at evaluating and qualifying biomarkers for a variety of toxicological endpoints. The Carcinogenicity Working Group of the Predictive Safety Testing Consortium has concentrated on sharing data to test the predictivity of two published hepatic gene expression signatures, including the signature by Fielden et al. (2007, Toxicol. Sci. 99, 90-100) for predicting nongenotoxic hepatocarcinogens, and the signature by Nie et al. (2006, Mol. Carcinog. 45, 914-933) for predicting nongenotoxic carcinogens. Although not a rigorous prospective validation exercise, the consortium approach created an opportunity to perform a meta-analysis to evaluate microarray data from short-term rat studies on over 150 compounds. Despite significant differences in study designs and microarray platforms between laboratories, the signatures proved to be relatively robust and more accurate than expected by chance. The accuracy of the Fielden et al. signature was between 63 and 69%, whereas the accuracy of the Nie et al. signature was between 55 and 64%. As expected, the predictivity was reduced relative to internal validation estimates reported under identical test conditions. Although the signatures were not deemed suitable for use in regulatory decision making, they were deemed worthwhile in the early assessment of drugs to aid decision making in drug development. These results have prompted additional efforts to rederive and evaluate a QPCR-based signature using these samples. When combined with a standardized test procedure and prospective interlaboratory validation, the accuracy and potential utility in preclinical applications can be ascertained.

Characterization of a Lactobacillus plantarum Strain Able to Produce Tyramine and Partial Cloning of a Putative Tyrosine Decarboxylase Gene

The aim of this article was to analyze the ability of wine Lactobacillus plantarum strains to form tyramine. Preliminary identification of L. plantarum strains was performed by amplification of the recA gene. Primers pREV and PlanF, ParaF and PentF were used respectively as reverse and forward primers in the polymerase chain reaction tests as previously reported. Furthermore, the gene encoding for the tyrosine decarboxylase (TDC) was partially cloned from one strain identified as L. plantarum. The strain was further analyzed by 16S rDNA sequence and confirmed as belonging to L. plantarum species. The tyrosine decarboxylase activity was investigated and tyramine was determined by the high-performance liquid chromatography method. Moreover, a negative effect of sugars such as glucose and fructose and L: -malic acid on tyrosine decarboxylase activity was observed. The results suggest that, occasionally, L. plantarum is able to produce tyramine in wine and this ability is apparently confined only to L. plantarum strains harboring the tdc gene.

Which lactic acid bacteria are responsible for histamine production in wine?

AIMS

To quantify the ability of 136 lactic acid bacteria (LAB), isolated from wine, to produce histamine and to identify the bacteria responsible for histamine production in wine.

METHODS AND RESULTS

A qualitative method based on pH changes in a plate assay was used to detect wine strains capable of producing high levels of histamine. Two quantitative, highly sensitive methods were used, an enzymatic method and HPLC, to quantify the histamine produced by LAB. Finally, an improved PCR test was carried out to detect the presence of histidine decarboxylase gene in these bacteria. The species exhibiting the highest frequency of histamine production is Oenococcus oeni. However, the concentration of histamine produced by this species is lower than that produced by strains belonging to species of Lactobacillus and Pediococcus. A correlation of 100% between presence of histidine decarboxylase gene and histamine production was observed. Wines containing histamine were analysed to isolate and characterize the LAB responsible for spoilage.

CONCLUSIONS

Oenococcus was able to synthesize low concentrations of histamine in wines, while Pediococcus parvulus and Lactobacillus hilgardii have been detected as spoilage, high histamine-producing bacteria in wines.

SIGNIFICANCE AND IMPACT OF THE STUDY

Information regarding histamine-producing LAB isolated from wines can contribute to prevent histamine formation during winemaking and storage.

Polyphasic study of wine Lactobacillus strains: taxonomic implications

One hundred and seventy-eight lactobacilli isolated from wine were characterized by a polyphasic approach. Strains were phenotypically identified at genus and species level by classical tests including the analysis of cell morphology, homo/heterofermentative character, sugar fermentation patterns, growth at different temperatures and the optical nature of the isomer of lactic acid produced from glucose. Molecular techniques such as random amplification of polymorphic DNA (RAPD), amplified 16S rDNA restriction analysis (16S-ARDRA), PFGE-RFLP and ribotyping were used to characterize strains, and their potential for identification and/or typing was evaluated. The information obtained with these techniques was processed with the BioNumerics software in order to analyse relationships existing between isolated strains and various reference species of the genus. Then, taxonomic dendrograms were obtained, and this information allowed the proposal of molecular procedures suitable for the identification and typing of these wine micro-organisms. The techniques useful for both identification and typing were RAPD and ribotyping, while 16S-ARDRA was only useful for identification and PFGE-RFLP only for typing purposes. The wine strains were identified as Lactobacillus brevis (19 strains), Lactobacillus collinoides (2 strains), Lactobacillus hilgardii (71 strains), Lactobacillus paracasei (13 strains), Lactobacillus pentosus (2 strains), Lactobacillus plantarum (34 strains) and Lactobacillus mali (10 strains).

Pulmonary neoplasia in two llamas (Lama glama)

Two llamas with pulmonary tumors were examined. Llama No. 1 had multiple nodules throughout the lung that consisted histologically of solid clusters of polygonal to spindle cells with rare glandular differentiation. Intravascular emboli were common. Similar neoplastic masses were present in the kidney, heart, and liver. Immunohistochemically, neoplastic cells were positive for broad-spectrum cytokeratins (CKs), high-molecular weight CKs, CKs 5/6, and vimentin. The diagnosis was pulmonary carcinoma. Llama No. 2 had pulmonary nodules without extrapulmonary involvement. Microscopically, neoplastic cells formed acini lined by simple epithelium and solid cords of squamous cells that sometimes surrounded acini. Neoplastic cells were strongly positive for broad-spectrum CKs and weakly positive for thyroid transcription factor-1. The diagnosis was adenosquamous carcinoma. Pulmonary tumors account for 23% of neoplasms in South American camelids in our laboratory, making this the second most common type of neoplasm after lymphosarcoma.

Improved enzymatic method for the rapid determination of histamine in wine

Fermented foods are frequently contaminated by histamine generated by microorganisms possessing histidine decarboxylase activity. The ingestion of large amounts of histamine can cause serious toxicological problems in man. Thus, it becomes important to set a reliable method for rapid histamine quantification in foods. The detection of bacteria exhibiting histidine decarboxylase activity is also important to estimate the risk of contamination of food. Previous enzymatic methods used to quantify histamine in fish gave erroneously high values due to interference when applied to wine. A new enzymatic method is described that allows the direct determination of histamine concentrations in this type of sample. It can be used for the detection of histamine in synthetic media, grape must or wine (white, rose, red) without polyphenols or sugar interferences. This new enzymatic method shows a good correlation (R2 = 0.996, p < 0.001) between the histamine concentrations and absorbances in the interval 0.4-160 mg l(-1). Comparison between this enzymatic method and a high-performance liquid chromatography method showed a high correlation (R2 =0.9987, p<0.001). A miniaturized enzymatic method is also proposed, which is particularly useful when high numbers of samples must be analysed.

The potential of positively-charged cellulose sponge for malolactic fermentation of wine, using Oenococcus oeni

Malolactic fermentation (MLF) is a secondary bioconversion developed in some wines involving malic acid decarboxylation. The induction of MLF in wine by cultures of free and immobilized Oenococcus oeni cells was investigated. This work reports on the effect of surface charges in the immobilization material, a recently described fibrous sponge, as well as the pH and the composition of the media where cells are suspended. A chemical treatment provided positive charge to the sponges (DE or DEAE) and gave the highest cell loadings and subsequent resistance to removal. Preculture media to grow the malolactic bacteria before the immobilization procedure were also evaluated. We have established favorable conditions for growth (Medium of Preculture), suspension solution (Tartrate-Phosphate Buffer), suspension pH (3.5-5.5) and immobilization matrix (DE or DEAE cellulose sponge) to induce MLF in red wine. The use of a semi-continuous system permitted a high-efficiency malic acid conversion by 2 x 10(9) cfu sponge(-)(1) in at least four subsequent batch fermentations.

Nucleotide sequence of plasmid p4028, a cryptic plasmid from Leuconostoc oenos

The Leuconostoc oenos plasmid p4028 was cloned in pBlueScript (SK+), and its complete nucleotide sequence was determined. The analysis of the nucleotide sequence revealed five open reading frames, all of them located on the same strand and grouped in two clusters separated by a short noncoding stretch. A similarity search against the other sequences deposited in the EMBL and GenBank databases showed that p4028 has no significant similarity with any of the sequences checked. Nevertheless, a putative ATP-binding motif was found in ORF2. A more detailed analysis of this ORF suggests that it could encode for a DNA-dependent ATPase.

Transposons Tn916 and Tn925 can transfer from Enterococcus faecalis to Leuconostoc oenos

The streptococcal transposons Tn916 and Tn925 were transferred to several strains of Leuconostoc (Ln.) oenos using the filter mating method. The insertion of both transposons into the chromosome occurred at different sites. Transconjugants of Ln. oenos carrying Tn916 could serve as donors in mating experiments with Lactococcus lactis LM2301. Further analysis of L. lactis LM2301 transconjugants showed that the insertion of the transposon Tn916 into the chromosome was site-specific. These studies establish a basis for the initiation of genetic studies in this Leuconostoc species since there are no efficient conjugal or transformation systems previously described for this microorganism.

An improved medium for distinguishing between homofermentative and heterofermentative lactic acid bacteria

An improved solid medium for differentiating between homofermentative and heterofermentative lactic acid bacteria is proposed. It was developed to support the growth of wine strains unable to grow in other media. However, it can be employed as a general medium for the lactic acid bacteria that utilize fructose.

Potential histamine H2-receptor antagonists. Synthesis, conformational studies and activity of novel 3-oxo-1,2,5-thiadiazole 1,1-dioxide derivatives

New histamine H2-receptor antagonists bearing a novel "urea equivalent", the 3-oxo-1,2,5-thiadiazole 1,1-dioxide ring, have been synthesized in a transamination reaction. Open chain derivatives have also been obtained. Theoretical conformational analysis of the compounds has been carried out using a molecular modelling program. Semiempirical CNDO/2 calculations have also been performed. The antisecretory and cytoprotective activities of the compounds have been evaluated.

Dynamics of Microbial Populations during Fermentation of Wines from the Utiel-Requena Region of Spain

The dynamics of fungi, yeasts, and lactic acid bacteria during fermentation of four musts were studied. Fungi disappeared quickly in the fermenting must. The lactic acid bacteria population diminished during alcoholic fermentation, then they increased and performed malolactic fermentation. Yeasts grew quickly, reaching maximum populations at different times depending on the vinification treatment.

Analysis of in vitro polyclonal B cell differentiation responses to bacterial peptidoglycan and pokeweed mitogen in rheumatoid arthritis

To gain insight into possible determinants of in vivo polyclonal B cell activation seen in rheumatoid arthritis (RA), we enumerated immunoglobulin secreting cells appearing in cultures of peripheral blood mononuclear cells that were stimulated with pokeweed mitogen (PWM) or a newly described polyclonal B cell activator, bacterial peptidoglycan. Peptidoglycan, the major constituent of the cell wall of gram positive bacteria, has properties which warrant its consideration in the pathogenesis of RA; including the ability to induce rheumatoid factor production as well as a RA like syndrome in experimental animals. RA patients as a group had similar immunoglobulin secreting cell responses in PWM stimulated cultures compared to arthritis controls and showed moderately depressed responses compared to healthy volunteers. However, their in vitro responses to peptidoglycan were markedly depressed when compared to those of both control groups. Of note, severely reduced peptidoglycan-induced responses were seen in 26 of 55 rheumatoid patients who demonstrated intact PWM-induced responses. These impaired responses to peptidoglycan were not due to (1) aberrant kinetic response; (2) shift in the dose-response pattern; (3) decreased cell survival in culture or (4) the inability of peptidoglycan to activate RA cells. Cell fractionation studies indicated that peptidoglycan reactive B cells were present in the blood of some patients but their reactivity was abrogated by suppressor T cells. These studies provide evidence of aberrant in vitro polyclonal B cell activation in patients with RA and provide a basis for further investigation of peptidoglycan as an immunopathogenetic agent in this disease.

Circulating immunoglobulin-secreting cells in rheumatoid arthritis

The level of circulating cells secreting IgG, IgM, and IgA (IgSC) provides insight into the degree of in vivo polyclonal B-cell activation (PBA). Patients with rheumatoid arthritis (RA) exhibit abnormalities in humoral immune responses suggestive of augmented in vivo polyclonal B-cell activation. Therefore, a protein A reverse hemolytic plaque assay was used to measure the level of circulating IgSC in 32 RA patients. The mean level of circulating IgSC in RA patients was 3602 +/- 747 (SEM) compared to a mean of 1407 +/- 443 in patients with other types of arthritis and 1253 +/- 216 (P less than 0.02) in healthy volunteers. Levels found in RA patients did not appear to reflect disease activity or concomitant corticosteroid therapy. However, a subset of RA patients receiving gold therapy had levels of IgSC (1381 +/- 501) similar to those seen in healthy volunteers (P greater than 0.5). These data are consistent with augmented in vivo polyclonal B-cell activation in RA. In addition they suggest that gold affects mechanisms controlling in vivo B-cell activation.