The Microbial Diversity of Traditional Spontaneously Fermented Lambic Beer

Lambic sour beers are the products of a spontaneous fermentation that lasts for one to three years before bottling. The present study determined the microbiota involved in the fermentation of lambic beers by sampling two fermentation batches during two years in the most traditional lambic brewery of Belgium, using culture-dependent and culture-independent methods. From 14 samples per fermentation, over 2000 bacterial and yeast isolates were obtained and identified. Although minor variations in the microbiota between casks and batches and a considerable species diversity were found, a characteristic microbial succession was identified. This succession started with a dominance of Enterobacteriaceae in the first month, which were replaced at 2 months by Pediococcus damnosus and Saccharomyces spp., the latter being replaced by Dekkera bruxellensis at 6 months fermentation duration.     

Habitat Use and Mobility of Two Threatened Coastal Dune Insects: Implications for Conservation

We studied the habitat use and mobility of the Grayling butterfly (Hipparchia semele) and the Blue-Winged Grasshopper (Oedipoda caerulescens), two threatened insects within spatially structured blond and grey dunes in a nature reserve along the Belgian coast. Although both species occur in the same biotope, H. semele were more abundant in open, dynamic sites with a relatively high amount of bare sand, while O. caerulescens preferred sheltered, more stable environments with a lower amount of bare sand. Unlike H. semele, substrate use varied in accordance to body colouration in O. caerulescens, especially on cold days, with light-coloured animals being more abundant on sand and dark-coloured animals more abundant on moss. During a mark-recapture-study, we marked 493 Grayling butterflies and 1289 Blue-Winged Grasshoppers. On average, both sexes of H. semele were equally mobile (about 150 m/day; maximum recorded distance of about 1700 m) while male O. caerulescens were significantly more mobile than females (daily average 47 vs. 5 m; maximum distances observed for O. caerulescens were about 800 m). The importance of habitat heterogeneity (within and among patches) and the consequences of habitat use and mobility of both species for the conservation of typical coastal dune habitats are discussed. The complementary use of species-specific information to site-based management measures is advocated.     

Phialomyces fusiformis sp. nov. from soil in Singapore is identified and described

Phialomyces fusiformis sp. nov., isolated from soil in Singapore, is described and illustrated. The species is similar to P. macrosporus-type species of the genus but differs in that it has longer, more ellipsoid-limoniform, fusiform and more coarsely ornamented conidia.     

Innovative development and validation of an HPLC/DAD method for the qualitative and quantitative determination of major cannabinoids in cannabis plant material

GC is commonly used for the analysis of cannabis samples, e.g. in forensic chemistry. However, as this method is based on heating of the sample, acidic forms of cannabinoids are decarboxylated into their neutral counterparts. Conversely, HPLC permits the determination of the original composition of plant cannabinoids by direct analysis. Several HPLC methods have been described in the literature, but most of them failed to separate efficiently all the cannabinoids or were not validated according to general guidelines. By use of an innovative methodology for modelling chromatographic responses, a simple and accurate HPLC/DAD method was developed for the quantification of major neutral and acidic cannabinoids present in cannabis plant material: Δ9-tetrahydrocannabinol (THC), THC acid (THCA), cannabidiol (CBD), CBD acid (CBDA), cannabigerol (CBG), CBG acid (CBGA) and cannabinol (CBN). Δ8-Tetrahydrocannabinol (Δ8-THC) was determined qualitatively. Following the practice of design of experiments, predictive multilinear models were developed and used in order to find optimal chromatographic analytical conditions. The method was validated following an approach using accuracy profiles based on β-expectation tolerance intervals for the total error measurement, and assessing the measurements uncertainty. This analytical method can be used for diverse applications, e.g. plant phenotype determination, evaluation of psychoactive potency and control of material quality.     

On the use of the transmission disequilibrium test to detect pseudo‐autosomal variants affecting traits with sex‐limited expression

We herein describe the realization of a genome‐wide association study for scrotal hernia and cryptorchidism in Norwegian and Belgian commercial pig populations. We have used the transmission disequilibrium test to avoid spurious associations due to population stratification. By doing so, we obtained genome‐wide significant signals for both diseases with SNPs located in the pseudo‐autosomal region in the vicinity of the pseudo‐autosomal boundary. By further analyzing these signals, we demonstrate that the observed transmission disequilibria are artifactual. We determine that transmission bias at pseudo‐autosomal markers will occur (i) when analyzing traits with sex‐limited expression and (ii) when the allelic frequencies at the marker locus differ between X and Y chromosomes. We show that the bias is due to the fact that (i) sires will preferentially transmit the allele enriched on the Y (respectively X) chromosome to affected sons (respectively daughters) and (ii) dams will appear to preferentially transmit the allele enriched on the Y (respectively X) to affected sons (respectively daughters), as offspring inheriting the other allele are more likely to be non‐informative. We define the conditions to mitigate these issues, namely by (i) extracting information from maternal meiosis only and (ii) ignoring trios for which sire and dam have the same heterozygous genotype. We show that by applying these rules to scrotal hernia and cryptorchidism, the pseudo‐autosomal signals disappear, confirming their spurious nature.     

A validated method for the quantification of enterodiol and enterolactone in plasma using isotope dilution liquid chromatography with tandem mass spectrometry

Enterolactone and enterodiol are phytoestrogens with structural similarity to endogenous estrogens. Because of their biological activities, they may affect the development of several diseases. To quantify enterodiol and enterolactone in plasma, we developed and validated a liquid chromatography-tandem mass spectrometry method with electrospray ionization using 13C3 labeled isotopes. The method consists of a simple enzymatic hydrolysis and ether extraction followed by a rapid LC separation (run-time of 11 min). Detection limits as low as 0.15 nM for enterodiol and 0.55 nM for enterolactone were achieved. The within-run R.S.D. ranges from 3 to 6% and the between-run R.S.D. ranges from 10 to 14% for both enterolignans. This method allows simple, rapid, and sensitive quantification, and is suitable for measuring large numbers of samples.     

Affinities of Phylacia and the daldinoid Xylariaceae, inferred from chemotypes of cultures and ribosomal DNA sequences

A chemotaxonomic evaluation using hplc profiling was undertaken to resolve the infrageneric and intergeneric affinities of over 150 strains of Xylariaceae. Daldinia placentiformis, Hypoxylon nicaraguense, H. polyporus, and Phylacia sagrana were found to contain 8-methoxy-1-naphthol, which is apparently absent in Annulohypoxylon, Hypoxylon, and related genera with bipartite stromata. D. placentiformis and other species of Daldinia and Entonaema produced this naphthol, 5-hydroxy-2-methylchromone, isosclerone derivatives, and ‘AB-5046’ phytotoxins. Phylacia sagrana differed from most Daldinia spp., except for D. caldariorum, by producing eutypine derivatives in addition to the above compounds. Indolylquinones were observed in H. nicaraguense and H. polyporus. Isosclerones were also identified in the A. multiforme complex, but Hypoxylon and other Annulohypoxylon and most Hypoxylon spp. studied Annulohypoxylon spp. contained 5-methylmellein as the major metabolite of their cultures. Based on the occurrence of the above metabolites, further mellein-type dihydroisocoumarins, teleomorphic and anamorphic Xylariaceae with Nodulisporium-like anamorphs (‘Hypoxyloideae’) were divided into various chemotypes. A comparison of their 5.8S/ITS nuc-rDNA sequences agreed in some important aspects with the above results: H. nicaraguense and H. polyporus appeared basal to a clade comprising Daldinia, Entonaema, and Ph. sagrana. The latter species appeared allied to D. caldariorum, but was distantly related to Pyrenomyxa morganii and Hypoxylon s. str.     

Microarray Analysis of Copy Number Variants on the Human Y Chromosome Reveals Novel and Frequent Duplications Overrepresented in Specific Haplogroups

Background

The human Y chromosome is almost always excluded from genome-wide investigations of copy number variants (CNVs) due to its highly repetitive structure. This chromosome should not be forgotten, not only for its well-known relevance in male fertility, but also for its involvement in clinical phenotypes such as cancers, heart failure and sex specific effects on brain and behaviour.

Results

We analysed Y chromosome data from Affymetrix 6.0 SNP arrays and found that the signal intensities for most of 8179 SNP/CN probes in the male specific region (MSY) discriminated between a male, background signals in a female and an isodicentric male containing a large deletion of the q-arm and a duplication of the p-arm of the Y chromosome. Therefore, this SNP/CN platform is suitable for identification of gain and loss of Y chromosome sequences. In a set of 1718 males, we found 25 different CNV patterns, many of which are novel. We confirmed some of these variants by PCR or qPCR. The total frequency of individuals with CNVs was 14.7%, including 9.5% with duplications, 4.5% with deletions and 0.7% exhibiting both. Hence, a novel observation is that the frequency of duplications was more than twice the frequency of deletions. Another striking result was that 10 of the 25 detected variants were significantly overrepresented in one or more haplogroups, demonstrating the importance to control for haplogroups in genome-wide investigations to avoid stratification. NO-M214(xM175) individuals presented the highest percentage (95%) of CNVs. If they were not counted, 12.4% of the rest included CNVs, and the difference between duplications (8.9%) and deletions (2.8%) was even larger.

Conclusions

Our results demonstrate that currently available genome-wide SNP platforms can be used to identify duplications and deletions in the human Y chromosome. Future association studies of the full spectrum of Y chromosome variants will demonstrate the potential involvement of gain or loss of Y chromosome sequence in different human phenotypes.