The biggest losers: habitat isolation deconstructs complex food webs from top to bottom.

Habitat fragmentation threatens global biodiversity. To date, there is only limited understanding of how the different aspects of habitat fragmentation (habitat loss, number of fragments and isolation) affect species diversity within complex ecological networks such as food webs. Here, we present a dynamic and spatially explicit food web model which integrates complex food web dynamics at the local scale and species-specific dispersal dynamics at the landscape scale, allowing us to study the interplay of local and spatial processes in metacommunities. We here explore how the number of habitat patches, i.e. the number of fragments, and an increase of habitat isolation affect the species diversity patterns of complex food webs (α-, ß-, γ-diversities). We specifically test whether there is a trophic dependency in the effect of these two factors on species diversity. In our model, habitat isolation is the main driver causing species loss and diversity decline. Our results emphasize that large-bodied consumer species at high trophic positions go extinct faster than smaller species at lower trophic levels, despite being superior dispersers that connect fragmented landscapes better. We attribute the loss of top species to a combined effect of higher biomass loss during dispersal with increasing habitat isolation in general, and the associated energy limitation in highly fragmented landscapes, preventing higher trophic levels to persist. To maintain trophic-complex and species-rich communities calls for effective conservation planning which considers the interdependence of trophic and spatial dynamics as well as the spatial context of a landscape and its energy availability.

Consanguinity and pregnancy outcomes in a multi-ethnic, metropolitan European population.

OBJECTIVE: The aim of the present study was to assess the risk of major anomalies in the offspring of consanguineous couples, including data on the prenatal situation. METHODS: Over 20 years (1993-2012), 35,391 fetuses were examined by prenatal sonography. In 675 cases (1.9%), parents were consanguineous, with 307 couples (45.5%) related as first cousins, 368 couples (54.5%) beyond first cousins. Detailed information was retrieved on 31,710 (89.6%) fetuses, (consanguineous 568: 1.8%). RESULTS: Overall prevalence of major anomalies among fetuses with non-consanguineous parents was 2.9% (consanguineous, 10.9%; first cousins, 12.4%; beyond first cousins, 6.5%). Adjusting the overall numbers for cases having been referred because of a previous index case, the prevalences were 2.8% (non-consanguineous) and 6.1% (consanguineous) (first cousin, 8.5%; beyond first cousin, 3.9%). Further adjustment for differential rates of trisomic pregnancies indicated 2.0%/5.9% congenital anomalies (non-consanguineous/consanguineous groups), that is, a consanguinity-associated excess of 3.9%, 6.1% in first cousin progeny and 1.9% beyond first cousin. CONCLUSIONS: The prevalence of major fetal anomalies associated with consanguinity is higher than in evaluations based only on postnatal life. It is important that this information is made available in genetic counselling programmes, especially in multi-ethnic and multi-religious communities, to enable couples to make informed decisions.

Identification of novel aberrant methylation of BASP1 and SRD5A2 for early diagnosis of hepatocellular carcinoma by genome-wide search.

A genome-wide study using expression profiles of 12,600 genes was conducted to identify methylated genes that could be used for early diagnosis of hepatocellular carcinoma (HCC). Of the 12,600 genes examined, we identified 23 genes with significantly lower expression levels in HCC tissues than in non-HCC liver tissues by our statistical and CpG mapping tests. Of these 23 genes, methylation analysis by direct sequencing with bisulfite treatment determined 4 genes that were aberrantly methylated in 20 HCC samples of TNM stages I and II. Further methylation analysis of the 4 genes by quantitative sequencing with 20 HCCs and the corresponding non-tumor liver tissues from an independent cohort of HCC patients revealed that 2 genes, BASP1 and SRD5A2, were aberrantly methylated in only HCC tissues, though not in any corresponding non-tumor liver tissues. Notably, in the cohort we found that BASP1 or SRD5A2 were aberrantly methylated when a cut-off value of 30% in the methylation rate was used, in all cases of 11 HCCs of TNM stages I and II, of 10 well-differentiated HCCs and of 4 small HCCs <2 cm in maximum diameter, but in none of the 20 corresponding non-HCC livers. Methylation-specific PCR for BASP1 and SRD5A2 reproduced the same results observed by direct sequencing. These results indicate that BASP1 and SRD5A2 might serve as useful biomarkers for early diagnosis of HCC.

The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C.

Hyperthermus butylicus, a hyperthermophilic neutrophile and anaerobe, is a member of the archaeal kingdom Crenarchaeota. Its genome consists of a single circular chromosome of 1,667,163 bp with a 53.7% G+C content. A total of 1672 genes were annotated, of which 1602 are protein-coding, and up to a third are specific to H. butylicus. In contrast to some other crenarchaeal genomes, a high level of GUG and UUG start codons are predicted. Two cdc6 genes are present, but neither could be linked unambiguously to an origin of replication. Many of the predicted metabolic gene products are associated with the fermentation of peptide mixtures including several peptidases with diverse specificities, and there are many encoded transporters. Most of the sulfur-reducing enzymes, hydrogenases and electron-transfer proteins were identified which are associated with energy production by reducing sulfur to H(2)S. Two large clusters of regularly interspaced repeats (CRISPRs) are present, one of which is associated with a crenarchaeal-type cas gene superoperon; none of the spacer sequences yielded good sequence matches with known archaeal chromosomal elements. The genome carries no detectable transposable or integrated elements, no inteins, and introns are exclusive to tRNA genes. This suggests that the genome structure is quite stable, possibly reflecting a constant, and relatively uncompetitive, natural environment.

Highly functionalized glyco-conjugated hexahydroazepindiones from saccharide imides via the Norrish type II reaction.

Starting from readily available protected 6-tosylates of D-glucose and D-mannose in both their pyranoside and furanoside forms as well as 6-tosylates of alpha-D-galactopyranose, the corresponding primary succinimido derivatives were obtained in good yield by nucleophilic displacement with potassium succinimide. These imido sugars were photochemically transformed into hexahydroazepindione derivatives such as by means of a Norrish type II reaction. As expected, the intramolecular alkylation proceeded via an 1,6 H-abstraction leading to a stabilized diradical. The regiochemistry of the photoreaction was controlled by configurational, conformational and electronic features and was sometimes influenced by the protecting groups. Using this route, a facile approach to a novel class of highly functionalized sugar derived heterocycles was developed.

Elevated levels of circulating cell-free DNA in the blood of patients with hepatitis C virus-associated hepatocellular carcinoma.

BACKGROUND: Circulating cell-free DNA is present in increased amounts in the blood of patients with one of several forms of cancer. MATERIALS AND METHODS: A real-time PCR assay with glutathione S-transferase pi (GSTP1) gene was used to measure cell-free DNA levels in the sera of 52 patients with hepatocellular carcinoma (HCC) associated with hepatitis C virus (HCV), which included 30 HCV carriers without known HCC and 16 HCV-negative non-cancer patients (controls). RESULTS: Cell-free DNA levels were significantly higher in the sera from HCC patients than in the sera from HCV carriers or the control subjects. Cell-free DNA levels were associated with the degree of tumor differentiation and size but not patient age, gender, TNM stage or levels of alpha-fetoprotein (AFP) or protein induced by vitamin K absence (PIVKA-II). The cell-free DNA assay had a sensitivity of 69.2% and a specificity of 93.3% in discriminating HCC and HCV carriers at the optimal cut-off value of 73.0 ng/ml, with an area of 0.90 (95% CI, 0.83-0.96) under the receiver operating characteristic curve. The discriminative power of cell-free DNA was superior to that of AFP or PIVKA-II. CONCLUSION: Our results showed that levels of circulating cell-free DNA are significantly increased in sera of patients with HCV-associated HCC, suggesting that circulating cell-free DNA may be a good biomarker specific for HCV-associated HCC.