Miocene Trace Fossils from Borneo

In the Miocene Belait formation of northern Sarawak, Brunei and Sabah burrows ofOphiomorpha Lundgren were found, described here asOphiomorpha borneensis n. ichnosp. A few associated spiral tunnels of theXenohelix-type were also found. Two species ofHäntzschelinia Vialov occurred on Labuan Island. A third type of structure was found in Brunei and it probably represents castings of an unknown lamellibranch. The burrows and castings were made in a brackish water environment, probably in the littoral zone of an embayment or delta.     

NCI-H716 cells as a model for endocrine differentiation in colorectal cancer

In colonic neoplasms, endocrine differentiation is encountered not only in carcinoid tumors but also in adenocarcinomas, where endocrine cells may represent a distinct line of differentiation in the tumor. The significance of endocrine differentiation in colorectal cancer is not well established, partly because of the paucity of tumor cell lines which can serve as a model for studying endocrine differentiation. In this report we describe the properties of NCI-H716 cells, a cell line derived from a poorly differentiated adenocarcinoma of the caecum, under various in vitro conditions and as xenografts in athymic mice. Phenotypical properties were immunohistochemically assessed using a panel of differentiation related antibodies, and also by Northern blot analysis and by electron microscopy. Receptors for biogenic amines and peptide hormones were analyzed by ligand binding assay. These studies show that:

Heterozygosity for a loss-of-function mutation in GALNT2 improves plasma triglyceride clearance in man

Genome-wide association studies have identified GALNT2 as a candidate gene in lipid metabolism, but it is not known how the encoded enzyme ppGalNAc-T2, which contributes to the initiation of mucin-type O-linked glycosylation, mediates this effect. In two probands with elevated plasma high-density lipoprotein cholesterol and reduced triglycerides, we identified a mutation in GALNT2. It is shown that carriers have improved postprandial triglyceride clearance, which is likely attributable to attenuated glycosylation of apolipoprotein (apo) C-III, as observed in their plasma. This protein inhibits lipoprotein lipase (LPL), which hydrolyses plasma triglycerides. We show that an apoC-III-based peptide is a substrate for ppGalNAc-T2 while its glycosylation by the mutant enzyme is impaired. In addition, neuraminidase treatment of apoC-III which removes the sialic acids from its glycan chain decreases its potential to inhibit LPL. Combined, these data suggest that ppGalNAc-T2 can affect lipid metabolism through apoC-III glycosylation, thereby establishing GALNT2 as a lipid-modifying gene.     

The involvement of sucrose,glucose and other metabolites in the synthesis of triterpenes and dopa in the laticifers of Euphorbia lathyris

A quantitative triterpene analysis was made of latex stem tissue of Euphorbia lathyris. Young plants seedlings of E. lathyris were incubated with various labelled precursors. Incorporation into triterpenes was obtained from [2-¹⁴C]mevalonic acid, [1-¹⁴C]acetate, [3-¹⁴C]pyruvate, [U-¹⁴C]sucrose, [U-¹⁴C]glucose, [U-¹⁴C]xylose, [U-¹⁴C]glyoxylate, [2,3-¹⁴C]succinic acid, [1-¹⁴C]glycerol [U-¹⁴C]serine. Both sugars tyrosine appeared to be effective precursors in DOPA synthesis inside the laticifers. Exogenously supplied mevalonic acid was only involved in triterpene synthesis outside the laticifers. GC-RC of triterpenes synthesized from [U-¹⁴C]glucose revealed the origin of these compounds in the latex. The labelled triterpenes obtained after incorporation of the other mentioned labelled precursors were only partly synthesized in the laticifers. For quantitative data on latex triterpene synthesis seedlings were incubated with [U-¹⁴C]sucrose, [U-¹⁴C]glucose, [U-¹⁴C]xylose [1-¹⁴C]acetate in the presence of increasing amounts of unlabelled substrate. From the amount of ¹⁴C incorporated into the triterpenes the amount of substrate directly involved in triterpene synthesis was calculated, as was the absolute triterpene yield. Sucrose showed the highest triterpene yield, equivalent to the daily increase of the triterpene content of growing seedlings. The possible significance of the other precursors in triterpene synthesis in the laticifers is discussed.     

Dreissenids’ breaking loose: differential attachment as a possible driver of the dominance shift between two invasive mussel species

Biological Invasions - Ponto-Caspian dreissenids are notorious freshwater invaders. Recently, widespread observations show a dominance shift from the early invader, Dreissena polymorpha, to its...     

Identification and QTL mapping of whitefly resistance components in Solanum galapagense

Solanum galapagense is closely related to the cultivated tomato and can show a very good resistance towards whitefly. A segregating population resulting from a cross between the cultivated tomato and a whitefly resistant S. galapagense was created and used for mapping whitefly resistance and related traits, which made it possible to study the genetic basis of the resistance. Quantitative trait loci (QTL) for adult survival co-localized with type IV trichome characteristics (presence, density, gland longevity and gland size). A major QTL (Wf-1) was found for adult survival and trichome characters on Chromosome 2. This QTL explained 54.1 % of the variation in adult survival and 81.5 % of the occurrence of type IV trichomes. A minor QTL (Wf-2) for adult survival and trichome characters was identified on Chromosome 9. The major QTL was confirmed in F3 populations. Comprehensive metabolomics, based on GCMS profiling, revealed that 16 metabolites segregating in the F2 mapping population were associated with Wf-1 and/or Wf-2. Analysis of the 10 most resistant and susceptible F2 genotypes by LCMS showed that several acyl sugars were present in significantly higher concentration in the whitefly resistant genotypes, suggesting a role for these components in the resistance as well. Our results show that whitefly resistance in S. galapagense seems to inherit relatively simple compared to whitefly resistance from other sources and this offers great prospects for resistance breeding as well as elucidating the underlying molecular mechanism(s) of the resistance.     

Flyway population delineation in Taiga Bean Geese Anser fabalis fabalis revealed by multi‐element feather stable isotope analysis

Fundamental to effective management of migratory waterbird populations is an understanding of their flyway delineation. Taiga Bean Geese Anser fabalis fabalis wintering in NW Denmark, Scotland and England are considered to originate from northern and central Sweden, southern and central Norway (‘Western flyway’), those wintering in southern Sweden, NE and southern Denmark are considered to originate from northern Fennoscandia and western Russia (‘Central flyway’), and those wintering in eastern Germany and Poland (which show far less favourable conservation status) are thought to come from western Siberia (‘Eastern 1 flyway’), although evidence to demonstrate this has largely been lacking. Evidence for different natal and moult origins of Taiga Bean Geese was investigated using stable isotope analyses of feathers of four elements (δ²H, δ¹³C, δ¹⁵N and δ³⁴S). There were significant differences in isotopic composition of feathers from Swedish (Central) and German (Eastern 1) wintering populations and those moulting in Sweden in late summer (Western), which validated the three proposed major management flyway units above. The strong continental gradient in the stable hydrogen isotope ratios in precipitation (δ²H_p) across the region was used to assign wintering birds geospatially to natal and moulting origin, indicating separate natal and moulting areas for German (n = 37, from western Siberia) and Swedish (n = 20, Fennoscandia and more western Russia) wintering birds. These results confirm the largely discrete nature of these three flyways and contribute significantly to our ability to deliver effective targeted and appropriate research, monitoring and management actions throughout the ranges of these flyways.     

Cell lineage and gene expression in the development of polychaetes

The developmental strategies of embryos within the various taxa of polychaetes are designed to set up the fate of the cell lines. Some of these traits of pattern formation are considered to be ancestral, but we also find a number of derived developmental characteristics, some of which might be useful indicators for phylogenetic relationships. A combination of ooplasmic segregation and anisotropic cleavage rapidly establishes the fate of several larval cell lines in the polychaete embryo. The setting-up of the primary trochoblasts basically concerns the same cell line (la²–ld²) in polychaetes and even in molluscs. Such mechanisms may thus be regarded as ancestral. The determination of the mesoderm precursor occurs very late in both equally cleaving annelids and mollusks, indicating that an equal cleavage pattern may be regarded as an ancestral trait. Since both disproportionate cytoplasmic distribution (either by spindle shift or polar lobe formation) and cell cycle asynchronies appear to speed up the development of the mesoderm-forming cell line, these strategies represent derived traits. An analysis of these derived traits of early development is given and is discussed in the light of the phylogenetic relationships among the polychaetes. These data are extended by an analysis of some of the postlarval structures in polychaetes and the molecular developmenta1 circuitry involved.     

Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting

MOTIVATION: Identification of residues that account for protein function specificity is crucial, not only for understanding the nature of functional specificity, but also for protein engineering experiments aimed at switching the specificity of an enzyme, regulator or transporter. Available algorithms generally use multiple sequence alignments to identify residue positions conserved within subfamilies but divergent in between. However, many biological examples show a much subtler picture than simple intra-group conservation versus inter-group divergence. RESULTS: We present multi-RELIEF, a novel approach for identifying specificity residues that is based on RELIEF, a state-of-the-art Machine-Learning technique for feature weighting. It estimates the expected 'local' functional specificity of residues from an alignment divided in multiple classes. Optionally, 3D structure information is exploited by increasing the weight of residues that have high-weight neighbors. Using ROC curves over a large body of experimental reference data, we show that (a) multi-RELIEF identifies specificity residues for the seven test sets used, (b) incorporating structural information improves prediction for specificity of interaction with small molecules and (c) comparison of multi-RELIEF with four other state-of-the-art algorithms indicates its robustness and best overall performance. AVAILABILITY: A web-server implementation of multi-RELIEF is available at www.ibi.vu.nl/programs/multirelief. Matlab source code of the algorithm and data sets are available on request for academic use.