(Table 1) Chemical composition of Fe-rich layered silicates from the East Korean Rise, Japan Sea

Mineral and chemical compositions of highly ferruginous layered silicates (HLS) of glauconite sands occurred on the East Korean Rise outside volcanic structures and on an unnamed volcano and the Chentsov Volcano have been studied. The use of cluster and discriminant analyses has resulted to more objectively distinguished groups among HLS, and the use of factor analysis - to illustrate correlations between chemical elements in different groups. It has been found that green mineral assemblages of the East Korean Rise are heterogeneous in terms of morphology, composition and origin, and their formation is a complex multistage process including both neoformation and degradation.

Sedimentation in the vicinity of Leg 92 Drill Sites: Studies of site survey cores

Surveys of the areas surrounding the sites drilled on the Leg 92 19°S transect showed that sedimentation at all except the oldest site is dominated by calcium carbonate deposition. The sediments in the area of the oldest site, west of the Austral Fracture Zone, are being deposited beneath the calcium carbonate compensation depth and are dominated by terrigenous and metal-rich hydrogenous and hydrothermal sediments. The noncarbonate sediments in all of the areas east of the Austral Fracture Zone are dominated by hydrothermal sediment similar in composition to that presently being deposited at the East Pacific Rise. Although no biogenic microfossils were present in smear slides of the sediment, geochemical partitioning suggests that a remnant signal of siliceous biogenic deposition may be preserved, especially in gravity core (GC) 8, which was collected from a high heat flow zone near Site 600. The siliceous sediment may also result from the deposition of amorphous hydrothermal silica from the higher concentrations of pore water SiO2 characteristic of the upwelling waters. Sedimentation on the broad plateaus that characterize each area is quite uniform and suggests that sites on these plateaus will be broadly representative of pelagic sedimentation in the area.

Isotopic survey of diagenetic carbonates, at DSDP Leg 63 Holes

Authigenic carbonates, principally calcium-rich dolomites, with extremely variable isotopic compositions were recovered in organic-rich marine sediments during Leg 63 drilling off southern California and Baja California. These carbonates occur as thin layers in fine-grained, diatomaceous sediments and siliceous rocks, mostly deposited during the Neogene. A combination of textural, geochemical, and isotopic evidence indicates these dolomites formed as cements and precipitates in shallow subsurface zones of high alkalinity spawned by abundant CO2 and methane production during progressive microbial decay of organic matter. Depths and approximate temperatures of formation estimated from oxygen isotopes are 87 to 658 meters and 10°C to 50°C, respectively. Within any sedimentary section, dolomites may form simultaneously at several depths or at different times within the same interval. Highly variable carbon isotopes (-30 to +16 per mil) reflect the isotopic reservoir in which the carbonates formed. Oxidation of organic matter through microbial reduction of sulfate at shallow depths favors light-carbon carbonates such as those at Sites 468 and 471; heavy-carbon carbonates at Site 467 most likely formed below this zone where HC**12O3**- is preferentially removed by reduction of CO2 to methane during methanogenesis. An important controlling factor is the sedimentation rate, which dictates both the preservation of organic matter on the sea floor and depth distribution of subsurface zones of organic-matter decay.

High-resolution digital elevation model (DEM) of a thermokarst depression in Siberian ice-rich permafrost deposits

This data set provides a high-resolution digital elevation model (DEM) of a thermokarst depression (~7 km²) on ice-complex deposits in the Arctic Lena Delta, Siberia. The DEM based on a geodetic field survey and was used for quantitative land surface analyses and detailed description of the thermokarst depression morphology. Detailed morphometrical analyses, volume calculations, and solar radiation modeling were performed and statistically analyzed by Ulrich et al. (2010) to investigate the asymmetrical thermokarst depression development and directed lake migration previously proposed by Morgenstern et al. (2008). Furthermore, the high-resolution DEM in combination with satellite data allowed detailed analyses of spatial and temporal landscape changes due to thermokarst development (Günther, 2009).

A gene cluster for macrolide antibiotic biosynthesis in Streptomyces venezuelae: Architecture of metabolic diversity

In a survey of microbial systems capable of generating unusual metabolite structural variability, Streptomyces venezuelae ATCC 15439 is notable in its ability to produce two distinct groups of macrolide antibiotics. Methymycin and neomethymycin are derived from the 12-membered ring macrolactone 10-deoxymethynolide, whereas narbomycin and pikromycin are derived from the 14-membered ring macrolactone, narbonolide. This report describes the cloning and characterization of the biosynthetic gene cluster for these antibiotics. Central to the cluster is a polyketide synthase locus (pikA) that encodes a six-module system comprised of four multifunctional proteins, in addition to a type II thioesterase (TEII). Immediately downstream is a set of genes for desosamine biosynthesis (des) and macrolide ring hydroxylation. The study suggests that Pik TEII plays a role in forming a metabolic branch through which polyketides of different chain length are generated, and the glycosyl transferase (encoded by desVII) has the ability to catalyze glycosylation of both the 12- and 14-membered ring macrolactones. Moreover, the pikC-encoded P450 hydroxylase provides yet another layer of structural variability by introducing regiochemical diversity into the macrolide ring systems. The data support the notion that the architecture of the pik gene cluster as well as the unusual substrate specificity of particular enzymes contributes to its ability to generate four macrolide antibiotics.

Dynamic expression of multiple scavenger receptor cysteine-rich genes in coelomocytes of the purple sea urchin

Coelomocytes, the heterogeneous population of sea urchin putative immune cells, were found to express a complex set of transcripts featuring scavenger receptor cysteine-rich (SRCR) repeats. SRCR domains define a metazoan superfamily of proteins, many of which are implicated in development and regulation of the immune system of vertebrates. Coelomocytes transcribe multiple SRCR genes from among a multigene family encoding an estimated number of 1,200 SRCR domains in specific patterns particular to each individual. Transcription levels for given SRCR genes may range from pronounced to undetectable, yet all tested animals harbor the genomic loci encoding these genes. Analysis of several SRCR genes revealed multiple loci corresponding to each type. In the case of one SRCR type, a cluster of at least three genes was detected within a 133-kb bacterial artificial chromosome insert, and conserved as well as unique regions were identified in sequences of three genomic clones derived from a single animal. Array hybridizations with repeated samples of coelomocyte messages revealed substantial alterations in levels of expression of many SRCR genes, with fluctuations of up to 10-fold in 1 week and up to 30-fold over a period of 3 months. This report is the first demonstration of genomic and transcriptional complexity in molecules expressed by invertebrate coelomocytes. The mechanisms controlling SRCR gene expression and the functional significance of this dynamic system await elucidation.

ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins

The adenylate uridylate-rich elements (AREs) mediate the rapid turnover of mRNAs encoding proteins that regulate cellular growth and body response to exogenous agents such as microbes, inflammatory and environmental stimuli. However, the full repertoire of ARE-containing mRNAs is unknown. Here, we explore the distribution of AREs in human mRNA sequences. Computational derivation of a 13-bp ARE pattern was performed using multiple expectation maximization for motif elicitations (MEME) and consensus analyses. This pattern was statistically validated for the specificity towards the 3′-untranslated region and not coding region. The computationally derived ARE pattern is the basis of a database which contains non-redundant full-length ARE-mRNAs. The ARE-mRNA database (ARED; http://rc.kfshrc.edu.sa/ared) reveals that ARE-mRNAs encode a wide repertoire of functionally diverse proteins that belong to different biological processes and are important in several disease states. Cluster analysis was performed using the ARE sequences to demonstrate potential relationships between the type and number of ARE motifs, and the functional characteristics of the proteins.

X-ray emission from clusters and groups of galaxies

Recent major advances in x-ray imaging and spectroscopy of clusters have allowed the determination of their mass and mass profile out to ≈1/2 the virial radius. In rich clusters, most of the baryonic mass is in the gas phase, and the ratio of mass in gas/stars varies by a factor of 2–4. The baryonic fractions vary by a factor of ≈3 from cluster to cluster and almost always exceed 0.09 h50−[3/2] and thus are in fundamental conflict with the assumption of Ω = 1 and the results of big bang nucleosynthesis. The derived Fe abundances are 0.2–0.45 solar, and the abundances of O and Si for low redshift systems are 0.6–1.0 solar. This distribution is consistent with an origin in pure type II supernova. The amount of light and energy produced by these supernovae is very large, indicating their importance in influencing the formation of clusters and galaxies. The lack of evolution of Fe to a redshift of z ≈ 0.4 argues for very early enrichment of the cluster gas. Groups show a wide range of abundances, 0.1–0.5 solar. The results of an x-ray survey indicate that the contribution of groups to the mass density of the universe is likely to be larger than 0.1 h50−2. Many of the very poor groups have large x-ray halos and are filled with small galaxies whose velocity dispersion is a good match to the x-ray temperatures.

The highly recombinogenic bz locus lies in an unusually gene-rich region of the maize genome

The bronze (bz) locus exhibits the highest rate of recombination of any gene in higher plants. To investigate the possible basis of this high rate of recombination, we have analyzed the physical organization of the region around the bz locus. Two adjacent bacterial artificial chromosome clones, comprising a 240-kb contig centered around the Bz-McC allele, were isolated, and 60 kb of contiguous DNA spanning the two bacterial artificial chromosome clones was sequenced. We find that the bz locus lies in an unusually gene-rich region of the maize genome. Ten genes, at least eight of which are shown to be transcribed, are contained in a 32-kb stretch of DNA that is uninterrupted by retrotransposons. We have isolated nearly full length cDNAs corresponding to the five proximal genes in the cluster. The average intertranscript distance between them is just 1 kb, revealing a surprisingly compact packaging of adjacent genes in this part of the genome. At least 11 small insertions, including several previously described miniature inverted repeat transposable elements, were detected in the introns and 3′ untranslated regions of genes and between genes. The gene-rich region is flanked at the proximal and distal ends by retrotransposon blocks. Thus, the maize genome appears to have scattered regions of high gene density similar to those found in other plants. The unusually high rate of intragenic recombination seen in bz may be related to the very high gene density of the region.

Mapping rat megalin: the second cluster of ligand binding repeats contains a 46-amino acid pathogenic epitope involved in the formation of immune deposits in Heymann nephritis.

Megalin (gp330), an epithelial endocytic receptor, is a major target antigen of Heymann nephritis (HN), an autoimmune disease in rats. To elucidate the mechanisms of HN, we have mapped a pathogenic epitope in megalin that binds anti-megalin antibodies. We focused our attention on four clusters of cysteine-rich, low density lipoprotein receptor (LDLR) ligand binding repeats in the extracellular domain of megalin because they represent putative ligand binding regions and therefore would be expected to be exposed in vivo and to be able to bind circulating antibodies. Rat megalin cDNA fragments I through IV encoding the first through fourth clusters of ligand-binding repeats, respectively, were expressed in a baculovirus system. All four expression products were detected by immunoblotting with two antisera capable of inducing passive HN (pHN). When antibodies eluted from glomeruli of rats with pHN were used for immunoblotting, only the expression product encoded by fragment II was detected. This indicates that the second cluster of LDLR ligand binding repeats is directly involved in binding anti-megalin antibodies and in the induction of pHN. To narrow the major epitope in this domain, fragment II was used to prepare proteins sequentially truncated from the C- and N-terminal ends by in vitro translation. Analysis of the truncated translation products by immunoprecipitation with anti-megalin IgG revealed that the fifth ligand-binding repeat (amino acids 1160-1205) contains the major epitope recognized. This suggests that a 46-amino acid sequence in the second cluster of LDLR ligand binding repeats contains a major pathogenic epitope that plays a key role in pHN. Identification of this epitope will facilitate studies on the pathogenesis of HN.

Z-DNA-forming sites within the human beta-globin gene cluster.

Agarose-encapsulated, metabolically active, permeabilized nuclei from human hematopoietic cell lines were tested for Z-DNA formation in the beta-globin gene cluster. Biotinylated monoclonal antibodies against Z-DNA were diffused into the nuclei and cross-linked to DNA with a 10-ns laser exposure at 266 nm. Following digestion with restriction enzymes, fragments that had formed Z-DNA were isolated. Seventeen regions with Z-DNA sequence motifs in the 73-kb region were studied by PCR amplification, and five were found in the Z conformation.