Average dip directions from intervals of dipmeter log in drill hole CRP-2A

Bedding dips in the CRP-2A drillhole were determined in two ways (1) analysis of a dipmeter log, and (2) identification of bed boundaries on digital images of the outer core surface. The two methods document the downhole increase in structural dip, to a maximum of 15° in the lowest 150 m of the hole. Dipmeter data, which are azimuthally oriented, indicate a 75° azimuth for structural tilting, in agreement with seismic reflection profiles. Core and log dips indicate that structural dip increases by 5-7° between 325 and 480 mbsf. Both, however, also exhibit high dip inhomogeneity because of depositional (e.g., cross bedding) and post-depositional (e.g., softsediment deformation) processes. This variability adds ambiguity to the search for angular unconformities within the CRP-2A drillhole. Dip directions of different lithologies are generally similar, as are dip directions for the four kinds of systems tracts. Downdip azimuths of sands and muds are slightly different from those of diamicts, possibly reflecting the divergence between ENE offshore dip and ESE glacial advance.

Shallow water foraminifera of ODP Hole 133-821A

Reworked shallow-water foraminifers that settled on the upper slope of the central Great Barrier Reef at Site 821 (water depth, 212.6 m) were used as indicators of the paleoclimatic and paleoenvironmental conditions that have controlled the Pleistocene evolution of the adjacent platform. Throughout the 400-m-thick sequence drilled, the nature, composition, and distribution of the shallow-water foraminiferal assemblages studied indicate that (1) all the species recorded are at present living in diverse tropical, reef-related areas of the Indo-Pacific and Atlantic provinces; (2) the composition of the microfaunal taphocoenoses is almost identical between the different stratigraphic intervals studied and the modern Great Barrier Reef environments; (3) inner-neritic, tropical environments have continued to develop since the middle Pleistocene; (4) high- to moderate-energy platform edges occurred repeatedly throughout Pleistocene time. These factors may suggest that, since the beginning of the Pleistocene, several reef-like tracts have grown successively on the central area of the northeastern Australian shelf edge. These tracts probably had a sufficiently evolved morphological zonation to act as shelters for foraminiferal biocoenoses of high species diversity.

Characteristics and stomach contents of Greenland sharks (Somniosus microcephalus) caught in Svalbard during June 2008-2009

Harbour seals in Svalbard have short longevity, despite being protected from human hunting and having limited terrestrial predation at their haulout sites, low contaminant burdens and no fishery by-catch issues. This led us to explore the diet of Greenland sharks (Somniosus microcephalus) in this region as a potential seal predator. We examined gastrointestinal tracts (GITs) from 45 Greenland sharks in this study. These sharks ranged from 229 to 381 cm in fork length and 136-700 kg in body mass; all were sexually immature. Seal and whale tissues were found in 36.4 and 18.2%, respectively, of the GITs that had contents (n = 33). Based on genetic analyses, the dominant seal prey species was the ringed seal (Pusa hispida); bearded seal (Erignathus barbatus) and hooded seal (Cystophora cristata) tissues were each found in a single shark. The sharks had eaten ringed seal pups and adults based on the presence of lanugo-covered prey (pups) and age determinations based on growth rings on claws (<1 year and adults). All of the whale tissue was from minke whale (Balenoptera acutorostrata) offal, from animals that had been harvested in the whale fishery near Svalbard. Fish dominated the sharks' diet, with Atlantic cod (Gadus morhua), Atlantic wolffish (Anarhichas lupus) and haddock (Melanogrammus aeglefinus) being the most important fish species. Circumstantial evidence suggests that these sharks actively prey on seals and fishes, in addition to eating carrion such as the whale tissue. Our study suggests that Greenland sharks may play a significant predatory role in Arctic food webs.

Sediment composition and sedimentation rates of four Holes in ODP Leg 166

To date, work on the Great Bahama Bank's western, leeward margin has centred chiefly on seismic-scale expressions of carbonate sequences and systems tracts. However, periplatform, slope sediments also exhibit very well developed cyclicity on scales of decimetres to several metres. It is these small-scale, high-frequency cycles within the larger-scale facies successions of the Quaternary which form the main topic of this paper. Previous studies have shown that the small-scale cycles correlate to the orbitally forced, high-frequency sea-level changes. Therefore these cycles should indicate how sea level has affected the slope development and thus platform-margin evolution during this period. Through detailed, high-resolution sequence stratigraphy of the Great Bahama Bank's leeward margin, obtained via delta18O isotope and mineralogical (XRD) analyses, confined by U/Th dating and nannofossil bioevents, a greater understanding of the bedding geometries within the Pleistocene-Holocene seismic sequences and clues as to the nature of the slope development has been achieved. The high-resolution seismic profiles indicate that since the Plio-Pleistocene change in geometry, in which the Great Bahama Bank developed into a rimmed platform, continued steepening and subsequent progradation of the leeward margin has typified slope development during the Quaternary, which is described as an accretionary slope. However, on the basis of our observations we conclude that only the early to lower middle Pleistocene section (isotope stages 45-20) and the Holocene (isotope stage 1) of the leeward margin is accretionary. This indicates that a degree of erosion and/or by-passing has occurred on the leeward margin since the lower middle Pleistocene (isotope stage 19). During the first part of this period (isotope stages 19-12) erosion and/or by-passing occurred in the middle to lower slope regions and toe-of-slope. By the end of the upper middle to late Pleistocene phase (isotope stages 11-2) erosion also occurred on the upper slope. This erosion by currents at the toe-of-slope and oversteepening of the upper and middle slopes have led to back-cutting upslope and resulted in the progressive retreat of the toe-of-slope towards the platform to the east. However, the rise in sea level since the Last Glacial Maximum to its present-day level has allowed high productivity on the platform top during the Holocene and the deposition of a thick sediment wedge on the slope and sedimentation across the entire leeward flanks. This has led to the redevelopment of an accretionary slope and continued westward progradation of the Great Bahama Bank's western, leeward margin.

Diffusion Tensor Imaging in Alzheimer's disease

Attentional control and Information processing speed are central concepts in cognitive psychology and neuropsychology. Functional neuroimaging and neuropsychological assessment have depicted theoretical models considering attention as a complex and non-unitary process. One of its component processes, Attentional set-shifting ability, is commonly assessed using the Trail Making Test (TMT). Performance in the TMT decreases with increasing age in adults, Mild Cognitive Impairment (MCI) and Alzheimer’s Disease (AD). Besides, speed of information processing (SIP) seems to modulate attentional performance. While neural correlates of attentional control have been widely studied, there are few evidences about the neural substrates of SIP in these groups of patients. Different authors have suggested that it could be a property of cerebral white matter, thus, deterioration of the white matter tracts that connect brain regions related to set-shifting may underlie the age-related, MCI and AD decrease in performance. The aim of this study was to study the anatomical dissociation of attentional and speed mechanisms. Diffusion tensor imaging (DTI) provides a unique insight into the cellular integrity of the brain, offering an in vivo view into the microarchitecture of cerebral white matter. At the same time, the study of ageing, characterized by white matter decline, provides the opportunity to study the anatomical substrates speeded or slowed information processing. We hypothesized that FA values would be inversely correlated with time to completion on Parts A and B of the TMT, but not the derived scores B/A and B-A.

Structural changes after videogame practice related to a brain network associated with intelligence

Here gray and white matter changes after four weeks of videogame practice were analyzed using optimized voxel-based morphometry (VBM), cortical surface and cortical thickness indices, and white matter integrity computed from several projection, commissural, and association tracts relevant to cognition. Beginning with a sample of one hundred young females, twenty right handed participants were recruited for the study and assigned to a practice or a control group carefully matched by their general cognitive ability scores. After the first scan, the practice group played ‘Professor Layton and The Pandora's Box’ 4 h per week during four weeks. A second scan was obtained at the end of practice and intelligence was measured again. Image analyses revealed gray and white matter changes in the practice group. Gray matter changes theoretically relevant for intelligence were observed for the practice group mainly in frontal clusters (Brodmann areas 9 and 10) and also in smaller parietal and temporal regions. White matter findings were focused in the hippocampal cingulum and the inferior longitudinal fasciculus. These gray and white matter changes presumably induced by practice did not interact with intelligence tests' scores.

MEG networks organization is related to white matter integrity

Many studies have assessed the characterization of anatomical or functional connectivity in mild cognitive impairment (MCI), however it is still unknown how they are related in the course of the pathology. Here we integrate the analysis of magnetoencephalographic (MEG) data with white matter (WM) integrity quantification from diffusion weighted imaging (DWI), to asses whether the damage in the WM tracts disrupt the organization of the functional networks.

The default mode network is functionally and structurally disrupted in amnestic mild cognitive impairment — a bimodal MEG–DTI study

Over the past years, several studies on Mild Cognitive Impairment (MCI) and Alzheimer's disease (AD) have reported Default Mode Network (DMN) deficits. This network is attracting increasing interest in the AD community, as it seems to play an important role in cognitive functioning and in beta amyloid deposition. Attention has been particularly drawn to how different DMN regions are connected using functional or structural connectivity. To this end, most studies have used functional Magnetic Resonance Imaging (fMRI), Positron Emission Tomography (PET) or Diffusion Tensor Imaging (DTI). In this study we evaluated (1) functional connectivity from resting state magnetoencephalography (MEG) and (2) structural connectivity from DTI in 26 MCI patients and 31 age-matched controls. Compared to controls, the DMN in the MCI group was functionally disrupted in the alpha band, while no differences were found for delta, theta, beta and gamma frequency bands. In addition, structural disconnection could be assessed through a decreased fractional anisotropy along tracts connecting different DMN regions. This suggests that the DMN functional and anatomical disconnection could represent a core feature of MCI.

Natural and experimental oral infection of nonhuman primates by bovine spongiform encephalopathy agents

Experimental lemurs either were infected orally with the agent of bovine spongiform encephalopathy (BSE) or were maintained as uninfected control animals. Immunohistochemical examination for proteinase-resistant protein (prion protein or PrP) was performed on tissues from two infected but still asymptomatic lemurs, killed 5 months after infection, and from three uninfected control lemurs. Control tissues showed no staining, whereas PrP was detected in the infected animals in tonsil, gastrointestinal tract and associated lymphatic tissues, and spleen. In addition, PrP was detected in ventral and dorsal roots of the cervical spinal cord, and within the spinal cord PrP could be traced in nerve tracts as far as the cerebral cortex. Similar patterns of PrP immunoreactivity were seen in two symptomatic and 18 apparently healthy lemurs in three different French primate centers, all of which had been fed diets supplemented with a beef protein product manufactured by a British company that has since ceased to include beef in its veterinary nutritional products. This study of BSE-infected lemurs early in their incubation period extends previous pathogenesis studies of the distribution of infectivity and PrP in natural and experimental scrapie. The similarity of neuropathology and PrP immunostaining patterns in experimentally infected animals to those observed in both symptomatic and asymptomatic animals in primate centers suggests that BSE contamination of zoo animals may have been more widespread than is generally appreciated.

Orientation-dependent and sequence-specific expansions of CTG/CAG trinucleotide repeats in Saccharomyces cerevisiae

A quantitative and selective genetic assay was developed to monitor expansions of trinucleotide repeats (TNRs) in yeast. A promoter containing 25 repeats allows expression of a URA3 reporter gene and yields sensitivity to the drug 5-fluoroorotic acid. Expansion of the TNR to 30 or more repeats turns off URA3 and provides drug resistance. When integrated at either of two chromosomal loci, expansion rates were 1 × 10−5 to 4 × 10−5 per generation if CTG repeats were replicated on the lagging daughter strand. PCR analysis indicated that 5–28 additional repeats were present in 95% of the expanded alleles. No significant changes in CTG expansion rates occurred in strains deficient in the mismatch repair gene MSH2 or the recombination gene RAD52. The frequent nature of CTG expansions suggests that the threshold number for this repeat is below 25 in this system. In contrast, expansions of the complementary repeat CAG occurred at 500- to 1,000-fold lower rates, similar to a randomized (C,A,G) control sequence. When the reporter plasmid was inverted within the chromosome, switching the leading and lagging strands of replication, frequent expansions were observed only when CTG repeats resided on the lagging daughter strand. Among the rare CAG expansions, the largest gain in tract size was 38 repeats. The control repeats CTA and TAG showed no detectable rate of expansions. The orientation-dependence and sequence-specificity data support the model that expansions of CTG and CAG tracts result from aberrant DNA replication via hairpin-containing Okazaki fragments.

Synpolydactyly phenotypes correlate with size of expansions in HOXD13 polyalanine tract

Synpolydactyly (SPD) is a dominantly inherited congenital limb malformation. Typical cases have 3/4 finger and 4/5 toe syndactyly, with a duplicated digit in the syndactylous web, but incomplete penetrance and variable expressivity are common. The condition has recently been shown to be caused by expansions of an imperfect trinucleotide repeat sequence encoding a 15-residue polyalanine tract in HOXD13. We have studied 16 new and 4 previously published SPD families, with between 7 and 14 extra residues in the tract, to analyze the molecular basis for the observed variation in phenotype. Although there is no evidence of change in expansion size within families, even over six generations, there is a highly significant increase in the penetrance and severity of phenotype with increasing expansion size, affecting both hands (P = 0.012) and feet (P < 0.00005). Affected individuals from a family with a 14-alanine expansion, the largest so far reported, all have a strikingly similar and unusually severe limb phenotype, involving the first digits and distal carpals. Affected males from this family also have hypospadias, not previously described in SPD, but consistent with HOXD13 expression in the developing genital tubercle. The remarkable correlation between phenotype and expansion size suggests that expansion of the tract leads to a specific gain of function in the mutant HOXD13 protein, and has interesting implications for the role of polyalanine tracts in the control of transcription.

Sequence variation in the Fanconi anemia gene FAA

Fanconi anemia (FA) is a genetically heterogeneous autosomal recessive syndrome associated with chromosomal instability, hypersensitivity to DNA crosslinking agents, and predisposition to malignancy. The gene for FA complementation group A (FAA) recently has been cloned. The cDNA is predicted to encode a polypeptide of 1,455 amino acids, with no homologies to any known protein that might suggest a function for FAA. We have used single-strand conformational polymorphism analysis to screen genomic DNA from a panel of 97 racially and ethnically diverse FA patients from the International Fanconi Anemia Registry for mutations in the FAA gene. A total of 85 variant bands were detected. Forty-five of the variants are probably benign polymorphisms, of which nine are common and can be used for various applications, including mapping studies for other genes in this region of chromosome 16q. Amplification refractory mutation system assays were developed to simplify their detection. Forty variants are likely to be pathogenic mutations. Seventeen of these are microdeletions/microinsertions associated with short direct repeats or homonucleotide tracts, a type of mutation thought to be generated by a mechanism of slipped-strand mispairing during DNA replication. A screening of 350 FA probands from the International Fanconi Anemia Registry for two of these deletions (1115–1118del and 3788–3790del) revealed that they are carried on about 2% and 5% of the FA alleles, respectively. 3788–3790del appears in a variety of ethnic groups and is found on at least two different haplotypes. We suggest that FAA is hypermutable, and that slipped-strand mispairing, a mutational mechanism recognized as important for the generation of germ-line and somatic mutations in a variety of cancer-related genes, including p53, APC, RB1, WT1, and BRCA1, may be a major mechanism for FAA mutagenesis.

The yeast Cac1 protein is required for the stable inheritance of transcriptionally repressed chromatin at telomeres

Cac1p is a subunit of yeast chromatin assembly factor I (yCAF-I) that is thought to assemble nucleosomes containing diacetylated histones onto newly replicated DNA [Kaufman, P. D., Kobayashi, R. & Stillman, B. (1997) Genes Dev. 11, 345–357]. Although cac1Δ cells could establish and maintain transcriptional repression at telomeres, they displayed a reduced heritability of the repressed state. Single-cell analysis revealed that individual cac1Δ cells switch from transcriptionally “off” to transcriptionally “on” more often per cell cycle than wild-type cells. In addition, cac1Δ cells were defective for transcriptional silencing near internal tracts of C1–3A sequence, but they showed no defect in silencing at the silent mating type loci when analyzed by a reverse transcription–PCR assay. Despite the loss of transcriptional silencing at telomeres and internal C1–3A tracts, subtelomeric DNA was organized into nucleosomes that had all of the features characteristic of silent chromatin, such as hypoacetylation of histone H4 and protection from methylation by the Escherichia coli dam methylase. Thus, these features of silent chromatin are not sufficient for stable maintenance of a silent chromatin state. We propose that the inheritance of the transcriptionally repressed state requires the specific pattern of histone acetylation conferred by yCAF-I-mediated nucleosome assembly.

Histone H1 Reduces the Frequency of Initiation in Xenopus Egg Extract by Limiting the Assembly of Prereplication Complexes on Sperm Chromatin

Somatic histone H1 reduces both the rate and extent of DNA replication in Xenopus egg extract. We show here that H1 inhibits replication directly by reducing the number of replication forks, but not the rate of fork progression, in Xenopus sperm nuclei. Density substitution experiments demonstrate that those forks that are active in H1 nuclei elongate to form large tracts of fully replicated DNA, indicating that inhibition is due to a reduction in the frequency of initiation and not the rate or extent of elongation. The observation that H1 dramatically reduces the number of replication foci in sperm nuclei supports this view. The establishment of replication competent DNA in egg extract requires the assembly of prereplication complexes (pre-RCs) on sperm chromatin. H1 reduces binding of the pre-RC proteins, XOrc2, XCdc6, and XMcm3, to chromatin. Replication competence can be restored in these nuclei, however, only under conditions that promote the loss of H1 from chromatin and licensing of the DNA. Thus, H1 inhibits replication in egg extract by preventing the assembly of pre-RCs on sperm chromatin, thereby reducing the frequency of initiation. These data raise the interesting possibility that H1 plays a role in regulating replication origin use during Xenopus development.

Analysis of microsatellite mutations in the mitochondrial DNA of Saccharomyces cerevisiae

In the nuclear genome of Saccharomyces cerevisiae, simple, repetitive DNA sequences (microsatellites) mutate at rates much higher than nonrepetitive sequences. Most of these mutations are deletions or additions of repeat units. The yeast mitochondrial genome also contains many microsatellites. To examine the stability of these sequences, we constructed a reporter gene (arg8m) containing out-of-frame insertions of either poly(AT) or poly(GT) tracts within the coding sequence. Yeast strains with this reporter gene inserted within the mitochondrial genome were constructed. Using these strains, we showed that poly(GT) tracts were considerably less stable than poly(AT) tracts and that alterations usually involved deletions rather than additions of repeat units. In contrast, in the nuclear genome, poly(GT) and poly(AT) tracts had similar stabilities, and alterations usually involved additions rather than deletions. Poly(GT) tracts were more stable in the mitochondria of diploid cells than in haploids. In addition, an msh1 mutation destabilized poly(GT) tracts in the mitochondrial genome.