Biochemical analysis of mouse FKBP60, a novel member of the FKPB family.

We have identified mouse and human FKBP60, a new member of the FKBP gene family. FKBP60 shares strongest homology with FKBP65 and SMAP. FKBP60 contains a hydrophobic signal peptide at the N-terminus, 4 peptidyl-prolyl cis/trans isomerase (PPIase) domains and an endoplasmic reticulum retention motif (HDEL) at the C-terminus. Immunodetection of HA-tagged FKBP60 in NIH-3T3 cells suggests that FKBP60 is segregated to the endoplasmic reticulum. Northern blot analysis shows that FKBP60 is predominantly expressed in heart, skeletal muscle, lung, liver and kidney. With N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide as a substrate, recombinant GST-FKBP60 is shown to accelerate effectively the isomerization of the peptidyl-prolyl bond. This isomerization activity is inhibited by FK506. mFKBP60 binds Ca2+ in vitro, presumably by its C-terminal EF-hand Ca2+ binding motif, and is phosphorylated in vivo. hFKBP60 has been mapped to 7p12 and/or 7p14 by fluorescence in situ hybridization (FISH).     

Arteriovenous malformation of the stomach

A patient with chronic anemia is presented who radiologically showed prominent rugae of the stomach. Angiography demonstrated an arteriovenous malformation with a large feeding artery and prominent draining veins.     

Habitat suitability of the Wadden Sea for restoration of Zostera marina beds

A conceptual model is proposed, describing potential Zostera marina habitats in the Wadden Sea, based on reported data from laboratory, mesocosm and field studies. Controlling factors in the model are dynamics, degree of desiccation, turbidity, nutrients and salinity. A distinction has been made between a higher and a lower zone of potential habitats, each suitable for different morphotypes of Z. marina. The model relates the decline of Z. marina in the Wadden Sea to increased sediment and water dynamics, turbidity, drainage of sediments (resulting in increased degree of desiccation) and total nutrient loads during the twentieth century. The upper and lower delineation of both the higher and the lower zone of potential Z. marina habitats appear to be determined by one or a combination of several of these factors. Environmental changes in one of these factors will therefore influence the borderlines of the zones. The lower zone of Z. marina will be mainly affected by increased turbidity, sediment dynamics, degree of desiccation during low tide and nutrient load. The higher zone will be affected by increases in water and sediment dynamics, desiccation rates and nutrient loads. Potential Z. marina habitats are located above approx. –0.80 m mean sea level (when turbidity remains at the same level as in the early 1990s) in sheltered, undisturbed locations, and preferably where some freshwater influence is present. At locations with a high, near-marine, salinity, the nutrient load has to be low to allow the growth of Z. marina. The sediment should retain enough water during low tide to keep the plants moist. Our results suggest that the return of Z. marina beds within a reasonable time-scale will require not only suitable habitat conditions, but also revegetation measures, as the changes in the environment resulting from the disappearance of Z. marina may impede its recovery, and the natural import of propagules will be unlikely. Furthermore, the lower zone of Z. marina may require a genotype that is no longer found in the Wadden Sea. Received: 26 April 1999 / Received in revised form: 15 October 1999 / Accepted: 16 October 1999     

The p53 isoforms are differentially modified by Mdm2

The discovery that the single p53 gene encodes several different p53 protein isoforms has initiated a flurry of research into the function and regulation of these novel p53 proteins. Full-length p53 protein level is primarily regulated by the E3-ligase Mdm2, which promotes p53 ubiquitination and degradation. Here, we report that all of the novel p53 isoforms are ubiquitinated and degraded to varying degrees in an Mdm2-dependent and -independent manner, and that high-risk human papillomavirus can degrade some but not all of the novel isoforms, demonstrating that full-length p53 and the p53 isoforms are differentially regulated. In addition, we provide the first evidence that Mdm2 promotes the NEDDylation of p53β. Altogether, our data indicates that Mdm2 can distinguish between the p53 isoforms and modify them differently.     

Comparison of bone marrow extracellular matrices.

We have compared the structure and composition of adult and fetal bovine bone marrow extracellular matrices. In contrast to fetal bone marrow, adult bone marrow has more oval fenestration and accumulation of adipocytes as well as lower protein content. These differences could be due to remodeling of bone marrow tissue as it develops. Zymogram analysis of matrix metalloproteinase (MMP) and tissue inhibitor of MMP (TIMP) activities showed that fetal, but not adult bone marrow extract contained a 96-kDa MMP and TIMP-1 and -2. These activities may contribute to the structural differences between adult and fetal bone marrow tissues.     

DFT studies of the phenol adsorption on boron nitride sheets

We perform first principles total energy calculations to investigate the atomic structures of the adsorption of phenol (C₆H₅OH) on hexagonal boron nitride (BN) sheets. Calculations are done within the density functional theory as implemented in the DMOL code. Electron-ion interactions are modeled according to the local-spin-density-approximation (LSDA) method with the Perdew-Wang parametrization. Our studies take into account the hexagonal h-BN sheets and the modified by defects d-BN sheets. The d-BN sheets are composed of one hexagon, three pentagons and three heptagons. Five different atomic structures are investigated: parallel to the sheet, perpendicular to the sheet at the B site, perpendicular to the sheet at the N site, perpendicular to the central hexagon and perpendicular to the B-N bond (bridge site). To determine the structural stability we apply the criteria of minimum energy and vibration frequency. After the structural relaxation phenol molecules adsorb on both h-BN and d-BN sheets. Results of the binding energies indicate that phenol is chemisorbed. The polarity of the system increases as a consequence of the defects presence which induces transformation from an ionic to covalent bonding. The elastic properties on the BN structure present similar behavior to those reported in the literature for graphene.     

The risks of using the chi-square periodogram to estimate the period of biological rhythms

The chi-square periodogram (CSP), developed over 40 years ago, continues to be one of the most popular methods to estimate the period of circadian (circa 24-h) rhythms. Previous work has indicated the CSP is sometimes less accurate than other methods, but understanding of why and under what conditions remains incomplete. Using simulated rhythmic time-courses, we found that the CSP is prone to underestimating the period in a manner that depends on the true period and the length of the time-course. This underestimation bias is most severe in short time-courses (e.g., 3 days), but is also visible in longer simulated time-courses (e.g., 12 days) and in experimental time-courses of mouse wheel-running and ex vivo bioluminescence. We traced the source of the bias to discontinuities in the periodogram that are related to the number of time-points the CSP uses to calculate the observed variance for a given test period. By revising the calculation to avoid discontinuities, we developed a new version, the greedy CSP, that shows reduced bias and improved accuracy. Nonetheless, even the greedy CSP tended to be less accurate on our simulated time-courses than an alternative method, namely the Lomb-Scargle periodogram. Thus, although our study describes a major improvement to a classic method, it also suggests that users should generally avoid the CSP when estimating the period of biological rhythms.