Von Hippel-Lindau disease: identification of deletion mutations by pulsed-field gel electrophoresis

Von Hippel-Lindau disease (VHL) is an inherited multisystem neoplastic disorder. We prepared a 2.5-megabase (Mb) restriction map of the region surrounding the VHL gene and identified and characterized overlapping deletions in three unrelated patients affected with VHL. The smallest nested deletion (100 kb) was located within a 510-kb NruI fragment detected by 19–63. The rearrangements detected will be useful in isolating and evaluating candidate cDNAs for the VHL gene. The detailed physical map will be useful in studying the organization and structure of genes in the VHL region.     

THE FINE STRUCTURE OF GREEN BACTERIA

The fine structure of several strains of green bacteria belonging to the genus Chlorobium has been studied in thin sections with the electron microscope. In addition to having general cytological features typical of Gram-negative bacteria, the cells of these organisms always contain membranous mesosomal elements, connected with the cytoplasmic membrane, and an elaborate system of isolated cortical vesicles, some 300 to 400 A wide and 1000 to 1500 A long. The latter structures, chlorobium vesicles, have been isolated in a partly purified state by differential centrifugation of cell-free extracts. They are associated with a centrifugal fraction that has a very high specific chlorophyll content. In all probability, therefore, the chlorobium vesicles are the site of the photosynthetic apparatus of green bacteria.     

Reduced Lysis upon Growth of Lactococcus lactis on Galactose Is a Consequence of Decreased Binding of the Autolysin AcmA

When Lactococcus lactis subsp. lactis IL1403 or L. lactis subsp. cremoris MG1363 is grown in a medium with galactose as the carbon source, the culture lyses to a lesser extent in stationary phase than when the bacteria are grown in a medium containing glucose. Expression of AcmA, the major autolysin of L. lactis, is not influenced by the carbon source. Binding studies with a fusion protein consisting of the MSA2 protein of Plasmodium falciparum and the C-terminal peptidoglycan-binding domain of AcmA revealed that cell walls of cells from both subspecies grown on galactose bind less AcmA than cell walls of cells grown on glucose. Cells grown on glucose or galactose and treated with trichloroacetic acid prior to AcmA binding bind similar amounts of AcmA. Analysis of the composition of the lipoteichoic acids (LTAs) of L. lactis IL1403 cells grown on glucose or galactose showed that the LTA composition is influenced by the carbon source: cells grown on galactose contain LTA with less galactose than cells grown on glucose. In conclusion, growth of L. lactis on galactose changes the LTA composition in the cell wall in such a way that less AcmA is able to bind to the peptidoglycan, resulting in a decrease in autolysis.     

Fluorinated indazoles as novel selective inhibitors of nitric oxide synthase (NOS): Synthesis and biological evaluation

In order to find new compounds with neuroprotective activity and NOS-I/NOS-II selectivity, we have designed, synthesized, and characterized 14 new NOS inhibitors with an indazole structure. The first group corresponds to 4,5,6,7-tetrahydroindazoles (4–8), the second to the N-methyl derivatives (9–12) of 7-nitro-1H-indazole (1) and 3-bromo-7-nitro-1H-indazole (2), and the latter to 4,5,6,7-tetrafluoroindazoles (13–17). Compound 13 (4,5,6,7-tetrafluoro-3-methyl-1H-indazole) inhibited NOS-I by 63% and NOS-II by 83%. Interestingly, compound 16 (4,5,6,7-tetrafluoro-3-perfluorophenyl-1H-indazole) inhibited NOS-II activity by 80%, but it did not affect to NOS-I activity. Structural comparison between these new indazoles further supports the importance of the aromatic indazole skeleton for NOS inhibition and indicate that bulky groups or N-methylation of 1 and 2 diminish their effect on NOS activity. The fluorination of the aromatic ring increased the inhibitory potency and NOS-II selectivity, suggesting that this is a promising strategy for NOS selective inhibitors.     

High-resolution structure and biochemical properties of a recombinant Proteus mirabilis catalase depleted in iron

Heme catalases are homotetrameric enzymes with a highly conserved complex quaternary structure, and their functional role is still not well understood. Proteus mirabilis catalase (PMC), a heme enzyme belonging to the family of NADPH-binding catalases, was efficiently overexpressed in E. coli. The recombinant catalase (rec PMC) was deficient in heme with one-third heme and two-thirds protoporphyrin IX as determined by mass spectrometry and chemical methods. This ratio was influenced by the expression conditions, but the enzyme-specific activity calculated relative to the heme content remained unchanged. The crystal structure of rec PMC was solved to a resolution of 2.0 A, the highest resolution obtained to date with PMC. The overall structure was quite similar to that of wild-type PMC, and it is surprising that the absence of iron had no effect on the structure of the active site. Met 53 close to the essential His 54 was found less oxidized in rec PMC than in the wild-type enzyme. An acetate anion was modeled in an anionic pocket, away from the heme group but important for the enzymatic reaction. An alternate conformation observed for Arg 99 could play a role in the formation of the H-bond network connecting two symmetrical subunits of the tetramer.     

Brain-derived neurotrophic factor gene Val66Met polymorphism modulates reversible cerebral vasoconstriction syndromes

Background

Reversible cerebral vasoconstriction syndrome (RCVS) could be complicated by cerebral ischemic events. Hypothetical mechanisms of RCVS involve endothelial dysfunction and sympathetic overactivity, both of which were reported to be related to brain-derived neurotrophic factor (BDNF). The study investigated the association between functional BDNF Val66Met polymorphism and RCVS.

Methods

Patients with RCVS and controls were prospectively recruited and genotyped for the BDNF Val66Met polymorphism. Magnetic resonance angiography (MRA) and transcranial color-coded Doppler sonography were employed to evaluate cerebral vasoconstriction. Genotyping results, clinical parameters, vasoconstriction scores, mean flow velocities of the middle cerebral artery (V_MCA), and Lindegaard indices were analyzed. Split-sample approach was employed to internally validate the data.

Principal Findings

Ninety Taiwanese patients with RCVS and 180 age- and gender-matched normal controls of the same ethnicity completed the study. The genotype frequencies did not differ between patients and controls. Compared to patients with Met/Met homozygosity, patients with Val allele had higher mean vasoconstriction scores of all arterial segments (1.60±0.72 vs. 0.87±0.39, p<0.001), V_MCA values (116.7±36.2 vs. 82.7±17.9 cm/s, p<0.001), and LI (2.41±0.91 vs. 1.89±0.41, p = 0.001). None of the Met/Met homozygotes, but 38.9% of the Val carriers, had V_MCA values of >120 cm/s (p<0.001). Split-sample validation by randomization, age, entry time or residence of patients demonstrated concordant findings.

Conclusions

Our findings link BDNF Val66Met polymorphism with the severity of RCVS for the first time and implicate possible pathogenic mechanisms for vasoconstriction in RCVS.     

Bacterial endophytes: recent developments and applications.

Endophytic bacteria have been found in virtually every plant studied, where they colonize the internal tissues of their host plant and can form a range of different relationships including symbiotic, mutualistic, commensalistic and trophobiotic. Most endophytes appear to originate from the rhizosphere or phyllosphere; however, some may be transmitted through the seed. Endophytic bacteria can promote plant growth and yield and can act as biocontrol agents. Endophytes can also be beneficial to their host by producing a range of natural products that could be harnessed for potential use in medicine, agriculture or industry. In addition, it has been shown that they have the potential to remove soil contaminants by enhancing phytoremediation and may play a role in soil fertility through phosphate solubilization and nitrogen fixation. There is increasing interest in developing the potential biotechnological applications of endophytes for improving phytoremediation and the sustainable production of nonfood crops for biomass and biofuel production.     

Chronomics analysis toolkit (CATkit)

Chronomics, and the study of biological rhythms, is a rapidly growing area of study. As biological researchers transition to awareness of the impact biological oscillators have on experimental outcomes, and the need to design experiments around genetic, molecular, physiological, and behavioral rhythms, there is increasing need to identify and characterize rhythmicity. There is a corresponding increase in demand for accessible software tools to analyze data for rhythms, both macroscopically and quantitatively. The chronomics analysis toolkit (CATkit), an R package for analysis of periodicities in time series, is a free and open source suite of rhythm analysis tools that runs on UNIX, Windows, and Macintosh platforms. It is particularly well suited to the often scarce, frequently noisy, biological data, and is also applicable to long and/or denser records. CATkit includes a variety of tools, providing visualization and inspection tools to aid in determining whether data meet key assumptions for analysis; as well as quantitative assessment, by cosinor, of mean, amplitude and phase at an assumed period (or periods), with a measure of uncertainty for each parameter.     

Molecular Mechanics: The Cross-conjugated Carbonyl Group in Heterocyclic Compounds. 2. Parameterisation (MM2) of the Adjacent C-O and C-N Bonds

The definition, in a previous paper, of a new type of carbon atom (type 44) in the MM2 force field, i.e. when it is cross-conjugated, implies the reparameterisation of the bonds adjacent to the carbonyl bond. By means of a statistical study based on data issued from the Cambridge Structural Data System, we propose here new σ dipole moments and new stretching parameters for the C(44)-O(41) and C(44)-N(40) bonds included in heterocyclic compounds. These stretching parameters, which are π-bond-order dependent, are quite satisfactory (mean of unsigned deviations: 0.023Å) within limited π-bond-order ranges: 0.25 to 0.32 for the C-O bond, 0.37 to 0.53, for the C-N bond. As for the C(44)=O(7) bond the parameters are generally inappropriate for compounds in which both atoms connected to the type 44 carbon are heteroatoms. The maximum deviation from the experimental bond length, for both bond types can reach ±0.03Å. Here also, part of the dispersion of the results could be attributed to the variation of the effective dielectric constant D from one crystal to another.