N-terminal amino acid sequence and some properties of isopenicillin-N synthetase from Cephalosporium acremonium

AbstractIsopenicillin-N synthetase (IPNS) was purified to homogeneity from Cephalosporium acremonium C0728. The enzyme existed in two states during purification; an oxidised state with a disulphide linkage and its reduced state. These two forms can be interconverted in the presence or absence of thiol agents, and separated by fast protein liquid chromatography (FPLC) with the strong anion exchange Mono-Q column. The enzyme is a monomer with a molecular mass of 38 kDa and pI 5.05. The first 50 amino acid N-terminal sequence of the enzyme was determined. The purified enzyme has an absolute requirement of Fe2+ and a 2-electron donor for activity

An Atlas of Computed Equivalent Widths of Quasar Broad Emission Lines

We present graphically the results of several thousand photoionization calculations of broad emission line clouds in quasars, spanning seven orders of magnitude in hydrogen ionizing flux and particle density. The equivalent widths of 42 quasar emission lines are presented as contours in the particle density - ionizing flux plane for a typical incident continuum shape, solar chemical abundances, and cloud column density of $N(H) = 10^{23} cm^{-2}$. Results are similarly given for a small subset of emission lines for two other column densities ($10^{22} cm^{-2}$ and $10^{24} cm^{-2}$), five other incident continuum shapes, and a gas metallicity of 5 \Zsun. These graphs should prove useful in the analysis of quasar emission line data and in the detailed modeling of quasar broad emission line regions. The digital results of these emission line grids and many more are available over the Internet.Comment: 16 pages, LaTeX (AASTeX aaspp4.sty); to appear in the 1997 ApJS: full contents of the 9 photoionization grids presented in this paper may be found at http://www.pa.uky.edu/~korista/grids/grids.htm

High Metal Enrichments in Luminous Quasars

We discuss observations of the broad emission line in luminous intermediate redshift quasars, with emphasis on Q0207 -398. This object has relatively sharp lines, allowing us to deconvolve the profiles into distinct components. In this paper we examine the high ionization region, which we show must be matter-bounded, partially transparent to ionizing radiation. We measure a large N V λ1240/He II λ1640 ratio in Q0207-398, but detailed calculations predict this ratio to be ~1 for standard cloud properties. We show that no choice of incident continuum, ionizing photon flux, density, or even the appeal to nonradiative energy sources, can reproduce the observed N V, C IV, O VI, He II spectrum with solar abundances. The intensity of the N V line is sensitive to the abundance of the gas because the abundance of nitrogen, a secondary element goes up roughly as the square of the metallicity. The lowest metallicity capable of reproducing the N V spectrum in Q0207 - 398 is Z ~ 5 Z☉, consistent with that inferred to exist in the cores of massive galaxies after epochs of rapid star formation. Our final model of the high-ionization emission region is one with many properties similar to those inferred for broad absorption-line QSO absorption-line clouds

Large-scale identification of polymorphic microsatellites using an in silico approach

<p>Abstract</p> <p>Background</p> <p>Simple Sequence Repeat (SSR) or microsatellite markers are valuable for genetic research. Experimental methods to develop SSR markers are laborious, time consuming and expensive. <it>In silico </it>approaches have become a practicable and relatively inexpensive alternative during the last decade, although testing putative SSR markers still is time consuming and expensive. In many species only a relatively small percentage of SSR markers turn out to be polymorphic. This is particularly true for markers derived from expressed sequence tags (ESTs). In EST databases a large redundancy of sequences is present, which may contain information on length-polymorphisms in the SSR they contain, and whether they have been derived from heterozygotes or from different genotypes. Up to now, although a number of programs have been developed to identify SSRs in EST sequences, no software can detect putatively polymorphic SSRs.</p> <p>Results</p> <p>We have developed PolySSR, a new pipeline to identify polymorphic SSRs rather than just SSRs. Sequence information is obtained from public EST databases derived from heterozygous individuals and/or at least two different genotypes. The pipeline includes PCR-primer design for the putatively polymorphic SSR markers, taking into account Single Nucleotide Polymorphisms (SNPs) in the flanking regions, thereby improving the success rate of the potential markers. A large number of polymorphic SSRs were identified using publicly available EST sequences of potato, tomato, rice, <it>Arabidopsis</it>, <it>Brassica </it>and chicken.</p> <p>The SSRs obtained were divided into long and short based on the number of times the motif was repeated. Surprisingly, the frequency of polymorphic SSRs was much higher in the short SSRs.</p> <p>Conclusion</p> <p>PolySSR is a very effective tool to identify polymorphic SSRs. Using PolySSR, several hundred putative markers were developed and stored in a searchable database. Validation experiments showed that almost all markers that were indicated as putatively polymorphic by polySSR were indeed polymorphic. This greatly improves the efficiency of marker development, especially in species where there are low levels of polymorphism, like tomato. When combined with the new sequencing technologies PolySSR will have a big impact on the development of polymorphic SSRs in any species.</p> <p>PolySSR and the polymorphic SSR marker database are available from <url>http://www.bioinformatics.nl/tools/polyssr/</url>.</p

What characteristics of primary care and patients are associated with early death in patients with lung cancer in the UK?

Background: The UK has poor lung cancer survival rates and high early mortality, compared to other countries. We aimed to identify factors associated with early death, and features of primary care that might contribute to late diagnosis. Methods: All cases of lung cancer diagnosed between 2000 and 2013 were extracted from The Health Improvement Network database. Patients who died within 90 days of diagnosis were compared with those who survived longer. Standardised chest X-ray (CXR) and lung cancer rates were calculated for each practice. Results: Of 20 142 people with lung cancer, those who died early consulted with primary care more frequently prediagnosis. Individual factors associated with early death were male sex (OR 1.17; 95% CI 1.10 to 1.24), current smoking (OR 1.43; 95% CI 1.28 to 1.61), increasing age (OR 1.80; 95% CI 1.62 to 1.99 for age ≥80 years compared to 65–69 years), social deprivation (OR 1.16; 95% CI 1.04 to 1.30 for Townsend quintile 5 vs 1) and rural versus urban residence (OR 1.22; 95% CI 1.06 to 1.41). CXR rates varied widely, and the odds of early death were highest in the practices which requested more CXRs. Lung cancer incidence at practice level did not affect early deaths. Conclusions: Patients who die early from lung cancer are interacting with primary care prediagnosis, suggesting potentially missed opportunities to identify them earlier. A general increase in CXR requests may not improve survival; rather, a more timely and appropriate targeting of this investigation using risk assessment tools needs further assessment

Constraint-based probabilistic learning of metabolic pathways from tomato volatiles

Clustering and correlation analysis techniques have become popular tools for the analysis of data produced by metabolomics experiments. The results obtained from these approaches provide an overview of the interactions between objects of interest. Often in these experiments, one is more interested in information about the nature of these relationships, e.g., cause-effect relationships, than in the actual strength of the interactions. Finding such relationships is of crucial importance as most biological processes can only be understood in this way. Bayesian networks allow representation of these cause-effect relationships among variables of interest in terms of whether and how they influence each other given that a third, possibly empty, group of variables is known. This technique also allows the incorporation of prior knowledge as established from the literature or from biologists. The representation as a directed graph of these relationship is highly intuitive and helps to understand these processes. This paper describes how constraint-based Bayesian networks can be applied to metabolomics data and can be used to uncover the important pathways which play a significant role in the ripening of fresh tomatoes. We also show here how this methods of reconstructing pathways is intuitive and performs better than classical techniques. Methods for learning Bayesian network models are powerful tools for the analysis of data of the magnitude as generated by metabolomics experiments. It allows one to model cause-effect relationships and helps in understanding the underlying processes

Testing cosmological variability of the proton-to-electron mass ratio using the spectrum of PKS 0528-250

Multidimensional cosmologies allow for variations of fundamental physical constants over the course of cosmological evolution, and different versions of the theories predict different time dependences. In particular, such variations could manifest themselves as changes of the proton-to-electron mass ratio \mu=m_p/m_e over the period of ~ 10^{10} years since the moment of formation of high-redshift QSO spectra. Here we analyze a new, high-resolution spectrum of the z=2.81080 molecular hydrogen absorption system toward the quasar PKS 0528-250 to derive a new observational constraint to the time-averaged variation rate of the proton-to-electron mass ratio. We find |\dot{\mu} / \mu| < 1.5 \times 10^{-14}/year, which is much tighter than previously measured limits.Comment: 9 pages, 2 tables, 3 figures, LaTeX (aas2pp4.sty and epsf.sty included). To be published in Ap