Separation of oxidatively damaged DNA Nucleobases and Nucleosides on Packed and Monolith C18 Columns by HPLC-UV-EC

This study involves the incorporation of a commercially available Phenomenex Onyx C18 monolith column into the separation and detection of oxidative DNA damage. It includes thorough investigation of monolith performance and a comparison of the performance of monolith columns with a commercially available packed Restek reverse phase Ultra C18 column for the separation of DNA bases and nucleosides. The performance of the monolith was examined using efficiency, resolution, plate height, asymmetry and retention times, and in each case showed improved or at least comparable results in the separation of a mix of DNA bases and nucleosides. A 90% reduction, from just under 40 min. to just under 4 min., was obtained in the elution time of this separation. To the best of our knowledge, this is the first report of a fast monolith column separation successfully coupled to both a UV-vis and EC detector, which is especially useful for analysis of oxidative DNA damage. The determination of 8-oxoG and 8-OH-dG, oxidation products of guanine and 2’-deoxyguanosine, respectively, may be compromised by their ease of oxidation and therefore the fast separation, selective and sensitive detection, with no artifactual oxidation, detailed in this report, is ideal

Towards a Molecular Inventory of Protostellar Discs

The chemical environment in circumstellar discs is a unique diagnostic of the thermal, physical and chemical environment. In this paper we examine the structure of star formation regions giving rise to low mass stars, and the chemical environment inside them, and the circumstellar discs around the developing stars.Comment: 9 page PDF, 550 kbyte

Nickel(II)-catalysed oxidative guanine and DNA damage beyond 8-oxoguanine

Oxidative DNA damage is one of the most important and most studied mechanisms of disease. It has been associated with a range of terminal diseases such as cancer, heart disease, hepatitis, and HIV, as well as with a variety of everyday ailments. There are various mechanisms by which this type of DNA damage can be initiated, through radiation and chemical oxidation, among others; however, these mechanisms have yet to be fully elucidated. A HPLC-UV-EC study of the oxidation of DNA mediated by nickel(II) obtained results that show an erratic, almost oscillatory formation of 8-oxoguanine (8-oxoG) from free guanine and from guanine in DNA. Sporadic 8-oxoG concentrations were also observed when 8-oxoG alone was subjected to these conditions. A HPLC-MS/MS study showed the formation of oxidised-guanidinohydantoin (oxGH) from free guanine at pH 11, and the formation of guanidinohydantoin (GH) from DNA at pH 5.5

Analysis of earthquake body wave spectra for potency and magnitude values: implications for magnitude scaling relations

We develop a simple methodology for reliable automated estimation of the low-frequency asymptote in seismic body wave spectra of small to moderate local earthquakes. The procedure corrects individual P- and S-wave spectra for propagation and site effects and estimates the seismic potency from a stacked spectrum. The method is applied to >11 000 earthquakes with local magnitudes 0 < M_L < 4 that occurred in the Southern California plate-boundary region around the San Jacinto fault zone during 2013. Moment magnitude M_w values, derived from the spectra and the scaling relation of Hanks & Kanamori, follow a Gutenberg–Richter distribution with a larger b-value (1.22) from that associated with the M_L values (0.93) for the same earthquakes. The completeness magnitude for the M_w values is 1.6 while for M_L it is 1.0. The quantity (M_w – M_L) linearly increases in the analysed magnitude range as M_L decreases. An average earthquake with M_L = 0 in the study area has an M_w of about 0.9. The developed methodology and results have important implications for earthquake source studies and statistical seismology

TarO : a target optimisation system for structural biology

This work was funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) Structural Proteomics of Rational Targets (SPoRT) initiative, (Grant BBS/B/14434). Funding to pay the Open Access publication charges for this article was provided by BBSRC.TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC Structural Proteomics of Rational Targets initiative.Publisher PDFPeer reviewe

MP745: A Long-Term Study of an Oak Pine Forest Ecosystem: A Brief Overview of the Holt Research Forest

This publication provides an overview of the long-term forest ecosystem project at the Holt Research Forest in Arrowsic, Maine. It is based on nearly 16 years of work by an interdisciplinary team from the College of Natural Sciences, Forestry, and Agriculture, including faculty, professional staff, visiting scientists, University of Maine graduate students, and undergraduate field assistants. We hope this publication will be useful to other researchers, to our workshop participants, and to others interested in forest ecosystem science.https://digitalcommons.library.umaine.edu/aes_miscpubs/1029/thumbnail.jp

Analysis of earthquake body wave spectra for potency and magnitude values: implications for magnitude scaling relations

We develop a simple methodology for reliable automated estimation of the low-frequency asymptote in seismic body wave spectra of small to moderate local earthquakes. The procedure corrects individual P- and S-wave spectra for propagation and site effects and estimates the seismic potency from a stacked spectrum. The method is applied to >11 000 earthquakes with local magnitudes 0 < M_L < 4 that occurred in the Southern California plate-boundary region around the San Jacinto fault zone during 2013. Moment magnitude M_w values, derived from the spectra and the scaling relation of Hanks & Kanamori, follow a Gutenberg–Richter distribution with a larger b-value (1.22) from that associated with the M_L values (0.93) for the same earthquakes. The completeness magnitude for the M_w values is 1.6 while for M_L it is 1.0. The quantity (M_w – M_L) linearly increases in the analysed magnitude range as M_L decreases. An average earthquake with M_L = 0 in the study area has an M_w of about 0.9. The developed methodology and results have important implications for earthquake source studies and statistical seismology

Obligate Heterodimerization of the Archaeal Alba2 Protein with Alba1 Provides a Mechanism for Control of DNA Packaging

SummaryOrganisms growing at elevated temperatures face a particular challenge to maintain the integrity of their genetic material. All thermophilic and hyperthermophilic archaea encode one or more copies of the Alba (Sac10b) gene. Alba is an abundant, dimeric, highly basic protein that binds cooperatively and at high density to DNA. Sulfolobus solfataricus encodes a second copy of the Alba gene, and the Alba2 protein is expressed at ∼5% of the level of Alba1. We demonstrate by NMR, ITC, and crystallography that Alba2 exists exclusively as a heterodimer with Alba1 at physiological concentrations and that heterodimerization exerts a clear effect upon the DNA packaging, as observed by EM, potentially by changing the interface between adjacent Alba dimers in DNA complexes. A functional role for Alba2 in modulation of higher order chromatin structure and DNA condensation is suggested

Biofortification of UK food crops with selenium

Se is an essential element for animals. In man low dietary Se intakes are associated with health disorders including oxidative stress-related conditions, reduced fertility and immune functions and an increased risk of cancers. Although the reference nutrient intakes for adult females and males in the UK are 60 and 75 μg Se/d respectively, dietary Se intakes in the UK have declined from >60 μg Se/d in the 1970s to 35 μg Se/d in the 1990s, with a concomitant decline in human Se status. This decline in Se intake and status has been attributed primarily to the replacement of milling wheat having high levels of grain Se and grown on high-Se soils in North America with UK-sourced wheat having low levels of grain Se and grown on low-Se soils. An immediate solution to low dietary Se intake and status is to enrich UK-grown food crops using Se fertilisers (agronomic biofortification). Such a strategy has been adopted with success in Finland. It may also be possible to enrich food crops in the longer term by selecting or breeding crop varieties with enhanced Se-accumulation characteristics (genetic biofortification). The present paper will review the potential for biofortification of UK food crops with Se