Determination of oligonucleotide molecular masses by MALDI mass spectrometry

MALDI mass spectrometry (MS) of 14- to 42-mer homogeneous oligonucleotides and their mixtures was carried out using a Vision 2000 instrument (Thermo BioAnalysis, Finnigan, United States). Conditions for the determination of oligonucleotide molecular masses were optimized by applying various matrices and operation modes. The most reproducible results with minimal uncontrolled decomposition of the oligonucleotides including their apurinization during the MALDI MS registration were obtained using 2,4,6-trihydroxyacetophenone as a matrix instead of 3-hydroxypicolinic acid usually employed in the mass spectrometry of oligonucleotides. Our approach allows the determination of molecular masses of oligonucleotides obtained by chemical synthesis and the evaluation of their component composition and purity. It was applied to the mass spectrometric analysis of oligonucleotides containing a 3-(methyl-C-phosphonate) group or a modified 1,N ⁶-ethenodeoxyadenosine unit.__________Translated from Bioorganicheskaya Khimiya, Vol. 31, No. 2, 2005, pp. 151–158.Original Russian Text Copyright © 2005 by Streletskii, Kozlova, Esipov, Kayushin, Korosteleva, Esipov.     

Land application of treated sewage sludge: quantifying pathogen risks from consumption of crops

AIMS: To predict the number of humans in the UK infected through consumption of root crops grown on agricultural land to which treated sewage sludge has been applied in accordance with the current regulations and guidance (Safe Sludge Matrix). METHODS AND RESULTS: Quantitative risk assessments based on the source, pathway, receptor approach are developed for seven pathogens, namely salmonellas, Listeria monocytogenes, campylobacters, Escherichia coli O157, Cryptosporidium parvum, Giardia, and enteroviruses. Using laboratory data for pathogen destruction by mesophilic anaerobic digestion, and not extrapolating experimental data for pathogen decay in soil to the full 30-month harvest interval specified by the Matrix, predicts 50 Giardia infections per year, but less than one infection per year for the other six pathogens. Assuming linear decay in the soil, a 12-month harvest interval eliminates the risks from all seven pathogens; the highest predicted being one infection of C. parvum in the UK every 45 years. Computer simulations show that a protective effect from binding of pathogens to particulate matter could potentially exaggerate the observed rate of decay in experimental systems. CONCLUSIONS: The results confirm, assuming pathogens behave according to our current understanding, that the risks to humans from consumption of vegetable crops are remote. Furthermore the harvest intervals stipulated by the Safe Sludge Matrix compensate for potential lapses in the operational efficiency of sludge treatment. SIGNIFICANCE AND IMPACT OF THE STUDY: The models demonstrate the huge potential impact of decay in the soil over the 12/30-month intervals specified by the Matrix, although lack of knowledge on the exact nature of soil decay processes is a source of uncertainty. The models enable the sensitivity of the predicted risks to changes in the operational efficiency of sewage sludge treatment to be assessed.     

Carved trees in grazed forests in boreal Sweden—analysis of remaining trees, interpretation of past land-use and implications for conservation

Culturally modified trees (CMTs) provide unique insights into traditional knowledge and uses of the forest ecosystems. In close relation to pre-industrial livestock herding in central Sweden, it was a custom to carve text and symbols on trees and use them as notice boards in the forest. The main aim of this study was to document and analyse remaining carved trees in a managed forest landscape of 160 km². The same area was surveyed twice, once in 1986 and once in 2003. 488 carved trees were documented and classified into legible themes that were interpreted in the light of past herding practices. Name was the most common theme, found in 85% of the carvings. Most of the carvings were made in the period from the 1750s until the early 1900s. The custom of carving on trees was closely related to important grazing areas and the need to establish rights to them. The main losses of carved trees nowadays are due to their natural death and decay as most of the carved trees are located in areas that are not targeted for management. A primary recommendation for preservation is therefore to continue documentation of the trees because of the noticeable deterioration in readability of the carvings.     

A Modified PCR System for Amplifying <Emphasis Type="Italic">β</Emphasis>-ketoacyl-ACP Synthase Gene Fragments with DNA from <Emphasis Type="Italic">Streptomyces luteogriseus</Emphasis>

Streptomyces luteogriseus strain 099, producing a new type of macrolide antibiotic with anti-coxB6 virus and anti-HIV protease activities, was isolated from soil. PCR was optimized to amplify β-ketoacyl-ACP synthase (KS) genes. The system was optimized around the use of higher concentrations of DMSO (15% vs. 10% v/v) and dNTP (500 μM vs. 50–200 μM) and a lower annealing temperature (55 °C vs. 60–70 °C) than the normal PCR method used to amplify high GC content DNA.     

The small GTPase ADP-ribosylation factor 6 negatively regulates dendritic spine formation

Actin cytoskeletal reorganization and membrane trafficking are important for spine morphogenesis. Here we investigated whether the small GTPase, ADP-ribosylation factor 6 (ARF6), which regulates actin dynamics and peripheral vesicular trafficking, is involved in the regulation of spine formation. The developmental expression pattern of ARF6 in mouse hippocampus was similar to that of the post-synaptic density protein-95, and these molecules colocalized in mouse hippocampal neurons. Overexpression of a constitutively active ARF6 mutant in cultured hippocampal neurons decreased the spine density, whereas a dominant-negative ARF6 mutant increased the density. These results demonstrate a novel function for ARF6 as a key regulator of spine formation.     

An alternatively-spliced exon in the 5'-UTR of human ALAS1 mRNA inhibits translation and renders it resistant to haem-mediated decay

Haem controls its own synthesis in non-erythroid cells primarily by regulation of ALAS1 mRNA stability. Alternative splicing of human ALAS1 generates two mRNAs with different 5'-UTRs: a major one, where exon 1B is omitted, and a minor form containing exon 1B. We show that, unlike the major ALAS1 mRNA, the minor form was resistant to haem-mediated decay. Furthermore, we demonstrate that the ALAS1 5'-UTR alone did not confer haem-mediated decay upon a heterologous mRNA and the inclusion of exon 1B inhibited translation. These data suggest that translation of ALAS1 mRNA itself might be required for destabilisation in response to haem.     

Rapid rates of newly synthesized mitochondrial protein degradation are significantly affected by the generation of mitochondrial free radicals

Exposure of biological material to high levels of free radicals causes extensive cellular damage. Reactive oxygen species (ROS) generated by mitochondria have been associated with a variety of diseases and aging. We investigated the effect of low-level mitochondrial ROS production on newly synthesized mitochondrial proteins which are potentially vulnerable to mitochondrial ROS due to their location and unfolded state. We show that elevated mitochondrial ROS increases the degradation of newly synthesized mitochondrial proteins with some proteins more sensitive than others. In the long term reduced assembly of mitochondrial complexes would affect mitochondrial function and may trigger a vicious cycle of mitochondrial ROS production.     

Responses of keratinocytes to substrate-bound vitronectin: growth factor complexes

Insulin-like growth factor-1 (IGF-I) can associate with the extracellular matrix protein vitronectin (VN) via select IGF-binding proteins, and the resulting complex stimulates responses in a variety of cell types. As VN can also associate with epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF), we hypothesized that the multimeric nature of VN could be exploited to deliver multiple growth factors to the cell surface. We report here that VN enhances bFGF but not EGF stimulated [(3)H]-leucine incorporation in the HaCAT keratinocyte cell line, with VN synergistically enhancing cell migration in response to both EGF and bFGF when presented as a VN-bound complex. Furthermore, the addition of EGF and/or bFGF to IGF-I:IGFBP-5:VN complexes significantly enhances both [(3)H]-leucine incorporation and migration of HaCAT cells above that induced by IGF:IGFBP-5:VN complexes alone. Indeed, similar responses are observed in primary cultures of human skin keratinocytes, highlighting the potential use of these novel complexes for a wide range of tissue repair applications.     

Affinity Modification of the Restriction Endonuclease <Emphasis Type="Italic">Sso</Emphasis>II by 2′-Aldehyde-Containing Double Stranded DNAs

Properties of 2'-aldehyde-containing double stranded DNAs (dsDNAs) have been studied for the first time as substrate analogs of the restriction endonuclease SsoII. These reactive oligonucleotides were successfully cross-linked to the restriction endonuclease SsoII by reductive amination, and conditions for DNA-protein conjugate trypsinolysis followed by the oligonucleotide-peptide conjugate purification were optimized. Use of MALDI-TOF mass spectrometry revealed that covalent linkage forms between the sugar moiety of the central pyrimidine nucleoside of the SsoII recognition site and Lys173 of the enzyme. The latter is probably involved in initial steps of enzyme-substrate recognition during dsDNA readout.