Hot and crispy : CRISPR-Cas systems in the hyperthermophile Sulfolobus solfataricus

The CRISPR (clustered regularly interspaced short palindromic repeats) and Cas (CRISPR-associated) genes are widely spread in bacteria and archaea, representing an intracellular defence system against invading viruses and plasmids. In the system, fragments from foreign DNA are captured and integrated into the host genome at the CRISPR locus. The locus is transcribed and the resulting RNAs are processed by Cas6 into small crRNAs (CRISPR RNAs) that guide a variety of effector complexes to degrade the invading genetic elements. Many bacteria and archaea have one major type of effector complex. However, Sulfolobus solfataricus strain P2 has six CRISPR loci with two families of repeats, four cas6 genes and three different types of effector complex. These features make S. solfataricus an important model for studying CRISPR-Cas systems. In the present article, we review our current understanding of crRNA biogenesis and its effector complexes, subtype I-A and subtype III-B, in S. solfataricus. We also discuss the differences in terms of mechanisms between the subtype III-B systems in S. solfataricus and Pyrococcus furiosus.PostprintPeer reviewe

Experimental and computational results on the interaction of carbon dioxide laser radiation with a dense plasma

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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

Inverse-opal conducting polymer monoliths in microfluidic channels

Inverse opal monolithic flow-through structures of polyaniline (PANI) were achieved in microfluidic channels for lab-on-a-chip (LOC) applications. In order to achieve the uniformly porous monolith, polystyrene (PS) colloidal crystal (CC) templates were fabricated in channel. An inverse opal PANI structure was achieved on-chip, through a two-step process involving the electrochemical growth of PANI and subsequent removal of the template. The effect of electropolymerisation on these structures is discussed. It was found that growth time is critical in achieving an ordered structure with well-defined flow-through pores. This is significant in order to fabricate optimal porous PANI structures that maximise surface area of the monolith and also provide well-defined flow profiles through the micro-channel

Bacteria SAVED from viruses

Increasingly, cyclic nucleotide second messengers are implicated in antiviral defense systems in bacteria and archaea as well as in eukaryotes. In this issue of Cell, Lowey et al. describe SAVED—a widespread, uncharacterized cyclic nucleotide sensor protein domain that activates cell defense systems. The structure of SAVED reveals links to the CRISPR system, which also generates cyclic nucleotides in response to viral infection.PostprintPeer reviewe

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

The CTA Sensitivity to Lorentz-Violating Effects on the Gamma-Ray Horizon

The arrival of TeV-energy photons from distant galaxies is expected to be affected by their QED interaction with intergalactic radiation fields through electron-positron pair production. In theories where high-energy photons violate Lorentz symmetry, the kinematics of the process $\gamma + \gamma\rightarrow e^+ + e^-$ is altered and the cross-section suppressed. Consequently, one would expect more of the highest-energy photons to arrive if QED is modified by Lorentz violation than if it is not. We estimate the sensitivity of Cherenkov Telescope Array (CTA) to changes in the $\gamma$-ray horizon of the Universe due to Lorentz violation, and find that it should be competitive with other leading constraints.Comment: 13 pages, 4 figures, typos corrected + references added, results unchanged. Matches version accepted by JCA