Towards a human proteomics atlas

Proteomics research has taken up an increasingly important role in life sciences over the past few years. Due to a strong push from publishers and funders alike, the community has also started to freely share its data in earnest, making use of public repositories such as the highly popular PRIDE database at EMBL-EBI. Reuse of these publicly available data has so far been confined to rather specific, targeted reanalyses, but this limited reuse is set to expand dramatically as repositories continue to grow exponentially. Examples of large-scale reuse are readily found in other omics disciplines, where more comprehensive public data have already accumulated over longer periods. Here, a typical example of integrative data reuse is provided by the construction of so-called expression atlases. We here therefore investigate the issues involved in using the human data currently stored in the PRIDE database to construct a robust, tissue-specific protein expression atlas from tandem-MS based label-free quantification.     

Deliquescence and efflorescence behavior of ternary inorganic/organic/water aerosol particles

The deliquescence behavior of ternary inorganic (ammonium sulfate and ammonium nitrate)/organic (glutaric acid and malonic acid)/water aerosol particles has been investigated at 293 K using a novel surface aerosol microscopy (SAM) technique. The results obtained for the deliquescence relative humidities (DRH) for particles of variable inorganic/organic contents show a eutectic behavior with the mixed particles showing deliquescence at lower DRH compared to the pure inorganic and organic components, respectively. This behavior has been quantitatively modeled using the extended aerosol inorganics (E-AIM) thermodynamic model of Clegg et al. in combination with the UNIFAC group activity approach to account for organic molecular solutes. In addition, we have investigated the crystallization behavior of supersatured and formerly deliquesced ternary solution droplets using space resolved Raman spectroscopy. It is found that such droplets produce solid particles in which the inorganic and organic phases show some spatial separation with the organic component being predominantly found at the outer part of the particle. Independent measurements of the contact angles of such ternary droplets reveal that their angles are within experimental error identical to those of the purely organic/water solutions.     

Development of a pressurized liquid extraction and clean-up procedure for the determination of alpha-endosulfan, beta-endosulfan and endosulfan sulfate in aged contaminated Ethiopian soils

Pressurized liquid extraction (PLE) was investigated for the extraction of two endosulfan isomers and their metabolite from two real contaminated soil samples. PLE for 3x10min at 100 degrees C was proven to be more exhaustive than Soxhlet extraction (SOX) in one soil sample. On the other soil sample investigated the method was found to be equally exhaustive as SOX. The use of hazardous organic solvents such as n-hexane, toluene, and diethyl ether has been avoided in PLE and clean-up. Instead less toxic solvents have been used both at the extraction step (acetone/n-heptane) and clean-up step (ethyl acetate/n-heptane). A column Florisil clean-up procedure that consumes relatively low solvent volumes has been optimized and applied to purify soil extracts. The developed analytical procedure was validated by applying it to a certified reference soil material (CRM811-050). A recovery of 103% total endosulfan residue was obtained versus certified values.     

Detection of artifacts and peptide modifications in liquid chromatography/mass spectrometry data using two-dimensional signal intensity map data visualization

We demonstrate how visualization of liquid chromatography/mass spectrometry data as a two-dimensional signal intensity map can be used to assess the overall quality of the data, for the identification of polymer contaminants and artifacts, as well as for the confirmation of post-translational modifications.     

Iron hydrogenase active site mimic holding a proton and a hydride

The first model of the iron hydrogenase active site has been prepared which concomitantly carries a proton and a hydride; the title species was characterized by IR and NMR spectroscopy and is reduced at more positive potential than any other mimic of this kind.     

Pyrromethene dyes (BODIPY) can form ground state homo and hetero dimers: photophysics and spectral properties

Homo and hetero dimerisation of two spectroscopically different BODIPY chromophores was studied, namely, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene and its 5-styryl-derivative. These exhibit very similar absorption and fluorescence spectral shape, but are mutually shifted by ca. 70 nm. For this reason the former and the latter are referred to as the green and red BODIPY, which here are denoted gB and rB, respectively. Various spectroscopic properties of the rB in different common solvents were determined. The calculated and experimental fluorescence quantum yield is found to be close to 100%, the fluorescence relaxation has a single exponential decay with a lifetime of about 4.5 ns, and the F?rster radius for donor-donor energy migration is 67+/-1A. The dimerisation in different solvents was examined by using custom synthesised; mono and bis BODIPY-labelled forms of 1,2-cis-diaminocyclohexane. It is shown that gB and rB can form ground state homo- as well as hetero dimers. The dimers are non-fluorescent, compatible with H-dimers and may act as excitation traps or as acceptors to the corresponding excited monomers.     

Sustainable synthesis and automated deposition: an accessible discovery screening library of fragment-like purines

A sub-library of 88 information-rich lead-like purine derivatives were prepared and deposited in an open access academic screening facility. The rationale for the synthesis of these rigid low complexity structures was the privileged character of the purine heterocycle associated with its inherent probability of interactions with multiple adenine-related targets. Although generally expected to be weak binders in many assays, such fragment-like compounds are estimated to match diverse binding sites. It is suggested that heterocycles with many anchor points for hydrogen bonds can be anticipated to undergo very specific interactions to produce more negative enthalpies and thus provide superior starting points for lead optimization than compounds that owe their activity to entropic effects. The in vitro cytotoxicity of the small compounds on a panel of human cancer cell lines has been investigated and some of them showed marked unselective or selective toxicity. This data may be useful if these fragments are to be incorporated into drug-like structures via metabolically cleavable connections. The sub-library will be implemented as part of the ChemBioNet ( www.chembionet.info ) library, and it is open to screening campaigns of academic research groups striving for a fragment-based approach in their biological assays.     

The role of optimization in some recent advances in data-driven decision-making

Mathematical Programming - In this paper, we present a new framework of bi-level unconstrained minimization for development of accelerated methods in Convex Programming. These methods use...