Species identification of Oetzi's clothing with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry based on peptide pattern similarities of hair digests

Identification of ancient biological samples from the 1991-discovered and more than 5300-year-old Tyrolean mummy, also called iceman or Oetzi, is very difficult. The species of origins of four animal-hair-bearing samples of the accoutrement of the mummy not yet diagnosed were identified by a special proteomics method. Ha 43/91/130 and Ha 6/91, two samples from his coat, and Ha 5/91, a sample from his leggings, were assigned to sheep. The upper leather of his moccasins, Ha 2/91, was made from cattle. Despite the enormous age of these samples with partial (bio)chemical alterations, reliable identification was possible using a recently developed matrix-assisted laser desorption/ionization time-of-flight mass spectrometric ((MALDI-TOF MS)-based analytical method. The method is exclusively based on the analysis of proteins and uses minute amounts of peptides directly derived from tryptic hair digests without any separation or enrichment steps. Unknown species are identified by comparison of their peptide ion patterns with known spectra stored in existing databases. Hereby, the correlation distance, a form of Euclidean distance, and deduced parameters are used to measure similarities.If more than one potential hit remains, specific diagnostic peptide ions are used to stepwise exclude incorrect matches. These ions are specific for orders, families, subfamilies/genera and/or even species. Peptide mass fingerprinting data combined with those from collision-induced dissociation spectra (combined MS & MS/MS) were used for interpretation with the MASCOT search engine and the NCBI database to find the potential parentage of hair proteins. For this technique, selected precursor ions were identified as specific diagnostic peptide ions. Copyright (c) 2008 John Wiley & Sons, Ltd.     

2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence

We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short ( approximately 50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is substituted by an abasic site analog. The corresponding cocrystal structure shows 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not essential for base flipping. However, in this structure, a shift of the 3' neighbor of the target base into the vacancy left after base flipping is observed, apparently replicating a stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide quenching measurements of M.TaqI complexes in solution provide evidence for an alternative binding site for the extra-helical target base within M.TaqI and suggest that the partner thymine assists in delivering the target base into the active site.     

On the crystalline cohomology of Deligne–Lusztig varieties

Let $X\to Y^0$ be an abelian prime-to-p Galois covering of smooth schemes over a perfect field k of characteristic $p>0$. Let Y be a smooth compactification of $Y^0$ such that $Y-Y^0$ is a normal crossings divisor on Y. We describe a logarithmic F-crystal on Y whose rational crystalline cohomology is the rigid cohomology of X, in particular provides a natural $W[F]$-lattice inside the latter; here W is the Witt vector ring of k. If a finite group G acts compatibly on X, $Y^0$ and Y then our construction is G-equivariant. As an example we apply it to Deligne–Lusztig varieties. For a finite field k, if $\mathbb{G}$ is a connected reductive algebraic group defined over k and $\mathbb{L}$ a k-rational torus satisfying a certain standard condition, we obtain a meaningful equivariant $W[F]$-lattice in the cohomology (ℓ-adic or rigid) of the corresponding Deligne–Lusztig variety and an expression of its reduction modulo p in terms of equivariant Hodge cohomology groups.     

Equivariant crystalline cohomology and base change

Given a perfect field of characteristic , a smooth proper -scheme , a crystal on relative to and a finite group acting on and , we show that, viewed as a virtual -module, the reduction modulo of the crystalline cohomology of is the de Rham cohomology of modulo . On the way we prove a base change theorem for the virtual -representations associated with -equivariant objects in the derived category of -modules.

     

Mellin and Green symbols for boundary value problems on manifolds with edges

We introduce the algebra of smoothing Mellin and Green symbols in a pseudodifferential calculus for manifolds with edges. In addition, we define scales of weighted Sobolev spaces with asymptotics based on the Mellin transform and analyze the mapping properties of the operators on these spaces. This will allow us to obtain complete information on the regularity and asymptotics of solutions to elliptic equations on these spaces.     

Darstellung,Eigenschaften und Molekülstrukturen von Dimethylaminomethylferrocenyl‐Verbindungen ausgewählter Elemente der Gruppen 13 und 14

Preparation, Properties, and Molecular Structures of Dimethylaminomethyl Ferrocenyl Compounds of selected Elements of Group 13 and 14 Dimethylmetalchlorides of gallium and indium react with dimethylaminomethylferrocenyllithium (FcNLi) to give the corresponding dimethylmetaldimethylaminomethylferrocenes 1 and 2 [Me₂MFcN; M=Ga, In]. In a similar manner dialkylmetaldichlorides of germanium and tin yield the expected chlordialkylmetaldimethylaminomethylferrocenes 3 – 5 [R₂(Cl)MFcN; M=Ge; R = Me ( 3 ), M=Sn; R=Me ( 4 ), Ph ( 5 )]. In a reaction of Me₃Al and Me₂AlCl with dimethylaminomethylferrocene the formation of the 1 : 1 adducts 7 and 8 could be observed. All compounds were characterised by ¹H and ¹³C nmr spectroscopy. The molecular structures of 1 , 3 , 4 and 7 were determined. 3 and 4 build in contrast to 1 monomeric molecules with chelat rings as a result of the M–N coordination. Compound 7 consist of monomeric molecules with 4 coordinated Al atoms.     

Coupling of a Nucleoside with DNA by a Methyltransferase

How to outwit a methyltransferase: Methyltransferases (Mtases) catalyze the transfer of the activated methyl group from the cofactor S-adenosyl-L -methionine ( 1 ) to acceptors R within a large variety of biomolecules. Through the use of the cofactor analogue 2 a whole nucleoside was coupled to DNA in a Mtase-catalyzed reaction.     

Intra- and inter-chain fluctuations in entangled polymer melts in bulk and confined to pore channels

It is known that topological restraints by “chain entanglements” severely affect chain dynamics in polymer melts. In this field-cycling NMR relaxometry and fringe-field NMR diffusometry study, melts of linear polymers in bulk and confined to pores in a solid matrix are compared. The diameter of the pore channels was 10 nm. It is shown that the dynamics of chains in bulk dramatically deviate from those observed under pore constraints. In the latter case, one of the most indicative signatures of the reptation model is verified 28 years after its prediction by de Gennes: The frequency and molecular mass dependencies of the spin-lattice relaxation time obey the power law T_! ∝ M⁰ v^3/4 on a time scale shorter than the longest Rouse relaxation time τ_R. The mean squared segment displacement in the pores was also found to be compatible to the reptation law < r²>∝ M^−1/2t^1/2 predicted for τ_R < t < τ_d, where τ_d is the so-called disengagement time. Contrary to these findings, bulk melts of entangled polymers show frequency and molecular mass dependencies significantly different from what one expects on the basis of the reptation model. The data can however be described with the aid of the renormalized Rouse theory.     

A 2D reversed-phase × ion-pair reversed-phase HPLC-MALDI TOF/TOF-MS approach for shotgun proteome analysis

The separation of complex peptide mixtures in shotgun proteome analysis using a 2D separation scheme encompassing reversed-phase × ion-pair reversed-phase (IP-RP) liquid chromatography coupled online to electrospray ion trap mass spectrometry (MS) has been shown earlier to be superior in terms of separation efficiency and technical robustness compared to the classically used separation scheme encompassing strong cation exchange × IP-RP-chromatography in shotgun proteome analysis. In the present study, this novel separation scheme was coupled offline to matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF)/TOF-MS for the analysis of the same sample, a tryptic digest of the cytosolic proteome of the bacterium Corynebacterium glutamicum. Compared to the earlier study, the MALDI-based platform led to a significantly increased number of peptides (7,416 vs. 2,709) and proteins (1,208 vs. 468, without single peptide-based identifications), respectively. This represents the majority of all predicted cytosolic proteins in C. glutamicum. The high proteome coverage, as well as the large number of low-abundant proteins identified with this improved analytical platform, pave the way for new biological studies. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.