Base Flip in DNA Studied by Molecular Dynamics Simulations of Differently-Oxidized Forms of Methyl-Cytosine

Distortions in the DNA sequence, such as damage or mispairs, are specifically recognized and processed by DNA repair enzymes. Many repair proteins and, in particular, glycosylases flip the target base out of the DNA helix into the enzyme’s active site. Our molecular dynamics simulations of DNA with intact and damaged (oxidized) methyl-cytosine show that the probability of being flipped is similar for damaged and intact methyl-cytosine. However, the accessibility of the different 5-methyl groups allows direct discrimination of the oxidized forms. Hydrogen-bonded patterns that vary between methyl-cytosine forms carrying a carbonyl oxygen atom are likely to be detected by the repair enzymes and may thus help target site recognition.     

Derivatization of Antibody Fab Fragments: A Designer Enzyme for Native Protein Modification

Bioconjugates, such as antibody–drug conjugates, have gained recent attention because of their increasing use in therapeutic and diagnostic applications. Commonly used conjugation reactions based upon chemoselective reagents exhibit a number of drawbacks: most of these reactions lack regio‐ and stereospecificity, thus resulting in loss of protein functionality due to random modifications. Enzymes provide an obvious solution to this problem, but the intrinsic (natural) substrate specificities of existing enzymes pose severe limitations to the kind of modifications that can be introduced. Here we describe the application of the novel trypsin variant trypsiligase for site‐specific modification of the C terminus of a Fab antibody fragment via a stable peptide bond. The suitability of this designed biocatalyst was demonstrated by coupling the Her2‐specific Fab to artificial functionalities of either therapeutic (PEG) or diagnostic (fluorescein) relevance. In both cases we obtained homogeneously modified Fab products bearing the artificial functionality exclusively at the desired position.     

Self‐Assembly of Ferromagnetic Organic–Inorganic Perovskite‐Like Films

Perovskite‐based organic–inorganic hybrids hold great potential as active layers in electronics or optoelectronics or as components of biosensors. However, many of these applications require thin films grown with good control over structure and thickness—a major challenge that needs to be addressed. The work presented here is an effort towards this goal and concerns the layer‐by‐layer deposition at ambient conditions of ferromagnetic organic–inorganic hybrids consisting of alternating CuCl₄‐octahedra and organic layers. The Langmuir‐Blodgett technique used to assemble these structures provides intrinsic control over the molecular organization and film thickness down to the molecular level. Magnetic characterization reveals that the coercive field for these thin films is larger than that for solution‐grown layered bulk crystals. The strategy presented here suggests a promising cost effective route to facilitate the excellently controlled growth of sophisticated materials on a wide variety of substrates that have properties relevant for the high density storage media and spintronic devices.     

Mechanical damage to Gram-negative bacteria by surface plating with the Drigalski-spatula technique

Colony counting by spreading bacterial suspensions on plating media by various techniques is of general concern. Comparative studies between hand plating (Drigalski-spatula technique) for different time intervals and spiral plating resulted in significant differences in colony counts. Lower counts of Gram-negative bacteria were obtained by using hand plating for more than 10 s, compared with short time hand plating (5 s) or spiral plating. Colony counting of Gram-positive bacteria showed no differences between both techniques. Further characterisation of Escherichia coli cells spread with the Drigalski-spatula technique by electron microscopy revealed a large number of damaged cells compared to control samples. The data clearly shows that the mechanical forces during hand plating are sufficient to damage E. coli cells.     

Performance assessment of onboard and scene-based methods for Airborne Prism Experiment spectral characterization

Accurate spectral calibration of airborne and spaceborne imaging spectrometers is essential for proper preprocessing and scientific exploitation of high spectral resolution measurements of the land and atmosphere. A systematic performance assessment of onboard and scene-based methods for in-flight monitoring of instrument spectral calibration is presented for the first time in this paper. Onboard and ground imaging data were collected at several flight altitudes using the Airborne Prism Experiment (APEX) imaging spectrometer. APEX is equipped with an in-flight characterization (IFC) facility allowing the evaluation of radiometric, spectral, and geometric system properties, both in-flight and on-ground for the full field of view. Atmospheric and onboard filter spectral features present in at-sensor radiances are compared with the same features in reference transmittances convolved to varying instrument spectral configurations. A spectrum-matching algorithm, taking advantage of the high sensitivity of measurements around sharp spectral features toward spectrometer spectral performance, is used to retrieve channel center wavelength and bandwidth parameters. Results showed good agreement between spectral parameters estimated using onboard IFC and ground imaging data. The average difference between estimates obtained using the O(2) and H(2)O features and those obtained using the corresponding filter features amounted to about 0.3 nm (0.05 of a spectral pixel). A deviation from the nominal laboratory instrument spectral calibration and an altitude-dependent performance was additionally identified. The relatively good agreement between estimates obtained by the two approaches in similar spectral windows suggests they can be used in a complementary fashion: while the method relying on atmospheric features can be applied without the need for dedicated calibration acquisitions, the IFC allows assessment at user-selectable wavelength positions by custom filters as well as for the system on-ground.     

From bulk to single-cell classification of the filamentous growing Streptomyces bacteria by means of Raman spectroscopy

Classification of Raman spectra recorded from single cells is commonly applied to bacteria that exhibit small sizes of approximately 1 to 2 μm. Here, we study the possibility to adopt this classification approach to filamentous bacteria of the genus Streptomyces. The hyphae can reach extensive lengths of up to 35 μm, which can correspond to a single cell identified in light microscopy. The classification of Raman bulk spectra will be demonstrated. Here, ultraviolet resonance Raman (UV RR) spectroscopy is chosen to classify six Streptomyces species by the application of a tree-like classifier. For each knot of the hierarchical classifier, estimated classification accuracies of over 94% are accomplished. In contrast to the classification of bulk spectra, the classification of single-cell spectra requires a homogenous substance distribution within the cell. Consequently, the bacterial cell chemistry can be represented by one individual spectrum. This requirement is not fulfilled when different spectra are processed from different locations within the cell. Bacteria of the investigated genus Streptomyces exhibit, besides the normal bacterial spectra, lipid-rich spectra. The occurrence of lipid enrichment depends on culture age and nutrition availability. With this study, we investigate the cell substance distribution, especially of lipid-rich fractions. The classification utilizing a tree-like classifier is also applied to the Streptomyces single-cell spectra, resulting in classification accuracies between 80 and 93% for the investigated Streptomyces species.     

Physicochemical and functional properties of a protein isolate produced from safflower (Carthamus tinctorius L.) meal by ultrafiltration

BACKGROUND: The protein isolate obtained from safflower meal by aqueous extraction and ultrafiltration was evaluated for its physicochemical and functional properties. RESULTS: Protein, ash and moisture contents of the safflower protein isolate were 901, 51 and 45 g kg^?1 respectively. Its water and oil absorption capacities were 2.22 mL H₂O g^?1 protein and 2.77 mL oil g^?1 protein respectively. Least gelation concentration was 20 g kg^?1 at pH 2, 6, 8 and 10 but 100 g kg^?1 at pH 4. Emulsifying properties were also affected by the pH: emulsifying activity and emulsion stability at pH 6 were 82.5 and 100% respectively. The highest foaming capacity (126%) occurred at pH 2; however, it increased by 104% with the addition of 0.25 g glucose g^?1 protein to the foam system. CONCLUSION: In the light of its functional properties found in this study, safflower protein isolate produced by ultrafiltration is recommended for use as an ingredient in food products such as salad dressing, meat products, mayonnaise, cakes, ice cream and desserts. Copyright © 2010 Society of Chemical Industry     

Lack of Pervasiveness of the Underconfidence-With-Practice Effect: Boundary Conditions and an Explanation Via Anchoring.

The authors investigated whether underconfidence in judgments of learning (JOLs) is pervasive across multiple study-test trials as suggested by A. Koriat, L. Sheffer, and H. Ma'ayan (2002) or whether underconfidence with practice (UWP) might be a kind of anchoring-and-adjustment effect, such that the occurrence or nonoccurrence of the UWP effect depends on whether recall is above a psychological anchor. Participants studied normatively difficult items or normatively easy items and made immediate JOLs or delayed JOLs. The UWP effect occurred for easy items, but for difficult items an overconfidence-with-practice (OWP) effect occurred for delayed JOLs and no bias occurred for immediate JOLs. The systematic occurrence of all 3 outcomes establishes boundary conditions for the UWP effect and confirms the hypothesis that underconfidence (or the lack thereof) may arise at least in part from an anchoring-and-adjustment mechanism. (PsycINFO Database Record (c) 2010 APA, all rights reserved)