Highly efficient methods for the one-pot synthesis of b-substituted enones

A mild and practically-convenient one-pot procedure for the direct b-substitution of enones has been developed using a conjugate addition–oxidation strategy with a full range of copper-based reagents and N-tert-butylphenylsulfinimidoyl chloride; alkyl- and aryl-substituted enones are delivered in good to excellent yields

Di-tert-butyl N,N′-(octa­hydro­penta­lene-2,5-di­yl)dicarbamate

In the molecule of the title compound, C18H32N2O4, the central bicyclo­[3.3.0]octane (octa­hydro­penta­lene) has a rigid ring junction. Both rings of the bicyclo­[3.3.0]octane unit adopt an envelope conformation, and the flexible tert-butyl­carbamoyl side chains each have an extended conformation. Such a constrained bicyclo­[3.3.0]octane aliphatic template is of inter­est with respect to the design of novel self-assembling motifs. Mol­ecules related by c-glide symmetry are linked via inter­molecular N—H⋯O hydrogen bonds, forming a two-dimensional layer structure. Neighboring layers are weakly associated along the a axis due to the close approach of the tert-butyl­carbamoyl groups (2.55 Å)

Information inequalities and Generalized Graph Entropies

In this article, we discuss the problem of establishing relations between information measures assessed for network structures. Two types of entropy based measures namely, the Shannon entropy and its generalization, the R\'{e}nyi entropy have been considered for this study. Our main results involve establishing formal relationship, in the form of implicit inequalities, between these two kinds of measures when defined for graphs. Further, we also state and prove inequalities connecting the classical partition-based graph entropies and the functional-based entropy measures. In addition, several explicit inequalities are derived for special classes of graphs.Comment: A preliminary version. To be submitted to a journa

High-fat diet impact on intestinal cholesterol conversion by the microbiota and serum cholesterol levels

Cholesterol-to-coprostanol conversion by the intestinal microbiota has been suggested to reduce intestinal and serum cholesterol availability, but the relationship between intestinal cholesterol conversion and the gut microbiota, dietary habits, and serum lipids has not been characterized in detail. We measured conserved proportions of cholesterol high and low-converter types in individuals with and without obesity from two distinct, independent low-carbohydrate high-fat (LCHF) dietary intervention studies. Across both cohorts, cholesterol conversion increased in previous low-converters after LCHF diet and was positively correlated with the fecal relative abundance of Eubacterium coprostanoligenes. Lean cholesterol high-converters had increased serum triacylglycerides and decreased HDL-C levels before LCHF diet and responded to the intervention with increased LDL-C, independently of fat, cholesterol, and saturated fatty acid intake. Our findings identify the cholesterol high-converter type as a microbiome marker, which in metabolically healthy lean individuals is associated with increased LDL-C in response to LCHF.publishedVersio

Information Indices with High Discriminative Power for Graphs

In this paper, we evaluate the uniqueness of several information-theoretic measures for graphs based on so-called information functionals and compare the results with other information indices and non-information-theoretic measures such as the well-known Balaban index. We show that, by employing an information functional based on degree-degree associations, the resulting information index outperforms the Balaban index tremendously. These results have been obtained by using nearly 12 million exhaustively generated, non-isomorphic and unweighted graphs. Also, we obtain deeper insights on these and other topological descriptors when exploring their uniqueness by using exhaustively generated sets of alkane trees representing connected and acyclic graphs in which the degree of a vertex is at most four

Tightening the knot in phytochrome by single molecule atomic force microscopy

A growing number of proteins have been shown to adopt knotted folds. Yet the biological roles and biophysical properties of these knots remain poorly understood. We have used protein engineering and atomic force microscopy to explore single-molecule mechanics of the figure-of-eight knot in the chromophore-binding domain of the red/far red photoreceptor, phytochrome. Under load, apo phytochrome unfolds at forces of ~47 pN, while phytochrome carrying its covalently bound tetrapyrrole chromophore unfolds at ~73 pN. These forces are among the lowest measured in mechanical protein unfolding, hence the presence of the knot does not automatically indicate a super-stable protein. Our experiments reveal a stable intermediate along the mechanical unfolding pathway, reflecting sequential unfolding of two distinct subdomains in phytochrome, potentially the GAF and PAS domains. For the first time, our experiments allow direct determination of knot size under load. In the unfolded chain, the tightened knot is reduced to 17 amino acids, resulting in apparent shortening of the polypeptide chain by 6.2 nm. Steered molecular dynamics simulations corroborate this number. Finally, we found that covalent phytochrome dimers created for these experiments retain characteristic photoreversibility, unexpectedly arguing against dramatic rearrangement of the native GAF dimer interface upon photoconversion.Comment: 12 pages plus five figures; has been submitted to Biophysical J. Replacement on 9/16 is ONLY to correct a typo in the meta data; the uploaded file is identical to first versio

Quantitative real-time RT-PCR of CD24 mRNA in the detection of prostate cancer

BACKGROUND: Gene expression profiling has recently shown that the mRNA for CD24 is overexpressed in prostate carcinomas (Pca) compared to benign or normal prostate epithelial tissues. Immunohistochemical studies have reported the usefulness of anti-CD24 for detecting prostate cancer over the full range of prostate specimens encountered in surgical pathology, e.g. needle biopsies, transurethral resection of prostate chips, or prostatectomies. It is a small mucin-like cell surface protein and thus promises to become at least a standard adjunctive stain for atypical prostate biopsies. We tested the usefulness of real-time RT-PCR for specific and sensitive detection of CD24 transcripts as a supplementary measure for discriminating between malignant and benign lesions in prostatic tissues. METHODS: Total RNA was isolated from snap-frozen chips in 55 cases of benign prostatic hyperplasia (BPH) and from frozen sections in 59 prostatectomy cases. The latter contain at least 50% malignant epithelia. Relative quantification of CD24 transcripts was performed on the LightCycler instrument using hybridization probes for detection and porphobilinogen deaminase transcripts (PBGD) for normalization. RESULTS: Normalized CD24 transcript levels showed an average 2.69-fold increase in 59 Pca-cases (mean 0.21) when compared to 55 cases of BPH (mean 0.08). This difference was highly significant (p < 0.0001). The method has a moderate specificity (47.3%) but a high sensitivity (86.4%) if the cutoff is set at 0.0498. CD24 expression levels among Pca cases were not statistically associated with the tumor and lymph-node stage, the grading (WHO), the surgical margins, or the Gleason score. CONCLUSION: The present study demonstrates the feasibility of quantitative CD24 RNA transcript detection in prostatic tissues even without previous laser microdissection

German cancer statistics 2004

Background: For years the Robert Koch Institute (RKI) has been annually pooling and reviewing the data from the German population-based cancer registries and evaluating them together with the cause-of-death statistics provided by the statistical offices. Traditionally, the RKI periodically estimates the number of new cancer cases in Germany on the basis of the available data from the regional cancer registries in which registration is complete; this figure, in turn, forms the basis for further important indicators. Methods: This article gives a brief overview of current indicators - such as incidence, prevalence, mortality, survival rates - on the most common types of cancer, as well as important ratios on the risks of developing and dying of cancer in Germany. Results: According to the latest estimate, there were a total of 436,500 new cancer cases in Germany in 2004. The most common cancer in men is prostate cancer with over 58,000 new cases per annum, followed by colorectal and lung cancer. In women, breast cancer remains the most common cancer with an estimated 57,000 new cases every year, also followed by colorectal cancer. These and further findings on selected cancer sites can be found in the current brochure on “Cancer in Germany”, which is regularly published by the RKI together with the Association of Population-based Cancer Registries in Germany (GEKID). In addition, the RKI made cancer-prevalence estimates and calculated current morbidity and mortality risks at the federal level for the first time. According to these figures, the 5-year partial prevalence - i.e. the total number of cancer patients diagnosed over the past five years who are currently still living - exceeds 600,000 in men; the figure is about the same among women. Here, too, the most common cancers are prostate cancer in men and breast cancer in women. The lifetime risk of developing cancer, which is more related to the individual, is estimated to be higher among men (48.5%) than among women (40.3%). In roughly rounded figures, therefore, about every second person in Germany develops cancer in the course of their lives. One in four men and one in five women die of cancer. Conclusions: In recent years, population-based cancer registration in Germany has come significantly closer to the aim of the complete, nationwide coverage of cancer. The continuous improvements in the data situation help describe cancer development in Germany

Connections between Classical and Parametric Network Entropies

This paper explores relationships between classical and parametric measures of graph (or network) complexity. Classical measures are based on vertex decompositions induced by equivalence relations. Parametric measures, on the other hand, are constructed by using information functions to assign probabilities to the vertices. The inequalities established in this paper relating classical and parametric measures lay a foundation for systematic classification of entropy-based measures of graph complexity

Extraction of Accurate Biomolecular Parameters from Single-Molecule Force Spectroscopy Experiments

The atomic force microscope (AFM) is able to manipulate biomolecules and their complexes with exquisite force sensitivity and distance resolution. This capability, complemented by theoretical models, has greatly improved our understanding of the determinants of mechanical strength in proteins and revealed the diverse effects of directional forces on the energy landscape of biomolecules. In unbinding experiments, the interacting partners are usually immobilized on their respective substrates via extensible linkers. These linkers affect both the force and contour length (Lc) of the complex at rupture. Surprisingly, while the former effect is well understood, the latter is largely neglected, leading to incorrect estimations of Lc, a parameter that is often used as evidence for the detection of specific interactions and remodeling events and for the inference of interaction regions. To address this problem, a model that predicts contour length measurements from single-molecule forced-dissociation experiments is presented that considers attachment position on the AFM tip, geometric effects, and polymer dynamics of the linkers. Modeled data are compared with measured contour length distributions from several different experimental systems, revealing that current methods underestimate contour lengths. The model enables nonspecific interactions to be identified unequivocally, allows accurate determination of Lc, and, by comparing experimental and modeled distributions, enables partial unfolding events before rupture to be identified unequivocally