Luminal and Tumor-Associated Gut Microbiome Features Linked to Precancerous Lesions Malignancy Risk: A Compositional Approach.

Colorectal cancer is the third most commonly diagnosed cancer worldwide. Human gut microbiome plays important roles in protecting against it, as well as contributing to its onset and progression. Identification of specific bacterial taxa associated with early stages of colorectal cancer may help develop effective microbiome-based diagnostics.

Evaluating a species phylogeny using ddRAD SNPs: Cyto-nuclear discordance and introgression in the salmonid genus Thymallus (Salmonidae).

Hybridization and introgression are very common among freshwater fishes due to the dynamic nature of hydrological landscapes. Cyclic patterns of allopatry and secondary contact provide numerous opportunities for interspecific gene flow, which can lead to discordant paths of evolution for mitochondrial and nuclear genomes. Here, we used double digest restriction-site associated DNA sequencing (ddRADseq) to obtain a genome-wide single nucleotide polymorphism (SNP) dataset comprehensive for allThymallus (Salmonidae)species to infer phylogenetic relationships and evaluate potential recent and historical gene flow among species.

Freshwater and brackish water fishes of Sakhalin Island (Russia) in inland and coastal waters: an annotated checklist with taxonomic comments.

Based on a critical analysis of scientific publications for the last 200 years and on the collected specimens, a complete annotated list of both typical freshwater ichthyofauna of Sakhalin Island, with the inclusion of marine species that can be found in brackish coastal waters, is reported for the first time. The annotated list includes 226 species classified in three classes, 26 orders, 68 families, 29 subfamilies, and 148 genera. For 160 species, information is provided on collection samples deposited in various museums around the world, 36 of which are type specimens.

Signal transfer in human protein tyrosine phosphatase PTP1B from allosteric inhibitor P00058.

Protein tyrosine phosphatases constitute a family of cytosolic and receptor-like signal transducing enzymes that catalyze the hydrolysis of phospho-tyrosine residues of phosphorylated proteins. PTP1B, encoded by , is a key negative regulator of insulin and leptin receptor signaling, linking it to two widespread diseases: type 2 diabetes mellitus and obesity. Here, we present crystal structures of the PTP1B apo-enzyme and a complex with a newly identified allosteric inhibitor, 2-(2,5-dimethyl-pyrrol-1-yl)-5-hydroxy-benzoic acid, designated as P00058.

Therapeutic effect of iodised serum milk protein, lycopene and their combination on benign prostatic hyperplasia induced in rats.

Benign prostatic hyperplasia (BPH) is a common chronic disease in ageing men. Synthetic inhibitors of 5α-reductase commonly used in BPH treatment have limited effectiveness and may cause side effects. Evaluation of iodised serum milk protein and lycopene therapeutic effect in rat BPH model was the aim of the present study.

Cations Derived from Fentanyls Generated by Atmospheric Pressure Photoionization in the Presence of Ammonia: An IMS-MS Study.

A set of fentanyl molecules when subjected to vacuum UV atmospheric pressure photoionization (VUV-APPI) in the presence of dopants (ammonia and anisole) shows two major bands in the ion mobility-mass spectrometry (IMS-MS) spectrum corresponding to (a) the protonated fentanyl, [M+H] and (b) a unique [M-74] ion. For the parent fentanyl, the [M-74] ion is at / 262 but, in the absence of ammonia, the product ion is shifted to / 245, corresponding to a difference of NH. Collision-induced dissociations (CID) of the [M-74] ions for the different fentanyls examined here show the pattern of neutral losses, namely NH and HN=CH, and the dominant product ion is at / 84 (shifted to / 98 for 3-methylfentanyl and / 142 and 231 for carfentanyl).

Construction of Recombinant Human GM-CSF and GM-CSF-ApoA-I Fusion Protein and Evaluation of Their Biological Activity.

In this study, two strains of the yeast were constructed, one of which produced authentic recombinant human granulocyte-macrophage colony-stimulating factor (ryGM-CSF), and the other was a chimera consisting of ryGM-CSF genetically fused with mature human apolipoprotein A-I (ApoA-I) (ryGM-CSF-ApoA-I). Both forms of the cytokine were secreted into the culture medium. The proteins' yield during cultivation in flasks was 100 and 60 mg/L for ryGM-CSF and ryGM-CSF-ApoA-I, respectively.

Iodine Bonded with Milk Protein Inhibits Benign Prostatic Hyperplasia Development in Rats.

Background: There is some evidence that Benign Prostatic Hyperplasia (BPH) may increase the risk of developing prostate cancer, so conducting research on effective BPH inhibitors is important.

Objective: This research studied the inhibitory effect of Iodized Serum Milk Protein (ISMP) on BPH in rats. ISMP is a concentrate of lactic protein containing 2.

Crystal structure of Staphylococcus aureus Zn-glyoxalase I: new subfamily of glyoxalase I family.

The crystal structures of protein SA0856 from Staphylococcus aureus in its apo-form and in complex with a Zn-ion have been presented. The 152 amino acid protein consists of two similar domains with α + β topology. In both crystalline state and in solution, the protein forms a dimer with monomers related by a twofold pseudo-symmetry rotation axis.

Factors and Regional Differences Associated with Endometriosis: A Multi-Country, Case-Control Study.

Introduction: The present study aimed to investigate clinical, lifestyle, and environmental factors associated with endometrioma (OMA) and/or deep infiltrating endometriosis (DIE) as determined by case-control comparison [women with superficial peritoneal endometriosis (SUP) or no endometriosis], and compare differences between factor associated with endometriosis at a national level.

Methods: This was three countries (China, Russia, and France), case-control study in 1008 patients. Patients were identified and enrolled during their first routine appointment with their physician post-surgery for a benign gynecologic indication, excluding pregnancy.

The structure of SAV1646 from Staphylococcus aureus belonging to a new `ribosome-associated' subfamily of bacterial proteins.

The crystal structure of the SAV1646 protein from the pathogenic microorganism Staphylococcus aureus has been determined at 1.7 Å resolution. The 106-amino-acid protein forms a two-layer sandwich with α/β topology.

Unambiguous characterization of analytical markers in complex, seized opiate samples using an enhanced ion mobility trace detector-mass spectrometer.

Ion mobility spectroscopy (IMS)-based trace-compound detectors (TCDs) are powerful and widely implemented tools for the detection of illicit substances. They combine high sensitivity, reproducibility, rapid analysis time, and resistance to dirt with an acceptable false alarm rate. The analytical specificity of TCD-IMS instruments for a given analyte depends strongly on a detailed knowledge of the ion chemistry involved, as well as the ability to translate this knowledge into field-robust analytical methods.

Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2.

The poly(ADP-ribose) polymerase (PARP) family represents a new class of therapeutic targets with diverse potential disease indications. PARP1 and PARP2 inhibitors have been developed for breast and ovarian tumors manifesting double-stranded DNA-repair defects, whereas tankyrase 1 and 2 (TNKS1 and TNKS2, also known as PARP5a and PARP5b, respectively) inhibitors have been developed for tumors with elevated β-catenin activity. As the clinical relevance of PARP inhibitors continues to be actively explored, there is heightened interest in the design of selective inhibitors based on the detailed structural features of how small-molecule inhibitors bind to each of the PARP family members.

Structural insights into Noonan/LEOPARD syndrome-related mutants of protein-tyrosine phosphatase SHP2 (PTPN11).

Background: The ubiquitous non-receptor protein tyrosine phosphatase SHP2 (encoded by PTPN11) plays a key role in RAS/ERK signaling downstream of most, if not all growth factors, cytokines and integrins, although its major substrates remain controversial. Mutations in PTPN11 lead to several distinct human diseases. Germ-line PTPN11 mutations cause about 50% of Noonan Syndrome (NS), which is among the most common autosomal dominant disorders.

Crystal structure of the CN-hydrolase SA0302 from the pathogenic bacterium Staphylococcus aureus belonging to the Nit and NitFhit Branch of the nitrilase superfamily.

The nitrilases include a variety of enzymes with functional specificities of nitrilase, amidase, and hydrolase reactions. The crystal structure of the uncharacterized protein SA0302 from the pathogenic microorganism Staphylococcus aureus is solved at 1.7 Å resolution.

Mode of action, in vitro activity, and in vivo efficacy of AFN-1252, a selective antistaphylococcal FabI inhibitor.

The mechanism of action of AFN-1252, a selective inhibitor of Staphylococcus aureus enoyl-acyl carrier protein reductase (FabI), which is involved in fatty acid biosynthesis, was confirmed by using biochemistry, macromolecular synthesis, genetics, and cocrystallization of an AFN-1252-FabI complex. AFN-1252 demonstrated a low propensity for spontaneous resistance development and a time-dependent reduction of the viability of both methicillin-susceptible and methicillin-resistant S. aureus, achieving a ≥2-log(10) reduction in S.

X-CHIP: an integrated platform for high-throughput protein crystallization and on-the-chip X-ray diffraction data collection.

The X-CHIP (X-ray Crystallization High-throughput Integrated Platform) is a novel microchip that has been developed to combine multiple steps of the crystallographic pipeline from crystallization to diffraction data collection on a single device to streamline the entire process. The system has been designed for crystallization condition screening, visual crystal inspection, initial X-ray screening and data collection in a high-throughput fashion. X-ray diffraction data acquisition can be performed directly on-the-chip at room temperature using an in situ approach.

Crystal structure of alkyl hydroperoxidase D like protein PA0269 from Pseudomonas aeruginosa: homology of the AhpD-like structural family.

Background: Alkyl hydroperoxidase activity provides an important antioxidant defense for bacterial cells. The catalytic mechanism requires two peroxidases, AhpC and AhpD, where AhpD plays the role of an essential adaptor protein.

Results: The crystal structure of a putative AhpD from Pseudomonas aeruginosa has been determined at 1.

Structure of Francisella tularensis peptidyl-tRNA hydrolase.

The rational design of novel antibiotics for bacteria involves the identification of inhibitors for enzymes involved in essential biochemical pathways in cells. In this study, the cloning, expression, purification, crystallization and structure of the enzyme peptidyl-tRNA hydrolase from Francisella tularensis, the causative agent of tularemia, was performed. The structure of F.

Crystal structure of a truncated urease accessory protein UreF from Helicobacter pylori.

Urease plays a central role in the pathogenesis of Helicobacter pylori in humans. Maturation of this nickel metalloenzyme in bacteria requires the participation of the accessory proteins UreD (termed UreH in H. pylori), UreF, and UreG, which form sequential complexes with the urease apoprotein as well as UreE, a metallochaperone.

Bond dissociation energies of solvated silver(I)-amide complexes: competitive threshold collision-induced dissociations and calculations.

Using competitive threshold collision-induced dissociation (TCID) measurements, experimental bond dissociation energies have been evaluated for the water, methanol, and acetonitrile adducts of silver(I)-amide complexes. The influence of the solvent molecules on the binding energy of silver(I) to acetamide, N-methylacetamide, and N,N-dimethylacetamide was investigated. Experimental results show that solvents decrease the amide binding energy by 4-6 kcal mol(-1).

Spiro-naphthyridinone piperidines as inhibitors of S. aureus and E. coli enoyl-ACP reductase (FabI).

Spiropiperidine naphthyridinone inhibitors of Staphylococcus aureus and Escherichia coli FabI have been prepared. Compounds 14a and 14c were identified as having sub-nanomolar E. coli FabI activity and are among the most potent FabI inhibitors yet described.

Threshold collision-induced dissociation measurements using a ring ion guide as the collision cell in a triple-quadrupole mass spectrometer.

A triple-quadrupole mass spectrometer has been modified for bond-dissociation energy measurements via threshold collision-induced dissociations (TCIDs) by replacing the conventional collision cell with a ring ion guide. Optimal operating conditions for the ring ion guide were determined or derived, and validated using a set of complexes for which bond dissociation energies are known. A comparison with reference data (within a range of 16-57 kcal/mol) indicates an accuracy approaching that of TCID determined on a guided ion-beam mass spectrometer.

Binding energies of the silver ion to alcohols and amides: a theoretical and experimental study.

The silver ion binding energies to alcohols (methanol, ethanol, n-propanol, i-propanol, and n-butanol) and to amides (acetamide, N-methylacetamide, N, N-dimethylacetamide, formamide, N-methylformamide, and N, N-dimethylformamide) have been calculated using density functional theory (DFT) and measured using the threshold collision-induced dissociation (TCID) method. For DFT, the combined basis sets of ECP28MWB for silver and 6-311++G(2df,2pd) for the other atoms were found to be optimal using a series of test calculations on Ag (+) binding to methanol and to formamide. In addition, the Ag (+) binding energies of all ligands were evaluated with nine functionals after full geometric optimizations.

Analytical method for the identification of a thin-strip defect in a planar waveguide.

Nondestructive reconstruction of the location and width of a thin-strip defect in a strongly confined planar waveguide is considered. Explicit reconstruction formulas are given for a quick reconstruction of a thin-strip defect whose width is small by measuring the scattered fields at the two end faces of the planar waveguide for two frequencies. Numerical results are given, and the analytical reconstruction method is shown to be reliable regardless of the location of the defect.