Facile synthesis of the cyclohexane fragment of enacloxins,a series of antibiotics isolated from Frateuria sp. W-315

An efficient and good yield synthesis of the cyclohexane moiety of enacyloxins, a series of antibiotics isolated from Frateuria sp. W-315, was achieved from d-quinic acid using a successive Barton–McCombie deoxygenation.     

High-impact sulfur compounds: constitutional and configurational assignment of sulfur-containing heterocycles

To unambiguously identify their structures and to evaluate their organoleptic properties, several constitutional und configurational isomers of dialkyl-tetrathianes and dialkyl-pentathiepanes were synthesized by two different synthetic protocols, and separated by preparative gas chromatography. Raman and NMR spectroscopy were used to differentiate between the constitutional 3,6-dialkyl-1,2,4,5-tetrathiane and the 4,6-dialkyl-1,2,3,5-tetrathiane isomers. Furthermore, cis- and trans-isomers of 3,6-dialkyl-1,2,4,5-tetrathianes were distinguished by temperature-dependent NMR experiments. Static, quantum-chemical simulations of the NMR spectra for these cis- and trans-isomers were calculated in the gas layer in order to confirm our experimental assignments. In addition, the assignment of 4,7-alkyl-1,2,3,5,6-pentathiepanes were deducted from their Raman spectra. Dialkyl-tetrathianes and dialkyl-pentathiepanes are interesting components to be used in flavor applications due to their unique olfactory impact and facets.     

Ecdysteroids from Vitex species: distribution and compilation of their 13C-NMR spectral data

Iridoids and ecdysteroids are found in some genera of the family Verbenaceae. In such cases, they are used as chemotaxonomic markers for the difficult task of taxonomic identification by using morphological characteristics of plants belonging to this family. The present work describes the distribution of ecdysteroids in plants from the genus Vitex from a review of previous work on seventeen Vitex species. In addition, (13)C-NMR data of the main ecdysteroids found in this genus are described. This study attempted to summarize previous research on ecdysteroids distribution in Vitex species with the addition of (13)C-NMR analysis to further refine the characterization of these compounds in the Verbenaceae family.     

6-phospho-alpha-D-glucosidase from Fusobacterium mortiferum: cloning, expression, and assignment to family 4 of the glycosylhydrolases.

The Fusobacterium mortiferum malH gene, encoding 6-phospho-alpha-glucosidase (maltose 6-phosphate hydrolase; EC 3.2.1.122), has been isolated, characterized, and expressed in Escherichia coli. The relative molecular weight of the polypeptide encoded by malH (441 residues; Mr of 49,718) was in agreement with the estimated value (approximately 49,000) obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the enzyme purified from F. mortiferum. The N-terminal sequence of the MalH protein obtained by Edman degradation corresponded to the first 32 amino acids deduced from the malH sequence. The enzyme produced by the strain carrying the cloned malH gene cleaved [U-14C]maltose 6-phosphate to glucose 6-phosphate (Glc6P) and glucose. The substrate analogs p-nitrophenyl-alpha-D-glucopyranoside 6-phosphate (pNP alphaGlc6P) and 4-methylumbelliferyl-alpha-D-glucopyranoside 6-phosphate (4MU alphaGlc6P) were hydrolyzed to yield Glc6P and the yellow p-nitrophenolate and fluorescent 4-methylumbelliferyl aglycons, respectively. The 6-phospho-alpha-glucosidase expressed in E. coli (like the enzyme purified from F. mortiferum) required Fe2+, Mn2+, Co2+, or Ni2+ for activity and was inhibited in air. Synthesis of maltose 6-phosphate hydrolase from the cloned malH gene in E. coli was modulated by addition of various sugars to the growth medium. Computer-based analyses of MalH and its homologs revealed that the phospho-alpha-glucosidase from F. mortiferum belongs to the seven-member family 4 of the glycosylhydrolase superfamily. The cloned 2.2-kb Sau3AI DNA fragment from F. mortiferum contained a second partial open reading frame of 83 residues (designated malB) that was located immediately upstream of malH. The high degree of sequence identity of MalB with IIB(Glc)-like proteins of the phosphoenol pyruvate dependent:sugar phosphotransferase system suggests participation of MalB in translocation of maltose and related alpha-glucosides in F. mortiferum.     

Complete resonance assignment of the first and second apple domains of MIC4 from Toxoplasma gondii, using a new NMRView-based assignment aid

Microneme protein 4 is involved in cell binding by the important parasite Toxoplasma gondii. We present here the backbone and side-chain assignments of the first two apple domains together with a new graphical aid for their assignment using NMRView. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Neutrons, magnets, and photons: a career in structural biology

The purpose of Reflections articles, it seems, is to give elderly scientists a chance to write about the "good old days," when everyone walked to school in the snow. They enjoy this activity so much that your editor, Martha Fedor, must have known that I would accept her invitation to write such an article, no matter how much I demurred at first. As everyone knows, flattery will get you everywhere. It may comfort the apprehensive reader to learn that there is not going to be much walking to school in the snow in this story. On the contrary, rather than thinking how hard I had it during my scientific career, I find it inconceivable that anyone could have had a smoother ride. At the time I began my career, science was an expanding enterprise in the United States that welcomed the young. Only in such an opportunity-rich environment would someone like me have stood a chance. The contrast between that world and the dog-eat-dog world young scientists confront today is stark.     

Pharmacological and structural characterization of long-sarafotoxins, a new family of endothelin-like peptides: Role of the C-terminus extension

Long-sarafotoxins (l-SRTXs) have recently been identified in both the venom of Atractaspis microlepidota and that of Atractaspis irregularis. They are characterized by different C-terminus extensions that follow the invariant Trp21, which plays a crucial role in endothelin-receptor binding. We initially determined the toxicity and three-dimensional structures of two chemically synthesized l-SRTXs that have different C-terminus extensions, namely SRTX-m (24 aa, including extension "D-E-P") and SRTX-i3 (25 aa, including extension "V-N-R-N"). Both peptides were shown to be highly toxic in mice and displayed the cysteine-stabilized α-helical motif that characterizes endothelins and short-SRTXs, to which a longer C-terminus with variable flexibility is added. To discern the functional and pharmacological consequences of the supplementary amino acids, different chimerical as well as truncated forms of SRTX were designed and synthesized. Thus, we either removed the extra-C-terminal residues of SRTX-m or i3, or grafted the latter onto the C-terminal extremity of a short-SRTX (s-SRTX) (ie. SRTX-b). Our competitive binding assays where SRTXs competed for iodinated endothelin-1 binding to cloned ET(A) and ET(B) receptor subtypes over-expressed in CHO cells, revealed the essential role of the C-terminus extensions for ET-receptor recognition. Indeed, l-SRTXs displayed an affinity three to four orders of magnitude lower as compared to SRTX-b for the two receptor subtypes. Moreover, grafting the C-terminus extension to SRTX-b induced a drastic decrease in affinity, while its removal (truncated l-SRTXs) yielded an affinity for ET-receptors similar to that of s-SRTXs. Furthermore, we established by intracellular Ca(2+) measurements that l-SRTXs, as well as s-SRTXs, display agonistic activities. We thus confirmed in these functional assays the major difference in potency for these two SRTX families as well as the crucial role of the C-terminus extension in their various pharmacological profiles. Finally, one of the chimeric toxin synthesized in this study appears to be one of the most potent and selective ligand of the ET(B) receptor known to date.     

Two new Polyangium species,P. aurulentum sp. nov. and P. jinanense sp. nov., isolated from a soil sample

Polyangium belongs to Polyangiaceae family of Myxococcales, a taxonomic group well-known for their extraordinary social lifestyle and diverse novel gene clusters of secondary metabolites. A yellow-golden strain, designated SDU3-1^T, and two rose pink strains, designated SDU13 and SDU14^T, were isolated from a soil sample. These three strains were aerobic, mesophilic, not salt-tolerant and were able to prey on living microorganisms. SDU13 and SDU14^T formed solitary sporangioles under starvation conditions, while SDU3-1^T had no fruiting body structures. They showed 95.9–97.0% (SDU3-1^T) or 98.7–98.9% (SDU13 and SDU14^T) 16S rRNA gene similarity with the type strains of Polyangium, but were phylogenetically separate from them based on the 16S rRNA gene and genome sequences. Their genomes were 12.3 Mbp (SDU3-1^T), 13.9 Mbp (SDU13) and 13.8 Mbp (SDU14^T) with the G + C content range of 68.3–69.4 mol%. The average nucleotide identity and DNA-DNA hybridization analyses of genomes further indicated that these three strains belonged to two new species in Polyangium. Their major fatty acids were C_18:1ω9c, C_16:0 and C_18:0. The polyphasic taxonomic characterization suggest that the three strains represent two novel species in the genus Polyangium, for which the names Polyangium aurulentum sp. nov. and Polyangium jinanense sp. nov. are proposed, and the type strains are SDU3-1^T (=CGMCC 1.16875^T = KCTC 72136^T) and SDU14^T (=CCTCC AB 2021123^T = KCTC 82625^T), respectively.     

Complete 1H and 13C NMR assignment of digeneaside, a low-molecular-mass carbohydrate produced by red seaweeds

Digeneaside (alpha-D-mannopyranosyl-(1-->2)-D-glycerate) was extracted from the red algae, Bostrychia binderii, and purified by adsorption and gel-filtration chromatography. HPLC and ESI-MS techniques were used to follow purification steps and characterize digeneaside. NMR spectroscopy experiments (1D 1H, 13C, DEPT and 2D HMQC, COSY and TOCSY) were used to fully assign the 1H and 13C spectra.     

Inhibitors of the tyrosine kinase EphB4. Part 4: Discovery and optimization of a benzylic alcohol series

Optimization of our bis-anilino-pyrimidine series of EphB4 kinase inhibitors led to the discovery of compound 12 which incorporates a key m-hydroxymethylene group on the C4 aniline. 12 displays a good kinase selectivity profile, good physical properties and pharmacokinetic parameters, suggesting it is a suitable candidate to investigate the therapeutic potential of EphB4 kinase inhibitors.     

Complete genome sequences of Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4, polysaccharide-degrading members of the family Flavobacteriaceae

Two members of the family Flavobacteriaceae were isolated from subseafloor sediments using artificial seawater with cellulose, xylan, and chitin as the sole carbon and energy sources. Here, we present the complete genome sequences of Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4, which both encode putatively novel enzymes involved in cellulose, hemicellulose, and chitin metabolism.     

Complete Genome Sequence of the Hyperthermophilic Archaeon Thermococcus sp. Strain CL1, Isolated from a Paralvinella sp. Polychaete Worm Collected from a Hydrothermal Vent

Thermococcus sp. strain CL1 is a hyperthermophilic, anaerobic, and heterotrophic archaeon isolated from a Paralvinella sp. polychaete worm living on an active deep-sea hydrothermal sulfide chimney on the Cleft Segment of the Juan de Fuca Ridge. To further understand the distinct characteristics of this archaeon at the genome level, its genome was completely sequenced and analyzed. Here, we announce the complete genome sequence (1,950,313 bp) of Thermococcus sp. strain CL1, with a focus on H(2)- and energy-producing capabilities and its amino acid biosynthesis and acquisition in an extreme habitat.     

Stereochemistry of Female-Specific Normonoterpenes,Sex Pheromone Candidates from the Acarid Mite,Tyreophagus sp. (Astigmata: Acaridae)

Two normonoterpenes were detected from an unidentified Tyreophagus sp. as new female-specific components. Both planar structures were identified to be 2,6-dimethyl-5-heptenal (1) and 2,6-dimethyl-5-hepten-1-ol (2) by GC/MS co-chromatography with synthetic 1 and 2. The stereochemistry of 2 was determined to be R by a GC analysis with a chiral column, while that of 1 was presumed to be similar to 2 based on the biosynthetic aspects.     

Wahlenbergia cordiformis sp. nov. (Campanulaceae: Campanuloideae), a new woody species from Western Cape,South Africa

Wahlenbergia cordiformis, a new species of the Lightfootia‐type is described and illustrated. It is currently only known from the farm Knolfontein, in the Swartruggens region, north east of Ceres in the Western Cape, South Africa. The closest relative of W. cordiformis is unclear, but it may be closely related to either W. tenella, W. nodosa, W. tenerrima, W. oligantha or W. neorigida. Wahlenbergia cordiformis is distinguished from them by its cordate, leaf‐like calyx lobes.     

Morphology and infraciliature of two new marine urostylid ciliates: Metaurostylopsis struederkypkeae n. sp. and Thigmokeronopsis stoecki n. sp. (Ciliophora, Hypotrichida) from China

ABSTRACT. The morphology and infraciliature of two new marine urostylid ciliates, Metaurostylopsis struederkypkeae n. sp. and Thigmokeronopsis stoecki n. sp., collected from the coastal waters off Qingdao (Tsingtao), China, have been investigated. Metaurostylopsis struederkypkeae n. sp. is characterized by the slender body shape, small size, rose-reddish cell colour, and having two kinds of pigment-like granules. The larger pigment-like granules are yellow–green or grass-green in colour, oval in shape, and flattened, whereas the smaller ones are wine-reddish. Infraciliature and nuclear apparatus are similar to the well-known Metaurostylopsis marina. Thigmokeronopsis stoecki n. sp. is characterized by its large size with dark brown cell colour and grass-green cortical granules, which are large, blood-cell shaped, and sparsely distributed. The thigmotactic ciliature is conspicuous: 11–14 rows of densely arranged cirri occupy the most postoral area. Keys are provided for all the known species in both genera.