On the halogenation of N(1),N(2)-di-t-Boc-5-hydroxy-piperazic acid esters and the conformational preferences of their 5-halo-piperazic acid products. The importance of A1,3 rotameric-strain in determining N(2)-acyl piperazic acid ring conformation

In this Letter, an unambiguous synthetic strategy is reported for the preparation of enantiomerically purecis-5-halo-piperazic acid derivatives in single diastereoisomer form. Contrary to the recent report by Shin and co-workers (Chem. Lett. 2001, 1172), in which it is claimed that the Ph₃P and N-chlorosuccinimide (NCS)-mediated chlorination of (3R,5S)-trans-N(1),N(2)-di-t-Boc-5-hydroxy-piperazic acid derivative 1proceeds with retention of configuration at C(5) to give 2, we now show that this and related Ph₃P-mediated halogenations all occur with S_N2 inversion at the alcohol center, as is customary for such reactions. Specifically, we demonstrate that the (3R,5S)-trans-5-Cl-piperazic acid derivative 2 claimed by Shin and co-workers (Chem. Lett. 2001, 1172) is in actual fact the chlorinated (3S,5R)-enantiomer 6, which must have been prepared from the cis-(3S,5S)-alcohol 3, a molecule whose synthesis is not formally described in the Shin paper. We further show here that the cis-(3R,5R)-5-Cl-Piz 13 claimed by Shin and co-workers inChem. Lett. 2001, 1172, is also (3S,5R)-trans-5-Cl-Piz 6. Authentic 13 has now been synthesized by us, for the very first time, here. Since Lindsley and Kennedy have recently utilized the now invalid Shin and co-workers’ retentive Ph₃P/NCS chlorination procedure on 1 in their synthetic approach to piperazimycin A (Tetrahedron Lett. 2010, 51, 2493), it follows that their claimed 5-Cl-Piz-containing dipeptide 25 probably has the alternate structure 26, where the 5-Cl-Piz residue has a 3,5-cis-configuration. The aforementioned stereochemical misassignments appear to have come from a mix-up of starting materials by Shin and co-workers (Chem. Lett. 2001, 1172), and an under-appreciation of the various steric and conformational effects that operate in N(2)-acylated piperazic acid systems, most especially rotameric A^1,3-strain. The latter has now been unambiguously delineated and defined here under the banner of the A^1,3-rotamer effect.

Biosynthesis and structure of the Burkholderia cenocepacia K56-2 lipopolysaccharide core oligosaccharide:truncation of the core oligosaccharide leads to increased binding and sensitivity to polymyxin B

Burkholderia cenocepacia is an opportunistic pathogen that displays a remarkably high resistance to antimicrobial peptides. We hypothesize that high resistance to antimicrobial peptides in these bacteria is because of the barrier properties of the outer membrane. Here we report the identification of genes for the biosynthesis of the core oligosaccharide (OS) moiety of the B. cenocepacia lipopolysaccharide. We constructed a panel of isogenic mutants with truncated core OS that facilitated functional gene assignments and the elucidation of the core OS structure in the prototypic strain K56-2. The core OS structure consists of three heptoses in the inner core region, 3-deoxy-d-manno-octulosonic acid, d-glycero-d-talo-octulosonic acid, and 4-amino-4-deoxy-l-arabinose linked to d-glycero-d-talo-octulosonic acid. Also, glucose is linked to heptose I, whereas heptose II carries a second glucose and a terminal heptose, which is the site of attachment of the O antigen. We established that the level of core truncation in the mutants was proportional to their increased in vitro sensitivity to polymyxin B (PmB). Binding assays using fluorescent 5-dimethylaminonaphthalene-1-sulfonyl-labeled PmB demonstrated a correlation between sensitivity and increased binding of PmB to intact cells. Also, the mutant producing a heptoseless core OS did not survive in macrophages as compared with the parental K56-2 strain. Together, our results demonstrate that a complete core OS is required for full PmB resistance in B. cenocepacia and that resistance is due, at least in part, to the ability of B. cenocepacia to prevent binding of the peptide to the bacterial cell envelope.

Strain dependent microstructural modifications of BiCrO3 epitaxial thin films

Strain-dependent microstructural modifications were observed in epitaxial BiCrO3 (BCO) thin films fabricated on single crystalline substrates, utilizing pulsed laser deposition. The following conditions were employed to modify the epitaxial-strain: (i) in-plane tensile strain, BCOSTO [BCO grown on buffered SrTiO3 (001)] and in-plane compressive strain, BCONGO [BCO grown on buffered NdGaO3 (110)] and (ii) varying BCO film thickness. A combination of techniques like X-ray diffraction, X-ray photoelectron spectroscopy (XPS) and high resolution transmission electron microscopy (TEM) was used to analyse the epitaxial growth quality and the microstructure of BCO. Our studies revealed that in the case of BCOSTO, a coherent interface with homogeneous orthorhombic phase is obtained only for BCO film with thicknesses, d < 50 nm. All the BCOSTO films with d = 50 nm were found to be strain-relaxed with an orthorhombic phase showing 1/2 <100> and 1/4 <101> satellite reflections, the latter oriented at 45° from orthorhombic diffraction spots. High angle annular dark field scanning TEM of these films strongly suggested that the satellite reflections, 1/2 <100> and 1/4 <101>, originate from the atomic stacking sequence changes (or “modulated structure”) as reported for polytypes, without altering the chemical composition. The unaltered stoichiometry was confirmed by estimating both valency of Bi and Cr cations by surface and in-depth XPS analysis as well as the stoichiometric ratio (1 Bi:1 Cr) using scanning TEM–energy dispersive X-ray analysis. In contrast, compressively strained BCONGO films exhibited monoclinic symmetry without any structural modulations or interfacial defects, up to d ~ 200 nm. Our results indicate that both the substrate-induced in-plane epitaxial strain and the BCO film thickness are the crucial parameters to stabilise a homogeneous BCO phase in an epitaxially grown film.

Predation on mayfly nymph, Baetis rhodani, by native and introduced Gammarus: direct effects and the facilitation of predation by salmonids.

1. In a series of laboratory experiments, we assessed the predatory nature of the native Irish amphipod, Gammarus duebeni celticus, and the introduced G. pulex, towards the mayfly nymph Baetis rhodani. We also investigated alterations in microhabitat use and drift behaviour of B. rhodani in the presence of Gammarus, and indirect predatory interactions with juvenile Atlantic salmon, Salmo salar. 2. In trials with single predators and prey, B. rhodani survival was significantly lower when Gammarus were free to interact with nymphs as than when Gammarus were isolated from them. The invader G. pulex reduced the survival of B. rhodani more rapidly than did the native G. d. celticus. Both Gammarus spp. were active predators. 3. In `patch' experiments, B. rhodani survival was significantly lower both when G. pulex and G. d. celticus were present, although the effect of the two Gammarus species did not differ. Again, active predation of nymphs by Gammarus was observed. Significantly more nymphs occurred on the top and sides of a tile, and per capita drifts were significantly higher, when Gammarus were present. Baetis rhodani per capita drift was also significantly higher in the presence of the introduced G. pulex than with the native G. d. celticus. 4. Gammarus facilitated predation by salmon parr of B. rhodani by significantly increasing fish–nymph encounters on exposed gravel and in the drift. There were no differential effects of the two Gammarus spp. on fish –B. rhodani encounters or consumption. 5. We conclude that Gammarus as a predator can have lethal, nonlethal, direct and indirect effects in freshwaters. We stress the need for recognition of this predatory role when assigning Gammarus spp. to a `Functional Feeding Group'.

Electrooxidation of the iodides [C(4)mim]I, LiI, NaI, KI, RbI, and CsI in the room temperature ionic liquid [C(4)mim][NTf2]

The electrochemical oxidation of 1-butyl-3-methylimidazolium iodide, [C(4)mim]I, has been investigated by cyclic voltammetry at a platinum microelectrode at varying concentrations in the RTIL 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [C(4)mim][NTf2]. Two oxidation peaks were observed. The first peak is assigned to the oxidation of iodide to triiodide, in an overall two-electron process: 3I(-)- 2e(-) -> I-3(-). At higher potentials, the electrogenerated triiodide oxidizes to iodine, in an overall one-electron process: I-3(-) - e(-) -> 3/2I(2). An average diffusion coefficient, D, for I- of 1.55 x 10(-11) m(2) s(-1) was obtained. A digital simulation program was used to simulate the voltammetric response, and kinetic parameters were successfully extracted. The parameters deduced from the simulation include D for I-, I-3(-), and I-2 and K-eq,K-2, the equilibrium constant for the reaction of iodide and iodine to form triiodide. Values for these parameters are of the same order as those previously published for the oxidation of Br- in the same RTIL [Allen et al. J. Electroanal. Chem. 2005, 575, 311]. Next, the cyclic voltammetry of five different inorganic iodide salts was studied by dissolving small amounts of the solid in [C(4)mim][NTf2]. Similar oxidation peaks were observed, revealing diffusion coefficients of ca. 0.55, 1.14, 1.23, 1.44, and 1.33 x 10(-11) m(2) s(-1) and solubilities of 714, 246, 54, 83, and 36 mM for LiI, NaI, KI, RbI, and CsI, respectively. The slightly smaller diffusion coefficients for the XI salts (compared to [C(4)mim]I) may indicate that I- is ion-paired with Li+, Na+, K+, Rb+, and Cs+ in the RTIL medium.

Complete Genome Sequence of Propionibacterium acnes Type IB Strain 6609

Propionibacterium acnes is an anaerobic Gram-positive bacterium that forms part of the normal human cutaneous microbiota and is thought to play a central role in acne vulgaris, a chronic inflammatory disease of the pilosebaceous unit (I. Kurokawa et al., Exp. Dermatol. 18:821-832, 2009). Here we present the whole genome sequence of P. acnes type IB strain 6609, which was recovered from a skin sample from a woman with no recorded acne history and is thus considered a nonpathogenic strain (I. Nagy, Microbes Infect. 8:2195-2205, 2006).

The synthesis, characterisation and reactivity of 2-phosphanylethylcyclopentadienyl complexes of cobalt, rhodium and iridium

2-Phosphanylethylcyclopentadienyl lithium compounds, Li[C5R'(4)(CH2)(2)PR2] (R = Et, R' = H or Me, R = Ph, R' = Me), have been prepared from the reaction of spirohydrocarbons C5R'(4)(C2H4) with LiPR2. C5Et4HSiMe2CH2PMe2, was prepared from reaction of Li[C5Et4] with Me2SiCl2 followed by Me2PCH2Li. The lithium salts were reacted with [RhCl(CO)2]2,[IrCl(CO)3] or [Co-2(CO)(8)] to give [M(C5R'(4)(CH2) 2PR2)(CO)] (M = Rh, R = Et, R' = H or Me, R= Ph, R' = Me; M = Ir or Co, R = Et, R' = Me), which have been fully characterised, in many cases crystallographically as monomers with coordination of the phosphorus atom and the cyclopentadienyl ring. The values of nu(CO) for these complexes are usually lower than those for the analogous complexes without the bridge between the cyclopentadienyl ring and the phosphine, the exception being [Rh(Cp'(CH2)(2)PEt2)(CO)] (Cp' = C5Me4), the most electron rich of the complexes. [Rh(C5Et4SiMe2CH2PMe2)(CO)] may be a dimer. [Co-2(CO)(8)] reacts with C5H5(CH2)(2)PEt2 or C5Et4HSiMe2CH2PMe2 (L) to give binuclear complexes of the form [Co-2(CO)(6)L-2] with almost linear PCoCoP skeletons. [Rh(Cp'(CH2)(2)PEt2)(CO)] and [Rh(Cp'(CH2)(2)PPh2)(CO)] are active for methanol carbonylation at 150 degrees C and 27 bar CO, with the rate using [Rh(Cp'(CH2)(2)PPh2)(CO)] (0.81 mol dm(-3) h(-1)) being higher than that for [RhI2(CO)(2)](-) (0.64 mol dm(-3) h(-1)). The most electron rich complex, [Rh(Cp'(CH2)(2)PEt2)(CO)] (0.38 mol dm(-3) h(-1)) gave a comparable rate to [Cp*Rh(PEt3)(CO)] (0.30 mol dm(-3) h(-1)), which was unstable towards oxidation of the phosphine. [Rh(Cp'(CH2)(2)PEt2)I-2], which is inactive for methanol carbonylation, was isolated after the methanol carbonylation reaction using [Rh(Cp'(CH2)(2)PEt2)(CO)].

Reconstitution of O-specific lipopolysaccharide expression in Burkholderia cenocepacia strain J2315, which is associated with transmissible infections in patients with cystic fibrosis

Burkholderia cenocepacia is an opportunistic bacterium that infects patients with cystic fibrosis. B. cenocepacia strains J2315, K56-2, C5424, and BC7 belong to the ET12 epidemic clone, which is transmissible among patients. We have previously shown that transposon mutants with insertions within the O antigen cluster of strain K56-2 are attenuated for survival in a rat model of lung infection. From the genomic DNA sequence of the O antigen-deficient strain J2315, we have identified an O antigen lipopolysaccharide (LPS) biosynthesis gene cluster that has an IS402 interrupting a predicted glycosyltransferase gene. A comparison with the other clonal isolates revealed that only strain K56-2, which produced O antigen and displayed serum resistance, lacked the insertion element inserted within the putative glycosyltransferase gene. We cloned the uninterrupted gene and additional flanking sequences from K56-2 and conjugated this plasmid into strains J2315, C5424, and BC7. All the exconjugants recovered the ability to form LPS O antigen. We also determined that the structure of the strain K56-2 O antigen repeat, which was absent from the LPS of strain J2315, consisted of a trisaccharide unit made of rhamnose and two N-acetylgalactosamine residues. The complexity of the gene organization of the K56-2 O antigen cluster was also investigated by reverse transcription-PCR, revealing several transcriptional units, one of which also contains genes involved in lipid A-core oligosaccharide biosynthesis.

Alpha-2 agonists for sedation of mechanically ventilated adults in intensive care units: a systematic review

BACKGROUND: Care of critically ill patients in intensive care units (ICUs) often requires potentially invasive or uncomfortable procedures, such as mechanical ventilation (MV). Sedation can alleviate pain and discomfort, provide protection from stressful or harmful events, prevent anxiety and promote sleep. Various sedative agents are available for use in ICUs. In the UK, the most commonly used sedatives are propofol (Diprivan(®), AstraZeneca), benzodiazepines [e.g. midazolam (Hypnovel(®), Roche) and lorazepam (Ativan(®), Pfizer)] and alpha-2 adrenergic receptor agonists [e.g. dexmedetomidine (Dexdor(®), Orion Corporation) and clonidine (Catapres(®), Boehringer Ingelheim)]. Sedative agents vary in onset/duration of effects and in their side effects. The pattern of sedation of alpha-2 agonists is quite different from that of other sedatives in that patients can be aroused readily and their cognitive performance on psychometric tests is usually preserved. Moreover, respiratory depression is less frequent after alpha-2 agonists than after other sedative agents.

OBJECTIVES: To conduct a systematic review to evaluate the comparative effects of alpha-2 agonists (dexmedetomidine and clonidine) and propofol or benzodiazepines (midazolam and lorazepam) in mechanically ventilated adults admitted to ICUs.

DATA SOURCES: We searched major electronic databases (e.g. MEDLINE without revisions, MEDLINE In-Process & Other Non-Indexed Citations, EMBASE and Cochrane Central Register of Controlled Trials) from 1999 to 2014.

METHODS: Evidence was considered from randomised controlled trials (RCTs) comparing dexmedetomidine with clonidine or dexmedetomidine or clonidine with propofol or benzodiazepines such as midazolam, lorazepam and diazepam (Diazemuls(®), Actavis UK Limited). Primary outcomes included mortality, duration of MV, length of ICU stay and adverse events. One reviewer extracted data and assessed the risk of bias of included trials. A second reviewer cross-checked all the data extracted. Random-effects meta-analyses were used for data synthesis.

RESULTS: Eighteen RCTs (2489 adult patients) were included. One trial at unclear risk of bias compared dexmedetomidine with clonidine and found that target sedation was achieved in a higher number of patients treated with dexmedetomidine with lesser need for additional sedation. The remaining 17 trials compared dexmedetomidine with propofol or benzodiazepines (midazolam or lorazepam). Trials varied considerably with regard to clinical population, type of comparators, dose of sedative agents, outcome measures and length of follow-up. Overall, risk of bias was generally high or unclear. In particular, few trials blinded outcome assessors. Compared with propofol or benzodiazepines (midazolam or lorazepam), dexmedetomidine had no significant effects on mortality [risk ratio (RR) 1.03, 95% confidence interval (CI) 0.85 to 1.24, I (2) = 0%; p = 0.78]. Length of ICU stay (mean difference -1.26 days, 95% CI -1.96 to -0.55 days, I (2) = 31%; p = 0.0004) and time to extubation (mean difference -1.85 days, 95% CI -2.61 to -1.09 days, I (2) = 0%; p < 0.00001) were significantly shorter among patients who received dexmedetomidine. No difference in time to target sedation range was observed between sedative interventions (I (2) = 0%; p = 0.14). Dexmedetomidine was associated with a higher risk of bradycardia (RR 1.88, 95% CI 1.28 to 2.77, I (2) = 46%; p = 0.001).

LIMITATIONS: Trials varied considerably with regard to participants, type of comparators, dose of sedative agents, outcome measures and length of follow-up. Overall, risk of bias was generally high or unclear. In particular, few trials blinded assessors.

CONCLUSIONS: Evidence on the use of clonidine in ICUs is very limited. Dexmedetomidine may be effective in reducing ICU length of stay and time to extubation in critically ill ICU patients. Risk of bradycardia but not of overall mortality is higher among patients treated with dexmedetomidine. Well-designed RCTs are needed to assess the use of clonidine in ICUs and identify subgroups of patients that are more likely to benefit from the use of dexmedetomidine.

STUDY REGISTRATION: This study is registered as PROSPERO CRD42014014101.

FUNDING: The National Institute for Health Research Health Technology Assessment programme. The Health Services Research Unit is core funded by the Chief Scientist Office of the Scottish Government Health and Social Care Directorates.

Biomarker responses to folic acid intervention in healthy adults: a meta-analysis of randomized controlled trials

BACKGROUND: The task of revising dietary folate recommendations for optimal health is complicated by a lack of data quantifying the biomarker response that reliably reflects a given folate intake.

OBJECTIVE: We conducted a dose-response meta-analysis in healthy adults to quantify the typical response of recognized folate biomarkers to a change in folic acid intake.

DESIGN: Electronic and bibliographic searches identified 19 randomized controlled trials that supplemented with folic acid and measured folate biomarkers before and after the intervention in apparently healthy adults aged ≥18 y. For each biomarker response, the regression coefficient (β) for individual studies and the overall pooled β were calculated by using random-effects meta-analysis.

RESULTS: Folate biomarkers (serum/plasma and red blood cell folate) increased in response to folic acid in a dose-response manner only up to an intake of 400 μg/d. Calculation of the overall pooled β for studies in the range of 50 to 400 μg/d indicated that a doubling of folic acid intake resulted in an increase in serum/plasma folate by 63% (71% for microbiological assay; 61% for nonmicrobiological assay) and red blood cell folate by 31% (irrespective of whether microbiological or other assay was used). Studies that used the microbiological assay indicated lower heterogeneity compared with studies using nonmicrobiological assays for determining serum/plasma (I(2) = 13.5% compared with I(2) = 77.2%) and red blood cell (I(2) = 45.9% compared with I(2) = 70.2%) folate.

CONCLUSIONS: Studies administering >400 μg folic acid/d show no dose-response relation and thus will not yield meaningful results for consideration when generating dietary folate recommendations. The calculated folate biomarker response to a given folic acid intake may be more robust with the use of a microbiological assay rather than alternative methods for blood folate measurement.

Genomotyping of Pseudomonas putida strains using P-putida KT2440-based high-density DNA microarrays: implications for transcriptomics studies

Pseudomonas putida KT2440 is the only fully sequenced P. putida strain. Thus, for transcriptomics and proteomics studies with other P. putida strains, the P. putida KT2440 genomic database serves as standard reference. The utility of KT2440 whole-genome, high-density oligonucleotide microarrays for transcriptomics studies of other Pseudomonas strains was investigated. To this end, microarray hybridizations were performed with genomic DNAs of subcultures of P. putida KT2440 (DSM6125), the type strain (DSM291(T)), plasmid pWW0-containing KT2440-derivative strain mt-2 (DSM3931), the solvent-tolerant P. putida S12, and several other Pseudomonas strains. Depending on the strain tested, 22 to 99% of all genetic elements were identified in the genomic DNAs. The efficacy of these microarrays to study cellular function was determined for all strains included in the study. The vast majority of DSM6125 genes encoding proteins of primary metabolism and genes involved in the catabolism of aromatic compounds were identified in the genomic DNA of strain S12: a prerequisite for reliable transcriptomics analyses. The genomotypic comparisons between Pseudomonas strains were used to construct highly discriminative phylogenetic relationships. DSM6125 and DSM3931 were indistinguishable and clustered together with strain S12 in a separate group, distinct from DSM291(T). Pseudomonas monteilii (DSM14164) clustered well with P. putida strains.

Effect of interleukin-6 polymorphisms on human longevity: A systematic review and meta-analysis

Several studies have assessed changes in frequency of -174 interleukin (IL)-6 single nucleotide polymorphism (SNP) with age. If IL-6 tracks with disability and age-related diseases, then there should be reduction, in the oldest old, of the frequency of homozgyous GG subjects, who produce higher IL-6 levels. However, discordant results have been obtained. To explore the relationship between this polymorphism and longevity, we analyzed individual data on long-living subjects and controls from eight case-control studies conducted in Europeans, using meta-analysis. There was no significant difference in the IL-6 genotype between the oldest old and controls (Odds Ratio [OR]=0.96; 95% C.I.: 0.77-1.20; p=0.71), but there was significant between-study heterogeneity (I(2)=55.5%). In a subgroup analyses when male centenarians from the three Italian studies were included, the frequency of the IL-6 -174 GG genotype was significantly lower than the other genotypes (OR=0.49; 95% C.I.: 0.31-0.80; p=0.004), with no evidence of heterogeneity (I(2)=0%). Our data supports a negative association between the GG genotype of IL-6 SNP and longevity in Italian centenarians, with males who carry the genotype being two times less likely to reach extreme old age compared with subjects carrying CC or CG genotypes. These findings were not replicated in other European groups suggesting a possible interaction between genetics, sex and environment in reaching longevity.