Identification of Burkholderia cenocepacia genes required for bacterial survival in vivo

Burkholderia cenocepacia (formerly Burkholderia cepacia complex genomovar III) causes chronic lung infections in patients with cystic fibrosis. In this work, we used a modified signature-tagged mutagenesis (STM) strategy for the isolation of B. cenocepacia mutants that cannot survive in vivo. Thirty-seven specialized plasposons, each carrying a unique oligonucleotide tag signature, were constructed and used to examine the survival of 2,627 B. cenocepacia transposon mutants, arranged in pools of 37 unique mutants, after a 10-day lung infection in rats by using the agar bead model. The recovered mutants were screened by real-time PCR, resulting in the identification of 260 mutants which presumably did not survive within the lungs. These mutants were repooled into smaller pools, and the infections were repeated. After a second screen, we isolated 102 mutants unable to survive in the rat model. The location of the transposon in each of these mutants was mapped within the B. cenocepacia chromosomes. We identified mutations in genes involved in cellular metabolism, global regulation, DNA replication and repair, and those encoding bacterial surface structures, including transmembrane proteins and cell surface polysaccharides. Also, we found 18 genes of unknown function, which are conserved in other bacteria. A subset of 12 representative mutants that were individually examined using the rat model in competition with the wild-type strain displayed reduced survival, confirming the predictive value of our STM screen. This study provides a blueprint to investigate at the molecular level the basis for survival and persistence of B. cenocepacia within the airways.

Holocene climate change, vegetation history and human impact in the Central Mediterranean: evidence from the Maltese Islands

Holocene climates and human impact in the Mediterranean basin have received much attention, but the Maltese Islands in the Central Mediterranean, although a pivotal area, have been little researched. Here, sedimentary and palynological data are presented for three cores from the Holocene coastal and shallowmarine
deposits of the Maltese Islands. These show deforestation from Pinus-Cupressaceae woodland in the early Neolithic, and then a long, but relatively stable history of agriculturally degraded environments to the present day. The major climate events which have affected the Italian and Balkan peninsulas to the
north, and Tunisia to the south, are not reflected in the pollen diagrams from the Maltese Islands because of the strong anthropogenic imprint on the Maltese vegetation from early in the Neolithic. Previous suggestions of environmentally-driven agricultural collapse at the end of the Neolithic appear, however,
to be substantiated and may be linked to regional aridification around 4300 cal. BP. Depopulation in early Medieval times is not supported by the current palynological evidence.

Extracellular Loop 2 of the Free Fatty Acid Receptor 2 Mediates Allosterism of a Phenylacetamide Ago-Allosteric Modulator

Allosteric agonists are powerful tools for exploring the pharmacology of closely related G protein-coupled receptors that have nonselective endogenous ligands, such as the short chain fatty acids at free fatty acid receptors 2 and 3 (FFA2/GPR43 and FFA3/GPR41, respectively). We explored the molecular mechanisms mediating the activity of 4-chloro-alpha-(1-methylethyl)-N-2-thiazolylbenzeneacetamide (4-CMTB), a recently described phenylacetamide allosteric agonist and allosteric modulator of endogenous ligand function at human FFA2, by combining our previous knowledge of the orthosteric binding site with targeted examination of 4-CMTB structure-activity relationships and mutagenesis and chimeric receptor generation. Here we show that 4-CMTB is a selective agonist for FFA2 that binds to a site distinct from the orthosteric site of the receptor. Ligand structure-activity relationship studies indicated that the N-thiazolyl amide is likely to provide hydrogen bond donor/acceptor interactions with the receptor. Substitution at Leu(173) or the exchange of the entire extracellular loop 2 of FFA2 with that of FFA3 was sufficient to reduce or ablate, respectively, allosteric communication between the endogenous and allosteric agonists. Thus, we conclude that extracellular loop 2 of human FFA2 is required for transduction of cooperative signaling between the orthosteric and an as-yet-undefined allosteric binding site of the FFA2 receptor that is occupied by 4-CMTB.

A silicone elastomer vaginal ring for HIV prevention containing two microbicides with different mechanisms of action

Vaginal rings are currently being developed for the long-term (at least 30 days) continuous delivery of microbicides against human immunodeficiency virus (HIV). Research to date has mostly focused on devices containing a single antiretroviral compound, exemplified by the 25 mg dapivirine ring currently being evaluated in a Phase III clinical study. However, there is a strong clinical rationale for combining antiretrovirals with different mechanisms of action in a bid to increase breadth of protection and limit the emergence of resistant strains. Here we report the development of a combination antiretroviral silicone elastomer matrix-type vaginal ring for simultaneous controlled release of dapivirine, a non-nucleoside reverse transcriptase inhibitor, and maraviroc, a CCR5-targeted HIV-1 entry inhibitor. Vaginal rings loaded with 25 mg dapivirine and various quantities of maraviroc (50– 400 mg) were manufactured and in vitro release assessed. The 25 mg dapivirine and 100 mg maraviroc formulation was selected for further study. A 24-month pharmaceutical stability evaluation was conducted, indicating good product stability in terms of in vitro release, content assay, mechanical properties and related substances. This combination ring product has now progressed to Phase I clinical testing.

Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus

Barrett's esophagus is an increasingly common disease that is strongly associated with reflux of stomach acid and usually a hiatus hernia, and it strongly predisposes to esophageal adenocarcinoma (EAC), a tumor with a very poor prognosis. We report the first genome-wide association study on Barrett's esophagus, comprising 1,852 UK cases and 5,172 UK controls in the discovery stage and 5,986 cases and 12,825 controls in the replication stage. Variants at two loci were associated with disease risk: chromosome 6p21, rs9257809 (P(combined) = 4.09 × 10(-9); odds ratio (OR) = 1.21, 95% confidence interval (CI) =1.13-1.28), within the major histocompatibility complex locus, and chromosome 16q24, rs9936833 (P(combined) = 2.74 × 10(-10); OR = 1.14, 95% CI = 1.10-1.19), for which the closest protein-coding gene is FOXF1, which is implicated in esophageal development and structure. We found evidence that many common variants of small effect contribute to genetic susceptibility to Barrett's esophagus and that SNP alleles predisposing to obesity also increase risk for Barrett's esophagus.

Missing Links, Cultural Modernity and the Dead: Anatomically Modern Humans in the Great Cave of Niah (Sarawak, Borneo)

The Great Cave of Niah in Sarawak (northern Borneo) came into the gaze of Western Science through the work of Alfred Russell Wallace, who came to Sarawak in the 1850s to search for ‘missing links’ in his pioneering studies of evolution and the natural history of Island Southeast Asia and Australasia. The work of Tom and Barbara Harrisson in the 1950s and 1960s placed the Great Cave, and particularly their key find, the ‘Deep Skull’, at the nexus of the evolving archaeological framework for the region: for decades the skull, dated in 1958 by adjacent charcoal to c.40,000 BP, was the oldest fossil of an anatomically modern human anywhere in the world and thus critical to ideas about human evolution and dispersal. Although several authorities later questioned the provenance and antiquity of the Deep Skull, renewed investigations of the Harrisson excavations since 2000 have shown that it can be attributed securely to a specific location in the Pleistocene stratigraphy, with direct U-series dating on a piece of the skull indicating an age for it of c.37,500 BP and the first evidence for associated human activity at the site going back to c.50,000 BP. The new work also indicates that the skull is part of a cultural deposit, perhaps a precursor to the long tradition in Borneo of processing of the dead and secondary burial. These indicators of cultural complexity chime with the complexity of the subsistence behaviour of the early users of the caves discussed by Philip Piper and Ryan Rabett in chapter ten of this volume.

Foraging-farming transitions at the Niah Caves, Sarawak, Borneo

The Niah Caves in Sarawak, Borneo, have captured evidence for people and economies of 8000 and 4000 years ago. Although not continuous on this site, these open two windows on to life at the cultural turning point, broadly equivalent to the transition from Mesolithic to Neolithic. They have much in common, inferring that the occupants, perhaps belonging to an older maritime dispersal, had a choosy appetite for the Neolithic package.

Oxygen isotopes from Phorcus (Osilinus) turbinatus shells as a proxy for sea surface temperature in the central Mediterranean: a case study from Malta.

The marine topshell, Phorcus (Osilinus) turbinatus, is a common component of many archaeological sites in the Mediterranean. This species has been successfully used as a palaeoclimate proxy in Italy. To test whether d18O from P. turbinatus shells can serve as a reliable palaeoclimate archive for other regions of the Mediterranean, we collected live P. turbinatus from the northeast coast of Malta each month for a year. The d18OSHELL values of the outermost growth increments of these live-collected shells ranged between-0.4 and+2.4‰. These values correspond to growing temperatures calculated from shell edge d18O of between 15 °C and 27 °C. Calculated shell edge sea surface temperatures are highly correlated with instrumental records of sea surface temperature recorded over the period of collection. The individuals analysed for this study are smaller than P. turbinatus from populations studied elsewhere in the Mediterranean. Nonetheless, d18OSHELL provides a robust record of sea surface temperatures, suggesting that smaller/younger shells in archaeological deposits can still provide reliable palaeothermometry records. This study extends the upper growth limit P. turbinatus by 2 °C compared with the previous studies of P. turbinatus in the Mediterranean and suggests that, contrary to the previous studies, growth shutdown does not occur in all P. turbinatus when sea surface temperatures exceed 25 °C. This may reflect the higher sample resolution that can be obtained from smaller/faster growing shells, or it may reflect actual higher growth tolerances of P. turbinatus populations in Malta. By showing that P. turbinatus precipitate their shells in d18O equilibrium with surrounding sea water, this study reinforces the potential for the stable isotope chemistry of P. turbinatus shells preserved in Mediterranean archaeological sites to provide a window into the climate and seasonality regimes of the past.

A 2300 yr record of sago and rice use from the southern Kelabit Highlands of Sarawak, Malaysian Borneo

Rice and sago are today important staples for many subsistence farmers and nomadic hunter-gatherers living in interior Borneo, but the cultural antiquity of these staples remains poorly understood. This study examines a 2300 yr sedimentary record from a palaeochannel near the village of Pa’Dalih in the southern Kelabit Highlands. Pollen and phytolith evidence indicate significant use of the sago palm Eugeissona near the channel during this period. Oryza phytoliths likely belonging to domesticated rice varieties are also recorded, although rice may have been used to a lesser extent than the sago palms. A rise in cultural activity takes place between c. 1715 and 1600 cal. BP, shown by increased frequency of fires.

Patterns of Holocene relative sea level change in the North of Britain and Ireland

Temporal and spatial patterns of relative sea level (RSL) change in the North of Britain and Ireland during the Holocene are examined. Four episodes, each defined by marked changes in the RSL trend, are identified. Each episode is marked by a rise to a culminating shoreline followed by a fall. Episode HRSL-1 dates from the Younger Dryas to early in the Holocene; HRSL-2 to HRSL-4 occurred later in the Holocene. There is extensive evidence for each episode, and on this basis the spatial distribution of the altitude data for three culminating shorelines and a shoreline formed at the time of the Holocene Storegga Slide tsunami (ca 8110 ± 100 cal. BP) is analysed. Ordinary Kriging is used to determine the general pattern, following which Gaussian Trend Surface Analysis is employed. Recognising that empirical measurements of RSL change can be unevenly distributed spatially, a new approach is introduced which enables the developing pattern to be identified. The patterns for the most widely occurring shorelines were analysed and found to be similar and common centre and axis models were developed for all shorelines. The analyses described provide models of the spatial pattern of Holocene RSL change in the area between ca 8100 cal. BP and ca 1000 cal. BP based on 2262 high resolution shoreline altitude measurements. These models fit the data closely, no shoreline altitude measurement lying more than −1.70 m or +1.82 m from the predicted value. The models disclose a similar pattern to a recently published Glacial Isostatic Adjustment model for present RSL change across the area, indicating that the overall spatial pattern of RSL change may not have varied greatly during the last ca 8000 years.

Apolipoprotein-defined lipoproteins and apolipoproteins:Associations with abnormal albuminuria in type 1 diabetes in the diabetes control and complications trial/epidemiology of diabetes interventions and complications cohort

Dyslipoproteinemia has been associated with nephropathy in diabetes, with stronger correlations in men than in women. We aimed to characterize and compare plasma lipoprotein profiles associated with normal and increased albuminuria in men and women using apolipoprotein-defined lipoprotein subclasses and simple apolipoprotein measures.

High concentrations of AGE-LDL and oxidized LDL in circulating immune complexes are associated with progression of retinopathy in type 1 diabetes

To determine whether immunocomplexes (ICs) containing advanced glycation end product (AGE)-LDL (AGE-LDL) and oxidized LDL (oxLDL) contribute to the development of retinopathy over a 16-year period in subjects with type 1 diabetes.