Within-host evolution of Staphylococcus aureus during asymptomatic carriage

Background Staphylococcus aureus is a major cause of healthcare associated mortality, but like many important bacterial pathogens, it is a common constituent of the normal human body flora. Around a third of healthy adults are carriers. Recent evidence suggests that evolution of S. aureus during nasal carriage may be associated with progression to invasive disease. However, a more detailed understanding of within-host evolution under natural conditions is required to appreciate the evolutionary and mechanistic reasons why commensal bacteria such as S. aureus cause disease. Therefore we examined in detail the evolutionary dynamics of normal, asymptomatic carriage. Sequencing a total of 131 genomes across 13 singly colonized hosts using the Illumina platform, we investigated diversity, selection, population dynamics and transmission during the short-term evolution of S. aureus. Principal Findings We characterized the processes by which the raw material for evolution is generated: micro-mutation (point mutation and small insertions/deletions), macro-mutation (large insertions/deletions) and the loss or acquisition of mobile elements (plasmids and bacteriophages). Through an analysis of synonymous, non-synonymous and intergenic mutations we discovered a fitness landscape dominated by purifying selection, with rare examples of adaptive change in genes encoding surface-anchored proteins and an enterotoxin. We found evidence for dramatic, hundred-fold fluctuations in the size of the within-host population over time, which we related to the cycle of colonization and clearance. Using a newly-developed population genetics approach to detect recent transmission among hosts, we revealed evidence for recent transmission between some of our subjects, including a husband and wife both carrying populations of methicillin-resistant S. aureus (MRSA). Significance This investigation begins to paint a picture of the within-host evolution of an important bacterial pathogen during its prevailing natural state, asymptomatic carriage. These results also have wider significance as a benchmark for future systematic studies of evolution during invasive S. aureus disease.

The neolithisation of Liguria (NW Italy): an environmental archaeological and palaeoenvironmental perspective

The archaeological evidence compiled for Liguria has enabled the formulation of a comprehensive model of Neolithic social, technological and economic development (∼7800–5700 cal yrs BP). The model indicates that during the Early and Middle Neolithic (∼7800–6300 cal yrs BP; ‘Impressed Ware’ and ‘Square Mouthed’ pottery cultures) human activity mainly focussed on low (coastal) and mid-altitude areas. By the Late Neolithic (∼6300–5700 cal yrs BP; ‘Chassey’ culture) farming practices were taking place over a wider range of altitudes and involved transhumant pastoralism. Complementary environmental archaeological and palaeoecological records from caves, open-air sites, lakes and mires indicate that human activities had a more significant impact on the environment than previously thought. This included clearance, especially Abies, Ulmus, Fraxinus and Tilia, and woodland utilisation and management (e.g. leaf foddering), as well as cereal cultivation and animal husbandry. The influence of Middle Holocene climatic changes, especially from ∼7800 cal yrs BP, on the direction of vegetation changes and socio-economic developments during the Neolithic remain uncertain.

Environmental impact of geometric earthwork construction in pre-Columbian Amazonia

There is considerable controversy over whether pre-Columbian (pre-A.D. 1492) Amazonia was largely “pristine” and sparsely populated by slash-and-burn agriculturists, or instead a densely populated, domesticated landscape, heavily altered by extensive deforestation and anthropogenic burning. The discovery of hundreds of large geometric earthworks beneath intact rainforest across southern Amazonia challenges its status as a pristine landscape, and has been assumed to indicate extensive pre-Columbian deforestation by large populations. We tested these assumptions using coupled local- and regional-scale paleoecological records to reconstruct land use on an earthwork site in northeast Bolivia within the context of regional, climate-driven biome changes. This approach revealed evidence for an alternative scenario of Amazonian land use, which did not necessitate labor-intensive rainforest clearance for earthwork construction. Instead, we show that the inhabitants exploited a naturally open savanna landscape that they maintained around their settlement despite the climatically driven rainforest expansion that began ∼2,000 y ago across the region. Earthwork construction and agriculture on terra firme landscapes currently occupied by the seasonal rainforests of southern Amazonia may therefore not have necessitated large-scale deforestation using stone tools. This finding implies far less labor—and potentially lower population density—than previously supposed. Our findings demonstrate that current debates over the magnitude and nature of pre-Columbian Amazonian land use, and its impact on global biogeochemical cycling, are potentially flawed because they do not consider this land use in the context of climate-driven forest–savanna biome shifts through the mid-to-late Holocene.

Postprandial enrichment of triacylglycerol-rich lipoproteins with omega-3 fatty acids: lack of an interaction with apolipoprotein E genotype?

Background: We have previously demonstrated that carrying the apolipoprotein (apo) E epsilon 4 (E4+) genotype disrupts omega-3 fatty acids (n − 3 PUFA) metabolism. Here we hypothesise that the postprandial clearance of n − 3 PUFA from the circulation is faster in E4+ compared to non-carriers (E4−). The objective of the study was to investigate the fasted and postprandial fatty acid (FA) profile of triacylglycerol-rich lipoprotein (TRL) fractions: Sf >400 (predominately chylomicron CM), Sf 60 − 400 (VLDL1), and Sf 20 − 60 (VLDL2) according to APOE genotype. Methods: Postprandial TRL fractions were obtained in 11 E4+ (ε3/ε4) and 12 E4− (ε3/ε3) male from the SATgenε study following high saturated fat diet + 3.45 g/d of docosahexaenoic acid (DHA) for 8-wk. Blood samples were taken at fasting and 5-h after consuming a test-meal representative of the dietary intervention. FA were characterized by gas chromatography. Results: At fasting, there was a 2-fold higher ratio of eicosapentaenoic acid (EPA) to arachidonic acid (P = 0.046) as well as a trend towards higher relative% of EPA (P=0.063) in theSf >400 fraction of E4+. Total n − 3 PUFA in the Sf 60 − 400 and Sf 20 − 60 fractions were not APOE genotype dependant. At 5 h, there was a trend towards a time × genotype interaction (P=0.081) for EPA in theSf >400 fraction. When sub-groups were form based on the level of EPA at baseline within the Sf >400 fraction, postprandial EPA (%) was significantly reduced only in the high-EPA group. EPA at baseline significantly predicted the postprandial response in EPA only in E4+ subjects (R2 = 0.816). Conclusion: Despite the DHA supplement contain very low levels of EPA, E4+ subjects with high EPA at fasting potentially have disrupted postprandial n − 3 PUFA metabolism after receiving a high-dose of DHA. Trial registration: Registered at clinicaltrials.gov/show/NCT01544855.

Apolipoprotein e genotype has a modest impact on the postprandial plasma response to meals of varying fat composition in healthy men in a randomized controlled trial

BACKGROUND:Apolioprotein E (APOE) genotype is reported to influence a person's fasting lipid profile and potentially the response to dietary fat manipulation. The impact of APOE genotype on the responsiveness to meals of varying fat composition is unknown. OBJECTIVE:We examined the effect of meals containing 50 g of fat rich in saturated fatty acids (SFAs), unsaturated fatty acids (UNSATs), or SFAs with fish oil (SFA-FO) on postprandial lipemia. METHOD:A randomized, controlled, test meal study was performed in men recruited according to the APOE genotype (n = 10 APOE3/3, n = 11 APOE3/E4). RESULTS:For the serum apoE response (meal × genotype interaction P = 0.038), concentrations were on average 8% lower after the UNSAT than the SFA-FO meal in APOE4 carriers (P = 0.015) only. In the genotype groups combined, there was a delay in the time to reach maximum triacylglycerol (TG) concentration (mean ± SEM: 313 ± 25 vs. 266 ± 27 min) and higher maximum nonesterified fatty acid (0.73 ± 0.05 vs. 0.60 ± 0.03 mmol/L) and glucose (7.92 ± 0.22 vs. 7.25 ± 0.22 mmol/L) concentrations after the SFA than the UNSAT meal, respectively (P ≤ 0.05). In the Svedberg flotation rate 60-400 TG-rich lipoprotein fraction, meal × genotype interactions were observed for incremental area under the curve (IAUC) for the TG (P = 0.038) and apoE (P = 0.016) responses with a 58% lower apoE IAUC after the UNSAT than the SFA meal (P = 0.017) in the E4 carriers. CONCLUSIONS:Our data indicate that APOE genotype had a modest impact on the postprandial response to meals of varying fat composition in normolipidemic men. The physiologic importance of greater apoE concentrations after the SFA-rich meals in APOE4 carriers may reflect an impact on TG-rich lipoprotein clearance from the circulation. This trial was registered at clinicaltrials.gov as NCT01522482.

The ecological impact of conquest and colonization on a medieval frontier landscape: combined palynological and geochemical analysis of lake sediments from Radzyń Chełminski, northern Poland

Slavic and German colonization of the southern Baltic between the 8th and 15th centuries A.D. is well-documented archaeologically and historically. Despite the large number of pollen profiles from Poland, few palaeoecological studies have examined the ecological impact of a process that was central to the expansion of European, Christian, societies. This study aims to redress this balance through multiproxy analysis of lake sediments from Radzyń Chełminski, Northern Poland, using pollen, element geochemistry (Inductively Coupled-Optical Emission Spectroscopy [ICP-OES]), organic content, and magnetic susceptibility. The close association between lake and medieval settlements presents the ideal opportunity to reconstruct past vegetation and land-use dynamics within a well-documented archaeological, historical, and cultural context. Three broad phases of increasing landscape impact are visible in the pollen and geochemical data dating from the 8th/9th, 10th/11th, and 13th centuries, reflecting successive phases of Slavic and German colonization. This involved the progressive clearance of oak-hornbeam dominated woodland and the development of an increasingly open agricultural landscape. Although the castles and towns of the Teutonic Order remain the most visible signs of medieval colonization, the palynological and geochemical data demonstrate that the major phase of woodland impact occurred during the preceding phase of Slavic expansion; Germans colonists were entering a landscape already significantly altered.

High prevalence of undernutrition and low dietary diversity in institutionalised elderly living in Sri Lanka

This research received no specific grant from any funding agency in the public, commercial and not-for-profit sectors. The authors wish to thank the participants, administrators and caregivers of the homes for elders for their enthusiastic cooperation and also the Nutrition Research Team of the Department of Applied Nutrition, Wayamba University of Sri Lanka, for their valuable assistance during the course of the study. The authors also wish to thank Mr. S. Rahanan for coordination and the assistance given in data collection especially in Tamil speaking participants. K.M.R designed and managed the study, interpreted the data and drafted the manuscript. M.P.P.M contributed to the data collection, data analysis and coordination of the study. M.W, K.G.J and J.A.L assisted in data interpretation and critical revision of the manuscript. The authors declare that there is no conflict of interest of any kind involved in this study or this publication. Ethical clearance for this study was obtained from the Ethical Review Committee of the Sri Lanka Medical Association (ERC/13-037).

Soil carbon and litter development along a reconstructed biodiverse forest chronosequence of South-Western Australia

Soil organic matter (SOM) increases with time as landscape is restored. Studying SOM development along restored forest chronosequences would be useful in clarifying some of the uncertainties in quantifying C turnover rates with respect to forest clearance and ensuing restoration. The development of soil organic matter in the mineral soils was studied at four depths in a 16-year-old restored jarrah forest chronosequence. The size-separated SOM fractionation along with δ13C isotopic shift was utilised to resolve the soil C temporal and spatial changes with developing vegetation. The restored forest chronosequence revealed several important insights into how soil C is developing with age. Litter accumulation outpaced the native forest levels in 12 years after restoration. The surface soils, in general, showed increase in total C with age, but this trend was not clearly observed at lower depths. C accumulation was observed with increasing restoration age in all three SOM size-fractions in the surface 0–2 cm depth. These biodiverse forests show a trend towards accumulating C in recalcitrant stable forms, but only in the surface 0–2 cm mineral soil. A significant reverse trend was observed for the moderately labile SOM fraction for lower depths with increasing restoration age. Correlating the soil δ13C with total C concentration revealed the re-establishment of the isotopically depleted labile to enriched refractory C continuum with soil depth for the older restored sites. This implied that from a pedogenic perspective, the restored soils are developing towards the original native soil carbon profile.

Climate-driven expansion of blanket bogs in Britain during the Holocene

Blanket bog occupies approximately 6 % of the area of the UK today. The Holocene expansion of this hyperoceanic biome has previously been explained as a consequence of Neolithic forest clearance. However, the present distribution of blanket bog in Great Britain can be predicted accurately with a simple model (PeatStash) based on summer temperature and moisture index thresholds, and the same model correctly predicts the highly disjunct distribution of blanket bog worldwide. This finding suggests that climate, rather than land-use history, controls blanket-bog distribution in the UK and everywhere else. We set out to test this hypothesis for blanket bogs in the UK using bioclimate envelope modelling compared with a database of peat initiation age estimates. We used both pollen-based reconstructions and climate model simulations of climate changes between the mid-Holocene (6000 yr BP, 6 ka) and modern climate to drive PeatStash and predict areas of blanket bog. We compiled data on the timing of blanket-bog initiation, based on 228 age determinations at sites where peat directly overlies mineral soil. The model predicts large areas of northern Britain would have had blanket bog by 6000 yr BP, and the area suitable for peat growth extended to the south after this time. A similar pattern is shown by the basal peat ages and new blanket bog appeared over a larger area during the late Holocene, the greatest expansion being in Ireland, Wales and southwest England, as the model predicts. The expansion was driven by a summer cooling of about 2 °C, shown by both pollen-based reconstructions and climate models. The data show early Holocene (pre-Neolithic) blanket-bog initiation at over half of the sites in the core areas of Scotland, and northern England. The temporal patterns and concurrence of the bioclimate model predictions and initiation data suggest that climate change provides a parsimonious explanation for the early Holocene distribution and later expansion of blanket bogs in the UK, and it is not necessary to invoke anthropogenic activity as a driver of this major landscape change.

Climate-driven expansion of blanket bogs in Britain during the Holocene

Blanket bog occupies approximately 6% of the area of the UK today. The Holocene expansion of this hyperoceanic biome has previously been explained as a consequence of Neolithic forest clearance. However, the present distribution of blanket bog in Great Britain can be predicted accurately with a simple model (PeatStash) based on summer temperature and moisture index thresholds, and the same model correctly predicts the highly disjunct distribution of blanket bog worldwide. This finding suggests that climate, rather than land-use history, controls blanket-bog distribution in the UK and everywhere else. We set out to test this hypothesis for blanket bogs in the UK using bioclimate envelope modelling compared with a database of peat initiation age estimates. We used both pollen-based reconstructions and climate model simulations of climate changes between the mid-Holocene (6000 yr BP, 6 ka) and modern climate to drive PeatStash and predict areas of blanket bog. We compiled data on the timing of blanketbog initiation, based on 228 age determinations at sites where peat directly overlies mineral soil. The model predicts that large areas of northern Britain would have had blanket bog by 6000 yr BP, and the area suitable for peat growth extended to the south after this time. A similar pattern is shown by the basal peat ages and new blanket bog appeared over a larger area during the late Holocene, the greatest expansion being in Ireland,Wales, and southwest England, as the model predicts. The expansion was driven by a summer cooling of about 2 °C, shown by both pollen-based reconstructions and climate models. The data show early Holocene (pre- Neolithic) blanket-bog initiation at over half of the sites in the core areas of Scotland and northern England. The temporal patterns and concurrence of the bioclimate model predictions and initiation data suggest that climate change provides a parsimonious explanation for the early Holocene distribution and later expansion of blanket bogs in the UK, and it is not necessary to invoke anthropogenic activity as a driver of this major landscape change.

Pre-Columbian ring ditch construction and land use on a “chocolate forest island” in the Bolivian Amazon

We present a palaeoecological investigation of pre-Columbian land use in the savannah “forest island” landscape of north-east Bolivian Amazonia. A 5700 year sediment core from La Luna Lake, located adjacent to the La Luna forest island site, was analysed for fossil pollen and charcoal. We aimed to determine the palaeoenvironmental context of pre-Columbian occupation on the site and assess the environmental impact of land use in the forest island region. Evidence for anthropogenic burning and Zea mays L. cultivation began ~2000 cal a BP, at a time when the island was covered by savannah, under drier-than-present climatic conditions. After ~1240 cal a BP burning declined and afforestation occurred. We show that construction of the ring ditch, which encircles the island, did not involve substantial deforestation. Previous estimates of pre-Columbian population size in this region, based upon labour required for forest clearance, should therefore be reconsidered. Despite the high density of economically useful plants, such as Theobroma cacao, in the modern forest, no direct pollen evidence for agroforestry was found. However, human occupation is shown to pre-date and span forest expansion on this site, suggesting that here, and in the wider forest island region, there is no truly pre-anthropogenic ‘pristine’ forest.

N-acetylcysteine protects against renal injury following bilateral ureteral obstruction

Background. Obstructive nephropathy decreases renal blood flow (RBF) and glomerular filtration rate (GFR), causing tubular abnormalities, such as urinary concentrating defect, as well as increasing oxidative stress. This study aimed to evaluate the effects of N-acetylcysteine (NAC) on renal function, as well as on the protein expression of aquaporin 2 (AQP2) and endothelial nitric oxide synthase (eNOS), after the relief of bilateral ureteral obstruction (BUO). Methods. Adult male Wistar rats were divided into four groups: sham (sham operated); sham operated + 440 mg/kg body weight (BW) of NAC daily in drinking water, started 2 days before and maintained until 48 h after the surgery; BUO (24-h BUO only); BUO + NAC-pre (24-h BUO plus 440 mg/kg BW of NAC daily in drinking water started 2 days before BUO); and BUO + NAC-post (24-h BUO plus 440 mg/kg BW of NAC daily in drinking water started on the day of BUO relief). Experiments were conducted 48 h after BUO relief. Results. Serum levels of thiobarbituric reactive substances, which are markers of lipid peroxidation, were significantly lower in NAC-treated rats than in the BUO group rats. The administration of NAC provided significant protection against post-BUO GFR drops and reductions in RBF. Renal cortices and BUO rats presented decreased eNOS protein expression of eNOS in the renal cortex of BUO group rats, whereas it was partially recovered in BUO + NAC-pre group rats. Urine osmolality was significantly lower in BUO rats than in sham group rats or NAC-treated rats, the last also presenting less interstitial fibrosis. Post-BUO downregulation of AQP2 protein expression was averted in the BUO + NAC-pre group rats. Conclusions. This study demonstrates that NAC administration ameliorates the renal function impairment observed 48 h after the relief of 24-h BUO. Oxidative stress is important for the suppression of GFR, RBF, tissue AQP2 and eNOS in the polyuric phase after the release of BUO.

Pulmonary Surfactant in Respiratory Syncytial Virus Bronchiolitis: The Role in Pathogenesis and Clinical Implications

Respiratory syncytial virus (RSV) bronchiolitis is the leading cause of lower respiratory tract infection, and the most frequent reason for hospitalization among infants throughout the world. In addition to the acute consequences of the disease, RSV bronchiolitis in early childhood is related to further development of recurrent wheezing and asthma. Despite the medical and economic burden of the disease, therapeutic options are limited to supportive measures, and mechanical ventilation in severe cases. Growing evidence suggests an important role of changes in pulmonary surfactant content and composition in the pathogenesis of severe RSV bronchiolitis. Besides the well-known importance of pulmonary surfactant in maintenance of pulmonary homeostasis and lung mechanics, the surfactant proteins SP-A and SP-D are essential components of the pulmonary innate immune system. Deficiencies of such proteins, which develop in severe RSV bronchiolitis, may be related to impairment in viral clearance, and exacerbated inflammatory response. A comprehensive understanding of the role of the pulmonary surfactant in the pathogenesis of the disease may help the development of new treatment strategies. We conducted a review of the literature to analyze the evidences of pulmonary surfactant changes in the pathogenesis of severe RSV bronchiolitis, its relation to the inflammatory and immune response, and the possible role of pulmonary surfactant replacement in the treatment of the disease. Pediatr Pulmonol. 2011; 46:415-420. (c) 2010 Wiley-Liss, Inc.

Lineage-Negative Bone Marrow Cells Protect Against Chronic Renal Failure

Progressive renal failure continues to be a challenge. The use of bone marrow cells represents a means of meeting that challenge. We used lineage-negative (Lin(-)) cells to test the hypothesis that Lin(-) cell treatment decreases renal injury. Syngeneic Fischer 344 rats were divided into four groups: sham ( laparotomy only, untreated); Nx (five-sixth nephrectomy and untreated); NxLC1 (five-sixth nephrectomy and receiving 2 x 10(6) Lin(-) cells on postnephrectomy day 15); and NxLC3 (five-sixth nephrectomy and receiving 2 x 10(6) Lin(-) cells on postnephrectomy days 15, 30, and 45). On postoperative day 16, renal mRNA expression of interleukin (IL)-1 beta, tumor necrosis factor-alpha, and IL-6 was lower in NxLC rats than in Nx rats. On postnephrectomy day 60, NxLC rats presented less proteinuria, glomerulosclerosis, anemia, renal infiltration of immune cells, and protein expression of monocyte chemoattractant protein-1, as well as decreased interstitial area. Immunostaining for proliferating cell nuclear antigen showed that, in comparison with sham rats, Nx rats presented greater cell proliferation, whereas NxLC1 rats and NxLC3 rats presented less cell proliferation than did Nx rats. Protein expression of the cyclin-dependent kinase inhibitor p21 and of vascular endothelial growth factor increased after nephrectomy and decreased after Lin(-) cell treatment. On postnephrectomy day 120, renal function (inulin clearance) was significantly better in Lin(-) cell-treated rats than in untreated rats. Lin(-) cell treatment significantly improved survival. These data suggest that Lin(-) cell treatment protects against chronic renal failure. STEM CELLS 2009; 27: 682-692

Relation of pretreatment sequence diversity in NS5A region of HCV genotype 1 with immune response between pegylated-INF/ribavirin therapy outcomes

Hepatitis C virus (HCV) infection frequently persists despite substantial virus-specific immune responses and the combination of pegylated interferon (INF)-alpha and ribavirin therapy. Major histocompatibility complex class I restricted CD8+ T cells are responsible for the control of viraemia in HCV infection, and several studies suggest protection against viral infection associated with specific HLAs. The reason for low rates of sustained viral response (SVR) in HCV patients remains unknown. Escape mutations in response to cytotoxic T lymphocyte are widely described; however, its influence in the treatment outcome is ill understood. Here, we investigate the differences in CD8 epitopes frequencies from the Los Alamos database between groups of patients that showed distinct response to pegylated alpha-INF with ribavirin therapy and test evidence of natural selection on the virus in those who failed treatment, using five maximum likelihood evolutionary models from PAML package. The group of sustained virological responders showed three epitopes with frequencies higher than Non-responders group, all had statistical support, and we observed evidence of selection pressure in the last group. No escape mutation was observed. Interestingly, the epitope VLSDFKTWL was 100% conserved in SVR group. These results suggest that the response to treatment can be explained by the increase in immune pressure, induced by interferon therapy, and the presence of those epitopes may represent an important factor in determining the outcome of therapy.