Testing the ancient marine redox record from oxygenic photosynthesis to photic zone euxina

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2015Tracing the evolution of Earth’s redox history is one of the great challenges of geobiology and geochemistry. The accumulation of photosynthetically derived oxygen transformed the redox state of Earth’s surface environments, setting the stage for the subsequent evolution of complex life. However, the timing of the advent of oxygenic photosynthesis relative to the Great Oxidation Event (GOE; ~2.4 Ga) is poorly constrained. After the deep ocean became oxygenated in the early Phanerozoic, hydrogen sulfide, which is toxic to most aerobes, may have transiently accumulated in the marine photic zone (i.e. photic zone euxinia; PZE) during mass extinctions and oceanic anoxic events. Here, the molecular fossil evidence for oxygenic photosynthesis and eukaryotes is reevaluated, where the results imply that currently existing lipid biomarkers are contaminants. Next, the stratigraphic distribution of green and purple sulfur bacteria biomarkers through geologic time is evaluated to test whether these compounds reflect a water column sulfide signal, which is implicit in their utility as PZE paleoredox proxies. Results from a modern case study underscore the need to consider allochthonous and microbial mat sources and the role of basin restriction as alternative explanations for these biomarkers in the geologic record, in addition to an autochthonous planktonic source.NSF graduate research fellowship (DGE-­‐‑1122374), the NASA Astrobiology Institute (NNA13AA90A), a grant from NASA Exobiology (NNX09AM88G), the Agouron Institute, the Joint Program Academics Program Office, and the PAOC Houghton fund

Gender and changing foodways in England’s late-medieval bourgeois households

By the late Middle Ages, new varieties of dishware, clothing, and furniture were increasingly produced in and imported into English cities. The acquisition, use, and care of an expanding array of manufactured goods, not only made merchant and artisan lives more comfortable, it made them who they were. Yet as material culture scholars have repeatedly shown, the use and meaning of objects is neither stable nor guaranteed. Archaeologists argue that the new variety of dishware available gradually changed urban eating habits, with consequences for gender relations within the household. By reading two late medieval literary descriptions of all-women’s dinner parties against these material changes, this article looks at the impact of changing material culture on household dynamics.À la fin de l’époque médiévale, la production et l’importation d’une nouvelle vaisselle, d’une nouvelle mode vestimentaire et d’un nouveau mobilier s’accélèrent dans les villes d’Angleterre. L’acquisition, l’usage et l’entretien d’une gamme de plus en plus large de produits manufacturés n’a pas seulement rendu plus aisée la vie des marchands et des artisans, mais les a transformés eux-mêmes. Cependant l’usage et le sens des objets – les spécialistes de la culture matérielle l’ont bien montré – n’est pas stable. Selon certains archéologues, la vaisselle qui commence à se répandre change peu à peu les habitudes de table avec des conséquences sur l’ordre de genre au sein du foyer. Cet article examine deux textes littéraires du Moyen Âge tardif qui décrivent des banquets exclusivement réservés aux femmes, pour évaluer l’effet de ces changements dans la culture matérielle sur les relations entre maris et femmes

Organic geochemistry of the early Toarcian oceanic anoxic event in Hawsker Bottoms, Yorkshire, England

A comprehensive organic geochemical investigation of the Hawsker Bottoms outcrop section in Yorkshire, England has provided new insights about environmental conditions leading into and during the Toarcian oceanic anoxic event (T-OAE; ~183 Ma). Rock-Eval and molecular analyses demonstrate that the section is uniformly within the early oil window. Hydrogen index (HI), organic petrography, polycyclic aromatic hydrocarbon (PAH) distributions, and tricyclic terpane ratios mark a shift to a lower relative abundance of terrigenous organic matter supplied to the sampling locality during the onset of the T-OAE and across a lithological transition. Unlike other ancient intervals of anoxia and extinction, biomarker indices of planktonic community structure do not display major changes or anomalous values. Depositional environment and redox indicators support a shift towards more reducing conditions in the sediment porewaters and the development of a seasonally stratified water column during the T-OAE. In addition to carotenoid biomarkers for green sulfur bacteria (GSB), we report the first occurrence of okenane, a marker of purple sulfur bacteria (PSB), in marine samples younger than ~1.64 Ga. Based on modern observations, a planktonic source of okenane's precursor, okenone, would require extremely shallow photic zone euxinia (PZE) and a highly restricted depositional environment. However, due to coastal vertical mixing, the lack of planktonic okenone production in modern marine sulfidic environments, and building evidence of okenone production in mat-dwelling Chromatiaceae, we propose a sedimentary source of okenone as an alternative. Lastly, we report the first parallel compound-specific δ[superscript 13]C record in marine- and terrestrial-derived biomarkers across the T-OAE. The δ[superscript 13]C records of short-chain n-alkanes, acyclic isoprenoids, and long-chain n -alkanes all encode negative carbon isotope excursions (CIEs), and together, they support an injection of isotopically light carbon that impacted both the atmospheric and marine carbon reservoirs. To date, molecular δ[superscript 13]C records of the T-OAE display a negative CIE that is smaller in magnitude compared to the bulk organic δ[superscript 13]C excursion. Although multiple mechanisms could explain this observation, our molecular, petrographic, and Rock-Eval data suggest that variable mixing of terrigenous and marine organic matter is an important factor affecting the bulk organic δ[superscript 13]C records of the T-OAE.NASA Astrobiology InstituteExobiology Program (U.S.)National Science Foundation (U.S.). Graduate Research Fellowshi

Millennial soil retention of terrestrial organic matter deposited in the Bengal Fan

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 8 (2018): 11997, doi:10.1038/s41598-018-30091-8.The abundance of organic carbon (OC) in vegetation and soils (~2,600 PgC) compared to carbon in the atmosphere (~830 PgC) highlights the importance of terrestrial OC in global carbon budgets. The residence time of OC in continental reservoirs, which sets the rates of carbon exchange between land and atmosphere, represents a key uncertainty in global carbon cycle dynamics. Retention of terrestrial OC can also distort bulk OC- and biomarker-based paleorecords, yet continental storage timescales remain poorly quantified. Using “bomb” radiocarbon (14C) from thermonuclear weapons testing as a tracer, we model leaf-wax fatty acid and bulk OC 14C signatures in a river-proximal marine sediment core from the Bay of Bengal in order to constrain OC storage timescales within the Ganges-Brahmaputra (G-B) watershed. Our model shows that 79–83% of the leaf-waxes in this core were stored in continental reservoirs for an average of 1,000–1,200 calendar years, while the remainder was stored for an average of 15 years. This age structure distorts high-resolution organic paleorecords across geologically rapid events, highlighting that compound-specific proxy approaches must consider storage timescales. Furthermore, these results show that future environmental change could destabilize large stores of old - yet reactive - OC currently stored in tropical basins.We acknowledge funding support from the Agouron Institute Postdoctoral Fellowship (K.L.F), the US National Science Foundation (Awards: OCE-1333387 and OCE-13333826), the Investment in Science Fund given primarily by WHOI Trustee and Corporation Members, and the Swiss National Science Foundation (Award: 200020_163162)

Accuracy and consequences of using trial-of-antibiotics for TB diagnosis (ACT-TB study) : protocol for a randomised controlled clinical trial

The clinical trial is funded by the Commonwealth Scholarship Commission and the Helse Nord RHF grant awarded to THD. This work is part of THD’s PhD work at London School of Hygiene & Tropical Medicine (LSHTM). LSHTM is the sponsor of this clinical trial (sponsor address: Keppel Street, Bloomsbury, London WC1E 7HT). ELC is funded by a Wellcome Trust Senior Research Fellowship in Clinical Science: WT200901.Introduction Over 40% of global tuberculosis case notifications are diagnosed clinically without mycobacteriological confirmation. Standard diagnostic algorithms include ‘trial-of-antibiotics’—empirical antibiotic treatment given to mycobacteriology-negative individuals to treat infectious causes of symptoms other than tuberculosis, as a ‘rule-out’ diagnostic test for tuberculosis. Potentially 26.5 million such antibiotic courses/year are prescribed globally for the 5.3 million/year mycobacteriology-negative patients, making trial-of-antibiotics the most common tuberculosis diagnostic, and a global-scale risk for antimicrobial resistance (AMR). Our systematic review found no randomised controlled trial (RCT) to support use of trial-of-antibiotic. The RCT aims to determine the diagnostic and clinical value and AMR consequences of trial-of-antibiotics. Methods and analysis A three-arm, open-label, RCT randomising (1:1:1) Malawian adults (≥18 years) seeking primary care for cough into: (a) azithromycin 500 mg one time per day for 3 days or (b) amoxicillin 1 g three times per day for 5 days or (c) standard-of-care (no immediate antibiotic). We will perform mycobacteriology tests (microscopy, Xpert MTB/RIF (Mycobacterium tuberculosis/rifampicin) and Mycobacterium tuberculosis culture) at baseline. We will use audiocomputer-assisted self-interview to assess clinical improvement at day 8. First primary outcome will be proportion of patients reporting day 8 improvement out of those with negative mycobacteriology (specificity). Second primary outcome will be day 29 incidence of a composite endpoint of either death or hospitalisation or missed tuberculosis diagnosis. To determine AMR impact we compare proportion of resistant nasopharyngeal Streptococcus pneumoniae isolates on day 29. 400 mycobacteriology-negative participants/arm will be required to detect a ≥10% absolute difference in diagnostic specificity with 80% power. We will estimate measures of effect by comparing outcomes in antibiotic arms (combined and individually) to standard-of-care. Ethics and dissemination The study has been reviewed and approved by Malawi College of Medicine Research and Ethics Committee, London School of Hygiene & Tropical Medicine (LSHTM) Research Ethics Committee and Regional Committee for Health and Research Ethics – Norway, and Malawi Pharmacy, Medicines and Poisons Board. We will present abstracts at relevant conferences, and prepare a manuscript for publication in a peer-reviewed journal.Publisher PDFPeer reviewe

Effect of the duration of antimicrobial exposure on the development of antimicrobial resistance (AMR) for macrolide antibiotics: protocol for a systematic review with a network meta-analysis

THD is funded by the Commonwealth Scholarship Commission and the Helse Nord RHF. This review is part of his PhD work at LSHTM. ELC is funded by a Wellcome Trust Senior Research Fellowship in Clinical Science: WT200901. HRS is supported by the Medical Research Council [MR/R008345/1].Background: Antimicrobial resistance generates a huge health and economic burden and has the potential to become the leading cause of death globally, but its underlying drivers are yet to be fully described. The association between a microbe’s exposure to antimicrobials and subsequent development of, or selection for, resistance is well documented, as are the exacerbating microbial and human factors. However, the nature and extent of this risk, and how it varies by antimicrobial class and duration of treatment, is poorly defined. The goal of our systematic review and network meta-analysis is to determine the relationship between the duration of antimicrobial exposure and selection for resistance. We will use macrolides as the antimicrobial class of interest and Streptococcus pneumoniae carriage as an indicator organism. Our secondary outcomes include duration of symptoms, risk of treatment failure and recurrence, and descriptions of resistance mechanisms. Methods:  We will conduct a systematic review, selecting studies if they are published randomised controlled trials (RCTs) which report the relationship between taking a macrolide for any indication and incidence of resistant Streptococcus pneumoniae in patients of any age group. We will use a predefined search strategy to identify studies meeting these eligibility criteria in MEDLINE, Embase, Global Health and the Cochrane Central Register of RCTs. Two authors will independently screen titles and abstracts, review the full texts and undertake data extraction. We will use the Cochrane Collaboration’s tool to assess the quality of included RCTs. If feasible, we will perform pair-wise meta-analysis modelling to determine the relationship between the duration of macrolide treatment and development of macrolide resistant Streptococcus pneumoniae. If the identified studies meet the assumptions for a network meta-analysis (NMA), we will additionally model this relationship using indirect comparisons. Our protocol utilises reporting guidance by Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) and the extensions for protocols (PRISMA-P) and network meta-analyses (PRISMA for NMA). Our review will also report to these standards. Discussion:  Establishing the relationship between the duration of antimicrobial exposure and development of, or selection for, resistance will inform the design of antimicrobial prescriptions, treatment guidelines and the behaviour of both physicians and patients. This work will therefore be a strong contribution towards the full realisation of current antimicrobial resistance stewardship strategies.Publisher PDFPeer reviewe

Invasive Group B Streptococcal Infection in Infants, Malawi

Incidence and serotype distribution of disease in Malawi are similar to those reported from industrialized countries, but case-fatality rate is high

Self-Report Versus Ultrasound Measurement of Uterine Fibroid Status

Much of the epidemiologic research on risk factors for fibroids, the leading indication for hysterectomy, relies on self-reported outcome. Self-report is subject to misclassification because many women with fibroids are undiagnosed. The purpose of this analysis was to quantify the extent of misclassification and identify associated factors