Permafrost organic matter quality and biolability in the Vault Lake thermokarst environment, Interior Alaska, USA

Thesis (Ph.D.) University of Alaska Fairbanks, 2017Warming and thawing of permafrost soils removes a major barrier to soil organic carbon (SOC) mineralization, leading to the mobilization and microbial degradation of previously frozen, inactive permafrost organic carbon (OC) into the greenhouse gases carbon dioxide (CO₂) and methane (CH₄). Many thermokarst (thaw) lakes formed in permafrost-dominated landscapes have high rates of CO₂ and CH₄ emission; however, the composition and biodegradability of the thawed permafrost OC as they relate to the relative magnitudes of anaerobic OC mineralization at different depths throughout the vertical profile of a thermokarst-lake talik system have, to my knowledge, never been measured. My research examined OC composition and mineralization potentials at the Vault Creek (VC) permafrost tunnel and Vault Lake, located 20 km north of Fairbanks, Alaska, USA, to better constrain these uncertainties. I found that, in a 590-cm long sediment core collected from the center of Vault Lake, whole-column CH₄ production is dominated by methanogenesis in the organic-rich mud facies, which occurred in the surface 0 to 152 cm. CH₄ production potential rates positively associated with substrate availability (carbon and nitrogen concentrations) and the relative abundances of terrestrially-derived organic matter compounds (alkanes, alkenes, lignin products, and phenols and phenolic precursors), measured using pyrolysis-gas chromatography-mass spectrometry. Temperature sensitivity analyses conducted on a subset of samples from the Vault Lake sediment core suggest century-scale time since permafrost thaw affects temperature sensitivities of CH₄ production. Freshly-thawed taberite sediments at the base of the talik (thaw bulb) were most sensitive to warming at lower incubation temperatures (0 °C to 3 °C), while the overlying taberite sediments thawed in situ longer periods of time (up to 400 years based on radiocarbon dating) did not experience statistically significant increases in CH₄ production until higher incubation temperatures (10 °C to 25 °C). Finally, using anaerobic incubations and ultrahigh-resolution mass spectrometry of water-extractable organic matter along a 12-m yedoma profile in the VC permafrost tunnel, I show that yedoma OC biolability increases with depth as indicated by increasing proportions of aliphatics and peptides (reduced, high H/C compounds). These compounds also positively correlated with anaerobic CO₂ and CH₄ production, and corresponded to high proportions (5.6% to 118 %) of OC mineralization rates in incubations. This suggests that as yedoma permafrost thaws beneath a thermokarst lake greenhouse gas production potentials may increase with thaw depth

Investigating the impact of a specialist CPD training programme for Teaching Assistants, related to supporting children with English as an Additional Language

This research emerged from education practice, specifically from the experiences of one local authority area within the North East of England. Akin to experiences across Europe (Koehler & Schneider, 2019), increasing numbers of economic migrants and asylum seekers in the area presented schools with a variety of new challenges, for which many felt ill equipped. Not only were schools required to support an increasing range of language repertoires and the needs of vulnerable groups, but specialist provision and training was sparse for teachers and even less for Teaching Assistants, who were regularly expected to care for, and educate, these children. There were also concerns over equality of opportunity in education for these children who had English as an addition language (EAL). The local authority area reflected the national pattern of a reduction in such specialist provision for schools. In response to a request for partnership working, a university in the North East of England developed a specialist Certificate of Education Practice with a focus upon offering continuous professional development (CPD) to Teaching Assistants to support EAL learners. This CPD was followed up by a real-time work-based project which aimed to consolidate the learning and effect relevant change within the area. To determine the impact of the programme, a small-scale evaluation was conducted by way of questionnaire and semi-structured interviews, aiming to glean responses from course attendees, their work-based advisors and Head Teachers or managers. The findings identified three themes: motivation, personal and professional development and impact on school. While the impact of the CPD from the perspectives of the teaching assistants is now more clearly defined, the wider impact from the perspectives of colleagues in other school roles remains anecdotal and unconfirmed

Thermokarst-lake methanogenesis along a complete talik (thaw bulb) profile

Thermokarst (thaw) lakes emit methane (CH4) to the atmosphere, with the carbon (C) originating from terrestrial sources such as the Holocene soils of the lakes’ watersheds, thaw of Holocene- and Pleistoceneaged permafrost soil beneath and surrounding the lakes, and decomposition of contemporary organic matter (OM) in the lakes. However, the relative magnitude of CH4 production in surface lake sediments versus deeper thawed permafrost horizons is not well understood. We assessed anaerobic CH4 production potentials from 22 depths along a 590 cm long lake sediment core from the center of an interior Alaska thermokarst lake, Vault Lake, that captured the entire package of surface lake sediments, the talik (thaw bulb), and the top 40 cm of thawing permafrost beneath the talik. We also studied the adjacent Vault Creek permafrost tunnel that extends through icerich yedoma permafrost soils surrounding the lake and into underlying fluvial gravel. Our results show, in the center of a first generation thermokarst-lake, whole-column CH4 production is dominated by methanogenesis in the organic-rich surface lake sediments [151 cm thick; mean ± SD 5.95 ± 1.67 μg C-CH4 per g dry weight sediment per day (g dw−1 d−1); 125.9 ± 36.2 μg C-CH4 per g organic carbon per day (g Corg−1 d−1)]. The organic-rich surface sediments contribute the most (67%) to whole-column CH4 production despite occupying a lesser fraction (26%) of sediment column thickness. High CH4 production potentials were also observed in recently-thawed permafrost (1.18 ± 0.61 μg C-CH4 g dw−1 d−1; 59.60 ± 51.5 μg CCH4 g Corg−1 d−1) at the bottom of the talik, but the narrow thicknesses (43 cm) of this horizon limited its overall contribution to total sediment column CH4 production in the core. Lower rates of CH4 production were observed in sediment horizons representing permafrost that has been thawed in the talik for longer periods of time. The thickest sequence in the Vault Lake core, which consisted of combined Lacustrine silt and Taberite facies (60% of total core thickness), had low CH4 production potentials, contributing only 21% of whole sediment column CH4 production potential. No CH4 production was observed in samples obtained from the permafrost tunnel, whose sediments represent a non-lake environment. Our findings imply that CH4 production is highly variable in thermokarstlake systems and that both modern OM supplied to surface sediments and ancient OM supplied to both surface and deep lake sediments by in situ thaw, as well as shore erosion of yedoma permafrost, are important to lake CH4 production. Knowing where CH4 originates and what proportion of produced CH4 is emitted will aid in estimations of how C release and processing in a thermokarst-lake environment differs from other thawing permafrost and non-permafrost environments. References: Heslop, J.K.; Walter Anthony, K.M.; Sepulveda-Jauregui, A.; Martinez-Cruz, K.; Bondurant, A.; Grosse, G. and Jones, M.C. [2015]: Thermokarst lake methanogenesis along a complete talik profile. Biogeosciences, 12:4317–4331, doi:10.5194/bg-12-4317-2015

Mechanistic evaluation of primary human hepatocyte culture using global proteomic analysis reveals a selective dedifferentiation profile

© 2016 The Author(s)The application of primary human hepatocytes following isolation from human tissue is well accepted to be compromised by the process of dedifferentiation. This phenomenon reduces many unique hepatocyte functions, limiting their use in drug disposition and toxicity assessment. The aetiology of dedifferentiation has not been well defined, and further understanding of the process would allow the development of novel strategies for sustaining the hepatocyte phenotype in culture or for improving protocols for maturation of hepatocytes generated from stem cells. We have therefore carried out the first proteomic comparison of primary human hepatocyte differentiation. Cells were cultured for 0, 24, 72 and 168 h as a monolayer in order to permit unrestricted hepatocyte dedifferentiation, so as to reveal the causative signalling pathways and factors in this process, by pathway analysis. A total of 3430 proteins were identified with a false detection rate of <1 %, of which 1117 were quantified at every time point. Increasing numbers of significantly differentially expressed proteins compared with the freshly isolated cells were observed at 24 h (40 proteins), 72 h (118 proteins) and 168 h (272 proteins) (p < 0.05). In particular, cytochromes P450 and mitochondrial proteins underwent major changes, confirmed by functional studies and investigated by pathway analysis. We report the key factors and pathways which underlie the loss of hepatic phenotype in vitro, particularly those driving the large-scale and selective remodelling of the mitochondrial and metabolic proteomes. In summary, these findings expand the current understanding of dedifferentiation should facilitate further development of simple and complex hepatic culture systems

2012 ACCF/AHA/ACP/AATS/PCNA/SCAI/STS guideline for the diagnosis and management of patients with stable ischemic heart disease

The recommendations listed in this document are, whenever possible, evidence based. An extensive evidence review was conducted as the document was compiled through December 2008. Repeated literature searches were performed by the guideline development staff and writing committee members as new issues were considered. New clinical trials published in peer-reviewed journals and articles through December 2011 were also reviewed and incorporated when relevant. Furthermore, because of the extended development time period for this guideline, peer review comments indicated that the sections focused on imaging technologies required additional updating, which occurred during 2011. Therefore, the evidence review for the imaging sections includes published literature through December 2011

Century-scale time since permafrost thaw affects temperature sensitivity of net methane production in thermokarst-lake and talik sediments

Permafrost thaw subjects previously frozen soil organic carbon (SOC) to microbial degradation to the greenhouse gases carbon dioxide (CO2) and methane (CH4).Emission of these gases constitutes a positive feedback to climate warming. Among numerous uncertainties in estimating the strength of this permafrost carbon feedback (PCF), two are: (i) how mineralization of permafrost SOC thawed in saturated anaerobic conditions responds to changes in temperature and (ii) how microbial communities and temperature sensitivities change over time since thaw. To address these uncertainties,we utilized a thermokarst-lake sediment core as a natural chronosequence where SOC thawed and incubated in situ under saturated anaerobic conditions for up to 400 years following permafrost thaw. Initial microbial communities were characterized, and sediments were anaerobically incubated in the lab at four temperatures (0 °C, 3 °C, 10 °C, and 25 °C) bracketing those observed in the lake's talik. Net CH4 production in freshly-thawed sediments near the downward-expanding thaw boundary at the base of the talik were most sensitive to warming at the lower incubation temperatures (0 °C to 3 °C), while the overlying sediments which had been thawed for centuries had initial low abundant methanogenic communities (b 0.02%) and did not experience statistically significant increases in net CH4 production potentials until higher incubation temperatures (10 °C to 25 °C). We propose these observed differences in temperature sensitivities are due to differences in SOM quality and functional microbial community composition that evolve over time; however further research is necessary to better constrain the roles of these factors in determining temperature controls on anaerobic C mineralization

Temperature sensitivity of methanogenesis in a thermokarst lake sediment core

Little is known about temperature sensitivity of permafrost organic carbon (OC) mineralization over time scales of years to centuries following thaw. Due to their formation and thaw histories, taliks (thaw bulbs) beneath thermokarst lakes provide a unique natural laboratory from which to examine how permafrost thawed in saturated anaerobic conditions responds to changes in temperature following long periods of time since thaw. We anaerobically incubated samples from a 590 cm thermokarst lake sediment core near Fairbanks, Alaska at four temperatures (0, 3, 10, and 25 ºC) bracketing observed talik temperatures. We show that since initial thaw ~400 yr BP CH4 production shifts from being most sensitive to at lower (0-3 ºC; Q10-EC=1.15E7) temperatures to being most sensitive at higher (10-25 ºC; Q10-EC=67) temperatures. Frozen sediments collected from beneath the talik, thawed at the commencement of the incubation, had significant (p ≤ 0.05) increases in CH4 production rates at lower temperatures but did not show significant CH4 production rate increases at higher temperatures (10-25 ºC). We hypothesize the thawing of sediments removed a major barrier to C mineralization, leading to rapid initial permafrost C mineralization and preferential mineralization of the most biolabile OC compounds. In contrast, sediments which had been thawed beneath the lake for longer periods of time did not experience statistically significant increases in CH4 production at lower temperatures (0-10 ºC), but had high temperature sensitivities at higher temperatures (10-25 ºC). We believe these rate increases are due to warmer temperatures in the experimental incubations crossing activation energy thresholds, allowing previously recalcitrant fractions of OC to be utilized, and/or the presence of different microbial communities adapted to thawed sediments. Recently-deposited sediments at shallow depths in the lake core experienced increases in CH4 production across all incubation temperatures (Q10-ST=4.4)

Impact of modern thermokarst on mineral element release: case study in Cape Bounty, Canada

Rapid permafrost thaw, exposing organic matter (OM) to decomposition, is also responsible for mineral alteration and nutrient release from previously perennially frozen materials. Ice-rich permafrost thaw creates local landscape degradations (subsidence) known as thermokarst structures, resulting in development of distinctive landforms. Two different types of structures are studied: an Active Layer Detachment (ALD) which is a one-time event, and a Retrogressive Thaw Slumps (RTS) which repeats annually during summer months. In the Cape Bounty Arctic Watershed Observatory (Canada), the total elemental content and mineral nutrient released from an ALD formed in 2007 and a RTS still very much active were compared. For the disturbed areas, results show an increase in total elemental content (for Al, Ca, Fe, K) with depth as compared to the undisturbed site, as well as an increase in plagioclase content. The mineral nutrient concentration released is also several times higher (Ca : 5 ; Na : 8 ; Mg : 5) for the RTS disturbed site compared to the undisturbed site. For ALD sites, there was no significant difference between the disturbed and the undisturbed areas. We hypothesize that the one-time ALD event was followed by a seasonal depletion of the total mineral nutrient content as well as the soluble mineral nutrient concentrations in disturbed and undisturbed soils since 2007. In contrast, RTS structures expose perennially frozen materials every summer after thaw and degradation. This study suggests that RTS development in the Arctic might constitute an important driver for mineral nutrient release by permafrost upon thawing, which might affect local to regional ecosystem chemistry. The data are also considered in the context of potential changes in organic carbon stability upon disturbanc

Peptide Ligands That Bind Selectively to Spores of Bacillus subtilis and Closely Related Species

As part of an effort to develop detectors for selected species of bacterial spores, we screened phage display peptide libraries for 7- and 12-mer peptides that bind tightly to spores of Bacillus subtilis. All of the peptides isolated contained the sequence Asn-His-Phe-Leu at the amino terminus and exhibited clear preferences for other amino acids, especially Pro, at positions 5 to 7. We demonstrated that the sequence Asn-His-Phe-Leu-Pro (but not Asn-His-Phe-Leu) was sufficient for tight spore binding. We observed equal 7-mer peptide binding to spores of B. subtilis and its most closely related species, Bacillus amyloliquefaciens, and slightly weaker binding to spores of the closely related species Bacillus globigii. These three species comprise one branch on the Bacillus phylogenetic tree. We did not detect peptide binding to spores of several Bacillus species located on adjacent and nearby branches of the phylogenetic tree nor to vegetative cells of B. subtilis. The sequence Asn-His-Phe-Leu-Pro was used to identify B. subtilis proteins that may employ this peptide for docking to the outer surface of the forespore during spore coat assembly and/or maturation. One such protein, SpsC, appears to be involved in the synthesis of polysaccharide on the spore coat. SpsC contains the Asn-His-Phe-Leu-Pro sequence at positions 6 to 10, and the first five residues of SpsC apparently must be removed to allow spore binding. Finally, we discuss the use of peptide ligands for bacterial detection and the use of short peptide sequences for targeting proteins during spore formation