The impact of microbial metabolism on marine dissolved organic matter

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Marine Science 3 (2011): 567-599, doi:10.1146/annurev-marine-120308-081003.Microbes mediate global biogeochemical cycles through their metabolism, and all metabolic processes begin with the interaction between the microbial cell wall or membrane and the external environment. For all heterotrophs and many autotrophs, critical growth substrates and factors are present within the dilute and heterogeneous mixture of compounds that constitutes dissolved organic matter (DOM). In short, the microbe--molecule interaction is one of the fundamental reactions within the global carbon cycle. Here, I summarize recent findings from studies that examine DOM--microbe interactions from either the DOM perspective (organic geochemistry) or the microbe perspective (microbial ecology). Gaps in our knowledge are highlighted and future integrative research directions are proposed.My research has been funded through the National Science Foundation, the Gordon and Betty Moore Foundation, and Woods Hole Oceanographic Institution internal resources

Defining and quantifying the resilience of responses to disturbance: a conceptual and modelling approach from soil science

There are several conceptual definitions of resilience pertaining to environmental systems and, even if resilience is clearly defined in a particular context, it is challenging to quantify. We identify four characteristics of the response of a system function to disturbance that relate to “resilience”: (1) degree of return of the function to a reference level; (2) time taken to reach a new quasi-stable state; (3) rate (i.e. gradient) at which the function reaches the new state; (4) cumulative magnitude of the function (i.e. area under the curve) before a new state is reached. We develop metrics to quantify these characteristics based on an analogy with a mechanical spring and damper system. Using the example of the response of a soil function (respiration) to disturbance, we demonstrate that these metrics effectively discriminate key features of the dynamic response. Although any one of these characteristics could define resilience, each may lead to different insights and conclusions. The salient properties of a resilient response must thus be identified for different contexts. Because the temporal resolution of data affects the accurate determination of these metrics, we recommend that at least twelve measurements are made over the temporal range for which the response is expected

Does codetermination affect the composition of variable versus fixed parts of executive compensation?

Contrary to previous literature we hypothesize that interests of labor may well – like that of shareholders – aim at securing the long-run survival of the firm. Consequently, employee representatives on the supervisory board could well have an interest in increasing incentive-based compensation to avoid excessive risk taking and short-run orientated decisions. We compile unique panel data on executive compensation over the periods 2006 to 2011 for 405 listed companies and use a Hausman-Taylor approach to estimate the effect of codetermination on the compensation design. Finally, codetermination has a significantly positive effect on performance-based components of compensation, which supports our hypothesis

Can a Multifaceted Intervention Including Motivational Interviewing Improve Medication Adherence, Quality of Life, and Mortality Rates in Older Patients Undergoing Coronary Artery Bypass Surgery? A Multicenter, Randomized Controlled Trial with 18-Month Follow-Up.

BACKGROUND: Patients undergoing coronary artery bypass graft (CABG) surgery are required to take a complex regimen of medications for extended periods, and they may have negative outcomes because they struggle to adhere to this regimen. Designing effective interventions to promote medication adherence in this patient group is therefore important. OBJECTIVE: The present study aimed to evaluate the long-term effects of a multifaceted intervention (psycho-education, motivational interviewing, and short message services) on medication adherence, quality of life (QoL), and mortality rates in older patients undergoing CABG surgery. METHODS: Patients aged over 65 years from 12 centers were assigned to the intervention (EXP; n = 144) or treatment-as-usual (TAU; n = 144) groups using cluster randomization at center level. Medication adherence was evaluated using the Medication Adherence Rating Scale (MARS), pharmacy refill rate, and lipid profile; QoL was evaluated using Short Form-36. Data were collected at baseline; 3, 6, and 18 months after intervention. Survival status was followed up at 18 months. Multi-level regressions and survival analyses for hazard ratio (HR) were used for analyses. RESULTS: Compared with patients who received TAU, the MARS, pharmacy refill rate, and lipid profile of patients in the EXP group improved 6 months after surgery (p < 0.01) and remained so 18 months after surgery (p < 0.01). QoL also increased among patients in the EXP group as compared with those who received TAU at 18 months post-surgery (physical component summary score p = 0.02; mental component summary score p = 0.04). HR in the EXP group compared with the TAU group was 0.38 (p = 0.04). CONCLUSION: The findings suggest that a multifaceted intervention can improve medication adherence in older patients undergoing CABG surgery, with these improvements being maintained after 18 months. QoL and survival rates increased as a function of better medication adherence. ClinicalTrials.gov NCT02109523

Characterization of Contaminants from a Sanitized Milk Processing Plant

Milk processing lines offer a wide variety of microenvironments where a diversity of microorganisms can proliferate. We sampled crevices and junctions where, due to deficient reach by typical sanitizing procedures, bacteria can survive and establish biofilms. The sampling sites were the holding cell, cold storage tank, pasteurizer and storage tank - transfer pump junction. The culturable bacteria that were isolated after the sanitation procedure were predominantly Pseudomonas spp., Serratia spp, Staphylococcus sciuri and Stenotrophomonas maltophilia. We assayed several phenotypic characteristics such as the ability to secrete enzymes and siderophores, as well as the capacity of the strains to form biofilms that might contribute to their survival in a mixed species environment. The Pseudomonas spp. isolates were found to either produce proteases or lecithinases at high levels. Interestingly, protease production showed an inverse correlation with siderophore production. Furthermore, all of the Serratia spp. isolates were strong biofilm formers and spoilage enzymes producers. The organisms identified were not mere contaminants, but also producers of proteins with the potential to lower the quality and shelf-life of milk. In addition, we found that a considerable number of the Serratia and Pseudomonas spp. isolated from the pasteurizer were capable of secreting compounds with antimicrobial properties

A Unique Human-Fox Burial from a Pre-Natufian Cemetery in the Levant (Jordan)

New human burials from northern Jordan provide important insights into the appearance of cemeteries and the nature of human-animal relationships within mortuary contexts during the Epipalaeolithic period (c. 23,000–11,600 cal BP) in the Levant, reinforcing a socio-ideological relationship that goes beyond predator-prey. Previous work suggests that archaeological features indicative of social complexity occur suddenly during the latest Epipalaeolithic phase, the Natufian (c. 14,500–11,600 cal BP). These features include sedentism, cemeteries, architecture, food production, including animal domestication, and burials with elaborate mortuary treatments. Our findings from the pre-Natufian (Middle Epipalaeolithic) cemetery of ‘Uyun al-Hammam demonstrate that joint human-animal mortuary practices appear earlier in the Epipalaeolithic. We describe the earliest human-fox burial in the Near East, where the remains of dogs have been found associated with human burials at a number of Natufian sites. This is the first time that a fox has been documented in association with human interments pre-dating the Natufian and with a particular suite of grave goods. Analysis of the human and animal bones and their associated artefacts provides critical data on the nature and timing of these newly-developing relationships between people and animals prior to the appearance of domesticated dogs in the Natufian

Activation of Methanogenesis in Arid Biological Soil Crusts Despite the Presence of Oxygen

Methanogenesis is traditionally thought to occur only in highly reduced, anoxic environments. Wetland and rice field soils are well known sources for atmospheric methane, while aerated soils are considered sinks. Although methanogens have been detected in low numbers in some aerated, and even in desert soils, it remains unclear whether they are active under natural oxic conditions, such as in biological soil crusts (BSCs) of arid regions. To answer this question we carried out a factorial experiment using microcosms under simulated natural conditions. The BSC on top of an arid soil was incubated under moist conditions in all possible combinations of flooding and drainage, light and dark, air and nitrogen headspace. In the light, oxygen was produced by photosynthesis. Methane production was detected in all microcosms, but rates were much lower when oxygen was present. In addition, the δ13C of the methane differed between the oxic/oxygenic and anoxic microcosms. While under anoxic conditions methane was mainly produced from acetate, it was almost entirely produced from H2/CO2 under oxic/oxygenic conditions. Only two genera of methanogens were identified in the BSC-Methanosarcina and Methanocella; their abundance and activity in transcribing the mcrA gene (coding for methyl-CoM reductase) was higher under anoxic than oxic/oxygenic conditions, respectively. Both methanogens also actively transcribed the oxygen detoxifying gene catalase. Since methanotrophs were not detectable in the BSC, all the methane produced was released into the atmosphere. Our findings point to a formerly unknown participation of desert soils in the global methane cycle

Neuronal lysosomal dysfunction releases exosomes harboring APP C-terminal fragments and unique lipid signatures

Defects in endolysosomal and autophagic functions are increasingly viewed as key pathological features of neurodegenerative disorders. A master regulator of these functions is phosphatidylinositol-3-phosphate (PI3P), a phospholipid synthesized primarily by class III PI 3-kinase Vps34. Here we report that disruption of neuronal Vps34 function in vitro and in vivo impairs autophagy, lysosomal degradation as well as lipid metabolism, causing endolysosomal membrane damage. PI3P deficiency also promotes secretion of unique exosomes enriched for undigested lysosomal substrates, including amyloid precursor protein C-terminal fragments (APP-CTFs), specific sphingolipids, and the phospholipid bis(monoacylglycero)phosphate (BMP), which normally resides in the internal vesicles of endolysosomes. Secretion of these exosomes requires neutral sphingomyelinase 2 and sphingolipid synthesis. Our results reveal a homeostatic response counteracting lysosomal dysfunction via secretion of atypical exosomes eliminating lysosomal waste and define exosomal APP-CTFs and BMP as candidate biomarkers for endolysosomal dysfunction associated with neurodegenerative disorders.Fan Wang for the kind gift of the Pi3kc3flox/flox mice. We thank Basant Abdulrahman and Hermann Schaetzl for providing the gene-edited Atg5 KO N2a cells. We are also grateful to Zhenyu Yue, Ralph Nixon, and Jean Gruenberg for the kind gift of anti-Atg14L, Cathepsin D, and BMP antibodies, respectively. We thank Thomas Südhof for sharing Cre recombinase lentiviruses. We thank the OCS Microscopy Core of New York University Langone Medical Center for the support of the EM work and Rocio Perez-Gonzalez and Efrat Levy of New York University for their support during optimization of the brain exosome isolation technique. We thank Elizabeta Micevska for the maintenance and genotyping of the animal colony and Bowen Zhou for the preliminary lipidomic analysis of conditional Pi3kc3 cKO mice. We also thank Rebecca Williams and Catherine Marquer for critically reading the manuscript. This work was supported by grants from the Fundação para a Ciência e Tecnologia (PD/BD/105915/2014 to A.M.M.); the National Institute of Health (R01 NS056049 to G.D.P., transferred to Ron Liem, Columbia University; T32-MH015174 to Rene Hen (Z.M.L.)). Z.M.L. and R.B.C. received pilot grants from ADRC grant P50 AG008702 to S.A.S.info:eu-repo/semantics/publishedVersio

The Green, Green Grass of Home: an archaeo-ecological approach to pastoralist settlement in central Kenya

© 2016 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This paper considers the ecological residues of pastoralist occupation at the site of Maili Sita in Laikipia, central Kenya, drawing links with the archaeological record so as to contribute a fresh approach to the ephemeral settlement sites of mobile herding communities, a methodological aspect of African archaeology that remains problematic. Variations in the geochemical and micromorphological composition of soils along transects across the site are compared with vegetation distributions and satellite imagery to propose an occupation pattern not dissimilar to contemporary Cushitic-speaking groups further north. We argue that Maili Sita exemplifies the broad migratory and cultural exchange networks in place during the mid- to late second millennium AD, with pastoralist occupants who were both physically and culturally mobile.British Academy (2002-5 Funding) European Union - Marie Curie Initiatives (EXT grant 2007-11