Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling

Many biological processes depend on the sequential assembly of protein complexes. However, studying the kinetics of such processes by direct methods is often not feasible. As an important class of such protein complexes, pore-forming toxins start their journey as soluble monomeric proteins, and oligomerize into transmembrane complexes to eventually form pores in the target cell membrane. Here, we monitored pore formation kinetics for the well-characterized bacterial pore-forming toxin aerolysin in single cells in real time to determine the lag times leading to the formation of the first functional pores per cell. Probabilistic modeling of these lag times revealed that one slow and seven equally fast rate-limiting reactions best explain the overall pore formation kinetics. The model predicted that monomer activation is the rate-limiting step for the entire pore formation process. We hypothesized that this could be through release of a propeptide and indeed found that peptide removal abolished these steps. This study illustrates how stochasticity in the kinetics of a complex process can be exploited to identify rate-limiting mechanisms underlying multistep biomolecular assembly pathways.

Carbon-Based Ocean Productivity and Phytoplankton Physiology from Space

Ocean biogeochemical and ecosystem processes are linked by net primary production (NPP) in the ocean's surface layer, where inorganic carbon is fixed by photosynthetic processes. Determinations of NPP are necessarily a function of phytoplankton biomass and its physiological status, but the estimation of these two terms from space has remained an elusive target. Here we present new satellite ocean color observations of phytoplankton carbon (C) and chlorophyll (Chl) biomass and show that derived Chl:C ratios closely follow anticipated physiological dependencies on light, nutrients, and temperature. With this new information, global estimates of phytoplankton growth rates (mu) and carbon-based NPP are made for the first time. Compared to an earlier chlorophyll-based approach, our carbon-based values are considerably higher in tropical oceans, show greater seasonality at middle and high latitudes, and illustrate important differences in the formation and demise of regional algal blooms. This fusion of emerging concepts from the phycological and remote sensing disciplines has the potential to fundamentally change how we model and observe carbon cycling in the global oceans.

Oxygen Production and Carbon Sequestration in an Upwelling Coastal Margin

We examined high-resolution cross-shelf distributions of particulate organic carbon (POC) and dissolved O(2) during the upwelling season off the Oregon coast. Oxygen concentrations were supersaturated in surface waters, and hypoxic in near-bottom waters, with greatly expanded hypoxic conditions late in the season. Simplified time-dependent mass balances on cross-shelf integrated concentrations of these two parameters, found the following: ( 1) The average net rate of photosynthesis generated 2.1 mmol O(2) m(-3) d(-1) and ( 2) essentially none of the corresponding net carbon fixation of 1.4 mmol m(-3) d(-1) could be accounted for in the observed standing stocks of POC. After examining other possible sinks for carbon, we conclude that most of the net production is being exported to the adjacent deep ocean. A simplified POC budget suggests that about a quarter of the export is via alongshore advection, and the remainder is due to some other process. We propose a simplistic conceptual model of across-shelf transport in which POC sinks to the bottom boundary layer where it comes into contact with mineral ballast material but is kept in suspension by high turbulence. When upwelling conditions ease, the BBL waters move seaward, carrying the suspended, ballasted POC with it where it sinks rapidly into the deep ocean at the shelf break. This suggests a mechanism whereby the duration and frequency of upwelling events and relaxations can determine the extent to which new carbon produced by photosynthesis in the coastal ocean is exported to depth rather than being respired on the shelf.

High-Frequency in Situ Optical Measurements During a Storm Event: Assessing Relationships Between Dissolved Organic Matter, Sediment Concentrations, and Hydrologic Processes

Dissolved organic matter (DOM) dynamics during storm events has received considerable attention in forested watersheds, but the extent to which storms impart rapid changes in DOM concentration and composition in highly disturbed agricultural watersheds remains poorly understood. In this study, we used identical in situ optical sensors for DOM fluorescence (FDOM) with and without filtration to continuously evaluate surface water DOM dynamics in a 415 km(2) agricultural watershed over a 4 week period containing a short-duration rainfall event. Peak turbidity preceded peak discharge by 4 h and increased by over 2 orders of magnitude, while the peak filtered FDOM lagged behind peak turbidity by 15 h. FDOM values reported using the filtered in situ fluorometer increased nearly fourfold and were highly correlated with dissolved organic carbon (DOC) concentrations (r(2) = 0.97), providing a highly resolved proxy for DOC throughout the study period. Discrete optical properties including specific UV absorbance (SUVA(254)), spectral slope (S(290-350)), and fluorescence index (FI) were also strongly correlated with in situ FDOM and indicate a shift toward aromatic, high molecular weight DOM from terrestrially derived sources during the storm. The lag of the peak in FDOM behind peak discharge presumably reflects the draining of watershed soils from natural and agricultural landscapes. Field and experimental evidence showed that unfiltered FDOM measurements underestimated filtered FDOM concentrations by up to similar to 60% at particle concentrations typical of many riverine systems during hydrologic events. Together, laboratory and in situ data provide insights into the timing and magnitude of changes in DOM quantity and quality during storm events in an agricultural watershed, and indicate the need for sample filtration in systems with moderate to high suspended sediment loads.

A Comparison of Hydrographically and Optically Derived Mixed Layer Depths

Efforts to understand and model the dynamics of the upper ocean would be significantly advanced given the ability to rapidly determine mixed layer depths (MLDs) over large regions. Remote sensing technologies are an ideal choice for achieving this goal. This study addresses the feasibility of estimating MLDs from optical properties. These properties are strongly influenced by suspended particle concentrations, which generally reach a maximum at pycnoclines. The premise therefore is to use a gradient in beam attenuation at 660 nm (c660) as a proxy for the depth of a particle-scattering layer. Using a global data set collected during World Ocean Circulation Experiment cruises from 1988-1997, six algorithms were employed to compute MLDs from either density or temperature profiles. Given the absence of published optically based MLD algorithms, two new methods were developed that use c660 profiles to estimate the MLD. Intercomparison of the six hydrographically based algorithms revealed some significant disparities among the resulting MLD values. Comparisons between the hydrographical and optical approaches indicated a first-order agreement between the MLDs based on the depths of gradient maxima for density and c660. When comparing various hydrographically based algorithms, other investigators reported that inherent fluctuations of the mixed layer depth limit the accuracy of its determination to 20 m. Using this benchmark, we found a similar to 70% agreement between the best hydrographical-optical algorithm pairings.

Distributions and Variability of Particulate Organic Matter in a Coastal Upwelling System

In this study we examined the spatial and temporal variability of particulate organic material (POM) off Oregon during the upwelling season. High-resolution vertical profiling of beam attenuation was conducted along two cross-shelf transects. One transect was located in a region where the shelf is relatively uniform and narrow (off Cascade Head (CH)); the second transect was located in a region where the shelf is shallow and wide (off Cape Perpetua (CP)). In addition, water samples were collected for direct analysis of chlorophyll, particulate organic carbon (POC), and particulate organic nitrogen (PON). Beam attenuation was highly correlated with POC and PON. Striking differences in distribution patterns and characteristics of POM were observed between CH and CP. Off CH, elevated concentrations of chlorophyll and POC were restricted to the inner shelf and were highly variable in time. The magnitude of the observed short-term temporal variability was of the same order as that of the seasonal variability reported in previous studies. Elevated concentrations of nondegraded chlorophyll and POM were observed near the bottom. Downwelling and rapid sinking are two mechanisms by which phytoplankton cells can be delivered to the bottom before being degraded. POM may be then transported across the shelf via the benthic nepheloid layer. Along the CP transect, concentrations of POM were generally higher than they were along the CH transect and extended farther across the shelf. Characteristics of surface POM, namely, C: N ratios and carbon: chlorophyll ratios, differed between the two sites. These differences can be attributed to differences in shelf circulation.

The relationship between leadership practices and a medication safety regime

Errors in healthcare are commonplace and have significant impact on mortality, morbidity, and costs. Other high-risk industries are credited with strong safety records. These successes are due in part to a strong, committed organizational culture and their leadership. A consistent pattern of effective leadership behaviors; creating change, establishing a vision and strategic actions, and enabling and inspiring the organization's members to act, is present in these high-risk industries. This research examined the relationship between leadership practices and a medication safety regime. The hypothesis is strong leadership practices have a positive relationship with the degree of sophistication of a medication safety program (safety performance). Leadership was used as a surrogate for organizational culture and was measured in this research through the Kouzes and Posner's Leadership Practices Inventory. The Institute of Medicine's 14 Selected Strategies to Improve Medication Safety was used to measure the development of a medication safety regime. Leadership practices towards safety were assessed by surveying 2,478 critical care Registered Nurses in the greater Houston area. A response rate of 19% was achieved. Thirteen hospitals participated in the medication safety regime assessment. Data from 386 RN respondents from 53 institutions provided an overall description of unit (ICU) and organization (hospital) leader's practices towards safety. There is some recognition of the medical error problem and that leaders exhibit moderate levels of leadership practices to promote safety. There were no differences noted in unit and hospital leaders' behaviors, with the exception that unit leaders promote change and enable staff to act more often than hospital leaders. There were no statistically significant relationships between overall leadership, or individual leadership practices and the organization's safety performance. There was a significant relationship between leadership and safety performance when other factors in organizational culture were considered. Teaching and Magnet hospitals also exhibited stronger behaviors towards safety. Organizational culture, as measured by academic affiliation and Magnet recognition, is strongly related to safety performance as measured by the degree of development of a medication safety regime. ^

A qualitative analysis of leadership styles and the selection of quality improvement in primary care practice

In the Practice Change Model, physicians act as key stakeholders, people who have both an investment in the practice and the capacity to influence how the practice performs. This leadership role is critical to the development and change of the practice. Leadership roles and effectiveness are an important factor in quality improvement in primary care practices.^ The study conducted involved a comparative case study analysis to identify leadership roles and the relationship between leadership roles and the number and type of quality improvement strategies adopted during a Practice Change Model-based intervention study. The research utilized secondary data from four primary care practices with various leadership styles. The practices are located in the San Antonio region and serve a large Hispanic population. The data was collected by two ABC Project Facilitators from each practice during a 12-month period including Key Informant Interviews (all staff members), MAP (Multi-method Assessment Process), and Practice Facilitation field notes. This data was used to evaluate leadership styles, management within the practice, and intervention tools that were implemented. The chief steps will be (1) to analyze if the leader-member relations contribute to the type of quality improvement strategy or strategies selected (2) to investigate if leader-position power contributes to the number of strategies selected and the type of strategy selected (3) and to explore whether the task structure varies across the four primary care practices.^ The research found that involving more members of the clinic staff in decision-making, building bridges between organizational staff and clinical staff, and task structure are all associated with the direct influence on the number and type of quality improvement strategies implemented in primary care practice.^ Although this research only investigated leadership styles of four different practices, it will offer future guidance on how to establish the priorities and implementation of quality improvement strategies that will have the greatest impact on patient care improvement. ^

The Comprehensive Assessment of Leadership for Learning: A Next Generation Formative Evaluation and Feedback System

Recent developments in federal policy have prompted the creation of state evaluation frameworks for principals and teachers that hold educators accountable for effective practices and student outcomes. These changes have created a demand for formative evaluation instruments that reflect current accountability pressures and can be used by schools to focus school improvement and leadership development efforts. The Comprehensive Assessment of Leadership for Learning (CALL) is a next generation, 360-degree on-line assessment and feedback system that reflect best practices in feedback design. Some unique characteristics of CALL include a focus on: leadership distributed throughout the school rather than as carried out by an individual leader; assessment of leadership tasks rather than perceptions of leadership practice; a focus on larger complex systems of middle and high school; and transparency of assessment design. This paper describes research contributing to the design and validation of the CALL survey instrument.

Major elements and trace ferrides in deep sea cores obtained during the Swedish Deep-Sea Expedition in 1947-1948

Samples from sediment cores collected during the Swedish Deep-Sea Expedition 1947-1948 have been analyzed in the Geochemical laboratory of the Geological Survey of Sweden. Most samples were placed at our disposal by Professor Hans Pettersson, leader of the expedition mentioned. For complementary studies, samples from the Atlantic and Indian oceans were included in our investigation and the samples placed at our disposal by Professor B. Kullenberg, Göteborg. From the Tyrrhenian Sea we got samples from Professor E. Norin, Uppsala.

Description and chemical composition of manganese deposits during the deep-sea expedition of the streamer Valdivia in 1898-1899

This monograph forms the fourth part of the tenth volume of the scientific results of the voyage of the German exploring ship Valdivia in the Atlantic and Indian Oceans, made during the years 1898-1899. These volumes are published under the editorship of Prof. Chun, the zoologist of Leipzig, who was leader of the expedition ; and Prof. E. Philippi with the cooperation of Sir John Murray. The nature of the materials brought up at various points during the voyage is well illustrated by a series of plates, similar to those accompanying the Challenger volumes. Among the concretions from the Agulhas Bank were found phosphatic nodules containing 33 per cent, of calcium carbonate, 28 of calcium phosphate, 14.6 of calcium sulphate, and 4.8 of magnesium carbonate, with some ferric oxide, alumina, and silica. These nodules were dredged at a depth of 155 metres. Off the coast of Namibia, a large quantity of manganese nodules were also dredged. Their chemical analysis performed at the Mineralogical Institute of the University Jena show similar composition as the nodules recovered by the "Challenger" at station 253 in the Pacific Ocean.

Properties of seawater and particulate matter (fluorescence) from a WETLabs Eco-FL sensor mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements made with a WETLabs Eco-FL sensor mounted on the flowthrough system between June 4th, 2011 and March 30th, 2012. Data was recorded approximately every 10s. Two issues affected the data: 1. Periods when the water 0.2µm filtered water were used as blanks and 2. Periods where fluorescence was affected by non-photochemical quenching (NPQ, chlorophyll fluorescence is reduced when cells are exposed to light, e.g. Falkowski and Raven, 1997). Median data and their standard deviation were binned to 5min bins with period of light/dark indicated by an added variable (so that NPQ affected data could be neglected if the user so chooses). Data was first calibrated using HPLC data collected on the Tara (there were 36 data within 30min of each other). Fewer were available when there was no evident NPQ and the resulting scale factor was 0.0106 mg Chl m-3/count. To increase the calibration match-ups we used the AC-S data which provided a robust estimate of Chlorophyll (e.g. Boss et al., 2013). Scale factor computed over a much larger range of values than HPLC was 0.0088 mg Chl m-3/count (compared to 0.0079 mg Chl m-3/count based on manufacturer). In the archived data the fluorometer data is merged with the TSG, raw data is provided as well as manufacturer calibration constants, blank computed from filtered measurements and chlorophyll calibrated using the AC-S. For a full description of the processing of the Eco-FL please see Taillandier, 2015.

Properties of seawater and particulate matter from a FRRF instrument, operating in a flow-through mode on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements made with a FRRF instrument, operating in a flow-through mode during the 2009-2012 part of the expedition. It operates by exciting chlorophyll fluorescence using a series of short flashes of controlled energy and time intervals (Kolber et al, 1998). The fluorescence transients produced by this excitation signal were analysed in real-time to provide estimates of abundance of photosynthetic pigments, the photosynthetic yields (Fv/Fm), the functional absorption cross section (a proxy for efficiency of photosynthetic energy acquisition), the kinetics of photosynthetic electron transport between Photosystem II and Photosystem I, and the size of the PQ pool. These parameters were measured at excitation wavelength of 445 nm, 470nm, 505 nm, and 535 nm, allowing to assess the presence and the photosynthetic performance of different phytoplankton taxa based on the spectral composition of their light harvesting pigments. The FRRF-derived photosynthetic characteristics were used to calculate the initial slope, the half saturation, and the maximum level of Photosynthesis vs Irradiance relationship. FRRF data were acquired continuously, at 1-minute time intervals.

Properties of seawater and particulate matter from a WETLabs ALFA hyperspectral laser spectrofluorometer mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements made with an Aquatic Laser Fluorescence Analyzer (ALFA) (Chekalyuk et al., 2014), connected in-line to the TARA flow through system during 2013. The ALFA instrument provides dual-wavelength excitation (405 and 514 nm) of laser-stimulated emission (LSE) for spectral and temporal analysis. It offers in vivo fluorescence assessments of phytoplankton pigments, biomass, photosynthetic yield (Fv/Fm), phycobiliprotein (PBP)-containing phytoplankton groups, and chromophoric dissolved organic matter (CDOM) (Chekalyuk and Hafez, 2008; 2013A). Spectral deconvolution (SDC) is used to assess the overlapped spectral bands of aquatic fluorescence constituents and water Raman scattering (R). The Fv/Fm measurements are spectrally corrected for non-chlorophyll fluorescence background produced by CDOM and other constituents (Chekalyuk and Hafez, 2008). The sensor was cleaned weakly following the manufacturer recommended protocol.

The rise and fall in the price of food, fuel and manufactured goods : interdependency between prices and technology determining comparative advantages and development paths

Green innovation, which enables us to extract energy from food crops, caused a food shortage in 2008. Countries suffering severe damage started to reconsider their agricultural policy with the aim of becoming more autonomous. The food price hike of the time looks like a reversal of the celebrated Singer-Prebisch thesis proposed in the 1950s. This paper examines the consequences of this trend on the comparative advantages and development strategies of developing countries. For that purpose, first, trends and short-run fluctuations in the prices of fuel and bio-energy crops are investigated. It is shown that the price series of fuels and the crops are synchronized only after the fuel extracting technology came into effect. Second, the reversal of the Singer-Prebisch thesis is underpinned by the generic form of an endogenous growth model developed by Rebelo (1991). It is shown that as an economy grows, appreciation of the non-reproducible, such as mineral resources and raw labor, over the reproducible, such as capital goods, is the norm rather than an anomaly. Third, the consequences of the food price hike and underlying capital accumulation on the development strategies of labor-abundant and low-income countries are explored. It is concluded that the impact of the food price hikes on the alteration of a development strategy is only incremental, without reinforcement from raw-labor-saving innovation. A case study of inventions by JUKI Corporation, a world-leader in the sewing machine market exemplifies the fact that, of all the major inventions the company have made, raw-labor-saving inventions have not dominated, although JUKI's machines are sold to one of the most raw-labor-intensive industries.