Increased bacterial growth efficiency with environmental variability: results from DOC degradation by bacteria in pure culture experiments.

This paper assesses how considering variation in DOC availability and cell maintenance in bacterial models affects Bacterial Growth Efficiency (BGE) estimations. For this purpose, we conducted two biodegradation experiments simultaneously. In experiment one, a given amount of substrate was added to the culture at the start of the experiment whilst in experiment two, the same amount of substrate was added, but using periodic pulses over the time course of the experiment. Three bacterial models, with different levels of complexity, (the Monod, Marr-Pirt and the dynamic energy budget – DEB – models), were used and calibrated using the above experiments. BGE has been estimated using the experimental values obtained from discrete samples and from model generated data. Cell maintenance was derived experimentally, from respiration rate measurements. The results showed that the Monod model did not reproduce the experimental data accurately, whereas the Marr-Pirt and DEB models demonstrated a good level of reproducibility, probably because cell maintenance was built into their formula. Whatever estimation method was used, the BGE value was always higher in experiment two (the periodically pulsed substrate) as compared to the initially one-pulsed-substrate experiment. Moreover, BGE values estimated without considering cell maintenance (Monod model and empirical formula) were always smaller than BGE values obtained from models taking cell maintenance into account. Since BGE is commonly estimated using constant experimental systems and ignore maintenance, we conclude that these typical methods underestimate BGE values. On a larger scale, and for biogeochemical cycles, this would lead to the conclusion that, for a given DOC supply rate and a given DOC consumption rate, these BGE estimation methods overestimate the role of bacterioplankton as CO<sub>2</sub> producers

Degradation state of organic matter in surface sediments from the Southern Beaufort Sea: a lipid approach

For the next decades significant climatic changes should occur in the Arctic zone. The expected destabilisation of permafrost and its consequences for hydrology and plant cover should increase the input of terrigenous carbon to coastal seas. Consequently, the relative importance of the fluxes of terrestrial and marine organic carbon to the seafloor will likely change, strongly impacting the preservation of organic carbon in Arctic marine sediments. Here, we investigated the lipid content of surface sediments collected on the Mackenzie basin in the Beaufort Sea. Particular attention was given to biotic and abiotic degradation products of sterols and monounsaturated fatty acids. By using sitosterol and campesterol degradation products as tracers of the degradation of terrestrial higher plant inputs and brassicasterol degradation products as tracers of degradation of phytoplanktonic organisms, it could be observed that autoxidation, photooxidation and biodegradation processes act much more intensively on higher plant debris than on phytoplanktonic organisms. Examination of oxidation products of monounsaturated fatty acids showed that photo- and autoxidation processes act more intensively on bacteria than on phytodetritus. Enhanced damages induced by singlet oxygen (transferred from senescent phytoplanktonic cells) in bacteria were attributed to the lack of an adapted antioxidant system in these microorganisms. The strong oxidative stress observed in the sampled sediments resulted in the production of significant amounts of epoxy acids and unusually high proportions of monounsaturated fatty acids with a <i>trans</i> double bond. The formation of epoxy acids was attributed to peroxygenases (enzymes playing a protective role against the deleterious effects of fatty acid hydroperoxides in vivo), while <i>cis/trans</i> isomerisation was probably induced by thiyl radicals produced during the reaction of thiols with hydroperoxides. Our results confirm the important role played by abiotic oxidative processes in the degradation of marine bacteria and do not support the generally expected refractory character of terrigenous material deposited in deltaic systems

The ineffectiveness of CSR : understanding garment company commitments to living wages in global supply chains

In the face of pressure from civil society, unions and consumers to improve labour standards for the workers producing their goods, companies at the helm of global garment supply chains have made commitments to pay living wages within their supply chains. Harnessing insights from the critical political economy literature on corporate social responsibility (CSR), we investigate the actions of garment companies to meet these commitments. We do so through analysis of original data from a survey of 20 leading garment companies, which we co-developed in 2018-2019, as well as publicly available information for garment companies and relevant multi-stakeholder initiatives. Based on this data, we argue there is very little evidence to suggest companies have made meaningful progress towards achieving commitments to pay living wages in their supply chains, challenging widespread assumptions about CSR’s benefits to workers. We argue that in the face of mounting evidence of CSR ineffectiveness, including our own, there is a need for new political economy research into the benefits that companies derive from CSR commitments that deflect attention from their core business models and the uneven value distribution within global supply chains

Breakdown of Scale Invariance in the Phase Ordering of Fractal Clusters

Our numerical simulations with the Cahn-Hilliard equation show that coarsening of fractal clusters (FCs) is not a scale-invariant process. On the other hand, a typical coarsening length scale and interfacial area of the FC exhibit power laws in time, while the mass fractal dimension remains invariant. The initial value of the lower cutoff is a relevant length scale. A sharp-interface model is formulated that can follow the whole dynamics of a diffusion controlled growth, coarsening, fragmentation and approach to equilibrium in a system with conserved order parameter.Comment: 4 pages, 4 figures, RevTex, submitted to PR

Gigwa v2—Extended and improved genotype investigator

The study of genetic variations is the basis of many research domains in biology. From genome structure to population dynamics, many applications involve the use of genetic variants. The advent of next-generation sequencing technologies led to such a flood of data that the daily work of scientists is often more focused on data management than data analysis. This mass of genotyping data poses several computational challenges in terms of storage, search, sharing, analysis, and visualization. While existing tools try to solve these challenges, few of them offer a comprehensive and scalable solution. Gigwa v2 is an easy-to-use, species-agnostic web application for managing and exploring high-density genotyping data. It can handle multiple databases and may be installed on a local computer or deployed as an online data portal. It supports various standard import and export formats, provides advanced filtering options, and offers means to visualize density charts or push selected data into various stand-alone or online tools. It implements 2 standard RESTful application programming interfaces, GA4GH, which is health-oriented, and BrAPI, which is breeding-oriented, thus offering wide possibilities of interaction with third-party applications. The project home page provides a list of live instances allowing users to test the system on public data (or reasonably sized user-provided data). This new version of Gigwa provides a more intuitive and more powerful way to explore large amounts of genotyping data by offering a scalable solution to search for genotype patterns, functional annotations, or more complex filtering. Furthermore, its user-friendliness and interoperability make it widely accessible to the life science community

Normal scaling in globally conserved interface-controlled coarsening of fractal clusters

Globally conserved interface-controlled coarsening of fractal clusters exhibits dynamic scale invariance and normal scaling. This is demonstrated by a numerical solution of the Ginzburg-Landau equation with a global conservation law. The sharp-interface limit of this equation is volume preserving motion by mean curvature. The scaled form of the correlation function has a power-law tail accommodating the fractal initial condition. The coarsening length exhibits normal scaling with time. Finally, shrinking of the fractal clusters with time is observed. The difference between global and local conservation is discussed.Comment: 4 pages, 3 eps figure

Crustal structure of the propagating TAMMAR ridge segment on the Mid-Atlantic Ridge, 21.5°N

Active ridge propagation frequently occurs along spreading ridges and profoundly affects ridge crest segmentation over time. The mechanisms controlling ridge propagation, however, are poorly understood. At the slow spreading Mid-Atlantic Ridge at 21.5°N a seismic refraction and wide-angle reflection profile surveyed the crustal structure along a segment controlled by rapid ridge propagation. Tomographic traveltime inversion of seismic data suggests that the crustal structure along the ridge axis is controlled by melt supply; thus, crust is thickest, 8 km, at the domed segment center and decreases in thickness toward both segment ends. However, thicker crust is formed in the direction of ridge propagation, suggesting that melt is preferentially transferred toward the propagating ridge tip. Further, while seismic layer 2 remains constant along axis, seismic layer 3 shows profound changes in thickness, governing variations in total crustal thickness. This feature supports mantle upwelling at the segment center. Thus, fluid basaltic melt is redistributed easily laterally, while more viscose gabbroic melt tends to crystallize and accrete nearer to the locus of melt supply. The onset of propagation seems to have coincided with the formation of thicker crust, suggesting that propagation initiation might be due to changes in the melt supply. After a rapid initiation a continuous process of propagation was established. The propagation rate seems to be controlled by the amount of magma that reaches the segment ends. The strength of upwelling may govern the evolution of ridge segments and hence ultimately controls the propagation length

MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data

Unraveling the genetic diversity held in genebanks on a large scale is underway, due to advances in Next-generation sequence (NGS) based technologies that produce high-density genetic markers for a large number of samples at low cost. Genebank users should be in a position to identify and select germplasm from the global genepool based on a combination of passport, genotypic and phenotypic data. To facilitate this, a new generation of information systems is being designed to efficiently handle data and link it with other external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS), the database for global ex situ-held banana genetic resources, has been developed to address those needs in a user-friendly way. In developing MGIS, we selected a generic database schema (Chado), the robust content management system Drupal for the user interface, and Tripal, a set of Drupal modules which links the Chado schema to Drupal. MGIS allows germplasm collection examination, accession browsing, advanced search functions, and germplasm orders. Additionally, we developed unique graphical interfaces to compare accessions and to explore them based on their taxonomic information. Accession-based data has been enriched with publications, genotyping studies and associated genotyping datasets reporting on germplasm use. Finally, an interoperability layer has been implemented to facilitate the link with complementary databases like the Banana Genome Hub and the MusaBase breeding database. Database URL:https://www.crop-diversity.org/mgis

The Petaca (late Oligocene-middle Miocene) and Yecua (late Miocene) formations of the Subandean-Chaco basin, Bolivia, and their tectonic significance

The Petaca (late Oligocene-middle Miocene) and Yecua (late Miocene) formations of the Subandean-Chaco basin, Bolivia, and their tectonic significance. The Petaca and Yecua formations are the first two units of the Cenozoic foreland fill in the central and southern Subandean belt of Bolivia. Their biostratigraphic dating permits to recognize a notable acceleration of tectonic subsidence at ≈10 Ma, which coincides with the ingression of shallow restricted-marine waters from the Río de la Plata area along the eastern edge of the Bolivian and northwestern Argentine Andes. The Yecua Formation was deposited some time between 10 and 8 Ma.Les formations Petaca (Oligocène terminal-Miocène moyen) et Yecua (Miocène terminal) du bassin sub-andin Chaco, Bolivie, et leur signification tectonique. Les formations Petaca et Yecua sont les deux premières unités du remplissage cénozoïque d'avant-pays dans la zone subandine centrale et méridionale de Bolivie. Leur datation biostratigraphique met en évidence une accélération notable de la subsidence tectonique vers ≈10 Ma, laquelle coïncide avec une incursion d'eaux marines restreintes peu profondes depuis la région du Río de la Plata, le long de la bordure orientale des Andes de Bolivie et du Nord-Ouest argentin. Le dépôt de la Formation Yecua est intervenu au cours de l'intervalle 10-8 Ma.Las formaciones Petaca (Oligoceno terminal-Mioceno medio) y Yecua (Mioceno terminal) de la cuenca subandina-chaqueña, Bolivia, y su significado tectónico. Las formaciones Petaca y Yecua son las dos primera s unidades del relleno de antepaís de la faja subandina centro y sur de Bolivia. Su datación bioestratigráfica evidencia una aceleración notable de la subsidencia tectónica alrededor de ≈10 Ma, la cual coincide con la ingresión de aguas marinas restringidas someras desde la región del Río de la Plata, a lo largo del borde oriental de los Andes bolivianos y del Norte argentino. La Formatión Yecua se depositó en el curso del intervalo 10-8 Ma.Marshall Larry G., Sempéré Thierry, Gayet Mireille. The Petaca (late Oligocene-middle Miocene) and Yecua (late Miocene) formations of the Subandean-Chaco basin, Bolivia, and their tectonic significance. In: Documents des Laboratoires de Géologie, Lyon, n°125, 1993. Paléontologie et stratigraphie d’Amérique latine. Table ronde européenne. Lyon, 7-8-9 juillet 1992. pp. 291-301