Assessing the Use of Molecular Barcoding and qPCR for Investigating the Ecology of Prorocentrum minimum (Dinophyceae), a Harmful Algal Species

Prorocentrum minimum is a species of marine dinoflagellate that occurs worldwide and can be responsible for harmful algal blooms (HABs). Some studies have reported it to produce tetrodotoxin; however, results have been inconsistent. qPCR and molecular barcoding (amplicon sequencing) using high-throughput sequencing have been increasingly applied to quantify HAB species for ecological analyses and monitoring. Here, we isolated a strain of P. minimum from eastern Australian waters, where it commonly occurs, and developed and validated a qPCR assay for this species based on a region of ITS rRNA in relation to abundance estimates from the cultured strain as determined using light microscopy. We used this tool to quantify and examine ecological drivers of P. minimum in Botany Bay, an estuary in southeast Australia, for over ~14 months in 2016-2017. We compared abundance estimates using qPCR with those obtained using molecular barcoding based on an 18S rRNA amplicon. There was a significant correlation between the abundance estimates from amplicon sequencing and qPCR, but the estimates from light microscopy were not significantly correlated, likely due to the counting method applied. Using amplicon sequencing, ~600 unique actual sequence variants (ASVs) were found, much larger than the known phytoplankton diversity from this region. P. minimum abundance in Botany Bay was found to be significantly associated with lower salinities and higher dissolved CO2 levels

Quantification Of The Efficiency Of Rumen Microbial Protein Synthesis In Steers Fed Green Tropical Grass

The rate of rumen microbial crude protein (MCP) supply to the intestines is a crucial element in the current rumen models to predict respond of ruminants to a certain diet. Data from tropical pastures always below predicted results from the existing rumen models. Thus, quantification of the rumen MCP supply from tropical grass will improve predictive rate under tropical feeding conditions. Four Brahman crossbred steers (457±20.1 kg) were used in a metabolism study. Pangola grass (Digitaria erianthe cv. Steudal) was harvested every morning and fed to the animals soon after. Parameters measured were EMPS, intake, fractional passage rates, and rumen ammonia concentration. The EMPS was estimated using purine derivative excretion in urine. Crude protein and water soluble carbohydrates content were 6.3 and 7.4% of dry matter (DM) respectively. DM intake was 1.6% live weight. Average rumen ammonia concentration was 69 mg/L whilst rumen passage rates were 7.84 and 6.92 %/h for fluid and solids respectively. EMPS was only 72 g MCP/kg digestible organic matter. It might be concluded that EMPS in steers consuming green pangola grass was below the minimum level for forage diets adopted in the current feeding standards

The primatologist as social actor

This communication explores the role of primatologists conducting fieldwork in human-impacted habitats and how they can become part of a complex social and political landscape. Cláudia Sousa was interested in how to avoid or mitigate negative interactions involving local populations, researchers and other stakeholders in biodiversity conservation programmes.Esta comunicação explora o papel dos primatólogos que conduzem trabalho de campo em habitats com impacto humano e como podem tornar-se parte de panoramas políticos e sociais complexos. Cláudia Sousa estava interessada em analisar como evitar ou mitigar as interações negativas envolvendo as populações, os investigadores e outras partes interessadas em programas de conservação da biodiversidade

Quantum transport and momentum conserving dephasing

We study numerically the influence of momentum-conserving dephasing on the transport in a disordered chain of scatterers. Loss of phase memory is caused by coupling the transport channels to dephasing reservoirs. In contrast to previously used models, the dephasing reservoirs are linked to the transport channels between the scatterers, and momentum conserving dephasing can be investigated. Our setup provides a model for nanosystems exhibiting conductance quantization at higher temperatures in spite of the presence of phononic interaction. We are able to confirm numerically some theoretical predictions.Comment: 7 pages, 4 figure

Extended Clausius Relation and Entropy for Nonequilibrium Steady States in Heat Conducting Quantum Systems

Recently, in their attempt to construct steady state thermodynamics (SST), Komatsu, Nakagwa, Sasa, and Tasaki found an extension of the Clausius relation to nonequilibrium steady states in classical stochastic processes. Here we derive a quantum mechanical version of the extended Clausius relation. We consider a small system of interest attached to large systems which play the role of heat baths. By only using the genuine quantum dynamics, we realize a heat conducting nonequilibrium steady state in the small system. We study the response of the steady state when the parameters of the system are changed abruptly, and show that the extended Clausius relation, in which "heat" is replaced by the "excess heat", is valid when the temperature difference is small. Moreover we show that the entropy that appears in the relation is similar to von Neumann entropy but has an extra symmetrization with respect to time-reversal. We believe that the present work opens a new possibility in the study of nonequilibrium phenomena in quantum systems, and also confirms the robustness of the approach by Komtatsu et al.Comment: 19 pages, 2 figure

Phase-space approach to dynamical density functional theory

We consider a system of interacting particles subjected to Langevin inertial dynamics and derive the governing time-dependent equation for the one-body density. We show that, after suitable truncations of the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy, and a multiple time scale analysis, we obtain a self-consistent equation involving only the one-body density. This study extends to arbitrary dimensions previous work on a one-dimensional fluid and highlights the subtelties of kinetic theory in the derivation of dynamical density functional theory

Sorting out Compositional Trends in Sedimentary Rocks of the Bradbury Group (Aeolus Palus), Gale Crater, Mars

Sedimentary rocks are composed of detrital grains derived from source rocks, which are altered by chemical weathering, sorted during transport, and cemented during diagenesis. Fluvio-lacustrine sedimentary rocks of the Bradbury group, observed on the floor of Gale crater by the Curiosity rover during its first 860 Martian solar days, show trends in bulk chemistry that are consistent with sorting of mineral grains during transport. The Bradbury group rocks are uniquely suited for sedimentary provenance analysis because they appear to have experienced negligible cation loss (i.e., open-system chemical weathering) at the scale of the Alpha Particle X-ray Spectrometer bulk chemistry analyses based on low Chemical Index of Alteration values and successful modeling of >90% of the (volatile-free) targets as mixtures of primary igneous minerals. Significant compositional variability between targets is instead correlated to grain-size and textural characteristics of the rocks; the coarsest-grained targets are enriched in Al_2O_3, SiO_2, and Na_2O, whereas the finer-grained targets are enriched in mafic components. This is consistent with geochemical and mineralogical modeling of the segregation of coarse-grained plagioclase from finer-grained mafic minerals (e.g., olivine and pyroxenes), which would be expected from hydrodynamic sorting of the detritus from mechanical breakdown of subalkaline plagioclase-phyric basalts. While the presence of a distinctive K_2O-rich stratigraphic interval shows that input from at least one distinctive alkali-feldspar-rich protolith contributed to basin fill, the dominant compositional trends in the Bradbury group are consistent with sorting of detrital minerals during transport from relatively homogeneous plagioclase-phyric basalts

Nonequilibrium fluctuation dissipation relations of interacting Brownian particles driven by shear

We present a detailed analysis of the fluctuation dissipation theorem (FDT) close to the glass transition in colloidal suspensions under steady shear using mode coupling approximations. Starting point is the many-particle Smoluchowski equation. Under shear, detailed balance is broken and the response functions in the stationary state are smaller at long times than estimated from the equilibrium FDT. An asymptotically constant relation connects response and fluctuations during the shear driven decay, restoring the form of the FDT with, however, a ratio different from the equilibrium one. At short times, the equilibrium FDT holds. We follow two independent approaches whose results are in qualitative agreement. To discuss the derived fluctuation dissipation ratios, we show an exact reformulation of the susceptibility which contains not the full Smoluchowski operator as in equilibrium, but only its well defined Hermitian part. This Hermitian part can be interpreted as governing the dynamics in the frame comoving with the probability current. We present a simple toy model which illustrates the FDT violation in the sheared colloidal system.Comment: 21 pages, 13 figures, submitted to Phys. Rev.

Towards a developmental state? Provincial economic policy in South Africa

This paper explores the meaning of the developmental state for spatial economic policy in South Africa. Two main questions are addressed: do provincial governments have a role to play in promoting economic prosperity, and to what extent do current provincial policies possess the attributes of a developmental state? These attributes are defined as the ability to plan longer term, to focus key partners on a common agenda, and to mobilise state resources to build productive capabilities. The paper argues that the developmental state must harness the power of government at every level to ensure that each part of the country develops to its potential. However, current provincial capacity is uneven, and weakest where support is needed most. Many provinces seem to have partial strategies and lack the wherewithal for sustained implementation. Coordination across government appears to be poor. The paper concludes by suggesting ways provincial policies could be strengthened