Approaches and tools to manipulate the carbonate chemistry

Although the chemistry of ocean acidifi cation is very well understood (see chapter 1), its impact on marine organisms and ecosystems remains poorly known. The biological response to ocean acidifi cation is a recent field of research, the fi rst purposeful experiments have only been carried out as late as the 1980s (Agegian, 1985) and most were not performed until the late 1990s. The potentially dire consequences of ocean acidifi cation have attracted the interest of scientists and students with a limited knowledge of the carbonate chemistry and its experimental manipulation. Perturbation experiments are one of the key approaches used to investigate the biological response to elevated p(CO2). Such experiments are based on measurements of physiological or metabolic processes in organisms and communities exposed to seawater with normal and altered carbonate chemistry. The basics of the carbonate chemistry must be understood to perform meaningful CO2 perturbation experiments (see chapter 1). Briefl y, the marine carbonate system considers € CO2 ∗(aq) [the sum of CO2 and H2CO3], € HCO3 −, € CO3 2−, H+, € OH− , and several weak acid-base systems of which borate-boric acid (€ B(OH)4 − , B(OH)3) is the most important. As discussed by Dickson (chapter 1), if two components of the carbonate chemistry are known, all the other components can be calculated for seawater with typical nutrient concentrations at given temperature, salinity, and pressure. One of the possible pairs is of particular interest because both components can be measured with precision, accuracy, and are conservative in the sense that their concentrations do not change with temperature or pressure. Dissolved inorganic carbon (DIC) is the sum of all dissolved inorganic carbon species while total alkalinity (AT) equals € [HCO3 − ] + 2 € [CO3 2− ] + € [B(OH)4 − ] + € [OH− ] - [H+] + minor components, and refl ects the excess of proton acceptors over proton donors with respect to a zero level of protons (see chapter 1 for a detailed defi nition). AT is determined by the titration of seawater with a strong acid and thus can also be regarded as a measure of the buffering capacity. Any changes in any single component of the carbonate system will lead to changes in several, if not all, other components. In other words, it is not possible to vary a single component of the carbonate system while keeping all other components constant. This interdependency in the carbonate system is important to consider when performing CO2 perturbation experiments. To adjust seawater to different p(CO2) levels, the carbonate system can be manipulated in various ways that usually involve changes in AT or DIC. The goal of this chapter is (1) to examine the benefi ts and drawbacks of various manipulation methods used to date and (2) to provide a simple software package to assist the design of perturbation experiments

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments

Relation Between Quantum Speed Limits And Metrics On U(n)

Recently, Chau [Quant. Inform. & Comp. 11, 721 (2011)] found a family of metrics and pseudo-metrics on $n$-dimensional unitary operators that can be interpreted as the minimum resources (given by certain tight quantum speed limit bounds) needed to transform one unitary operator to another. This result is closely related to the weighted $\ell^1$-norm on ${\mathbb R}^n$. Here we generalize this finding by showing that every weighted $\ell^p$-norm on ${\mathbb R}^n$ with 1\le p \le \limitingp induces a metric and a pseudo-metric on $n$-dimensional unitary operators with quantum information-theoretic meanings related to certain tight quantum speed limit bounds. Besides, we investigate how far the correspondence between the existence of metrics and pseudo-metrics of this type and the quantum speed limits can go.Comment: minor amendments, 6 pages, to appear in J.Phys.

Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing

Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure

The assessment of quality of life in acute cough with the Leicester Cough Questionnaire (LCQ-acute)

INTRODUCTION: Acute cough has a significant impact on physical and psychosocial health and is associated with an impaired quality of life (QOL). The Leicester Cough Questionnaire (LCQ) is a validated cough-related health status questionnaire designed for patients with chronic cough. The purpose of this study was to validate the LCQ for the assessment of health related QOL in patients with acute cough and determine the clinical minimal important difference (MID). METHODS: 10 subjects with cough due to acute upper respiratory tract infection underwent focused interviews to investigate the face validity of the LCQ. The LCQ was also evaluated by a multidisciplinary team. 30 subjects completed the revised LCQ-acute and a cough visual analogue score (VAS: 0-100 mm) within one week of onset of cough and again 0.9. There was a significant correlation between LCQ-acute and VAS (ρ = -0.48, p = 0.007). The LCQ-acute and its domains were highly responsive to change; effect sizes 1.7-2.3. The MID for total LCQ and VAS were 2.5 and 13 mm respectively. CONCLUSION: The LCQ-acute is a brief, simple and valid instrument to assess cough specific health related QOL in patients with acute cough. It is a highly responsive tool suggesting that it will be particularly useful to assess the effect of antitussive therapy

Identification of H3K4me1-associated proteins at mammalian enhancers.

Enhancers act to regulate cell-type-specific gene expression by facilitating the transcription of target genes. In mammalian cells, active or primed enhancers are commonly marked by monomethylation of histone H3 at lysine 4 (H3K4me1) in a cell-type-specific manner. Whether and how this histone modification regulates enhancer-dependent transcription programs in mammals is unclear. In this study, we conducted SILAC mass spectrometry experiments with mononucleosomes and identified multiple H3K4me1-associated proteins, including many involved in chromatin remodeling. We demonstrate that H3K4me1 augments association of the chromatin-remodeling complex BAF to enhancers in vivo and that, in vitro, H3K4me1-marked nucleosomes are more efficiently remodeled by the BAF complex. Crystal structures of the BAF component BAF45C indicate that monomethylation, but not trimethylation, is accommodated by BAF45C's H3K4-binding site. Our results suggest that H3K4me1 has an active role at enhancers by facilitating binding of the BAF complex and possibly other chromatin regulators

Low energy physical properties of high-Tc superconducting Cu oxides: A comparison between the resonating valence bond and experiments

In a recent review by Anderson and coworkers\cite{Vanilla}, it was pointed out that an early resonating valence bond (RVB) theory is able to explain a number of unusual properties of high temperature superconducting (SC) Cu-oxides. Here we extend previous calculations \cite{anderson87,FC Zhang,Randeria} to study more systematically low energy physical properties of the plain vanilla d-wave RVB state, and to compare results with the available experiments. We use a renormalized mean field theory combined with variational Monte Carlo and power Lanczos methods to study the RVB state of an extended $t-J$ model in a square lattice with parameters suitable for the hole doped Cu-oxides. The physical observable quantities we study include the specific heat, the linear residual thermal conductivity, the in-plane magnetic penetration depth, the quasiparticle energy at the antinode $(\pi, 0)$, the superconducting energy gap, the quasiparticle spectra and the Drude weight. The traits of nodes (including $k_{F}$, the Fermi velocity $v_{F}$ and the velocity along Fermi surface $v_{2}$), as well as the SC order parameter are also studied. Comparisons of the theory and the experiments in cuprates show an overall qualitative agreement, especially on their doping dependences.Comment: 12 pages, 14 figures, 1 tabl

Longitudinal spin transport in diluted magnetic semiconductor superlattices: the effect of the giant Zeeman splitting

Longitudinal spin transport in diluted magnetic semiconductor superlattices is investigated theoretically. The longitudinal magnetoconductivity (MC) in such systems exhibits an oscillating behavior as function of an external magnetic field. In the weak magnetic field region the giant Zeeman splitting plays a dominant role which leads to a large negative magnetoconductivity. In the strong magnetic field region the MC exhibits deep dips with increasing magnetic field. The oscillating behavior is attributed to the interplay between the discrete Landau levels and the Fermi surface. The decrease of the MC at low magnetic field is caused by the $s-d$ exchange interaction between the electron in the conduction band and the magnetic ions.Comment: 6 pages, 9 figures, submitted to Phys. Rev.

Rapid default transition of CD4 T cell effectors to functional memory cells

The majority of highly activated CD4 T cell effectors die after antigen clearance, but a small number revert to a resting state, becoming memory cells with unique functional attributes. It is currently unclear when after antigen clearance effectors return to rest and acquire important memory properties. We follow well-defined cohorts of CD4 T cells through the effector-to-memory transition by analyzing phenotype, important functional properties, and gene expression profiles. We find that the transition from effector to memory is rapid in that effectors rested for only 3 d closely resemble canonical memory cells rested for 60 d or longer in the absence of antigen. This is true for both Th1 and Th2 lineages, and occurs whether CD4 T cell effectors rest in vivo or in vitro, suggesting a default pathway. We find that the effector–memory transition at the level of gene expression occurs in two stages: a rapid loss of expression of a myriad of effector-associated genes, and a more gradual gain of expression of a cohort of genes uniquely associated with memory cells rested for extended periods