Spectrophotometric measurements of pH in-situ: laboratory and field evaluations of instrumental performance

Automated in-situ instrumentation has been developed for precise and accurate measurements of a variety of analytes in natural waters. In this work we describe the use of 'SEAS' (spectrophotometric elemental analysis system) instrumentation for measurements of solution pH. SEAS-pH incorporates a CCD-based spectrophotometer, an incandescent light source, and dual pumps for mixing natural water samples with a sulfonephthalein indicator. The SEAS-pH optical cell consists of either a liquid core waveguide (LCW, Teflon AF-2400) or a custom-made PEEK cell. Long optical path lengths allow use of indicators at low concentrations, thereby precluding large indicator-induced pH perturbations. Laboratory experiments show that pH measurements obtained using LCW and PEEK optical cells are indistinguishable from measurements obtained using conventional spectrophotometric cells and high-performance spectrophotometers. Deployments in the Equatorial Pacific and the Gulf of Mexico demonstrate that SEAS-pH instruments are capable of obtaining vertical pH profiles with high spatial resolution. SEAS-pH deployments at a fixed river-site (Hillsborough River, FL) demonstrate the capability of SEAS for observations of diel pH cycles with high temporal resolution. The in-situ precision of SEAS-pH is assessed as 0.0014 pH units, and the system's measurement frequency is approximately 0.5 Hz. This work indicates that in-situ instrumentation can be used to provide accurate, precise, and highly resolved observations of carbon-system transformations in the natural environment.     

Genomic structure,cloning and expression of two phospholipase D isoenzymes from white cabbage

Phospholipase D (PLD) from cabbage is interesting as biocatalyst in phospholipid transformation. To provide the basis for genetic engineering of the enzyme, gene cloning and sequencing were carried out. We have recently identified two isoenzymes, PLD1 and PLD2, on the basis of their cDNAs, here we describe their genomic structure consisting of 3404 and 3614 bp, respectively. Based on their sequence, PLD1 and PLD2 can be assigned to the α‐type of plant PLDs, they contain two HKD motifs and the C2 domain with a phosphatidylinositol 4,5‐bisphosphate (PIP₂) binding motif. Starting from pld1 cDNA, expression studies were carried out. Whereas expression using constructs with StrepTactin or Glutathion S‐transferase tags was not successful, soluble active enzyme was produced from constructs without tag. pld2 was expressed accordingly. Both enzymes were purified by Ca²⁺‐mediated hydrophobic interaction chromatography to high purity. N‐terminal sequencing of PLD1 and PLD2 revealed that the Met‐free N‐termini of both enzymes correspond to sequences derived from the coding region of the pld1 and pld2 genes, respectively. Both recombinant enzymes showed highest hydrolytic activities at pH 5.5 to 5.6, independent of Ca²⁺ concentration (10—100 mM). The optimum Ca²⁺ concentration was 45 mM for PLD1 and PLD2. Both enzymes showed comparable activities in hydrolysis and transphosphatidylation of phospholipids.     

Layer‐by‐Layer Coated Gold Nanoparticles: Size‐Dependent Delivery of DNA into Cells

Because nanoparticles are finding uses in myriad biomedical applications, including the delivery of nucleic acids, a detailed knowledge of their interaction with the biological system is of utmost importance. Here the size‐dependent uptake of gold nanoparticles (AuNPs) (20, 30, 50 and 80 nm), coated with a layer‐by‐layer approach with nucleic acid and poly(ethylene imine) (PEI), into a variety of mammalian cell lines is studied. In contrast to other studies, the optimal particle diameter for cellular uptake is determined but also the number of therapeutic cargo molecules per cell. It is found that 20 nm AuNPs, with diameters of about 32 nm after the coating process and about 88 nm including the protein corona after incubation in cell culture medium, yield the highest number of nanoparticles and therapeutic DNA molecules per cell. Interestingly, PEI, which is known for its toxicity, can be applied at significantly higher concentrations than its IC₅₀ value, most likely because it is tightly bound to the AuNP surface and/or covered by a protein corona. These results are important for the future design of nanomaterials for the delivery of nucleic acids in two ways. They demonstrate that changes in the nanoparticle size can lead to significant differences in the number of therapeutic molecules delivered per cell, and they reveal that the toxicity of polyelectrolytes can be modulated by an appropriate binding to the nanoparticle surface.     

Sustainability standards for bioenergy—A means to reduce climate change risks?

The paper discusses the importance of standards for sustainable bioenergy production. Sustainability of bioenergy production is crucial if bioenergy is supposed to contribute effectively to climate change mitigation. First, a brief overview of current bioenergy policies and of initiatives and legislation for bioenergy sustainability are given. Then, the authors show that under free market conditions undersupply of sustainable bioenergy will prevail. Two types of market failures are identified: information asymmetry and externalities in bioenergy production. Due to these market failures bioenergy is less sustainable than it could be. It is shown that mandatory certification and subsequent labeling can help to overcome the information asymmetry and lead to a more efficient market outcome since consumers can choose products according to their preferences. The authors conclude, however, that the existence of production externalities asks for stronger market intervention, for example in the form of binding minimum standards or taxes. The paper discusses the efficiency and feasibility of such policy measures and shows that mandatory certification combined with binding minimum standards can be an adequate policy choice to regulate the bioenergy market.     

Addressing the numbers problem in directed evolution

Our previous contribution to increasing the efficiency of directed evolution is iterative saturation mutagenesis (ISM) as a systematic means of generating focused libraries for the control of substrate acceptance, enantioselectivity, or thermostability of enzymes. We have now introduced a crucial element to knowledge-guided targeted mutagenesis in general that helps to solve the numbers problem in directed evolution. We show that the choice of the amino acid (aa) alphabet, as specified by the utilized codon degeneracy, provides the experimenter with a powerful tool in designing "smarter" randomized libraries that require considerably less screening effort. A systematic comparison of two different codon degeneracies was made by examining the relative quality of the identically sized enzyme libraries in relation to the degree of oversampling required in the screening process. The specific example in our case study concerns the conventional NNK codon degeneracy (32 codons/20 aa) versus NDT (12 codons/12 aa). The model reaction is the hydrolytic kinetic resolution of a chiral trans-disubstituted epoxide, catalyzed by the epoxide hydrolase from Aspergillus niger. The NDT library proves to be of much higher quality, as measured by the dramatically higher frequency of positive variants and by the magnitude of catalyst improvement (enhanced rate and enantioselectivity). We provide a statistical analysis that constitutes a useful guide for the optimal design and generation of "smarter" focused libraries. This type of approach accelerates the process of laboratory evolution considerably and can be expected to be broadly applicable when engineering functional proteins in general.     

Occurrence of perfluoroalkyl compounds in surface waters from the North Pacific to the Arctic Ocean

Perfluoroalkyl compounds (PFCs) were determined in 22 surface water samples (39-76°N) and three sea ice core and snow samples (77-87°N) collected from North Pacific to the Arctic Ocean during the fourth Chinese Arctic Expedition in 2010. Geographically, the average concentration of ∑PFC in surface water samples were 560 ± 170 pg L(-1) for the Northwest Pacific Ocean, 500 ± 170 pg L(-1) for the Arctic Ocean, and 340 ± 130 pg L(-1) for the Bering Sea, respectively. The perfluoroalkyl carboxylates (PFCAs) were the dominant PFC class in the water samples, however, the spatial pattern of PFCs varied. The C(5), C(7) and C(8) PFCAs (i.e., perfluoropentanoate (PFPA), perfluoroheptanoate (PFHpA), and perfluorooctanoate (PFOA)) were the dominant PFCs in the Northwest Pacific Ocean while in the Bering Sea the PFPA dominated. The changing in the pattern and concentrations in Pacific Ocean indicate that the PFCs in surface water were influenced by sources from the East-Asian (such as Japan and China) and North American coast, and dilution effect during their transport to the Arctic. The presence of PFCs in the snow and ice core samples indicates an atmospheric deposition of PFCs in the Arctic. The elevated PFC concentration in the Arctic Ocean shows that the ice melting had an impact on the PFC levels and distribution. In addition, the C(4) and C(5) PFCAs (i.e., perfluorobutanoate (PFBA), PFPA) became the dominant PFCs in the Arctic Ocean indicating that PFBA is a marker for sea ice melting as the source of exposure.     

Suppression of Fusarium graminearium growth by differently structured starch types

We investigated the growth behavior and amylolytic enzymes of Fusarium graminearum cultivated on different types of native starch granules including barley (A‐type crystalline polymorph), potato and Curcuma zedoaria (B‐type crystalline polymorph), cassava (C‐type crystalline polymorph), and high AM maize (A + Vh‐type crystalline polymorphs). F. graminearum grew poorly on B‐type starches and the accumulation of biomass was similar to that obtained for fungi cultivated under carbohydrate starvation conditions. In comparison, three‐ to fivefold higher accumulation of fungal biomass was observed for growth on the A‐, C‐ and A + Vh‐type starches. Fungal glucoamylase and α‐amylase activity increased over time in the presence of native starch granules. Interestingly, resistant B‐type starches induced the highest amylolytic activity indicating that F. graminearum interacts with B‐type granules although only limited degradation occur. Starch degradation products maltose and malto‐oligosacharides was found to increase glucoamylase and α‐amylase activity, whereas glucose acted as a catabolite repressor.     

Single-channel blind estimation of arterial input function and tissue impulse response in DCE-MRI

Multipass dynamic MRI and pharmacokinetic modeling are used to estimate perfusion parameters of leaky capillaries. Curve fitting and nonblind deconvolution are the established methods to derive the perfusion estimates from the observed arterial input function (AIF) and tissue tracer concentration function. These nonblind methods are sensitive to errors in the AIF, measured in some nearby artery or estimated by multichannel blind deconvolution. Here, a single-channel blind deconvolution algorithm is presented, which only uses a single tissue tracer concentration function to estimate the corresponding AIF and tissue impulse response function. That way, many errors affecting these functions are reduced. The validity of the algorithm is supported by simulations and tests on real data from mouse. The corresponding nonblind and multichannel methods are also presented.     

Antibacterial Surface Coatings from Zinc Oxide Nanoparticles Embedded in Poly(N‐isopropylacrylamide) Hydrogel Surface Layers

Despite multiple research approaches to prevent bacterial colonization on surfaces, device‐associated infections are currently responsible for about 50% of nosocomial infections in Europe and significantly increase health care costs, which demands development of advanced antibacterial surface coatings. Here, novel antimicrobial composite materials incorporating zinc oxide nanoparticles (ZnO NP) into biocompatible poly(N‐isopropylacrylamide) (PNIPAAm) hydrogel layers are prepared by mixing the PNIPAAm prepolymer with ZnO NP, followed by spin‐coating and photocrosslinking. Scanning electron microscopy (SEM) characterization of the composite film morphology reveals a homogeneous distribution of the ZnO NP throughout the film for every applied NP/polymer ratio. The optical properties of the embedded NP are not affected by the matrix as confirmed by UV‐vis spectroscopy. The nanocomposite films exhibit bactericidal behavior towards Escherichia coli (E. coli) for a ZnO concentration as low as ≈0.74 μg cm^?2 (1.33 mmol cm^?3), which is determined by inductively coupled plasma optical emission spectrometry. In contrast, the coatings are found to be non‐cytotoxic towards a mammalian cell line (NIH/3T3) at bactericidal loadings of ZnO over an extended period of seven days. The differential toxicity of the ZnO/hydrogel nanocomposite thin films between bacterial and cellular species qualifies them as promising candidates for novel biomedical device coatings.