The structure of cyanobacterial phycobilisomes: a model

Phycobilisomes, supramolecular complexes of water-soluble accessory pigments, serve as the major light-harvesting antennae in cyanobacteria and red algae. Regular arrays of these organelles are found on the surface of the thylakoid membranes of these organisms. In the present study, the hemi-discoidal phycobilisomes of several species of cyanobacteria were examined in thin sections of cells and by negative staining after isolation and fixation. Their fundamental structures were found to be the same. Isolated phycobilisomes possessed a triangular core assembled from three stacks of disc-shaped subunits. Each stack contained two discs which were 12 nm in diameter and 6–7 nm thick. Each of these discs was probably subdivided into halves 3–3.5 nm thick. Radiating from each of two sides of the triangular core were three rods 12 nm in diameter. Each rod consisted of stacks of 2 to 6 disc-shaped subunits 6 nm thick. These discs were subdivided into halves 3 nm thick.The average number of discs of 6 nm thickness forming the peripheral rods varied among the strains studied. For certain chromatically adapting strains, the average rod length was dependent upon the wavelength of light to which cells were exposed during growth. Analyses of phycobilisomes by spectroscopic techniques, polyacrylamide gel electrophoresis, and electron microscopy were compared. These analyses suggested that the triangular core was composed of allophycocyanin and that the peripheral rods contained phycocyanin and phycoerythrin (when present). A detailed model of the hemi-discoidal phycobilisome is proposed. This model can account for many aspects of phycobiliprotein assembly and energy transfer.Abbreviations PBS phycobilisome(s) - PBP phycobiliprotein(s) - AP allophycocyanin - PC phycocyanin - PE phycoerythrin - PEC phycoerythrocyanin - AP-B allophycocyanin B - C- cyanobacterial - R- rhodophytan - B- Bangiophycean - SDS sodium dodecyl sulfate - LPP Lyngbya-Plectonema-Phormidium group - Na-KPO₄ buffers NaH₂PO₄ titrated with a solution of KH₂PO₄ of equivalent molarity to a given pH     

Image analysis as a tool for quantitative phycology: a computational approach to cyanobacterial taxa identification

In the following work we discuss the application of image processing and pattern recognition to the field of quantitative phycology. We overview the area of image processing and review previously published literature pertaining to the image analysis of phycological images and, in particular, cyanobacterial image processing. We then discuss the main operations used to process images and quantify data contained within them. To demonstrate the utility of image processing to cyanobacteria classification, we present details of an image analysis system for automatically detecting and classifying several cyanobacterial taxa of Lake Biwa, Japan. Specifically, we initially target the genus Microcystis for detection and classification from among several species of Anabaena. We subsequently extend the system to classify a total of six cyanobacteria species. High-resolution microscope images containing a mix of the above species and other nontargeted objects are analyzed, and any detected objects are removed from the image for further analysis. Following image enhancement, we measure object properties and compare them to a previously compiled database of species characteristics. Classification of an object as belonging to a particular class membership (e.g., “Microcystis,”“A. smithii,”“Other,” etc.) is performed using parametric statistical methods. Leave-one-out classification results suggest a system error rate of approximately 3%. Received: September 6, 1999 / Accepted: February 6, 2000     

A retained viability index (RVI10) for evaluation of a cyanobacterial powder fertilizer

The preparation of a dry and powder fertilizer based on five nitrogen-fixing cyanobacterial strains is described. Tolypothrix tenuis and Nostoc muscorum resisted the drying and milling processes and showed a suitable recovering capacity in liquid media of different pH and salinity. Although a decrease in the cellular viability was observed with the storage time, the biomass of Nostoc muscorum retained viability for 16 months. The results were evaluated in terms of the retained viability index (RVI₁₀) specifically designed for the fertilizer material.     

The efficiency of combined coagulant and ballast to remove harmful cyanobacterial blooms in a tropical shallow system

We tested the hypothesis that a combination of coagulant and ballast could be efficient for removal of positively buoyant harmful cyanobacteria in shallow tropical waterbodies, and will not promote the release of cyanotoxins. This laboratory study examined the efficacy of coagulants [polyaluminium chloride (PAC) and chitosan (made of shrimp shells)] alone, and combined with ballast (lanthanum modified bentonite, red soil or gravel) to remove the natural populations of cyanobacteria collected from a shallow eutrophic urban reservoir with alternating blooms of Cylindrospermopsis and Microcystis. PAC combined with ballast was effective in settling blooms dominated by Microcystis or Cylindrospermopsis. Contrary to our expectation, chitosan combined with ballast was only effective in settling Cylindrospermopsis-dominated blooms at low pH, whereas at pH ≥ 8 no effective flocculation and settling could be evoked. Chitosan also had a detrimental effect on Cylindrospermopsis causing the release of saxitoxins. In contrast, no detrimental effect on Microcystis was observed and all coagulant-ballast treatments were effective in not only settling the Microcystis dominated bloom, but also lowering dissolved microcystin concentrations. Our data show that the best procedure for biomass reduction also depends on the dominant species.     

Cover as a simple predictor of biomass for two shrubs in Tibet

Knowledge of the quantitative relationship between plant cover and its corresponding biomass for shrubs is not well known, especially for those on the Tibetan Plateau. Based on investigations of 35 sites, 90 plots and 95 standard individuals for two typical shrub species (Rhododendron nivale Hook. f. and Sophora moorcroftiana (Benth.) Baker) across Tibet, we developed allometric models for biomass estimation from measurements of crown diameter and/or height. We found that the parameters of crown projection area (CPA), height and their product (volume) were all significantly (p < 0.01) correlated with dry mass of different organs for both species at individual level. The CPA rather than volume best predicted aboveground dry mass. This is because that the bulk density declined significantly with increasing plant height, leading to the inappropriateness for plant height itself being employed as a parameter in biomass estimation, especially for shrubs in smaller size groups. At community level, cover was tightly correlated with the aboveground, belowground and total biomass (R² = 0.97–0.99). Therefore, biomass for the two shrubs can be simply estimated by measuring plant cover, which enables rapid estimation of shrubland carbon stock at large scales by using satellite data and repeated experiments over time. This non-destructive method using cover to estimate shrub biomass can be applied not only in arid ecosystems but also in alpine or subalpine environment.     

Micro and macroalgal biomass: A renewable source for bioethanol

Population outburst together with increased motorization has led to an overwhelming increase in the demand for fuel. In the milieu of economical and environmental concern, algae capable of accumulating high starch/cellulose can serve as an excellent alternative to food crops for bioethanol production, a green fuel for sustainable future. Certain species of algae can produce ethanol during dark-anaerobic fermentation and thus serve as a direct source for ethanol production. Of late, oleaginous microalgae generate high starch/cellulose biomass waste after oil extraction, which can be hydrolyzed to generate sugary syrup to be used as substrate for ethanol production. Macroalgae are also harnessed as renewable source of biomass intended for ethanol production. Currently there are very few studies on this issue, and intense research is required in future in this area for efficient utilization of algal biomass and their industrial wastes to produce environmentally friendly fuel bioethanol.     

Discussion for animal experiments in space: ethical standard and responsibility of researchers for space experiments using laboratory animals.

International efforts to standardize regulations and study designs and to promote the principles of Reduction, Replacement, and Refinement (the 3 Rs) have reduced and refined animal use. In NASA ARC and KSC, researchers are responsible only for activities related directly to the conduct of their animal experiments. The IACUC plays an important role in conformity with NIH policies. Even if researchers design protocols of the space life science in Japan, the animal experiments should be carried out under the global harmonized conditions in accordance with NIH/NASA policies, guides and rules. It is important that researchers himself must look forward the ethical animal experiment.     

The ethical acceptability of animal experiments: a proposal for a system to support decision-making

We describe a system to support decision-making on the ethical acceptability of animal experiments for scientific researchers and others responsible for ethical decision-making in animal experiments. The system consists of eight steps. Each step contains a number of substantive questions or a computational rule, leading to a well-articulated moral judgment on specific animal experiments. The system comprises a number of moral assumptions and pre-emptive norms, but leaves enough room for moral discretion and personal responsibility. The general ethical ideas behind the moral choices and assumptions are sketched and potential objections to the overall approach are discussed.     

Global solutions to regional problems: Collecting global expertise to address the problem of harmful cyanobacterial blooms. A Lake Erie case study

In early August 2014, the municipality of Toledo, OH (USA) issued a ‘do not drink’ advisory on their water supply directly affecting over 400,000 residential customers and hundreds of businesses (Wilson, 2014). This order was attributable to levels of microcystin, a potent liver toxin, which rose to 2.5 μg L⁻¹ in finished drinking water. The Toledo crisis afforded an opportunity to bring together scientists from around the world to share ideas regarding factors that contribute to bloom formation and toxigenicity, bloom and toxin detection as well as prevention and remediation of bloom events. These discussions took place at an NSF- and NOAA-sponsored workshop at Bowling Green State University on April 13 and 14, 2015. In all, more than 100 attendees from six countries and 15 US states gathered together to share their perspectives. The purpose of this review is to present the consensus summary of these issues that emerged from discussions at the Workshop. As additional reports in this special issue provide detailed reviews on many major CHAB species, this paper focuses on the general themes common to all blooms, such as bloom detection, modeling, nutrient loading, and strategies to reduce nutrients.     

Low filtering rates of <Emphasis Type="Italic">Daphnia magna</Emphasis> in a hypertrophic lake: laboratory and in situ experiments using synthetic microspheres

Zooplankton grazing was measured in Albufera of València (Spain), a shallow turbid hypertrophic lagoon dominated by filamentous bluegreens, during the period of Daphnia magna growth, to evaluate the role of this cladoceran in maintaining a clear water phase which takes place after flushing for rice cultivation practices. We found extremely low ingestion and clearance rates (CR) on latex beads in situ, using a Haney trap suggesting potentially strong inhibition of grazing by the filamentous cyanobacteria, still flourishing in the lagoon. To test the effect of filaments, we undertook laboratory feeding experiments using six different dilutions of the lagoon water to vary filament concentrations, and four different bead concentrations. A highly significant power function between CR and water dilution associated with filament concentrations was found, indicating that the ability of Daphnia to exploit smaller edible algae and thereby control phytoplankton growth would depend on filament concentration levels in the lagoon. From our results only the two more diluted treatments, 9 × 10³ and 18 × 10³ filament ml⁻¹ showed CRs not far from the range of what would be normally expected on the basis of the general relationship of feeding rate as a function of total food concentration. This means that at lower food concentrations, filaments reduce D. magna CR by increasing total food concentration beyond the incipient limiting level, as well as by moderate mechanical interference with the animal’s feeding. However, at lagoon water concentrations above 25% (corresponding to filament concentrations of 75 × 10⁵ filaments ml⁻¹), extremely low CR’s, which did not respond to any food addition, were obtained for D. magna. From these results we can infer that at concentrations beyond the above-mentioned critical level, feeding inhibition by filamentous cyanobacteria is most probably due entirely to mechanical interference. Guest editor: Piet Spaak Cladocera: Proceedings of the 7th International Symposium on Cladocera     

A method for examining temporal changes in cyanobacterial harmful algal bloom spatial extent using satellite remote sensing

Cyanobacterial harmful algal blooms (CyanoHAB) are thought to be increasing globally over the past few decades, but relatively little quantitative information is available about the spatial extent of blooms. Satellite remote sensing provides a potential technology for identifying cyanoHABs in multiple water bodies and across geo-political boundaries. An assessment method was developed using MEdium Resolution Imaging Spectrometer (MERIS) imagery to quantify cyanoHAB surface area extent, transferable to different spatial areas, in Florida, Ohio, and California for the test period of 2008 to 2012. Temporal assessment was used to evaluate changes in satellite resolvable inland waterbodies for each state of interest. To further assess cyanoHAB risk within the states, the World Health Organization’s (WHO) recreational guidance level thresholds were used to categorize surface area of cyanoHABs into three risk categories: low, moderate, and high-risk bloom area. Results showed that in Florida, the area of cyanoHABs increased largely due to observed increases in high-risk bloom area. California exhibited a slight decrease in cyanoHAB extent, primarily attributed to decreases in Northern California. In Ohio (excluding Lake Erie), little change in cyanoHAB surface area was observed. This study uses satellite remote sensing to quantify changes in inland cyanoHAB surface area across numerous water bodies within an entire state. The temporal assessment method developed here will be relevant into the future as it is transferable to the Ocean Land Colour Instrument (OLCI) on Sentinel-3A/3B missions.     

Protein extraction from biomass in a bioethanol refinery - Possible dietary applications: Use as animal feed and potential extension to human consumption

The economy of the production of lignocellulosic ethanol could be supported by the simultaneous use of different components of the biomass other than sugars. Among these, protein is present at high concentration in leaves and is a candidate for different possible utilizations. Among dietary applications, plant protein may be used as animal feed and possibly extended to human consumption, in close similarity to leaf protein concentrates already proposed in the past. This would be especially beneficial for developing countries. For this aim, protein quality plays a crucial role: separating only the noble fraction of protein in biomass and preserving its nutritional value, while simultaneously obtaining good yields and limiting drawbacks on other steps of the production chain is particularly challenging from a technical viewpoint. In this review, we compare the possible extraction of protein from dry biomass with the more commonly studied situation in which freshly harvested material is used, with special focus on dietary implications.     

Synchrotron Protein Footprinting: A Technique to Investigate Protein-Protein Interactions

Abstract

Traditional approaches for macromolecular structure elucidation, including NMR, crystallography and cryo-EM have made significant progress in defining the structures of protein-protein complexes. A substantial number of macromolecular structures, however, have not been examined with atomic detail due to sample size and heterogeneity, or resolution limitations of the technique; therefore, the general applicability of each method is greatly reduced. Synchrotron footprinting attempts to bridge the gap in these methods by monitoring changes in accessible surface areas of discrete macromolecular moieties. As evidenced by our previous studies on RNA folding and DNA-protein interactions, the three-dimensional structure is probed by examining the reactions of these moieties with hydroxyl radicals generated by synchrotron X-rays. Here we report the application of synchrotron foot- printing to the investigation of protein-protein interactions, as the novel technique has been utilized to successfully map the contact sites of gelsolin segment-1 in the gelsolin segment 1/actin complex. Footprinting results demonstrate that phenylalanine 104, located on the actin binding helix of gelsolin segment 1, is protected from hydroxyl radical modification in the presence of actin. This change in reactivity results from the specific protection of gel- solin segment-1, consistent with the substantial decrease in solvent accessibility of F104 upon actin binding, as calculated from the crystal structural of the gelsolin segment 1/actin complex. The results presented here establish synchrotron footprinting as a broadly applicable method to probe structural features of macromolecular complexes that are not amenable to conventional approaches.     

Design and development of a simple laboratory model to detect <Superscript>15</Superscript>N enrichment in cyanobacterial biomass and extra cellular ammonia using <Superscript>15</Superscript>N gas

A laboratory scale working model that could detect the ¹⁵N enrichment in cyanobacterial biomass and extracellular ammonia, using ¹⁵N gas under in vitro conditions was designed and fabricated. Using the model, ¹⁵N enrichment of 0.48% atom excess was detected in the cyanobacterial biomass on the 30 d after inoculation. The ¹⁵N enrichment increased linearly in the extracellular ammoniacal fraction from the 20 d onward. The model would prove to be a useful tool to quantify the extent of ¹⁵N enrichment under in vitro conditions using ¹⁵N gas.     

Energy valorization of industrial biomass: Using a batch frying process for sewage sludge

This paper studies the energy valorization of sewage sludge using a batch fry–drying process. Drying processes was carried out by emerging the cylindrical samples of the sewage sludge in the preheated recycled cooking oil. Experimental frying curves for different conditions were determined. Calorific values for the fried sewage sludge were hence determined to be around 24 MJ kg⁻¹, showing the auto-combustion potential of the fried sludge. A one-dimensional model allowing for the prediction of the water removal during frying was developed. Another water replacement model for oil intake in the fried sewage sludge was also developed. Typical frying curves were obtained and validated against the experimental data.     

A general algorithm for peak-tracking in multi-dimensional NMR experiments

We present an algorithmic method allowing automatic tracking of NMR peaks in a series of spectra. It consists in a two phase analysis. The first phase is a local modeling of the peak displacement between two consecutive experiments using distance matrices. Then, from the coefficients of these matrices, a value graph containing the a priori set of possible paths used by these peaks is generated. On this set, the minimization under constraint of the target function by a heuristic approach provides a solution to the peak-tracking problem. This approach has been named GAPT, standing for General Algorithm for NMR Peak Tracking. It has been validated in numerous simulations resembling those encountered in NMR spectroscopy. We show the robustness and limits of the method for situations with many peak-picking errors, and presenting a high local density of peaks. It is then applied to the case of a temperature study of the NMR spectrum of the Lipid Transfer Protein (LTP).     

Protein kinases and protein phosphatases in prokaryotes: a genomic perspective

For many years, the regulation of protein structure and function by phosphorylation and dephosphorylation was considered a relatively recent invention that arose independently in each phylogenetic domain. Over time, however, incidents of apparent domain trespass involving the presence of 'eukaryotic' protein kinases or protein phosphatases in prokaryotic organisms were reported with increasing frequency. Today, genomics has provided the means to examine the phylogenetic distribution of 'eukaryotic' protein kinases and protein phosphatases in a comprehensive and systematic manner. The results of these genome searches challenge previous conceptions concerning the origins and evolution of this versatile regulatory mechanism.