The light-harvesting polypeptides of Rhodopseudomonas viridis. The complete amino-acid sequences of B1015-alpha, B1015-beta and B1015-gamma

Three low molecular mass polypeptides have been isolated by using the technique of organic solvent extraction of thylakoid membranes or whole cells from Rhodopseudomonas viridis. Their primary structures were determined by long liquid phase sequencer runs, combined with the isolation and sequence analysis of the C-terminal o-iodosobenzoic acid fragment and carboxypeptidase degradation. The polypeptide which consists of 58 amino-acids and is 46% homologous to the antenna polypeptide B880-alpha from Rhodospirillum rubrum was designated as B1015-alpha (1 His residue). The sequence homology between the second polypeptide, named B1015-beta (55 amino acids, 2 His residues) and B880-beta from Rs. rubrum is 52%. For the third polypeptide consisting of 36 amino acids and exhibiting a high hydrophobicity, no equivalent polypeptide has so far been found in other purple bacteria. The molar ratio of these three organic solvent soluble polypeptides from Rp. viridis was estimated to be 1:1:1. Accordingly, the 36 amino-acid polypeptide is likely to be an additional constituent of the light-harvesting complex B1015, consequently termed as B1015-gamma. According to hydrophathy profiles, the transmembrane arrangement of B1015-alpha and B1015-beta within the thylakoid membrane is supposed to be similar. B1015-gamma, however, shows a somewhat different hydropathy profile. A particular feature of this polypeptide is its high amount of aromatic amino acids. It is postulated that B1015-gamma is involved in the formation of regular arrays of light-harvesting complexes.     

Feeding patterns of four macroinvertebrate taxa in the headwaters of the Buffalo River,eastern Cape

Gut content analysis, field and laboratory observations, and food choice experiments were used to assign four abundant macroinvertebrate taxa in the headwaters of the Buffalo River, eastern Cape, to functional feeding groups. The mayfly Adenophlebia auriculata (Leptophlebiidae) was classified as a collector: brusher; while the caddisflies, Dyschimus ensifer (Pisuliidae) and Goerodes caffrariae (Lepidostomatidae), and stoneflies Afronemoura spp. (Notonemouridae) were classified as shredders. The effects of organism size, season and biotope on dietary composition were tested, with size accounting for most of the dietary variability within each taxon. Larger individuals consumed more material, larger items, and, in the case of A. auriculata, a wider variety of food-types. There was little variation in the feeding of the taxa in different seasons or biotopes. Shredders ingested mainly leaf fragments, and this, rather than the size of particles in the gut, is a more useful basis for the shredder designation. A. auriculata was the most opportunistic feeder, and items in its diet additional to fine detritus varied seasonally and in the various biotopes. Of the shredders, Afronemoura spp. and D. ensifer were more varied in their diet, augmenting the staple intake of leaf material with other items. G. caffrariae was the most specialised feeder, being exclusively a shredder, regardless of biotope or season. Despite criticisms of the applicability of the FFG concept in the literature, we conclude that these taxa can reasonably be accommodated in functional feeding classes, and that the results are useful in describing the functions performed by the organisms in the river. The relationship between feeding function and river process is emphasised: we suggest that collectors contribute primarily to organic particle retention, while shredders facilitate organic particle size reduction and mobilisation, and the enhancement of substrates for microbial colonisation. An emphasis on river function is a useful context within which to view the FFG concept.     

Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway

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Quantifying HDL proteins by mass spectrometry: how many proteins are there and what are their functions?

Introduction: Many lines of evidence indicate that low levels of HDL cholesterol increase the risk of cardiovascular disease (CVD). However, recent clinical studies of statin-treated subjects with established atherosclerosis cast doubt on the hypothesis that elevating HDL cholesterol levels reduces CVD risk.

Areas covered: It is critical to identify new HDL metrics that capture HDL’s proposed cardioprotective effects. One promising approach is quantitative MS/MS-based HDL proteomics. This article focuses on recent studies of the feasibility and challenges of using this strategy in translational studies. It also discusses how lipid-lowering therapy and renal disease alter HDL’s functions and proteome, and how HDL might serve as a platform for binding proteins with specific functional properties.

Expert commentary: It is clear that HDL has a diverse protein cargo and that its functions extend well beyond its classic role in lipid transport and reverse cholesterol transport. MS/MS analysis has demonstrated that HDL might contain >80 different proteins. Key challenges are demonstrating that these proteins truly associate with HDL, are functionally important, and that MS-based HDL proteomics can reproducibly detect biomarkers in translational studies of disease risk.     

Discovery of Mcl-1 inhibitors based on a thiazolidine-2,4-dione scaffold

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William E. Vidaver (1921–2017): an innovator,enthusiastic scientist,inspiring teacher and a wonderful friend

William (Bill) E. Vidaver (February 2, 1921–August 31, 2017), who did his Ph.D. with Laurence (Larry) R. Blinks at Stanford (1964) and a postdoc with C. Stacy French (1965), taught and did research at Simon Fraser University (SFU) for almost 30 years. Here he published over 80 papers in photosynthesis-related areas co-authored by his graduate students, postdocs, visiting professors and SFU colleagues. He developed a unique high-pressure cuvette for the study of oxygen exchange and studied high-pressure effects in photosynthesis. Ulrich (Uli) Schreiber, as a postdoctoral fellow from Germany, introduced measurements on chlorophyll (Chl) a fluorescence to Bill’s lab, leading to the discovery of reversible inhibition of excitation energy transfer between photosynthetic pigments and of a pivotal role of O₂ in the oxidation of the electron transport chain between Photosystem II (PS II) and PS I. Bill’s and Uli’s work led to a patent of a portable chlorophyll fluorometer, the first available commercially, which was later modified to measure whole plantlets. The latter was used in pioneering measurement of the health of forest and crop plants undergoing in vitro clonal micropropagation. With several other researchers (including Doug Bruce, the late Radovan Popovic, and Sarah Swenson), he localized the quenching site of O₂ and showed a dampening effect on measurements of the four-step process of O₂ production by endogenous oxygen uptake. Bill is remembered as a hard-working but fun-loving person with a keen mind and strong sense of social justice.     

Unexpected spatial stability of water chemistry in headwater stream networks

Understanding how water and solutes enter and propagate through freshwater landscapes in the Anthropocene is critical to protecting and restoring aquatic ecosystems and ensuring human water security. However, high hydrochemical variability in headwater streams, where most carbon and nutrients enter river networks, has hindered effective modelling and management. We developed an analytical framework informed by landscape ecology and catchment hydrology to quantify spatiotemporal variability across scales, which we tested in 56 headwater catchments, sampled periodically over 12 years in western France. Unexpectedly, temporal variability in dissolved carbon, nutrients and major ions was preserved moving downstream and spatial patterns of water chemistry were stable on annual to decadal timescales, partly because of synchronous variation in solute concentrations. These findings suggest that while concentration and flux cannot be extrapolated among subcatchments, periodic sampling of headwaters provides valuable information about solute sources and subcatchment resilience to disturbance.     

Effective water model for Monte Carlo simulations of proteins

We present an effective theory for water. Our goal is to formulate on accurate model for the effects of solvation on protein dynamics, without incurring the huge computational cost and the slow temporal evolution typical of molecular dynamics simulations of liquids. We replace the individual water molecules in an all-atom potential with a local dielectric density field, with self interactions given by the Landau-Ginzburg free energy and external interactions by Lennard-Jones forces at the surface of the protein atoms. We explore conformational space with finite temperature Monte Carlo dynamics, using parallel Langevin and Fourier acceleration algorithms well suited to data-parallel computer architectures such as the Connection Machine. To establish the validity of our approximations, we compare our electrostatic contribution to the solvalion energy with the results of Lim, Bashford, and Karplus using a conventional static continuum dielectric cavity model, and the non electrostatic contributions with estimates of hydrophohic surface free energy. Our model can also accommodate ionic charges and temperature fluctuations, We propose future investigations extending our effective theory of solvation to include explicit orientational entropy and hydroxen-bonding terms. © 1995 John Wiley & Sons, Inc.     

Water balance of conifer logs in early stages of decomposition

Seasonal and long-term changes in the water balance of conifer logs during the first 8 years of decomposition were studied in an old-growth Pseudotsuga/Tsuga forest in the Oregon Cascade Mountains. Measurements were made of the moisture content of outer bark, inner bark, sapwood, and heartwood and of the flow of water into and out of logs of four species (Abies amabilis, Pseudotsuga menziesii, Thuja plicata, and Tsuga heterophylla). After the logs had decomposed from 1 to 2 years, 38–47% of the canopy throughfall landing upon them ran off the surface, 29–34% leached from the bottom, and 21–30% was absorbed and evaporated. After 8 years of decomposition, water entering and then leaching from logs increased 1.3 times while runoff decreased a similar amount. The proportion of water stored by and evaporated from logs in this study indicates that in old growth forests they may intercept 2–5% of the canopy throughfall to the forest floor and that, even in early stages of decomposition, they may affect the hydrological cycle of Pacific Northwest old-growth forests.This is paper 2945 of the Forest Research Laboratory, Oregon State University, Corvallis