Advances in clinical cancer proteomics: SELDI-ToF-mass spectrometry and biomarker discovery.

For most cancers, survival rates depend on the early detection of the disease. So far, no biomarkers exist to cope with this difficult task. New proteomic technologies have brought the hope of discovering novel early cancer-specific biomarkers in complex biological samples and/or of the setting up of new clinically relevant test systems. Novel mass spectrometry-(MS) based technologies in particular, such as surface-enhanced laser desorption/ionisation time of flight (SELDI-ToF-MS), have shown promising results in the recent literature. Here, proteomic profiles of control and disease states are compared to find biomarkers for diagnosis. This paper aims to address the authors' own work and that of other groups in clinical cancer proteomics based on SELDI-ToF-MS. Shortcomings and hopes for the future are discussed.     

Biomarkers Reveal Diverse Microbial Communities in Black Smoker Sulfides from Turtle Pits (Mid-Atlantic Ridge,Recent) and Yaman Kasy (Russia,Silurian)

The steep biogeochemical gradients near deep sea hydrothermal vents provide various niches for microbial life. Here we present biosignatures of such organisms enclosed in a modern and an ancient hydrothermal sulfide deposit (Turtle Pits, Mid-Atlantic Ridge, Recent; Yaman Kasy, Russia, Silurian). In the modern sulfide we found high amounts of specific bacterial and archaeal biomarkers with δ¹³C values between ?8 and ?37‰ VPDB. Our data indicate the presence of thermophilic members of the autotrophic Aquificales using the reductive tricarboxylic acid (rTCA) cycle as well as of methanogenic and chemolithoheterotrophic Archaea. In the ancient sample, most potential biomarkers of thermophiles were obscured by compounds derived from allochthonous organic matter (OM), except for an acyclic C₄₀ biphytane and its C₃₉ breakdown product. Both samples contained high amounts of unresolved complex mixtures (UCM) of hydrocarbons. Apparently, OM in the sulfides had to withstand high thermal stress, indicated by highly mature hopanes, steranes, and cheilanthanes with up to 41 carbon atoms.     

Long Term Variability in the Structure of Kelp Communities in Northern Chile and the 1997–98 ENSO

This is the first study on the south eastern Pacific coast of South America which details long term, interannual variability in the structure of subtidal rocky-bottom kelp-dominated communities before, during, and after the El Niño Southern Oscillation (ENSO) event of 1997–1998 in northern Chile (23^°S). The temporal patterns of the main components of these ecosystems, which included Macrocystis integrifolia, Lessonia trabeculata, echinoids and asteroids, were evaluated seasonally between 1996 and 2004. M. integrifolia demonstrated high interannual variability in temporal patterns of abundance. The 1997–1998 ENSO did not significantly modify the temporal patterns of Macrocystis, although local extinction of M. integrifolia beds occurred during negative thermal anomalies in 1999–2000 (La Niña event), facilitating the establishment of urchin dominated “barren grounds”. The abundance of Lessonia trabeculata showed little temporal variability, and this species dominated the deeper regions of the kelp assemblage (8–13 m depth). The structure of the kelp communities in the study area is regulated by a trophic cascade which modulates alternation between kelp dominated areas and sea urchin barrens. In this context, frequent and intense upwelling of cold water high in nutrients favors the establishment and persistence of kelp assemblages. During ENSO, coastal upwellings can mitigate superficial warming of coastal water and increase the nutrient concentration in the water column. Superficial warming during the 1997–1998 ENSO induced spawning by different species of echinoderms, which resulted in major recruitment of these species during 1999. Top-down events, such as the decrease in densities of the asteroids after the 1997–1998 ENSO event, favored increases in densities of benthic grazers, which caused significant decreases in abundance of M. integrifolia. The re-establishment of the adult fraction of the carnivore (starfish) guild coincided with a decrease in the density of sea urchins and thus re-establishment of the kelp. In the temperate south eastern Pacific, oceanographic events, which act on different spatial-temporal scales, trigger trophic cascades that act at local levels, producing interannual variability in the structure of kelp communities. On the other hand, considering the high macroinvertebrate diversity associated with kelp assemblages, the transitions between kelp-dominated areas and sea urchin barrens do not appear to significantly affect the biodiversity of these assemblages of benthic invertebrates.     

Some herbaceous lycopods from the Westphalian D of Germany

This paper deals with compression fossils of two Late Carboniferous herbaceous lycopods. New fertile material of Selaginellites gutbieri (Göppert, 1837) Kidston, 1911 was collected from its type locality Oelsnitz (Westphalian D; Erzgebirge-Basin). The three-dimensionally preserved strobili clearly show micro- and megasporangia. In addition a sterile large-leaved form is described from the Westphalian D of the Saar Basin.     

Multi-sensor plant imaging: Towards the development of a stress-catalogue

Agricultural production is limited by a wide range of abiotic (e.g. drought, waterlogging) and biotic (pests, diseases and weeds) stresses. The impact of these stresses can be minimized by appropriate management actions such as irrigation or chemical pesticide application. However, further optimization requires the ability to diagnose and quantify the different stresses at an early stage. Particularly valuable information of plant stress responses is provided by plant imaging, i.e. non-contact sensing with spatial resolving power: (i) thermal imaging, detecting changes in transpiration rate and (ii) fluorescence imaging monitoring alterations in photosynthesis and other physiological processes. These can be supplemented by conventional video imagery for study of growth. An efficient early warning system would need to discriminate between different stressors. Given the wide range of sensors, and the association of specific plant physiological responses with changes at particular wavelengths, this goal seems within reach. This is based on the organization of the individual sensor results in a matrix that identifies specific signatures for multiple stress types. In this report, we first review the diagnostic effectiveness of different individual imaging techniques and then extend this to the multi-sensor stress-identification approach.     

Helical Growth of the Arabidopsis Mutant tortifolia2 Does Not Depend on Cell Division Patterns but Involves Handed Twisting of Isolated Cells

Several factors regulate plant organ growth polarity. tortifolia2 (tor2), a right-handed helical growth mutant, has a conservative replacement of Arg-2 with Lys in the α-tubulin 4 protein. Based on a published high-resolution (2.89 Å) tubulin structure, we predict that Arg-2 of α-tubulin forms hydrogen bonds with the GTPase domain of β-tubulin, and structural modeling suggests that these contacts are interrupted in tor2. Consistent with this, we found that microtubule dynamicity is reduced in the tor2 background. We investigated the developmental origin of the helical growth phenotype using tor2. One hypothesis predicts that cell division patterns cause helical organ growth in Arabidopsis thaliana mutants. However, cell division patterns of tor2 root tips appear normal. Experimental uncoupling of cell division and expansion suggests that helical organ growth is based on cell elongation defects only. Another hypothesis is that twisting is due to inequalities in expansion of epidermal and cortical tissues. However, freely growing leaf trichomes of tor2 mutants show right-handed twisting and cortical microtubules form left-handed helices as early as the unbranched stage of trichome development. Trichome twisting is inverted in double mutants with tor3, a left-handed mutant. Single tor2 suspension cells also exhibit handed twisting. Thus, twisting of tor2 mutant organs appears to be a higher-order expression of the helical expansion of individual cells.     

Fractionation and characterization of chitosan by analytical SEC and H NMR after semi-preparative SEC

Heterogeneity in molecular weight and degree of deacetylation (DDA) of chitosans from different sources and preparation methods were studied by fractionating chitosans, using semi-preparative SEC, and then determining molecular weight profiles of fractions by analytical SEC with multi-angle laser light scattering (SEC–MALLS), and degree of deacetylation (DDA) by ¹H NMR. Fractionation of two high molecular weight chitosans from different manufacturers, produced fractions that spanned a wide range of molecular weight (number-average M_n), from 65 to 400 kDa in one case, that was not evident when unfractionated material was directly analyzed by SEC providing M_n = 188 kDa and PDI = M_w/M_n = 1.73. In a second case, fractions ranged from 20 to 600 kDa with unfractionated M_n = 145 kDa and PDI = 1.83. Fractionation of low molecular weight chitosans also showed a broad range of molecular weight in the original material, however, the fractions obtained with the TSKgel G4000W column in the M_n range of 5–100 kDa were essentially monodisperse with PDIs between 1.0 and 1.4. The DDA of one low molecular weight chitosan (10 kDa) produced by nitrous acid degradation was dependent on the M_n of the fraction. This semi-preparative fractionation procedure revealed important compositional heterogeneities of chitosans not evident in unfractionated material, and permitted the production of monodisperse low molecular weight chitosans with homogeneous properties.     

A decade of crystallization drops: Crystallization of the cbb3 cytochrome c oxidase from Pseudomonas stutzeri

The cbb₃ cytochrome c oxidases are distant members of the superfamily of heme copper oxidases. These terminal oxidases couple O₂ reduction with proton transport across the plasma membrane and, as a part of the respiratory chain, contribute to the generation of an electrochemical proton gradient. Compared with other structurally characterized members of the heme copper oxidases, the recently determined cbb₃ oxidase structure at 3.2 Å resolution revealed significant differences in the electron supply system, the proton conducting pathways and the coupling of O₂ reduction to proton translocation. In this paper, we present a detailed report on the key steps for structure determination. Improvement of the protein quality was achieved by optimization of the number of lipids attached to the protein as well as the separation of two cbb₃ oxidase isoenzymes. The exchange of n‐dodecyl‐β‐d ‐maltoside for a precisely defined mixture of two α‐maltosides and decanoylsucrose as well as the choice of the crystallization method had a most profound impact on crystal quality. This report highlights problems frequently encountered in membrane protein crystallization and offers meaningful approaches to improve crystal quality.     

Cultivation of Gigartina skottsbergii (Gigartinales, Rhodophyta): Recent advances and challenges for the future

This study integrates landings statistics and biological studies of the red algaGigartina skottsbergii Setchell & Gardner. The analysis of the landings and carrageenan production in Chile suggeststhat this resource will suffer a strong harvesting pressure during the nextyears. Biological results on sporulation, germination, sporeling growth and survivorship in laboratory,indoor tanks and field conditions, indicated that cultivation of this species istechnically feasible, as spores can be seeded on ropes and other substrata. Vegetative propagation of this species through tissue fragmentationis also possible. Vegetative fragments of this carrageenophyte have 20 to30% higher growth rates than whole fronds in suspended culture systems. Protoplast production can be also explored for bypassing restrictions inspore availability. Major advantages that encourage the cultivation of G. skottsbergii include its gel quantity and quality, its pathogen-freecondition, a high reproduction potential and its regeneration capacity. Onthe other hand, the major constraints are related to its relatively slowgrowth as compared to other carrageenophytes, limited availability ofspores and high mortality during juvenile stages.     

VEGF and therapeutic opportunities in cardiovascular diseases

In the past ten years, alternative revascularization strategies have come from bench to bedside focusing on the growth of new vessels to replace the old. Hypoxia and vascular endothelial growth factor may induce capillary growth; however, atherosclerosis affects large conductance vessels, which can only be replaced by functional collateral arteries.