Quantitative approach to the fine structure of both symbionts of nine Umbilicaria species

Protoplasma - The ultrastructure of the photobiont and mycobiont of nine Umbilicaria species has been studied. The stereological parameter Vv (volume density) has been estimated for the most...     

A strategy for finding regions of similarity in complete genome sequences

MOTIVATION: Complete genomic sequences will become available in the future. New methods to deal with very large sequences (sizes beyond 100 kb) efficiently are required. One of the main aims of such work is to increase our understanding of genome organization and evolution. This requires studies of the locations of regions of similarity. RESULTS: We present here a new tool, ASSIRC ('Accelerated Search for SImilarity Regions in Chromosomes'), for finding regions of similarity in genomic sequences. The method involves three steps: (i) identification of short exact chains of fixed size, called 'seeds', common to both sequences, using hashing functions; (ii) extension of these seeds into putative regions of similarity by a 'random walk' procedure; (iii) final selection of regions of similarity by assessing alignments of the putative sequences. We used simulations to estimate the proportion of regions of similarity not detected for particular region sizes, base identity proportions and seed sizes. This approach can be tailored to the user's specifications. We looked for regions of similarity between two yeast chromosomes (V and IX). The efficiency of the approach was compared to those of conventional programs BLAST and FASTA, by assessing CPU time required and the regions of similarity found for the same data set. AVAILABILITY: Source programs are freely available at the following address: ftp://ftp.biologie.ens. fr/pub/molbio/assirc.tar.gz CONTACT: vincens@biologie.ens.fr, hazout@urbb.jussieu.fr      

The weathering action of saxicolous lichens in maritime Antarctica

Summary Xanthoria elegans (Link) Th Fr. and Lecidea lapicida (Ach.) were studied on volcanic andesite, and Rhizocarpon geographicum (L.) DC. and Bacidia stipata Lamb on a volcanigenic sediment, using light microscopy, infrared spectroscopy, X-ray diffraction and transmission electron microscopy. Feldspars were present in the rocklichen interface to a lesser extent than in the underlying rock. R. geographicum was found to alter the minerals in the rock on which it grew without producing any new minerals in the rock/lichen interface, in contrast to the observations for this species on granite in temperate regions. Beneath of the thallus of L. lapicida there was calcium oxalate and some micas of the illite type, which may have been degradation products of various phyllosilicates in the rock. B. stipata, an endemic Antarctic lichen, had the greatest capacity to weather the rock and had weddellite (dihydrate calcium oxalate) and calcite in the contact area as well as many bacteria. The presence of crystalline oxalate, imogolite, allophane, carbonates (calcite) and amorphous material not found in the parent rock indicates biomineralization processes attributable to the lichens.     

Concentric bodies in three lichen species

The existence of concentric bodies in the lichen species: Parmelia conspersa, Rhizocarpon geographicum and Umbilicaria pustulata is reported. By first time the presence of these structures in the ascospores of the lichen R. geographicum is described.     

NEW ULTRASTRUCTURAL ASPECTS OF PYRENOIDS OF THE LICHEN PHOTOBIONT TREBOUXZA (MICROTHAMNIALES,CHLOROPHYTA)1

The pyrenoid structure of Trebouxia, a photobiont of two lichen species, Umbilicaria cinereorufescens (Schaer.) Frey and Parmelia sulcata Taylor, was investigated. In both lichen species, the pyrenoid of the photobiont exhibited straight, unbranched, long or short tubules. In the first lichen species, multiple pyrenoids were observed occasionally, while in the second one, homogeneous masses, called protein bodies, appeared between the thylakoids. These protein bodies were previously observed in some other species of the family Umbilicariaceae. Serial sections from single pyrenoids showed that tubules of the Impressa-type pyrenoid were closely associated with pyrenoglobuli. The three-dimensional reconstruction of a complete chloroplast of a P. sulcata algal cell showed that the protein bodies were spatially separate structures. Immunolocalization techniques to detect the presence of ribulose-bisphosphate carboxylase (Rubisco) in the chloroplast showed that this enzyme was present primarily in the pyrenoid matrix. When protein bodies were present in the chloroplast, Rubisco appeared to be localized in these structures. The presence of pyrenoid satellites and protein bodies with reactivity to anti-Rubisco may be related to the nutritional conditions of the thalli.     

Study of lichens with different state of hydration by the combination of low temperature scanning electron and confocal laser scanning microscopies.

The use of techniques such as low temperature scanning electron microscopy (LTSEM) and confocal laser scanning microscopy (CLSM) allows the study of lichen thalli in different states of hydration and also near the natural state. The spatial organization of desiccated thalli, with reduced, very compact algal layers, is different from that of hydrated ones. Sometimes, the observation with transmission electron microscopy (TEM) of photobiont pyrenoids from desiccated thalli reports pyrenoids with a central part of a weak stained matrix lacking pyrenoglobuli, named "empty zones". "Empty zones" are not distinguishable with LTSEM and do not present immunolabelling with rubisco antibody in TEM. These zones could be originated by an expansion process during rehydration produced in chemical fixation.     

Water Distribution in Foliose Lichen Species: Interactions between Method of Hydration, Lichen Substances and Thallus Anatomy

Three lichens (Neofuscelia pokornyi, N. pulla and Xanthoriaparietina) from a semi-arid habitat were examined using low-temperaturescanning electron microscopy to evaluate the effects of hydrationmethod, lichen substances and thallus anatomy on the water distributionof hydrated thalli. In theNeofuscelia species, extracellularwater within the thallus was observed in association with cracksin its otherwise impervious upper cortex, while X. parietinashowed abundant extracellular water between medullary hyphae.Spraying the thalli followed by maintenance for 14–20h in a water-saturated atmosphere led to the disappearance ofthe external water film in X. parietina but not in the Neofusceliaspecies. Surface water was abundant in specimens of all speciesimmediately after spraying for 15 min. No extracellular waterwas observed inside the thallus 14–20 h after spraying,but after rinsing with acetone its presence was detected inall three species. Hydric strategy correlated with cortex hygroscopicity:X. parietina, an aero-hygrophytic species, had a more hygroscopicupper cortex than theNeofuscelia species, which are substrate-hygrophytic.The hygroscopicity of the upper cortex was linked with the amountof extracellular water in the thalline interior. Differencesbetween X. parietina and Neofuscelia in the polarity and distributionof their lichen substances agreed with species differences inthe presence and distribution of free water both as a film overthe surface and inside the thallus. Lichen substances appearto play a role in the maintenance of air-filled intrathallinespaces in species whose anatomy, habitat, or both, favour water-loggedconditions. Copyright 2000 Annals of Botany Company Lichen, water relations, semi-arid, lichen substances, LTSEM, thallus anatomy, extracellular water, Neofuscelia pokornyi(Körb.) Essl., Neofuscelia pulla(Ach.) Essl., Xanthoria parietina(L.) Th. Fr     

Interaction between Calcite and Phosphorus in Biomineralization Processes in Tufa Carbonates

Using electron microscopy techniques (SEM, LTSEM) coupled with analytical methods (XRD and EDS) the role of phosphorus has been assessed in the formation of freshwater calcite deposits (tufa) in a small pond of the Ruidera Lakes (Spain). Differences between the cell walls and sheaths of bacteria and eukaryotic algae as well as the existence of additional layers of extracellular polymeric substances (EPS) were features that lead to differences in the process of induced calcite biomineralization. Phosphorus has influence in the biomineralization of the EPS, sheaths and cell walls of cyanobacteria allowing for fossil preservation whereas does not participate in the calcite precipitation around algae and mosses. This variability may explain the different positive or negative roles played by natural or artificial inputs of phosphorus in hard water lakes and the different morphological features of calcite precipitates associated with eukaryotic and cyanobacteria picoplankton found in natural environments. The biomineralization observed is in agreement with the isotopic composition of the tufa layers that reflect the variations in environmental conditions around biological communities. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

New approaches to the study of Antarctic lithobiontic microorganisms and their inorganic traces,and their application in the detection of life in Martian rocks

Microbial life in the harsh conditions of Antarctica's cold desert may be considered an analogue of potential life on early Mars. In order to explore the development and survival of this epilithic and endolithic form of microbial life, our most sophisticated, state-of-the-art visualization technologies have to be used to their full potential. The study of any ecosystem requires a knowledge of its components and the processes that take place within it. If we are to understand the structure and function of each component of the microecosystems that inhabit lithic substrates, we need to be able to quantify and identify the microorganisms present in each lithobiontic ecological niche and to accurately characterize the mineralogical features of these hidden microhabitats. Once we have established the techniques that will allow us to observe and identify these microorganisms and mineral substrates in situ, and have confirmed the presence of water, the following questions can be addressed: How are the microorganisms organized in the fissures or cavities? Which microorganisms are present and how many are there? Additional questions that logically follow include: What are the existing water relationships in the microhabitat and what effects do the microorganisms have on the mineral composition? Mechanical and chemical changes in minerals and mineralization of microbial cells can give rise to physical and/or chemical traces (biomarkers) and to microbial fossil formation. In this report, we describe the detection of chains of magnetite within the Martian meteorite ALH84001, as an example of the potential use of SEM-BSE in the search for plausible traces of life on early Mars. Electronic Publication