16 resultados para DEINOCOCCUS-RADIODURANS


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Il passo preliminare del presente elaborato è quello di mettere a punto un metodica solida e riproducibile per la sovraespressione della subunità α di D. radiodurans per via eterologa. L’ospite ideale per realizzare la sovraespressione è E. coli, microorganismo ampiamente discusso e impiegato per via della sua semplice manipolazione. Per realizzare la sovraespressione il ceppo di E. coli prescelto è stato trasformato con il plasmide pBAD-dnaE e la proteina in esame è stata ottenuta come corpi di inclusione (biologicamente inattiva). Successivamente alla fase di rinaturazione e alla purificazione tramite cromatografia liquida dell’enzima è stato possibile ottenere quantità sufficienti di proteina pura e biologicamente attiva con la quale condurre saggi spettrofotometrici di attività enzimatica per valutare il comportamento dell’enzima in vitro simulando le condizioni di substrato attese in vivo. È proprio in quest’ultimo frangente che si condensa lo scopo di questo lavoro. La conduzione dei saggi di attività enzimatica in condizioni ricombinative e non ricombinative (quindi in presenza o meno di RecAEc nell’ambiente di reazione) ci ha consentito di comprendere meglio il comportamento della pol III-α durante la fase di strand invasion mediata dalla ricombinasi e la successiva sintesi del neofilamento, contribuendo a chiarire alcuni aspetti dei meccanismi che intervengono lungo la via di riparazione del genoma danneggiato in D. radiodurans ancora poco discussi. Inoltre l’elaborazione di un sistema di espressione per la singola subunità α getterebbe le basi per sviluppare un sistema di co-espressione più complesso ove siano coinvolte anche altre subunità dell’oloenzima (τ-δ-δ’), in modo da poter verificare la tipologia di subassemblaggio che spontaneamente avverrebbe in vivo e gli stimoli relativi tra le diverse subunità che ne migliorerebbero l’efficienza.

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Asparaginyl-tRNA (Asn-tRNA) and glutaminyl-tRNA (Gln-tRNA) are essential components of protein synthesis. They can be formed by direct acylation by asparaginyl-tRNA synthetase (AsnRS) or glutaminyl-tRNA synthetase (GlnRS). The alternative route involves transamidation of incorrectly charged tRNA. Examination of the preliminary genomic sequence of the radiation-resistant bacterium Deinococcus radiodurans suggests the presence of both direct and indirect routes of Asn-tRNA and Gln-tRNA formation. Biochemical experiments demonstrate the presence of AsnRS and GlnRS, as well as glutamyl-tRNA synthetase (GluRS), a discriminating and a nondiscriminating aspartyl-tRNA synthetase (AspRS). Moreover, both Gln-tRNA and Asn-tRNA transamidation activities are present. Surprisingly, they are catalyzed by a single enzyme encoded by three ORFs orthologous to Bacillus subtilis gatCAB. However, the transamidation route to Gln-tRNA formation is idled by the inability of the discriminating D. radiodurans GluRS to produce the required mischarged Glu-tRNAGln substrate. The presence of apparently redundant complete routes to Asn-tRNA formation, combined with the absence from the D. radiodurans genome of genes encoding tRNA-independent asparagine synthetase and the lack of this enzyme in D. radiodurans extracts, suggests that the gatCAB genes may be responsible for biosynthesis of asparagine in this asparagine prototroph.

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Predicted highly expressed (PHX) and putative alien genes determined by codon usages are characterized in the genome of Deinococcus radiodurans (strain R1). Deinococcus radiodurans (DEIRA) can survive very high doses of ionizing radiation that are lethal to virtually all other organisms. It has been argued that DEIRA is endowed with enhanced repair systems that provide protection and stability. However, predicted expression levels of DNA repair proteins with the exception of RecA tend to be low and do not distinguish DEIRA from other prokaryotes. In this paper, the capability of DEIRA to resist extreme doses of ionizing and UV radiation is attributed to an unusually high number of PHX chaperone/degradation, protease, and detoxification genes. Explicitly, compared with all current complete prokaryotic genomes, DEIRA contains the greatest number of PHX detoxification and protease proteins. Other sources of environmental protection against severe conditions of UV radiation, desiccation, and thermal effects for DEIRA are the several S-layer (surface structure) PHX proteins. The top PHX gene of DEIRA is the multifunctional tricarboxylic acid (TCA) gene aconitase, which, apart from its role in respiration, also alerts the cell to oxidative damage.

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This review reports the Brazilian history in astrobiology, as well as the first delineation of a vision of the future development of the field in the country, exploring its abundant biodiversity, highly capable human resources and state-of-the-art facilities, reflecting the last few years of stable governmental investments in science, technology and education, all conditions providing good perspectives on continued and steadily growing funding for astrobiology-related research. Brazil is growing steadily and fast in terms of its worldwide economic power, an effect being reflected in different areas of the Brazilian society, including industry, technology, education, social care and scientific production. In the field of astrobiology, the country has had some important landmarks, more intensely after the First Brazilian Workshop on Astrobiology in 2006. The history of astrobiology in Brazil, however, is not so recent and had its first occurrence in 1958. Since then, researchers carried out many individual initiatives across the country in astrobiology-related fields, resulting in an ever growing and expressive scientific production. The number of publications, including articles and theses, has particularly increased in the last decade, but still counting with the effort of researchers working individually. That scenario started to change in 2009, when a formal group of Brazilian researchers working with astrobiology was organized, aiming at congregating the scientific community interested in the subject and to promote the necessary interactions to achieve a multidisciplinary work, receiving facilities and funding from the University de Sao Paulo and other funding agencies. Received 29 February 2012, accepted 17 May 2012, first published online 18 July 2012

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Synthetic biology has shown that the metabolic behavior of mammalian cells can be altered by genetic devices such as epigenetic and hysteretic switches, timers and oscillators, biocomputers, hormone systems and heterologous metabolic shunts. To explore the potential of such devices for therapeutic strategies, we designed a synthetic mammalian circuit to maintain uric acid homeostasis in the bloodstream, disturbance of which is associated with tumor lysis syndrome and gout. This synthetic device consists of a modified Deinococcus radiodurans-derived protein that senses uric acids levels and triggers dose-dependent derepression of a secretion-engineered Aspergillus flavus urate oxidase that eliminates uric acid. In urate oxidase-deficient mice, which develop acute hyperuricemia, the synthetic circuit decreased blood urate concentration to stable sub-pathologic levels in a dose-dependent manner and reduced uric acid crystal deposits in the kidney. Synthetic gene-network devices providing self-sufficient control of pathologic metabolites represent molecular prostheses, which may foster advances in future gene- and cell-based therapies.

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We have combined high-resolution atomic force microscopy (AFM) imaging and force spectroscopy to gain insight into the interaction forces between the individual protomers of the hexagonally packed intermediate (HPI) layer of Deinococcus radiodurans. After imaging the HPI layer, the AFM stylus was attached to individual protomers by enforced stylus-sample contact to allow force spectroscopy experiments. Imaging of the HPI layer after recording force-extension curves allowed adhesion forces to be correlated with structural alterations. By using this approach, individual protomers of the HPI layer were found to be removed at pulling forces of ≈300 pN. Furthermore, it was possible to sequentially unzip entire bacterial pores formed by six HPI protomers. The combination of high-resolution AFM imaging of individual proteins with the determination of their intramolecular forces is a method of studying the mechanical stability of supramolecular structures at the level of single molecules.

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Caenorhabditis elegans dauer formation is an alternative larval developmental pathway that the worm can take when environmental conditions become detrimental. Animals can survive several months in this stress-resistant stage and can resume normal development when growth conditions improve. Although the worms integrate a variety of sensory information to commit to dauer formation, it is currently unknown whether they also monitor internal cellular damage. The Ro ribonucleoprotein complex, which was initially described as a human autoantigen, is composed of one major 60-kDa protein, Ro60, that binds to one of four small RNA molecules, designated Y RNAs. Ro60 has been shown to bind mutant 5S rRNA molecules in Xenopus oocytes, suggesting a role for Ro60 in 5S rRNA biogenesis. Analysis of ribosomes from a C. elegans rop-1(−) strain, which is null for the expression of Ro60, demonstrated that they contain a high percentage of mutant 5S rRNA molecules, thereby strengthening the notion of a link between the rop-1 gene product and 5S rRNA quality control. The Ro particle was recently shown to be involved in the resistance of Deinococcus radiodurans to UV irradiation, suggesting a role for the Ro complex in stress resistance. We have studied the role of rop-1 in dauer formation. We present genetic and biochemical evidence that rop-1 interacts with dauer-formation genes and is involved in the regulation of the worms' entry into the dauer stage. Furthermore, we find that the rop-1 gene product undergoes a proteolytic processing step that is regulated by the dauer formation pathway via an aspartic proteinase. These results suggest that the Ro particle may function in an RNA quality-control checkpoint for dauer formation.

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The ribonucleotide reductases from three ancient eubacteria, the hyperthermophilic Thermotoga maritima (TM), the radioresistant Deinococcus radiodurans (DR), and the thermophilic photosynthetic Chloroflexus aurantiacus, were found to be coenzyme-B12 (class II) enzymes, similar to the earlier described reductases from the archaebacteria Thermoplasma acidophila and Pyrococcus furiosus. Reduction of CDP by the purified TM and DR enzymes requires adenosylcobalamin and DTT. dATP is a positive allosteric effector, but stimulation of the TM enzyme only occurs close to the temperature optimum of 80–90°C. The TM and DR genes were cloned by PCR from peptide sequence information. The TM gene was sequenced completely and expressed in Escherichia coli. The deduced amino acid sequences of the two eubacterial enzymes are homologous to those of the archaebacteria. They can also be aligned to the sequence of the large protein of the aerobic E. coli ribonucleotide reductase that belongs to a different class (class I), which is not dependent on B12. Structure determinations of the E. coli reductase complexed with substrate and allosteric effectors earlier demonstrated a 10-stranded β/α-barrel in the active site. From the conservation of substrate- and effector-binding residues we propose that the B12-dependent class II enzymes contain a similar barrel.

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Les ribozymes sont des ARN catalytiques fréquemment exploités pour le développement d’outils biochimiques et d’agents thérapeutiques. Ils sont particulièrement intéressants pour effectuer l’inactivation de gènes, en permettant la dégradation d’ARNm ou d’ARN viraux associés à des maladies. Les ribozymes les plus utilisés en ce moment pour le développement d’agents thérapeutiques sont les ribozymes hammerhead et hairpin, qui permettent la reconnaissance spécifique d’ARN simple brin par la formation de structures secondaires stables. In vivo, la majorité des ARN adoptent des structures secondaires et tertiaires complexes et les régions simples brins sont parfois difficiles d’accès. Il serait intéressant de pouvoir cibler des ARN repliés et un motif d’ARN intéressant à cibler est la tige-boucle d’ARN qui peut être importante dans le repliement global des ARN et pour accomplir des fonctions biologiques. Le ribozyme VS de Neurospora fait la reconnaissance de son substrat replié en tigeboucle de façon spécifique par une interaction kissing-loop, mais il n’a jamais été exploité pour faire la reconnaissance d’un ARN cible très différent de son substrat naturel. Le but des travaux présentés dans cette thèse est de déterminer si le ribozyme VS possède l’adaptabilité nécessaire pour l’ingénierie de ribozymes qui clivent des ARN cibles différents du substrat naturel. Dans le cadre de cette thèse, le ribozyme VS a été modifié pour l’adapter à différents substrats et des études de cinétiques ont été réalisées pour évaluer l’impact de ces modifications sur l’activité de clivage du ribozyme. Dans un premier temps, le ribozyme a été modifié pour faire la reconnaissance et le clivage de substrats possédant différentes longueurs de tiges Ib. Le ribozyme a été adapté avec succès à ces substrats de différentes longueurs de tige Ib, avec une activité qui est similaire à celle du ribozyme avec un substrat sans modification. Dans un deuxième temps, c’est l’interaction kissing-loop I/V du ribozyme qui a été substituée de façon rationnelle, dans le but de savoir si un ribozyme VS mutant peut reconnaitre et cliver un substrat ayant une boucle différente de celle de son substrat naturel. L’interaction kissing-loop I/V a été substituée pour les interactions kissing-loop TAR/TAR* de l’ARN du VIH-1 et L22/L88 de l’ARN 23S de Deinococcus radiodurans. La réaction de iii clivage des ribozymes comportant ces nouvelles interactions kissing-loop est toujours observée, mais avec une activité diminuée. Finalement, la sélection in vitro (SELEX) de ribozymes a été effectuée pour permettre un clivage plus efficace d’un substrat mutant avec une nouvelle boucle. Le SELEX a permis la sélection d’un ribozyme qui clive un substrat avec une boucle terminale mutée pour celle de l’ARN TAR du VIH-1 et cela avec une activité de clivage très efficace. L’ensemble de ces études démontre que le ribozyme VS peut être modifié de diverses façons pour la reconnaissance spécifique de différents substrats, tout en conservant une bonne activité de clivage. Ces résultats montrent le grand potentiel d’ingénierie du ribozyme VS et sont prometteurs pour la poursuite d’études d’ingénierie du ribozyme VS, en vue du clivage d’ARN cibles repliés en tige-boucle complètement différents du substrat naturel du ribozyme VS.

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Les ribozymes sont des ARN catalytiques fréquemment exploités pour le développement d’outils biochimiques et d’agents thérapeutiques. Ils sont particulièrement intéressants pour effectuer l’inactivation de gènes, en permettant la dégradation d’ARNm ou d’ARN viraux associés à des maladies. Les ribozymes les plus utilisés en ce moment pour le développement d’agents thérapeutiques sont les ribozymes hammerhead et hairpin, qui permettent la reconnaissance spécifique d’ARN simple brin par la formation de structures secondaires stables. In vivo, la majorité des ARN adoptent des structures secondaires et tertiaires complexes et les régions simples brins sont parfois difficiles d’accès. Il serait intéressant de pouvoir cibler des ARN repliés et un motif d’ARN intéressant à cibler est la tige-boucle d’ARN qui peut être importante dans le repliement global des ARN et pour accomplir des fonctions biologiques. Le ribozyme VS de Neurospora fait la reconnaissance de son substrat replié en tigeboucle de façon spécifique par une interaction kissing-loop, mais il n’a jamais été exploité pour faire la reconnaissance d’un ARN cible très différent de son substrat naturel. Le but des travaux présentés dans cette thèse est de déterminer si le ribozyme VS possède l’adaptabilité nécessaire pour l’ingénierie de ribozymes qui clivent des ARN cibles différents du substrat naturel. Dans le cadre de cette thèse, le ribozyme VS a été modifié pour l’adapter à différents substrats et des études de cinétiques ont été réalisées pour évaluer l’impact de ces modifications sur l’activité de clivage du ribozyme. Dans un premier temps, le ribozyme a été modifié pour faire la reconnaissance et le clivage de substrats possédant différentes longueurs de tiges Ib. Le ribozyme a été adapté avec succès à ces substrats de différentes longueurs de tige Ib, avec une activité qui est similaire à celle du ribozyme avec un substrat sans modification. Dans un deuxième temps, c’est l’interaction kissing-loop I/V du ribozyme qui a été substituée de façon rationnelle, dans le but de savoir si un ribozyme VS mutant peut reconnaitre et cliver un substrat ayant une boucle différente de celle de son substrat naturel. L’interaction kissing-loop I/V a été substituée pour les interactions kissing-loop TAR/TAR* de l’ARN du VIH-1 et L22/L88 de l’ARN 23S de Deinococcus radiodurans. La réaction de iii clivage des ribozymes comportant ces nouvelles interactions kissing-loop est toujours observée, mais avec une activité diminuée. Finalement, la sélection in vitro (SELEX) de ribozymes a été effectuée pour permettre un clivage plus efficace d’un substrat mutant avec une nouvelle boucle. Le SELEX a permis la sélection d’un ribozyme qui clive un substrat avec une boucle terminale mutée pour celle de l’ARN TAR du VIH-1 et cela avec une activité de clivage très efficace. L’ensemble de ces études démontre que le ribozyme VS peut être modifié de diverses façons pour la reconnaissance spécifique de différents substrats, tout en conservant une bonne activité de clivage. Ces résultats montrent le grand potentiel d’ingénierie du ribozyme VS et sont prometteurs pour la poursuite d’études d’ingénierie du ribozyme VS, en vue du clivage d’ARN cibles repliés en tige-boucle complètement différents du substrat naturel du ribozyme VS.

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This final thesis is aimed at summarizing the research program I have carried out during my PhD studies, that has been dealing with the design, the preparation, characterization and applications of new Re(I), Ru(II), and Ir(III) metal complexes containing anionic ligands such as 5-aryl tetrazolates [R-CN4]- or their neutral analogues, N-alkyltetrazoles [R-CN4-R1]. Chapter 1 consists of a brief introduction on tetrazoles and metal-tetrazolato complexes, and on the photophysical properties of d6 transition metal complexes. In chapter 2, the synthesis, characterization and study of the photophysical properties of new luminescent Ir(III)-tetrazolate complexes are discussed. Moreover, the application of one of the new Ir(III)-CN complexes as emissive core in the fabrication of an OLED device is reported. In chapter 3, the study of the antimicrobial activity of new Ru(II)-alkyltetrazole complexes is reported. When the pentatomic ring was substituted with a long alkyl residue, antimicrobial activity toward Deinococcus radiodurans was observed. In chapter 4, a new family of luminescent Re(I)-tetrazolate complexes is reported. In this study, different N-alkyl tetrazoles play the role of diimine (diim) ligands in the preparation of new Re(I) tricarbonyl complexes. In addition, absorption and emission titration experiments were performed to study their interaction with Bovine Serum Albumin (BSA). In chapter 5, the synthesis and characterization of new luminescent Re(I)-tetrazolate complexes are discussed. The use of sulfonated diimine ligands in the preparation of new Re(I) tricarbonyl complexes led to the first example Re(I) complexes for the luminescent staining of proteins. In chapter 6, the synthesis, a new family of Ir(III)-NO2 tetrazole complexes displaying unexpected photophysical properties are discussed. Moreover, the possibility to tune the luminescent output of such systems upon chemical modification of the pending nitro group was verified by performing reduction tests with sodium dithionite; this represents encouraging evidence for their possible application as hypoxia-responsive luminescent probes in bioimaging.

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Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments.

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Interest in water treatment by electrochemical methods has grown in recent years. Electrochemical oxidation has been applied particularly successfully to degrade different organic pollutants and disinfect drinking water. This study summarizes the effectiveness of the electrochemical oxidation technique in inactivating different primary biofilm forming paper mill bacteria as well as sulphide and organic material in pulp and paper mill wastewater in laboratory scale batch experiments. Three different electrodes, borondoped diamond (BDD), mixed metal oxide (MMO) and PbO2, were employed as anodes. The impact on inactivation efficiency of parameters such as current density and initial pH or chloride concentration of synthetic paper machine water was studied. The electrochemical behaviour of the electrodes was investigated by cyclic voltammetry with MMO, BDD and PbO2 electrodes in synthetic paper mill water as also with MMO and stainless steel electrodes with biocides. Some suggestions on the formation of different oxidants and oxidation mechanisms were also presented during the treatment. Aerobic paper mill bacteria species (Deinococcus geothermalis, Pseudoxanthomonas taiwanensis and Meiothermus silvanus) were inactivated effectively (>2 log) at MMO electrodes by current density of 50 mA/cm2 and the time taken three minutes. Increasing current density and initial chloride concentration of paper mill water increased the inactivation rate of Deinococcus geothermalis. The inactivation order of different bacteria species was Meiothermus silvanus > Pseudoxanthomonas taiwanensis > Deinococcus geothermalis. It was observed that inactivation was mainly due to the electrochemically generated chlorine/hypochlorite from chloride present in the water and also residual disinfection by chlorine/hypochlorite occurred. In real paper mill effluent treatment sulphide oxidation was effective with all the different initial concentrations (almost 100% reduction, current density 42.9 mA/cm2) and also anaerobic bacteria inactivation was observed (almost 90% reduction by chloride concentration of 164 mg/L and current density of 42.9 mA/cm2 in five minutes). Organic material removal was not as effective when comparing with other tested techniques, probably due to the relatively low treatment times. Cyclic voltammograms in synthetic paper mill water with stainless steel electrode showed that H2O2 could be degraded to radicals during the cathodic runs. This emphasises strong potential of combined electrochemical treatment with this biocide in bacteria inactivation in paper mill environments.

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The frequency of adenine mononucleotides (A), dinucleotides (AA) and clusters, and the positions of clusters, were studied in 502 molecules of the 5S rRNA.All frequencies were reduced in the evolutive lines of vertebrates, plants and fungi, in parallel with increasing organismic complexity. No change was observed in invertebrates. All frequencies were increased in mitochondria, plastids and mycoplasmas. The presumed relatives to the ancestors of the organelles, Rhodobacteria alfa and Cyanobacteria, showed intermediate values, relative to the eubacterial averages. Firmibacterid showed very high number of cluster sites.Clusters were more frequent in single-stranded regions in all organisms. The routes of organelles and mycoplasmas accummulated clusters at faster rates in double-stranded regions. Rates of change were higher for AA and clusters than for A in plants, vertebrates and organeltes, higher for cluster sites and A in mycoplasmas, and higher for AA and A in fungi. These data indicated that selection pressures acted more strongly on adenine clustering than on adenine frequency.It is proposed that AA and clusters, as sites of lower informational content. have the property of tolerating positional variation in the sites of other molecules (or other regions of the same molecule) that interact with the adenines. This reasoning was consistent with the degrees of genic polymorphism. low in plants and vertebrates and high in invertebrates. In the eubacteria endosymbiontic or parasitic to eukaryotes, the more tolerant RNA would be better adapted to interactions with the homologous nucleus-derived ribosomal proteins: the intermediate values observed in their precursors were interpreted as preadaptive.Among other groups, only the Deinococcus-Thermus eubacteria showed excessive AA and cluster contents, possibly related to their peculiar tolerance to mutagens, and the Ciliates showed excessive AA contents, indicative of retention of primitive characters.

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Diversity of endolithic Dry Valley rock microorganisms was studied by evaluating the presence of morphotypes in enrichments. Storage of rock samples for 16 h over dry ice affected the diversity of endolithic organisms, especially that of algae and fungi. Diversity in various samples depended on rock location and exposure, on the rock type, and to some extent on the pH of the pulverized rock samples. In most cases sandstone contained more morphotypes than dolerite or granite. Presence of many different phototrophs resulted in greater diversity of the heterotrophs in the enrichments. Samples from Linnaeus Terrace and Battleship Promontory had higher morphotype (MT) numbers than those from more exposed sites such as New Mountain, University Valley, Dais, or Mt. Fleming. Beacon sandstone (13 samples) from Linnaeus Terrace varied greatly with respect to MT numbers, although the pH values ranged only from 4.2-5.3. The highest MT number of 24 per sample was obtained from the upper surface of a flat boulder tilted to the North. Only two MT's were found in a hard sandstone sample from the wind-exposed and more shaded east side of the Terrace. 15 sandstone samples from Battleship Promontory contained more diverse populations: there occurred a total of 131 different MT's in these samples as compared to only 68 in Linnaeus Terrace samples. Cysts of colorless flagellates were found in some Battleship Promontory samples; rnost samples were populated with a wealth of different cyanobacteria. Studies on the distribution of actinomycete morphotypes in Linnaeus Terrace sandstone revealed great differences between individual boulders. Identification tests and lipid analyses made with representative strains of the isolated 1500 pure cultures led to genus names such as Caulobacter, Blastobacter, Hyphomicrobium, Micrococcus, Arthrobacter, Brevibacterium, Corynebacterium, Bifidobacterium, Mycobacterium, Nocardia (Amycolata), Micromonospora, Streptomyces, Blastococcus, and Deinococcus. Our data demonstrate the great diversity of Antarctic endolithic microbial populations.