Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes

Many prokaryotic organisms have adapted to incredibly extreme habitats. The genomes of such extremophiles differ from their non-extremophile relatives. For example, some proteins in thermophiles sustain high temperatures by being more compact than homologs in non-extremophiles. Conversely, some proteins have increased volumes to compensate for freezing effects in psychrophiles that survive in the cold. Here, we revealed that some differences in organisms surviving in extreme habitats correlate with a simple single feature, namely the fraction of proteins predicted to have long disordered regions. We predicted disorder with different methods for 46 completely sequenced organisms from diverse habitats and found a correlation between protein disorder and the extremity of the environment. More specifically, the overall percentage of proteins with long disordered regions tended to be more similar between organisms of similar habitats than between organisms of similar taxonomy. For example, predictions tended to detect substantially more proteins with long disordered regions in prokaryotic halophiles (survive high salt) than in their taxonomic neighbors. Another peculiar environment is that of high radiation survived, e.g. by Deinococcus radiodurans. The relatively high fraction of disorder predicted in this extremophile might provide a shield against mutations. Although our analysis fails to establish causation, the observed correlation between such a simplistic, coarse-grained, microscopic molecular feature (disorder content) and a macroscopic variable (habitat) remains stunning.     

Low-pH-mediated elevations in cytosolic calcium are inhibited by aluminium: a potential mechanism for aluminium toxicity

Aluminium, the most abundant metal in the earth's crust, is highly toxic to most plant species. One of the prevailing dogmas is that aluminium exerts this effect by disrupting cellular calcium homeostasis. However, recent research gives strongly conflicting results: aluminium was shown to provoke either an increase or a decrease in cytosolic free calcium concentration ([Ca2+]c). To solve this question, we have adopted a novel approach: [Ca2+]c measurements in intact plant roots as opposed to isolated cells, and the correlative measurements of intracellular and external pH. The results obtained show that plant roots respond to low external pH by a sustained elevation in [Ca2+]c. In the presence of aluminium, this pH-mediated elevation in [Ca2+]c does not occur, therefore any potential calcium-mediated protection against low pH is likely to be irreversibly inhibited. The severity of the inhibitory effect of aluminium on [Ca2+]c depends on the concentration of external calcium, thus perhaps explaining why the effects of aluminium toxicity are ameliorated in calcium-rich soils. It seems possible that a primary toxic effect of aluminium might be to impair calcium-mediated plant defence responses against low pH.     

Genome analysis of Pseudomonas aeruginosa by field inversion gel electrophoresis

Abstract The genome of Pseudomonas aeruginosa was analysed by digestion with rare-cutting restriction endonucleases and subsequent field inversion gel electrophoresis (FIGE). P. aeruginosa strain PAO and the 17 IATS strains were investigated. Each strain displayed a unique pattern of restriction fragments. Digestion with Dra I and Ssp I yielded, respectively 7–11 and 2–5 fragments of more than 130 kb in size, indicating the non-random occurrence of AT-rich sequences in the P. aeruginosa genome. The genome size of P. aeruginosa PAO was estimated to be (2.2 ± 0.3) × 10⁶ bp. The applications of DNA fingerprinting for gene cloning, construction of a physical chromosome map, and epidemiological studies, are discussed.     

Clonal descent and microevolution of Neisseria meningitidis during 30 years of epidemic spread

Serogroup A meningococci of subgroups III, IV-1 and IV-2 are probably descended from a common ancestor that existed in the nineteenth century. The 10.5 kb sequences spanning five distinct chromosomal loci, encoding cell-surface antigens, a secreted protease or housekeeping genes and intergenic regions, were almost identical in strains of those subgroups isolated in 1966, 1966 and 1917 respectively. During the subsequent two to three decades, all of these loci varied as a result of mutation, translocation or import of DNA from unrelated neisseriae. Thus, microevolution occurs frequently in naturally transformable bacteria. Many variants were isolated only once or within a single geographical location and disappeared thereafter. Other variants achieved genetic fixation within months or a few years. The speed with which sequence variation is either eliminated or fixed may reflect sequential bottlenecks associated with epidemic spread and contrasts with the results of phylogenetic analyses from bacteria that do not cause epidemics.     

Vorkommen und Ausbildung der Fingerkrallen bei rezenten V?geln

Zusammenfassung Mit vorliegender Studie werden die Lücken der Kenntnisse über das Vorkommen von Fingerkrallen bei rezenten Vögeln so weit geschlossen, daß nunmehr Vertreter aller Ordnungen und der meisten Familien untersucht sind. Die Gruppierung der Ordnungen nach dem Vorkommen bzw. Fehlen von Fingerkrallen zeigt die Tendenz ihrer Reduktion auf. Trotz solcher allgemeinen Tendenz gibt es Arten, bei denen die Fingerkrallen während der Ontogenese an Größe zunehmen. Einige funktionelle, ontogenetische und phylogenetische Aspekte werden diskutiert. Der Zusammenhang zwischen Rückbildung der Fingerkrallen und Flügelbefiederung ist angedeutet. Möglicherweise werden die Krallen durch Federn verdrängt, und ihre Funktion, schützende Hülle des Fingerendes zu sein, fällt weg. Zwei weitere Ursachen der Reduktion werden in Betracht gezogen: Veränderungen der Ontogenese und genetische Veränderungen. Während die Ergebnisse für die Taxonomie nur einen geringen Wert haben, sind sie für die Rekonstruktion der Evolution des Vogelflügels und die aktuelle Urvogelforschung von Bedeutung.

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Occurrence and expression of claws on fingers of recent birds

Summary The present study completes the gaps in our knowledge about the occurrence and expression of claws on fingers of recent birds in so far as individuals from all orders and from most families were examined. The results are presented in a systematic overview. The grouping of the orders according to the presence or absence of claws shows a tendency towards their reduction. However, in spite of this overall trend, there exist species in which the claws on the fingers increase in size during ontogeny. Several functional, ontogenetic and phylogenetic aspects are discussed. The correlation between reduction of the finger claws and wing feathering is mentioned. Probably the claws are ousted by feathers, and therefore their function can be explained as a protective sheath for the finger. Two further causes of reduction are considered: changes of the ontogeny and genetic changes. Although the results are of little value for taxonomy, they may be relevant for the reconstruction of the evolution of bird wings and for present research on the origin of birds.

     

Purification of Neuronal Cell Surface Proteins and Generation of Epitope-Specific Monoclonal Antibodies Against Cell Adhesion Molecules

To establish a procedure for the purification of a broad spectrum of cell surface proteins, three separate methods based on different principles were compared with the aid of four marker proteins. Membrane preparation by sedimentation-flotation centrifugation, temperature-induced phase separation with Triton X-114, and lectin affinity chromatography were used separately as well as in combination. The two-step procedure of membrane preparation and lectin affinity chromatography provided by far the best enrichment of cell surface marker proteins. This result was further substantiated by screening greater than 6,600 hybridoma cultures that originated from mice that had been immunized with protein fractions obtained by different purification protocols. In addition, it was found that solubilized glycoproteins used as immunogens led to many more cell surface-specific monoclonal antibodies than glycoproteins immobilized on lectin-agarose beads. Three monoclonal antibodies that recognize distinct epitopes of cell adhesion molecules (CAMs) were isolated. Monoclonal antibody C4 bound to a detergent-labile epitope of G4 (neuron-glia CAM). Monoclonal antibody D1 recognized specifically nonreduced neural CAM (N-CAM) with intact disulfide bridges, and monoclonal antibody D3 recognized only the 180-kilodalton isoform of N-CAM. Because of these specificities, these monoclonal antibodies promise to be useful tools for the elucidation of the structural organization of adhesion molecules.