Signal peptide analogs derived from two chloroplast precursors interact with the signal recognition system of the chloroplast envelope

We have used synthetic peptides representing segments of the signal sequences of preferredoxin (pFd) and the precursor of the small subunit of ribulose-1,5-bisphosphate carboxylase (pS) to study interactions with the signal sequence recognition system at the chloroplast surface. Peptides representing the COOH-terminal 30 amino acids of the pFd and pS signal peptides were able to completely and reversibly inhibit the import of their homologous precursors into isolated chloroplasts at a 2.5 microM concentration. Import was blocked at the level of precursor binding to the chloroplast. This inhibition of precursor binding and import was not due to disruption of chloroplast integrity as incubation of isolated chloroplasts with the peptides did not cause measurable perturbation of the envelope membranes. The peptides also were able to block the import of the heterologous precursor protein, suggesting that pS and pFd share a common signal sequence recognition system. Visualization of the bound peptides at the chloroplast surface by indirect immunofluorescence microscopy using antipeptide antibodies gave a marked punctate staining pattern. This pattern is consistent with the localization of chloroplast import receptor(s) at contact zones between the inner and outer envelope membranes.     

Eubacterium acidaminophilum sp. nov., a versatile amino acid-degrading anaerobe producing or utilizing H2 or formate

An obligately anaerobic, rod-shaped bacterium was isolated on alanine in co-culture with H₂-scavenging Desulfovibrio and obtained in pure culture with glycine as sole fermentation substrate. The isolated strain, al-2, was motile by a polar to subpolar flagellum and stained Gram-positive. The guanine plus cytosine content of the DNA was 44.0 mol%. Strain al-2 grew in defined, reduced glycine media supplemented with biotin. The pure culture fermented 4 mol glycine to 3 mol acetate, 4 mol ammonia and 2 mol CO₂. Under optimum conditions (34°C, pH 7.3), the doubling time on glycine was 60 min and the molar growth yield 7.6 g cell dry mass. Serine was fermented to acetate, ethanol, CO₂, H₂ and ammonia. In addition, betaine, sarcosine or creatine served as substrates for growth and acetate production if H₂, formate or e.g. valine were added as H-donors. In pure culture on alanine under N₂, strain al-2 grew very poorly and produced H₂ up to a partial pressure of 3.6 kPa (0.035 atm). Desulfovibrio species, Methanospirillum hungatei and Acetobacterium woodii served as H₂-scavengers that allowed good syntrophic growth on alanine. The co-cultures also grew on aspartate, leucine, valine or malate. Alanine and aspartate were stoichiometrically degraded to acetate and ammonia, whereas the reducing equivalents were recovered as H₂S, CH₄ or newly synthetized acetate, respectively. Growth of strain al-2 in co-culture with the hydrogenase-negative, formate-utilizing Desulfovibrio baarsii indicated that a syntrophy was also possible by interspecies formate transfer. Growth on glycine, or on betaine, sarcosine or creatine (plus H-donors) depended strictly on the addition of selenite (0.1 M); selenite was not required for fermentation of serine, or for degradation of alanine, aspartate or valine by the co-cultures. Cell-free extracts of glycine-grown cells contained active glycine reductase, glycine decarboxylase and reversible methyl viologen-dependent formate dehydrogenase in addition to the other enzymes necessary for an oxidation to CO₂. In all reactions NADP was the preferred H-carrier. Both formate and glycine could be synthesized from bicarbonate. Serine-grown cells did not contain serine hydroxymethyl transferase but serine dehydratase and other enzymes commonly involved in pyruvate metabolism to acetate, CO₂ and H₂. The enzymes involved in glycine metabolism were repressed during growth on serine. By its morphology and physiology, strain al-2 did not resemble described amino acid-degrading species. Therefore, the new isolate is proposed as type strain of a new species, Eubacterium acidaminophilum.     

Toad radiation reveals into-India dispersal as a source of endemism in the Western Ghats-Sri Lanka biodiversity hotspot

Background  

High taxonomic level endemism in the Western Ghats-Sri Lanka biodiversity hotspot has been typically attributed to the subcontinent's geological history of long-term isolation. Subsequent out of – and into India dispersal of species after accretion to the Eurasian mainland is therefore often seen as a biogeographic factor that 'diluted' the composition of previously isolated Indian biota. However, few molecular studies have focussed on into-India dispersal as a possible source of endemism on the subcontinent. Using c. 6000 base pairs of mitochondrial and nuclear DNA, we investigated the evolutionary history and biogeography of true toads (Bufonidae), a group that colonized the Indian Subcontinent after the Indo-Asia collision.     

A Year in the Life of a Shinto Shrine

. Year in the Life of. Shinto Shrine. John K. Nelson. Seattle: University of Washington Press, 1996. 286 pp.     

Reconstructing biochemical pathways from time course data

Time series data on biochemical reactions reveal transient behavior, away from chemical equilibrium, and contain information on the dynamic interactions among reacting components. However, this information can be difficult to extract using conventional analysis techniques. We present a new method to infer biochemical pathway mechanisms from time course data using a global nonlinear modeling technique to identify the elementary reaction steps which constitute the pathway. The method involves the generation of a complete dictionary of polynomial basis functions based on the law of mass action. Using these basis functions, there are two approaches to model construction, namely the general to specific and the specific to general approach. We demonstrate that our new methodology reconstructs the chemical reaction steps and connectivity of the glycolytic pathway of Lactococcus lactis from time course experimental data.     

Is the intrinsic disorder of proteins the cause of the scale-free architecture of protein-protein interaction networks?

In protein-protein interaction (PPI) networks certain topological properties appear to be recurrent: network maps are considered scale-free. It is possible that this topology is reflected in the protein structure. In this paper, we investigate the role of protein disorder in the network topology. We find that the disorder of a protein (or of its neighbors) is independent of its number of PPIs. This result suggests that protein disorder does not play a role in the scale-free architecture of protein networks.     

A clock and wavefront mechanism for somite formation

Somitogenesis, the sequential formation of a periodic pattern along the antero-posterior axis of vertebrate embryos, is one of the most obvious examples of the segmental patterning processes that take place during embryogenesis and also one of the major unresolved events in developmental biology. In this article, we develop a mathematical formulation of a new version of the Clock and Wavefront model proposed by Pourquié and co-workers (Dubrulle, J., McGrew, M.J., Pourquié, O., 2001. FGF signalling controls somite boundary position and regulates segmentation clock control of spatiotemporal Hox gene activation. Cell 106, 219-232). Dynamic expression of FGF8 in the presomitic mesoderm constitutes the wavefront of determination which sweeps along the body axis interacting as it moves with the segmentation clock to gate cells into somites. We also show that the model can mimic the anomalies formed when progression of the wavefront is disturbed and make some experimental predictions that can be used to test the hypotheses underlying the model.     

Comparison of survey methods for wintering grassland birds

ABSTRACT Although investigators have evaluated the efficacy of survey methods for assessing densities of breeding birds, few comparisons have been made of survey methods for wintering birds, especially in grasslands. In winter, social behavior and spatial distributions often differ from those in the breeding season. We evaluated the degree of correspondence between density estimates based on different survey methods. Surveys were conducted during two winters (2001–2002 and 2002–2003) on 16 grassland sites in southwestern Oklahoma. Line‐transect (using a detection function to account for birds present but not detected) and area‐search (where density was based on the total count within a given area) methods were employed. Observations on line transects were also analyzed as strip transects, where density was based on total count within a given strip width and no detection function was used. Savannah Sparrows (Passerculus sandwichensis), LeConte's Sparrows (Ammodramus leconteii), Song Sparrows (Melospiza melodia), Smith's Longspurs (Calcarius pictus), Chestnut‐collared Longspurs (C. ornatus), and Eastern Meadowlarks (Sturnella magna) were sufficiently abundant to allow comparison. Area‐search density estimates tended to be higher than line‐transect estimates for Savannah Sparrows, Song Sparrows, and Eastern Meadowlarks, suggesting that some individuals initially located close to the transect line were not detected on line transects. The area‐search and line‐transect methods gave similar density estimates for Chestnut‐collared and Smith's longspurs. Area‐search estimates of Eastern Meadowlarks were significantly higher in the second year of the study only. For this species, area‐search estimates did not differ from those of strip transects covering an equal area, so the reason for the differing meadowlark estimates is not clear. Higher density estimates using the area‐search method likely resulted from: (1) birds that might escape detection by hiding were more likely detected (flushed) during area searches because of the repeated passes through the area, and (2) birds close to the line in line transects escape detection by hiding, biasing those estimates low. We also evaluated the correspondence of density rankings for the six species as determined by the different survey methods and for the same species across survey sites. Correlations among the six species of the area‐search results with those of line transects and strip transects generally were high, increasing in 2002–2003 when densities of birds were greater. All three methods provided similar density rankings among species. Density rankings within species across sites for the four non‐longspur species generally were concordant for the three methods, suggesting that any of them will adequately reflect among‐site differences, especially when densities vary greatly across sites. Further research is needed to determine the extent to which grassland birds are missed on line transects. We suggest that workers using line transects to study these species give careful consideration and make additional efforts to satisfy the distance‐sampling assumption that all birds on or near the line are detected. If density is measured as a total count in a fixed area, we recommend that observers pass within <10 m of all points in the area.