The bacteriorhodopsin proton pump: effect of crosslinkings of lysine residues

All six available lysine residues in bacteriorhodopsin were amidinated with dimethyl-3,3'-dithiobispropionimidate, which is a crosslinking agent. The photocycle was studied by measuring light absorption and electric signals. The data show an essential change in the photocycle: instead of single components, the rise of the signal due to the M intermediate can be decomposed into two components, and the decay into three. The life-times and the intensities of these components and in general the proton pumping activity of bacteriorhodopsin depend only negligibly upon pH. Changes upon removing the crosslinks are not significantly different from those in the crosslinked samples. The lysine residues therefore may not be considered of primary importance in proton translocation.     

Correlation of pause sites in MDV-1 RNA replication with kinetic refolding of the growing chain. A Monte Carlo simulation of the Markov process

We consider a template-instructed MDV-1 RNA replication catalyzed by Q beta replicase. The relaxation of the effective binding of the growing chain to the enzyme is simulated, considering a Markov process where refolding events in the chain are concomitant with chain elongation events. When realistic transition probabilities are considered, it becomes evident that the pause sites in replication are due to relaxation of the binding by folding of the growing chain.     

The role of humans in the diversification of a threatened island raptor

Background  

Anthropogenic habitat modifications have led to the extinction of many species and have favoured the expansion of others. Nonetheless, the possible role of humans as a diversifying force in vertebrate evolution has rarely been considered, especially for species with long generation times. We examine the influence that humans have had on the colonization and phenotypic and genetic differentiation of an insular population of a long-lived raptor species, the Egyptian vulture (Neophron percnopterus).     

Some meteorological conditions associated with forest fires in Galicia (Spain)

The present paper offers data on the effect of certain meteorological parameters on the outbreak of forest fires in Galicia (Spain). In a day-to-day analysis, the values of the stability of the air column and the saturation deficit at the lower levels are related to the number of fires occurring in the following 24 h.     

Patterns of co‐occurrences in a killifish metacommunity are more related with body size than with species identity

Body size may be more important than species identity in determining species interactions and community structure. However, co‐occurrence of organisms has commonly been analysed from a taxonomic perspective and the body size is rarely taken into account. On six sampling occasions, we analysed patterns of killifish co‐occurrences in nestedness (tendency for less rich communities to be subsamples of the richest), checkerboard structure (tendency for species segregation), and modularity (tendency for groups to co‐occur more frequently than random expectation) in a pond metacommunity located in Uruguay. We contrasted co‐occurrence patterns among species and body size‐classes (individuals from different species were combined into size categories). The analysis was performed at two spatial scales: ponds (communities) and sample units within ponds. Observed nestedness was frequently smaller than the null expectation, with significantly greater deviations for body size‐classes than for species, and for sample units than for communities. At the sample unit level, individuals tended to segregate (i.e. clump into a checkerboard pattern) to a larger extent by body size rather than by taxonomy. Modularity was rarely detected, but nevertheless indicated a level of taxonomic organization not evident in nestedness or checkerboard indices. Identification of the spatial scale and organization at which ecological forces determine community structure is a basic requirement for advancement of robust theory. In our study system, these ecological forces probably structured the community by body sizes of interacting organisms rather than by species identities.     

Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures

Coprolites are fossilized feces that can be used to provide information on the composition of the intestinal microbiota and, as we show, possibly on diet. We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement on Vieques Island, Puerto Rico. While more is known about the Saladoid culture, it is believed that both societies co-existed on this island approximately from 5 to 1170 AD. By extracting DNA from the coprolites, followed by metagenomic characterization, we show that both cultures can be distinguished from each other on the basis of their bacterial and fungal gut microbiomes. In addition, we show that parasite loads were heavy and also culturally distinct. Huecoid coprolites were characterized by maize and Basidiomycetes sequences, suggesting that these were important components of their diet. Saladoid coprolite samples harbored sequences associated with fish parasites, suggesting that raw fish was a substantial component of their diet. The present study shows that ancient DNA is not entirely degraded in humid, tropical environments, and that dietary and/or host genetic differences in ancient populations may be reflected in the composition of their gut microbiome. This further supports the hypothesis that the two ancient cultures studied were distinct, and that they retained distinct technological/cultural differences during an extended period of close proximity and peaceful co-existence. The two populations seemed to form the later-day Taínos, the Amerindians present at the point of Columbian contact. Importantly, our data suggest that paleomicrobiomics can be a powerful tool to assess cultural differences between ancient populations.     

Neomorph and leaf differentiation as alternative morphogenetic pathways in soybean tissue culture.

Somatic embryogenesis and organogenesis were induced on immature cotyledons of different soybean cultivars. The anatomical investigation of morphogenesis proved neomorph differentiation instead of somatic embryos, and leaf formation instead of shoot development. While normal embryos were induced in 0-3.1% of the explants, neomorphs developed at a much higher rate i.e. in 10.5-78.9% depending on the genotype. Likewise organogenesis preferably followed the pathway of leaflet development (3.1-26.3%) than that of shoot tip formation (0-2.6%). Low plant regeneration frequency of soybean can partly be explained with these two alternative abortive pathways of morphogenesis probably induced with higher frequency than the normal pathways by the generally used in vitro methods.     

Techniques for the detection of pathogenic Cryptococcus species in wood decay substrata and the evaluation of viability in stored samples

In this study, we evaluated several techniques for the detection of the yeast form of Cryptococcus in decaying wood and measured the viability of these fungi in environmental samples stored in the laboratory. Samples were collected from a tree known to be positive for Cryptococcus and were each inoculated on 10 Niger seed agar (NSA) plates. The conventional technique (CT) yielded a greater number of positive samples and indicated a higher fungal density [in colony forming units per gram of wood (CFU.g^-1) ] compared to the humid swab technique (ST). However, the difference in positive and false negative results between the CT-ST was not significant. The threshold of detection for the CT was 0.05.10³ CFU.g^-1, while the threshold for the ST was greater than 0.1.10³ CFU^-1. No colonies were recovered using the dry swab technique. We also determined the viability of Cryptococcus in wood samples stored for 45 days at 25ºC using the CT and ST and found that samples not only continued to yield a positive response, but also exhibited an increase in CFU.g^-1, suggesting that Cryptococcus is able to grow in stored environmental samples. The ST.1, in which samples collected with swabs were immediately plated on NSA medium, was more efficient and less laborious than either the CT or ST and required approximately 10 min to perform; however, additional studies are needed to validate this technique.