Combinatorial minimization and secondary structure determination of a nucleotide synthase ribozyme

We previously isolated from random sequences ribozymes able to form a glycosidic linkage between a ribose sugar and 4-thiouracil in a reaction that mimics protein-catalyzed nucleotide synthesis. Here we report on two serial in vitro selection experiments that defined the core motif of one of the nucleotide synthase ribozymes and provided improved versions of this ribozyme. The first selection experiment started from a degenerate sequence pool based on the previously isolated sequence and used a selection-amplification protocol that allowed the sequence requirements at the 3' terminus of the ribozyme to be interrogated. Comparing the active sequences identified in this experiment revealed the complicated secondary structure of the nucleotide synthase ribozyme. A second selection was then performed to remove nonessential sequence from the ribozyme. This selection started with a pool with variation introduced in both the sequence and the length of the nonconserved loops and joining regions. This pool was generated using a partial reblocking/deblocking strategy on a DNA synthesizer, allowing the combinatorial synthesis of both point deletions and point substitutions. The consensus ribozyme motif that emerged was an approximately 71 nt pseudoknot structure with five stems and two important joining segments. Comparative sequence analysis and a cross-linking experiment point to the probable location of nucleotide synthesis. The prototype isolate from the second selection was nearly 35 times more efficient than the initial isolate and at least 10(8) times more efficient than an upper limit of an as-yet undetectable uncatalyzed reaction, supporting the idea that RNA-catalyzed nucleotide synthesis might have been important in an RNA world.     

Assessing the function of geophagy in a Malagasy rain forest lemur

Geophagy has been observed in nearly every long‐term study of folivorous primates. Yet despite frequent observations of this behavior, conclusive explanations for soil consumption remain ambiguous. This study tests the most frequently proposed hypotheses for geophagy using data collected on the geophagic behavior of the Milne‐Edwards’ sifaka (Propithecus edwardsi) living in two forests with varying levels of disturbance within Ranomafana National Park, Madagascar. Field data were collected from December 2002 to November 2003, during which time soil samples were collected for mineral analyses from 102 sites selected for geophagy and 42 control sites at which no geophagy was recorded. Results indicate that control soils differ significantly between the two study sites and that this difference is primarily attributable to varying levels of habitat disturbance. The frequency of soil consumption also does not vary significantly by sex or between logged and unlogged habitats. Soil consumption significantly correlated with fruit/seed consumption overall, but to a lesser degree in logged compared with unlogged sites. Clay minerals found in soils likely prevent absorption of dietary toxins in the gut and/or may mediate gut pH. This provides strong evidence for the protection hypothesis for geophagy, which may be especially important in areas where logging, or other forms of habitat disturbance, has been experienced. Abstract in French is available with online material.     

Related Arabidopsis serine carboxypeptidase-like sinapoylglucose acyltransferases display distinct but overlapping substrate specificities

The Arabidopsis (Arabidopsis thaliana) genome encodes 51 proteins annotated as serine carboxypeptidase-like (SCPL) enzymes. Nineteen of these SCPL proteins are highly similar to one another, and represent a clade that appears to be unique to plants. Two of the most divergent proteins within this group have been characterized to date, sinapoyl-glucose (Glc):malate sinapoyltransferase and sinapoyl-Glc:choline sinapoyltransferase. The fact that two of the least related proteins within this clade are acyltransferases rather than true serine carboxypeptidases suggests that some or all of the remaining members of this group may have similar activities. The gene that encodes sinapoyl-Glc:malate sinapoyltransferase (sinapoyl-Glc accumulator1 [SNG1]: At2g22990) is one of five SCPL genes arranged in a cluster on chromosome 2. In this study, an analysis of deletion mutant lines lacking one or more genes in this SCPL gene cluster reveals that three of these genes also encode sinapoyl-Glc-dependent acyltransferases. At2g23000 encodes sinapoyl-Glc:anthocyanin acyltransferase, an enzyme that is required for the synthesis of the sinapoylated anthocyanins in Arabidopsis. At2g23010 encodes an enzyme capable of synthesizing 1,2-disinapoyl-Glc from two molecules of sinapoyl-Glc, an activity shared by SNG1 and At2g22980. Sequence analysis of these SCPL proteins reveals pairwise percent identities that range from 71% to 78%, suggesting that their differing specificities for acyl acceptor substrates are due to changes in a relatively small subset of amino acids. The study of these SCPL proteins provides an opportunity to examine enzyme structure-function relationships and may shed light on the role of evolution of hydroxycinnamate ester metabolism and the SCPL gene family in Arabidopsis and other flowering plants.     

Density is more important than predation risk for predicting growth and developmental outcomes in tadpoles of spotted tree frog,Litoria spenceri (Dubois 1984)

The diverse benefits of group living include protection against predators through dilution effects and greater group vigilance. However, intraspecific aggregation can decrease developmental rates and survival in prey species. We investigated the impact on tadpole development and behaviour of the interaction between population density and predation risk. Spotted tree frog (Litoria spenceri: Hylidae, Dubois 1984) tadpoles were kept at one of three different densities (two tadpoles per litre, five tadpoles per litre or 10 tadpoles per litre) until metamorphosis in the presence or absence of predatory cues. We aimed to determine the influence of population density, predation and the interaction of both factors in determining growth rates in tadpoles. Tadpoles were measured weekly to assess growth and development and filmed to quantify differences in activity and feeding frequency between groups. Generally, tadpoles housed without predators had longer developmental periods when housed with a predator, but there was no effect on tail length or total length. There was no effect of either predation cues or density on percentage of individuals feeding or moving. Although the effects of the presence of predators alone may appear to be less than the effects of the presence of competitors, the prioritisation of competitiveness over predator avoidance may increase vulnerability of tadpoles to the lethal threat of predators. This is particularly important in species such as L. spenceri, which is at risk from introduced fish predators.     

An increasing citation black hole in ecology and evolution

Citations published in online supplementary material (OSM) are invisible to search engines used to calculate citation counts, potentially negatively impacting popular performance indices and journal rankings that rely on citation counts for quantification. To quantify the number of citations that are “lost” in OSM, we conducted a systematic survey of supplementary citation practices in four high‐ranking, society‐run journals from two geographical locations (Europe and North America). In 2012, 6% of all citations were only included in the OSM and were therefore not included in citation counts. We found a significant increase in the number of references invisible to citation counting services over the last two decades. A solution to this problem is urgently required and could include journal indexing of citations in OSM or the inclusion of all references in the main text.     

Application of phage display to high throughput antibody generation and characterization

We have created a high quality phage display library containing over 10¹⁰ human antibodies and describe its use in the generation of antibodies on an unprecedented scale. We have selected, screened and sequenced over 38,000 recombinant antibodies to 292 antigens, yielding over 7,200 unique clones. 4,400 antibodies were characterized by specificity testing and detailed sequence analysis and the data/clones are available online. Sensitive detection was demonstrated in a bead based flow cytometry assay. Furthermore, positive staining by immunohistochemistry on tissue microarrays was found for 37% (143/381) of antibodies. Thus, we have demonstrated the potential of and illuminated the issues associated with genome-wide monoclonal antibody generation.     

Integrating sequence and structural biology with DAS

Background  

The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence.     

Improved double immunofluorescence for confocal laser scanning microscopy.

Reliable double immunofluorescence labeling for confocal laser scanning microscopy requires good separation of the signals generated by the fluorochromes. We have successfully overcome the limitation of a single argon ion laser in achieving effective excitation of dyes with well-separated emission spectra by employing the novel sulfonated rhodamine fluorochromes designated Alexa 488 and Alexa 568. The more abundant antigen was visualized using the red-emitting Alexa 568, with amplification of the signal by a biotinylated bridging antibody and labeled streptavidin. This was combined with the green-emitting Alexa 488, which yielded brighter images than fluorescein but exhibited comparable photodegradation. With appropriate controls to ensure the absence of crosstalk between fluorescence channels, these dyes permitted unequivocal demonstration of co-localization. This combination of fluorochromes may also offer advantages for users of instruments equipped with alternative laser systems.