A sequence variation in the human cystatin D gene resulting in an amino acid (Cys/Arg) polymorphism at the protein level

A polymorphism in the coding region of the human cystatin D gene has been detected by direct sequencing of amplified DNA from different individuals. The variation, resulting from a T/C transition in exon 1 of the gene, causes an amino acid variation, Cys/Arg, at the protein level. An allele-specific oligonucleotide hybridization assay was developed and used to demonstrate this polymorphism in the population. The deduced frequencies were 0.55 and 0.45 for the Cys and Arg variant-encoding alleles, respectively.     

DNA sequences specific for Caucasian G3m(b) and (g) allotypes: allotyping at the genomic level

Assignment of the G3m(g) and (b) correlative amino acid residues was performed at the genomic level by direct sequencing of DNA from nine Caucasian individuals. Two oligonucleotide primers were used for subclass-specific enzymatic amplification of a DNA segment comprising a major portion of the second and third constant region domains (C_H2 and C_H3) fo the human IgG3 heavy chain gene. Comparison of the sequences of amplified DNA from individuals serologically typed as homozygous for G3m(b) or G3m(g) or as heterozygous, G3m(b,g), revealed differences in the codons for the amino acid residues 291, 296, and 384. Proline, phenylalanine, and serine at these positions corresponded to G3m(b), and leucine, tyrosine, and asparagine to G3m(g). Heterozygotic individuals, typed G3m(b,g), displayed both the G3m(b) and G3m(g) codons at these three positions. The polymorphism at each of these three codons could be identified either as the appearance, or the loss, of recognition sites for the two restriction endonucleases, Nsp BII and Rsa I. This allowed the development of a polymerase chain reaction (PCR)-based assay permitting the distinction of G3m ^b and G3m ^g alleles by analyzing the electrophoretical mobility of the DNA fragments generated by digestion of the PCR-products with Nsp BII and Rsa I. Correspondence to: R. Grubb.     

New insights on the comma-less theory

The comma-less hypothesis represents a theoretical effort to describe one of the steps in the early evolution of the translation apparatus. This hypothesis emphasizes the advantages that a RNY coding pattern would have provided in a primitive RNA adaptor-catalyst system. This theory has been debated for years, both in conceptual and statistical terms, and no consensus about its validity has been ascertained. In this work, a statistical model refuting this theory was reconsidered. This new approach eliminates the bias due to the absence of stop codons in the open reading frame, and to the amino acid composition of bacterial genes. The results obtained support the biological significance of the RNY coding pattern.     

Decline of the breeding population of <Emphasis Type="Italic">Pygoscelis antarctica</Emphasis> and <Emphasis Type="Italic">Pygoscelis adeliae</Emphasis> on Penguin Island,South Shetland,Antarctica

This work is a quantitative analysis of the population of breeding pairs of Pygoscelis adeliae and Pygoscelis antarctica, which use Penguin Island as a breeding area. There was a decrease in the populations of P. adeliae and P. antarctica by 75 and 66%, respectively, from the breeding season of 1979/1980 to 2003/2004. A mixed breeding colony of both species was also documented, according to published data which has existed since 1979/1980. The P. antarctica has an advantage over P. adeliae in this mixed breeding situation, where the breeding pairs of the former increased by 127%, indicating an interspecies competition for nesting ground.     

Molecular phylogeny endorses the relationship between carnivorous and filter‐feeding tunicates (Tunicata,Ascidiacea)

Tatián, M., Lagger, C., Demarchi, M. & Mattoni, C. (2011). Molecular phylogeny endorses the relationship between carnivorous and filter‐feeding tunicates (Tunicata, Ascidiacea).—Zoologica Scripta, 40, 603–612. The phylogeny of the tunicates (animals considered the closest relatives to the vertebrates) is not yet completely defined, especially the evolutionary relationships within the class. Molecular studies do not include particular benthic deep‐sea species that show morphological changes in the evolution from filter feeding into a carnivorous‐feeding habit. According only to morphological features, these animals are considered as a part of the Class Ascidiacea (Family Hexacrobylidae), but also as a different class, Sorberacea, belonging to the Phylum Tunicata. In this study, we present a phylogenetic analysis based on 18S rDNA sequences, which clearly included these animals in Ascidiacea but in the Family Molgulidae, faster‐evolving ascidians with a high evolution rate. This finding supports the idea that carnivory in Molgulidae represents a more recent adaptation to life in the ocean deep bottoms, where organisms have to adapt themselves to a less plentiful particulate organic carbon supply. Based on molecular and morphological evidence, we propose the following new synonymy: Hexacrobylidae Seeliger 1906 = Molgulidae Lacaze‐Duthiers, 1877 .     

Building multiple nests is associated with reduced breeding performance in a south temperate population of Grass Wrens Cistothorus platensis platensis

Grass Wrens Cistothorus platensis build two types of non-breeding nest structures: platforms and dummy nests. Platforms are rudimentary accumulations of grasses concealed between vegetation. Dummy and breeding nests are dome-shaped with a similar structural layer. We used a nest-removal experiment and observational data to evaluate several hypotheses regarding the adaptive significance of building multiple nests in a south temperate population of Grass Wrens. Building non-breeding nests was not a strategy of males to attract additional females, as most of these nests were built after pair formation and both sexes collaborated during building. Building non-breeding nests was not a post-pairing display as the presence of multiple nests did not increase female investment in the breeding attempt: clutch size and female provisioning to nestlings did not differ between experimental and control territories where no non-breeding nests were removed. Similarly, in non-manipulated territories, clutch size and female provisioning were not correlated with the number of non-breeding nests or with males’ nest-building effort. Contrary to this hypothesis, the number of non-breeding nests was associated with delayed clutch initiation and reduced hatching success. The presence of non-breeding nests did not reduce nest predation and brood parasitism, which did not differ between experimental and control territories. We did not detect differences in concealment between non-breeding and breeding nests, suggesting that non-breeding nests were not the result of abandonment before egg-laying to reduce subsequent nest predation. Dummy nests did not provide shelter; they were not used frequently for roosting over the breeding season and were not maintained during the non-breeding season. We suggest that building non-breeding nests may be an attempt by males to manipulate the decision of females to breed with a mate they might otherwise reject or to start reproduction earlier than optimal for the females.     

Unexpected diversity of ferredoxin-dependent thioredoxin reductases in cyanobacteria

Thioredoxin reductases control the redox state of thioredoxins (Trxs)—ubiquitous proteins that regulate a spectrum of enzymes by dithiol–disulfide exchange reactions. In most organisms, Trx is reduced by NADPH via a thioredoxin reductase flavoenzyme (NTR), but in oxygenic photosynthetic organisms, this function can also be performed by an iron-sulfur ferredoxin (Fdx)-dependent thioredoxin reductase (FTR) that links light to metabolic regulation. We have recently found that some cyanobacteria, such as the thylakoid-less Gloeobacter and the ocean-dwelling green oxyphotobacterium Prochlorococcus, lack NTR and FTR but contain a thioredoxin reductase flavoenzyme (formerly tentatively called deeply-rooted thioredoxin reductase or DTR), whose electron donor remained undefined. Here, we demonstrate that Fdx functions in this capacity and report the crystallographic structure of the transient complex between the plant-type Fdx1 and the thioredoxin reductase flavoenzyme from Gloeobacter violaceus. Thereby, our data demonstrate that this cyanobacterial enzyme belongs to the Fdx flavin-thioredoxin reductase (FFTR) family, originally described in the anaerobic bacterium Clostridium pasteurianum. Accordingly, the enzyme hitherto termed DTR is renamed FFTR. Our experiments further show that the redox-sensitive peptide CP12 is modulated in vitro by the FFTR/Trx system, demonstrating that FFTR functionally substitutes for FTR in light-linked enzyme regulation in Gloeobacter. Altogether, we demonstrate the FFTR is spread within the cyanobacteria phylum and propose that, by substituting for FTR, it connects the reduction of target proteins to photosynthesis. Besides, the results indicate that FFTR acquisition constitutes a mechanism of evolutionary adaptation in marine phytoplankton such as Prochlorococcus that live in low-iron environments.