Frequent non-reciprocal exchange in microsatellite-containing-DNA-regions of vertebrates

Microsatellites are DNA-fragments containing short repetitive motifs with 2–10 bp. They are highly variable in most species and distributed throughout the whole genome. It is broadly accepted that their high degree of variability is closely associated with mispairing of DNA-strands during the replication phase, termed slippage, although recombination is also observed. The aim of this study is to demonstrate evidence that non-reciprocal recombination processes changing the total genomic structure are common in microsatellites and flanking regions. We sequenced DNA fragments from birds in which microsatellites are located, and analyzed the structure of the microsatellites and their flanking regions. Additionally, other data and those from literature of three microsatellite regions of primates coding for the Ataxin-2, the Huntingtin and the TATA-box binding protein were analyzed. The structures of seven avian and three primate microsatellites support the hypothesis that non-reciprocal recombination is a common process that may also contribute considerably to the variation at microsatellite loci. We conclude that results of population genetic studies that are analyzed statistically with methods based on stepwise mutation models should be interpreted with caution if no detailed information on the allelic variation of microsatellites is available.     

The tendency of lentiviral open reading frames to become A-rich: constraints imposed by viral genome organization and cellular tRNA availability

Human immunodeficiency virus type 1 (HIV-1) and other lentiviridae demonstrate a strong preference for the A-nucleotide, which can account for up to 40% of the viral RNA genome. The biological mechanism responsible for this nucleotide bias is currently unknown. The increased A-content of these viral genomes corresponds to the typical use of synonymous codons by all members of the lentiviral family (HIV, SIV, BIV, FIV, CAEV, EIAV, visna) and the human spuma retrovirus, but not by other retroviruses like the human T-cell leukemia viruses HTLV-I and HTLV-II. In this article, we analyzed A-bias for all codon groups in all open reading frames of several lentiviruses. The extent of lentiviral codon bias could be related to host cellular translation. By calculating codon bias indices (CBIs), we were able to demonstrate an inverse correlation between the extent of codon bias and the rate of translation of individual reading frames in these viruses. Specifically, the shift toward A-rich codons is more pronounced in pol than in gag lentiviral genes. Since it is known that Gag synthesis exceeds Pol synthesis by a factor of 20 due to infrequent ribosomal frame-shifting during translation of the gap-pol mRNA molecule, we propose that the aminoacyl-tRNA availability in the host cell restricts the lentiviral preference for A-rich codons. In addition, less A-nucleotides were found in regions of the viral genome encoding multiple functions; e.g., overlapping reading frames (tat-rev-env) or in genes that overlap regulatory sequences (nef-LTR region). Finally, the characteristics of lentiviral codon usage are presented as a phylogenetic tree without the need for prior sequence alignment.Correspondence to: B. Berkhout     

ASSESSMENT OF POTENTIAL BIAS WITH SNOWSHOE HARE FECAL PELLET-PLOT COUNTS

Abstract: The fecal pellet-plot method has been used extensively for snowshoe hare (Lepus americanus) population studies across the species' range, but potential biases associated with the technique have not been addressed adequately. We studied hare pellet-plots in northern Idaho to quantify pellet decomposition rates across environmental gradients, and conducted feeding trials on captive hares to assess the role of diet on pellet production rates. We found that across our study area pellet numbers tended to be higher on plots with high vegetative cover, which likely was a reflection of hare habitat choice rather than lesser pellet decomposition in such habitat. A pellet decomposition experiment indicated that pellet persistence was negatively related to moisture level, and that pellets produced by hares during summer decomposed more quickly than those from winter. We found that only 19% of fecal pellets collected from plots located across northern Idaho were produced by hares during winter. There was a correlation between pellet numbers from plots that were pre-cleared 1 year earlier and estimated numbers of hares on 6 study areas. A similar correlation was lacking for pellet counts from uncleared plots, implying that hare population estimation via pellet-plot counts should involve plot pre-clearing. In captive studies, juvenile hares produced slightly fewer pellets per day per gram of food ingested than adults, but pellet production was similar across diets comprised of 10 different browse species. We conclude that for our study area the fecal pellet-plot method may be subject to notable pellet decomposition bias, and therefore recommend that use of the method elsewhere across the species' range be preceded by assessment of both the pellet-hare density relationship and pellet decomposition rates across habitats.     

Nucleosomal Positioning and Genetic Divergence Study Based on DNA Flexibility Map

Abstract

Based on worm like chain model, DNA structural parameters—tilt, roll and rise, derived from crystallographic database have been used to determine the flexibility of DNA that regulates the nucleosomal translational positioning. Theoretically derived data has been compared to the experimental values available in Ioshikhes and Trifonov's database. The methodology has been extended to determine the flexibility of 18S rRNA genome in eukarya, where yeast shows a distinct difference when compared with mammals like human, mouse and rabbit.     

A Combined Product Estimator in Sample Survey

For the estimation of the population mean in stratified random sampling a ‘Combined Product Estimator’ is proposed which is more efficient than the ‘Combined Ratio’ and ‘Separate Ratio’ estimators. Also, the proposed estimator have exact expressions for bias and mean square error. An empirical illustration is given to compare the efficiencies of different estimators.     

A journey through time: exploring temporal patterns amongst digitized plant specimens from Australia

Online access to species occurrence records has opened new windows into investigating biodiversity patterns across multiple scales. The value of these records for research depends on their spatial, temporal, and taxonomic quality. We assessed temporal patterns in records from the Australasian Virtual Herbarium, asking: (1) How temporally consistent has collecting been across Australia? (2) Which areas of Australia have the most reliable records, in terms of temporal consistency and inventory completeness? (3) Are there temporal trends in the completeness of attribute information associated with records? We undertook a multi-step filtering procedure, then estimated temporal consistency and inventory completeness for sampling units (SUs) of 50?km ×?50?km. We found temporal bias in collecting, with 80% of records collected over the period 1970–1999. South-eastern Australia, the Wet Tropics in north-east Queensland, and parts of Western Australia have received the most consistent sampling effort over time, whereas much of central Australia has had low temporal consistency. Of the SUs, 18% have relatively complete inventories with high temporal consistency in sampling. We also determined that 25% of digitized records had missing attribute information. By identifying areas with low reliability, we can limit erroneous inferences about distribution patterns and identify priority areas for future sampling.     

Lineage-Biased Hematopoietic Stem Cells Are Regulated by Distinct Niches

1. Download high-res image (196KB)
2. Download full-size image