Diversification of hAT transposase paralogues in the sugarcane genome

Transposons are abundant components of eukaryotic genomes, and play important role in genome evolution. The knowledge about these elements should contribute to the understanding of their impact on the host genomes. The hAT transposon superfamily is one of the best characterized superfamilies in diverse organisms, nevertheless, a detailed study of these elements was never carried in sugarcane. To address this question we analyzed 32 cDNAs similar to that of hAT superfamily of transposons previously identified in the sugarcane transcriptome. Our results revealed that these hAT-like transposases cluster in one highly homogeneous and other more heterogeneous lineage. We present evidences that support the hypothesis that the highly homogeneous group is a domesticated transposase while the remainder of the lineages are composed of transposon units. The first is common to grasses, clusters significantly with domesticated transposases from Arabidopsis, rice and sorghum and is expressed in different tissues of two sugarcane cultivars analyzed. In contrast, the more heterogeneous group represents at least two transposon lineages. We recovered five genomic versions of one lineage, characterizing a novel transposon family with conserved DDE motif, named SChAT. These results indicate the presence of at least three distinct lineages of hAT-like transposase paralogues in sugarcane genome, including a novel transposon family described in Saccharum and a domesticated transposase. Taken together, these findings permit to follow the diversification of some hAT transposase paralogues in sugarcane, aggregating knowledge about the co-evolution of transposons and their host genomes.

Evaluation of primary epidermal lamellar density in the forefeet of near-term fetal Australian feral and domesticated horses

Objective: To investigate the density of the primary epidermal lamellae (PEL) around the solar circumference of the forefeet of near-term fetal feral and nonferal (ie, domesticated) horses. Sample: Left forefeet from near-term Australian feral (n = 14) and domesticated (4) horse fetuses. Procedures: Near-term feral horse fetuses were obtained from culled mares within 10 minutes of death; fetuses that had died in utero 2 weeks prior to anticipated birth date and were delivered from live Thoroughbred mares were also obtained. Following disarticulation at the carpus, the left forefoot of each fetus was frozen during dissection and data collection. In a standard section of each hoof, the stratum internum PEL density was calculated at the midline center (12 o'clock) and the medial and lateral break-over points (11 and 1 o'clock), toe quarters (10 and 2 o'clock), and quarters (4 and 6 o'clock). Values for matching lateral and medial zones were averaged and expressed as 1 density. Density differences at the 4 locations between the feral and domesticated horse feet were assessed by use of imaging software analysis. Results: In fetal domesticated horse feet, PEL density did not differ among the 4 locations. In fetal feral horse feet, PEL density differed significantly among locations, with a pattern of gradual reduction from the dorsal to the palmar aspect of the foot. The PEL density distribution differed significantly between fetal domesticated and feral horse feet. Conclusions and Clinical Relevance: Results indicated that PEL density distribution differs between fetal feral and domesticated horse feet, suggestive of an adaptation of feral horses to environment challenges.

The genome of the domesticated apple (Malus × domestica Borkh.)

We report a high-quality draft genome sequence of the domesticated apple (Malus × domestica). We show that a relatively recent (>50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy of eudicots. Phylogenetic reconstruction of Pyreae and the genus Malus, relative to major Rosaceae taxa, identified the progenitor of the cultivated apple as M. sieversii. Expansion of gene families reported to be involved in fruit development may explain formation of the pome, a Pyreae-specific false fruit that develops by proliferation of the basal part of the sepals, the receptacle. In apple, a subclade of MADS-box genes, normally involved in flower and fruit development, is expanded to include 15 members, as are other gene families involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol.

The 'rise' of Aboriginal women, from domesticated cow to cash cow

The recent claims from former Queensland Labor MP Gary Johns that “a lot of poor women in this country, a large proportion of whom are Aboriginal, are used as cash cows” who are “kept pregnant and producing children for the cash” are somewhat alarming, but not surprising...

Increasing seedstock production of domesticated giant tiger prawns

DEEDI has been approached to perform an important outdoor pond experiment using the heated nursery ponds at Bribie Island Aquaculture Research Centre to get tiger prawn broodstock out of expensive clear-water tank systems and into ponds. This approach will enable a faster and more cost-effective adoption of existing selective breeding technology. Additional benefits will involve increased profitability and sustainability of genetic selection programs, improved understanding of prawn maturation benefiting other tiger prawn research and improved collaboration between DEEDI and CSIRO.

A transposase-independent mechanism gives rise to precise excision of IS256 from insertion sites in Staphylococcus epidermidis.

The mobile element IS256 causes phase variation of biofilm formation in Staphylococcus epidermidis by insertion and precise excision from the icaADBC operon. Precise excision, i.e., removal of the target site duplications (TSDs) and restoration of the original DNA sequence, occurs rarely but independently of functional transposase. Instead, the integrity of the TSDs is crucial for precise excision. Excision increased significantly when the TSDs were brought into closer spatial proximity, suggesting that excision is a host-driven process that might involve most likely illegitimate recombination.

Domesticated domesticated! Some comments on the translation into English of José Carlos Somoza's La Caverna de las ideas

In order to cater for an extended readership, crime fiction, like most popular genres, is based on the repetition of a formula allowing for the reader's immediate identification. This first domestication is followed, at the time of its translation, by a second process, which wipes out those characteristics of the source text that may come into conflict with the dominant values of the target culture. An analysis of the textual and paratextual strategies used in the English translation of José Carlos Somoza's La caverna de las ideas (2000) shows the efforts to make the novel more easily marketable in the English-speaking world through the elimination of most of the obstacles to easy readability.

California : A history of Upper and Lower California from their first discovery to the present time, comprising an account of the climate, soil, natural productions, agriculture, commerce, Sc. A full view of the missionary establishments and condition of the free and domesticated indians. With an appendix relation to steam navigation in the Pacific. Illustrated with a new map, plans of the harbours, and numerous engravings

UANL

Identification and validation of candidate genes associated with domesticated and improved traits in soybean

Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 traitassociated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene Glyma15 g17480 (GmZTL3). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.

Ecological niche similarities of Peponapis bees and non-domesticated Cucurbita species

Peponapis bees are considered specialized pollinators of Cucurbita flowers, a genus that presents several species of economic value (squashes and pumpkins). Both genera originated in the Americas, and their diversity dispersion center is in Mexico. Ten species of Peponapis and ten species of Cucurbita (only non-domesticated species) were analyzed considering the similarity of their ecological niche characteristics with respect to climatic conditions of their occurrence areas (abiotic variables) and interactions between species (biotic variables). The similarity of climatic conditions (temperature and precipitation) was estimated through cluster analyses. The areas of potential occurrence of the most similar species were obtained through ecological niche modeling and summed with geographic information system tools. Three main clusters were obtained: one with species that shared potential occurrence areas mainly in deserts (P. pruinosa, P. timberlakei, C. digitata, C. palmata, C. foetidissima), another in moist forests (P. limitaris, P. atrata, C. lundelliana, C. o. martinezii) and a third mainly in dry forests (C. a. sororia, C. radicans, C. pedatifolia, P. azteca, P. smithi, P. crassidentata, P. utahensis). Some species with similar ecological niche presented potential shared areas that are also similar to their geographical distribution, like those occurring predominantly on deserts. However, some clustered species presented larger geographical areas, such as P. pruinosa and C. foetidissima suggesting other drivers than climatic conditions to shape their distributions. The domestication of Cucurbita and also the natural history of both genera were considered also as important factors. (C) 2011 Elsevier B.V. All rights reserved.

High female mortality resulting in herd collapse in free-ranging domesticated reindeer (Rangifer tarandus tarandus) in Sweden

Reindeer herding in Sweden is a form of pastoralism practised by the indigenous Sami population. The economy is mainly based on meat production. Herd size is generally regulated by harvest in order not to overuse grazing ranges and keep a productive herd. Nonetheless, herd growth and room for harvest is currently small in many areas. Negative herd growth and low harvest rate were observed in one of two herds in a reindeer herding community in Central Sweden. The herds (A and B) used the same ranges from April until the autumn gathering in October-December, but were separated on different ranges over winter. Analyses of capture-recapture for 723 adult female reindeer over five years (2007-2012) revealed high annual losses (7.1% and 18.4%, for herd A and B respectively). A continuing decline in the total reindeer number in herd B demonstrated an inability to maintain the herd size in spite of a very small harvest. An estimated breakpoint for when herd size cannot be kept stable confirmed that the observed female mortality rate in herd B represented a state of herd collapse. Lower calving success in herd B compared to A indicated differences in winter foraging conditions. However, we found only minor differences in animal body condition between the herds in autumn. We found no evidence that a lower autumn body mass generally increased the risk for a female of dying from one autumn to the next. We conclude that the prime driver of the on-going collapse of herd B is not high animal density or poor body condition. Accidents or disease seem unlikely as major causes of mortality. Predation, primarily by lynx and wolverine, appears to be the most plausible reason for the high female mortality and state of collapse in the studied reindeer herding community.

RFLP and cytogenetic evidence on the origin and evolution of allotetraploid domesticated peanut, Arachis hypogaea (Leguminosae)

Nuclear restriction fragment length polymorphism (RFLP) analysis was used to determine the wild diploid Arachis species that hybridized to form tetraploid domesticated peanut. Results using 20 previously mapped cDNA clones strongly indicated A. duranensis as the progenitor of the A genome of domesticated peanut and A. ipaensis as the B genome parent. A large amount of RFLP variability was found among the various accessions of A. duranensis, and accessions most similar to the A genome of cultivated peanut were identified. Chloroplast DNA RFLP analysis determined that A. duranensis was the female parent of the original hybridization event. Domesticated peanut is known to have one genome with a distinctly smaller pair of chromosomes ('A'), and one genome that lacks this pair. Cytogenetic analysis demonstrated that A. duranensis has a pair of 'A' chromosomes, and A. ipaensis does not. The cytogenetic evidence is thus consistent with the RFLP evidence concerning the identify of the progenitors. RFLP and cytogenetic evidence indicate a single origin for domesticated peanut in Northern Argentina or Southern Bolivia, followed by diversification under the influence of cultivation.