The Tnt1 family member Retrosol copy number and structure disclose retrotransposon diversification in different Solanum species

Eukaryotic genome expansion/retraction caused by LTR-retrotransposon activity is dependent on the expression of full length copies to trigger efficient transposition and recombination-driven events. The Tnt1 family of retrotransposons has served as a model to evaluate the diversity among closely related elements within Solanaceae species and found that members of the family vary mainly in their U3 region of the long terminal repeats (LTRs). Recovery of a full length genomic copy of Retrosol was performed through a PCR-based approach from wild potato, Solanum oplocense. Further characterization focusing on both LTR sequences of the amplified copy allowed estimating an approximate insertion time at 2 million years ago thus supporting the occurrence of transposition cycles after genus divergence. Copy number of Tnt1-like elements in Solanum species were determined through genomic quantitative PCR whereby results sustain that Retrosol in Solanum species is a low copy number retrotransposon (1-4 copies) while Retrolyc1 has an intermediate copy number (38 copies) in S. peruvianum. Comparative analysis of retrotransposon content revealed no correlation between genome size or ploidy level and Retrosol copy number. The tetraploid cultivated potato with a cellular genome size of 1,715 Mbp harbours similar copy number per monoploid genome than other diploid Solanum species (613-884 Mbp). Conversely, S. peruvianum genome (1,125 Mbp) has a higher copy number. These results point towards a lineage specific dynamic flux regarding the history of amplification/activity of Tnt1-like elements in the genome of Solanum species.

Copy number variants on the X chromosome in women with primary ovarian insufficiency

Objective: To investigate whether submicroscopic copy number variants (CNVs) on the X chromosome can be identified in women with primary ovarian insufficiency (POI), defined as spontaneous secondary amenorrhea before 40 years of age accompanied by follicle-stimulating hormone levels above 40 IU/L on at least two occasions. Design: Analysis of intensity data of single nucleotide polymorphism (SNP) probes generated by genomewide Illumina 370k CNV BeadChips, followed by the validation of identified loci using a custom designed ultra-high-density comparative genomic hybridization array containing 48,325 probes evenly distributed over the X chromosome. Setting: Multicenter genetic cohort study in the Netherlands. Patient(s): 108 Dutch Caucasian women with POI, 97 of whom passed quality control, who had a normal karyogram and absent fragile X premutation, and 235 healthy Dutch Caucasian women as controls. Intervention(s): None. Main Outcome Measure(s): Amount and locus of X chromosomal microdeletions or duplications. Result(s): Intensity differences between SNP probes identify microdeletions and duplications. The initial analysis identified an overrepresentation of deletions in POI patients. Moreover, CNVs in two genes on the Xq21.3 locus (i.e., PCDH11X and TGIF2LX) were statistically significantly associated with the POI phenotype. Mean size of identified CNVs was 262 kb. However, in the validation study the identified putative Xq21.3 deletions samples did not show deviations in intensities in consecutive probes. Conclusion(s): X chromosomal submicroscopic CNVs do not play a major role in Caucasian POI patients. We provide guidelines on how submicroscopic cytogenetic POI research should be conducted. (Fertil Steril (R) 2011;95:1584-8. (C) 2011 by American Society for Reproductive Medicine.)

Related changes in biodiversity, insolation and climate in the Atlantic rainforest since the last interglacial

The long-term Colonia record is located in the Atlantic rainforest domain in Brazil (23 degrees 52`S 46 degrees 42`20 `` W 900 m a.s.l.). The 780 cm long core CO3 provides a coverage of a complete interglacial/glacial cycle for the first time in a neotropical rainforest. Information on the behavior of tropical climates compared to global changes in temperatures indicates specific climate responses in terms of precipitation at these latitudes. Winter extratropical circulation was very active during the last interglacial and most of the glacial. Floristic composition of the rainforest changed several times in each phase of expansion, twice during the interglacial, and three times during glacial episodes. Araucaria was well developed in the area of Sao Paulo until the beginning of the first dry phase of the glacial at ca. 50,000 yr B.P. Changes in insolation controlled the expansion of the rainforest and the tropical hydrological cycle as evidenced by a strong precession signal. However precession had no impact on regional climatic features. The two interglacials (MIS 5e and Holocene) showed completely different patterns attesting to the continuous evolution of the forest. The biodiversity index (Shannon-Wiener Index) remained high during both the interglacial and glacial attesting to the permanence of small patches of rainforest refugia during drier phases. The lowest Shannon-Wiener Indexes were recorded between 23,000 and 12,000 yr B.P. and 40,000 and 30,000 yr B.P. and characterize two marked phases of stress for the rainforest. (C) 2008 Elsevier B.V. All rights reserved.

Lacustrine sediments provide geochemical evidence of environmental change during the last millennium in southeastern Brazil

A 172 cm-long sediment core was collected from a small pristine lake situated within a centripetal drainage basin in a tropical karst environment (Ribeira River valley, southeastern Brazil) in order to investigate the paleoenvironmental record provided by the lacustrine geochemistry. Sediments derived from erosion of the surrounding cambisoils contain quartz, kaolinite, mica, chlorite and goethite. Accelerator mass spectroscopy (AMS) (14)C dating provided the geochronological framework. Three major sedimentary units were identified based on the structure and color of the sediments: Unit III from 170 to 140 cm (1030 +/- 60-730 +/- 60 yr BP), Unit II from 140 to 90 cm (730 +/- 60-360 +/- 60 yr BP) and Unit I from 90 to 0 cm (360 +/- 60-0 yr BP). Results of major and trace element concentrations were analysed through multivariate statistical techniques. Factor analysis provided three factors accounting for 72.4% of the total variance. F1 and F2 have high positive loadings from K, Ba, Cs, Rb, Sr, Sc, Th, light rare earth element (LREE), Fe, Cr, Ti, Zr, Hf and Ta, and high negative loadings from Mg, Co, Cu, Zn, Br and loss on ignition (LOI). F3, with positive loadings from V and non-metals As and Sb, accounts for a low percentage (9.7%) of the total variance, being therefore of little interpretative use. The profile distribution of F1 scores reveals negative values in Units I and III, and positive values in Unit II, meaning that K, Ba, Cs, Rb, Sr, Sc, Th, LREE, Fe, Cr, Ti, Zr, Hf and Ta are relatively more concentrated in Unit II, and Mg, Co, Cu, Zn and Br are relatively more abundant in Units I and III. The observed fluctuations in the geochemical composition of the sediments are consistent with slight variations of the erosion intensity in the catchment area as a possible response to variations of climatic conditions during the last millennium. (c) 2009 Elsevier GmbH. All rights reserved.

Generalizations of Pelczynski`s decomposition method for Banach spaces containing a complemented copy of their squares

Suppose that X and Y are Banach spaces isomorphic to complemented subspaces of each other. In 1996, W. T. Gowers solved the Schroeder- Bernstein Problem for Banach spaces by showing that X is not necessarily isomorphic to Y. However, if X-2 is complemented in X with supplement A and Y-2 is complemented in Y with supplement B, that is, { X similar to X-2 circle plus A Y similar to Y-2 circle plus B, then the classical Pelczynski`s decomposition method for Banach spaces shows that X is isomorphic to Y whenever we can assume that A = B = {0}. But unfortunately, this is not always possible. In this paper, we show that it is possible to find all finite relations of isomorphism between A and B which guarantee that X is isomorphic to Y. In order to do this, we say that a quadruple (p, q, r, s) in N is a P-Quadruple for Banach spaces if X is isomorphic to Y whenever the supplements A and B satisfy A(p) circle plus B-q similar to A(r) circle plus B-s . Then we prove that (p, q, r, s) is a P-Quadruple for Banach spaces if and only if p - r = s - q = +/- 1.