Genetic dissection of vitamin E biosynthesis in tomato

Vegetables are critical for human health as they are a source of multiple vitamins including vitamin E (VTE). In plants, the synthesis of VTE compounds, tocopherol and tocotrienol, derives from precursors of the shikimate and methylerythritol phosphate pathways. Quantitative trait loci (QTL) for alpha-tocopherol content in ripe fruit have previously been determined in an Solanum pennellii tomato introgression line population. In this work, variations of tocopherol isoforms (alpha, beta, gamma, and delta) in ripe fruits of these lines were studied. In parallel all tomato genes structurally associated with VTE biosynthesis were identified and mapped. Previously identified VTE QTL on chromosomes 6 and 9 were confirmed whilst novel ones were identified on chromosomes 7 and 8. Integrated analysis at the metabolic, genetic and genomic levels allowed us to propose 16 candidate loci putatively affecting tocopherol content in tomato. A comparative analysis revealed polymorphisms at nucleotide and amino acid levels between Solanum lycopersicum and S. pennellii candidate alleles. Moreover, evolutionary analyses showed the presence of codons evolving under both neutral and positive selection, which may explain the phenotypic differences between species. These data represent an important step in understanding the genetic determinants of VTE natural variation in tomato fruit and as such in the ability to improve the content of this important nutriceutical.

Differential staining and microchromosomal variation in karyotypes of four Brazilian species of Tupinambinae lizards (Squamata : Teiidae)

Kayotypes of four neotropical teiid lizard species (Tupinambinae) were herein studied after conventional as well as silver staining and CBG-banding: Crocodilurus amazonicus (2n = 34), Tupinambis teguixin (2n = 36), Tupinambis merianae and Tupinambis quadrilineatus (2n = 38). The karyological data for T. quadrilineatus as well as those obtained using differential staining for all species were unknown until now. The karyotypes of all species presented 12 macrochromosomes identical in morphology, but differed in the number of microchromosomes: 22 in C. amazonicus, 24 in T. teguixin and 26 in T. quadrilineatus and T. merianae. The Ag-NOR located at the secondary constriction at the distal end of pair 2 is shared by all species, contrasting with the variability observed for this character in species of the related Teiinae. CBG-banding revealed a species-specific pattern in T. quadrilineatus with conspicuous interstitial C-blocks at the proximal region of the long arm of pair 4 and the whole heterochromatic short arm of pair 6. The karyological data reported here corroborates the relationship hypothesis obtained for Tupinambis based on molecular characters. T. teguixin presents the putative ancestral karyotype for the genus with 2n = 36 whereas T. merianae and T. quadrilineatus exhibit 2n = 38, due to an additional pair of microchromosomes.

Chromosome polymorphism in Astyanax fasciatus (Teleostei, Characidae). 2-Chromosomal location of a satellite DNA

Studies about composition of repetitive sequences and their chromosomal location have been helpful to evolutionary studies in many distinct organisms. In order to keep on assessing the possible relationships among different cytotypes of Astyanax fasciatus (Teleostei, Characiformes) in the Mogi-Guacu River (Sao Paulo State, Brazil), C-banding, chromomycin A 3 staining, and fluorescent in situ hybridization with a repetitive DNA sequence (As51) isolated from Astyanax scabripinnis were performed in the present work. The constitutive heterochromatin was distributed in terminal regions on long arms of submetacentric, subtelocentric, and acrocentric chromosomes and in the terminal region on short arms of a pair of submetacentric chromosomes in both standard cytotypes. This latter heterochromatic site was also GC-rich, as revealed by chromomycin A(3) staining, corresponding to the nucleolar organizer region (NOR), as shown by previous studies. The sites of the satellite As51 DNA were located in terminal regions on long arms of several chromosomes. Some variant karyotypic forms, which diverge from the two standard cytotypes, also presented distinctive chromosomes carrying As51 satellite DNA. It is possible that the standard 2n = 46 cytotype represents an invader population in the Mogi-Guacu River able to interbreed with the resident standard 2n = 48 cytotype. Therefore, the variant karyotypes would be related to a possible viable offspring, where complementary chromosomal rearrangements could favor new locations of the satellite DNA analyzed. Copyright (C) 2008 S. Karger AG, Basel

Natural History of the Lutz`s Frog Cycloramphus lutzorum Heyer, 1983 (Anura: Cycloramphidae) in the Brazilian Atlantic Forest: Description of the Advertisement Call, Tadpole, and Karyotype

We describe the advertisement call, tadpole, karyotype, and additional information on the natural history of Cycloramphus lutzorum from southern Brazil. Sonograms were generated from digitally recorded calls. Tadpoles were collected in the field for description in the lab, and an adult was collected for karyotyping. Data on seasonal activity were gathered monthly from November 2005 to November 2007. All tadpoles (N = 21), juveniles (N = 18), and adults (N = 52) were found exclusively in streams. Reproduction, as identified by calling frogs, occurred from July through November. Frogs call all day long, but mostly at dusk, from rock crevices inside the stream edges near the splash zone. The call is short and loud, with 11 pulsed notes, of 491-641 ms, with a dominant frequency of 0.98-1.39 kHz. We describe the exotrophic and semiterrestrial tadpoles, always found in constantly humid vertical rock walls in the stream. Tadpoles of C. lutzorum are recognized by differences in labial tooth row formula, eye diameter, body shape, position of nares, and development of tail. Like congeneric species, the karyotype of C. lutzorum comprises 26 metacentric and submetacentric chromosomes. Cycloramphus lutzorum is restricted to and adapted for living in fast flowing streams, many of which are threatened by deforestation, pollution, and habitat loss. Therefore, we recommend the status of C. lutzorum be changed from its current ""Data Deficient"" to ""Near Threatened (NT)"" in the IUCN species red list.

Karyotypes of a Cryptic Diploid Form of the Unisexual Leposoma percarinatum (Squamata, Gymnophthalmidae) and the Bisexual Leposoma ferreirai from the Lower Rio Negro, Amazonian Brazil

Karyotypes of Leposoma show a clear differentiation between species of the scincoides group from Brazilian Atlantic Forest (2n = 52, without distinctive size groups of chromosomes) and those of the parietale group from the Amazon (2n = 44, with 20M + 24m). In a previous study, we found that in the parietale group the parthenoform Leposoma percarinatum from the state of Mato Grosso, Brazil, exhibited a triploid karyotype (3n = 66) with 30 macrochromosomes and 36 microchromosomes. It was suggested that this karyotype arose after hybridization between a bisexual species with N = 22 (10M + 12m) and a hypothetical unisexual cryptic diploid form of the L. percarinatum complex. Herein, we describe the karyotypes for two species of the parietale group occurring sympatrically in the Arquipelago das Anavilhanas, lower Rio Negro, in Amazonian Brazil. The first represents a distinctive diploid parthenogenetic clone of the L. percarinatum complex, and the other is the recently described Leposoma ferreirai. Both species have 44 biarmed chromosomes clearly represented by 20 macrochromosomes and 24 microchromosomes and present Ag-NORs in one pair of the smallest sized microchromosomes; heteromorphism of size for these regions was detected in L. percarinatum. C-banding revealed blocks of constitutive heterochromatin on the telomeric and pericentromeric regions of macrochromosomes and some microchromosomes. The description of a diploid karyotype (2n = 44, 20M + 24m) for the L. percarinatum complex and its sympatric congener L. ferreirai provides new insight for a better understanding of the origin of parthenogenesis in the L. percarinatum complex.

The R2 mobile element of Rhynchosciara americana: Molecular, cytological and dynamic aspects

Ribosomal RNA genes are encoded by large units clustered (18S, 5S, and 28S) in the nucleolar organizer region in several organisms. Sometimes additional insertions are present in the coding region for the 28S rDNA. These insertions are specific non-long terminal repeat retrotransposons that have very restricted integration targets within the genome. The retrotransposon present in the genome of Rhynchosciara americana, RaR2, was isolated by the screening of a genomic library. Sequence analysis showed the presence of conserved regions, such as a reverse transcriptase domain and a zinc finger motif in the amino terminal region. The insertion site was highly conserved in R. americana and a phylogenetic analysis showed that this element belongs to the R2 clade. The chromosomal localization confirmed that the RaR2 mobile element was inserted into a specific site in the rDNA gene. The expression level of RaR2 in salivary glands during larval development was determined by quantitative RT-PCR, and the increase of relative expression in the 3P of the fourth instar larval could be related to intense gene activity characteristic of this stage. 5`-Truncated elements were identified in different DNA samples. Additionally, in three other Rhynchosciara species, the R2 element was present as a full-length element.

Genes of cathepsin L-like proteases in Trypanosoma rangeli isolates: Markers for diagnosis, genotyping and phylogenetic relationships

We have sequenced genes encoding cathepsin L-like (CatL-like) cysteine proteases from isolates of Trypanosoma rangeli from humans, wild mammals and Rhodnius species of Central and South America. Phylogenetic trees of sequences encoding mature CatL-like enzymes of T rangeli and homologous genes from other trypanosomes, Leishmania spp. and bodonids positioned sequences of T rangeli (rangelipain) closest to T cruzi (cruzipain). Phylogenetic tree of kinetoplastids based on sequences of CatL-like was totally congruent with those derived from SSU rRNA and gGAPDH genes. Analysis of sequences from the CatL-like catalytic domains of 17 isolates representative of the overall phylogenetic diversity and geographical range of T rangeli supported all the lineages (A-D) previously defined using ribosomal and spliced leader genes. Comparison of the proteolytic activities of T rangeli isolates revealed heterogeneous banding profiles of cysteine proteases in gelatin gels, with differences even among isolates of the same lineage. CatL-like sequences proved to be excellent targets for diagnosis and genotyping of T rangeli by PCR. Data from CatL-like encoding genes agreed with results from previous studies of kDNA markers, and ribosomal and spliced leader genes, thereby corroborating clonal evolution, independent transmission cycles and the divergence of T rangeli lineages associated with sympatric species of Rhodnius. (c) 2009 Elsevier B.V. All rights reserved.

Comparative genomics of the neglected human malaria parasite Plasmodium vivax

The human malaria parasite Plasmodium vivax is responsible for 25 - 40% of the similar to 515 million annual cases of malaria worldwide. Although seldom fatal, the parasite elicits severe and incapacitating clinical symptoms and often causes relapses months after a primary infection has cleared. Despite its importance as a major human pathogen, P. vivax is little studied because it cannot be propagated continuously in the laboratory except in non- human primates. We sequenced the genome of P. vivax to shed light on its distinctive biological features, and as a means to drive development of new drugs and vaccines. Here we describe the synteny and isochore structure of P. vivax chromosomes, and show that the parasite resembles other malaria parasites in gene content and metabolic potential, but possesses novel gene families and potential alternative invasion pathways not recognized previously. Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species.

Quantitative analysis of indexed publications on seventeen model organisms in nine countries, from 1974 to 2006

Developed countries have an even distribution of published papers on the seventeen model organisms. Developing countries have biased preferences for a few model organisms which are associated with endemic human diseases. A variant of the Hirsch-index, that we call the mean (mo)h-index (""model organism h-index""), shows an exponential relationship with the amount of papers published in each country on the selected model organisms. Developing countries cluster together with low mean (mo)h-indexes, even those with high number of publications. The growth curves of publications on the recent model Caenorhabditis elegans in developed countries shows different formats. We also analyzed the growth curves of indexed publications originating from developing countries. Brazil and South Korea were selected for this comparison. The most prevalent model organisms in those countries show different growth curves when compared to a global analysis, reflecting the size and composition of their research communities.

A quasispecies approach to the evolution of sexual replication in unicellular organisms

This study develops a simplified model describing the evolutionary dynamics of a population composed of obligate sexually and asexually reproducing, unicellular organisms. The model assumes that the organisms have diploid genomes consisting of two chromosomes, and that the sexual organisms replicate by first dividing into haploid intermediates, which then combine with other haploids, followed by the normal mitotic division of the resulting diploid into two new daughter cells. We assume that the fitness landscape of the diploids is analogous to the single-fitness-peak approach often used in single-chromosome studies. That is, we assume a master chromosome that becomes defective with just one point mutation. The diploid fitness then depends on whether the genome has zero, one, or two copies of the master chromosome. We also assume that only pairs of haploids with a master chromosome are capable of combining so as to produce sexual diploid cells, and that this process is described by second-order kinetics. We find that, in a range of intermediate values of the replication fidelity, sexually reproducing cells can outcompete asexual ones, provided the initial abundance of sexual cells is above some threshold value. The range of values where sexual reproduction outcompetes asexual reproduction increases with decreasing replication rate and increasing population density. We critically evaluate a common approach, based on a group selection perspective, used to study the competition between populations and show its flaws in addressing the evolution of sex problem.