Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa

Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the American continent, and induces diverse disease phenotypes. Previous molecular analyses indicated three distinct groups of X.fastidiosa isolates that were expected to be genetically divergent. Here we report the genome sequence of X. fastidiosa (Temecula strain), isolated from a naturally infected grapevine with Pierce's disease (PD) in a wine-grape-growing region of California. Comparative analyses with a previously sequenced X.fastidiosa strain responsible for citrus variegated chlorosis (CVC) revealed that 98% of the PD X.fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain 9a5c genes. Furthermore, the average amino acid identity of the open reading frames in the strains is 95.7%. Genomic differences are limited to phage-associated chromosomal rearrangements and deletions that also account for the strain-specific genes present in each genome. Genomic islands, one in each genome, were identified, and their presence in other X.fastidiosa strains was analyzed. We conclude that these two organisms have identical metabolic functions and are likely to use a common set of genes in plant colonization and pathogenesis, permitting convergence of functional genomic strategies.

CYTOGENETIC STUDIES ON THE SUBFAMILY HYPOPTOPOMATINAE (PISCES, SILURIFORMES, LORICARIIDAE) .3. ANALYSIS OF 7 SPECIES

Cytogenetic studies carried out on nine species belonging to five genera of the subfamily Hypoptopomatinae showed that this group has a relatively constant diploid number, 2n = 54, with only one species having 2n = 72 chromosomes. Nevertheless, the karyotypic formulae, NOR position and C-band pattern are very different among species and sometimes among local populations, with species having undifferentiated sex chromosomes and species having the XX/XY or the ZZ/ZW mechanisms. The population structure of species belonging to the subfamily Hypoptopomatinae suggests that many chromosome rearrangements have been fixed in the different species and populations due to their geographic isolation and these karyotypic differences may be very important today for species definition.

Chromosome breakpoint distribution in nonmelanoma skin cancers

We have identified chromosome regions that may be sites of genes activated as a result of chromosomal rearrangements observed in 61 of the 86 skin tumors referenced in the literature. The data showed that most of the breakpoints were distributed throughout the genome and some tended to cluster. Highest frequencies of breakpoints were observed in chromosomes with high relative length, except chromosomes 14 and 15 that were more often affected in malignant tumors, despite their size. Our work provides a starting point for more detailed studies that may allow identification of these genes as important keys in the development and progression of skin cancers. (C) Elsevier B.V., 1997.

Cytogenetic study of neoplastic and nonneoplastic cells of the skin

We describe the cytogenetic study of six neoplastic and eight nonneoplastic skin samples from sun-exposed body sites or sites close to tumors. The cytogenetic findings revealed that chromosome rearrangements are common in sun-exposed normal skin, similar to the situation in cutaneous tumors, and suggest that such karyotypic abnormalities might be indicative of the genetic instability caused by specific mutations and resulting from carcinogenic exposure of the tissue.

Cytogenetics of three breeds of river buffalo (Bubalus bubalis L.), with evidence of a fragile site on the X chromosome

The cytogenetic study of 182 river buffalo (Bubalus bubalis L., 2n=50) of Murrah, Mediterranean and Jaffarabadi breeds, from the State of São Paulo, was carried out to characterize their chromosomes and to detect possible chromosomal abnormalities. The karyotypes were indistinguishable with conventional staining as well as with C and replication R banding techniques. In about 44% of the sample (8 males and 72 females), an X marker chromosome due to a fragile site was shown. The frequency of metaphases expressing the fragility site on the X was highly variable, from 2.86 to 41.03%. In females, the fragile site, rarely appeared on both X chromosomes. Most of the metaphases showed only 1 marker chromosome. In R-banded metaphases using 5-bromodeoxyuridine (BrdU) treatment, it corresponded in general to the late replicating X chromosome. No correlation between the X fragile site and altered phenotype was found. Structural and numerical chromosome rearrangements were ruled out in the present sample of buffalo. (C) 1998 by Elsevier B.V.

CYTOGENETIC AND DNA CONTENT IN 6 GENERA OF THE FAMILY CALLICHTHYIDAE (PISCES, SILURIFORMES)

Cytogenetic studies involving conventional Giemsa staining, C-banding analysis and silver staining of NORs were performed on nine species belonging to six genera of the family Callichthyidae. The diploid number ranged from 2n = 44 to 2n = 100, the number of chromosomal pairs with NORs ranged from 1 to 4 and constitutive heterochromatin was mainly distributed in the centromeric and/or pericentromeric position of the chromosomes. The DNA content of erythrocytes from six species studied ranged from 1.18 +/- 0.07 to 2.77 +/- 0.22 pg/nucleus. The extensive variability in karyotypes and in nuclear DNA content detected are in accordance with the initial hypothesis that chromosome rearrangements and polyploidy have played a significant role in the evolutionary history of Callichthyidae.

Helium ion irradiation of polymer films deposited from TMS-Ar plasmas

Polymer films synthesized from plasmas of a tetramethylsilane - Ar mixture were modified by irradiation with 170 keV He ions at fluences ranging from 1 x 10(14) to 1 x 10(16) cm(-2). As revealed by infrared spectroscopy, the ion beam produced intense bond rearrangements, such as the depletion of bonding groups (C-H and Si-H), and induced the formation of new ones, such as O-H and Si-O. From the nanoindentation measurements, a remarkable increase in the surface hardness of the films was observed as the ion fluence was increased. The increases in hardness were accompanied by an increase in the film compaction as shown by using a combination of RBS and film thickness measurements. From both hardness and infrared measurements A was concluded that, under the He ion bombardment, the polymer structure is transformed into a silicon oxycarbide network.

Genetic relationships between Brazilian species of Molossidae and Phyllostomidae (Chiroptera, Mammalia)

A comparative analysis of G-banded karyotypes was performed for seven species of Chiroptera, representing two families (Phyllostomidae and Molossidae). Despite the differences in diploid and fundamental numbers, extensive homologies between six karyotypes were identified: A . planirostris, P. lineatus, S. lilium, G. soricina, P. hastatus (Phyllostomidae) and M. rufus (Molossidae). Robertsonian rearrangements and pericentric inversions account for the differences between the karyotypes of phyllostomid and molossid species. The homologies and rearrangements observed reinforce the monophiletic origin of phyllostomids and the inclusion of species in different subfamilies. In situ hybridization with genomic DNA revealed considerable conservation of the karyotypes, including C. perspicillata, that did not show G-band homologies with the other species analyzed. For the first time, chromosomal evidence is presented of a common origin for Phyllostomidae and Molossidae.

Chromosomal evolution in Gekkonidae. I. Chromosome painting between Gekko and Hemidactylus species reveals phylogenetic relationships within the group

Geckos are a large group of lizards characterized by a rich variety of species, different modes of sex determination and diverse karyotypes. In spite of many unresolved questions on lizards' phylogeny and taxonomy, the karyotypes of most geckos have been studied by conventional cytogenetic methods only. We used flow-sorted chromosome-specific painting probes of Japanese gecko (Gekko japonicus), Mediterranean house gecko (Hemidactylus turcicus) and flat-tailed house gecko (Hemidactylus platyurus) to reveal homologous regions and to study karyotype evolution in seven gecko species (Gekko gecko, G. japonicus, G. ulikovskii, G. vittatus, Hemidactylus frenatus, H. platyurus and H. turcicus). Generally, the karyotypes of geckos were found to be conserved, but we revealed some characteristic rearrangements including both fissions and fusions in Hemidactylus. The karyotype of H. platyurus contained a heteromorphic pair in all female individuals, where one of the homologues had a terminal DAPI-negative and C-positive heterochromatic block that might indicate a putative sex chromosome. Among two male individuals studied, only one carried such a polymorphism, and the second one had none, suggesting a possible ZZ/ZW sex determination in some populations of this species. We found that all Gekko species have retained the putative ancestral karyotype, whilst the fission of the largest ancestral chromosome occurred in the ancestor of modern Hemidactylus species. Three common fissions occurred in the ancestor of Mediterranean house and flat-tailed house geckos, suggesting their sister group relationships. PCR-assisted mapping on flow-sorted chromosome libraries with conserved DMRT1 gene primers in G. japonicus indicates the localization of DMRT1 gene on chromosome 6.

Cytogenetic studies of three species of Glandulocaudinae (Pisces, Characiformes, Characidae)

Cytogenetic studies of three species of the subfamily Glandulocaudinae showed that Mimagoniates microlepis presents 2n = 52 chromosomes (6M + 20SM + 18ST + 8A), Mimagoniates lateralis presents 2n = 52 chromosomes (6M + 20SM + 16ST + 10A) and Glandalocauda melanogenys presents 2n = 52 chromosomes (4M + 12SM + 22ST + 14A). The number of NOR-bearing chromosome pairs ranged from two to four. Differences in number and position of NORs at the species and population levels were detected, suggesting that several chromosome rearrangements occurred in the evolutionary process of this group. Some aspects related to the chromosome evolution of the Glandulocaudinae are discussed.

Karyotype studies of some species of Dalechampia plum. (Euphorbiaceae)

Karyotype studies in eight species of Dalechampia, including 10 natural populations, revealed chromosome numbers (2n = 36, 46, 138 and 198) differing from two numbers cited in the literature (2n = 44 and 72). The basic number x = 6, as in the genus Acalypha, may be considered ancestral in Dalechampia. Analysis of Chromosome number, haploid chromosome length and karyotype symmetry suggests that the major chromosome mechanism acting in karyotype evolution of Dalechampia is polyploidy, but differences in chromosome morphology may be caused by chromosome rearrangements.

Genetic relatedness of Plasmodium falciparum isolates and the origin of allelic diversity at the merozoite surface protein-1 (MSP-1) locus in Brazil and Vietnam

Background: Despite the extensive polymorphism at the merozoite surface protein-1 (MSP-1) locus of Plasmodium falciparum, that encodes a major repetitive malaria vaccine candidate antigen, identical and nearly identical alleles frequently occur in sympatric parasites. Here we used microsatellite haplotyping to estimate the genetic distance between isolates carrying identical and nearly identical MSP-1 alleles. Methods: We analyzed 28 isolates from hypoendemic areas in north-western Brazil, collected between 1985 and 1998, and 23 isolates obtained in mesoendemic southern Vietnam in 1996. MSP-1 alleles were characterized by combining PCR typing with allele-specific primers and partial DNA sequencing. The following single-copy microsatellite markers were typed: Polyα, TA42 (only for Brazilian samples), TA81, TA1, TA87, TA109 (only for Brazilian samples), 2490, ARAII, PfG377, PfPK2, and TA60. Results: The low pair-wise average genetic distance between microsatellite haplotypes of isolates sharing identical MSP-1 alleles indicates that epidemic propagation of discrete parasite clones originated most identical MSP-1 alleles in parasite populations from Brazil and Vietnam. At least one epidemic clone propagating in Brazil remained relatively unchanged over more than one decade. Moreover, we found no evidence that rearrangements of MSP-1 repeats, putatively created by mitotic recombination events, generated new alleles within clonal lineages of parasites in either country. Conclusion: Identical MSP-1 alleles originated from co-ancestry in both populations, whereas nearly identical MSP-1 alleles have probably appeared independently in unrelated parasite lineages.

Comparative cytogenetic studies in species of the subfamily Callichthyinae (Teleostei: Siluriformes: Callichthyidae)

In the present study, the karyotype of three species (nine populations) of the Callichthyinae subfamily were investigated with the objective of better understanding the pattern of relationship among the genera that compose the subfamily. Among the four populations of Callichthys callichthys studied, two showed 2n=56 chromosomes and two 2n=58 chromosomes. Up to eight additional microchromosomes were observed in the sample from Marilia. The three populations of Hoplosternum littorale displayed the same number of chromosomes, 2n=60, and karyotypic constitution, 6M+2SM+52A. The two populations of Megalechis personata showed 2n=62 chromosomes and similar karyotypic formulae, 8M+54A and 6M+2SM+54A. Terminal Ag-NORs were found in one chromosome pair of C. callichthys, H. littorale, and M. personata from Itiquira, and in two pairs in M. personata from Rio Branco. The populations of C. callichthys showed C-band positive segments in centromeric and pericentromeric position and the populations of H. littorale and M. personata exhibited C-band positive segments in centromeric and/or interstitial position. Contrarily to the extensive chromosome rearrangements verified in the Corydoradinae subfamily, in the Callichthyinae subfamily a small number of changes seems to have occurred in its karyotypic evolution.

Velocardiofacial syndrome with a rare t(2;22)

Rearrangements involving chromosomes 2 and 22 were described not only as acquired abnormalities in a variety of human neoplasias but also in the constitutional karyotype suggesting the existence of a greater fragility in some specific regions in these chromosomes. Patients with DiGeorge and Velocardiofacial syndromes have a deletion on 22q11 leading to haploinsufficiency for one or more gene(s). We report a patient with velocardiofacial syndrome in which cytogenetic and fluorescence in situ hybridization analysis showed a rare t(2;22) and deletion in the 22q11 region. © 2007 Lippincott Williams & Wilkins, Inc.

The influence of seasonalness on the structural characteristics of aquatic humic substances extracted from Negro River (Amazon state) waters: Interactions with Hg(II)

In this work, humic substances were extracted from water samples collected monthly from the Negro River basin in the Amazon state (Brazil) to study their properties in the Amazonian environment and interactions with the mercury ion considering the influence of seasonalness in this formation. The C/H, C/N and C/O atomic ratio parameters, functional groups, concentration of semiquinone-type free radicals, pH, pluviometric and fluviometric indices, and mercury concentrations were interpreted using hierarchical cluster analysis (HCA) and principal component analysis (PCA). The statistical analyses showed that when the pluviometric index was greater and the fluviometric index was smaller, the degree of humification of aquatic substances was greater. The following decreasing order of the degree of humification of the AHS collected monthly was established: Nov/02 to Feb/03 > Mar/02 to May/02 > Jun/02 to Oct/02. The greatest concentrations of mercury were detected in more humidified samples. These results suggest that due to inter and/or intra-molecular rearrangements, the degree of humification of aquatic humic substances is related to its affinity for Hg(II) ions. ©2007 Sociedade Brasileira de Química.