High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane

P>Modern sugarcane (Saccharum spp.) is the leading sugar crop and a primary energy crop. It has the highest level of `vertical` redundancy (2n = 12x = 120) of all polyploid plants studied to date. It was produced about a century ago through hybridization between two autopolyploid species, namely S. officinarum and S. spontaneum. In order to investigate the genome dynamics in this highly polyploid context, we sequenced and compared seven hom(oe)ologous haplotypes (bacterial artificial chromosome clones). Our analysis revealed a high level of gene retention and colinearity, as well as high gene structure and sequence conservation, with an average sequence divergence of 4% for exons. Remarkably, all of the hom(oe)ologous genes were predicted as being functional (except for one gene fragment) and showed signs of evolving under purifying selection, with the exception of genes within segmental duplications. By contrast, transposable elements displayed a general absence of colinearity among hom(oe)ologous haplotypes and appeared to have undergone dynamic expansion in Saccharum, compared with sorghum, its close relative in the Andropogonea tribe. These results reinforce the general trend emerging from recent studies indicating the diverse and nuanced effect of polyploidy on genome dynamics.

Non-homologous sex chromosomes in two species of the genus Eigenmannia (Teleostei : Gymnotiformes)

The Neotropical genus Eigenmannia is a fish group with unknown species diversity where representatives possess a broad range of chromosomal sex determining systems namely XY/XX, X1X2Y/X1X1X2X2, ZZ/ZW as well as homomorphic sex chromosomes. To test the homology of two heteromorphic XY sex chromosome systems present in two sympatric populations, reciprocal cross-species FISH experiments were performed using probes derived by microdissection of X and Y chromosomes present in analyzed specimens of Eigenmannia virescens and Eigenmannia sp.2, respectively. While X and Y paint probes hybridized to species-specific sex chromosomes, in reciprocal cross-FISH both probes hybridized exclusively to autosomes. The result suggests multiple independent origins of the XY systems in the analyzed populations. Copyright (C) 2008 S. Karger AG, Basel.

Protection against high-dose homologous infection in calves immunized with intestine or membrane extracts from Haemonchus placei

Control of Haemonchus placei, one of the most important cattle nematodes in Brazil, relies on the use of anthelmintics. However, there is a need for integrated control, which includes active immunization. The aim of this work was to assess the protection afforded to calves by immunization with adult H. placei extracts against a high-dose challenge infection, a condition frequently found in the tropics. Holstein calves aged 8-10 months were immunized four times with intestinal extracts (Group D) or with a Triton X-100-soluble fraction of adult H. placei (Group A), challenge-infected with 120,000 infective larvae and sacrificed 40 days later. Immunized animals had higher IgG titers than the controls against tested fractions after the 2nd immunization, peaking after the 4th. Sera from both immunized groups recognized bands of similar apparent mass in both antigenic preparations, some of which were similar in molecular weight to Haemonchus contortus antigens with known protective effect to sheep. Egg counts were 49% and 57% lower in Groups A and D than in controls, respectively. High levels of protection were observed in two of the four calves in Group D, as evidenced by very low worm numbers recovered at necropsy, absence of eggs in the uteri of the recovered females and reduced worm length. Group D animals also showed milder signs of anemia than the other infected animals. Results demonstrate that protection against homologous high-dose challenge can be achieved by immunizing calves with H. placei gut antigens. (C) 2007 Elsevier B.V. All rights reserved.

Healing process in anastomosis of homologous venous grafts preserved in glutaraldehyde implanted aorta of rabbits

Aim. Autologous vein (AV) is sometimes not suitable or present for a vascular restoration. Homologous vein preserved in glutaraldehyde may be an alternative to AV, but little is yet known about this graft and its healing process after implantation in arteries. The purpose of this study was to compare the initial healing process of glutaraldehyde-tanned homologous venous grafts (group 1) with fresh autologous venous grafts (group 2), at 4 or 15 days.Methods. Forty Norfolk rabbits were allocated in 2 groups of 20 animals each. The grafts was interposed in the infra-renal aorta of the rabbit. Anastomotic tensile strength (TS), hydroxyproline (HP) determination, and histology (HA) were performed.Results. TS increased in both groups, from the 4th to 15th day, (p < 0.01) in both proximal (G1: from 364.5 &PLUSMN; 98.3 g to 491.8 &PLUSMN; 107.3 g; G2: from 366.26 &PLUSMN; 85.15 g to 518.46 &PLUSMN; 82.79 g) and distal anastomosis (GI: from 363.53 &PLUSMN; 96.26 g to 507.32 &PLUSMN; 91.01 g; G2: from 352.30 &PLUSMN; 102.41 g to 528.67 &PLUSMN; 48.58 g), with no difference between the groups. HP did not change (p > 0.10) in this same period and was similar in both groups, in the proximal (GI: from 677.99 +/- 153.98 mug/100 mg to 914.92 +/- 459.83 mug/100 mg; G2: from 668.65 +/- 170.28 mug/100 mg to 669.46 +/- 319.80 mug/100 mg) as well as in the distal anastomosis (G1:from 740.07 +/- 213.53 mug/100 mg to 923.52 +/- 270.57 mug/100 mg; G2: from 737.66 +/- 266.76 mug/100 mg to 707.68 +/- 171.25 mug/100 mg). Initial inflammatory and reparative features of the anastomosis were similar in both groups.Conclusion. We can conclude that the healing process of the glutaraldehyde-tanned homologous vein graft was similar to that of the fresh autologous venous graft.

Glutaraldehyde-treated homologous vein graft as a vein substitute: experimental study in rabbits

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

When decisions on homologous structures cause ambiguous taxa relationships: the Neomorphinae (Aves, Cuculidae) example

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evaluation of homologous, heterologous, and affinity conjugates for the serodiagnosis of Toxoplasma gondii and Neospora caninum in maned wolves (Chrysocyon brachyurus)

Use of serological tests in the diagnosis of infectious diseases in wild animals has several limitations, primarily the difficulty of obtaining species-specific reagents. Wild canids, such as maned wolves (Chrysocyon brachyurus), are highly predisposed to infection by Toxoplasma gondii and, to a lesser extent, to Neospora caninum. The aim of the present study was to evaluate homologous, heterologous, and affinity conjugates in enzyme-linked immunosorbent assays (ELISAs) and indirect fluorescent antibody tests (IFATs) for detecting immunoglobulin (Ig) G antibodies against T. gondii and N. caninum in maned wolves. Serum samples were obtained from 59 captive animals in Brazil and tested by ELISA for T. gondii serology and IFAT for N. caninum serology using 3 different enzymatic and fluorescent conjugates: homologous (guinea pig anti-maned wolf IgG-peroxidase and -fluorescein isothiocyanate [FITC]), heterologous (rabbit anti-dog IgG-peroxidase and -FITC), and affinity (protein A-peroxidase and -FITC). Seropositivity to T. gondii was comparable among the homologous (69.5%), heterologous (74.6%), and affinity (71.2%) enzymatic conjugates. A significant positive correlation was found between the antibody levels determined by the 3 enzymatic conjugates. The highest mean antibody levels (ELISA index = 4.5) were observed with the protein A-peroxidase conjugate. The same seropositivity to N. caninum (8.5%) was found with the homologous and heterologous fluorescent conjugates, but protein A-FITC was not able to detect or confirm any positive samples with homologous or heterologous conjugates. Our results demonstrate that homologous, heterologous, and affinity conjugates might be used in ELISA for serological assays of T. gondii in wild canids, whereas for N. caninum infection, only the homologous or heterologous fluorescent conjugates have been shown to be useful. © American Society of Parasitologists 2005.

Quasi-homologous spherically symmetric branes and their symmetry breaking

We revisit the dynamical system-based approach of spherically symmetric vacuum braneworlds, pointing out and studying the existence of a transcritical bifurcation as the dark pressure parameter changes its sign, we analyze some consequences of not discard the brane cosmological constant. For instance, it is noteworthy that the existence of an isothermal state equation between the dark fluid parameters cannot be obtained via the requirement of a quasi-homologous symmetry of the vacuum. © 2013 Springer-Verlag Berlin Heidelberg and Società Italiana di Fisica.

Grafts of porcine small intestinal submucosa seeded with cultured homologous smooth muscle cells for bladder repair in dogs

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Relationship between B-Cell-specific moloney murine leukemia virus integration site 1 (BMI-1) and homologous recombination regulatory genes in invasive ductal breast carcinomas

B-cell-specific Moloney murine leukemia virus integration site 1 (Bmi-1) is a Polycomb group protein that is able to induce telomerase activity, enabling the immortalization of epithelial cells. Immortalized cells are more susceptible to double-strand breaks (DSB), which are subsequently repaired by homologous recombination (HR). BRCA1 is among the HR regulatory genes involved in the response to DNA damage associated with the RAD51 protein, which accumulates in DNA damage foci after signaling H2AX, another important marker of DNA damage. Topoisomerase III beta (topoIII beta) removes HR intermediates before chromosomal segregation, preventing damage to cellular DNA structure. In breast carcinomas positive for BMI-1 the role of proteins involved in HR remains to be investigated. The aim of this study was to evaluate the association between BMI-1 and homologous recombination proteins. Using tissue microarrays containing 239 cases of primary breast tumors, the expression of Bmi-1, BRCA-1, H2AX, Rad51, p53, Ki-67, topoIII beta, estrogen receptors (ER), progesterone receptors (PR), and HER-2 was analyzed by immunohistochemistry. We observed high Bmi-1 expression in 66 cases (27.6%). Immunohistochemical overexpression of BMI-1 was related to ER (p=0.004), PR (p<0.001), Ki-67 (p<0.001), p53 (p=0.003), BRCA1 (p=0.003), H2AX (p=0.024) and topoIII beta (p<0,001). Our results show a relationship between the expression of BMI-1 and HR regulatory genes, suggesting that Bmi-1 overexpression might be an important event in HR regulation. However, further studies are necessary to understand the mechanisms in which Bmi-1 could regulate HR pathways in invasive ductal breast carcinomas.

Repertoire, Genealogy and Genomic Organization of Cruzipain and Homologous Genes in Trypanosoma cruzi, T. cruzi-Like and Other Trypanosome Species

Trypanosoma cruzi, the agent of Chagas disease, is a complex of genetically diverse isolates highly phylogenetically related to T. cruzi-like species, Trypanosoma cruzi marinkellei and Trypanosoma dionisii, all sharing morphology of blood and culture forms and development within cells. However, they differ in hosts, vectors and pathogenicity: T. cruzi is a human pathogen infective to virtually all mammals whilst the other two species are non-pathogenic and bat restricted. Previous studies suggest that variations in expression levels and genetic diversity of cruzipain, the major isoform of cathepsin L-like (CATL) enzymes of T. cruzi, correlate with levels of cellular invasion, differentiation, virulence and pathogenicity of distinct strains. In this study, we compared 80 sequences of genes encoding cruzipain from 25 T. cruzi isolates representative of all discrete typing units (DTUs TcI-TcVI) and the new genotype Tcbat and 10 sequences of homologous genes from other species. The catalytic domain repertoires diverged according to DTUs and trypanosome species. Relatively homogeneous sequences are found within and among isolates of the same DTU except TcV and TcVI, which displayed sequences unique or identical to those of TcII and TcIII, supporting their origin from the hybridization between these two DTUs. In network genealogies, sequences from T. cruzi clustered tightly together and closer to T. c. marinkellei than to T. dionisii and largely differed from homologues of T. rangeli and T. b. brucei. Here, analysis of isolates representative of the overall biological and genetic diversity of T. cruzi and closest T. cruzi-like species evidenced DTU- and species-specific polymorphisms corroborating phylogenetic relationships inferred with other genes. Comparison of both phylogenetically close and distant trypanosomes is valuable to understand host-parasite interactions, virulence and pathogenicity. Our findings corroborate cruzipain as valuable target for drugs, vaccine, diagnostic and genotyping approaches.

Mechanistic study of cell death induction by O 6-methylating agents, focusing on the role of homologous recombination as a molecular target for sensitization of tumor cells to chemotherapeutic alkylating agents

Chemotherapeutic SN1‑methylating agents are important anticancer drugs. They induce several covalent modifications in the DNA, from which O6‑methylguanine (O6MeG) is the main toxic lesion. In this work, different hypotheses that have been proposed to explain the mechanism of O6MeG‑triggered cell death were tested. The results of this work support the abortive processing model, which states that abortive post‑replicative processing of O6MeG‑driven mispairs by the DNA mismatch repair (MMR) machinery results in single‑strand gaps in the DNA that, upon a 2nd round of DNA replication, leads to DNA double‑strand break (DSB) formation, checkpoint activation and cell death. In this work, it was shown that O6MeG induces an accumulation of cells in the 2nd G2/M‑phase after treatment. This was accompanied by an increase in DSB formation in the 2nd S/G2/M‑phase, and paralleled by activation of the checkpoint kinases ATR and CHK1. Apoptosis was activated in the 2nd cell cycle. A portion of cells continue proliferating past the 2nd cell cycle, and triggers apoptosis in the subsequent generations. An extension to the original model is proposed, where the persistence of O6MeG in the DNA causes new abortive MMR processing in the 2nd and subsequent generations, where new DSB are produced triggering cell death. Interestingly, removal of O6MeG beyond the 2nd generation lead to a significant, but not complete, reduction in apoptosis, pointing to the involvement of additional mechanisms as a cause of apoptosis. We therefore propose that an increase in genomic instability resulting from accumulation of mis‑repaired DNA damage plays a role in cell death induction. Given the central role of DSB formation in toxicity triggered by chemotherapeutic SN1‑alkylating agents, it was aimed in the second part of this thesis to determine whether inhibition of DSB repair by homologous recombination (HR) or non‑homologous end joining (NHEJ) is a reasonable strategy for sensitizing glioblastoma cells to these agents. The results of this work show that HR down‑regulation in glioblastoma cells impairs the repair of temozolomide (TMZ)‑induced DSB. HR down‑regulation greatly sensitizes cells to cell death following O6‑methylating (TMZ) or O6‑chlorethylating (nimustine) treatment, but not following ionizing radiation. The RNAi mediated inhibition in DSB repair and chemo‑sensitization was proportional to the knockdown of the HR protein RAD51. Chemo‑sensitization was demonstrated for several HR proteins, in glioma cell lines proficient and mutated in p53. Evidence is provided showing that O6MeG is the primary lesion responsible for the increased sensitivity of glioblastoma cells following TMZ treatment, and that inhibition of the resistance marker MGMT restores the chemo‑sensitization achieved by HR down‑regulation. Data are also provided to show that inhibition of DNA‑PK dependent NHEJ does not significantly sensitized glioblastoma cells to TMZ treatment. Finally, the data also show that PARP inhibition with olaparib additionally sensitized HR down‑regulated glioma cells to TMZ. Collectively, the data show that processing of O6MeG through two rounds of DNA replication is required for DSB formation, checkpoint activation and apoptosis induction, and that O6MeG‑triggered apoptosis is also executed in subsequent generations. Furthermore, the data provide proof of principle evidence that down‑regulation of HR is a reasonable strategy for sensitizing glioma cells to killing by O6‑alkylating chemotherapeutics.