Browsing by Issue Date, starting with "2005"
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- The making of gametes in higher plantsPublication . Boavida, L.; Becker, J.D.; Feijó, J.A.Higher plants have evolved to be one of the predominant life forms on this planet. A great deal of this evolutionary success relies in a very short gametophytic phase which underlies the sexual reproduction cycle. Sexual plant reproduction takes place in special organs of the flower. In most species the processes of gametogenesis, pollination, syngamy and embryogenesis are sequentially coordinated to give rise to a functional seed in a matter of few weeks. Any of these processes is so intricately complex and precisely regulated that it becomes no wonder that each involves more specific genes and cellular processes than any other function in the plant life cycle. While variability generation - the evolutionary output of the sexual cycle - is the same as in any other Kingdom, plants do it using a completely original set of mechanisms, many of which are not yet comprehended. In this paper, we cover the fundamental features of male and female gametogenesis. While the physiological and cellular bases of these processes have been continuously described since the early nineteen century, recent usage of Arabidopsis and other species as central models has brought about a great deal of specific information regarding their genetic regulation. Transcriptomics has recently enlarged the repertoire and pollen became the first gametophyte to have a fully described transcriptome in plants. We thus place special emphasis on the way this newly accumulated genetic and transcriptional information impacts our current understanding of the mechanisms of gametogenesis.
- The multigenic structure of the MHC locus contributes to positive selection efficiency: A role for MHC class II gene-genespecificPublication . Monteiro, Miguel Caetano; Couceiro, Sofia; Penha-Gonçalves, CarlosThe study of T cell positive selection in the thymus has long been focused on the specificity of the MHC-TCR interactions, making use of genetically manipulated mice that display TCR specificities or selecting peptides of limited diversity. However, little is known on the role of the MHC molecules irrespective of the peptide specificity and the implications of MHC multigenic structure in thymic positive selection have not been addressed. Here, we investigated the effect of MHC class II genetic configuration on the positive selection efficiency of naturally generated pre-selection repertoires in the mouse thymus. Analysis of positively selected thymocyte populations in MHC-congenic and -transgenic mice revealed that expression of I-E molecule in the thymic cortex increases positive selection efficiency of CD4 cells by approximately 50%.We show that increments in positive selection attributable to either the I-A and I-E genes are not due to increased MHC class II expression in the thymic cortex and are not affected by the number of MHC alleles. Collectively, our findings imply that MHC class II generestricted TCR specificities significantly contribute to positive selection efficiency, introducing the notion that multigenic structure of the MHC locus serves to increase selection of non-overlapping TCR repertoires.
- Gametophyte interaction and sexual reproduction: how plants make a zygotePublication . Boavida, L.C.; Vieira, A.M.; Becker, J.D.; Feijó, J.A.The evolutionary success of higher plants relies on a very short gametophytic phase, which underlies the sexual reproduction cycle. Sexual plant reproduction takes place in special organs of the flower: pollen, the male gametophyte, is released from the anthers and then adheres, grows and interacts along various tissues of the female organs, collectively known as the pistil. Finally, it fertilizes the female gametophyte, the embryo sac. Pollen is released as bi or tricellular, highly de-hydrated and presumably containing all the biochemical components and transcripts to germinate. Upon hydration on the female tissues, it develops a cytoplasmic extension, the pollen tube, which is one of the fastest growing cells in nature. Pollen is completely "ready-to-go", but despite this seemingly simple reaction, very complex interactions take place with the female tissues. In higher animals, genetic mechanisms for sex determination establish striking developmental differences between males and females. In contrast, most higher plant species develop both male and female structures within the same flower, allowing self-fertilization. Outcrossing is ensured by self-incompatibility mechanisms, which evolved under precise genetic control, controlling self-recognition and cell-to-cell interaction. Equally important is pollen selection along the female tissues, where interactions between different cell types with inherent signalling properties correspond to check-points to ensure fertilization. Last but not least, pollen-pistil interaction occurs in a way that enables the correct targeting of the pollen tubes to the receptive ovules. In this review, we cover the basic mechanisms underlying sexual plant reproduction, from the structural and cellular determinants, to the most recent genetic advances.
- Cyclooxygenase-2 (COX-2) expression by in vitro produced bovine embryos. Preliminary results = Expressão da ciclo-oxigenase-2 (COX-2) em embriões bovinos produzidos in vitro. Resultados preliminaresPublication . Marques, C.C.; Horta, A.E.; Vasques, M.I.; Baptista, M.C.; Becker, J.D.; Pimenta, J.; Pereira, R.M.Expression of the two isoforms of cyclooxygenase enzyme, cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2), by in vitro produced bovine embryos was examined. Cumulus-oocyte complexes were recovered from ovaries of slaughtered animals and subsequently in vitro matured and in vitro fertilized. Presumptive zygotes were cultured in serum containing medium (TCM 199+10% bovine superovulated oestrus serum) on a granulosa cell monolayer for 12 days.
- Increased polyclonal immunoglobulin reactivity toward human and bacterial proteins is associated with clinical protection in human Plasmodium infectionPublication . Fesel, C.; Goulart, L.F.; Neto, A.S.; Coelho, A.; Fontes, C.J.F.; Braga, E.M.; Vaz, N.M.The observed difference in polyclonal antibody production seems related to intrinsic activation states of infected individuals, rather than to parasite-antigen specific immune responses. However, it appears influenced by preceding stimuli. This supports the idea that acquired clinical immunity may not exclusively depend on antigen-specific responses, but also on the individual polyclonal reaction.
- Nonequilibrium model for estimating parameters of deleterious mutationsPublication . Gordo, I.; Dionisio, F.Deleterious mutations are of extreme evolutionary importance because, even though they are eliminated by natural selection, their continuous pressure creates a pool of variability in natural populations. They are of potential relevance for the existence of several features in evolution, such as sexual reproduction, and pose a risk to small asexual populations. Despite their extreme importance, the deleterious mutation rate and the effects of each mutation on fitness are poorly known quantities. Here we analyze a simple model that can be applied to simple experiments, in microorganisms, aiming at the quantification of these values.
- Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control and gene expression regulationPublication . Pina, C.; Pinto, F.; Feijó, J.A.; Becker, J.D.Upon germination, pollen forms a tube that elongates dramatically through female tissues to reach and fertilize ovules. While essential for the life cycle of higher plants, the genetic basis underlying most of the process is not well understood. We previously used a combination of flow cytometry sorting of viable hydrated pollen grains and GeneChip array analysis of onethird of the Arabidopsis (Arabidopsis thaliana) genome to define a first overview of the pollen transcriptome. We now extend that study to approximately 80% of the genome of Arabidopsis by using Affymetrix Arabidopsis ATH1 arrays and perform comparative analysis of gene family and gene ontology representation in the transcriptome of pollen and vegetative tissues. Pollen grains have a smaller and overall unique transcriptome (6,587 genes expressed) with greater proportions of selectively expressed (11%) and enriched (26%) genes than any vegetative tissue. Relative gene ontology category representations in pollen and vegetative tissues reveal a functional skew of the pollen transcriptome toward signaling, vesicle transport, and the cytoskeleton, suggestive of a commitment to germination and tube growth. Cell cycle analysis reveals an accumulation of G2/Massociated factors that may play a role in the first mitotic division of the zygote. Despite the relative underrepresentation of transcription-associated transcripts, nonclassical MADS box genes emerge as a class with putative unique roles in pollen. The singularity of gene expression control in mature pollen grains is further highlighted by the apparent absence of small RNA pathway components.
- The evolution of a conjugative plasmid and its ability to increase bacterial fitness.Publication . Dionisio, F.; Conceição, I.C.; Marques, A.C.R.; Fernandes, L.; Gordo, I.Conjugative plasmids are extra-chromosomal DNA elements that are capable of horizontal transmission and are found in many natural isolated bacteria. Although plasmids may carry beneficial genes to their bacterial host, they may also cause a fitness cost. In this work, we studied the evolution of the R1 plasmid and we found that, in spite of the R1 plasmid conferring an initial cost to its host, after 420 generations the cost disappeared in all five independent evolution experiments. In fact, in two of these five experiments evolved conjugative plasmids actually conferred a fitness advantage to their hosts. Furthermore, the relative fitness of the ancestral clone bearing one of the evolved plasmids is significantly higher than both the plasmid-free ancestral cells and the evolved cells carrying the evolved plasmid. Given that the R1 plasmid may spread among different species of enterobacteria, we wondered what the effect of the evolved plasmid would be inside Salmonella enterica cells. We found that the evolved plasmid is also able to dramatically increase the relative fitness of these cells. Our results suggest that even if general usage of antibiotics is halted, conjugative plasmids that have been selected with antibiotics in previous years can still persist among bacterial populations or even invade new strains.
- Scaling, genetic drift and clonal interference in the extinction pattern of asexual populationsPublication . Rosas, A.; Gordo, I.; Campos, P.R.A.We investigate the dynamics of loss of favorable mutations in an asexual haploid population. In the current work, we consider homogeneous as well as spatially structured population models. We focus our analysis on statistical measurements of the probability distribution of the maximum population size N(sb) achieved by those mutations that have not reached fixation. Our results show a crossover behavior which demonstrates the occurrence of two evolutionary regimes. In the first regime, which takes place for small N(sb) , the probability distribution is described by a power law with characteristic exponent theta(d) =1.8 +/- 0.01. This power law is not influenced by the rate of beneficial mutations. The second regime, which occurs for intermediate to large values of N(sb), has a characteristic exponent theta(c) which increases as the rate of beneficial mutations grows. These results establish where genetic drift and clonal interference become the main underlying mechanism in the extinction of advantageous mutations.
- The reinfection thresholdPublication . Gomes, M. G. M.; White, L. J.; Medley, G. F.Thresholds in transmission are responsible for critical changes in infectious disease epidemiology. The epidemic threshold indicates whether infection invades a totally susceptible population. The reinfection threshold indicates whether self-sustained transmission occurs in a population that has developed a degree of partial immunity to the pathogen (by previous infection or vaccination). In models that combine susceptible and partially immune individuals, the reinfection threshold is technically not a bifurcation of equilibria as correctly pointed out by Breban and Blower. However, we show that a branch of equilibria to a reinfection submodel bifurcates from the disease-free equilibrium as transmission crosses this threshold. Consequently, the full model indicates that levels of infection increase by two orders of magnitude and the effect of mass vaccination becomes negligible as transmission increases across the reinfection threshold. (c) 2005 Elsevier Ltd. All rights reserved