A specific group of genes respond to cold dehydration stress in cut Alstroemeria flowers whereas ambient dehydration stress accelerates developmental senescence expression patterns

Petal development and senescence entails a normally irreversible process. It starts with petal expansion and pigment production, and ends with nutrient remobilization and ultimately cell death. In many species this is accompanied by petal abscission. Post-harvest stress is an important factor in limiting petal longevity in cut flowers and accelerates some of the processes of senescence such as petal wilting and abscission. However, some of the effects of moderate stress in young flowers are reversible with appropriate treatments. Transcriptomic studies have shown that distinct gene sets are expressed during petal development and senescence. Despite this, the overlap in gene expression between developmental and stress-induced senescence in petals has not been fully investigated in any species. Here a custom-made cDNA microarray from Alstroemeria petals was used to investigate the overlap in gene expression between developmental changes (bud to first sign of senescence) and typical post-harvest stress treatments. Young flowers were stressed by cold or ambient temperatures without water followed by a recovery and rehydration period. Stressed flowers were still at the bud stage after stress treatments. Microarray analysis showed that ambient dehydration stress accelerates many of the changes in gene expression patterns that would normally occur during developmental senescence. However, a higher proportion of gene expression changes in response to cold stress were specific to this stimulus and not senescence related. The expression of 21 transcription factors was characterized, showing that overlapping sets of regulatory genes are activated during developmental senescence and by different stresses.

Análise da variabilidade imunológica e da expressão dos genes FREPs entre as espécies Biomphalaria glabrata e B. straminea com diferentes perfis de suscetibilidade ao parasito Schistosoma mansoni

Algumas espécies do gênero Biomphalaria se apresentam como potenciais hospedeiras ao parasito Schistosoma mansoni, estando a suscetibilidade a este parasito, neste gênero, ligada ao sistema interno de defesa de cada espécie de Biomphalaria. Um dos componentes importantes no sistema imune de invertebrados é a enzima fenoloxidase, que ainda apresenta muitos aspectos desconhecidos no sistema de defesa do gênero Biomphalaria. Foi relatado também que os genes de proteínas relacionadas ao fibrinogênio (FREPs) possuem importância na resposta imune de Biomphalaria glabrata, entre esses, as subfamílias dos FREPs 3 e 4 são diferencialmente expressas em linhagens susceptíveis e resistentes frente a infecção com trematódeos. No entanto os trabalhos existentes em sua maioria estudam a espécie Biomphalaria glabrata, excluindo a espécie Biomphalaria straminea, amplamente distribuída no Brasil e principal responsável pela disseminação da esquistossomose. Tendo em vista a falta de conhecimento sobre a resposta imune destes moluscos hospedeiros, principalmente em relação à expressão de genes imune relevantes e ao tipo de resposta, o presente trabalho se propôs a estudar a variação do número de hemócitos, da produção de fenoloxidase e da expressão dos genes dos FREP 3 e FREP 4 envolvidos com a ligação a antígenos de trematódeos, nas espécies Biomphalaria glabrata, Biomphalaria straminea pós-infecção com S. mansoni, bem como em caramujos pré-expostos a antígenos de S. mansoni. Para isso, os caramujos de cada espécie foram divididos em 2 grupos: pré-expostos e não expostos a antígenos de S. mansoni. Esses grupos foram divididos em sadios e infectados com a cepa LE de S. mansoni. Em B. glabrata não houve alteração no número de hemócitos, porém B. straminea mostrou uma queda após duas horas de infecção. A atividade da fenoloxidase variou após a sensibilização na espécie menos susceptível (B. straminea) e não variou em B. glabrata, também foi identificado que os hemócitos produtores da fenoloxidase são os granulócitos e hialinócitos. Quanto à expressão dos genes, o FREP 3 e 4 apresentaram níveis basais de expressão aumentados após a sensibilização, com perfil de expressão diferente entre as espécies estudadas. Esses resultados confirmam que a resposta imune varia em diversos aspectos entre as espécies do gênero Biomphalaria, e que nas espécies estudadas a enzima fenoloxidase não parece ter o mesmo papel que no sistema de defesa de insetos, diferindo apenas após a sensibilização, que tem influência na expressão dos genes imuno relevantes do FREPs

Estudo da influência dos alelos do HLA classe I e II e do polimorfismo dos genes de citocinas na infecção pelo HTLV-1

INTRODUÇÃO: O vírus linfotrópico para células T humanas (HTLV-1) é o principal agente causador da Paraparesia Espástica Tropical / Mielopatia associada ao HTLV-1 (PET/MAH) e da Leucemia da célula T do Adulto (LTA). A maioria dos indivíduos infectados permanece assintomática, somente 2 a 5% irão desenvolver uma das duas doenças. Fatores da interação HTLV-1/ hospedeiro estão envolvidos no risco de desenvolver doença. A lesão neurológica na PET/MAH parece ser consequência de uma reação inflamatória, desencadeada pelo reconhecimento de células infectadas por linfócitos T citotóxicos, com consequente liberação de citocinas e lesão medular. OBJETIVO: Identificar marcadores genéticos, que possam ajudar no prognóstico e tratamento dos pacientes portadores do HTLV-1. MÉTODOS: Nas amostras de 117 portadores do HTLV-1 assintomáticos e 171 pacientes com acometimento neurológico em acompanhamento na cidade do Rio de Janeiro, foram realizadas as tipificações dos genes do HLA Classe I e II, dos polimorfismos dos genes das citocinas -308TNF-\03B1,-174IL-6, +874IFN-\03B3, códon 10 e 25TGF-\03B21 e -1082 - 819-592IL-10, e a quantificação da carga proviral. Os dados foram organizados em um banco de dados no programa SPSS. As frequências alélicas e genotípicas foram obtidas por contagem direta. O equilíbrio de Hardy-Weinberg foi avaliado para os polimorfismos das citocinas no sitio http://bioinfo.iconcologia.net/ubbweb/SNPStats_web, em relação ao HLA foram utilizadas as ferramentas disponíveis no sítio \201CLos Alamos HIV database tools\201D. As comparações entre os grupos foram realizadas através de tabelas de contingência 2x2 (quiquadrado, exato de Fisher e odds ratios), valores de p\22640,05 foram considerados significantes RESULTADOS E CONCLUSÕES: O alelo A*02 não influencia a condição clínica nem os níveis da carga proviral. Os alelos A*29 e B*44 foram mais frequentes entre os indivíduos assintomáticos e a sua presença influenciou os níveis da carga proviral sugerindo proteção ao desenvolvimento de doença neurológica. O alelo A*68 foi mais frequente entre os pacientes com doença neurológica, porém sua presença não influenciou nos níveis da carga proviral. O alelo C*04 foi mais frequente entre os portadores assintomáticos e não influenciou os níveis de carga proviral, já o alelo DRB1*03 predominou entre os pacientes com doença neurológica e a sua presença entre os indivíduos assintomáticos acarretou níveis mais elevados de carga proviral, sugerindo ser um possível fator de risco para o desenvolvimento de doença neurológica. Na análise do polimorfismo genético das citocinas, o polimorfismo de IL-10, com perfil fenotípico de baixo produtor da citocina foi mais frequente no grupo dos assintomáticos, enquanto que o fenótipo de produtor intermediário predominou entre os sintomáticos. O perfil fenotípico da população estudada foi caracterizado como: baixo produtor da citocina -308TNF-\03B1, intermediário a alto produtor para códon 10 e códon 25 TGF-\03B2, baixo a intermediário produtor para -1082,-819,- 592 IL-10, alto produtor para -174 IL-6 e baixo a intermediário produtor para +874IFN-\03B3

Effect of wheat dwarfing genes on nitrogen-use efficiency

Near isogenic lines (NILs) varying for alleles for reduced height (Rht) and photoperiod insensitivity (Ppd-D1a) in a cvar Mercia background (rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht8c+Ppd-D1a, Rht-D1c, Rht12) were compared at a field site in Berkshire, UK, but within different systems (‘organic’, O, in 2005/06, 2006/07 and 2007/08 growing seasons v. ‘conventional’, C, in 2005/06, 2006/07, 2007/08 and 2008/09). In 2007 and 2008, further NILs (rht (tall), Rht-B1b, Rht-D1b, Rht-B1c, Rht-B1b+Rht-D1b, Rht-D1b+Rht-B1c) in both Maris Huntsman and Maris Widgeon backgrounds were added. The contrasting systems allowed NILs to be tested in diverse rotational and agronomic, but commercially relevant, contexts, particularly with regard to the assumed temporal distribution of nitrogen availability, and competition from weeds. For grain, nitrogen-use efficiency (NUE; grain dry matter (DM) yield/available N; where available N=fertilizer N+soil mineral N), recovery of N in the grain (grain N yield/available N), N utilization efficiency to produce grain (NUtEg; grain DM yield/above-ground crop N yield), N harvest index (grain N yield/above-ground crop N yield) and dry matter harvest index (DMHI; grain DM yield/above-ground crop DM yield) all peaked at final crop heights of 800–950 mm. Maximum NUE occurred at greater crop heights in the organic system than in the conventional system, such that even adding just a semi-dwarfing allele (Rht-D1b) to the shortest background, Mercia, reduced NUE in the organic system. The mechanism of dwarfing (gibberellin sensitive or insensitive) made little difference to the relationship between NUE and its components with crop height. For above-ground biomass: dwarfing alleles had a greater effect on DM accumulation compared with N accumulation such that all dwarfing alleles could reduce nitrogen utilization efficiency (NUtE; crop DM yield/crop N yield). This was particularly evident at anthesis in the conventional system when there was no significant penalty for severe dwarfism for N accumulation, despite a 3-tonne (t)/ha reduction in biomass compared to the tallest lines. Differences between genotypes for recovery of N in the grain were thus mostly a function of net N uptake after anthesis rather than of remobilized N. This effect was compounded as dwarfing, except when coupled with Ppd-D1a, was associated with delayed anthesis. In the organic experiments there was greater reliance on N accumulated before anthesis, and genotype effects on NUE were confounded with effects on N accumulated by weeds, which was negatively associated with crop height. Optimum height for maximizing wheat NUE and its components, as manipulated by Rht alleles, thus depend on growing system, and crop utilization (i.e. biomass or grain production).

Comparisons of host mitochondrial, nuclear and endosymbiont bacterial genes reveal cryptic fig wasp species and the effects of Wolbachia on host mtDNA evolution and diversity

Background Figs and fig-pollinating wasp species usually display a highly specific one-to-one association. However, more and more studies have revealed that the "one-to-one" rule has been broken. Co-pollinators have been reported, but we do not yet know how they evolve. They may evolve from insect speciation induced or facilitated by Wolbachia which can manipulate host reproduction and induce reproductive isolation. In addition, Wolbachia can affect host mitochondrial DNA evolution, because of the linkage between Wolbachia and associated mitochondrial haplotypes, and thus confound host phylogeny based on mtDNA. Previous research has shown that fig wasps have the highest incidence of Wolbachia infection in all insect taxa, and Wolbachia may have great influence on fig wasp biology. Therefore, we look forward to understanding the influence of Wolbachia on mitochondrial DNA evolution and speciation in fig wasps. Results We surveyed 76 pollinator wasp specimens from nine Ficus microcarpa trees each growing at a different location in Hainan and Fujian Provinces, China. We found that all wasps were morphologically identified as Eupristina verticillata, but diverged into three clades with 4.22-5.28% mtDNA divergence and 2.29-20.72% nuclear gene divergence. We also found very strong concordance between E. verticillata clades and Wolbachia infection status, and the predicted effects of Wolbachia on both mtDNA diversity and evolution by decreasing mitochondrial haplotypes. Conclusions Our study reveals that the pollinating wasp E. verticillata on F. microcarpa has diverged into three cryptic species, and Wolbachia may have a role in this divergence. The results also indicate that Wolbachia strains infecting E. verticillata have likely resulted in selective sweeps on host mitochondrial DNA.

Amphioxus type I keratin cDNA and the evolution of intermediate filament genes

We report the cloning of an intermediate filament (IF) cDNA from the cephalochordate amphioxus that encodes a protein assignable to the type I keratin group. This is the first type I keratin reported from an invertebrate. Molecular phylogenetic analyses reveal that amphioxus also possesses a type II keratin, and that the genes encoding short-rod IF proteins underwent different patterns of duplication in vertebrates and their closest relatives, the cephalochordates. Extensive IF gene duplication and divergence may have facilitated the origin of new specialised cell types in vertebrates.

Complex history of a chromosomal paralogy region: insights from amphioxus aromatic amino acid hydroxylase genes and insulin-related genes

Aromatic amino acid hydroxylase (AAAH) genes and insulin-like genes form part of an extensive paralogy region shared by human chromosomes 11 and 12, thought to have arisen by tetraploidy in early vertebrate evolution. Cloning of a complementary DNA (cDNA) for an amphioxus (Branchiostoma floridae) hydroxylase gene (AmphiPAH) allowed us to investigate the ancestry of the human chromosome 11/12 paralogy region. Molecular phylogenetic evidence reveals that AmphiPAH is orthologous to vertebrate phenylalanine (PAH) genes; the implication is that all three vertebrate AAAH genes arose early in metazoan evolution, predating vertebrates. In contrast, our phylogenetic analysis of amphioxus and vertebrate insulin-related gene sequences is consistent with duplication of these genes during early chordate ancestry. The conclusion is that two tightly linked gene families on human chromosomes 11 and 12 were not duplicated coincidentally. We rationalize this paradox by invoking gene loss in the AAAH gene family and conclude that paralogous genes shared by paralogous chromosomes need not have identical evolutionary histories.

Clustered Fox genes in lophotrochozoans and the evolution of the bilaterian Fox gene cluster

FoxC, FoxF, FoxL1 and FoxQ1 genes have been shown to be clustered in some animal genomes, with mesendodermal expression hypothesised as a selective force maintaining cluster integrity. Hypotheses are, however, constrained by a lack of data from the Lophotrochozoa. Here we characterise members of the FoxC, FoxF, FoxL1 and FoxQ1 families from the annelid Capitella teleta and the molluscs Lottia gigantea and Patella vulgata. We cloned FoxC, FoxF, FoxL1 and FoxQ1 genes from C. teleta, and FoxC, FoxF and FoxL1 genes from P. vulgata, and established their expression during development. We also examined their genomic organisation in C. teleta and L. gigantea, and investigated local syntenic relationships. Our results show mesodermal and anterior gut expression is a common feature of these genes in lophotrochozoans. In L. gigantea FoxC, FoxF and FoxL1 are closely linked, while in C. teleta Ct-foxC and Ct-foxL1 are closely linked, with Ct-foxF and Ct-foxQ1 on different scaffolds. Adjacent to these genes there is limited evidence of local synteny. This demonstrates conservation of genomic organisation and expression of these genes can be traced in all three bilaterian Superphyla. These data are evaluated against competing theories for the long-term maintenance of gene clusters.

Evolutionary genomics of the Fox genes: origin of gene families and the ancestry of gene clusters

Over the past decade genomic approaches have begun to revolutionise the study of animal diversity. In particular, genome sequencing programmes have spread beyond the traditional model species to encompass an increasing diversity of animals from many different phyla, as well as unicellular eukaryotes that are closely related to the animals. Whole genome sequences allow researchers to establish, with reasonable confidence, the full complement of any particular family of genes in a genome. Comparison of gene complements from appropriate genomes can reveal the evolutionary history of gene families, indicating when both gene diversification and gene loss have occurred. More than that, however, assembled genomes allow the genomic environment in which individual genes are found to be analysed and compared between species. This can reveal how gene diversification occurred. Here, we focus on the Fox genes, drawing from multiple animal genomes to develop an evolutionary framework explaining the timing and mechanism of origin of the diversity of animal Fox genes. Ancient linkages between genes are a prominent feature of the Fox genes, depicting a history of gene clusters, some of which may be relevant to understanding Fox gene function.

Gene duplication and an accelerated evolutionary rate in 11S globulin genes are associated with higher protein synthesis in dicots as compared to monocots

Background: Seed storage proteins are a major source of dietary protein, and the content of such proteins determines both the quantity and quality of crop yield. Significantly, examination of the protein content in the seeds of crop plants shows a distinct difference between monocots and dicots. Thus, it is expected that there are different evolutionary patterns in the genes underlying protein synthesis in the seeds of these two groups of plants. Results: Gene duplication, evolutionary rate and positive selection of a major gene family of seed storage proteins (the 11S globulin genes), were compared in dicots and monocots. The results, obtained from five species in each group, show more gene duplications, a higher evolutionary rate and positive selections of this gene family in dicots, which are rich in 11S globulins, but not in the monocots. Conclusion: Our findings provide evidence to support the suggestion that gene duplication and an accelerated evolutionary rate may be associated with higher protein synthesis in dicots as compared to monocots.

Divergent evolutionary pattern of starch biosynthetic pathway genes in grasses and dicots

Starch is the most widespread and abundant storage carbohydrate in crops and its production is critical to both crop yield and quality. As regards the starch content in the seeds of crop plants, there are distinct difference between grasses (Poaceae) and dicots. However, few studies have described the evolutionary pattern of genes in the starch biosynthetic pathway in these two groups of plants. In this study, therefore, an attempt was made to compare the evolutionary rate, gene duplication and selective pattern of the key genes involved in this pathway between the two groups, using five grasses and five dicots as materials. The results showed (i) distinct differences in patterns of gene duplication and loss between grasses and dicots; duplication in grasses mainly occurred prior to the divergence of grasses, whereas duplication mostly occurred in individual species within the dicots; there is less gene loss in grasses than in dicots; (ii) a considerably higher evolutionary rate in grasses than in dicots in most gene families analyzed; (iii) evidence of a different selective pattern between grasses and dicots; positive selection may have occurred asymmetrically in grasses in some gene families, e.g. AGPase small subunit. Therefore, we deduced that gene duplication contributes to, and a higher evolutionary rate is associated with, the higher starch content in grasses. In addition, two novel aspects of the evolution of the starch biosynthetic pathway were observed.

Identifying antimicrobial resistance genes of human clinical relevance within Salmonella isolated from food animals in Great Britain

To investigate the occurrence of antimicrobial resistance genes of human clinical relevance in Salmonella isolated from livestock in Great Britain. Two hundred and twenty-five Salmonella enterica isolates were characterized using an antimicrobial resistance gene chip and disc diffusion assays. Plasmid profiling, conjugation experiments and identification of Salmonella genomic island 1 (SGI1) were performed for selected isolates. Approximately 43% of Salmonella harboured single or multiple antimicrobial resistance genes with pig isolates showing the highest numbers where 96% of Salmonella Typhimurium harboured one or more resistance genes. Isolates harbouring multiple resistances divided into three groups. Group 1 isolates harboured ampicillin/streptomycin/sulphonamide/tetracycline resistance and similar phenotypes. This group contained isolates from pigs, cattle and poultry that were from several serovars including Typhimurium, 4,[5],12:i:-, Derby, Ohio and Indiana. All Group 2 isolates were from pigs and were Salmonella Typhimurium. They contained a non-sul-type class 1 integron and up to 13 transferrable resistances. All Group 3 isolates harboured a class 1 integron and were isolated from all animal species included in the study. Most isolates were Salmonella Typhimurium and harboured SGI1. Salmonella isolated from livestock was shown to harbour antimicrobial resistance genes although no or little resistance to third-generation cephalosporins or ciprofloxacin, respectively, was detected. The preponderance in pigs of multidrug-resistant Salmonella Typhimurium makes it important to introduce control measures such as improved biosecurity to ensure that they do not pass through the food chain and limit human therapeutic options.