Applications of gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other teleost fish species

Evolutionary genetics incorporates traditional population genetics and studies of the origins of genetic variation by mutation and recombination, and the molecular evolution of genomes. Among the primary forces that have potential to affect the genetic variation within and among populations, including those that may lead to adaptation and speciation, are genetic drift, gene flow, mutations and natural selection. The main challenges in knowing the genetic basis of evolutionary changes is to distinguish the adaptive selection forces that cause existent DNA sequence variants and also to identify the nucleotide differences responsible for the observed phenotypic variation. To understand the effects of various forces, interpretation of gene sequence variation has been the principal basis of many evolutionary genetic studies. The main aim of this thesis was to assess different forms of teleost gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other species. Firstly, the level of Darwinian adaptive evolution affected coding regions of the growth hormone (GH) gene during the teleost evolution was investigated based on the sequence data existing in public databases. Secondly, a target gene approach was used to identify within population variation in the growth hormone 1 (GH1) gene in salmon. Then, a new strategy for single nucleotide polymorphisms (SNPs) discovery in salmonid fishes was introduced, and, finally, the usefulness of a limited number of SNP markers as molecular tools in several applications of population genetics in Atlantic salmon was assessed. This thesis showed that the gene sequences in databases can be utilized to perform comparative studies of molecular evolution, and some putative evidence of the existence of Darwinian selection during the teleost GH evolution was presented. In addition, existent sequence data was exploited to investigate GH1 gene variation within Atlantic salmon populations throughout its range. Purifying selection is suggested to be the predominant evolutionary force controlling the genetic variation of this gene in salmon, and some support for gene flow between continents was also observed. The novel approach to SNP discovery in species with duplicated genome fragments introduced here proved to be an effective method, and this may have several applications in evolutionary genetics with different species - e.g. when developing gene-targeted markers to investigate quantitative genetic variation. The thesis also demonstrated that only a few SNPs performed highly similar signals in some of the population genetic analyses when compared with the microsatellite markers. This may have useful applications when estimating genetic diversity in genes having a potential role in ecological and conservation issues, or when using hard biological samples in genetic studies as SNPs can be applied with relatively highly degraded DNA.

Molecular and Clinical Characteristics of Pituitary Adenoma Predisposition (PAP)

Pituitary adenomas are common benign neoplasms. Although most of them are sporadic, a minority occurs in familial settings. Heterozygous germline mutations in the aryl hydrocarbon receptor interacting protein (AIP) gene were found to underlie familial pituitary adenomas, a condition designated as pituitary adenoma predisposition (PAP). PAP confers incomplete penetrance of mostly growth hormone (GH) secreting adenomas in young patients, who often lack a family history of pituitary adenomas. This thesis work aimed to clarify the molecular and clinical characteristics of PAP. Applying the multiplex ligation-dependent probe amplification assay (MLPA), we found large genomic AIP deletions to account for a subset of PAP. Therefore, MLPA could be considered in PAP suspected patients with no AIP mutations found with conventional sequencing. We generated an Aip mouse model to examine pituitary tumorigenesis in vivo. The heterozygous Aip mutation conferred complete penetrance of pituitary adenomas that were mostly GH-secreting, rendering the phenotype of the Aip mouse similar to that of PAP patients. We suggest that AIP may function as a candidate gatekeeper gene in somatotrophs. To clarify molecular mechanisms of tumorigenesis, we elucidated the expression of AIP-related molecules in human and mouse pituitary tumors. The expression of aryl hydrocarbon receptor nuclear translocator (ARNT) was reduced in mouse Aip-deficient adenomas, and similar ARNT reduction was also evident in human AIP mutation positive adenomas. This suggests that in addition to participating in the hypoxia pathway, estrogen receptor signaling and xenobiotic response pathways, ARNT may play a role in AIP-related tumorigenesis. We also studied the characteristics and the response to therapy of PAP patients and found them to have an aggressive disease phenotype with young age at onset. Therefore, improvement in treatment outcomes of PAP patients would require their efficient identification and earlier diagnosis of the pituitary adenomas. The possible role of the RET proto-oncogene in tumorigenesis of familial AIP mutation negative pituitary adenomas was evaluated, but none of the found RET germline variants were considered pathogenic. Surprisingly, RET immunohistochemistry suggested possible underexpression of RET in AIP mutation positive pituitary adenomas an observation that merits further investigation.

Nature of the inhibition by noradrenaline of induction by cortisol of hepatic tryptophan pyrrolase

Administration of noradrenaline inhibited the induction of hepatic trytophan pyrrolase by Cortisol but not by tryptophan. The selective inhibition of pyrrolase was specific to noradrenaline, whereas adrenaline and rat growth hormone also inhibited tyrosine aminotransferase. None of those three hormones had any effect on the incorporation of [32P]-orthophosphate into RNA, stimulated by cortisol. Other biogenic amines, polypeptide hormones and steroid analogues were not inhibitory to the induction of tryptophan pyrrolase by cortisol. The α-adrenergic agonist, phenylephrine, potentiated the noradrenaline inhibition whereas Image -threo-3,4-dihydroxyphenylserine, its precursor, together with pargyline had no effect on the induction process of pyrrolase. These results support the view that noradrenaline exerts its inhibitory action at the cell membrane via the α-receptor, and is not mediated directly by an intracellular mechanism.

Isolation of the murine interleukin 2 gene and characterization of its regulatory architecture

Interleukin 2 (IL2) is the primary growth hormone used by mature T cells and this lymphokine plays an important role in the magnification of cell-mediated immune responses. Under normal circumstances its expression is limited to antigen-activated type 1 helper T cells (T_H1) and the ability to transcribe this gene is often regarded as evidence for commitment to this developmental lineage. There is, however, abundant evidence than many non-T_H1 T cells, under appropriate conditions, possess the ability to express this gene. Of paramount interest in the study of T-cell development is the mechanisms by which differentiating thymocytes are endowed with particular combinations of cell surface proteins and response repertoires. For example, why do most helper T cells express the CD4 differentiation antigen?

As a first step in understanding these developmental processes the gene encoding IL2 was isolated from a mouse genomic library by probing with a conspecific IL2 cDNA. The sequence of the 5' flanking region from + 1 to -2800 was determined and compared to the previously reported human sequence. Extensive identity exists between +1 and -580 (86%) and sites previously shown to be crucial for the proper expression of the human gene are well conserved in both sequence location in the mouse counterpart.

Transient expression assays were used to evaluate the contribution of various genomic sequences to high-level gene expression mediated by a cloned IL2 promoter fragment. Differing lengths of 5' flanking DNA, all terminating in the 5' untranslated region, were linked to a reporter gene, bacterial chloramphenicol acetyltransferase (CAT) and enzyme activity was measured after introduction into IL2-producing cell lines. No CAT was ever detected without stimulation of the recipient cells. A cloned promoter fragment containing only 321 bp of upstream DNA was expressed well in both Jurkat and EL4.El cells. Addition of intragenic or downstream DNA to these 5' IL2-CAT constructs showed that no obvious regulatory regions resided there. However, increasing the extent of 5' DNA from -321 to -2800 revealed several positive and negative regulatory elements. One negative region that was well characterized resided between -750 and -1000 and consisted almost exclusively of alternating purine and pyrimidines. There is no sequence resembling this in the human gene now, but there is evidence that there may have once been.

No region, when deleted, could relax either the stringent induction-dependence on cell-type specificity displayed by this promoter. Reagents that modulated endogenous IL2 expression, such as cAMP, cyclosporin A, and IL1, affected expression of the 5' IL2-CAT constructs also. For a given reagent, expression from all expressible constructs was suppressed or enhanced to the same extent. This suggests that these modulators affect IL2 expression through perturbation of a central inductive signal rather than by summation of the effects of discrete, independently regulated, negative and positive transcription factors.

Produtividade Total dos Fatores: revisão da literatura e uma aplicação exploratória para a cultura do milho usando os dados dos censos agropecuários

Este trabalho pretende contribuir para o entendimento sobre a produtividade na agricultura brasileira, bem como propõe uma reflexão sobre o debate da produtividade total dos fatores. Para isso, buscou-se, antes de tudo, debater as medidas de produtividade, sobretudo as medidas de produtividade total dos fatores e, em seguida, apresentar estimativas da produtividade total na agricultura no Brasil e no mundo. Propõem-se também uma estimativa preliminar dessa metodologia para o cálculo da produtividade total dos fatores na cultura do milho através do índice de Tornqvist. O objetivo é, então, revisar a literatura teórica e empírica sobre a produtividade total dos fatores na agricultura e calcular as produtividades parciais e totais na cultura do milho para os estados brasileiros. Apesar da maior parte dos resultados encontrados no cálculo da produtividade total para a cultura do milho no Brasil não terem sido consistentes, a conclusão geral do levantamento bibliográfico foi que tanto a agricultura brasileira quanto a agricultura mundial, independente da metodologia utilizada, apresentou uma tendência ao crescimento da produtividade total dos fatores.

Sinalização da grelina no coração de camundongos obesos após hipernutrição durante a lactação

A grelina é um ligante endógeno do receptor secretagogo do hormônio do crescimento (GHSR), potente estimulador da liberação do hormônio de crescimento (GH), ingestão alimentar, e adiposidade. Além disso, sua ação hormonal inclui regulação do metabolismo energético cardíaco. Entretanto, a hipernutrição no início da vida leva ao desenvolvimento da obesidade, induz hipertrofia cardíaca, compromete a função cardíaca, e gera insuficiência cardíaca na vida adulta. Avaliar proteínas chaves no processo de sinalização da grelina no remodelamento cardíaco no coração de camundongos obesos após a hipernutrição na lactação. A obesidade foi induzida por redução de ninhada e camundongos adultos (180 dias) foram divididos em: grupo hiperalimentado, GH com obesidade decorrente de hipernutrição na lactação e controle, GC. Cardiomiócitos (cmi) do ventrículo esquerdo foram analisados por microscopia de luz e estereologia, o conteúdo e fosforilação de proteínas cardíacas: receptor de grelina (hormônio do crescimento secretagogo receptor 1a, GHSR-1a), proteína quinase-B (AKT e pAKT), phosphatidil inositol 3-quinase (PI3K), proteína quinase ativada por AMP (AMPK e pAMPK), m-TOR, pmTOR, Bax, Bcl2 e actina foram analizados por western blotting. A expressão gênica do GHSR-1a foi analisada por PCR em tempo real. A respirometria de alta resolução dos cardiomiócitos foi analisada por oxígrafo OROBOROS. Significância estatística (P< 0,05) determinada por teste t-Student não-pareado. Nossos dados demonstram que a hipernutrição na lactação induz aumento no peso corporal, iniciado aos 10 dias de idade, persistindo até os 180 dias de idade. A glicemia, peso do fígado, e da gordura visceral foram maiores no grupo GH. Além disso, o grupo GH também apresentou aumento no peso do coração e razão peso do coração/CT (comprimento da tíbia), indicando hipertrofia e remodelamento cardíaco, aumento na expressão e conteúdo de GHSR-1a no coração, associado ao maior conteúdo de PI3K e maior conteúdo e fosforilação de AKT, diminuição no conteúdo de Bcl2. Em contraste, o conteúdo e fosforilação da AMPK e mTOR no coração não foram diferentes entre os grupos. Os níveis de grelina plasmático no GH foram menores. A respiração do GH com grelina foi menor que no GC com grelina. A incubação das fibras cardíacas com grelina resultou em aumento do fluxo respiratório após adição de citocromo c nos grupos com grelina, indicando dano à membrana mitocondrial e extravazamento de citocromo c. Os grupos GC com grelina e GH sem grelina apresentaram RCR menor comparado ao GC sem grelina, indicando desacoplamento mitocondrial. Nossos resultados mostram que a hipernutrição na lactação induz diminuição do nível de grelina plasmática e aumento da expressão do GHS-R1a no cardiomiócito do animal quando adulto. Tal processo determina aumento da sensibilidade a grelina no coração, processo que ocorre independentemente de variações do AMPK e mTOR. Sugerimos uma redução no efeito protetor da ação da grelina na AMPK. Também, demonstramos que o remodelamento do miocárdio nestes animais adultos associa-se a GHSR-1a, PI3K, e fosforilação da AKT, mas não com AMPK e mTOR na vida adulta.

Molecular evolution of GH in primates: characterisation of the GH genes from slow loris and marmoset defines an episode of rapid evolutionary change

Pituitary growth hormone (GH), like several other protein hormones, shows an unusual episodic pattern of molecular evolution in which sustained bursts of rapid change are imposed on long periods of very slow evolution (near-stasis). A marked period of rap

Motilin and ghrelin gene experienced episodic evolution during primitive placental mammal evolution

Motilin and ghrelin, members of a structure-function-related hormone family, play important roles in gastrointestinal function, regulation of energy homeostasis and growth hormone secretion. We observed episodic evolution in both of their prehormone gene sequences during primitive placental mammal evolution, during which most of the nonsynonymous changes result in radical substitution. Of note, a functional obestatin hormone might have only originated after this episodic evolution event. Early in placental mammal evolution, a series of biology complexities evolved. At the same time the motilin and ghrelin prehormone genes, which play important roles in several of these processes, experienced episodic evolution with dramatic changes in their coding sequences. These observations suggest that some of the lineage-specific physiological adaptations are due to episodic evolution of the motilin and ghrelin genes.

Study on some biological and feeding factors of spined loach Cobitis taenia from the Babolrud, Talar and Siahrud Rivers

Spined loach, Cobitis taenia, is a predominant fish in the river systems of the southern Caspian Sea basin. Although there is evidence of the geographical divergence of this taxon, but no information is available on morphological differences within the species populations. This study was designed to evaluate some biological factors including; morphometric and meristic characters, length-weight, age-growth, condition factor, diet, reproduction, variation and differentiation, in the Babolrud, Talar and Siahrud Rivers in south of the Caspian Sea basin. Age, sex ratio, fecundity, ova diameter and gonadosomatic index were estimated. Also, regression analyses was tested the relation between fecundity and fish length, weight, gonad weight, and also age. Totally 858 fish of which 721 were matures, were collected from these rivers by electrofishing. 37 morphometric characters, 9 meristic characters and 78 truss network system characters were estimated. Resulats of DFA analysis based on data of morphometric and meristic showd that these populations are highly (94.5%) varios from each other. In discriminate function analysis, the proportion of individuals correctly classified into their original groups was 61%, 65.4% and 86.5% for upstream and downstream, respectively. Clustering based on Euclidean distances among groups of centroids using an UPGMA and also principal component analysis’ results for morphometric data indicated that these populations from these three rivers were clearly distinct from each other. Regression equations between length and weight in these three populations were significantly different from Folton factor (b=3), that showed the fish has a negative Alometric growth process. Condition factor was estimated between 0.8912 to 1.2736 and 0.8131 to 1.4489 for males and females, respectively. Sex ratio (female: male) in these populations was 1.2816:1. The difference between the number of females and males was significant and females were more than males. The female and male specimens reach maturity by Tl more than 40 and 30 mm and at the age of 2+ and 1+, respectively. The mean of ova diameter was 0.5824±0.2882. The spawning took place from May to late July, at the water temperature from 18.7 to 24.0°C. The GSI values average at the beginning of the reproduction period was about 9%, with ranged from 2 to 26% in ripe mature females. The absolute and relative fecundity were 2109±792 and 579±208 respectively. The absolute fecundity was significantly related to body weight and gonads weight. Based on the pattern of gonado-somatic index, it was concluded that this fish has prolong active reproductive period, which is a type of adaptation by short-lived small fishes to environmental conditions. The macroscopic and histological results showed that the female and male have 5 and 4 stages in their maturation process, respectively. The RLG index was about 0.4732, which showed the fish is a carnivorous species. Significant difference was observed between fishes with different length and diet. The main foods of the fish were Trichoptera, Chironomidae larvae and Ephemeroptera which were their prefered food as well, however it was estimated that the food selection and diet are affected by environmental conditions.

两种不同终止子在转基因鲤鱼中的促生长效应

转基因构建体中启动子的选择会直接影响转植基因的活性,近年来有研究表明转基因构建体中终止子的选择会一定程度地影响转植基因的活性。为了更好地筛选转基因构建体和培育快速生长的转"全鱼"生长激素(Growth hormone,GH)基因鱼,文章用鲤鱼β-actin基因终止子和生长激素基因终止子分别构建了转基因构建体,显微注射得到转"全鱼"GH基因鱼P0代养殖群体,比较两种不同终止子构建体的活性。统计分析发现,生长激素基因终止子构建体的养殖群体的体重频率呈正态分布且平均体重显著高于β-actin基因终止子构建体的养

Identification of the Angel-related elements in cyprinid fishes and their phylogenetic implications

Angel-related element belongs to the family of miniature inverted-repeat transposable elements (MITEs). In this paper we report the identification of an Angel-related element in the series Leuciscini of cyprinid fishes, which is located in the second intron of the growth hormone (GH) gene. We have also found that this element is absent in orthologous locus in the series Barbini of cyprinid fishes, that provides new evidence for the monophyly of the series Leuciscini. The insertion of Angel-related element into the GH gene might take place in the common ancestor of the series Leuciscini after its divergence from the series Barbini. The high sequence divergence and relatively broad species distribution of Angel-related elements implies that they might be ancient transposons which appeared about 26 million years ago.

Integration of double-fluorescence expression vectors into zebrafish genome for the selection of site-directed knockout/knockin

Production of zebrafish by modifying endogenous growth hormone (GH) gene through homologous recombination is described here. We first constructed the targeting vectors pGHT1.7k and pGHT2.8k, which were used for the knockout/knockin of the endogenous GH gene of zebrafish, and injected these two vectors into the embryos of zebrafish. Overall, the rate of targeted integration with the characteristic of germ line transmission in zebrafish was 1.7x10(-6). In one experimental patch, the integrating efficiency of pGHT2.8k was higher than that of pGHT1.7k, but the lethal effect of pGHT2.8k was stronger than that of pGHT1.7k. The clones with the correct integration of target genes were identified by a simple screening procedure based on green fluorescent protein (GFP) and RFP dual selection, which corresponded to homologous recombination and random insertion, respectively. The potential homologous recombination zebrafish was further bred to produce a heterozygous F-1 generation, selected based on the presence of GFP. The potential targeted integration of exogenous GH genes into a zebrafish genome at the P-0 generation was further verified by polymerase chain reaction and Southern blot analysis. Approximately 2.5% of potential founder knockout and knockin zebrafish had the characteristic of germ line transmission. In this study, we developed an efficient method for producing the targeted gene modification in zebrafish for future studies on genetic modifications and gene functions using this model organism.

Developments in transgenic fish in the people's Republic of China

In the People's Republic of China, genetically modified (GM) fish are being developed primarily to produce desirable alterations to growth rates or feed-conversion efficiency. Up to the present, no transgenic fish have been commercially approved for human consumption. This review introduces advances in the People's Republic of China in transgenic fish studies, biosafety studies of fast-growth GM fish, and the regulation of GM fish.

Molecular analysis of silver crucian carp (Carassius auratus gibelio Bloch) clones by SCAR markers

Random amplified polymorphic DNA (RAPD) molecular markers specific for one, two or three clones have been identified from five gynogenetic clones of silver crucian carp (Carassius auratus gibelio Bloch) using RAPD markers developed earlier. In this study, three RAPD markers (RA1-PA, RA2-EF and RA4-D) produced by Opj-1, and two RAPD DNA fragments (RA3-PAD and RA5-D) produced by Opj-7, were selected for molecular cloning and sequencing. Sequence data indicated that there were identical 801-bp nucleotide sequences in the shared marker RA1-PA cloned respectively from clones P and A, and the shared marker RA2-EF (which was cloned from clones E and F), were also of identical 958-by nucleotide sequences. The nucleotide sequences of the shared marker RA3-PAD fragments were also similar for 1181 by among clones P, A and D. The specific fragment RA4-D was composed of 628 bp, and the fragment RA5-D from clone D contained 385 nucleotides. According to the nucleotide sequences, we designed and synthesized five pairs of sequence characterized amplified regions (SCAR) primers to identify the specific fragments in these gynogenetic clones of silver crucian carp. Only individuals from clones P and A amplified a specific band using a pair of SCI-PA primers synthesized according to the marker RA1-PA sequences, whereas no products were detected in individuals from clones D, E and F. The PCR products amplified using SC2-EF and SC3-PAD primers were as expected. Furthermore, the pair of SC4-D primers amplified specific bands only in individuals from clone D, although weak bands could be produced in all individuals of the five clones when lower annealing temperatures were used. However, an additional pair of SC5-D primers designed from the RA5-D marker sequences could amplify a DNA band in individuals from clones P, A and D, and the same weak band was produced in clone E, whereas no products were detected in individuals from clone F. Searches in GenBank revealed that the 385-bp DNA fragment from RA5-D was homologous to the 5' end of gonadotropin I beta subunit 2 gene and growth hormone gene. No homologous sequences were found for other markers in GenBank. The SCAR markers identified in this study will offer a powerful, easy, and rapid method for discrimination of different clones and for genetic analyses that examine their origins and unique reproductive modes in crucian carp. Furthermore, they will likely benefit future selective breeding programs as reliable and reproducible molecular markers. (C) 2001 Elsevier Science B.V. All rights reserved.

Embryonic and genetic manipulation in fish

Fishes, the biggest and most diverse community in vertebrates are good experimental models for studies of cell and developmental biology by many favorable characteristics. Nuclear transplantation in fish has been thoroughly studied in China since 1960s. Fish nuclei of embryonic cells from different genera were transplanted into enucleated eggs generating nucleo-cytoplasmic hybrids of adults. Most importantly, nuclei of cultured goldfish kidney cells had been reprogrammed in enucleated eggs to support embryogenesis and ontogenesis of a fertile fish. This was the first case of cloned fish with somatic cells. Based on the technique of microinjection, recombinant MThGH gene has been transferred into fish eggs and the first batch of transgenic fish were produced in 1984. The behavior of foreign gene was characterized and the onset of the foreign gene replication occurred between the blastula to gastrula stages and random integration mainly occurred at later stages of embryogenesis. This eventually led to the transgenic mosaicism. The MThGH-transferred common carp enhanced growth rate by 2-4 times in the founder juveniles and doubled the body weight in the adults. The transgenic common carp were more efficient in utilizing dietary protein than the controls. An "all-fish" gene construct CAgcGH has been made by splicing the common carp beta-actin gene (CA) promoter onto the grass carp growth hormone gene (gcGH) coding sequence. The CAgcGH-transferred Yellow River Carp have also shown significantly fast-growth trait. Combination of techniques of fish cell culture, gene transformation with cultured cells and nuclear transplantation should be able to generate homogeneous strain of valuable transgenic fish to fulfil human requirement in 21(st) century.