Large-scale screen for genes involved in gonad development

The vertebrate gonad develops from the intermediate mesoderm as an initially bipotential organ anlage, the genital ridge. In mammals, Sry acts as a genetic switch towards testis development. Sox9 has been shown to act downstream of Sry in testis development, while Dax1 appears to counteract Sry. Few more genes have been implicated in early gonad development. However, the genetic networks controlling early differentiation events in testis and ovary are still far from being understood. In order to provide a broader basis for the molecular analysis of gonad development, high-throughput gene expression analysis was utilized to identify genes specifically expressed in the gonad. In total, among 138 genes isolated which showed tissue specific expression in the embryo, 79 were detected in the developing gonad or sex ducts. Twenty-seven have not been functionally described before, while 40 represent known genes and 12 are putative mouse orthologues. Forty-five of the latter two groups (86%) have not been described previously in the fetal gonad. In addition, 21 of the gonad specific genes showed sex-dimorphic expression suggesting a role in sex determination and/or gonad differentiation. Eighteen of the latter (86%) have not been described previously in the fetal gonad. In total we provide new data on 72 genes which may play a role in gonad or sex duct development and/or sex determination. Thus we have generated a large gene resource for the investigation of these processes, and demonstrate the suitability of high-throughput gene expression screening for the genetic analysis of organogenesis.     

The Transformer Genes of the Fern Ceratopteris Simultaneously Promote Meristem and Archegonia Development and Repress Antheridia Development in the Developing Gametophyte

The sex of the haploid gametophyte of the fern Ceratopteris is determined by the presence or absence of the pheromone antheridiogen, which, when present, promotes male development and represses female development of the gametophyte. Several genes involved in sex determination in Ceratopteris have been identified by mutation. In this study, the epistatic interactions among new and previously described sex-determining mutants have been characterized. These results show that sex expression is regulated by two sets of genes defined by the FEM1 and TRA loci. Each promotes the expression of either male or female traits and simultaneously represses the expression of the other. A model describing how antheridiogen regulates the expression of these genes and the sex of the gametophyte is described. The observation that some gametophytic sex-determining mutants have phenotypic effects on the sporophyte plant indicates that sex determination in the Ceratopteris gametophyte is regulated by a mechanism that also regulates sporophyte development.     

The CK1 gene family: expression patterning in zebrafish development

Protein kinase CK1 is a ser/thr protein kinase family which has been identified in the cytosol cell fraction, associated with membranes as well as in the nucleus. Several isoforms of this gene family have been described in various organisms: CK1alpha, CK1beta, CK1delta, CK1epsilon and CK1gamma. Over the last decade, several members of this family have been involved in development processes related to wnt and sonic hedgehog signalling pathways. However, there is no detailed temporal information on the CK1 family in embryonic stages, even though orthologous genes have been described in several different vertebrate species. In this study, we describe for the first time the cloning and detailed expression pattern of five CK1 zebrafish genes. Sequence analysis revealed that zebrafish CK1 proteins are highly homologous to other vertebrate orthologues. Zebrafish CK1 genes are expressed throughout development in common and different territories. All the genes studied in development show maternal and zygotic expression with the exception of CK1epsilon. This last gene presents only a zygotic component of expression. In early stages of development CK1 genes are ubiquitously expressed with the exception of CK1epsilon. In later stages the five CK1 genes are expressed in the brain but not in the same way. This observation probably implicates the CK1 family genes in different and also in redundant functions. This is the first time that a detailed comparison of the expression of CK1 family genes is directly assessed in a vertebrate system throughout development.     

Probing the microenvironment of intracellular bacterial pathogens

The identification of bacterial genes regulated in response to the intracellular environment is crucial to the understanding of host-pathogen interactions. Several techniques have been developed to identify and characterize bacterial genes that are induced during the intracellular infection and, potentially, may play a role in pathogenesis. This review discusses the strategies that have been utilized to examine differential gene expression by bacterial pathogens during the intracellular infection. Furthermore, a number of the differentially expressed genes are described.     

In vivo incorporation of Drosophila H2a histone into mammalian chromatin.

Hybrid prokaryotic/eukaryotic expression vectors have been used to introduce Drosophila histone genes into CV-1 African green monkey tissue culture cells. Transfection of CV-1 cells with Drosophila genes under the control of insect DNA promoter sequences results in low level expression of histone genes. On the other hand, when the Drosophila H2a gene is juxtaposed downstream from the long terminal repeat sequence of Rous sarcoma virus (RSV) expression of the insect gene is considerably more efficient; both 3' polyadenylated insect histone messenger RNA and putative Drosophila H2a histone protein can be readily detected in the transduced cells. Using this RSV/H2a vector, we have been able to demonstrate the presence of Drosophila H2a histone in monomer nucleosome preparations isolated from transfected CV-1 cells. These results suggest the feasibility of 'remodeling' cellular chromatin in vivo in precisely defined ways. The techniques described may be generally applicable to other genes coding for chromosomal proteins.     

Genetic Engineering of Insect-Resistant Crop Plants with Bacillus thuringiensis Crystal Protein Genes

Bacillus thuringiensis, a soil bacterium, produces crystalline proteins which are toxic to the Insect larvae, The toxicity Is brought about by the protein fragments released due to the action of mid-gut proteases and their binding to the receptors on the epithelial membrane, which In turn loses Its selective permeability. The genes (cry) coding for these Insecticidal crystal proteins have been cloned, characterized and mobilized Into a number of crop plants. Such transgenic plants were shown to be resistant to insects. However, the expression of these bacterial genes in higher plants has been limited because of differential codon usage. Various strategies for maximizing the expression of these genes in transgenic plants have been described. In addition, alternative approaches have been suggested for circumventing the development of resistance in insects to the crystal proteins.     

Extensive transcriptomic studies on the roles played by abscisic acid and auxins in the development and ripening of strawberry fruits

Strawberry is an ideal model for studying the molecular biology of the development and ripening of non-climacteric fruits. Hormonal regulation of gene expression along all these processes in strawberries is still to be fully elucidated. Although auxins and ABA have been pointed out as the major regulatory hormones, few high-throughput analyses have been carried out to date. The role for ethylene and gibberellins as regulatory hormones during the development and ripening of the strawberry fruit remain still elusive. By using a custom-made and high-quality oligo microarray platform done with over 32,000 probes including all of the genes actually described in the strawberry genome, we have analysed the expression of genes during the development and ripening in the receptacles of these fruits. We classify these genes into two major groups depending upon their temporal and developmental expression. First group are genes induced during the initial development stages. The second group encompasses genes induced during the final maturation and ripening processes. Each of these two groups has been also divided into four sub-groups according their pattern of hormonal regulation. By analyzing gene expression, we clearly show that auxins and ABA are the main and key hormones that combined or independently are responsible of the development and ripening process. Auxins are responsible for the receptacle fruit development and, at the same time¸ prevent ripening by repressing crucial genes. ABA regulates the expression of the vast majority of genes involved in the ripening. The main genes expressed under the control of these hormones are presented and their physiological rule discussed. We also conclude that ethylene and gibberellins do not seem to play a prominent role during these processes.     

A low diversity of ANTP class homeobox genes in Placozoa

Homeobox genes of the ANTP and PRD classes play important roles in body patterning of metazoans, and a large diversity of these genes have been described in bilaterian animals and cnidarians. Trichoplax adhaerens (Phylum Placozoa) is a small multicellular marine animal with one of the simplest body organizations of all metazoans, showing no symmetry and a small number of distinct cell types. Only two ANTP class genes have been described from Trichoplax: the Hox/ParaHox gene Trox-2 and a gene related to the Not family. Here we report an extensive screen for ANTP class genes in Trichoplax, leading to isolation of three additional ANTP class genes. These can be assigned to the Dlx, Mnx and Hmx gene families. Sequencing approximately 12-20 kb around each gene indicates that none are part of tight gene clusters, and in situ hybridization reveals that at least two have spatially restricted expression around the periphery of the animal. The low diversity of ANTP class genes isolated in Trichoplax can be reconciled with the low anatomical complexity of this animal, although the finding that these genes are assignable to recognized gene families is intriguing.     

Interactions between the rabbit CSN1 gene and the nuclear matrix of stably transfected HC11 mammary epithelial cells vary with its level of expression

The expression of casein genes is specific to the mammary gland and maximal during lactation. However, among the numerous mammary cell lines described so far, only a few express some casein genes. The regulatory regions of casein genes have been largely described but the mechanisms explaining the mammary specific expression of these genes, and their silencing in most mammary cell lines, have not yet been fully elucidated. To test the hypothesis that the nuclear location of the casein genes may affect their expression, we transfected HC11 mouse mammary cell line with a 100 kb DNA fragment surrounding the rabbit alpha S1 casein gene. We derived stable clones which express or not the transfected rabbit casein gene, in the same cellular context, independently of the number of transgene copies. Metaphase spreads were prepared from the different clones and the transfected genes were localized. Unexpectedly, we observed that in the original HC11 cell line the number of chromosomes per metaphase spread is close to 80, suggesting that HC11 cells have undergone a duplication event, since the mouse karyotype is 2n = 40. In alpha S1 casein expressing cells, the expression level does not clearly correlate with a localization of the transfected DNA proximal to the centromeres or the telomeres. Analysis of the localization of the transfected DNA in nuclear halos allows us to conclude that when expressed, transfected DNA is more closely linked to the nuclear matrix. The next step will be to study the attachment of the endogenous casein gene in mammary nuclei during lactation.     

Feeding conditions control the expression of genes involved in sterol metabolism in peripheral blood mononuclear cells of normoweight and diet-induced (cafeteria) obese rats

Peripheral blood mononuclear cells (PBMC) are easily obtainable cells from blood whose gene expression profiles have been proven to be highly robust in distinguishing a disease state from healthy state. Sterol metabolism is of physiological importance, and although its nutritional response in liver has been described, it is poorly studied in PBMC. To examine if PBMC sterol metabolism reflects diet-induced physiological responses, we analysed the whole genome gene expression response of PBMC and focused on sterol metabolism-related genes affected by different feeding conditions (ad libitum feeding, fasting, and refeeding) in normoweight (control) rats and in diet-induced (cafeteria) obese rats.Our results of microarray analysis show that, in control rats, 21 genes involved in sterol metabolism were regulated by the different feeding conditions, whereas in cafeteria-obese rats, only seven genes showed a changed expression. Most of the genes identified were classified into three pathways: sterol biosynthesis, cholesterol transport and uptake and sterol signaling. The expression profile of these genes was similar to that previously described for liver, decreasing in response to fasting conditions and recovering the levels found in fed animals after 6-h-refeeding. In addition, our data and the comparable expression pattern of sterol metabolism-related genes between PBMC and liver suggest similar sterol regulatory element-binding protein-mediated regulatory mechanisms in response to feeding conditions in both tissues.In conclusion, the expression of genes involved in sterol metabolism is highly controlled by feeding conditions in PBMC of control rats, but this control is impaired in cafeteria-obese animals. The pathophysiological significance of this impairment requires further investigation.     

Efficient Cloning of cDNAs of Retinoic Acid-Responsive Genes in P19 Embryonal Carcinoma Cells and Characterization of a Novel Mouse Gene, Stra1 (Mouse LERK-2/Eplg2)

Pluripotent mouse P19 embryonal carcinoma (EC) cells have been extensively used as a developmental model system because they can differentiate in the presence of retinoic acid (RA) into derivatives of all three germ layers depending on RA dosage and culture conditions. The expression of several genes has been shown to be induced in RA-treated P19 EC cells and, interestingly, some of these genes may play important roles during mouse embryogenesis. In view of the increasing evidence that RA is a crucial signaling molecule during vertebrate development, we have initiated a study aimed at the systematic isolation of genes whose expression is induced in P19 cells at various times after exposure to RA. We describe here an efficient differential subtractive hybridization cloning strategy which was used to identify additional RA-responsive genes in P19 cells. Fifty different cDNA fragments corresponding to RA-induced genes were isolated. Ten cDNAs represent known genes, 4 of which have already been described as RA-inducible, while the remaining 40 correspond to novel genes. Many of these cDNA sequences represent low-abundance mRNAs. Kinetic analysis of mRNA accumulation following RA treatment allowed us to characterize four classes of RA-responsive genes. We also report the sequence and expression pattern in mouse embryos and adult tissues of one of these novel RA-inducible genes, Stral, and show that it corresponds to the mouse ligand for the Cek5 receptor protein-tyrosine kinase.     

Effect of paraquat exposure on nitric oxide-responsive genes in rat mesencephalic cells

When neural cells are exposed to paraquat, nitric oxide generation increases primarily due to an increase in the expression of the inducible isoform of nitric oxide synthase. The nitric oxide generated has controversial actions in paraquat exposure, as both protective and harmful effects have been described previously. While the actions mediated by nitric oxide in neural cells have been well described, there is evidence that nitric oxide may also be an important modulator of the expression of several genes during paraquat exposure. To better understand the actions of nitric oxide and its potential role in paraquat-induced gene expression, we examined changes in GCH1, ARG1, ARG2, NOS1, NOS2, NOS3, NOSTRIN, NOSIP, NOS1AP, RASD1, DYNLL1, GUCY1A3, DDAH1, DDAH2 and CYGB genes whose expression is controlled by or involved in signaling by the second messenger nitric oxide, in rat mesencephalic cells after 3, 6, 12 and 24 h of paraquat exposure. A qPCR strategy targeting these genes was developed using a SYBR green I-based method. The mRNA levels of all the genes studied were differentially regulated during exposure. These results demonstrate that nitric oxide-related genes are regulated following paraquat exposure of mesencephalic cells and provide the basis for further studies exploring the physiological and functional significance of nitric oxide-sensitive genes in paraquat-mediated neurotoxicity.     

Gene cloning and expression in lactic streptococci

Abstract Recent developments have made the mesophilic lactic streptococci, widely used in dairy fermentations, accessible to genetic manipulation. Several host-vector systems have been described which currently are used in the cloning and expression of homologous and heterologous genes. The essential elements of these systems, the various cloning strategies and the first successful cloning experiments are described with emphasis on the molecular organization of proteinase genes. In addition, the organization and nucleotide sequence of signals which are involved in gene expression in lactic streptococci are summarized.     

Representation of differential expression: a new approach to study differential gene expression in trypanosomatids

During the past five years, several methods have been described that allow the isolation and cloning of stage-specific or cell-specific genes. The characterization of genes expressed at different stages of parasite development is of the utmost importance for the understanding of the mechanisms involved in the regulation of gene expression. Here, Samuel Goldenberg and Marco Aurelio Krieger describe a method for the amplification and cloning of Trypanosoma cruzi genes expressed specifically at different times of the metacyclogenesis process. This method, representation of differential expression (RDE), should be useful for the isolation and cloning of any trypanosomatid gene transcribing differentially expressed messenger RNA.     

Cell surface proteins of a group A streptococcus type M4: The IgA receptor and a receptor related to M proteins are coded for by closely linked genes

Summary Two genes coding for cell surface proteins were cloned from a group A streptococcus type M4: the gene for an IgA binding protein and the gene for a fibrinogen binding protein. Both proteins were purified and partially characterized after expression in Escherichia coli. There was no immunological cross-reaction between the two proteins. The IgA binding protein, called protein Arp4, is similar to an IgA receptor previously purified from another strain of group A streptococci, but the proteins are not identical. Characterization of many independent clones showed that the two proteins described here are coded for by closely linked genes. Bacterial mutants have been found which have simultaneously lost the ability to express both genes, and a simple method to isolate such mutants is described. The existence of these variants indicates that expression of the two cell surface proteins may be coordinately regulated. Binding of fibrinogen is a characteristic property of streptococcal M proteins, and the available evidence suggests that the fibrinogen binding protein is indeed an M protein.     

Analysis of histone acetyltransferase and deacetylase families of Vitis vinifera

Histone acetyltransferases (HATs) and deacetylases (HDACs) play critical roles in the regulation of chromatin structure and gene expression. In plants, these genes are emerging as crucial players in all aspects of development. As part of our study regarding the growth and development of grapevine (Vitis vinifera), we report the genome-wide analysis of HAT and HDAC genes. This analysis revealed the presence of 7 and 13 genes coding for putative HATs and HDACs, respectively. In this work, we present a complete analysis of these families with regards to their phylogenetic relationships with orthologous genes identified in other sequenced plant genomes, their genome location, gene structure and expression. The genes identified can be grouped into different families as has been previously described for other eukaryotic species. The organ-specific expression pattern of HAT and HDAC genes indicates that some genes have different expression profiles, and their potential involvement during grape development is discussed.