Expression Of New Gene Research Articles

Class 1 Integron (Inti1) Gene In Gram Negative Multi-Drug Resistant Bacteria Isolated From Clinical Samples In Bayelsa State, Nigeria

Background and Objective: Integrons are common features of bacterial genomes that allow efficient capture and expression of new genes which are embedded in gene cassettes. Class 1 integron are mostly identified among clinical Gram-negative bacteria as the major factor responsible for drug resistance. This study was aimed at detecting the presence of the integron-integrase 1 gene (inti1) in Gram negative bacteria. Materials and Methods: The isolates were determined using Standard Bacteriological methods. Antibiotic susceptibility testing was carried out using Modified Kirby Bauer disc-diffusion method and the genomic DNA was extracted by boiling method. The presence of Inti1 gene was determined using Polymerase Chain Reaction. Results: A total of 121 clinical samples were collected, of which 99 (81.8%) were urine samples, 5 (4.13%) were Endocervical swabs, 4 (3.31%) were sputum samples, 4 (3.31%) were High vaginal swabs, 6 (4.95%) were wound samples and 3 (2.48%) were ear swabs, 45 (37.2%) samples were collected from males and 76 (62.8%) were collected from females. The findings showed that out of 121 samples analysed, a total of 95 isolates were obtained from the samples with E.coli having a high prevalence of 32 (33.7%), followed by Klebsiella oxytoca 30 (31.6%), Klebsiella pneumonia 21 (22.1%), Pseudomonas aeruginosa 6 (6.31%), Enterobacter aerogenes 3 (3.2%) and Citrobacter fruendii 3 (3.2%). Antibiotics susceptibility pattern showed the resistance percentage of each of the antibiotics used; Gentamicin (50.5%) Pefloxacine (68.4), Narivid (67.4%), Streptomycin (81.1%), Septrin (66.3%) Chloramphenicol (70.5%), Spectinomycin (53.7%), Ciprofloxacin (56.8%), Amoxacillin (53.7%) and Augmentin (88.4%). Out of the 30 isolates selected for molecular analysis, the Inti 1 gene was detected in 26 isolates. Conclusion: This study showed that there is high prevalence of class 1 integron in multi-drug resistant Gram-negative bacteria. To prevent the development of multi-drug resistance bacteria, the indiscriminate use of antibiotics should be avoided.

Expression of new genes in vertebrate tooth development and p63 signaling.

p63 is an evolutionarily ancient transcription factor essential to vertebrate tooth development. Our recent gene expression screen comparing wild-type and "toothless" p63-/- mouse embryos implicated in tooth development several new genes that we hypothesized act downstream of p63 in dental epithelium, where p63 is also expressed. Via in situ hybridization and immunohistochemistry, we probed mouse embryos (embryonic days 10.5-14.5) and spotted gar fish embryos (14 days postfertilization) for these newly linked genes, Cbln1, Cldn23, Fermt1, Krt15, Pltp and Prss8, which were expressed in mouse and gar dental epithelium. Loss of p63 altered expression levels but not domains. Expression was comparable between murine upper and lower tooth organs, implying conserved gene functions in maxillary and mandibular dentitions. Our meta-analysis of gene expression databases supported that these genes act within a p63-driven gene regulatory network important to tooth development in mammals and more evolutionary ancient vertebrates (fish, amphibians). Cbln1, Cldn23, Fermt1, Krt15, Pltp, and Prss8 were expressed in mouse and fish dental epithelium at placode, bud, and/or cap stages. We theorize that these genes participate in cell-cell adhesion, cell polarity, and extracellular matrix signaling to support dental epithelium integrity, folding, and epithelial-mesenchymal cross talk during tooth development.

Origin of new genes after zygotic genome activation in vertebrate.

New genes are drivers of evolutionary innovation and phenotypic evolution. Expression of new genes in early development raises the possibility that new genes could originate and be recruited for functions in embryonic development, but this remains undocumented. Here, based on temporal gene expression at different developmental stages in Xenopus tropicalis, we found that young protein-coding genes were significantly enriched for expression in developmental stages occurring after the midblastula transition (MBT), and displayed a decreasing trend in abundance in the subsequent stages after MBT. To complement the finding, we demonstrate essential functional attributes of a young orphan gene, named as Fog2, in morphological development. Our data indicate that new genes could originate after MBT and be recruited for functions in embryonic development, and thus provide insights for better understanding of the origin, evolution, and function of new genes.

Dynamic gene expression analysis of maternal, cytoplasmic and embryo genetic systems for linolenic and erucic acid contents in rapeseed (Brassica napus L.)

The genetic effects including genetic main effects and genotype × environment (GE) interaction effects were analyzed for linolenic acid content (LLAC) and erucic acid content (EAC) in rapeseed using unconditional and conditional genetic models for diploid seed quantitative traits. The results from unconditional analysis revealed that GE effects were important for both traits during seed development. Also the higher magnitude of embryo effects at different developmental times indicated that seed selection would be useful for improving these quality traits in rapeseed. The conditional analysis showed that new expression of genes from maternal and embryo genetic systems occurred during different developmental stages and their magnitude could be influenced by the GE effects. The total narrow-sense heritability was high for both LLAC and EAC, with general heritability being more prominent for EAC at 15 days (32.87 %), 29 days (31.44 %), 36 days (60.55 %) and 43 days (76.45 %), and GE interaction heritability dominating for LLAC at 22 days (40.57 %), 29 days (60.91 %), 36 days (63.83 %) and 43 days (47.45 %) after flowering, respectively. Phenotypic and genotypic correlations for both traits were positive among some pairwise developmental times indicating that genes expressed at these times complemented each other to improve LLAC or EAC in rapeseed. Significant negative correlation between LLAC and EAC at most developmental times indicated that it may not be possible to simultaneously reduce the contents of both traits by indirect selection.

Plant Promoters: An Approach of Structure and Function

With current advances in genomics, several technological processes have been generated, resulting in improvement in different segments of molecular research involving prokaryotic and eukaryotic systems. A widely used contribution is the identification of new genes and their functions, which has led to the elucidation of several issues concerning cell regulation and interactions. For this, increase in the knowledge generated from the identification of promoters becomes considerably relevant, especially considering that to generate new technological processes, such as genetically modified organisms, the availability of promoters that regulate the expression of new genes is still limited. Considering that this issue is essential for biotechnologists, this paper presents an updated review of promoters, from their structure to expression, and focuses on the knowledge already available in eukaryotic systems. Information on current promoters and methodologies available for studying their expression are also reported.

Emerging Role of Neuronal Exosomes in the Central Nervous System

Exosomes are small extracellular vesicles, which stem from endosomes fusing with the plasma membrane, and can be recaptured by receiving cells. They contain lipids, proteins, and RNAs able to modify the physiology of receiving cells. Functioning of the brain relies on intercellular communication between neural cells. These communications can modulate the strength of responses at sparse groups of specific synapses, to modulate circuits underlying associations and memory. Expression of new genes must then follow to stabilize the long-term modifications of the synaptic response. Local changes of the physiology of synapses from one neuron driven by another, have so far been explained by classical signal transduction to modulate transcription, translation, and posttranslational modifications. In vitro evidence now demonstrates that exosomes are released by neurons in a way depending on synaptic activity; these exosomes can be retaken by other neurons suggesting a novel way for inter-neuronal communication. The efficacy of inter-neuronal transfer of biochemical information allowed by exosomes would be far superior to that of direct cell-to-cell contacts or secreted soluble factors. Indeed, lipids, proteins, and RNAs contained in exosomes secreted by emitting neurons could directly modify signal transduction and protein expression in receiving cells. Exosomes could thus represent an ideal mechanism for inter-neuronal transfer of information allowing anterograde and retrograde signaling across synapses necessary for plasticity. They might also allow spreading across the nervous system of pathological proteins like PrPsc, APP fragments, phosphorylated Tau, or Alpha-synuclein.

The construction of gallbladder carcinoma cell line GBC-SD with stable expression of DMBT1 and its growth properties HE Too

Objective To establish the cell line CBC-SD of gallbladder carcinoma with stable expression of a new candidate tumor suppressor gene DMBT1 and analyze its proliferation features. Methods GBC-SD was transfected with the plasmid pTRexDest30_DMBT18kb.2 by Lipofectamine 2000 and subsequently screened with G418 for 5-6 weeks. The expression of DMBT1 niRNA and protein was detected by reverse transcription-PCR, Western blot and immunocytochemistry;cell proliferation was evaluated by MTT method,and cell apoptosis in serum-free medium was assessed with DAPI staining. Results After selection with G418 for 5-6 weeks, macroscopic resistant cell cloning was formed in the experimental group and the control group, whereas all the cells died in the untreated group. RT-PCR and Western blot revealed that the relative expression levels of DMBT1 protein and mRNA in the experimental group were 0. 82±0. 11 and 0. 87±0. 12 respectively,P<0. 01 versus the control group (0.24±0.03 and 0. 29±0. 03 respectively) ,equivalent to the findings of immunocytochemistry. The growth curves indicated that the experimental group showed a slackened pace of proliferation versus the control group, the inhibition ratio of proliferation of cells cultured for 72 h in serum-free medium was (43.3±5.0)%. DAPI staining showed that apoptosis rate of cells culture in serum-free medium in the experimental group was (22.0±2.5)% versus (7.0±1. 1 )% in the control group. Conclusion The gallbladder carcinoma cell line that stably expressed DMBT1 was successfully established. DMBT1 over-expression in vitro suppresses proliferation of the gallbladder carcinoma cells and induces their apoptosis in serum-free medium. Key words: Gallbladder carcinoma; Proliferation; Transfection

Fungal-bacterial biofilms: their development for novel biotechnological applications

The attachment of microbes on biotic or abiotic surfaces to form biofilm structures has a great impact on biodegradation and biosynthesis in nature. Various interactions in such biofilms and their extracellular polymeric substances (EPS) layer make them considerably different in physiology and action, compared to that of their individual microbes in planktonic (free swimming) mode of growth. Expression of new genes is up-regulated in the biofilm cells, due in part to the cellular interactions, compared with the planktonic cells. Formation of fungal-bacterial biofilms (FBB) by bacterial colonization on biotic fungal surface gives the biofilm enhanced metabolic activities compared to monocultures, and perhaps multi-species bacterial or fungal biofilms on abiotic surfaces. Incorporation of a N2-fixing rhizobial strain to the FBB to form fungal-rhizobial biofilms (FRB) has been shown to improve potential biofilm applications in N-deficient settings and in the production of biofilmed inocula for biofertilizers and biocontrol in plants. Their applications in agricultural and environmental settings, enzyme technology, drug discovery studies and energy research are being investigated. Thus, it has already been shown that the use of the FBB is a promising technology for many applications. This review deals with the different areas in which FBB/FRB have been seen to be applied with successful results as well as the numerous emerging avenues in which they show promising potential.

Focusing of Gene Expression as the Basis of Stem Cell Differentiation

In a prior report (Stem Cells Dev 14(4):354-366, 2005), we employed two-dimensional gel electrophoresis followed by advanced proteomics and the Database for Annotation, Visualization and Integrated Discovery (DAVID) to compare the protein expression profiles of mesenchymal stem cells to that of fully differentiated osteoblasts. These data were reported to advance technical approaches to define the basis of differentiation, but also led us to suggest that osteogenic differentiation of stem cells may result from the focusing of gene expression in functional clusters (e.g., calcium-regulated signaling proteins or adherence proteins) rather than simply from the induced expression of new genes, as many have assumed. Here, we have employed these analytical techniques to compare protein expression by mesenchymal stem cells directly with that of cells derived from them after induced osteogenic differentiation. Our results support the concept of gene focusing as the basis of differentiation. Specifically, induced differentiation results in a decrease in the number of mesenchymal cell markers and calcium-mediated signaling molecules expressed by their differentiated progeny. This effect was seen in parallel to increased expression of specific extracellular matrix (ECM) molecules and their receptors. These results strongly imply that changes in the ECM have a direct impact on stem cell differentiation, and that osteogenic differentiation of stem cells directed by matrix clues results from focusing of the expression of genes involved in Ca2+-dependent signaling pathways.

Developmental quantitative genetic analysis of body weight and morphological traits in red common carp, Cyprinus carpio L.

Developmental genetic analysis was conducted for body weight, total length, standard length and body height in red common carp by a mixed genetic model with additive–dominance effects, based on complete diallel crosses made by Xingguo red common carp ( Cyprinus carpio var. singuonensis), purse red common carp ( Cyprinus carpio var. wuyuanensis) and Oujiang color common carp ( Cyprinus carpio var. color). Unconditional genetic analysis revealed that the traits of body weight, total length and standard length were mainly controlled by dominance effects before June but by additive effects after June, which suggests a high potential for heterosis during the early developmental period and an opportunity for selection during the late developmental periods for common carp. Through conditional genetic analysis, lots of new expression of genes of additive effects for body weight, total length and standard length existed during April to August and significant new expression of genes from dominance effects for these three traits at the other period. New expression from additive and dominance effect genes for body height occurred intermittently during the ontogeny. The conditional genetic procedure is a useful tool to understand the expression of genes controlling developmental quantitative traits at a specific developmental period ( t − 1 → t) during ontogeny. It is also important to determine the appropriate developmental period ( t − 1 → t) for trait measurement in developmental quantitative genetic analysis in fish.

Genetic engineering in conifer forestry: Technical and social considerations

Over the past 20 years, DNA-based biotechnologies have been applied to agricultural production and many crops with new and useful attributes have been cultivated in various countries. The adoption of this new technology by farmers has been swift, and benefits in terms of increased production per unit land and environmental benefits are becoming obvious. In forestry, the application of biotechnology is somewhat lagging behind and to date there are no commercial plantations with genetically modified trees. However, most tree species used in plantation forestry have been genetically transformed, and results demonstrate the successful and correct expression of new genes in these plants. At the same time, this new technology is being viewed with concern, very similar to the concerns voiced over the use of genetic engineering in agriculture. This paper discusses some of the issues involved for world forestry, with particular focus on future demand for timber and timber products and how modern biotechnology can contribute to meet the growing demand. Tree genetic engineering techniques will be outlined, and results reviewed for a number of species. Concerns over the use of this new technology will be described and analyzed in relation to scientific considerations.

Developmental regulation of homeobox gene expression in dorsal root ganglion neurons is not recapitulated during regeneration of the crushed sciatic nerve

The adult peripheral nervous system is able to regenerate after injury. Regeneration is associated with the expression of new genes and proteins. Proteins abundant in developing axons increase in expression after injury, whereas proteins involved in neurotransmission are downregulated. It has been hypothesized that molecular mechanisms underlying regeneration-associated alterations in gene expression may be a recapitulation of developmental processes. These gene expression changes are likely to be regulated by changes in the gene expression of transcription factors. As homeobox genes play important roles in embryonic development of the nervous system, it makes them candidates for a regulatory role in the process of regeneration. Here we show that the relative mRNA expression levels of Isl1 decreased shortly after crush, but those of DRG11, Lmx1b, and Pax3 did not change after crush. These data indicate that the developmental expression patterns of the homeobox genes studied here are not recapitulated during regeneration of the dorsal root ganglia neurons. We conclude that developmental gene expression programs controlled by these homeobox genes are not directly involved in sciatic nerve regeneration.

A new evaluation of our life-support system.

After more than 150 years of research in microbiology, new technologies and new insights into the microbial world have sparked a revolution in the field. This is a much needed development, not only to renew interest in prokaryote research, but also to meet many emerging challenges in medicine, agriculture and industrial processes. Although many microbiologists—such as Emil von Behring, Robert Koch, Jacques Monod, Francois Jacob, Andre Lwoff, Alexander Fleming, Selman A. Waksman and Joshua Lederberg—grace the list of Nobel laureates, attention moved away from microbiology as biologists focused their interest on eukaryotic cells and higher organisms in the 1970s and 1980s. Furthermore, from the beginning, research on prokaryotes has suffered from an anthropocentric view, regarding as interesting only those organisms that cause disease or that can be exploited for industrial or agricultural use. But the advent of new technologies, some of which have been driven by a need to understand eukaryotes, may change this. We are increasingly realizing how little we know about microbes in general, their diversity, the mechanisms of their evolution and adaptation and their modes of existence within, and communication with, their environment and higher organisms. As bacteria have succeeded in occupying virtually all ecological niches on this planet, ranging from arctic regions to oceanic hot springs, they hold an immense wealth of genetic information that we have barely started to explore and that may provide many useful applications for humans. The new technologies that allow us to sequence and annotate whole genomes more rapidly and to analyse the expression of thousands of genes in a single experiment are likely to speed up this change, particularly as microbes are well suited for high‐throughput analysis. Any microbial genome can now be sequenced within a few hours and, in the near future, new bioinformatics tools will enable scientists not …

Mammary expression of new genes to combat mastitis.

ABSTRACTContinual advances in the ability to produce transgenic animals make it likely that such animals will become important components of animal agriculture. The full benefit of the technology, and justification of its initial cost outlay, will be dependent on the establishment within these animals of new traits not easily achievable by other means. Potential applications include enhanced nutrient digestibility with reduced fecal losses, significantly altered milk composition with superior nutritional properties, and enhanced disease resistance. Our goal is to enhance mastitis resistance of dairy cows by enabling the cells of the mammary gland to secrete additional antibacterial proteins. Proof of concept has been obtained through experimentation with a transgenic mouse model. Three lines of mice were developed that produce varying levels of lysostaphin in their milk. This protein has potent anti-staphylococcal activity and its secretion into milk confers substantial resistance to infection caused by intramammary challenge with Staphylococcus aureus, a major mastitis pathogen. Additional antibacterial proteins are being sought that will complement lysostaphin. A potential benefit of transgenic application of antibacterial proteins is the concomitant sparing in the agricultural use of antibiotics currently used as human therapeutics. Antibacterial proteins, such as lysostaphin, are not typically used as injectable or oral therapeutics because of immune-mediated or digestive destruction of their activity. In contrast, the immune system of transgenic animals will not consider the transgenic protein as being foreign. In addition we are exploring the potential of involution or mastitis responsive promoter elements for use in subsequent transgenic experiments designed to restrict lysostaphin production to these important time points. It is anticipated that genomics will play a role in unveiling candidate genes whose promoter elements will enable desired temporal expression patterns. The transgenic approach to insertion of new genetic material into agriculturally important animals is feasible but requires extensive prior evaluation of the transgene and transgene product in model systems.

Genetic analysis of transparency and chalkiness area at different filling stages of rice ( Oryza sativa L.)

Seven cytoplasmic male sterile lines and five restorer lines of indica rice ( Oryza sativa L.) were used to analyze genetic effects on transparency and chalkiness area at four filling stages. A developmental genetic model for quantitative traits of triploid endosperm in cereal crops were used for the data analysis. The unconditional analysis showed that the accumulated genetic effects of genes expressed from the initial time (at flowering and fertilization) to the filling time t were all significant for transparency and chalkiness area. These results indicated that the genetic effects of the triploid endosperm, cytoplasmic and diploid maternal plant were all of importance for both traits at various filling stages, especially for maternal additive and dominance effects on transparency. The relatively high endosperm and maternal additive effects on transparency and chalkiness area indicated that the two traits could be improved by selection in early generations. From the conditional analysis for the net genetic effects of genes expressed during time t−1 to time t, new expression of genes in endosperm, cytoplasm and maternal plant for transparency and chalkiness area was found at most of the filling stages, especially from 8 to 14 days after flowering for transparency and from 1 to 14 days after flowering for chalkiness area. Predicted genetic effects and conditional genetic effects at different filling stages showed that transparency and chalkiness area of offspring could be improved by using some parents, such as Zuo 5, because of their better endosperm additive and cytoplasmic effects.

Systemic acquired resistance

Plants can be induced to switch on defense reactions to a broad range of pathogens as a result of prior exposure to pathogens or to various chemicals or physical stress. Induced resistance is expressed locally, at the site of the infection or systemically, at sites remotely located from the initial infection. Upon recognition of the initial stimulus by the plant, a signal transduction pathway is set in motion, that includes intra and intercellular signals, and results in the activation of defense mechanisms, mostly by expression of new genes. This brief review will focus on some of the recent advances in the understanding of systemic acquired resistance and on the role played by salicylic acid in this process.

Analysis of mechanisms underlying adaptation processes

A system of elementary adaptation mechanisms is presented. The adaptations are considered as transients to a new homeostatic condition induced by an environmental change. We propose to distinguish adaptation mechanisms not directly related to gene expression (changes in the rate of synthesis and degradation of proteins, protein-ligand interactions, changes in viscosity of the membrane lipids) and the mechanisms relying on gene expression (changes in expression of already functioning genes, expression of new genes, mutations). Most of these mechanisms have phenotypic nature and just one (mutations) is genotypic. By the nature and time pattern of the environmental influence the adaptation processes can be divided into four types: phenotypic adaptations under rapidly (A) or gradually (B) alternating environmental factors, genotypic adaptations induced by an instant change (mutation) (C), and step adaptational changes (several or many mutations) (D). We propose a model based on a (second-order) linear differential equation qualitatively describing all four types of the adaptation processes.

Self-renewing stem cells

Cancer patients that receive high-dose chemotherapy depend on transplants of bone-marrow stem cells, but until now, the number of cells available for therapy has been limited by the amount that can be harvested from any one donor. A team led by Irving Weissman, professor at Stanford University, California, has reported that β-catenin instructs hematopoietic stem cells (HSCs) isolated from blood or bone marrow to self-renew, rather than terminally differentiate into mature blood cells in culture. Thus, the number of HSCs can be expanded in vitro. Cytoplasmic levels of β-catenin are raised as a result of signaling through the frizzled receptor, leading to the expression of new genes. The effect of β-catenin on stem-cell division can be reversed by the addition of axin, which acts to bring β-catenin into contact with an enzyme that triggers its degradation. Interestingly, this novel role for β-catenin implicates it in the development of leukemia, which occurs when blood-forming cells start to divide uncontrollably. MK

Integrative Food-Grade Expression System Based on the Lactose Regulon of Lactobacillus casei

The lactose operon from Lactobacillus casei is regulated by very tight glucose repression and substrate induction mechanisms, which made it a tempting candidate system for the expression of foreign genes or metabolic engineering. An integrative vector was constructed, allowing stable gene insertion in the chromosomal lactose operon of L. casei. This vector was based on the nonreplicative plasmid pRV300 and contained two DNA fragments corresponding to the 3' end of lacG and the complete lacF gene. Four unique restriction sites were created, as well as a ribosome binding site that would allow the cloning and expression of new genes between these two fragments. Then, integration of the cloned genes into the lactose operon of L. casei could be achieved via homologous recombination in a process that involved two selection steps, which yielded highly stable food-grade mutants. This procedure has been successfully used for the expression of the E. coli gusA gene and the L. lactis ilvBN genes in L. casei. Following the same expression pattern as that for the lactose genes, beta-glucuronidase activity and diacetyl production were repressed by glucose and induced by lactose. This integrative vector represents a useful tool for strain improvement in L. casei that could be applied to engineering fermentation processes or used for expression of genes for clinical and veterinary uses.

Historical perspectives of cellular oxygen sensing and responses to hypoxia.

The responses to acute and chronic hypoxia begin with oxygen sensing, and this historical perspective is written in line with this concept. The earliest pertinent work started with studies on fermentation in yeast in the 17th century, before the discovery of oxygen. It required 200 yr to localize the oxygen sensing within the cells and another 100 yr to discover the cellular oxidation reactions. Today, the consensus is that the mitochondrial respiratory chain is in part the site of oxygen sensing. In addition, membrane-bound NAD(P)H oxidase possibly takes part in oxygen sensing. Oxygen-sensing mechanisms occur in a tissue-specific fashion. For example, the carotid body responds to hypoxia promptly by eliciting a ventilatory response, whereas erythropoietin production in response to hypoxia requires more time, involving new expression of genes. The mechanism has therefore moved from the cells to genes.