Identification Of Putative Genes Research Articles

Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability.

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

Biodegradation of phenol by Candida tropicalis sp.: Kinetics, identification of putative genes and reconstruction of catabolic pathways by genomic and transcriptomic characteristics

Candida tropicalis sp. was isolated with predominant biodegradation capability to phenol compounds, even with high concentration or in acid environment. The biodegradation of phenol was evaluated at the following concentrations 10–1750 mg L−1, the strain exhibited well biodegradation efficiency. The maximum specific growth rate was 0.660 h−1 and the specific biodegradation rates was 0.47 mg (phenol) [(mg (VSS) h]−1. Differentially expressed genes were screened out, and results revealed a complete process of energy and carbon metabolism. The genes’ arrangements and phylogenetic information showed the unique genetic characteristics of the strain. Catabolic pathways were reconstructed and some key phenol-degrading genes were obviously upregulated, including pheA, catA, OXCT and fadA. A notable detail that CMBL encoding carboxymethylenebutenolidase was speculated to be involved in a shortened pathway of phenol biodegradation, thereby contributing to the reconstruction of the novel phenol catabolic pathway through the hydrolases of dienelactone. Finally, key enzymes were verified by the analysis of specific activity.

Degradation of Phenol by Candida Tropicalis Sp.: Kinetics, Identification of Putative Genes and Reconstruction of Catabolic Pathways by Genomic and Transcriptomic Characteristics

Degradation of Phenol by Candida Tropicalis Sp.: Kinetics, Identification of Putative Genes and Reconstruction of Catabolic Pathways by Genomic and Transcriptomic Characteristics

Mapping of candidate genes involved in fatty acid synthesis in Brassica rapa

Oilseed crops are valuable sources of oil content and fatty acid constituents. Brassica rapa is a well-known oilseed and vegetable crop grown throughout the world. B. rapa has higher genomic similarities with model plant A. thaliana . The genetic regulation of fatty acid biosynthesis is well studied in A. thaliana as well as in B. napus. However, only little information on genetic regulation of fatty acid biosynthesis has been known in B. rapa . The objective of this work was to identify and map the genes involved in fatty acid biosynthesis process in B. rapa DH population (Yellow Sarson, YS-143 x Pak Choi, PC-175). 172 lines of DH68 population was used for genotyping of markers. Comparative mapping was performed to predict positions of genes in B. rapa using two approaches; homology with chiifu sequence and genomic block synteny A. thaliana and B. rapa . Primers were designed for 18 candidate genes and their 16 paralogs genes in B. rapa using Chiifu sequence. Among 31 markers genotyped, 13 markers were mapped in DH68 population are in agreement with predicted positions in genomic blocks. Thus, the research will be useful to co-localise QTLs with candidate gene, identification of putative genes as well as cis and trans positions of genes in future.

Identification of putative genes related to the survival of Arabidopsis thaliana shoot tips after cryopreservation

Identification of putative genes related to the survival of Arabidopsis thaliana shoot tips after cryopreservation

Abstract POSTER-TECH-1130: Identification of putative genes involved in early steps of epithelial ovarian cancer pathogenesis

Abstract Epithelial ovarian cancer (EOC) is a deadly q disease and the related statistics are alarming with 15000 lives claimed in USA each year. EOC is a subtle disease since the majority of patients at presentation are diagnosed with a higher stage disease characterized by an aggressive potential. Early diagnosis seems to be of importance since complete cure can reach up to 90% if the disease is diagnosed at an early stage. Therefore, biological markers to detect patients at an early stage of the disease progression are urgently needed. In this study, the focus was centered on the transcription factor E2F5 used as biomarker and highly expressed at early stages of EOC pathogenesis. Therefore, we hypothesize that downstream genes regulated by this transcription factor might be also involved in the early events leading to ovarian cancer and can therefore potentially serve as useful biomarkers. Chromatin Immuno-Precipitation (ChIP) was performed using two ovarian cancer cell lines SK-OV-3 and OVCAR-3 and an antibody against E2F5 transcription factor. The enriched chromatin was cloned and sequenced before using available databases for BLAST and identification of downstream regulated genes. A short list of relevant genes, all involved in cancer, was obtained and analysis for their putative role in early detection of EOC is ongoing. The selected genes will be also validated using frozen human ovarian tissues available in our institution. ChIP is a robust technology to identify genes regulated by E2F5 with a putative potential to play a crucial role in the early steps of ovarian cancer pathogenesis. Citation Format: Yahya Tamimi, Ikram Burney, Moza Al-Kalbani, Ritu Lakhtari, Roseline Godbout, Mansour Al-Moundhri. Identification of putative genes involved in early steps of epithelial ovarian cancer pathogenesis [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr POSTER-TECH-1130.

Abstract 4182: A screen for genes that define the strong gender bias nature of hepatocellular carcinoma using a transposon mutagenesis murine model

Abstract Introduction: Hepatocellular carcinoma (HCC) is a deadly disease where many of the underlying associated genetic mechanisms remain undiscovered. Although HCC has been relatively rare in the US, the growing number of patients with cirrhosis (due to hepatitis infection and/or obesity-related fatty liver) has accounted for a surge in the incidence of HCC. Using the conditional Sleeping Beauty (SB) transposon somatic insertional mutagenesis system in transgenic mice, a novel unbiased HCC genetic screen was performed to elucidate the important genes responsible for this disease1. Methods: Triple transgenic (containing the conditional SB transposase, transposon mutagenic vector and liver-specific Cre transgenes) and quadruple transgenic (as above plus a conditional dominant negative p53 allele) mice were generated and aged for tumorigenesis1. Results: Using this system combined with a conditional p53-deficient background, we were able to identify many HCC cancer candidate genes. In addition, liver tumor nodules were also isolated from experimental mice without a predisposed genetic background. Liver tumors were prevalent in male experimental mice, mimicking the strong gender bias in the incidence of HCC seen in humans. Liver tumors were isolated from female experimental mice with and without a p53-deficient background, only after a prolonged latency (>432-days). From wild-type female liver tumors, we identified 17 candidate genes including the Pten tumor suppressor gene. From p53-deficient female liver tumors, we identified 6 candidate genes including some genes that are implicated in the miRNA18a pathway. This miRNA pathway has been associated with increased incidence of HCC in female patients. Conclusion: SB system allows for the identification of putative genes involved in HCC development in female mice. Finally, our ultimate goal is that candidate genes will be useful in generating possible therapeutic agents for the treatment of HCC and increase our knowledge in defining the underlying genetic mechanisms associated with the strong gender bias nature of this deadly disease. 1. Keng, V.W., et al. (2009). A conditional transposon-based insertional mutagenesis screen for genes associated with mouse hepatocellular carcinoma. Nat Biotechnol. 27, 264-74. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4182.

Drosophila Proteome; Exome Re-sequencing; Sequencing in Nanopores

BioTechniquesVol. 46, No. 1 NIH Grant WatchOpen AccessDrosophila Proteome; Exome Re-sequencing; Sequencing in NanoporesK. Nybo† & B. Perry††K. Nybo††is assistant editor at BioTechniques.Search for more papers by this author & B. Perry††††is president of NIH Sales, Rockville, MD.Search for more papers by this authorPublished Online:25 Apr 2018https://doi.org/10.2144/000113054AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInReddit BioTechniques and NIH Sales reviewed grants made by the National Institutes of Health during 2008. Here are some highlights from among the largest R01 and R03 grants awarded last year.The Protein Complex Map of the Drosophila Proteome, $2,182,909(5R01HG003616-04, National Human Genome Research Institute)Spyridon Artavanis-Tsakonas (Harvard University Medical School, Boston, MA)Goal: To completely map protein interactions in Drosophila melanogaster. This will be accomplished by isolation of purified proteins that complex with tagged proteins and mass spectrometric analysis.Development and Implementation of Genome-wide Exome Re-sequencing for Medical Genetics, $1,784,943(1R01HL095045-01, National Heart, Lung, and Blood Institute)Stacey Gabriel (Massachusetts Institute of Technology, Cambridge, MA)Goal: To optimize and validate a cost-effective approach for whole-exon sequencing that will be used to sequence hundreds of samples at production scale. Next-generation sequencing technology will be employed. Data acquired from this project will facilitate broad, unbiased surveys of DNA-based variation in disease at a large enough scale to disclose statistically significant correlations.Electronic Sequencing in Nanopores, $1,685,766(2R01HG003703-04 and 5R01HG003703-03, National Human Genome Research Institute)Daniel Branton and Jene Golovchenko (Harvard University, Cambridge, MA)Goal: To create a nanopore detector chip for an instrument that generates base-dependent electronic signals from single strands of DNA as they pass through carbon nanotube probes. Inclusion of the resulting nanopores in the sequencing machine will resolve approximately 104 bases per second, allowing high quality sequencing of a mammalian genome within 20 hours for $1000.Tetrahymena Genome Sequencing Project, $1,373,429(7R01GM067012-04, National Institute of General Medical Sciences)Jonathan Eisen (University of California, Davis, Davis, CA)Goal: To complete whole-genome shotgun-sequencing, assembly, and annotation of the T. thermophila genome. Specifically, the project will result in sequence of high enough quality for post-genomic analysis, discovery of all genes, identification of putative genes, and prediction of gene function. The data will be immediately released on a TIGR website, a manually-curated Tetrahymena Genome Database, and a Tetrahymena-specific section on the NCBI website.Automated Alignment of MRI Rodent Brain to Sterotaxic Atlases, $175,750(1R03EB008134-01A1, National Institute of Biomedical Imaging and BioEngineering)Joseph Madeville (Massachusetts General Hospital, Boston, MA)Goal: To modify an optimized functional rodent MRI analysis scheme for open source distribution to the research community. The software resulting from this project will automate registration of MRI data to standardized stereotaxic coordinates and provide the means for transcribing anatomic regions based on histological atlases. This software will enable the use of extensive analysis packages developed for human MRI for rodent data.Application of Bioinformatics to Retinal Gene Regulation, $159,658(5R03EY015684-03, National Eye Institute)Jiang Qian (Johns Hopkins University, Baltimore, MD)Goal: To develop two algorithms for deciphering the transcriptional regulatory networks associated with retinal gene expression. Completion of the program will identify cis-regulatory motifs and predict transcription factor targets in retinal gene expression. Once established, these regulatory networks will be integrated with microarray data for prediction of transcription factor targets.FiguresReferencesRelatedDetails Vol. 46, No. 1 Follow us on social media for the latest updates Metrics History Published online 25 April 2018 Published in print January 2009 Information© 2009 Author(s)PDF download

Identification of Putative Gene Based Markers of Renal Toxicity

Identification of Putative Gene Based Markers of Renal Toxicity

Expanding functional spaces of enzymes by utilizing whole genome treasure for library construction

A huge database resulted from whole genome sequencings has provided a possibility of new information that is likely to extent the scope and thus changes the way of approach for the functional assigning of putative open reading frames annotated by whole genome sequence analyses. These are mainly realized by ease, one-step identification of putative genes using genomics or proteomics tools. A major challenge remained in biotechnology may translate these informations into better ways to screen or select a gene as a representative sequence. Further attempts to mine the related whole genes or partial DNA fragments from whole genome treasure, and then the incorporation of these sequences into a representative template, will result in the use of genetic information that can be translated into functional proteins or allowed the generation of new lineages as a valuable pool. Such screens enable rapid biochemical analysis and easy isolation of the target activity, thereby accelerating the screening of novel enzymes from the expanded library with related sequences. Information-based PCR amplification of whole genes and reconstitution of functional DNA fragments will provide a platform for expanding the functional spaces of potential enzymes, especially when used mixed- and metagenome as gene resources.

The neurobiology of autism: new pieces of the puzzle.

The neurobiologic basis of autism is reviewed, with discussion of evidence from genetic, magnetic resonance imaging, neuropathology, and functional neuroimaging studies. Although autism is a behaviorally valid syndrome, it is remarkably heterogeneous and involves multiple developmental domains as well as a wide range of cognitive, language, and socioemotional functioning. Although multiple etiologies are implicated, recent advances have identified common themes in pathophysiology. Genetic factors play a primary role, based on evidence from family studies, identification of putative genes using genome-wide linkage analyses, and comorbidities with known genetic mutations. The RELN gene, which codes for an extracellular protein guiding neuronal migration, has been implicated in autism. Numerous neuropathologic changes have been described, including macroencephaly, acceleration and then deceleration in brain growth, increased neuronal packing and decreased cell size in the limbic system, and decreased Purkinje cell number in the cerebellum. Abnormalities in organization of the cortical minicolumn, representing the fundamental subunit of vertical cortical organization, may underlie the pathology of autism and result in altered thalamocortical connections, cortical disinhibition, and dysfunction of the arousal-modulating system of the brain. The role of acquired factors is speculative, with insufficient evidence to link the measles-mumps-rubella (MMR) vaccine with autism or to change immunization practices.

Identification of putative genes in bean (Phaseolus vulgaris) genomic (Bng) RFLP clones and their conversion to STSs.

A set of 79 previously mapped bean (Phaseolus vulgaris) genomic (Bng) clones were partially sequenced. BLAST database searches detected homologies between 59 of these clones and genes from a variety of plants, especially Arabidopsis thaliana. Some matches in the database to the Bng clones included a putative P-glycoprotein-ABC transporter from Arabidopsis, an early nodulin-binding protein (ENBPI) from Medicago truncatula, a lon-protease protein from spinach, a branched-chain amino-acid aminotransferase from Arabidopsis, and a vacuolar sorting receptor (BP-80) from Pisum sativum. Additional matches were found for genes involved in isoprenoid biosynthesis, sulfur metabolism, proline biosynthesis, and floral development. Sequence tagged site (STSs) were produced for 16 of the clones, 2 of which contain simple sequence repeats (SSRs). Polymorphisms were detected for six of the STSs.

Identification of Putative Gene Encoded on ORF 16 of the 81kb Contig of Arabidopsis thaliana Chromosome III as .ALPHA.-Mannosidase.

We isolated cDNA corresponding to open reading frame (ORF) 16 of the 81 kb contig of Arabidopsis thaliana chromosome III [Quigley., Nucleic Acids Res., 24, 4313-4318 (1996)] and expressed alpha-mannosidase activity in tobacco suspension-cultured cells, which revealed that ORF16 encodes alpha-mannosidase. We also suggested that Arabidopsis harbors three genes encoding alpha-mannosidase by homology search against the database.

IAP retrotransposons in the mouse liver as reporters of ageing

IAP are endogenous retrovirus-like elements present at a thousand copies in the murine genome. They can modulate the level of expression of the tagged genes into which they have inserted, and conversely their activity could be influenced by the level of activity of the genes and/or DNA sequences into which they are embedded. In this report, we have analysed by Northern blots the pattern of expression of the IAP-related transcripts in the organs of young and ageing mice. We show that IAP transcripts of unexpected size (namely 10 kb and 6 kb) are induced in the liver of ageing mice from all inbred and hybrid strains tested. These transcripts are not detected in young mice, and their intensity disclose variations depending on the strain, as those observed for the two canonical 7.2 and 5.4 kb IAP transcripts. It is suggested that these age-dependent IAP transcripts originate from unique sites within the mouse genome that are ‘tagged’ by an IAP sequence, which would be sensitive both to strain-dependent cellular factors acting at the level of all IAPs, and to an age-dependent liver-specific cellular factor and/or DNA state, responsible for the position-dependent effect. These age-dependent transcripts should allow the identification of putative genes or factors of ‘senescence’.