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Background: TRIM proteins, recognized as a class of E3 ubiquitin ligases, are increasingly acknowledged for their antipathogen immune functions in mammals and fish. In the Chinese soft-shelled turtle (Pelodiscus sinensis), a secondary aquatic reptile that occupies a unique evolutionary position, the TRIM gene has rarely been reported. Methods and results: In the present study, 48 PsTRIM proteins were identified from the genome of Pelodiscus sinensis via Hidden Markov Model (HMM) searches and Signal Transduction ATPases with Numerous Domains (SMART) analysis. These PsTRIMs were found across 43 distinct scaffolds, and phylogenetic analyses classified them into three principal clades. The PsTRIMs feature a conserved assembly of either RING-B-box-coiled-coil (RBCC) or B-box-coiled-coil (BBC) domains at the N-terminus, in addition to eight unique domains at the C-terminus, including the B30.2 domain, 19 of which were identified. Expression profiling revealed ubiquitous expression of the 48 PsTRIMs across various P. sinensis tissues. Notably, seven PsTRIMs exhibited significant differential expression in liver transcriptomes following infection with Aeromonas hydrophila. Weighted gene coexpression network analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis implicated PsTRIM14 and PsTRIM28 as key players in host defense against bacterial invasion. Real-time quantitative PCR results indicated that PsTRIM1, PsTRIM2, PsTRIM14, and PsTRIM28 experienced marked upregulation in P. sinensis livers at 12 h post-infection with A. hydrophila. Conclusions: Our study is the first to comprehensively identify and analyze the functions of TRIM genes in P. sinensis, unveiling their considerable diversity and potential roles in modulating immune responses. [ABSTRACT FROM AUTHOR]

Background: Light is essential for kiwifruit development, in which photoresponse factors contributes greatly to the quality formation. 'Light sensitive hypocotyls, also known as light-dependent short hypocotyls' (LSH) gene family can participate in fruit development as photoresponse factor. However, the key LSH gene that determine kiwifruit development remains unclear. This study aim to screen and identify the key gene AaLSH9 in A. arguta. Materials and methods: Genome-wide identification of the LSH gene family was used to analyse LSH genes in kiwifruit. Homologous cloning was used to confirm the sequence of candidate LSH genes. qRT-PCR and cluster analysis of expression pattern were used to screen the key AaLSH9 gene. Subcellular localization of AaLSH9 in tobacco leaves and overexpression of AaLSH9 in Arabidopsis thaliana hy5 mutant plants were used to define the acting place in cell and identify molecular function, respectively. Results: We identified 15 LSH genes, which were divided into two sub-families namely A and B. Domain analysis of A and B showed that they contained different domain organizations, which possibly played key roles in the evolution process. Three LSH genes, AaLSH2, AaLSH9, and AaLSH11, were successfully isolated from Actinidia arguta. The expression pattern and cluster analysis of these three AaLSH genes suggested AaLSH9 might be a key photoresponse gene participating in fruit development in A. arguta. Subcellular localization showed AaLSH9 protein was located in the nucleus. The overexpression of AaLSH9 gene in Arabidopsis thaliana hy5 mutant plants partially complemented the long hypocotyls of hy5 mutant, implying AaLSH9 played a key role as photoresponse factor in cells. In addition, the seed coat color of A. thaliana over-expressing AaLSH9 became lighter than the wide type A.thaliana. Finally, AaCOP1 was confirmed as photoresponse factor to participate in developmental process by stable transgenic A. thaliana. Conclusions: AaLSH9 can be involved in kiwifruit (A. arguta) development as key photoresponse factor. Our results not only identified the photoresponse factors AaLSH9 and AaCOP1 but also provided insights into their key role in fruit quality improvement in the process of light response. [ABSTRACT FROM AUTHOR]

Background: Drought stress is a major constraint for rice production worldwide. Reproductive stage drought stress (RSDS) leads to heavy yield losses in rice. The prospecting of new donor cultivars for identification and introgression of QTLs of major effect (Quantitative trait locus) for drought tolerance is crucial for the development of drought-resilient rice varieties. Methods and results: Our study aimed to map QTLs associated with yield and its related traits under RSDS conditions. A saturated linkage map was constructed using 3417 GBS (Genotyping by sequencing) derived SNP (Single nucleotide polymorphism) markers spanning 1924.136 cM map length with an average marker density of 0.56 cM, in the F3 mapping population raised via cross made between the traditional ahu rice cultivar, Koniahu (drought tolerant) and a high-yielding variety, Disang (drought susceptible). Using the Inclusive composite interval mapping approach, 35 genomic regions governing yield and related traits were identified in pooled data from 198 F3 and F4 segregating lines evaluated for two consecutive seasons under both RSDS and irrigated control conditions. Of the 35 QTLs, 23 QTLs were identified under RSDS with LOD (Logarithm of odds) values ranging between 2.50 and 7.83 and PVE (phenotypic variance explained) values of 2.95–12.42%. Two major QTLs were found to be linked to plant height (qPH1.29) and number of filled grains per panicle (qNOG5.12) under RSDS. Five putative QTLs for grain yield namely, qGY2.00, qGY5.05, qGY6.16, qGY9.19, and qGY10.20 were identified within drought conditions. Fourteen QTL regions having ≤ 10 Mb QTL interval size were further analysed for candidate gene identification and a total of 4146 genes were detected out of these 2263 (54.63%) genes were annotated to at least one gene ontology (GO) term. Conclusion: Several QTLs associated with grain yield and yield components and putative candidate genes were identified. The putative QTLs and candidate genes identified could be employed to augment drought resilience in rice after further validation through MAS strategies. [ABSTRACT FROM AUTHOR]

Particle Swarm Optimization (PSO) has a limitation of early convergence and needs to be improved to find the global optima. The main objective here is to improve its exploration capability without deteriorating the exploitation capability. For this purpose, a modified version of PSO, namely Elitist Random Swapped Particle Swarm Optimization (ERSPSO), has been proposed. The elitist (fittest) particles in the swarm guide the other particles to improve their position. To enhance exploration in the search process a swapping of the randomly selected parts of the elitist particle positions (candidate solution) has been made. Consequently, a perturbation is applied to further improve the exploration. The proposed ERSPSO has been applied to the full benchmark set of 25 functions (CEC 2005) as well as complex real life problems like 'Gene selection by sample classification'. The new variant ERSPSO has been validated by the statistical metrics, convergence plot, sensitivity analysis using convergence behaviour, p-values using Wilcoxon rank sum test and Friedman rank test. For sample classification in Gene selection, VkNN (a new variant of kNN) is proposed which performs better than kNN in classification accuracy. The combined ERSPSO-VkNN is tested in 6 microarray datasets including 4 diseases. In most of the datasets (5 datasets out of 6) ERSPSO-VkNN performs better than the state-of-the-art methods. In different datasets, the percentage of classification accuracy of ERSPSO-VkNN varies between 89.29 and 100%. Finally, a biological verification is performed to show that many of the selected genes are biologically significant according to the reporting in current literature. [ABSTRACT FROM AUTHOR]

Main conclusion: In Magnolia polytepala, the formation of floral organization and color was attributed to tissue-dependent differential expression levels of MADS-box genes and anthocyanin biosynthetic genes. In angiosperms, the diversity of floral morphology and organization suggests its value in exploring plant evolution. Magnolia polytepala, an endemic basal angiosperm species in China, possesses three green sepal-like tepals in the outermost whorl and pink petal-like tepals in the inner three whorls, forming unique floral morphology and organization. However, we know little about its underlying molecular regulatory mechanism. Here, we first reported the full-length transcriptome of M. polytepala using PacBio sequencing. A total of 16 MADS-box transcripts were obtained from the transcriptome data, including floral homeotic genes (e.g., MpAPETALA3) and other non-floral homeotic genes (MpAGL6, etc.). Phylogenetic analysis and spatial expression pattern reflected their putative biological function as their homologues in Arabidopsis. In addition, nine structural genes involved in anthocyanin biosynthesis pathway had been screened out, and tepal color difference was significantly associated with their tissue-dependent differential expression levels. This study provides a relatively comprehensive investigation of the MADS-box family and anthocyanin biosynthetic genes in M. polytepala, and will facilitate our understanding of the regulatory mechanism underlying floral organization and color in basal angiosperms. [ABSTRACT FROM AUTHOR]

The most challenging issue in diagnosing and treating neurological disorders is gene identification that causes the disease. Classification of the genes that cause or initiate different genes leading to diseases with neurological disorders like Parkinson's disease, is a grave challenge in biomedical research. Detecting neurological disorders has a significant contribution in genetics, which require the deployment of machine learning methods which are still in its infancy. For exploring protein sequences (genes), computational analysis is a vital technique, since a manual comparison of multiple sequences results in impracticality. It helps to find a gene in the sequence and to combine protein sequences into a class of similar sequence. There are many traditional methods available for detection of Parkinson's disease. However, relatively less comparative work is done on Machine Learning techniques using protein sequences for evaluation of Parkinson's disease. This paper demonstrates the comparison of multiple classification methods to identify Parkinson's disease using hydrophobicity and Amino Acid Composition as feature extraction methods. Classification methods are then combined to propose a 2-level ensemble method based on the false prediction rate. The performance of these methods is evaluated using Precision, Recall, F-Score and ROC curves. Experimental results have demonstrated that Random Forest, SVM, Neural Network (PCANNET) and Naïve Bayes classifiers individually performed best based on their performance metrics under 5-fold cross validation, whereas the proposed method outperforms Random Forest and SVM by 1.96%, NB by 1.1% and PCANNET by 1.68% respectively. Further, statistical analysis has been added to validate the proposed method. [ABSTRACT FROM AUTHOR]

The MYB family, one of the largest transcription factor (TF) families, plays an important role in plant growth, development, and stress response. Although genome-wide analysis of the MYB family has been performed in many species based on sequence similarity, predicting the potential functions of the MYB genes and classifying the regulators into specific metabolic pathways remains difficult. In this study, using a hidden Markov model search and co-expression regulatory network analysis, we demonstrated a process to screen and identify potential MYB TFs in the anthocyanin biosynthesis pathway of Gossypium hirsutum. As a result, we identified 617 and 784 MYB genes (812 in total) from the previously reported and recently released genomes, respectively. Using 126 structural genes involved in the anthocyanin biosynthesis pathway as targets for several co-expression network analyses, we sorted out 31 R2R3-MYB genes, which are potential regulators in the specific pathway. Phylogenetic and collinearity analyses indicated that 83.9% of the 31 MYB genes originated from whole genome duplication or polyploidization. In addition, we revealed relatively specific regulatory relationships between the MYB TFs and their target structural genes. Approximately, 71% of the MYBs could regulate only a single anthocyanin-related structural gene. Moreover, we found that the A- and D- subgenome homoeologs of MYB TFs in G. hirsutum rarely co-regulate the same target gene. The current study not only demonstrated an easy method to rapidly predict potential TFs in a specific metabolic pathway, but also enhanced our understanding of the evolution, gene characteristics, expression, and regulatory pattern of MYB TFs in G. hirsutum. [ABSTRACT FROM AUTHOR]

Thermopsis turcica Kit Tan, Vural & Küçüködük is an herbaceous perennial, endemic and listed as endangered species by IUCN in Turkey. This plant is noted for its unusual floral structure characterized by a 2-4 carpellary ovary. In this study, a DPD ( NADP+)-like gene was partially sequenced for the first time in T. turcica. Since there is no previous molecular genetic information available for T. turcica, RT-PCR was performed using degenerate primers targeted to conserved sequences of WUS protein homologues from related legume species. Amplified cDNAs of the expected size were sequenced and analyzed using bioinformatics tools. The analysis strongly suggested that a 283 bp PCR product was part of a dihydropyrimidine dehydrogenase (NADP+)-like coding sequence with a Flavin mononucleotide binding domain. The putative gene was named Tt- DPD and the partial CDS submitted to the NCBI database (accession number KT182937). This gene has not been identified previously in T. turcica. The DPD (NADP+) enzyme is the rate-limiting step in pyrimidine degradation, which is essential for the biosynthesis of beta-alanine and pantothenates in plants; it has also been shown to be required for normal seed development in Arabidopsis. Expression of Tt- DPD was monitored by both endpoint and real-time RT-PCR. High expression of the identified gene was observed in the mid-developmental stage of the pistil of T. turcica. The findings presented here provide a starting point for understanding the roles of this gene in pyrimidine catabolism in T. turcica. [ABSTRACT FROM AUTHOR]

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases of rice (Oryza sativa) worldwide. Identification and utilization of resistance genes in rice breeding is considered to be an effective and economical method to control this disease. Hanghui 1179 (HH1179) is a new native rice restorer line developed in South China. The hybrids derived from HH1179 show broad-spectrum resistance against rice blast in South China, and a further understanding of the genetic resistance in HH1179 will provide useful information for breeding resistant cultivars. In the present study, we used bulked segregant analysis combined with specific-length amplified fragment sequencing to identify a dominant gene from HH1179 that provides resistance against the rice blast isolate GD13-14. Association analysis indicated that the resistance gene is located on chromosome 6 and we mapped the target gene to a 100.8 kb region (between markers InDel-8 and RM19818) that contains the Pi2/ Pi9/Piz/Piz-t/Pi50 gene cluster. Candidate gene prediction and cDNA sequencing indicated that the target resistance gene in HH1179 is Pi2. Our findings will be valuable for resistance breeding with restorer line HH1179. [ABSTRACT FROM AUTHOR]

The advent of next generation sequencing has made possible massive availability of sequence information for in-depth structural and functional analysis of the genes and their encoded biological state in model and non-model organisms. In this study, we demonstrate a combinatorial approach for finding protein coding genes using ab initio and extrinsic evidence-based methods in monsonia ( Monsonia burkeana Planch. ex harv). This is an important herbal tea crop, yet little is known about its coding genes. To our knowledge, this is the first description of protein coding genes with detailed functional annotation in M. burkeana. This study demonstrates that (1) regions of transcript assembly potentially encode protein coding genes, (2) homologous evidence with known functions reliably assigns functions to the identified genes (3) conserved domains suggest evolutionary and functional relationship of the crop with other lineage and (4) accuracy of finding coding genes in alignment free models and in RNA-seq alignment based transcript assembly performs well. This study provides a glimpse of functional information of the protein coding region at the transcriptome level and can be used as the basis for further investigation of the underlying genetic composition and molecular functions associated with M. burkeana. [ABSTRACT FROM AUTHOR]

Bacteria of the genus Methylobacillus are methanotrophs, a metabolic feature that is widespread in the phylum Proteobacteria. The study demonstrates the isolation and characterization of a newly isolated Methylobacillus sp. V29b. which grows on methanol, protocatechuate, monobutyl phthalate, dibutyl phthalate, diethyl phthalate, benzyl butyl phthalate, dioctyl phthalate and diisodecyl phthalate. Methylobacillus sp. V29b was characterized with scanning electron microscopy, transmission electron microscopy, Gram staining, antibiotics sensitivity tests and biochemical characterization. It degrades 70 % of the initial DBP in minimal salt medium and 65 % of the initial DBP in samples contaminated with DBP. DBP biodegradation kinetics was explained by the Monod growth inhibition model. Values for maximum specific growth rate ( µ ) and half-velocity constant ( K ) are 0.07 h and 998.2 mg/l, respectively. Stoichiometry for DBP degradation was calculated for Methylobacillus sp. V29b. Four metabolic intermediates, dibutyl phthalate (DBP), monobutyl phthalate, phthalic acid and pyrocatechol, were identified. Based on the metabolic intermediates identified, a chemical pathway for DBP degradation was proposed. Six genes for phthalic acid degradation were identified from the genome of Methylobacillus sp. V29b. [ABSTRACT FROM AUTHOR]

The Human Genome Project was launched at the end of the 1980s. Since then, the cloning and identification of functional genes has been a major focus of research across the world. In China too, the potentially profound impact of such studies on the life sciences and on human health was realized, and relevant studies were initiated in the 1990s. To advance China's involvement in the Human Genome Project, in the mid-1990s, Committee of Experts in Biology from National High Technology Research and Development Program of China (863 Program) proposed the 'two 1%' goal. This goal envisaged China contributing 1% of the total sequencing work, and cloning and identifying 1% of the total human functional genes. Over the past 20 years, tremendous achievement has been accomplished by Chinese scientists. It is well known that scientists in China finished the 1% of sequencing work of the Human Genome Project, whereas, there is no comprehensive report about 'whether China had finished cloning and identifying 1% of human functional genes'. In the present study, the GenBank database at the National Center of Biotechnology Information, the PubMed search tool, and the patent database of the State Intellectual Property Office, China, were used to retrieve entries based on two screening standards: (i) Were the newly cloned and identified genes first reported by Chinese scientists? (ii) Were the Chinese scientists awarded the gene sequence patent? Entries were retrieved from the databases up to the cut-off date of 30 June 2011 and the obtained data were analyzed further. The results showed that 589 new human functional genes were first reported by Chinese scientists and 159 gene sequences were patented (). This study systematically summarizes China's contributions to human functional genomics research and answers the question 'has China finished cloning and identifying 1% of human functional genes?' in the affirmative. [ABSTRACT FROM AUTHOR]

Phosphorus (P) is one of the essential nutrient elements for plant growth and development because of its low availability and mobility in soil. To investigate genes which are involved in Pi starvation response in leaves and roots of Brassica napus, a survey of genes induced in Pi starvation was done by macroarray analysis. Among 3,000 cDNA clones, 94 genes were identified to be up-regulated, while 46 genes were detected to be down-regulated by Pi starvation in B. napus. The Pi starvation-induced genes represent a large range of functional categories including cell defense, cellular signal transduction, cellular transport, biogenesis of cellular components, protein synthesis, proteins with binding function, regulation of metabolism and so on. By comparative analysis, over 40% genes were overlapped with Pi starvation-induced genes in Arabidopsis, but the remaining was not identified in Arabidopsis. From the genes identified by macroarray analysis, 22 genes were selected for further quantitative reverse transcription (RT)-PCR assay and confirmed as Pi starvation-induced genes convincingly. The temporal expression patterns of 22 genes in roots and leaves were different during Pi starvation. Most of the 22 genes were expressed at relatively low level in leaves and roots, and at relatively high level in other tissues. The data presented in this study will facilitate the understanding of molecular mechanism of Pi starvation response in B. napus. [ABSTRACT FROM AUTHOR]

The bacteria Burkholderia cenocepacia, which cause pulmonary infections in people with low immunity and in children with inherited diseases such as cystic fibrosis, were studied. The virulence of these bacteria is related with their ability to form viscous biofilms in the lung bronchi and alveoli of patients. Data on the possibility of producing mutants with an altered changed biofilm formation ability using insertion mutagenesis and their characteristics in vivo and in vitro are presented. Three genes involved in the genetic regulation of biofilm formation were identified by cloning and sequencing fragments of mutant genes. Two of the identified genes are the global regulatory genes ompR and tetR, and their mutations result in a decrease or higher ability to form biofilms of B. cenocepacia. Proteomic analysis identified the proteins in mutant strains with a different expression level than in the initial strains. The adhesive properties of the biofilms formed by initial and mutant strains of Burkholderia were evaluated using light and scanning microscopy in an analysis of the interaction between these strains and abiotic surfaces and cell cultures of pulmonary epithelium HL. It was shown that mutant strains with a low ability to form biofilms were characterized by a disturbed adhesion process. [ABSTRACT FROM AUTHOR]

The subtelomere and a portion of the associated telomeric region (together named 3RTAS) of chromosome IIIR from the Arabidopsis thaliana ecotypes Columbia (Col) and Wassilewskija (Ws) were specifically amplified by polymerase chain reaction and subsequently cloned and sequenced. The centromere-proximal portion of 3RTAS from both ecotypes contained two newly identified potential genes, one encoding the chloroplast luminal 19-kDa protein precursor and the other encoding three potential alternatively spliced CCCH-type zinc finger proteins. The telomere-proximal portion of 3RTAS from the Col ecotype contained short duplicated fragments derived from chromosomes I, II, and III, and that from the Ws ecotype contained a duplicated fragment derived from chromosome V. Each duplicated fragment has diverged somewhat in sequence from that of the ectopic template. Small patches of homologous nucleotides were found within the flanking sequences of both the duplicated fragments and the corresponding ectopic template sequences. The structural characteristics of these duplicated fragments suggest that they are filler DNAs captured by non-homologous end joining during double-strand break repair. Our characterization of 3RTAS not only filled up a gap in the chromosome IIIR sequence of A. thaliana but also identified new genes with unknown functions. [ABSTRACT FROM AUTHOR]

Low levels of high-density lipoprotein cholesterol (HDL-C) are an independent risk factor for cardiovascular disease. To identify novel genetic variants that contribute to HDL-C, we performed genome-wide scans and quantitative association studies in two study samples: a Quebec-wide study consisting of 11 multigenerational families and a study of 61 families from the Saguenay–Lac St-Jean (SLSJ) region of Quebec. The heritability of HDL-C in these study samples was 0.73 and 0.49, respectively. Variance components linkage methods identified a LOD score of 2.61 at 98 cM near the marker D16S515 in Quebec-wide families and an LOD score of 2.96 at 86 cM near the marker D16S2624 in SLSJ families. In the Quebec-wide sample, four families showed segregation over a 25.5-cM (18 Mb) region, which was further reduced to 6.6 Mb with additional markers. The coding regions of all genes within this region were sequenced. A missense variant in CHST6 segregated in four families and, with additional families, we observed a P value of 0.015 for this variant. However, an association study of this single-nucleotide polymorphism (SNP) in unrelated Quebec-wide samples was not significant. We also identified an SNP (rs11646677) in the same region, which was significantly associated with a low HDL-C (P=0.016) in the SLSJ study sample. In addition, RT-PCR results from cultured cells showed a significant difference in the expression of CHST6 and KIAA1576, another gene in the region. Our data constitute additional evidence for a locus on chromosome 16q23-24 that affects HDL-C levels in two independent French-Canadian studies. [ABSTRACT FROM AUTHOR]

Salvia miltiorrhiza Bge. is a well-known traditional Chinese herb. Its roots have been formulated and used clinically for the treatment of various diseases. However, little genetic information has so far been available and this fact has become a major obstacle for molecular studies. To address this lack of genetic information, an Expressed Sequence Tag (EST) library from whole plantlets of S. miltiorrhiza was generated. From the 12959 cDNA clones that were randomly selected and subjected to single-pass sequencing from their 5′ ends, 10288 ESTs (with sizes⩾100 bp) were selected and assembled into 1288 contigs, leaving 2937 singletons, for a total of 4225 unigenes. These were analyzed using BLASTX (against protein databases), RPS-BLAST (against a conserved domain database) as well as the web-based KEGG Automatic Annotation Server for metabolic enzyme assignment. Based on the metabolic enzyme assignment, expression patterns of 14 secondary metabolic enzyme genes in different organs and under different treatments were verified using real-time PCR analysis. Additionally, a total of 122 microsatellites were identified from the ESTs, with 89 having sufficient flanking sequences for primer design. This set of ESTs represents a significant proportion of the S. miltiorrhiza transcriptome, and gives preliminary insights into the gene complement of S. miltiorrhiza. They will prove useful for uncovering secondary metabolic pathways, analyzing cDNA-array based gene expression, genetic manipulation to improve yield of desirable secondary products, and molecular marker identification. [ABSTRACT FROM AUTHOR]

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Recent work on gene concepts has been influenced by recognition of the extent to which RNA transcripts from a given DNA sequence yield different products in different cellular environments. These transcripts are altered in many ways and yield many products based, somehow, on the sequence of nucleotides in the DNA. I focus on alternative splicing of RNA transcripts (which often yields distinct proteins from the same raw transcript) and on 'gene sharing', in which a single gene produces distinct proteins with the exact same amino acid sequence. These are instances of molecular pleiotropy, in which distinct molecules are derived from a single putative gene. In such cases the cellular and external environments play major roles in determining which protein is produced. Where there is molecular pleiotropy, alternative gene concepts are naturally deployed; molecular epigenesis (revision of sequence-based information by altering molecular conformations or by action of noninformational molecules) plays a major role in orderly development. These results show that gene concepts in molecular biology do, and should, have both structural and functional components. They also show the need for a plurality of gene concepts and reveal fundamental difficulties in stabilizing gene concepts solely by reference to nucleotide sequence. [ABSTRACT FROM AUTHOR]

This is a review of the approaches that can be used to analyze genetic changes in ovarian cancer. Traditional gene localization methods are discussed, followed by a section on gene identification techniques. Once a putative disease-associated gene has been cloned, mutations have to be identified and analyzed. There are numerous mutation detection methods, and the most common ones are outlined. In the penultimate section, the role of immunohistochemistry as a surrogate method for mutation analysis is considered. Finally, the possible use of functional assays is discussed. At present, it would appear that DNA chip technology for the detection of mutations, and microarray analysis of gene expression, are two important techniques likely to have a significant impact on the genetic analysis of ovarian cancer. [ABSTRACT FROM AUTHOR]

The fully sequenced genomes of Arabidopsis, rice, tomato, potato, maize, wheat, and soybean offer large amounts of information about cellular and developmental biology. It is a central challenge of genomics to use this information in discovering the function of proteins and identifying developmentally important genes. Although classical genetic approaches to gene identification which rely on disruption of a gene leading to a recognizable phenotype continues to be an extremely successful one, T-DNA mediated gene trap tagging which has been developed that utilize random integration of reporter gene constructs has also proven to be an extremely powerful tool in plant cellular developmental biology. In this review, how gene trap tagging, promoter trap tagging, and enhancer trap tagging detection systems have been applied to plant biology is described and these gene identification techniques could be useful to the plant molecular biology and plant biotechnology community. [ABSTRACT FROM AUTHOR]

Functional identification of genes is an efficient way to study many biological processes in lower eukaryotes. However, an effective approach in mammalian cells is still under development. We designed a functional gene identification procedure and applied it in a study of tumor necrosis factor (TNF)-induced cell killing. This procedure employed a specially designed retroviral vector that allows random truncation of genes, efficiently selecting clones in which a gene was disrupted and quickly identifying disrupted genes. We have identified several novel genes by a preliminary test of this approach and confirmed by reconttitution that the genes we identified are required for TNF cytotoxicity in L929 cells. Because of the efficient identification of these components in TNF-induced cell killing, we have already been able to outline the killing pathway of TNF in L929 cells. Application of this method could be widespread because it can be used in studying any cellular responses if a specific selection assay can be set up. [ABSTRACT FROM AUTHOR]

Genes for resistance to Puccinia graminis tritici and Puccinia recondita tritici identified in four South African wheats were: Sr6, Sr8a, Sr9e, and Lr13 in 'W3762'; Sr5, Sr8a, Sr9b, Sr12, Sr24, Lr13, and Lr24 in 'W3760'; Sr2, Sr24, SrC, Lr13, and Lr24 in 'W3751'; and Sr7a, Sr23, Sr36, and Lr16 in 'W3755'. Genes Sr2, Sr9e, and Sr24 also conferred adult plant resistance to the predominant pathotypes of P. graminis tritici. Genes Sr7a, Sr23, and SrC, when present alone, did not confer acceptable adult plant resistance, even though low seedling reactions were associated with them when tested with the same pathotypes. Genetic recombination between Lr13 and Sr9e was estimated at 12.5%±2.3%. [ABSTRACT FROM AUTHOR]

'Chris' wheat possessed genes Sr5, Sr7a, Sr8a, Sr9g and Sr12. 'W3746', derived from the cross 'Chris'/'Baart', possessed Sr7a and Sr12. The response conferred by Sr7a was influenced by the genetic background. Although Sr7a or Sr12 alone conferred no observable resistance upon adult plants, the adult resistances of 'Chris' and 'W3746' to predominant pathotypes appeared to be associated with the interaction of Sr7a and Sr12, or genes at closely linked loci. [ABSTRACT FROM AUTHOR]