Transcriptional factor DLX3 promotes the gene expression of enamel matrix proteins during amelogenesis.

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Zhang, Zhichun; Tian, Hua; Lv, Ping; Wang, Weiping; Jia, Zhuqing; Wang, Sainan; Zhou, Chunyan; Gao, Xuejun

2015-01-01

Mutation of distal-less homeobox 3 (DLX3) is responsible for human tricho-dento-osseous syndrome (TDO) with amelogenesis imperfecta, indicating a crucial role of DLX3 in amelogenesis. However, the expression pattern of DLX3 and its specific function in amelogenesis remain largely unknown. The aim of this study was to investigate the effects of DLX3 on enamel matrix protein (EMP) genes. By immunohistochemistry assays of mouse tooth germs, stronger immunostaining of DLX3 protein was identified in ameloblasts in the secretory stage than in the pre-secretory and maturation stages, and the same pattern was found for Dlx3 mRNA using Realtime PCR. In a mouse ameloblast cell lineage, forced expression of DLX3 up-regulated the expression of the EMP genes Amelx, Enam, Klk4, and Odam, whereas knockdown of DLX3 down-regulated these four EMP genes. Further, bioinformatics, chromatin immunoprecipitation, and luciferase assays revealed that DLX3 transactivated Enam, Amelx, and Odam through direct binding to their enhancer regions. Particularly, over-expression of mutant-DLX3 (c.571_574delGGGG, responsible for TDO) inhibited the activation function of DLX3 on expression levels and promoter activities of the Enam, Amelx, and Odam genes. Together, our data show that DLX3 promotes the expression of the EMP genes Amelx, Enam, Klk4, and Odam in amelogenesis, while mutant-DLX3 disrupts this regulatory function, thus providing insights into the molecular mechanisms underlying the enamel defects of TDO disease.

Transcriptional factor DLX3 promotes the gene expression of enamel matrix proteins during amelogenesis.

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Zhichun Zhang

Full Text Available Mutation of distal-less homeobox 3 (DLX3 is responsible for human tricho-dento-osseous syndrome (TDO with amelogenesis imperfecta, indicating a crucial role of DLX3 in amelogenesis. However, the expression pattern of DLX3 and its specific function in amelogenesis remain largely unknown. The aim of this study was to investigate the effects of DLX3 on enamel matrix protein (EMP genes. By immunohistochemistry assays of mouse tooth germs, stronger immunostaining of DLX3 protein was identified in ameloblasts in the secretory stage than in the pre-secretory and maturation stages, and the same pattern was found for Dlx3 mRNA using Realtime PCR. In a mouse ameloblast cell lineage, forced expression of DLX3 up-regulated the expression of the EMP genes Amelx, Enam, Klk4, and Odam, whereas knockdown of DLX3 down-regulated these four EMP genes. Further, bioinformatics, chromatin immunoprecipitation, and luciferase assays revealed that DLX3 transactivated Enam, Amelx, and Odam through direct binding to their enhancer regions. Particularly, over-expression of mutant-DLX3 (c.571_574delGGGG, responsible for TDO inhibited the activation function of DLX3 on expression levels and promoter activities of the Enam, Amelx, and Odam genes. Together, our data show that DLX3 promotes the expression of the EMP genes Amelx, Enam, Klk4, and Odam in amelogenesis, while mutant-DLX3 disrupts this regulatory function, thus providing insights into the molecular mechanisms underlying the enamel defects of TDO disease.

Uued muutused nõuavad enam selgitustööd / Katrin Saks

Index Scriptorium Estoniae

Saks, Katrin, 1956-

2008-01-01

Euroopa Liidu otsustest ja nende tähtsusest ning selgitamise vajadusest. Ilmunud ka Koit 22. jaan. 2008, lk. 6, pealkiri kujul: Muutused nõuavad poliitikutelt järjest enam selgitustööd, Meie Maa 22. jaan. 2008, lk. 2 ; Sakala 24. jaan. 2008, lk. 2 ; Valgamaalane 22. jaan. 2008, lk. 2 ; Virumaa Teataja 25. jaan. 2008, lk. 11 ; Lääne Elu 24. jaan. 2008, lk. 2 ; Pärnu Postimees 5. veeb. 2008, lk. 19

[Correlation and concordance between the national test of medicine (ENAM) and the grade point average (GPA): analysis of the peruvian experience in the period 2007 - 2009].

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Huamaní, Charles; Gutiérrez, César; Mezones-Holguín, Edward

2011-03-01

To evaluate the correlation and concordance between the 'Peruvian National Exam of Medicine' (ENAM) and the Mean Grade Point Average (GPA) in recently graduated medical students in the period 2007 to 2009. We carried out a secondary data analysis, using the records of the physicians applying to the Rural and Urban Marginal Service in Health of Peru (SERUMS) processes for the years 2008 to 2010. We extracted from these registers, the grades obtained in the ENAM and GPA. We performed a descriptive analysis using medians and 1st and 3rd quartiles (q1/q3); we calculated the correlation between both scores using the Spearman correlation coefficient, additionally, we conducted a lineal regression analysis, and the concordance was measured using the Bland and Altman coefficient. A total of 6 117 physicians were included, the overall median for the GPA was 13.4 (12.7/14.2) and for the ENAM was 11.6 (10.2/13.0).Of the total assessed, 36.8% failed the TEST. We observed an increase in annual median of ENAM scores, with the consequent decrease in the difference between both grades. The correlation between ENAM and PPU is direct and moderate (0.582), independent from the year, type of university management (Public or Private) and location. However, the concordance between both ratings is regular, with a global coefficient of 0.272 (CI 95%: 0.260 to 0.284). Independently of the year, location or type of university management, there is a moderate correlation between the ENAM and the PPU; however, there is only a regular concordance between both grades.

Molecular Basis of Human Enamel Defects

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Chatzopoulos Georgios

2014-03-01

Full Text Available During eruption of teeth in the oral cavity, the effect of gene variations and environmental factors can result in morphological and structural changes in teeth. Amelogenesis imperfecta is a failure which is detected on the enamel of the teeth and clinical picture varies by the severity and type of the disease. Classification of the types of amelogenesis imperfecta is determined by histological, genetic, clinical and radiographic criteria. Specifically, there are 4 types of amelogenesis imperfecta (according to Witkop: hypoplastic form, hypo-maturation form, hypo-calcified form, and hypo-maturation/hypoplasia form with taurodontism and 14 subcategories. The diagnosis and classification of amelogenesis imperfecta has traditionally been based on clinical presentation or phenotype and the inheritance pattern. Several genes can be mutated and cause the disease. Millions of genes, possibly more than 10,000 genes produce proteins that regulate synthesis of enamel. Some of the genes and gene products that are likely associated with amelogenesis imperfecta are: amelogenin (AMELX, AMELY genes, ameloblastin (AMBN gene, enamelin (ENAM gene, enamelysin (MMP20 gene, kalikryn 4 (KLK 4 gene, tuftelins (Tuftelin gene, FAM83H (FAM83H gene and WDR72 (WDR72 gene. Particular attention should be given by the dentist in recognition and correlation of phenotypes with genotypes, in order to diagnose quickly and accurately such a possible disease and to prevent or treat it easily and quickly. Modern dentistry should restore these lesions in order to guarantee aesthetics and functionality, usually in collaboration with a group of dentists.

Amelogenesis imperfecta caused by N-terminal enamelin point mutations in mice and men is driven by endoplasmic reticulum stress.

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Brookes, Steven J; Barron, Martin J; Smith, Claire E L; Poulter, James A; Mighell, Alan J; Inglehearn, Chris F; Brown, Catriona J; Rodd, Helen; Kirkham, Jennifer; Dixon, Michael J

2017-05-15

'Amelogenesis imperfecta' (AI) describes a group of inherited diseases of dental enamel that have major clinical impact. Here, we identify the aetiology driving AI in mice carrying a p.S55I mutation in enamelin; one of the most commonly mutated proteins underlying AI in humans. Our data indicate that the mutation inhibits the ameloblast secretory pathway leading to ER stress and an activated unfolded protein response (UPR). Initially, with the support of the UPR acting in pro-survival mode, Enamp.S55I heterozygous mice secreted structurally normal enamel. However, enamel secreted thereafter was structurally abnormal; presumably due to the UPR modulating ameloblast behaviour and function in an attempt to relieve ER stress. Homozygous mutant mice failed to produce enamel. We also identified a novel heterozygous ENAMp.L31R mutation causing AI in humans. We hypothesize that ER stress is the aetiological factor in this case of human AI as it shared the characteristic phenotype described above for the Enamp.S55I mouse. We previously demonstrated that AI in mice carrying the Amelxp.Y64H mutation is a proteinopathy. The current data indicate that AI in Enamp.S55I mice is also a proteinopathy, and based on comparative phenotypic analysis, we suggest that human AI resulting from the ENAMp.L31R mutation is another proteinopathic disease. Identifying a common aetiology for AI resulting from mutations in two different genes opens the way for developing pharmaceutical interventions designed to relieve ER stress or modulate the UPR during enamel development to ameliorate the clinical phenotype. © The Author 2017. Published by Oxford University Press.

A Community Seismic Experiment in the ENAM Primary Site

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Van Avendonk, H. J.

2012-12-01

Eastern North America (ENAM) was chosen as a GeoPRISMS Rift Initiation and Evolution primary site because it represents a mature continental margin with onshore and offshore rift basins in which the record of extension and continental break-up is preserved. The degree to which syn-rift magmatism and preexisting lithospheric weaknesses controlled the evolution of the margin can be further investigated if we image its 3-D structure at small and large length scales with active-source and earthquake seismic imaging. In the Summer of 2012 we submitted a proposal to the US National Science Foundation for an ambitious plan for data acquisition on a 400 km wide section of the mid-Atlantic East Coast margin around Cape Hatteras, from unextended continental lithosphere onshore to mature oceanic lithosphere offshore. This area includes an important along-strike transition in the morphology of the margin from the Carolina Trough to the Baltimore Canyon Trough, and two major fracture zones that are associated with significant offsets at the modern Mid-Atlantic Ridge. The study area also covers several features representing the post-rift modification of the margin by slope instability and fluid flow. As the Earthscope Transportable Array reaches the East Coast of the US in 2013 and 2014, we will have an unprecedented opportunity to image the detailed structure of the rifted margin. To make effective use of the research infrastructure, including the seismic vessel R/V Marcus Langseth, the Earthscope seismic instrumentation, and US OBS Instrument Pool, we propose to collect a suite of seismic data at the mid-Atlantic margin in the context of a community-driven experiment with completely open data access. This multi-faceted seismic experiment offers an immense opportunity for education of young scientists. We propose an integrated education effort during and after acquisition. The science and field parties for data acquisition will largely consist of young scientists, who will be

Amelogenesis imperfecta

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Aldred Michael

2007-04-01

Full Text Available Abstract Amelogenesis imperfecta (AI represents a group of developmental conditions, genomic in origin, which affect the structure and clinical appearance of enamel of all or nearly all the teeth in a more or less equal manner, and which may be associated with morphologic or biochemical changes elsewhere in the body. The prevalence varies from 1:700 to 1:14,000, according to the populations studied. The enamel may be hypoplastic, hypomineralised or both and teeth affected may be discoloured, sensitive or prone to disintegration. AI exists in isolation or associated with other abnormalities in syndromes. It may show autosomal dominant, autosomal recessive, sex-linked and sporadic inheritance patterns. In families with an X-linked form it has been shown that the disorder may result from mutations in the amelogenin gene, AMELX. The enamelin gene, ENAM, is implicated in the pathogenesis of the dominant forms of AI. Autosomal recessive AI has been reported in families with known consanguinity. Diagnosis is based on the family history, pedigree plotting and meticulous clinical observation. Genetic diagnosis is presently only a research tool. The condition presents problems of socialisation, function and discomfort but may be managed by early vigorous intervention, both preventively and restoratively, with treatment continued throughout childhood and into adult life. In infancy, the primary dentition may be protected by the use of preformed metal crowns on posterior teeth. The longer-term care involves either crowns or, more frequently these days, adhesive, plastic restorations.

Pengaruh Relationship Marketing Dan Customer Satisfaction Terhadap Customer Loyalty Pada Penjualan Sepeda Motor Honda Di PT Enam Tiga Sejahtera Tahun 2013

OpenAIRE

., Kadek Rai Suwena, S.Pd., M.Pd.; ., Dr. Iyus Akhmad Haris,M.Pd; ., Jumati

2014-01-01

Penelitian ini bertujuan untuk mengetahui pengaruh; (1) relationship marketing terhadap customer satisfaction, (2) relationship marketing terhadap customer loyalty, (3) customer satisfaction terhadap customer loyalty, (4) pengaruh relationship marketing terhadap customer loyalty melalui customer satisfaction. Populasi dalam penelitian ini adalah pelanggan yang telah membeli membeli sepeda motor Honda di PT Enam Tiga Sejahtera tahun 2013, jumlah sampel sebanyak 97 responden, dengan teknik peng...

Missense Mutation in Fam83H Gene in Iranian Patients with Amelogenesis Imperfecta.

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Pourhashemi, S Jalal; Ghandehari Motlagh, Mehdi; Meighani, Ghasem; Ebrahimi Takaloo, Azadeh; Mansouri, Mahsa; Mohandes, Fatemeh; Mirzaii, Maryam; Khoshzaban, Ahad; Moshtaghi, Faranak; Abedkhojasteh, Hoda; Heidari, Mansour

2014-12-01

Amelogenesis Imperfecta (AI) is a disorder of tooth development where there is an abnormal formation of enamel or the external layer of teeth. The aim of this study was to screen mutations in the four most important candidate genes, ENAM, KLK4, MMP20 and FAM83H responsible for amelogenesis imperfect. Geneomic DNA was isolated from five Iranian families with 22 members affected with enamel malformations. The PCR amplifications were typically carried out for amplification the coding regions for AI patients and unaffected family members. The PCR products were subjected to direct sequencing. The pedigree analysis was performed using Cyrillic software. One family had four affected members with autosomal dominant hypocalcified amelogenesis imperfecta (ADHPCAI); pedigree analysis revealed four consanguineous families with 18 patients with autosomal recessive hypoplastic amelogenesis imperfecta (ARHPAI). One non-synonymous single-nucleotide substitution, c.1150T>A, p. Ser 342Thr was identified in the FAM83H, which resulted in ADHCAI. Furthermore, different polymorphisms or unclassified variants were detected in MMP20, ENAM and KLK4. Our results are consistent with other studies and provide further evidence for pathogenic mutations of FAM83H gene. These findings suggest different loci and genes could be implicated in the pathogenesis of AI.

Bmp2 deletion causes an amelogenesis imperfecta phenotype via regulating enamel gene expression.

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Guo, Feng; Feng, Junsheng; Wang, Feng; Li, Wentong; Gao, Qingping; Chen, Zhuo; Shoff, Lisa; Donly, Kevin J; Gluhak-Heinrich, Jelica; Chun, Yong Hee Patricia; Harris, Stephen E; MacDougall, Mary; Chen, Shuo

2015-08-01

Although Bmp2 is essential for tooth formation, the role of Bmp2 during enamel formation remains unknown in vivo. In this study, the role of Bmp2 in regulation of enamel formation was investigated by the Bmp2 conditional knock out (Bmp2 cKO) mice. Teeth of Bmp2 cKO mice displayed severe and profound phenotypes with asymmetric and misshaped incisors as well as abrasion of incisors and molars. Scanning electron microscopy analysis showed that the enamel layer was hypoplastic and enamel lacked a typical prismatic pattern. Teeth from null mice were much more brittle as tested by shear and compressive moduli. Expression of enamel matrix protein genes, amelogenin, enamelin, and enamel-processing proteases, Mmp-20 and Klk4 was reduced in the Bmp2 cKO teeth as reflected in a reduced enamel formation. Exogenous Bmp2 up-regulated those gene expressions in mouse enamel organ epithelial cells. This result for the first time indicates Bmp2 signaling is essential for proper enamel development and mineralization in vivo. © 2015 Wiley Periodicals, Inc.

New insights into the functions of enamel matrices in calcified tissues

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Satoshi Fukumoto

2014-05-01

Full Text Available Ameloblasts secrete enamel matrix proteins, including amelogenin, ameloblastin, enamelin, amelotin, and Apin/odontogenic ameloblast-associated protein (Apin/ODAM. Amelogenin is the major protein component of the enamel matrix. Amelogenin, ameloblastin, and enamelin are expressed during the secretory stage of ameloblast, while amelotin and Apin/ODAM are expressed during the maturation. Amelogenin and ameloblastin are also expressed in osteoblasts, and they regulate bone formation. In addition, recent studies show the importance of protein–protein interactions between enamel matrix components for enamel formation. In a mouse model mimicking a mutation of the amelogenin gene in amelogenesis imperfect (AI in humans, the mutated amelogenin forms a complex with ameloblastin, which accumulates in the endoplasmic reticulum/Golgi apparatus and causes ameloblast dysfunction resulting in AI phenotypes. Ameloblastin is a cell adhesion molecule that regulates cell proliferation. It inhibits odontogenic tumor formation and regulates osteoblast differentiation through binding to CD63. Amelotin interacts with Apin/ODAM, but not ameloblastin, while Apin/ODAM binds to ameloblastin. These interactions may be important for enamel mineralization during amelogenesis. The enamel matrix genes are clustered on human chromosome 4 except for the amelogenin genes located on the sex chromosomes. Genes for these enamel matrix proteins evolved from a common ancestral gene encoding secretory calcium-binding phosphoprotein.

Defining a new candidate gene for amelogenesis imperfecta: from molecular genetics to biochemistry.

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Urzúa, Blanca; Ortega-Pinto, Ana; Morales-Bozo, Irene; Rojas-Alcayaga, Gonzalo; Cifuentes, Víctor

2011-02-01

Amelogenesis imperfecta is a group of genetic conditions that affect the structure and clinical appearance of tooth enamel. The types (hypoplastic, hypocalcified, and hypomature) are correlated with defects in different stages of the process of enamel synthesis. Autosomal dominant, recessive, and X-linked types have been previously described. These disorders are considered clinically and genetically heterogeneous in etiology, involving a variety of genes, such as AMELX, ENAM, DLX3, FAM83H, MMP-20, KLK4, and WDR72. The mutations identified within these causal genes explain less than half of all cases of amelogenesis imperfecta. Most of the candidate and causal genes currently identified encode proteins involved in enamel synthesis. We think it is necessary to refocus the search for candidate genes using biochemical processes. This review provides theoretical evidence that the human SLC4A4 gene (sodium bicarbonate cotransporter) may be a new candidate gene.

Molecular decay of enamel matrix protein genes in turtles and other edentulous amniotes

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Meredith Robert W

2013-01-01

Full Text Available Abstract Background Secondary edentulism (toothlessness has evolved on multiple occasions in amniotes including several mammalian lineages (pangolins, anteaters, baleen whales, birds, and turtles. All edentulous amniote clades have evolved from ancestors with enamel-capped teeth. Previous studies have documented the molecular decay of tooth-specific genes in edentulous mammals, all of which lost their teeth in the Cenozoic, and birds, which lost their teeth in the Cretaceous. By contrast with mammals and birds, tooth loss in turtles occurred in the Jurassic (201.6-145.5 Ma, providing an extended time window for tooth gene degradation in this clade. The release of the painted turtle and Chinese softshell turtle genomes provides an opportunity to recover the decayed remains of tooth-specific genes in Testudines. Results We queried available genomes of Testudines (Chrysemys picta [painted turtle], Pelodiscus sinensis [Chinese softshell turtle], Aves (Anas platyrhynchos [duck], Gallus gallus [chicken], Meleagris gallopavo [turkey], Melopsittacus undulatus [budgerigar], Taeniopygia guttata [zebra finch], and enamelless mammals (Orycteropus afer [aardvark], Choloepus hoffmanni [Hoffmann’s two-toed sloth], Dasypus novemcinctus [nine-banded armadillo] for remnants of three enamel matrix protein (EMP genes with putative enamel-specific functions. Remnants of the AMBN and ENAM genes were recovered in Chrysemys and retain their original synteny. Remnants of AMEL were recovered in both testudines, although there are no shared frameshifts. We also show that there are inactivated copies of AMBN, AMEL and ENAM in representatives of divergent avian lineages including Galloanserae, Passeriformes, and Psittaciformes, and that there are shared frameshift mutations in all three genes that predate the basal split in Neognathae. Among enamelless mammals, all three EMP genes exhibit inactivating mutations in Orycteropus and Choloepus. Conclusions Our results

Exclusion of known gene for enamel development in two Brazilian families with amelogenesis imperfecta.

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Santos, Maria C L G; Hart, P Suzanne; Ramaswami, Mukundhan; Kanno, Cláudia M; Hart, Thomas C; Line, Sergio R P

2007-01-31

Amelogenesis imperfecta (AI) is a genetically heterogeneous group of diseases that result in defective development of tooth enamel. Mutations in several enamel proteins and proteinases have been associated with AI. The object of this study was to evaluate evidence of etiology for the six major candidate gene loci in two Brazilian families with AI. Genomic DNA was obtained from family members and all exons and exon-intron boundaries of the ENAM, AMBN, AMELX, MMP20, KLK4 and Amelotin gene were amplified and sequenced. Each family was also evaluated for linkage to chromosome regions known to contain genes important in enamel development. The present study indicates that the AI in these two families is not caused by any of the known loci for AI or any of the major candidate genes proposed in the literature. These findings indicate extensive genetic heterogeneity for non-syndromic AI.

Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales.

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Deméré, Thomas A; McGowen, Michael R; Berta, Annalisa; Gatesy, John

2008-02-01

The origin of baleen in mysticete whales represents a major transition in the phylogenetic history of Cetacea. This key specialization, a keratinous sieve that enables filter-feeding, permitted exploitation of a new ecological niche and heralded the evolution of modern baleen-bearing whales, the largest animals on Earth. To date, all formally described mysticete fossils conform to two types: toothed species from Oligocene-age rocks ( approximately 24 to 34 million years old) and toothless species that presumably utilized baleen to feed (Recent to approximately 30 million years old). Here, we show that several Oligocene toothed mysticetes have nutrient foramina and associated sulci on the lateral portions of their palates, homologous structures in extant mysticetes house vessels that nourish baleen. The simultaneous occurrence of teeth and nutrient foramina implies that both teeth and baleen were present in these early mysticetes. Phylogenetic analyses of a supermatrix that includes extinct taxa and new data for 11 nuclear genes consistently resolve relationships at the base of Mysticeti. The combined data set of 27,340 characters supports a stepwise transition from a toothed ancestor, to a mosaic intermediate with both teeth and baleen, to modern baleen whales that lack an adult dentition but retain developmental and genetic evidence of their ancestral toothed heritage. Comparative sequence data for ENAM (enamelin) and AMBN (ameloblastin) indicate that enamel-specific loci are present in Mysticeti but have degraded to pseudogenes in this group. The dramatic transformation in mysticete feeding anatomy documents an apparently rare, stepwise mode of evolution in which a composite phenotype bridged the gap between primitive and derived morphologies; a combination of fossil and molecular evidence provides a multifaceted record of this macroevolutionary pattern.

Tragedy in Savar: Management of Victims in Enam Medical College Hospital

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Mithun Alamgir

2014-01-01

Full Text Available Background: Rana Plaza collapse is the worst and deadliest man-made industrial disaster in the history of garment sector in the world. Around 1200 people died and thousands more were injured. Most of the victims of the disaster were treated in Enam Medical College Hospital (EMCH. We conducted this study to give an overview on the disaster victims and services provided by EMCH. Objective: The study was done to observe the length of time between accident and admission in EMCH, length of time between admission and discharge, to observe the numbers, types and sites of injuries to the victims, medical measures given to the victims and finally to observe the status of the victims at the time of discharge. Materials and Methods: This descriptive type of observational study was carried out among the victims of Rana Plaza tragedy during the period of May to October 2013. All admitted patients in EMCH were included in the study. Purposive nonprobability sampling technique was applied in this research work. Data were collected from the hospital record. After collection, data were manually compiled, edited and analyzed. Results: Among 621 victims treated in different wards, 276 (44.45% were admitted to the hospital on the day of accident. Among the admitted patients, 255 (41.06% stayed in the hospital for 1--3 days,133 (21.42% for 4--7 days and 88 (14.17% for more than 10 days. Fracture and dislocation were present in 32.70% patients, lacerated injury in 18.20%, abrasion in 15.78%, bruise in 13.53%, incised wound in 15.45% and punctured wound in 4.34% patients. Single injury was present in 56.68% and rest had multiple injuries. Lower limbs were the most (33.01% affected part of the body followed by head and neck (22.06%, upper limbs (18.52%, thorax (17.55% and abdomen (8.86%. Two hundred seventy two patients (43.80% were improved after treatment and 56 (9.02% were fully cured; 23.83% of the victims were referred to higher medical centers for special

Proses Pengambilan Keputusan Adopsi Inovasi Teknologi Budidaya Kedelai Jenuh Air (Kasus: Labuhan Ratu Enam, Lampung Timur

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Nur Elisa Faizaty

2016-12-01

Full Text Available The expansion of crop land to suboptimal land (especially in the outside of Java Island should be set up as source of agriculture crop production growth. Saturated-soil Cultivation (SSC Technology is able to improve the productivity of soybean plants up to 4.0 tons/ha in the suboptimal land. This research is aims to examine the decision making process on innovation adoption of soybean Saturated-soil Cultivation (SSC Technology, conducted in Labuan Ratu Enam Village, East Lampung Regency. Main approaches were used in this research is Rogers’ theory of innovation diffusion. Decision process was divided into four main group of analysis: i communication channel and general description of stages in the innovation decision, ii influential variables of respondents’ characteristics on the knowledge stage using Kruskall-Wallis test, iii influential variables of the innovation’s attributes on the persuasion stage using Spearman Correlation test, and iv correlation between the stages of innovation decision process using Spearman Correlation test and Mann-Whitney test. The results  shows that i interpersonal channel is chosen as the way to diffuse SSC innovation to 25 potential farmer adopters through discussion, direct practice, and guidance; ii the influential variables of individuals’ characteristics are leve of nonformal education and level of motivation, while level of formal education and farming experience is not significant difference in their knowledge level about SSC; iii there is significant correlation between the level of respondents’ persuasion and their perception on the innovation complexity and triability, but not compatability and observability; iv each stage of SSC innovation-decision, one stage to another in sequence, has significant positive correlation.

Comparison of Two Mouse Ameloblast-like Cell Lines for Enamel-specific Gene Expression

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Juni eSarkar

2014-07-01

Full Text Available Ameloblasts are ectoderm-derived cells that produce an extracellular enamel matrix that mineralizes to form enamel. The development and use of immortalized cell lines, with a stable phenotype, is an important contribution to biological studies as it allows for the investigation of molecular activities without the continuous need for animals. In this study we compare the expression profiles of enamel-specific genes in two mouse derived ameloblast-like cell lines: LS8 and ALC cells. Quantitative PCR analysis indicates that, relative to each other, LS8 cells express greater mRNA levels for genes that define secretory-stage activities (Amelx, Ambn, Enam and Mmp20, while ALC express greater mRNA levels for genes that define maturation-stage activities (Odam and Klk4. Western blot analyses show that Amelx, Ambn and Odam proteins are detectable in ALC, but not LS8 cells. Unstimulated ALC cells form calcified nodules, while LS8 cells do not. These data provide greater insight as to the suitability of both cell lines to contribute to biological studies on enamel formation and biomineralization, and highlight some of the strengths and weaknesses when relying on enamel epithelial organ-derived cell lines to study molecular activities of amelogenesis.

Neanderthal and Denisova tooth protein variants in present-day humans.

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Clément Zanolli

Full Text Available Environment parameters, diet and genetic factors interact to shape tooth morphostructure. In the human lineage, archaic and modern hominins show differences in dental traits, including enamel thickness, but variability also exists among living populations. Several polymorphisms, in particular in the non-collagenous extracellular matrix proteins of the tooth hard tissues, like enamelin, are involved in dental structure variation and defects and may be associated with dental disorders or susceptibility to caries. To gain insights into the relationships between tooth protein polymorphisms and dental structural morphology and defects, we searched for non-synonymous polymorphisms in tooth proteins from Neanderthal and Denisova hominins. The objective was to identify archaic-specific missense variants that may explain the dental morphostructural variability between extinct and modern humans, and to explore their putative impact on present-day dental phenotypes. Thirteen non-collagenous extracellular matrix proteins specific to hard dental tissues have been selected, searched in the publicly available sequence databases of Neanderthal and Denisova individuals and compared with modern human genome data. A total of 16 non-synonymous polymorphisms were identified in 6 proteins (ameloblastin, amelotin, cementum protein 1, dentin matrix acidic phosphoprotein 1, enamelin and matrix Gla protein. Most of them are encoded by dentin and enamel genes located on chromosome 4, previously reported to show signs of archaic introgression within Africa. Among the variants shared with modern humans, two are ancestral (common with apes and one is the derived enamelin major variant, T648I (rs7671281, associated with a thinner enamel and specific to the Homo lineage. All the others are specific to Neanderthals and Denisova, and are found at a very low frequency in modern Africans or East and South Asians, suggesting that they may be related to particular dental traits or

Analisis Kerentanan Pulau-Pulau Kecil di Kecamatan Togean Kabupaten Tojo Una Una Provinsi Sulawesi Tengah (Studi Kasus P. Kukumbi, P. Enam, P. Mogo, P. Kadidiri, P. Pagempa, P. Tongkabo

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Mohamad Akbar

2017-04-01

Full Text Available This research was conducted in small islands area to Togean District, TojoUna-Una Regency Central Celebes by ecological and sosio-economic approach.  Methods those used in this research were vulnerability index, MCDM (multi criteria dimension making and Geographycal information system (SIG approach.  Data was collected bt participative and explorative approach.  Data analysed parameters using vulnerability, assessment method involved vulnerability variable parameters i.e. area characteristic, area degradation, sea level rise, human impact, economic exposure, economic remoteness.  The results shows the range ofcomposit vulnerability index for ecological (CVI-Ek is 0.00-0.77, economic (CVI-En is 0.00-0.75, and composite vulnerability ecological-economic (CVI-EE is 0.00-0.76.  Enam island (0.76and tongkabo island (0.66 is rated to high vulnerable (0.67, Mogo Island (0.14, Kukumbi Island (0.12, Pagempa Island (0.09 and Kadidiri Island (0.07, is considerednon vulnerable.  MCDM analysis result that is used to determine small island management model in Togean District, shows ecological criteria is most important compared with economy criteria and social criteria.  Analysis of SMART technique  shows the type small islands  sustainability management  scenario in Togean District, those are scenario A (adaptation, 0.94 and scenario B ( without adaptation, 0.55. Keywords : small island, composite vulnerability index, sustainability, togean district.

Dentin bond strength of two resin-ceramic computer-aided design/computer-aided manufacturing (CAD/CAM) materials and five cements after six months storage.

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Flury, Simon; Schmidt, Stefanie Zita; Peutzfeldt, Anne; Lussi, Adrian

2016-10-01

The aim was to investigate dentin bond strength of two resin-ceramic materials and five cements after 24 h and six months storage. Cylinders (n=15/group) of Lava Ultimate (3M ESPE) and VITA ENAMIC (VITA Zahnfabrik) were cemented to mid-coronal dentin of 300 extracted human molars with RelyX Ultimate (3M ESPE), PANAVIA F2.0 (Kuraray), Variolink II (Ivoclar Vivadent), els cem (Saremco Dental), or Ketac Cem Plus (3M ESPE). Shear bond strength (SBS) was measured after 24 h or six months storage (37°C, 100% humidity) and statistically analyzed (significance level: α=0.05). SBS varied markedly between Lava Ultimate and VITA ENAMIC, between the five cements, and between storage of either 24 h or six months. After six months, SBS was highest when Lava Ultimate was cemented with RelyX Ultimate and when VITA ENAMIC was cemented with RelyX Ultimate or with Variolink II. Lava Ultimate was somewhat more sensitive to storage than was VITA ENAMIC.

Juhan Parts : kasvu nimel tuleb kõvasti pingutada / Juhan Parts ; interv. Frank Sprenk-Dorn

Index Scriptorium Estoniae

Parts, Juhan, 1966-

2007-01-01

Majandus- ja kommunikatsiooniminister vastab küsimustele, mis olid tema arvates möödunud aastal Eesti majandust kõige enam mõjutanud sündmused ja mis muutused majanduses jäid möödunud aasta jooksul kõige enam silma nii negatiivse kui ka positiivse poole pealt

Factores asociados a la calificación del Examen Nacional de Medicina 2012 en internos de la UNMSM

Directory of Open Access Journals (Sweden)

Fernando Ricardo Arenas-Significación

2014-01-01

Full Text Available Introducción: El Examen Nacional de Medicina (ENAM es una herramienta que mide los conocimientos y el raciocinio clínico del interno como una forma de aproximarse a evaluar la calidad educativa. Objetivo: Determinar los factores asociados a la calificación del ENAM 2012 en internos de la Universidad Nacional Mayor de San Marcos (UNMSM. Diseño: Estudio transversal. Lugar: Facultad de Medicina Humana de la UNMSM, Lima, Perú. Participantes: Internos de Medicina Humana 2012. Intervenciones: Se analizó fuentes secundarias con el método de regresión logística binaria. Se determinó los coeficientes de correlación de Pearson y Spearman, así como la prueba t student. Principales medidas de resultados: Promedios de las calificaciones del ENAM, pertenencia a la promoción ingresante, sede hospitalaria de internado, orden de mérito según promedio ponderado universitario (PPU. Resultados: Los factores asociados a un mejor puntaje en el ENAM fueron pertenecer a la promoción ingresante 2006, realizar internado en EsSalud y ubicarse en el tercio superior y medio. Conclusiones: La pertenencia a la promoción ingresante 2006, la sede hospitalaria de internado y el orden de mérito según el PPU fueron factores asociados a obtener una calificación mayor o igual a trece en el ENAM 2012.

Interaction between the enamel matrix proteins amelogenin and ameloblastin

International Nuclear Information System (INIS)

Ravindranath, Hanumanth H.; Chen, Li-Sha; Zeichner-David, Margaret; Ishima, Rieko; Ravindranath, Rajeswari M.H.

2004-01-01

Enamel matrix consists of amelogenin and non-amelogenins. Though amelogenin is not involved in nucleation of minerals, the enamel mineralization is impaired when amelogenin or other matrix protein (ameloblastin/enamelin) genes are mutated. We hypothesize that amelogenin may promote enamel mineralization by interacting with the calcium-binding matrix proteins. Specific binding of amelogenin to N-acetylglucosamine (GlcNAc), GlcNAc-mimicking peptides (GMps), and their carrier proteins and the identification of amelogenin-trityrosyl-motif-peptide (ATMP) as a GlcNAc/GMp-binding domain in amelogenin favor the hypothesis. This study tested the interaction of amelogenin with ameloblastin, a carrier of GMp sequence at intermittent sites. Neither GlcNAc nor sialic acids were identified in the recombinant-ameloblastin. Amelogenin bound to recombinant-ameloblastin in both Western blots and in ELISA. More specifically, [ 3 H]ATMP bound to both recombinant and native ameloblastins. Dosimetry and Scatchard analyses showed the specific interaction between ATMP and ameloblastin, suggesting that amelogenin may interact with ameloblastin to form a heteromolecular assembly

Interaction between the enamel matrix proteins amelogenin and ameloblastin.

Science.gov (United States)

Ravindranath, Hanumanth H; Chen, Li-Sha; Zeichner-David, Margaret; Ishima, Rieko; Ravindranath, Rajeswari M H

2004-10-22

Enamel matrix consists of amelogenin and non-amelogenins. Though amelogenin is not involved in nucleation of minerals, the enamel mineralization is impaired when amelogenin or other matrix protein (ameloblastin/enamelin) genes are mutated. We hypothesize that amelogenin may promote enamel mineralization by interacting with the calcium-binding matrix proteins. Specific binding of amelogenin to N-acetylglucosamine (GlcNAc), GlcNAc-mimicking peptides (GMps), and their carrier proteins and the identification of amelogenin-trityrosyl-motif-peptide (ATMP) as a GlcNAc/GMp-binding domain in amelogenin favor the hypothesis. This study tested the interaction of amelogenin with ameloblastin, a carrier of GMp sequence at intermittent sites. Neither GlcNAc nor sialic acids were identified in the recombinant-ameloblastin. Amelogenin bound to recombinant-ameloblastin in both Western blots and in ELISA. More specifically, [(3)H]ATMP bound to both recombinant and native ameloblastins. Dosimetry and Scatchard analyses showed the specific interaction between ATMP and ameloblastin, suggesting that amelogenin may interact with ameloblastin to form a heteromolecular assembly.

Store-operated Ca2+ Entry Modulates the Expression of Enamel Genes.

Science.gov (United States)

Nurbaeva, M K; Eckstein, M; Snead, M L; Feske, S; Lacruz, R S

2015-10-01

Dental enamel formation is an intricate process tightly regulated by ameloblast cells. The correct spatiotemporal patterning of enamel matrix protein (EMP) expression is fundamental to orchestrate the formation of enamel crystals, which depend on a robust supply of Ca2+. In the extracellular milieu, Ca2+ -EMP interactions occur at different levels. Despite its recognized role in enamel development, the molecular machinery involved in Ca2+ homeostasis in ameloblasts remains poorly understood. A common mechanism for Ca2+ influx is store-operated Ca2+ entry (SOCE). We evaluated the possibility that Ca2+ influx in enamel cells might be mediated by SOCE and the Ca2+ release-activated Ca2+ (CRAC) channel, the prototypical SOCE channel. Using ameloblast-like LS8 cells, we demonstrate that these cells express Ca2+ -handling molecules and mediate Ca2+ influx through SOCE. As a rise in the cytosolic Ca2+ concentration is a versatile signal that can modulate gene expression, we assessed whether SOCE in enamel cells had any effect on the expression of EMPs. Our results demonstrate that stimulating LS8 cells or murine primary enamel organ cells with thapsigargin to activate SOCE leads to increased expression of Amelx, Ambn, Enam, Mmp20. This effect is reversed when cells are treated with a CRAC channel inhibitor. These data indicate that Ca2+ influx in LS8 cells and enamel organ cells is mediated by CRAC channels and that Ca2+ signals enhance the expression of EMPs. Ca2+ plays an important role not only in mineralizing dental enamel but also in regulating the expression of EMPs. © International & American Associations for Dental Research 2015.

"Mitte kunagi enam!" / Heino Piirsalu

Index Scriptorium Estoniae

Piirsalu, Heino

2007-01-01

Refereering Norra Reservohvitseride Assotsiatsiooni presidendi brigaadikindral Sigurd Hellstromi ettekandest "The Norwegian Home Guard - vital coponent in Norway's Homeland Defence" ( Norra kodukaitse - Norra kodumaakaitse vitaalne komponent) Liitlaste Reservohvitseride Ühingu sümpoosionil 6. juulil 2006. aastal Viterbos. 1946. aastal loodud Norra kodukaitsest

Identification of Pathogenic Leptospira in Rat and Shrew Populations Using rpoB Gene and Its Spatial Distribution in Boyolali District

Directory of Open Access Journals (Sweden)

Dyah Widiastuti

2016-08-01

Ngemplak dan Desa Jeron Kecamatan Nogosari, Kabupaten Boyolali. Pemeriksaan Polymerase Chain Reaction dilakukan pada 104 sampel ginjal tikus dari dua lokasi penelitian. Analisis spasial sederhana dilakukan untuk memetakan sebaran tikus yang positif Leptospira. Terdapat enam sampel positif gen rpoB Leptospira pada Rattus tanezumi, Rattus argentiventer dan Suncus murinus. Lima dari keenam sampel menunjukkan hubungan kekerabatan yang paling dekat dengan Leptospira borgpetersenii serovar Sejroe berdasarkan gen rpoB. Satu isolat tidak memiliki hubungan kekerabatan yang dekat dengan serovar manapun yang masuk dalam cluster. Analisis spasial berdasarkan jarak aktivitas harian tikus menunjukkan tikus positif Leptospira ditemukan berada dalam kisaran 30 meter dan 150 meter dari penderita leptospirosis.

Impact of three endocrine disruptors, Bisphenol A, Genistein and Vinclozolin on female rat enamel.

Science.gov (United States)

Jedeon, K; Berdal, A; Babajko, A

2016-06-28

Concerns about the potential adverse effectsof endocrine disruptors (EDs) have been increasingover the last three decades. BisphenolA (BPA), genistein (G) and vinclozolin (V) arethree widely used EDs sharing similar effects.Since populations are exposed to many diverseEDs simultaneously, we demonstratedrecently their impact alone or combined onmale rat tooth enamel. The purpose of thisstudy was therefore to assess their effects onfemale rat tooth enamel in order to understandwhy they are differentially sensitive. Ratswere exposed daily in utero and after birth tolow doses of EDs during the critical fetal andsuckling periods when amelogenesis takesplace. Enamel of rats exposed to EDs presentedopaque areas of hypomineralization. Theproportion of affected rats was the highestin the groups of rats treated with BPA aloneand higher in males than in females (in all thegroups). Comparison of enamel key gene expressionlevels showed modulations of Klk4and Enamelin in males but no significant variationsin females. These findings show thatfemale rats are less affected than males bythe three EDs chosen in this study and suggestthat enamel hypomineralization may differbetween males and females.

Nii enam ei saa / Mart Laar

Index Scriptorium Estoniae

Laar, Mart, 1960-

2001-01-01

Ilmunud ka: Pärnu Postimees 15. sept., lk. 2; Järva Teataja 15. sept., lk. 2; Põhjarannik 15. sept., lk. 2; Severnoje Poberezhje 15. sept., lk. 2; Lääne- Harju Ekspress 15. sept., lk. 4; Nädaline 15. sept., lk. 2; Võrumaa Teataja 15. sept., lk. 4; Lääne Elu 15. sept., lk. 2; Hiiumaa 15. sept., lk. 2; Meie Maa 15. sept., lk. 2; Valgamaalane 15. sept., lk. 2; Sakala 14. sept., lk. 2; Vooremaa 18. sept., lk. 2. Pärnumaa salaviinatragöödia. Autor: Isamaaliit

Microsoft enam ei kasva / Richart Waters

Index Scriptorium Estoniae

Waters, Richart

2003-01-01

Autor selgitab Microsoft'i näitel, miks väikese kasvuga ettevõte vajab teistsugust firmakultuuri ning dividendipoliitikat. Diagrammid: Käive, täiskohaga töötajate arv, töötajate antud aktsiaoptsioonid. Lisa: Microsofti elulugu. Vt. samas: Üheksa aastaga 59 firmat

Detection of Vibrio harveyi using hemolysin primer in tiger shrimp Penaeus monodon

Directory of Open Access Journals (Sweden)

Irma Suriyani

2015-05-01

Full Text Available ABSTRACT This study was aimed to analyze the sensitivity and ability of primer hemolysin in detecting pathogenetic Vibrio on tiger shrimp post-larvae (PL exposed under different exposure times in media inoculated with Vibrio harveyi. The PL of tiger shrimp were infected with 106 cfu/mL of V. harveyi by immersion method for three, six, 12, 24, 48 and 72 hours. The presence of hemolisin genes was detected by PCR techniques. The electrophoresis detected narrow hemolysin genes after PL were exposed for three and six hours. Clear visible bands of DNA Vibrio were observed for 12 hours of exposure. In contrast, no detected hemolysin gene of Vibrio was observed for PL exposed within 24, 48, and 72 hours. The rapid detection on Vibrio pathogenic for tiger shrimp PL should be conducted within three to 12 hours of exposure. No recommendation in utilizing this rapid detection for tiger shrimp PL exposed beyond 12 hours of V. harveyi. Keywords: specific primer, luminous Vibrio bacteria, pathogenic, PCR method, hemolysin gene  ABSTRAK Penelitian ini bertujuan untuk mengetahui kemampuan atau sensitivitas primer hemolisin dalam mendeteksi Vibrio patogen dengan lama pemaparan berbeda. Penelitian ini dilakukan dengan menginfeksikan Vibrio harveyi pada benur udang dengan metode perendaman pada konsentrasi 106 cfu/mL. Pengambilan sampel dilakukan pada waktu tiga, enam, 12, 24, 48, dan 72 jam pascainfeksi. Keberadaan gen hemolisin pada bakteri V. harveyi dideteksi menggunakan teknik polymerase chain reaction (PCR. Hasil elektroforesis memperlihatkan bahwa pada pemaparan tiga dan enam jam keberadaan gen hemolisin dari bakteri Vibrio patogen yang diinfeksikan sudah dapat terdeteksi pada benur walaupun masih terlihat tipis. Pada pemaparan 12 jam terlihat sangat jelas pita-pita DNA dari bakteri patogen. Sedangkan pada pemaparan 24, 48, dan 72 jam sudah tidak terdeteksi lagi gen hemolisin dari bakteri Vibrio. Hal ini diduga disebabkan terjadinya penurunan populasi

Enamel protein regulation and dental and periodontal physiopathology in MSX2 mutant mice.

Science.gov (United States)

Molla, Muriel; Descroix, Vianney; Aïoub, Muhanad; Simon, Stéphane; Castañeda, Beatriz; Hotton, Dominique; Bolaños, Alba; Simon, Yohann; Lezot, Frédéric; Goubin, Gérard; Berdal, Ariane

2010-11-01

Signaling pathways that underlie postnatal dental and periodontal physiopathology are less studied than those of early tooth development. Members of the muscle segment homeobox gene (Msx) family encode homeoproteins that show functional redundancy during development and are known to be involved in epithelial-mesenchymal interactions that lead to crown morphogenesis and ameloblast cell differentiation. This study analyzed the MSX2 protein during mouse postnatal growth as well as in the adult. The analysis focused on enamel and periodontal defects and enamel proteins in Msx2-null mutant mice. In the epithelial lifecycle, the levels of MSX2 expression and enamel protein secretion were inversely related. Msx2+/- mice showed increased amelogenin expression, enamel thickness, and rod size. Msx2-/- mice displayed compound phenotypic characteristics of enamel defects, related to both enamel-specific gene mutations (amelogenin and enamelin) in isolated amelogenesis imperfecta, and cell-cell junction elements (laminin 5 and cytokeratin 5) in other syndromes. These effects were also related to ameloblast disappearance, which differed between incisors and molars. In Msx2-/- roots, Malassez cells formed giant islands that overexpressed amelogenin and ameloblastin that grew over months. Aberrant expression of enamel proteins is proposed to underlie the regional osteopetrosis and hyperproduction of cellular cementum. These enamel and periodontal phenotypes of Msx2 mutants constitute the first case report of structural and signaling defects associated with enamel protein overexpression in a postnatal context.

MODEL PEMBELAJARAN TEACHING FACTORY UNTUK MENINGKATKAN KOMPETENSI SISWA DALAM MATA PELAJARAN PRODUKTIF

Directory of Open Access Journals (Sweden)

Dadang Hidayat M.

2011-11-01

Full Text Available Abstract: The Model of Teaching Factory to Promote Students' Competence in Productive Sub­jects. The present article reports on a research project using the model of six-step teaching factory known as Model TF-6M. This R & D project was aimed at promoting students' competences regarding productive subjects at Vocational Schools. The six steps in the teaching factory model include receiving orders, ana­lyzing orders, stating readiness in executing orders, execution of orders, doing quality control, and handing over products to customers. Prior to the implementation of the steps, the students and teachers made some agreements on the setting up of industrial atmosphere in the school, exercising communication skills, and exercising analysis of orders. The model was developed in the time blocks of six weeks in the fourth semester and six weeks in the fifth semester, which was subsequently followed with an exam on the competences. The results indicate that the model was effective in promoting students' productive competences. Abstrak: Model Pembelajaran Teaching Factory untuk Meningkatkan Kompetensi Siswa dalam Mata Pelajaran Produktif. Model teaching factory enam langkah adalah model pembelajaran hasil penelitian dengan menggunakan metode R&D. Model ini bertujuan meningkatkan kompetensi produktif siswa SMK. Enam langkah dari satu siklus model ini, yaitu menerima pemberi order, menganalisis order, menyatakan kesiapan mengerjakan order, mengerjakan order, melakukan quality control, dan menyerahkan order. Sebelum siklus model dilaksanakan, siswa dengan guru melakukan kesepakatan menciptakan iklim industri di sekolah, melakukan latihan berkomunikasi, dan berlatih menganalisis order. Model dilakukan dalam blok waktu enam minggu pada semester empat, enam minggu pada semester lima dan dilanjutkan dengan uji kompetensi. Hasil penelitian menunjukkan model ini efektif meningkatkan kompetensi produktif siswa.

Constantinople vs. Moscow / Aleksei Gynter

Index Scriptorium Estoniae

Gynter, Aleksei

2000-01-01

Konstantinoopoli patriarhi Bartholomeose visiit Eestisse ei toonud leevendust kahe õigeusu kogukonna vastasseisule, vaid puhus Konstantinoopolile ja Moskvale alluvate kirikute tüli veelgi enam lõkkele

Comparative temporospatial expression profiling of murine amelotin protein during amelogenesis.

Science.gov (United States)

Somogyi-Ganss, Eszter; Nakayama, Yohei; Iwasaki, Kengo; Nakano, Yukiko; Stolf, Daiana; McKee, Marc D; Ganss, Bernhard

2012-01-01

Tooth enamel is formed in a typical biomineralization process under the guidance of specific organic components. Amelotin (AMTN) is a recently identified, secreted protein that is transcribed predominantly during the maturation stage of enamel formation, but its protein expression profile throughout amelogenesis has not been described in detail. The main objective of this study was to define the spatiotemporal expression profile of AMTN during tooth development in comparison with other known enamel proteins. A peptide antibody against AMTN was raised in rabbits, affinity purified and used for immunohistochemical analyses on sagittal and transverse paraffin sections of decalcified mouse hemimandibles. The localization of AMTN was compared to that of known enamel proteins amelogenin, ameloblastin, enamelin, odontogenic ameloblast-associated/amyloid in Pindborg tumors and kallikrein 4. Three-dimensional images of AMTN localization in molars at selected ages were reconstructed from serial stained sections, and transmission electron microscopy was used for ultrastructural localization of AMTN. AMTN was detected in ameloblasts of molars in a transient fashion, declining at the time of tooth eruption. Prominent expression in maturation stage ameloblasts of the continuously erupting incisor persisted into adulthood. In contrast, amelogenin, ameloblastin and enamelin were predominantly found during the early secretory stage, while odontogenic ameloblast-associated/amyloid in Pindborg tumors and kallikrein 4 expression in maturation stage ameloblasts paralleled that of AMTN. Secreted AMTN was detected at the interface between ameloblasts and the mineralized enamel. Recombinant AMTN protein did not mediate cell attachment in vitro. These results suggest a primary role for AMTN in the late stages of enamel mineralization. Copyright © 2011 S. Karger AG, Basel.

Lehmakauplemisega me enam ei tegele / Villu Reiljan

Index Scriptorium Estoniae

Reiljan, Villu, 1953-

2001-01-01

Ilmunud ka: Virumaa Teataja, 6. sept. 2001, lk. 7; Järva Teataja, 6. sept. 2001, lk. 2; Nädaline, 6. sept. 2001, lk. 4; Koit, 6. sept. 2001, lk. 6; Vooremaa, 6. sept. 2001, lk. 8; Valgamaalane, 8. sept. 2001, lk. 2; Võrumaa Teataja (märgitud autorina Janno Reiljan), 8. sept. 2001, lk. 2; Pärnu Postimees, 13. sept. 2001, lk. 2. Enne presidendivalimiste otsustavaid voore on Riigikogu poliitikud jätkuvalt mõjutamas nii avalikku kui ka valijameeste arvamust. Autor: ERL. Parlamendisaadik

Digitaalse kirjaoskuseta enam ei saa / Andres Jõesaar

Index Scriptorium Estoniae

Jõesaar, Andres, 1959-

2015-01-01

Digikirjaoskusest, ristmeedia tootmisest. Hea lugu ja selle oskuslik edasiandmine digitehnoloogia vahendusel. Balti Filmi- ja Meediakooli ristmeedia tootmise bakalaureuse õppekava teise aasta tudengite tööst "Monsters to clowns", mis on lastega seotud ja lastele suunatud rahvusvaheline ristmeediaprojekt

Taevas ei olegi enam piir / Siim Tuksam

Index Scriptorium Estoniae

Tuksam, Siim, 1986-

2015-01-01

Artikkel tutvustab mängustuudio Hello Games poolt loodud uut videomängu "No Man`s Sky". See on seiklusmäng, kus saab lennata planeedilt planeedile, avastada kosmost, planeete, loomi, taimi, koguda maavarasid ja pidada kosmoselahinguid. Kogu see universum on protseduuriliselt genereeritud ja eksisteerib vaid koodis

Nomos versus logos / Hent Kalmo

Index Scriptorium Estoniae

Vipp, Kaupo

2010-01-01

Naftatipust ja ohejeldamatule tarbimisele järgnevast energiakriisist. Autori hinnangul peaks Eesti kujundama taktikalisi otsuseid riikliku energiajulgeoleku osas ega tohiks toetuda enam pelgalt ortodokssele majanduskäsitlusele

"Matrix : Revolutsiooni" esilinastusele on ostetud üle 700 pileti

Index Scriptorium Estoniae

2003-01-01

Andy ja Larry Wachowski ulmefilmide triloogia 3. osa "Matrix : Revolutsioon" ("The Marix Revolutions") jõuab 5. novembril esilinastuseni korraga enam kui 50 riigis, sealhulgas MPDE vahendusel ka Eestis

Kaubandussanktsioonide otstarbekusest / Jeffrey D. Sachs

Index Scriptorium Estoniae

Sachs, Jeffrey D.

2003-01-01

Autor leiab, et kaubandus- ja finantssanktsioonide rakendamine diktaatorlikele režiimidele on vale lähenemine, kuna rahvusvaheline marginaalitsemine haavab tavalisi kodanikke enam kui despootlikke süsteeme.

Some leaders, despite reputations, offer Latvians hope through crisis / Arta Ankrava

Index Scriptorium Estoniae

Ankrava, Arta

2009-01-01

DnB Nord Latvia Barometer küsitlusest selgus, et kõige enam usaldatakse ekspresident Vaira Vike-Freiberga, Riia linnapea Nils Usakovsi ja Ventspilsi endise linnapea Aivars Lembergsi majandusprognoose

Drivers of the Estonian accounting system in the harmonization process with the European framework / Toomas Haldma

Index Scriptorium Estoniae

Haldma, Toomas, 1957-

2005-01-01

Analüüsi tulemusena selgus, et enam on mõjutanud Eesti arvestussüsteemi raamatupidamisregulatsioonide eristumine maksundusest, arenev arvestuse kutseala ja arvestuse riiklike regulatsioonide paindlikkus ning strateegiline suunitlus

Matsirahvas vajab matside ülikooli / Lembit Nei

Index Scriptorium Estoniae

Nei, Lembit, 1957-

2000-01-01

Eesti Põllumajandusülikool, mida haridusminister hävitada tahab, ei tegele enam ammu ainult klassikalise põllumajandusliku kõrghariduse andmisega, vaid loodusressursside säästva kasutamise õpetamisega

Tänavu sünnib ligi 300 last rohkem kui mullu / Mirko Ojakivi

Index Scriptorium Estoniae

Ojakivi, Mirko

2005-01-01

Demograafilistest protsessidest Eestis lõppeval aastal. TÜ inimgeograafia õppetooli vanemteaduri Tiit Tammaru prognoose lähitulevikuks. Lisa: Rummo rõõmustab edasimineku üle. Graafik: Ligi 300 last enam

Opredelilis pretendentõ na glavnuju nagradu

Index Scriptorium Estoniae

2006-01-01

USAs tehti teatavaks Sõltumatu Vaimu Auhinna (Independent Spirit Award) nominendid. Kõige enam nominatsioone said "Half Nelson" (režii Ryan Fleck) ja "Little Miss Sunshine" (Jonathan Dayton, Valerie Faris)

Pokoja net kak net / Evelyn Sepp

Index Scriptorium Estoniae

Sepp, Evelyn, 1972-

2007-01-01

Riigikogu liige loodab, et peale valimisi kaitseminister Jürgen Ligi poolt kokku kutsutud sõjahaudade komisjon ei kiirusta enam oma otsuste tegemisega, millega võiks kaasneda pronkssõduri teisaldamine

Muusikamaailm / Priit Kuusk

Index Scriptorium Estoniae

Kuusk, Priit, 1938-

1999-01-01

La Scalaga ei olda enam rahul, Dresdenis tuli lavale Richard Straussi ooper "Ariadne Naxoselt", uus orkestriteos John Adamsilt, Müncheni muusikabiennaali uudiseid, suri üks rahvusvahelise kooriliikumise silmapaistvamaid tegelasi

Genes and Gene Therapy

Science.gov (United States)

... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

Elitaarne Harvard reformib õppekavasid : Ameerika kõrghariduse lipulaev tahab rõhuda teadusainetele / Neeme Raud

Index Scriptorium Estoniae

Raud, Neeme

2004-01-01

Harvardi ülikool Ameerikas kavatseb muuta tudengite õppekavasid nii, et need vastaksid senisest enam tänapäeva nõuetele, suuremat rõhku hakatakse panema teadusainetele ja rahvusvahelistele suhetele

Kuulujututurunduse abil Eestis veel müüa ei õnnestu / Katrin Rohtla

Index Scriptorium Estoniae

Rohtla, Katrin, 1966-

2007-01-01

Maailmas on üha enam levimas kuulujututurundus (buzzmarketing), kus ettevõtted annavad trenditeadlikele arvamusliidritele testimiseks tooteid lootuses, et nood tooteid oma tutvusringkonnale edasi tutvustaksid. Kommenteerivad Merit Raju ja Meelis Vill

Microsoft tirib ebaseadusliku tarkvara pärast firmasid kohtupinki / Henrik Ilves

Index Scriptorium Estoniae

Ilves, Henrik

2008-01-01

Microsoft Corporation esitas hagi BREM Kinnisvarahoolduse ja ettevõtete juhtide vastu. BREM-is on kasutatud piraattarkvara ning Microsoft Corporation taotleb kahju hüvitamist. Lisa: Enam kui pooled on piraadid

Planning, design and implementation of the enhancing child ...

African Journals Online (AJOL)

African Journal of Food, Agriculture, Nutrition and Development ... The Enhancing Child Nutrition through Animal Source Management (ENAM) project ... community development, research and capacity building initiative with the goal of ...

Maailma ristteedel / Tiiu Reimo

Index Scriptorium Estoniae

Reimo, Tiiu, 1953-

2010-01-01

Infoteaduse ja raamatukogunduse alastest õppeprogrammidest. Raamatuajalugu on kujunenud interdistsiplinaarseks uurimisvaldkonnaks, iseseisva teadusdistsipliinina õpetatakse seda üha enam ka Põhjamaades, Baltimaades on raamatu ja raamatukogude ajalugu olnud raamatukogunduse õpetamise lahutamatu osa

Millest kõneleb sinu Instagrami konto? / Kadri Eisenschmidt

Index Scriptorium Estoniae

Eisenschmidt, Kadri

2015-01-01

Fotod sotsiaalvõrgustikes on üha enam identiteedi loomise ja kommunikatsiooni vahendid. Autor kaitses hiljuti magistritöö, mis kirjeldas pildilise enesepresentatsiooni tegureid Instagramis nelja Eesti poliitiku kasutajaprofiilide näitel

Rahvas toetab Rüütlit

Index Scriptorium Estoniae

2005-01-01

BNS/Faktumi korraldatud telefoniküsitluse andmetel toetaksid enam kui pooled inimesed president Arnold Rüütli kandideerimist teiseks ametiajaks 2006. aastal. Ilmunud ka Hiiu Leht, 2005/May/27, lk. 4

Nebolshaja sensatsija / Ilja Sundelevitsh

Index Scriptorium Estoniae

Sundelevitsh, Ilja

2001-01-01

Venemaa ei seo enam majandusliku koostöö arengut nii rangelt Eesti astumisega NATO-sse. Kommentaar Vene Riigiduuma rahvusvaheliste asjade komisjoni aseesimehelt Leonid Slutskilt. Lühiintervjuu A. Tarandiga. Parlamendisaadik (A. Tarand)

Rol mezhdu proshlõm i budushtshim / Mart Laar ; interv. Josef Kats

Index Scriptorium Estoniae

Laar, Mart, 1960-

2006-01-01

Parlamendisaadik ning ekspeaminister Mart Laarile meeldib kõige enam tema roll ajaloolasena, otsusest esitada oma kandidatuur peaministri kohale kevadistel parlamendivalimistel, 1940. a. sündmuste mõju Eesti arengule, venelased Eestis

Culture, place and location / Dorothee Bauerle-Willert

Index Scriptorium Estoniae

Bauerle-Willert, Dorothee

2003-01-01

Kultuuri seotusest ja seosetusest koha ja paigaga - globaliseerumise tingimustes riikide ja rahvaste piirid ei lange enam kokku kultuuri piiridega, mistõttu kultuuri mõistmisel muutub oluliseks pinge koha ja kohatuse vahel

Eesti noorte väärtused / Ilmar Mikiver

Index Scriptorium Estoniae

Mikiver, Ilmar, 1920-2010

2004-01-01

Eesti koolinoored on uuringute andmeil enam orienteeritud Ameerika kui Euroopa väärtusorientatsioonile - domineerib pragmatism: edukus, suurem töökoormus karjääri nimel, materiaalne kindlustatus, isiklik heaolu

Amelotin Gene Structure and Expression during Enamel Formation in the Opossum Monodelphis domestica

Science.gov (United States)

Gasse, Barbara; Liu, Xi; Corre, Erwan; Sire, Jean-Yves

2015-01-01

Amelotin (AMTN) is an ameloblast-secreted protein that belongs to the secretory calcium-binding phosphoprotein family, which also includes the enamel matrix proteins amelogenin, ameloblastin and enamelin. Although AMTN is supposed to play an important role in enamel formation, data were long limited to the rodents, in which it is expressed during the maturation stage. Recent comparative studies in sauropsids and amphibians revealed that (i) AMTN was expressed earlier, i.e. as soon as ameloblasts are depositing the enamel matrix, and (ii) AMTN structure was different, a change which mostly resulted from an intraexonic splicing in the large exon 8 of an ancestral mammal. The present study was performed to know whether the differences in AMTN structure and expression in rodents compared to non-mammalian tetrapods dated back to an early ancestral mammal or were acquired later in mammalian evolution. We sequenced, assembled and screened the jaw transcriptome of a neonate opossum Monodelphis domestica, a marsupial. We found two AMTN transcripts. Variant 1, representing 70.8% of AMTN transcripts, displayed the structure known in rodents, whereas variant 2 (29.2%) exhibited the nonmammalian tetrapod structure. Then, we studied AMTN expression during amelogenesis in a neonate specimen. We obtained similar data as those reported in rodents. These findings indicate that more than 180 million years ago, before the divergence of marsupials and placentals, changes occurred in AMTN function and structure. The spatiotemporal expression was delayed to the maturation stage of amelogenesis and the intraexonic splicing gave rise to isoform 1, encoded by variant 1 and lacking the RGD motif. The ancestral isoform 2, housing the RGD, was initially conserved, as demonstrated here in a marsupial, then secondarily lost in the placental lineages. These findings bring new elements towards our understanding of the non-prismatic to prismatic enamel transition that occurred at the onset of

Amelotin Gene Structure and Expression during Enamel Formation in the Opossum Monodelphis domestica.

Directory of Open Access Journals (Sweden)

Barbara Gasse

Full Text Available Amelotin (AMTN is an ameloblast-secreted protein that belongs to the secretory calcium-binding phosphoprotein family, which also includes the enamel matrix proteins amelogenin, ameloblastin and enamelin. Although AMTN is supposed to play an important role in enamel formation, data were long limited to the rodents, in which it is expressed during the maturation stage. Recent comparative studies in sauropsids and amphibians revealed that (i AMTN was expressed earlier, i.e. as soon as ameloblasts are depositing the enamel matrix, and (ii AMTN structure was different, a change which mostly resulted from an intraexonic splicing in the large exon 8 of an ancestral mammal. The present study was performed to know whether the differences in AMTN structure and expression in rodents compared to non-mammalian tetrapods dated back to an early ancestral mammal or were acquired later in mammalian evolution. We sequenced, assembled and screened the jaw transcriptome of a neonate opossum Monodelphis domestica, a marsupial. We found two AMTN transcripts. Variant 1, representing 70.8% of AMTN transcripts, displayed the structure known in rodents, whereas variant 2 (29.2% exhibited the nonmammalian tetrapod structure. Then, we studied AMTN expression during amelogenesis in a neonate specimen. We obtained similar data as those reported in rodents. These findings indicate that more than 180 million years ago, before the divergence of marsupials and placentals, changes occurred in AMTN function and structure. The spatiotemporal expression was delayed to the maturation stage of amelogenesis and the intraexonic splicing gave rise to isoform 1, encoded by variant 1 and lacking the RGD motif. The ancestral isoform 2, housing the RGD, was initially conserved, as demonstrated here in a marsupial, then secondarily lost in the placental lineages. These findings bring new elements towards our understanding of the non-prismatic to prismatic enamel transition that occurred at

Отказ от киноленты осложняет работу PÖFF

Index Scriptorium Estoniae

2011-01-01

Traditsioonilise filmilindi kadumine seab PÖFFi korraldajad tulevikus keerulisse olukorda, kuna festivalile filme valides pole teada, mis formaadis need saadetakse. Üha enam levib maailmas DCP (Digital Cinema Package) ehk digiteeritud salvestis

Martin Anderson valis "Joonase lähetamise" / Priit Kuusk

Index Scriptorium Estoniae

Kuusk, Priit, 1938-

2000-01-01

M. Anderson kommenteeris ameerika muusikaajakirjas "Fanfare" viit talle kõige enam mõju avaldanud heliplaati, sh. R. Tobiase oratooriumi "Joonase lähetamine" CD-plaati (BIS). M. Andersoni huvist eesti muusika vastu

Suurosalusega juht kasulikum investorile / Tarvo Vaarmets

Index Scriptorium Estoniae

Vaarmets, Tarvo

2007-01-01

Bloombergi kolumnist ja finantskonsultant Greaf Cristal järeldas USA suurettevõtete juhte ja finantsandmeid uurides, et osalus motiveerib tegevjuhte enam kui palk. Diagramm: Berkshire Hathaway aktsia tõusis mullu 23 protsenti

Kaheksas loomispäev? : inimgenotehnika eetilisi ja õiguslikke probleeme / Jaan Sootak

Index Scriptorium Estoniae

Sootak, Jaan, 1948-

1994-01-01

Kunstliku viljastamise liigist IVF, mis on meditsiiniliselt kõige keerulisem ning õiguslikult ja eetiliselt kõige enam probleeme tekitav. Ilmunud ka: Sootak, Jaan. Kuri karjas : [artiklite kogumik]. Tartu, 2009, lk. 106-127

2018-05-21T06:43:30Z https://www.ajol.info/index.php/all/oai oai:ojs ...

African Journals Online (AJOL)

... of ghanaian women's experiences in income generation and family care Butler, LM ... Women who were doing well in business before the ENAM interventions did ... women employed multiple strategies to overcome business challenges.

Eesti Raudtee jagunemine avab ukse erakapitalile / Henrik Ilves

Index Scriptorium Estoniae

Ilves, Henrik

2008-01-01

Eesti Raudtee on alustanud jagunemist, mille käigus asutatakse kaks tütarfirmat: infrastruktuuri haldav aktsiaselts EVR Infra ning vedusid korraldav aktsiaselts EVR Cargo. Vt. samas: Guido Sammelselg: ei iial enam

Ei geneetiliselt muundatud toidule! / Roy Strider

Index Scriptorium Estoniae

Strider, Roy, 1974-

2007-01-01

Jätkates mõttevahetust geneetiliselt muundatud toidu kahjulikkuse või ohutuse üle, kirjutab autor, et teadus pole tänapäeval enam mitte inimeste teenistuses, vaid korporatsioonide ja riikide palgalehel

TINGKAT HIDUP DAN PERTUMBUHAN AVOKAD HASIL SAMBUNG PUCUK ENTRES YANG DISIMPAN DALAM PELEPAH BATANG PISANG

Directory of Open Access Journals (Sweden)

Lazarus Agus Sukamto

2014-01-01

Full Text Available Buah avokad mempunyai kandungan nutrisi yang sangat baik bagi masyarakat khususnya kandungan lemak tidak jenuh dan protein yang tertinggi bila dibandingkan jenis buah lain. Untuk tujuan komersial, tanaman avokad perlu diperbanyak secara vegetatif untuk memperoleh bibit yang telah terbukti kualitas dan kuantitas tinggi, serta berbuah lebih awal. Keberhasilan penyambungan sangat dipengaruhi oleh kesegaran entres. Penelitian ini bertujuan untuk mengetahui keberhasilan dan pertumbuhan sambungan tanaman avokad dengan menggunakan entres yang disimpan dalam pelepah batang pisang selama dua hingga sembilan hari. Parameter pengamatan meliputi persentase tingkat hidup sambungan, pertumbuhan panjang, jumlah daun, jumlah cabang, dan panjang percabangan batang atas setiap bulan sampai enam bulan. Data pertumbuhan dianalisis secara statistik dengan ANOVA dan uji lanjut Duncan. Lama penyimpanan entres berpengaruh terhadap tingkat hidup hasil sambungan dan pertumbuhan batang atas avokad. Rerata tingkat hidup bibit sambungan avokad terus menurun dari 99,5% pada umur satu bulan sampai 71% pada umur enam bulan setelah penyambungan, tetapi tidak mengalami penurunan setelah lima bulan penyambungan. Penyimpanan entres avokad dalam pelepah pisang dapat dipertahankan kesegarannya selama sembilan hari, yaitu tingkat hidup sambungan 60% - 84% enam bulan setelah penyambungan. Ada kecenderungan bahwa makin lama penyimpanan entres, makin menurun pertumbuhan batang atas avokad; sebaliknya makin lama umur penyambungan, makin meningkat pertumbuhan batang atas avokad, kecuali jumlah cabangnya yang relatif tidak meningkat setelah dua bulan penyambungan.

TÜ jätkab tõusu maailma juhtivate teadusülikoolide edetabelites

Index Scriptorium Estoniae

2011-01-01

Eluteaduste valdkonnas (life sciences: bioloogia, meditsiin, psühholoogia) on TÜ enam kui 15 tuhande ülikooli seas 301.-350. kohal. Sellel aastal jõuti esmakordselt 1% mõjukamate institutsioonide hulka ka geoteadustes

Terror kui näitemäng meedias / Mart Raudsaar

Index Scriptorium Estoniae

Raudsaar, Mart, 1973-

2005-01-01

Terrorirünnakute iseloom on muutunud üha verisemaks ning see tendents jätkub. Terroristid ihalevad üha enam ülemaailmset rambivalgust. Teoreetikud arutavad, kas ja kuivõrd tuleks piirata terrorismi meediakajastust

Ansip lays flowers at Bronze Soldier, while government seeks to bridge gap in society

Index Scriptorium Estoniae

2007-01-01

Peaminister Andrus Ansip asetas pärja Pronkssõdurile ja kohtus rahvusvähemuste esindajatega. Eesti meediaruumis oleks vaja enam tähelepanu venekeelsele infole. Linnapea Edgar Savisaare käitumisest rahutuste ajal

II samba eduks peaks liitujaid olema üle 50% / Kaja Koovit

Index Scriptorium Estoniae

Koovit, Kaja, 1968-

2002-01-01

Edukaks pensionireformi läbiviimiseks peaks teise samba kasuks otsustama enam kui pooled võimalikest liitujatest, väidab Ida-Euroopa pensionisüsteemi üks käivitajatest EBRD direktor Jonathan Wollett

Multikulti lõpp ehk immigratsiooni müütide ajastu hakkab otsa saama / Heiki Suurkask

Index Scriptorium Estoniae

Suurkask, Heiki, 1972-

2011-01-01

Euroopa on hakanud endasse sulguma, sest ei tea enam, kuidas immigrantide massiga toime tulla. Sallimatust immigrantide vastu Euroopas küll on, kuid see pole üheski riigis valdavaks muutunud. Immigrantidega seotud probleemidest

Vastutustundlik ettevõtlus - millega tegu ja kellele seda on vaja / Triinu Gröön

Index Scriptorium Estoniae

Gröön, Triinu

2005-01-01

Ettevõtte ühiskondlik vastutus (Corporate Social Responsibility ehk CSR) on mõiste ja kontseptsioonina arenenud 1960-ndatest alates ning on üha enam jõudnud rahvusvahelisse juhtimiskirjandusse, samuti konverentside päevakavadesse

Investorid on hakanud mässama / Tõnis Oja

Index Scriptorium Estoniae

Oja, Tõnis, 1957-

2009-01-01

Viimastel aastatel on üha enam tekitanud nurinat börsiettevõtete juhtide palgad ja boonused. Viimati hääletasid juhtide kompensatsioonipaketi maha Briti-Hollandi naftafirma Royal Dutch Shell aktsionärid

Disaini ABC jõuab ettevõtjateni / Riin Kranna-Rõõs

Index Scriptorium Estoniae

Kranna-Rõõs, Riin

2007-01-01

ABCDisaini seminaridest eesti ettevõtjatele teemal kuidas konkurentsis püsida, kui allhange enam ei toimi. Korraldab Eesti Kunstiakadeemia Disaini Innovatsioonikeskus. Esinevad Martin Pärn, Kristjan Jagomägi ja Kristjan Mändmaa

Ülikoolide pingereastamisest / Lauri Randveer

Index Scriptorium Estoniae

Randveer, Lauri

2006-01-01

Euroopa juhtivaid ülikoole koondava Coimbra grupi ülikoolide rektorite aastakoosoleku raames toimunud seminaril Tartu Ülikoolis "International Ranking of Universities" arutleti viimastel aastatel üha enam kõlapinda leidnud ülikoolide pingereastamisest

Uganda elanikud tarbivad enim alkoholi / Villu Zirnask

Index Scriptorium Estoniae

Zirnask, Villu, 1966-

2007-01-01

Maailma tervishoiuorganisatsiooni (WHO) statistika järgi tarbivad maailmas kõige enam alkoholi Uganda elanikud - aastas 17,6 liitrit puhast alkoholi vanema kui 15-aastase elaniku kohta. Lisaks tabel alkoholi tarbimise kohta maailmas

Nord Stream tuleb Venemaa gaasihiiule raskel ajal / Jaanus Piirsalu ; kommenteerinud Mihhail Kortšemkin

Index Scriptorium Estoniae

Piirsalu, Jaanus, 1973-

2010-01-01

Gazpromi tähtsus "energeetikarelvana" on hakanud kahanema - Euroopas on gaasi tarbimine vähenenud, mitmed gaasitootjad pakuvad Euroopale Vene gaasiga hinna poolest edukalt konkureerivat vedelgaasi, USA-s toodetakse üha enam kildagaasi

Gene expression and gene therapy imaging

International Nuclear Information System (INIS)

Rome, Claire; Couillaud, Franck; Moonen, Chrit T.W.

2007-01-01

The fast growing field of molecular imaging has achieved major advances in imaging gene expression, an important element of gene therapy. Gene expression imaging is based on specific probes or contrast agents that allow either direct or indirect spatio-temporal evaluation of gene expression. Direct evaluation is possible with, for example, contrast agents that bind directly to a specific target (e.g., receptor). Indirect evaluation may be achieved by using specific substrate probes for a target enzyme. The use of marker genes, also called reporter genes, is an essential element of MI approaches for gene expression in gene therapy. The marker gene may not have a therapeutic role itself, but by coupling the marker gene to a therapeutic gene, expression of the marker gene reports on the expression of the therapeutic gene. Nuclear medicine and optical approaches are highly sensitive (detection of probes in the picomolar range), whereas MRI and ultrasound imaging are less sensitive and require amplification techniques and/or accumulation of contrast agents in enlarged contrast particles. Recently developed MI techniques are particularly relevant for gene therapy. Amongst these are the possibility to track gene therapy vectors such as stem cells, and the techniques that allow spatiotemporal control of gene expression by non-invasive heating (with MRI guided focused ultrasound) and the use of temperature sensitive promoters. (orig.)

Some empirical tests on the integration of economic activity between the euro area and the accession countries / Iikka Korhonen

Index Scriptorium Estoniae

Korhonen, Iikka

2003-01-01

Uurimusest, mille tulemusena selgus, et esimesena liitumisläbirääkimisi alustanud EL-i kandidaatriigid on enam integreeritud majandustegevusse eurotsoonis ning on lisaks liitumisele EL-iga valmis varem liituma ka Euroopa Rahaliiduga. Tabelid.

Liberalism surub käe inimese taskusse / Arvo Sarapuu

Index Scriptorium Estoniae

Sarapuu, Arvo, 1953-

2004-01-01

Riigi makstav dotatsioon küünib kuni 60 protsendini bussiveo hinnast ega kata enam Euroopa Liiduga liitumisega kaasnenud kütuse kallinemist, rääkimata vajadusest pidevalt investeerida busside uuendamisse, kirjutab autor

Ingrid Rüütel ne hotshet bõt prosto pervoi ledi Estonii

Index Scriptorium Estoniae

2001-01-01

Eesti presidendiproua loodab, et ta positsioon võimaldab rahvuskultuuri senisest enam toetada. Ilmunud ka Sillamjaeskii Vestnik (2001/Sep/24) lk. 1. Pealk. ajalehes Molodjozh Estonii (2001/Sep/24) lk. 3: Zabotõ pervoi ledi

Matrix - kultusfilm, mis muutus müüdiks / Rando Tooming

Index Scriptorium Estoniae

Tooming, Rando

2003-01-01

Andy ja Larry Wachowski ulmefilmide triloogia 3. osa "Matrix : Revolutsioon" ("The Marix Revolutions") jõuab 5. novembril esilinastuseni korraga enam kui 50 riigis, sealhulgas MPDE vahendusel ka Eestis. Eesti filmikriitikute arvamusi Matrix'i fenomenist

Investorid on dilemma ees / Ain Kivisaar

Index Scriptorium Estoniae

Kivisaar, Ain, 1978-

2007-01-01

Keskmise kuupalga eest ei saa enam ruutmeetritki elamispinda ei meil ega mujal. Aktiivsel investoril pole muud teha, kui heita kõrvale tavatarkus ja usaldada enda sisetunnet. Diagramm: Keskmise kuupalga ja korteri ruutmeetri hinna suhe

Shkoda veab Tšehhi majanduskasvu / Krister Paris

Index Scriptorium Estoniae

Paris, Krister, 1977-

2004-01-01

Kesk-Euroopa suurim autotootja Shkoda on Tšehhi suurimaid tööandjaid, tootes aastas ligi pool miljonit sõidukit, millest enam kui 80% läheb ekspordiks. Lisad: Suurimaks tootjaks saab Slovakkia; Shkoda

Kanada koolimõrv nõudis ühe ohvri / Rein Kärner

Index Scriptorium Estoniae

Kärner, Rein

1999-01-01

Veidi enam kui nädal pärast tapatalguid Colorado osariigi Littletoni koolis laskis Kanadas Taberi väikelinnas W. R. Myersi keskkoolis sama kooli endine õpilane Jason Lang maha oma endise koolikaaslase

Prisma külmutab hindu / Väinu Rozental

Index Scriptorium Estoniae

Rozental, Väinu, 1957-

2011-01-01

Prisma Peremarket otsustas enam kui 20 põhitoote hinnad aasta lõpuni külmutada. Arvamust avaldavad Rimi ja Säästumarketi turundus- ja kommunikatsioonijuht Andrija Lilleoja ja ASi Leibur juhatuse esimees Asso Lankots

Magister = magister? / Arvo Meri

Index Scriptorium Estoniae

Meri, Arvo

2002-01-01

Vastavalt uuele kõrgharidusstandardile on magistriõpe üks osa kõrgharidusest, mille peaksid läbima enamik üliõpilastest. Magistriõppe läbimine enam teaduskraadi ei anna, see on spetsialistiõpe

Boliivia natsionaliseerib maagaasitööstuse / Heiki Suurkask

Index Scriptorium Estoniae

Suurkask, Heiki, 1972-

2006-01-01

Boliivia president Juan Evo Morales riigistas oma dekreediga kõik Boliivia maagaasivarud, mis kutsus esile Brasiilia presidendi meelepaha. Lisad: Boliivia kokakasvatajate võimuaeg; Ameerika läheb üha enam punast värvi

Swedbank kaalub tasude alandamist / Andrus Karnau

Index Scriptorium Estoniae

Niitra, Sirje, 1948-

2009-01-01

Tallinna külastanud Swedbanki investeerimisfondide juht Carina Tovi teatas, et pank kaalub pensionifondide tasude vähendamist ega võta enam valitsemistasu, kui panga pensionifondid on ostnud mõne oma panga fondi osakuid

Kakskümmend kuus tankisti ja meer / Kaarel Tarand

Index Scriptorium Estoniae

Tarand, Kaarel, 1966-

2005-01-01

Et Riigikogu liikmed ei tohi enam paralleelselt kohalikes omavalitsustes töötada, hakkab nende asendusliikmetena Tallinna volikogus tööle massiliselt isikuid, kellest laiem avalikkus peale nende erakondliku kuuluvuse midagi ei tea

Irlandskaja svinina budet otpravlena na pererabotku / Hindrek Riikoja

Index Scriptorium Estoniae

Riikoja, Hindrek

2008-01-01

Eestisse on eksporditud Iirimaalt sealiha, millel kahtlustatakse lubatust mitu korda enam vähki tekitavate doksiinide sisaldust. Vt. samas: Saasteallikaks võis olla loomasööda töötlemisel kasutatav õli; Dioksiinid

Klein : üleilmastumiseks pole kütust / Naomi Klein ; interv. Nathan Gardels, tõlk. Külli-Riin Tigasson

Index Scriptorium Estoniae

Klein, Naomi

2008-01-01

Energia kallinemise ja veokulude suurenemisega aeglustub globaliseerumine, Hiina muutub tarbimiskapitalismi omaksvõtuga sarnasemaks läänega ning lääs sarnaneb üha enam Hiinaga seoses kodanike vabaduse ohverdamisega jälgimistegevusele

PENGELOLAAN ASET WAKAF OLEH LNW IBADURRAHMAN DURI DALAM MENINGKATKAN KESEJAHTERAAN UMMAT

Directory of Open Access Journals (Sweden)

Fitrianto Fitrianto

2017-08-01

Full Text Available LNW Ibadurrahman  merupakan salah satu Nazir wakaf yang mengelola harta wakaf di Duri. Tata kelola wakaf oleh LNW Ibadurrahman melalui 16 (enam belas jenis program  wakaf uang tunai seperti, wakaf perkebunan,balai latihan kerja, rumah yatim, pendidikan pesantren belading, Maqdis Ibad, pembebas Riau Menghafal, Warung Maqdis, Koperasi Ibadurrahman, TK maqdis, dan Bisnis Tiketing Haji dan Umrah. Melalui  enam belas program wakaf uang tersebut,  LNW Ibadurrahman menggunakannya langsung uang wakaf sesuai dalam  membangun, mengelola dan memproduktifkan infrastruktur sebagai aset wakaf. Sedangkan program  wakaf uang tunai  lainnya diproduktifkan sebagai aset wakaf yang menghasilkan nilai surplus wakaf seperti usaha perkebunan karet, perkebunan sawit dan permodalan bisnis (Koperasi, tiketing dan Warung Maqdis. LNW Ibadurrahman menggunakan nilai surplus wakaf yang ada dalam pemberdayaan aset-aset wakaf dan kesejahteraan ummat

Globoside accelerates the differentiation of dental epithelial cells into ameloblasts

Institute of Scientific and Technical Information of China (English)

Takashi Nakamura; Yuta Chiba; Masahiro Naruse; Kan Saito; Hidemitsu Harada; Satoshi Fukumoto

2016-01-01

Tooth crown morphogenesis is tightly regulated by the proliferation and differentiation of dental epithelial cells. Globoside (Gb4), a globo-series glycosphingolipid, is highly expressed during embryogenesis as well as organogenesis, including tooth development. We previously reported that Gb4 is dominantly expressed in the neutral lipid fraction of dental epithelial cells. However, because its functional role in tooth development remains unknown, we investigated the involvement of Gb4 in dental epithelial cell differentiation. The expression of Gb4 was detected in ameloblasts of postnatal mouse molars and incisors. A cell culture analysis using HAT-7 cells, a rat-derived dental epithelial cell line, revealed that Gb4 did not promote dental epithelial cell proliferation. Interestingly, exogenous administration of Gb4 enhanced the gene expression of enamel extracellular matrix proteins such as ameloblastin, amelogenin, and enamelin in dental epithelial cells as well as in developing tooth germs. Gb4 also induced the expression of TrkB, one of the key receptors required for ameloblast induction in dental epithelial cells. In contrast, Gb4 downregulated the expression of p75, a receptor for neurotrophins (including neurotrophin-4) and a marker of undifferentiated dental epithelial cells. In addition, we found that exogenous administration of Gb4 to dental epithelial cells stimulated the extracellular signal-regulated kinase and p38 mitogen-activated protein kinase signalling pathways. Furthermore, Gb4 induced the expression of epiprofin and Runx2, the positive regulators for ameloblastin gene transcription. Thus, our results suggest that Gb4 contributes to promoting the differentiation of dental epithelial cells into ameloblasts.

Маленьким кинотеатрам грозит закрытие / Ханнели Руди

Index Scriptorium Estoniae

Руди, Ханнели

2011-01-01

Üha enam levib maailmas DCP (Digital Cinema Package) ehk filmi digiteeritud salvestis. Eestis on vaid Tallinna ja Tartu kinodes tehnika, millega vaadata DCP filme. Probleemi analüüsib Kultuuriministeeriumi filminõunik Edit Sepp

Does Estonia need foreign policy? / Alexander Astrov

Index Scriptorium Estoniae

Astrov, Alexander

2003-01-01

Autori arvates vajab Eesti kindlaksmääratud poliitikasuundade asemel rohkem välispoliitikat laiemas mõttes, vajalik oleks loobuda viimase aastakümne eesmärgikesksest ratsionaalsusest enam kontekstitundliku tegutsemis- ja mõtlemisviisi kasuks

Lõuna-Osseetia : tohutu möödapanek / Gwynne Dyer ; tõlk. Kaspar Siplane

Index Scriptorium Estoniae

Dyer, Gwynne

2008-01-01

Ilmunud ka: Vesti Dnja 19. aug. lk. 5. Autor annab ülevaate Venemaa ja Gruusia vahelise sõjalise konflikti kronoloogiast ning usub, et Gruusia ei taasta enam kunagi kontrolli Lõuna-Osseetia ja Abhaasia üle

Rahvas palkab 101 töötajat / Tarmo Pikner

Index Scriptorium Estoniae

Pikner, Tarmo

2003-01-01

Saare Maavalitsuse arengu- ja planeeringu osakonna juhataja Tarmo Pikneri sõnul on piirkondlike erinevustega arvestamine meie riigi seadusandluses enam kui puudulik. Igal Riigikogu liikmel peaks olema ette näidata tema panus Eesti riigi seadusloomesse

Küüditatuid mälestati kontserdiga Kohilas ja Raplas / Inge Põlma

Index Scriptorium Estoniae

Põlma, Inge

2009-01-01

1941. aastal küüditatute mälestuseks toimunud kontsertidest "Me ei näinud teda enam kunagi" 14. juunil Raplas Maarja-Magdaleena kirikus ja Kohilas EAÕ Angerja Issanda kirikus, esines ansambel Tallinn Baroque

Eksminister jäi Citigroupis jänni / Tõnis Oja

Index Scriptorium Estoniae

Oja, Tõnis, 1957-

2009-01-01

USA endine rahandusminister ja Citigroupi nõukogu liige Robert Rubin teatas, et astub nõuniku kohalt tagasi ning ei lase end enam nõukogu liikmeks tagasi valida. Diagramm: Citigroupi aktsia hind ja majandusnäitajad

Üle poole rahvast toetab Rüütli teist ametiaega

Index Scriptorium Estoniae

2005-01-01

BNS/Faktumi korraldatud telefoniküsitluse andmetel toetaksid enam kui pooled inimesed president Arnold Rüütli kandideerimist teiseks ametiajaks 2006. aastal. Lisa: Eelistatuimad presidendikandidaadid. Ilmunud ka Pärnu Postimees, 2005/May/25, lk. 7

Raha tahab ringlusesse / Ralf-Martin Soe

Index Scriptorium Estoniae

Soe, Ralf-Martin

2009-01-01

Skype asutajate ettevõte Ambient Sound Investment paigutab üha enam raha uutesse ettevõtetesse välismaal, sest Eestis napib ideid. Vt. samas: Skype asutajad võivad firma eBaylt tagasi osta. Diagramm: Investeeringud

Erakondade erastatud Eesti: kuidas edasi? / Peeter Jalakas

Index Scriptorium Estoniae

Jalakas, Peeter, 1961-

2009-01-01

Autori hinnangul meenutavad Eesti erakonnad üha enam äriühinguid, mille tõttu valitseb riigis erakondlik egoism ning kodanike rahulolematus - olukorra parandamiseks oleks vaja muuta olemasolevat valitsemissüsteemi ning luua kahekojaline parlament

Optimismi viljad = The Fruits of Optimism / Tõnu Laigu

Index Scriptorium Estoniae

Laigu, Tõnu

2005-01-01

Mida võtta ette 1950-1990 massilise tüüpelamuehituse käigus Euroopas ja Eestis ehitatud elurajoonidega, mis ei vasta keskkonna, halva ehituskvaliteedi jm. põhjuste tõttu enam vajadustele. Bibliograafia lk. 55

Imaging gene expression in gene therapy

International Nuclear Information System (INIS)

Wiebe, Leonard I.

1997-01-01

Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on 'suicide gene therapy' of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k + ) has been use for 'suicide' in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k + gene expression where the H S V-1 t k + gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([ 18 F]F H P G; [ 18 F]-A C V), and pyrimidine- ([ 123 / 131 I]I V R F U; [ 124 / 131I ]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [ 123 / 131I ]I V R F U imaging with the H S V-1 t k + reporter gene will be presented

Imaging gene expression in gene therapy

Energy Technology Data Exchange (ETDEWEB)

Wiebe, Leonard I. [Alberta Univ., Edmonton (Canada). Noujaim Institute for Pharmaceutical Oncology Research

1997-12-31

Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on `suicide gene therapy` of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k{sup +}) has been use for `suicide` in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k{sup +} gene expression where the H S V-1 t k{sup +} gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([{sup 18} F]F H P G; [{sup 18} F]-A C V), and pyrimidine- ([{sup 123}/{sup 131} I]I V R F U; [{sup 124}/{sup 131I}]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [{sup 123}/{sup 131I}]I V R F U imaging with the H S V-1 t k{sup +} reporter gene will be presented

Volta tehas peitis saksa sõjavangide läkitust / Andri Maimets

Index Scriptorium Estoniae

Maimets, Andri, 1979-

2002-01-01

Kunagise Volta suurtehase tsaariaegse peakontori remonditööde käigus tuli päevavalgele kaks ajaloolist kirja, millest vanema olid enam kui pool sajandit tagasi seina taha peitnud II maailmasõjas vangi langenud sakslased

Десятка самых прибыльных актеров / Кая Коовит

Index Scriptorium Estoniae

Коовит, Кая, 1968-

2010-01-01

10 kõige enam teenivat Hollywoodi näitlejat (Quigley Publishing' andmeil) on Denzel Washington, Shia LaBeouf, Brad Pitt, Meryl Streep, Tom Hanks, Robert Downey jr., George Clooney, Matt Damon, Johnny Depp ja Sandra Bullock

Londoni terror sundis inglasi heitma pilgu endasse / Arko Olesk

Index Scriptorium Estoniae

Olesk, Arko, 1981-

2006-01-01

Aasta pärast Londonis toimunud enesetaputerroristide rünnakut, tunnevad Suurbritannias elavad moslemikogukonnad end valitsuse poolt hüljatuna ning on asunud üha enam toetama islamiäärmuslust. Kaart: Aastatagune terroripäev

Analysis of the assimilation of SAPARD support programme in Lithuania / Vida Čiulevičiene, Jonas Čiulevičius, Rolandas Kripaitis

Index Scriptorium Estoniae

Čiulevičiene, Vida

2003-01-01

Analüüsist selgus, et arvuliselt on kõige enam toetuse taotlusi esitatud põllumajandustootmise investeeringute tegemiseks, kuid rahalises väljenduses on suurim saaduste töötlemise ja turustamise valdkonna taotluste osakaal. Tabelid

Mahetootjad andsid loomadele geneetiliselt muundatud sööta / Hindrek Riikoja

Index Scriptorium Estoniae

Riikoja, Hindrek

2005-01-01

Loodusliku toidu eest seisvate mahetalunike söötadest leiti enam kui pooltel juhtudel geneetiliselt muundatud organisme (GMO), millest lõviosa moodustas Eestisse toodud muundatud soja. Lisa: mis on GMO? Vt. ka lk.1 ja 2

Anton Starkopf Kumus / Juta Kivimäe

Index Scriptorium Estoniae

Kivimäe, Juta, 1952-

2010-01-01

Näitus "Anton Starkopf. Eesti skulptuurilegend" Kumu Kunstimuuseumis 30. maini 2010. Näituse koostas ja kujundas Ahti Seppet. Eksponeeritakse 73 skulptuuri ja enam kui 70 joonistust aastaist 1911-1966. Anton Starkopfi (1889-1966) elust ja loomingust

Bagatellid : Maailm / Nele-Eva Steinfeld

Index Scriptorium Estoniae

Steinfeld, Nele-Eva

2009-01-01

Muusikasõnumeid maailmast: Pianist Krystian Zimerman teatas, et ta ei esine enam Ameerika Ühendriikides. Steve Reich pälvis Pulitzeri auhinna. Tenor Rolando Villazon katkestab tervislikel põhjustel esinemised. Jose Carreras lõpetab esinemised ooperis

Saaremaa maaelu ja põllumajandus said mullu ligi 140 miljonit toetust / Ain Lember

Index Scriptorium Estoniae

Lember, Ain

2005-01-01

Saare maakond sai 2004. aastal enam kui 138 miljoni krooni eest maaelu- ja põllumajandustoetusi, mis teeb iga maal elava inimese kohta 6760 krooni. Tabelid: Toetussumma maakonna lõikes; Toetussumma iga maal elava inimese kohta (kroonides)

Organisatsiooni riskijuhtimise tulevikusuunad ja siseauditi roll / Iivi Maspanov, Kersti Käbin

Index Scriptorium Estoniae

Maspanov, Iivi, 1950-

2004-01-01

Autorite hinnangul on riskijuhtimise eesmärgiks kogu organisatsiooni tegevust ja eesmärkide täitmist ohustavate riskide määratlemine, hindamine ja maandamine. Siseauditi funktsioon on üha enam muutumas kontrollijast konsulteerijaks. Skeem

Vene president Putin otsib endale sobivat mantlipärijat / Heiki Suurkask

Index Scriptorium Estoniae

Suurkask, Heiki, 1972-

2006-01-01

Venemaa president Vladimir Putin kavatseb 2008. aastal enam mitte presidendiks kandideerida ning otsib järgmist presidenti. Telekanal CNN pakkus kandidaatidena asepeaminister Dmitri Medvedjevit ja kaitseminister Sergei Ivanovi. Lisa: President ise küsib, ise vastab

Kampaania korras tagasi keskaega / Heiki Suurkask

Index Scriptorium Estoniae

Suurkask, Heiki, 1972-

2009-01-01

Autori sõnul pole kiirkorras kavandatava haldusreformiga, mis näeb omavalitsusi ainult teeninduspiirkondadena, mõistetud viimase sajandi saavutusi; kohalik omavalitsus pole ammu enam administreerimise ja haldamise organ, vaid see on lahutamatu osa demokraatlikust ühiskonnakorrast

Börs asub väikeinvestorit firma ülevõtmisel kaitsma / Margus Simson

Index Scriptorium Estoniae

Simson, Margus

1999-01-01

Börsireglemendi muudatuse järgi peab ettevõtte aktsiatest enam kui 50% omandav investor tegema võrdse pakkumise kõikidele aktsionäridele. Diagramm: registreeritud väärtpaberikontosid, väärtpaberid riikide kaupa

Kehaline kasvatus - mängule kadunud aeg ja ruum? / Joe Noormets

Index Scriptorium Estoniae

Noormets, Joe

2004-01-01

Autori väitel on üldhariduskooli kehalise kasvatuse tundidesse tunginud üha enam spordile omaseid tegevusmudeleid ja väärtusorientatsioone; mäng ja mängulisus on kehalises kasvatuses kaduma läinud

Soomes kolleeg, Eestis kollanokk / Krister Kivi, Kristina Fogel, Piret Tilk...[jt.

Index Scriptorium Estoniae

2004-01-01

Tartu Ülikooli arstiteaduskonna lõpetajaid ajab välismaale tunne, et nende oskusi väärtustatakse seal enam. Vestlusest kuuenda kursuse üliõpilaste Kristina Fogeli, Piret Tilga ja Pille Pärgmäega

Report raises questions about Ignalina shutdown

Index Scriptorium Estoniae

2004-01-01

Balti riikide, Valgevene ja Venemaa energiafirmade juhid saatsid Leedu peaministrile Algirdas Brazauskasele kirja, milles märgivad, et viie riigi energiatööstus ei oleks peale Ignalina tuumajaama esimese reaktori sulgemist enam usaldusväärne

Üritusturundusfirmad Orangetime ja Rodeo Marketing ühinesid

Index Scriptorium Estoniae

2005-01-01

Ühinenud agentuuri nimeks jääb Orangetime ja seda hakkab juhtima Hardi Kinnas, kes prognoosib aasta lõpuks käibe enam kui 50%-list kasvu 14-15 miljoni kroonini. Lisa: Orangetime'i suuremaid kliente

Aastaaruannete esitamise uus kord

Index Scriptorium Estoniae

2010-01-01

Alates 1. jaan. 2010 hakkas kehtima majandusaasta aruannete esitamise uus kord, mille järgi ei saa enam aruandeid esitada paberil ega üles laadida pdf-failina. Väljavõte Registrite ja Infosüsteemide Keskuse juhendist

Nokia pole ainus langev täht. RIM on hädas / Fredy-Edwin Esse

Index Scriptorium Estoniae

Esse, Fredy-Edwin

2011-01-01

Kanada tehnoloogiafirma Research In Motion kaotab ühe enam Põhja-Ameerikas turgu konkurentidele nagu Apple ja teised firmad, kes kasutavad Google'i Android operatsioonisüsteemi. Ka BlackBerry Playbook ei ole suutnud iPadiga konkureerida. Graafik

Analiz vmesto emotsii / Josef Kats

Index Scriptorium Estoniae

Kats, Josef, 1977-

2007-01-01

Peaminister Andrus Ansipi ja välisminister Urmas Paeti sõnul on valitsus küsinud Vene-Saksa gaasijuhtme ehitamiseks vajalike teadusuuringute läbiviimiseks nõu enam kui 20 asutuselt, nende alusel tuleb teha kaalutletud otsus

Terroristijaht keskendub pakistanlastele / Heiki Suurkask

Index Scriptorium Estoniae

Suurkask, Heiki, 1972-

2005-01-01

Egiptuse politsei otsib kuut pakistanlast, keda kahtlustatakse Sharm el-Sheikis toimunud terrorirünnakute toimepanekus. Pakistan peab Egiptuse võimude kahtlustusi alusetuks, riigi presidendi väitel al-Qaidat enam Pakistanis ei eksisteeri. Kaart, graafik: Egiptuse turism

Eesti üldhariduse finantsreformi olemus ja probleemid / Janno Reiljan, Ele Reiljan

Index Scriptorium Estoniae

Reiljan, Janno, 1951-2018

2005-01-01

Läbiviidav reform võib täiendavate investeerimisvahendite eraldamisest hoolimata kohalikele omavalitsustele pandavate pikaajaliste võlakohustuste ja õpikulude kaasrahastamise kohustuse koosmõjul üldhariduse koolivõrgu regionaalse tasakaalustamise asemel senisest enam tasakaalust välja viia

Kõrva-nina-kurguarstid võivad lõpetada öövalve / Urmas Seaver

Index Scriptorium Estoniae

Seaver, Urmas, 1973-

2006-01-01

Arstide nappuse tõttu võib Põhja-Eesti regionaalhaigla lõpetada kõrva-nina-kurguhaiguste ööpäevase valve. Sellisel juhul ei saaks pealinnas ja kogu Põhja-Eestis öösel vastavalt erialaarstilt enam abi

Norma tulemuste taga on eksport Venemaale / Virge Lahe

Index Scriptorium Estoniae

Lahe, Virge

2008-01-01

Autode turvavarustuse tootja AS-i Norma teise kvartali puhaskasum oli 25,4 miljonit krooni, mis on kaks korda enam kui 2007. aasta teises kvartalis, edaspidi võib kasumit survestada terasehinna tõus. Diagramm: Norma kasum on kasvanud

Kurjakuulutav Grantham Sünge / Rich Karlgaard

Index Scriptorium Estoniae

Karlgaard, Rich

2013-01-01

Majandusanalüütik Jeremy Granthami prognoosi kohaselt ei asu USA sisemajanduse kogutoodang enam kunagi tõusuteele. Autor toob paralleele Briti majandus- ja rahvastikuteadlase Thomas Malthuse prognoosidega ning loodab, et ka Grantham eksib, nagu Malthus omal ajal

Graham Watson: Eesti vajab enam riigi sekkumist majandusse

Index Scriptorium Estoniae

Watson, Graham

2009-01-01

18. aprillil pidasid keskerakondlased Tallinnas Euroopa Parlamendi valimiste konverentsi. Euroopa Parlamendi demokraatide ja liberaalide fraktsiooni juht Graham Watson saatis Keskerakonnale videotervituse

Miks Coca-Cola enam ei kihise? / Neeme Raud

Index Scriptorium Estoniae

Raud, Neeme, 1969-

2004-01-01

Autor teeb USA äriajakirjanduse põhjal ülevaate Coca-Cola Company maine, turupositsiooni ja aktsiakursi langemise põhjustest alates 1997. aastast. Analüütikute sõnul on korporatsioon olnud ebaedukas tippkaadri voolavuse, sisekonfliktide, pidevate ümberkorralduste ja töötajate koondamiste tõttu. Praegune peadirektor Neville Isdelle on püstitanud eesmärgiks firma sisekultuuri parandamise, et keskenduda liidripositsiooni kindlustamisele turul. Diagramm: Karastusjookidel gaas väljas. Vt. samas: Coca-Cola ja Pepsi - üheskoos alla

Haigla ei asenda enam vanglat / Väino Linde

Index Scriptorium Estoniae

Linde, Väino, 1959-

2006-01-01

Kohtuotsuse täitmise edasilükkamisest tervisliku seisundi tõttu. Sama ka Vooremaa 12. aug. 2006, lk. 2 ; Järva Teataja 12. aug. 2006, lk. 2, pealkiri kujul : Haigla pole vangla asendaja ; Vali Uudised 11. aug. 2006, lk. 2 ; Hiiu Leht 11. aug. 2006, lk. 2 ; Elva Postipoiss 12. aug. 2006, lk. 2 ; Valgamaalane 12. sep. 2006, lk. 2

USA toetab arvatust enam Ukraina opositsiooni / Neeme Raud

Index Scriptorium Estoniae

Raud, Neeme, 1969-

2004-01-01

Briti ajalehe The Guardian kommentaatori Ian Traynor'i sõnul on Ukraina sündmuste puhul tegemist viimase nelja aasta jooksul juba neljanda USA poolt korraldatud ja finantseeritud ettevõtmisega endises idablokis, kus soovitakse vanameelseid režiime võimult tõugata. Sarnase skeemi järgi on tema hinnangul toimunud valimistejärgsed rahutused Jugoslaavias, Gruusias ja Valgevenes

Estonian Attitudes towards the German Exercise of Power in Estonia 1941-1944 / Kari Alenius

Index Scriptorium Estoniae

Alenius, Kari, 1966-

2012-01-01

Eestlaste suhtumisest Saksa okupatsioonivõimudesse perioodil 1941-1944. Perioodi võib jagada kolmeks etapiks. 1941. aastal suhtuti sakslastesse heatahtlikult. Pettumus hakkas süvenema 1942. aasta talvel. Alates 1942. aasta kevadest polnud enam üksmeele leidmine võimalik

USA üritab Assange'i ja sõnavabadust risti lüüa / Birgitta Jónsdóttir ; intervjueerinud Askur Alas

Index Scriptorium Estoniae

Jónsdóttir, Birgitta

2011-01-01

Intervjuu Islandi parlamendisaadiku ja Wikileaksi endise kaastöötajaga USA nõudmisest, et Twitter annaks USA-le saadiku isiklikku infot, põhjusest, miks ta pole enam Wikileaksiga seotud. Ta usub, et samasuguseid internetisaite ja organisatsioone tekib veelgi

Optimism lubab uut kasvu. Kui kõrgelt lennatakse logistikas sel aastal? / Rivo Sarapik

Index Scriptorium Estoniae

Sarapik, Rivo, 1981-

2011-01-01

2010. aastal kasvas tarbeautode müük kolmandiku võrra, Tallinna Sadam käitles kaupu 16% võrra enam kui aasta varem. Transiidikeskus loodab konteinerkäibe ja ro-ro kaupade 20-protsendilist kasvu. Graafikud, diagrammid

Ehitusel käib pingeline töö tuisus ja tormis / Kristiina Viiron

Index Scriptorium Estoniae

Viiron, Kristiina, 1971-

2006-01-01

Ehitustööd pole enam seotud aastaajaga; nii Haapsalu Uksetehase AS, AS Lasita Aken kui ka AS Columbia Kivi valmistavad toodangut umbes samas koguses kui suvel. Ehitusmaterjalide tootmismahud on kasvanud umbes 20%. Lisa: Pausi nõuab tehnoloogia

President ei pruugi uuesti kandideerida

Index Scriptorium Estoniae

2006-01-01

Proua Ingrid Rüütel viitas Kanal 2 uudistesaates "Reporter" võimalusele, et Arnold Rüütel enam uueks ametiajaks ei kandideeri. Ilmunud ka Eesti Päevaleht, 2006/Mar/1, lk. 5 ; Koit, 2006/Mar/2, lk. 2

The most ambitious innovation project in Estonia / Raivo Murde

Index Scriptorium Estoniae

Murde, Raivo

2010-01-01

Tänavu jaanuaris EAS-ile esitatud 14 tehnoloogia arenduskeskuse loomise taotlusest valiti välja kaheksa arenduskeskust, keda toetatakse Euroopa Regionaalarengu Fondi rahadest enam kui 900 miljoni krooniga, arenduskeskustega liitunud ettevõtted investeerivad keskustesse ligi 400 miljonit krooni

Las fun'il tulla / Priit Pullerits

Index Scriptorium Estoniae

Pullerits, Priit, 1965-

2006-01-01

Taliolümpiamängudel pole murdmaasuusatamine enam ammuilmma A ja O. Autori arvates peavad Eesti riigi-, olümpia- ja spordijuhid kiiremas korras hakkama mõtlema, kuidas arendada meil nn uusi talialasid, nagu lumelauasõitu ja vigursuusatamist

Juhendamine juhtimise asemel / Vahur Murutar

Index Scriptorium Estoniae

Murutar, Vahur, 1961-

2003-01-01

Rets. rmt.: Patrick J. McKenna, David H. Maister. Esimene võrdsete seas. Fontes, Pärnu Konverentsid 2003. Autor selgitab McKenna ja Maisteri raamatule tuginedes, mida eeldab maailmas üha enam populaarsust koguv juhi roll meeskonna treenerina

Is European integration causing Europe to become more nationalist? Evidence from the 2007 - 9 financial crisis / Alina Polyakova, Neil Fligstein

Index Scriptorium Estoniae

Polyakova, Alina

2016-01-01

Artiklis käsitletakse eurointegratsiooni ühtse identiteedi kujunemise aspektis. Väidetakse, et EL-i integratsioon on tegelikult viinud selleni, et Euroopa kodanikud väärtustavad euroidentideedist enam rahvuslikku identiteeti ja soovivad, et nende riikide valitsused kaitseksid neid

Вручены награды "Золотого глобуса"

Index Scriptorium Estoniae

2011-01-01

Hollywoodi Välisajakirjanike Assotsiatsioon jagas 68. korda Kuldgloobuseid. Kõige enam auhindu kogus film "Sotsiaalvõrgustik": parim film, parim režissöör (David Fincher), parim stsenaarium (Aaron Sorkin) ja soundtrack (Trent Reznor, Atticus Ross). Ka teistest auhinnatutest

Iiri parlamendi Euroopa asjade ühiskomisjoni liikme hr. Bernard Durkani ettekanne / Bernard Durkan

Index Scriptorium Estoniae

Durkan, Bernard

2002-01-01

Ilmunud ka: Proceedings of the 8th International conference Estonia and the European Union : Estonia on its way to a changing Europe : October 31-November 2, 2001. - Tallinn, lk. 69-73. EL institutsioonid peaksid enam aitama riike probleemsituatsioonide lahendamisel

Küpros sattus mereväebaasi plahvatuse tagajärjel kriisi / Martin Rits

Index Scriptorium Estoniae

Rits, Martin

2011-01-01

Juunis juhtunud Evangelos Florakise mereväebaasi plahvatus viis Küprose tõsisesse poliitilisse ja majandusliku kriisi. Välis- ja kaitseminister astus tagasi ning riigi krediidireiting on langenud. Enam kui poole saare elektrist tootnud Vassiliko elektrijaam on seiskunud. Kaart

Kibuvits üllatab ja pakub leevendust / Ain Raal

Index Scriptorium Estoniae

Raal, Ain, 1961-

2005-01-01

Taani teadlased avastasid-eraldasid kibuvitsaseemnetest ja viljakestadest uue põletikuvastase toimeaine galaktolipiidi (GOPO). Seda lipiidi sisaldub kõige enam koer-kibuvitsa alamliigis Hyben Vital Litos. Nüüdseks on GOPO saamisviis ja nimi patenteeritud nii Euroopas kui ka USAs

Teatrilugu Variuselt

Index Scriptorium Estoniae

2008-01-01

Variuse lavastusest "His Master's Voice", mille idee tekkis, kui Eesti Rahvusraamatukogule anti Taani Rahvusliku Heliarhiivi poolt üle enam kui 200 matriitsi eesti muusikaga, mis salvestatud 1939. a. suurkontsernis The Gramophone Company, mille harukontor His Master's Voice asus Kopenhaagenis

"Kuhu kadunud oled ..." : [luuletused] / Aleksandr Belonogov

Index Scriptorium Estoniae

Belonogov, Aleksandr

2004-01-01

Sisu: "Kuhu kadunud oled ..." ; "Puude juured haaravad ..." ; "Nagu hiljuti eraldi teelt ..." ; "Kui kord enam mõista ma ..." ; Käänded ; Väravale on kirjutatud ; Rahvas ütleb. Eluloolisi andmeid autori kohta lk. 361. Luuletused paralleelselt udmurdi ja eesti keeles

Karzai nõuab USA-lt võitu, ähvardades muidu rahu teha / Heiki Suurkask

Index Scriptorium Estoniae

Suurkask, Heiki, 1972-

2008-01-01

Afganistani president Hamid Karzai nõuab USA-lt ajakava selle kohta, millal NATO kavatseb Talibani üle võidu saavutada. Afganistanis visiidil viibinud USA president George W. Bush avaldas toetust Barack Obama kavale keskenduda veelgi enam Afganistanis sõdimisele

Eestist saab politseiriik / Roy Strider

Index Scriptorium Estoniae

Strider, Roy, 1974-

2007-01-01

Autori väitel ei ole politsei pärast kavandatavat avaliku koosoleku seaduse muutmist enam kohustatud inimestele teatama, kui nende eraelu puutumatust on jälitustoiminguga riivatud. Autori sõnul tähendab see, et Eestist saab politseiriik

GoGene: gene annotation in the fast lane.

Science.gov (United States)

Plake, Conrad; Royer, Loic; Winnenburg, Rainer; Hakenberg, Jörg; Schroeder, Michael

2009-07-01

High-throughput screens such as microarrays and RNAi screens produce huge amounts of data. They typically result in hundreds of genes, which are often further explored and clustered via enriched GeneOntology terms. The strength of such analyses is that they build on high-quality manual annotations provided with the GeneOntology. However, the weakness is that annotations are restricted to process, function and location and that they do not cover all known genes in model organisms. GoGene addresses this weakness by complementing high-quality manual annotation with high-throughput text mining extracting co-occurrences of genes and ontology terms from literature. GoGene contains over 4,000,000 associations between genes and gene-related terms for 10 model organisms extracted from more than 18,000,000 PubMed entries. It does not cover only process, function and location of genes, but also biomedical categories such as diseases, compounds, techniques and mutations. By bringing it all together, GoGene provides the most recent and most complete facts about genes and can rank them according to novelty and importance. GoGene accepts keywords, gene lists, gene sequences and protein sequences as input and supports search for genes in PubMed, EntrezGene and via BLAST. Since all associations of genes to terms are supported by evidence in the literature, the results are transparent and can be verified by the user. GoGene is available at http://gopubmed.org/gogene.

Radionuclide reporter gene imaging for cardiac gene therapy

International Nuclear Information System (INIS)

Inubushi, Masayuki; Tamaki, Nagara

2007-01-01

In the field of cardiac gene therapy, angiogenic gene therapy has been most extensively investigated. The first clinical trial of cardiac angiogenic gene therapy was reported in 1998, and at the peak, more than 20 clinical trial protocols were under evaluation. However, most trials have ceased owing to the lack of decisive proof of therapeutic effects and the potential risks of viral vectors. In order to further advance cardiac angiogenic gene therapy, remaining open issues need to be resolved: there needs to be improvement of gene transfer methods, regulation of gene expression, development of much safer vectors and optimisation of therapeutic genes. For these purposes, imaging of gene expression in living organisms is of great importance. In radionuclide reporter gene imaging, ''reporter genes'' transferred into cell nuclei encode for a protein that retains a complementary ''reporter probe'' of a positron or single-photon emitter; thus expression of the reporter genes can be imaged with positron emission tomography or single-photon emission computed tomography. Accordingly, in the setting of gene therapy, the location, magnitude and duration of the therapeutic gene co-expression with the reporter genes can be monitored non-invasively. In the near future, gene therapy may evolve into combination therapy with stem/progenitor cell transplantation, so-called cell-based gene therapy or gene-modified cell therapy. Radionuclide reporter gene imaging is now expected to contribute in providing evidence on the usefulness of this novel therapeutic approach, as well as in investigating the molecular mechanisms underlying neovascularisation and safety issues relevant to further progress in conventional gene therapy. (orig.)

Changed work: a challenge to organisations and their members / Merike Karotom

Index Scriptorium Estoniae

Karotom, Merike

2003-01-01

Eesti töösfääri arenguid on kõige enam mõjutanud üleminek turumajandusele, sellega kaasnev restruktureerimine ja omandireformi läbiviimine, mille tõttu on järsult kahanenud tööhõive. Tabel

Müüdid ja põhitõed maailmapildi kujunemisel / Aino Pervik

Index Scriptorium Estoniae

Pervik, Aino, 1932-

2005-01-01

Eestimaal toimivast edumüüdist, mis on ka enam-vähem ainuke põlvkondi ühendav tõekspidamine ja maailmapildi kujunemisest lastel, mis peaks vastama ka tegelikult sellele, mis inimese ümber toimub ning lastekirjanduse osast selle kujunemisel

Region-building and security: The multiple borders of the Baltic Sea region after EU enlargement / Katharina Koch

Index Scriptorium Estoniae

Koch, Katharina

2015-01-01

Artikkel käsitleb Läänemere riikide (sh Eesti) piire, täpsemalt, kuidas piiride rajamine ja nende kaotamine mõjutab riikidevahelist koostööd, aluseks enam kui 20 antud teemat käsitleva dokumendi analüüs

Kosovo kõnelused ummikseisus / Arko Olesk

Index Scriptorium Estoniae

Olesk, Arko, 1981-

2007-01-01

ÜRO erisaadik Martti Ahtisaari tõdes Viinis, et Kosovo ja Serbia juhtide läbirääkimised on ammendunud ja pooled ei jõudnud kokkuleppele enam kui aasta kestnud kõneluste tulemusel Kosovo provintsi saatuse üle. Lisa: Kosovo

Venemaa langeb impordisõltuvusse / Villu Zirnask

Index Scriptorium Estoniae

Zirnask, Villu, 1966-

2007-01-01

Autori väitel on nii Vene era- kui ka riigifirmad ja pangad hakanud üha enam kasutama välisfinantseerimist. Kui import kasvab kiirelt, siis eksport on stagneerunud. Ohud Vene majanduskasvule. Tabel: Vene import kasvab suure kiirusega. Graafik: Majanduskasv

3 + 2 = 450 : 3+2 õppesüsteem tõi kaasa kuni 450 tudengiga hiigelloengud / Anu Mõistlik, Jüri Saar

Index Scriptorium Estoniae

Mõistlik, Anu, 1980-

2002-01-01

Vastne õppekord pakib loengusaali sadu noori. 3+2 tuleku otsustas kuue inimese hääletus. Vanade õppekavade ained kaovad järjestikku tunniplaanidest. Teadusmagistreid enam ei tule. Ainepunktide ülekandmiseks peab üliõpilane ise vaeva nägema

Adidas suutis tulemustega üllatada / Virge Lahe

Index Scriptorium Estoniae

Lahe, Virge

2007-01-01

Spordiriiete ja -tarvete tootja Adidase kasum oli teises kvartalis 104 mln eurot, mis on 27 protsenti enam kui mullu samal perioodil. Ettevõtte hinnangul tuli kasumikasv liitumisest Reebokiga. Diagramm: Adidase aktsia on viimasel ajal kõikunud 45 euro ümber

Bioenergia kasutus põllumajandus- ja metsandusettevõtetes investeeringutoetuse saajate näitel / Jaana Prants

Index Scriptorium Estoniae

Prants, Jaana

2015-01-01

Põllumajandus- ja metsandusettevõtjad pööravad üha enam tähelepanu energiakasutuse arengusuundadele ja keskkonnasõbralikuma energiatootmise võimalustele, et leida uusi väljundeid oma ettevõtte tootmisprotsessist tulenevate jäätmete kasutuseks ja efektiivsemaks energiakasutuseks

Harmooniline töötaja on väärtuslik / Kristine Täht

Index Scriptorium Estoniae

Täht, Kristine

2005-01-01

Rahvastikuministri nõuniku hinnangul on ühiskond seda jätkusuutlikum, mida rohkem on tema arengusse kaasatud õnnelikke inimesi. Selleks peaksid aga riik ja ettevõtjad senisest enam pöörama tähelepanu töötajate eraelule

Internet - rohi või mürk? / Kristjan Port

Index Scriptorium Estoniae

Port, Kristjan

2007-01-01

Vietnami valitsus püüab seksiteemaliste veebisaitide programmiga suurendada sündivust. Seevastu Jaapani perekonna planeerimise ühingu arvates on internet ventiil, mille kaudu jaapanlased oma seksuaalse energia maha laevad, nii et seda ei jagu enam iibe tõstmiseks

Tamm ja Asi / Karen Jagodin

Index Scriptorium Estoniae

Jagodin, Karen, 1982-

2007-01-01

Näitus "Sisearhitektid Väino Tamm & Vello Asi" Eesti Arhitektuurimuuseumis kuni 2. IX. Kuna valminud objektidest ei ole enam ühtegi originaalkujul alles, on eksponeeritud võimalikult suurel hulgal valmimisjärgseid fotosid, millest enamiku on teinud Rein Vainküla

Maailma turism 2006 / Piret Kallas

Index Scriptorium Estoniae

Kallas, Piret

2007-01-01

2006. aastal tehti kogu maailmas 842 miljonit ööbimisega välisreisi, mis on 4,5 protsenti enam kui 2005. aastal. Maailma turismitrendid 2006-2007, prognoos 2007. aastaks. Euroopa turismi arengust 2006. aastal. Allikas: UNWTO World Tourism Barometer, jaan. 2007

E.E.L.K. Peapiiskopi valimised / Thomas Vaga, Ivar Nippak

Index Scriptorium Estoniae

Vaga, Thomas, 1938-

2007-01-01

21. detsembril teatas häältelugemiskomisjon, et kaks enam hääli saanud kandidaati on Thomas Vaga ja Andres Taul. Samade kandidaatide vahel toimub korduv hääletus. Uued valimismaterjalid saadetakse välja 2007. aasta jaanuaris

Pangad nopivad odava kinnisvara / Birjo Must ; kommenteerinud Hannes Kuhlbach, Meelis Šokman

Index Scriptorium Estoniae

Must, Birjo

2010-01-01

Võrreldes 2010. a. algusega on SEB makseraskustes klientidelt ostetud kinnisvara mahu neljakordistanud, Swedbank on mahu enam kui kahekordistanud. Kommenteerivad SEB kinnisvarahaldusfirma Estectus OÜ juht Hannes Kuhlbach ja Swedbanki Eesti kinnisvarahalduse ettevõtte Ektornet Residential Estonia OÜ juht Meelis Šokman

Gene cluster statistics with gene families.

Science.gov (United States)

Raghupathy, Narayanan; Durand, Dannie

2009-05-01

Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In distantly related genomes, clusters of homologous gene pairs are evidence of candidate homologous regions. Demonstrating the statistical significance of such "gene clusters" is an essential component of comparative genomic analyses. However, currently there are no practical statistical tests for gene clusters that model the influence of the number of homologs in each gene family on cluster significance. In this work, we demonstrate empirically that failure to incorporate gene family size in gene cluster statistics results in overestimation of significance, leading to incorrect conclusions. We further present novel analytical methods for estimating gene cluster significance that take gene family size into account. Our methods do not require complete genome data and are suitable for testing individual clusters found in local regions, such as contigs in an unfinished assembly. We consider pairs of regions drawn from the same genome (paralogous clusters), as well as regions drawn from two different genomes (orthologous clusters). Determining cluster significance under general models of gene family size is computationally intractable. By assuming that all gene families are of equal size, we obtain analytical expressions that allow fast approximation of cluster probabilities. We evaluate the accuracy of this approximation by comparing the resulting gene cluster probabilities with cluster probabilities obtained by simulating a realistic, power-law distributed model of gene family size, with parameters inferred from genomic data. Surprisingly, despite the simplicity of the underlying assumption, our method accurately approximates the true cluster probabilities. It slightly overestimates these probabilities, yielding a conservative test. We present additional simulation results indicating the best choice of parameter values for data

Gene therapy prospects--intranasal delivery of therapeutic genes.

Science.gov (United States)

Podolska, Karolina; Stachurska, Anna; Hajdukiewicz, Karolina; Małecki, Maciej

2012-01-01

Gene therapy is recognized to be a novel method for the treatment of various disorders. Gene therapy strategies involve gene manipulation on broad biological processes responsible for the spreading of diseases. Cancer, monogenic diseases, vascular and infectious diseases are the main targets of gene therapy. In order to obtain valuable experimental and clinical results, sufficient gene transfer methods are required. Therapeutic genes can be administered into target tissues via gene carriers commonly defined as vectors. The retroviral, adenoviral and adeno-associated virus based vectors are most frequently used in the clinic. So far, gene preparations may be administered directly into target organs or by intravenous, intramuscular, intratumor or intranasal injections. It is common knowledge that the number of gene therapy clinical trials has rapidly increased. However, some limitations such as transfection efficiency and stable and long-term gene expression are still not resolved. Consequently, great effort is focused on the evaluation of new strategies of gene delivery. There are many expectations associated with intranasal delivery of gene preparations for the treatment of diseases. Intranasal delivery of therapeutic genes is regarded as one of the most promising forms of pulmonary gene therapy research. Gene therapy based on inhalation of gene preparations offers an alternative way for the treatment of patients suffering from such lung diseases as cystic fibrosis, alpha-1-antitrypsin defect, or cancer. Experimental and first clinical trials based on plasmid vectors or recombinant viruses have revealed that gene preparations can effectively deliver therapeutic or marker genes to the cells of the respiratory tract. The noninvasive intranasal delivery of gene preparations or conventional drugs seems to be very encouraging, although basic scientific research still has to continue.

Gene-gene interactions and gene polymorphisms of VEGFA and EG-VEGF gene systems in recurrent pregnancy loss.

Science.gov (United States)

Su, Mei-Tsz; Lin, Sheng-Hsiang; Chen, Yi-Chi; Kuo, Pao-Lin

2014-06-01

Both vascular endothelial growth factor A (VEGFA) and endocrine gland-derived vascular endothelial growth factor (EG-VEGF) systems play major roles in angiogenesis. A body of evidence suggests VEGFs regulate critical processes during pregnancy and have been associated with recurrent pregnancy loss (RPL). However, little information is available regarding the interaction of these two major major angiogenesis-related systems in early human pregnancy. This study was conducted to investigate the association of gene polymorphisms and gene-gene interaction among genes in VEGFA and EG-VEGF systems and idiopathic RPL. A total of 98 women with history of idiopathic RPL and 142 controls were included, and 5 functional SNPs selected from VEGFA, KDR, EG-VEGF (PROK1), PROKR1 and PROKR2 were genotyped. We used multifactor dimensionality reduction (MDR) analysis to choose a best model and evaluate gene-gene interactions. Ingenuity pathways analysis (IPA) was introduced to explore possible complex interactions. Two receptor gene polymorphisms [KDR (Q472H) and PROKR2 (V331M)] were significantly associated with idiopathic RPL (P<0.01). The MDR test revealed that the KDR (Q472H) polymorphism was the best loci to be associated with RPL (P=0.02). IPA revealed EG-VEGF and VEGFA systems shared several canonical signaling pathways that may contribute to gene-gene interactions, including the Akt, IL-8, EGFR, MAPK, SRC, VHL, HIF-1A and STAT3 signaling pathways. Two receptor gene polymorphisms [KDR (Q472H) and PROKR2 (V331M)] were significantly associated with idiopathic RPL. EG-VEGF and VEGFA systems shared several canonical signaling pathways that may contribute to gene-gene interactions, including the Akt, IL-8, EGFR, MAPK, SRC, VHL, HIF-1A and STAT3.

Gene doping: gene delivery for olympic victory

OpenAIRE

Gould, David

2012-01-01

With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called ‘gene doping’. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted...

FunGene: the functional gene pipeline and repository.

Science.gov (United States)

Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

2013-01-01

Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

FunGene: the Functional Gene Pipeline and Repository

Directory of Open Access Journals (Sweden)

Jordan A. Fish

2013-10-01

Full Text Available Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer.While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/ offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

Mining disease genes using integrated protein-protein interaction and gene-gene co-regulation information.

Science.gov (United States)

Li, Jin; Wang, Limei; Guo, Maozu; Zhang, Ruijie; Dai, Qiguo; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Xuan, Ping; Zhang, Mingming

2015-01-01

In humans, despite the rapid increase in disease-associated gene discovery, a large proportion of disease-associated genes are still unknown. Many network-based approaches have been used to prioritize disease genes. Many networks, such as the protein-protein interaction (PPI), KEGG, and gene co-expression networks, have been used. Expression quantitative trait loci (eQTLs) have been successfully applied for the determination of genes associated with several diseases. In this study, we constructed an eQTL-based gene-gene co-regulation network (GGCRN) and used it to mine for disease genes. We adopted the random walk with restart (RWR) algorithm to mine for genes associated with Alzheimer disease. Compared to the Human Protein Reference Database (HPRD) PPI network alone, the integrated HPRD PPI and GGCRN networks provided faster convergence and revealed new disease-related genes. Therefore, using the RWR algorithm for integrated PPI and GGCRN is an effective method for disease-associated gene mining.

Gene-gene, gene-environment, gene-nutrient interactions and single nucleotide polymorphisms of inflammatory cytokines.

Science.gov (United States)

Nadeem, Amina; Mumtaz, Sadaf; Naveed, Abdul Khaliq; Aslam, Muhammad; Siddiqui, Arif; Lodhi, Ghulam Mustafa; Ahmad, Tausif

2015-05-15

Inflammation plays a significant role in the etiology of type 2 diabetes mellitus (T2DM). The rise in the pro-inflammatory cytokines is the essential step in glucotoxicity and lipotoxicity induced mitochondrial injury, oxidative stress and beta cell apoptosis in T2DM. Among the recognized markers are interleukin (IL)-6, IL-1, IL-10, IL-18, tissue necrosis factor-alpha (TNF-α), C-reactive protein, resistin, adiponectin, tissue plasminogen activator, fibrinogen and heptoglobins. Diabetes mellitus has firm genetic and very strong environmental influence; exhibiting a polygenic mode of inheritance. Many single nucleotide polymorphisms (SNPs) in various genes including those of pro and anti-inflammatory cytokines have been reported as a risk for T2DM. Not all the SNPs have been confirmed by unifying results in different studies and wide variations have been reported in various ethnic groups. The inter-ethnic variations can be explained by the fact that gene expression may be regulated by gene-gene, gene-environment and gene-nutrient interactions. This review highlights the impact of these interactions on determining the role of single nucleotide polymorphism of IL-6, TNF-α, resistin and adiponectin in pathogenesis of T2DM.

Volta läbi saja aasta / Sten Grundig

Index Scriptorium Estoniae

Grundig, Sten

2005-01-01

Ilmunud ka: Delovõje Vedomosti 14. sept. lk. 4. Volta tehas valmistab täna mootoreid peamiselt rasketööstuse ettevõtetele, kus valmistatakse tõsteseadeid, kompressoreid, pumpasid. Vt. samas: uus suund - tuulegeneraatorid. Lisa: Voltast vahvliküpsetajaid enam ei tule

Iraagi hall kardinal usub uude riiki / Muhsen Naif Al-Faisal Al-Jarba ; interv. Ivar Soopan

Index Scriptorium Estoniae

Al-Jarba, Muhsen Naif Al-Faisal

2004-01-01

Iraagi presidendi ja peaministri nõuniku sõnul tahab Iraak üles ehitada tõelise armee, politsei, piirivalve. Pärast seda koalitsiooniarmeed enam ei vajata. Rahu kogu Lähis-Idas sõltub Iisraelist, ütleb nõunik. Vt. samas: Kuidas ma tutvusin sheigiga

Kas tulevik on kohal? / Kristjan Port

Index Scriptorium Estoniae

Port, Kristjan, 1960-

2012-01-01

Arvuti- ja tehnoloogiaettevõte IBM tõi 2008. aastal välja viis innovaatilist ideed, mis nende arvates viie aasta pärast kõige enam meie tööd ja elu mõjutavad. Kas need ennustused on täitunud?

Heategevus tänapäeva Eestis / Liis Klaar

Index Scriptorium Estoniae

Klaar, Liis

2002-01-01

Autor leiab, et Eestis on heategevus sarnaselt teistele ühiskondlikele ettevõtmistele veel välja arendamata ja väärib senisest enam riiklikku tähelepanu ning tunnustust. Ülevaade heategevuse korraldusest Eestis ja mujal. Autor:Rahvaerakond Mõõdukad. Parlamendisaadik

Charismatic aspect of transformational leadership and its role in creating organizational culture / Gerda Mihhailova, Kulno Türk

Index Scriptorium Estoniae

Mihhailova, Gerda

2006-01-01

Ettevõtte kasvu- ja küpsusfaasis vajatakse autorite hinnangul enam nn. klassikalisi juhte, karismaatilised juhid sobivad pigem radikaalseid muutusi nõudvatesse situatsioonidesse, nagu näiteks ettevõtte rajamine või selle langusfaasist välja toomine. Skeemid. Tabel. Lisa lk. 194

Soomlased teevad silma Eesti toidutööstusele / Silva Männik

Index Scriptorium Estoniae

Männik, Silva, 1974-

2004-01-01

EL-iga liitumise eel plaanivad mitmed Soome ettevõtjad investeerida Eesti toiduainetööstustesse ja viia Eesti tooted Soome turule. Diagrammid: Soomlane sööb üha enam Eesti toitu. Kommenteerivad Joakim Helenius ja Ain Hanschmidt. Lisa: Näiteid soomlaste tehingutest

Mitmekesisus ühenäolisuse asemel: suundumused arhitektuuris ja poliitikas 1980-ndate lõpul = Diversity versus uniformity: tendencies in architecture and politics since the late 1980`s / Udo Kultermann ; tõlkinud Jüri Pärni

Index Scriptorium Estoniae

Kultermann, Udo

1993-01-01

Endise Nõukogude Liidu ja sotsialistlike maade arhitektuuri suunamisel ei domineeri enam bürokraatlik tsentraliseeritud juhtimissüsteem. Arhitektid ja tellijad hakkavad otsuste tegemisel arvestama kohalikke ja regionaalseid olusid, mis on inimkesksemad, öeldes lahti poliitilisest ja kultuurilisest ühenäolisusest

Klaaspudelist loobumine vähendab Coca-Cola brändi eeliseid / Eda-Liis Kann

Index Scriptorium Estoniae

Kann, Eda-Liis, 1979-

2005-01-01

BRAND sense uuringu kohaselt, milles uuriti pakendi mõju brändilojaalusele, eelistab enam kui 60% Ameerika ja Suurbritannia tarbijaist juua kokakoolat klaaspudelist. Majanduslikel põhjustel on Coca-Cola Company aga viimased kümme aastat tegelenud klaaspudelite poelettidelt ära korjamisega. Diagramm

Hotellid loobuvad suuri kulutusi nõudvatest tärnidest / Andres Reimer

Index Scriptorium Estoniae

Reimer, Andres

2009-01-01

Meriton loobub hotellide taset näitavatest tärnidest ega ole oma uutele hotellidele Conference & Spa ja Old Town enam tärne taotlenud, kuid väikesed, luksust hindavale kliendile orienteeritud Tallinna majutuskohad tärnisüsteemist ei loobu

Kullad lennus / Silvia Viidik

Index Scriptorium Estoniae

Viidik, Silvia, 1972-

2008-01-01

Nafta hind on turul dramaatiliselt langenud, hoolimata tootmise vähendamisest. Kui nafta ja rahaturud enam investeerimiseks kindlust ei anna, pöörduvad pilgud muude väärtuslike toorainete, näiteks kulla, poole. Diagramm: Nafta ja kulla hinna muutus

Jäik määrus ähvardab puisniite / Tsipe Aavik

Index Scriptorium Estoniae

Aavik, Tsipe, 1981-

2005-01-01

Põllumajanduse Registrite ja Informatsiooni Ameti lubadus jätta ühtsest pindalatoetusest ilma talunikud, kelle karja- ja heinamaal kasvab enam kui 50 puud või kus üle 50 % pindalast on kaetud põõsastega, kätkeb endas ohtu traditsioonilistele põllumajandusmaastikele

EL nõuab USA vangilaagri sulgemist / Krister Paris

Index Scriptorium Estoniae

Paris, Krister, 1977-

2006-01-01

EL on seisukohal, et Guantanamo vangla tuleb sulgeda. Amnesty International nimetas kolme enesetappu Guantanamo vanglas aastatepikkuse õigusevastase ja lõputu vangistuse tagajärjeks. Vangilaagi komandant aga peab neid enesetappe osaks USA-vastasest asümmeetrilisest sõjast. Lisa: Enam kui 40 enesetapukatset

Küberkiusaja käib varjuna lapse kannul / Sigrid Kõiv

Index Scriptorium Estoniae

Kõiv, Sigrid

2008-01-01

Üle kolmandiku õpilastest on netikiusamist kogenud ja enam kui veerand õpilastest on ise selles osalenud, näitab Tartu Ülikooli magistrandi Karin Naruskovi uurmistöö. Kiusajate kõige menukamateks vahenditeks on MSN ja Rate. Kommenteerib IBM Eesti juht Valdo Randpere

Liibanonis röövitu: "Eesti palugu abi Hezbollah'lt!" / Krister Kivi

Index Scriptorium Estoniae

Kivi, Krister, 1975-

2011-01-01

USA ajakirjanik Charles Glass, kes 24 aastat tagasi võeti Beirutis pantvangiks ja sealt põgenes, on veendunud, et ideoloogilistel põhjustel Liibanonis inimesi enam ei röövita. Liibanonis röövitud eestlaste vabastamiseks tuleb kasutada kõiki kanaleid

Tallink City eskiis valmib sügiseks

Index Scriptorium Estoniae

2006-01-01

Septembris 2006 jõuab Tallinna linnavalitsuse ette Lasnamäele plaanitava lõbustuskeskuse Tallink City detailplaneeringu eskiis. Laevandusfirmas Tallink Grupp suurosalust omav Infortar plaanib 2010. aastaks rajada enam kui 160000 m2 suuruse linnaku (mäesuusahall, suusatunnel) Punasele tänavale

Suicide genes or p53 gene and p53 target genes as targets for cancer gene therapy by ionizing radiation

International Nuclear Information System (INIS)

Liu Bing; Chinese Academy of Sciences, Beijing; Zhang Hong

2005-01-01

Radiotherapy has some disadvantages due to the severe side-effect on the normal tissues at a curative dose of ionizing radiation (IR). Similarly, as a new developing approach, gene therapy also has some disadvantages, such as lack of specificity for tumors, limited expression of therapeutic gene, potential biological risk. To certain extent, above problems would be solved by the suicide genes or p53 gene and its target genes therapies targeted by ionizing radiation. This strategy not only makes up the disadvantage from radiotherapy or gene therapy alone, but also promotes success rate on the base of lower dose. By present, there have been several vectors measuring up to be reaching clinical trials. This review focused on the development of the cancer gene therapy through suicide genes or p53 and its target genes mediated by IR. (authors)

Neighboring Genes Show Correlated Evolution in Gene Expression

Science.gov (United States)

Ghanbarian, Avazeh T.; Hurst, Laurence D.

2015-01-01

When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. PMID:25743543

THE INFLUENCE OF SOCIAL STATUS AND SOLIDARITY TO THE QUANTITY OF UTTERANCES IN JANE AUSTEN’S NOVELS

Directory of Open Access Journals (Sweden)

Citra Suryanovika

2018-03-01

Fokus penelitian pada ujaran yang disampaikan oleh tokoh utama perempuan dalam enam novel Jane Austen. Penelitian bertujuan menelaah pengaruh status sosial dan solidaritas pada kuantitas ujaran. Hasil penelitian menunjukkan 1,738 dengan rincian 266 ujaran Elinor Dashwood, 368 ujaran Elizabeth Bennet, 194 ujaran Fanny Price, 473 ujaran Emma Woodhouse, 113 ujaran Anne Elliot, and 324 ujaran Catherine Morland. Berdasarkan peringkat, status sosial tinggi Emma Woodhouse menghasilkan jumlah ujaran paling banyak, dibandingkan dengan lima tokoh lainnya, namun Fanny Price dengan status sosial paling bawah berada di peringkat kelima dari enam tokoh yang ditelaah. Telaah keakraban menunjukkan 66,7% jumlah ujaran dengan skala solidaritas tinggi, dan 33,3% ujaran dengan skala solidaritas rendah. Berdasarkan hasil analisa, dapat disimpulkan bahwa penentu kuantitas ujaran bukan hanya ditentukan oleh status sosial dan solidaritas karakter, tapi juga ditentukan oleh ketertarikan dan rasa penasaran. Kata kunci: Status Sosial, Skala Solidaritas, Ujaran, Jane Austen.

A PRELIMINARY STUDY OF MALAYAN FILARIASIS IN PUDING VILLAGE, JAMBI PROVINCE (SUMATERA, INDONESIA

Directory of Open Access Journals (Sweden)

Sudomo M.

2012-09-01

Full Text Available Beberapa daerah di Propinsi Jambi akan dikembangkan menjadi daerah transmigrasi, satu di antara­nya adalah daerah Kumpeh yang terletak berdekatan dengan daerah endemik filariasis malayi. Desa yang paling dekat dengan lokasi transmigrasi tersebut adalah desa Puding. Penelitian pendahuluan tentang penyakit filariasis telah dikerjakan di desa Puding untuk mengetahui tingkat endemisitas, periodisitas B. malayi, fauna nyamuk, jenis nyamuk yang potensial menjadi vektor filariasis, hospes reservoir dan keadaan sosial-ekonomi-budaya penduduk setempat. Mf rate pada penduduk desa Puding adalah 18,7% dan dari B. malayi jenis subperiodiknokturna. Nyamuk yang tertangkap terdiri dari enam genera yaitu genus Anopheles, Aedes, Culex, Coquilletidia, Mansonia dan Tripteroides. Dari enam genera tersebut yang potensial untuk menjadi vektor filariasis adalah genus Mansonia dan ini didukung dengan diketemukannyd larva stadium L3 (infektif Brugia sp di tubuh nyamuk tersebut. Keadaan sosial-ekonomi-budaya, khususnya menyangkut adat istiadat dan kebiasaan penduduk setempat, telah dipelajari.

Gene Therapy

Science.gov (United States)

Gene therapy Overview Gene therapy involves altering the genes inside your body's cells in an effort to treat or stop disease. Genes contain your ... that don't work properly can cause disease. Gene therapy replaces a faulty gene or adds a new ...

Imaging reporter gene for monitoring gene therapy

International Nuclear Information System (INIS)

Beco, V. de; Baillet, G.; Tamgac, F.; Tofighi, M.; Weinmann, P.; Vergote, J.; Moretti, J.L.; Tamgac, G.

2002-01-01

Scintigraphic images can be obtained to document gene function at cellular level. This approach is presented here and the use of a reporter gene to monitor gene therapy is described. Two main ways are presented: either the use of a reporter gene coding for an enzyme the action of which will be monitored by radiolabeled pro-drug, or a cellular receptor gene, the action of which is documented by a radio labeled cognate receptor ligand. (author)

Gene-Gene and Gene-Environment Interactions in the Etiology of Breast Cancer

National Research Council Canada - National Science Library

Adegoke, Olufemi

2003-01-01

The objective of this CDA is to evaluate the gene-gene and gene-environment interactions in the etiology of breast cancer in two ongoing case-control studies, the Shanghai Breast Cancer Study (SBCS...

Gene doping: gene delivery for olympic victory.

Science.gov (United States)

Gould, David

2013-08-01

With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called 'gene doping'. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted from the engineered cells or is retained locally to, or inside engineered cells will, to some extent, determine the likelihood of detection. It is clear that effective gene delivery technologies now exist and it is important that detection and prevention plans are in place. © 2012 The Author. British Journal of Clinical Pharmacology © 2012 The British Pharmacological Society.

Differentiating for loyalty / Ivar Soone

Index Scriptorium Estoniae

Soone, Ivar, 1975-

2004-01-01

Autor väidab, et kui on suudetud tekitada tarbija seotus ja sellel põhinev lojaalsus, saab turundaja võtta kasumit seda enam, mida kõrgema astme lojaalsusega on tegemist. Selline kasumi juhtimine muutub jätkusuutlikkuse ning konkurentsieelise hoidmisel üha olulisemaks. Graafikud. Tabelid

Pariisis jagati Cesare / Aare Ermel

Index Scriptorium Estoniae

Ermel, Aare, 1957-2013

2006-01-01

Sel aastal sai prantsuse rahvuslike filmiauhindade Cesaride jagamisel kõige enam (8) auhindu J. Audiard'i mängufilm "Mu süda jättis vahele löögi" ("De battre mon coeur s'est arrete"). Näitlejapreemiad said Michel Bouquet, Nathalie Baye

Koolirõõmuta kool on lapsele kui sunnitöö / Ene-Silvia Sarv ; intervjueerinud Karin Klaus

Index Scriptorium Estoniae

Sarv, Ene-Silvia, 1945-

2013-01-01

Intervjuu Pärnus hariduskonverentsil "Õnnelik õpilane, õnnelik õpetaja" esinenud Tallinna ülikooli lektori Ene-Silvia Sarvega, kes rääkis oma ettekandes, milline paistab tänapäeva kool õpilaste silme läbi ja mis mõjutab koolikliimat kõige enam

Skandinavija ne protiv Baltiiskoi AES / Senta Alas

Index Scriptorium Estoniae

Alas, Senta

2006-01-01

Taani keskkonnaministri Connie Hedegaardi sõnade kohaselt ei kavatse Taani ehitada oma territooriumile tuumajaama, kuid samas ei mõista hukka ka Balti riikide püüdlusi hakata enam kasutama tuumaenergiat ning ehitada jaam Leetu. Minister esines pressikonverentsil seoses novembris Nairobis toimuva ülemaailmse kliimakonverentsiga

Rae valda kerkib esimene energiamajade elurajoon / Linda-Mari Väli

Index Scriptorium Estoniae

Väli, Linda-Mari

2009-01-01

Harjumaal Rae vallas asuvasse Järvekülla kavandatavast Eesti esimesest energiamajade elamurajoonist. 13. märtsil kuulutati A&A Kinnisvara OÜ korraldatud arhitektuurikonkursi võitjaks austerlanna Ursula Schneider, kelle töö hõlmab enam kui sajale leibkonnale mõeldud ridaelamute arhitektuurilist lahendust

Kaitseväelastel pole alust kogu missiooni eest lisapalka nõuda / Holger Roonemaa

Index Scriptorium Estoniae

Roonemaa, Holger

2007-01-01

Afganistanis teeninud kolm Eesti kaitseväelast nõuavad kaitseväelt Tallinna halduskohtus igaüks enam kui poolt miljonit krooni. Tööõigusbüroo Labour Consulting juristi Katrin Sarapi sõnul pole selliseks nõudeks alust. Vt. samas: Rahanõudjad teenivad edasi

Dolly looja pettub tehtus / Priit Ennet

Index Scriptorium Estoniae

Ennet, Priit

2007-01-01

Ajaloolise kloonlamba Dolly loonud Shoti teadlane Ian Wilmut ei kavatse edaspidi enam embrüoid kunstlikult valmistada ja loobub seega uurimissuunast. Intervjuus ajalehele Daily Telegraph tunnistab Wilmut, et Jaapani teadlaste avastatud konkureeriva meetodiga on inimese embrüonaalseid tüvirakke loodetavasti palju lihtsam toota

Uus menüü kasvatas McDonald'si käivet / Annika Matson

Index Scriptorium Estoniae

Matson, Annika, 1976-

2003-01-01

USA kiirtoiduketi McDonald's vähemalt aasta tegutsenud söögikohtade käive kasvas enam kui 6% eelkõige tänu uuele menüüle ja edukale reklaamikampaaniale. Diagrammid: McDonald'si käive ja kasum kasvasid 13%

Tarbijakaitse võitleb internetipettuste vastu / Maris Kärdi

Index Scriptorium Estoniae

Kärdi, Maris

2005-01-01

1. veebr. algas ühekuuline enam kui 30 erinevat riiki hõlmav kampaania, milles pööratakse avalikkuse tähelepanu segadusse ajavatele massiturunduse pettustele. Kampaania algatajaks on rahvusvaheline rakendusasutuste vaheline koostöövõrgustik ICPEN (International Consumer Protection and Enforcement Network)

Pensionikoorem riigil järjest raskem kanda / Raivo Sormunen

Index Scriptorium Estoniae

Sormunen, Raivo, 1976-

2008-01-01

Ilmunud ka: Delovõje Vedomosti 3. sept. lk. 4. Eesti riigil võib kuluda 2009. aastal pensionide maksmiseks 2,7 miljardit krooni enam kui sel aastal. Samas oodatakse riigieelarve tulude kasvuks kõigeks 1,5 miljardit krooni. Diagrammid: Pensionikulude osakaal riigieelarves; II pensionisamba fondide seis

Artificial landscapes / Dorothée Bauerle- Willert

Index Scriptorium Estoniae

Bauerle- Willert, Dorothée

2008-01-01

Maastik ei ole enam osa loodusest, vaid juba 18. sajandist alates on tehislikkus modernismi peamisi kategooriaid. C. Baudelaire', W. Benjamini ja L.Aragoni kujutelmi moodsast linnast kui tehisloodusest, kui virtuaalsest maastikust. Ka V. Nedeljkoviî ja N. Jeremiî videoprojektist "L2 and the Towers"

Genes2FANs: connecting genes through functional association networks

Science.gov (United States)

2012-01-01

Background Protein-protein, cell signaling, metabolic, and transcriptional interaction networks are useful for identifying connections between lists of experimentally identified genes/proteins. However, besides physical or co-expression interactions there are many ways in which pairs of genes, or their protein products, can be associated. By systematically incorporating knowledge on shared properties of genes from diverse sources to build functional association networks (FANs), researchers may be able to identify additional functional interactions between groups of genes that are not readily apparent. Results Genes2FANs is a web based tool and a database that utilizes 14 carefully constructed FANs and a large-scale protein-protein interaction (PPI) network to build subnetworks that connect lists of human and mouse genes. The FANs are created from mammalian gene set libraries where mouse genes are converted to their human orthologs. The tool takes as input a list of human or mouse Entrez gene symbols to produce a subnetwork and a ranked list of intermediate genes that are used to connect the query input list. In addition, users can enter any PubMed search term and then the system automatically converts the returned results to gene lists using GeneRIF. This gene list is then used as input to generate a subnetwork from the user’s PubMed query. As a case study, we applied Genes2FANs to connect disease genes from 90 well-studied disorders. We find an inverse correlation between the counts of links connecting disease genes through PPI and links connecting diseases genes through FANs, separating diseases into two categories. Conclusions Genes2FANs is a useful tool for interpreting the relationships between gene/protein lists in the context of their various functions and networks. Combining functional association interactions with physical PPIs can be useful for revealing new biology and help form hypotheses for further experimentation. Our finding that disease genes in

The genetics of amelogenesis imperfecta: a review of the literature Genética da amelogênese imperfeita: uma revisão da literatura

Directory of Open Access Journals (Sweden)

Maria Cristina Leme Godoy dos Santos

2005-09-01

Full Text Available A melogenesis imperfecta (AI is a group of inherited defects of dental enamel formation that show both clinical and genetic heterogeneity. Enamel findings in AI are highly variable, ranging from deficient enamel formation to defects in the mineral and protein content. Enamel formation requires the expression of multiple genes that transcribes matrix proteins and proteinases needed to control the complex process of crystal growth and mineralization. The AI phenotypes depend on the specific gene involved, the location and type of mutation, and the corresponding putative change at the protein level. Different inheritance patterns such as X-linked, autosomal dominant and autosomal recessive types have been reported. Mutations in the amelogenin, enamelin, and kallikrein-4 genes have been demonstrated to result in different types of AI and a number of other genes critical to enamel formation have been identified and proposed as candidates for AI. The aim of this article was to present an evaluation of the literature regarding role of proteins and proteinases important to enamel formation and mutation associated with AI.A melogênese imperfeita é um grupo de doenças hereditárias que causa defeito na formação esmalte dental e mostra heterogeneidade clínica e genética. O esmalte é afetado com alta variabilidade, desde deficiência na formação do esmalte até defeitos no conteúdo mineral e protéico. A formação do esmalte requer a expressão de múltiplos genes que transcrevem proteínas e proteinases importantes para controlar o complexo processo de crescimento dos cristais e mineralização. O fenótipo da AI depende do gene envolvido, sua localização e tipo de mutação, e a conseqüente alteração na proteína. Diferentes padrões hereditários com ligado ao X, autossômico dominante e autossômico recessivo já foram descritos. Mutações nos genes correspondentes da amelogenina, enamelina, e calicreína-4 demonstraram resultar em

Classifying genes to the correct Gene Ontology Slim term in Saccharomyces cerevisiae using neighbouring genes with classification learning

Directory of Open Access Journals (Sweden)

Tsatsoulis Costas

2010-05-01

Full Text Available Abstract Background There is increasing evidence that gene location and surrounding genes influence the functionality of genes in the eukaryotic genome. Knowing the Gene Ontology Slim terms associated with a gene gives us insight into a gene's functionality by informing us how its gene product behaves in a cellular context using three different ontologies: molecular function, biological process, and cellular component. In this study, we analyzed if we could classify a gene in Saccharomyces cerevisiae to its correct Gene Ontology Slim term using information about its location in the genome and information from its nearest-neighbouring genes using classification learning. Results We performed experiments to establish that the MultiBoostAB algorithm using the J48 classifier could correctly classify Gene Ontology Slim terms of a gene given information regarding the gene's location and information from its nearest-neighbouring genes for training. Different neighbourhood sizes were examined to determine how many nearest neighbours should be included around each gene to provide better classification rules. Our results show that by just incorporating neighbour information from each gene's two-nearest neighbours, the percentage of correctly classified genes to their correct Gene Ontology Slim term for each ontology reaches over 80% with high accuracy (reflected in F-measures over 0.80 of the classification rules produced. Conclusions We confirmed that in classifying genes to their correct Gene Ontology Slim term, the inclusion of neighbour information from those genes is beneficial. Knowing the location of a gene and the Gene Ontology Slim information from neighbouring genes gives us insight into that gene's functionality. This benefit is seen by just including information from a gene's two-nearest neighbouring genes.

Muusikamaailm : Esiettekannetest rikas aprill. Bachi passioonid Moskvas. MacMillani löökpillikontserdi edu / Priit Kuusk

Index Scriptorium Estoniae

Kuusk, Priit, 1938-

2000-01-01

Heliloojate teoste esiettekannetest aprillis 2000. Bachi aasta tähistamisest Moskvas ئ 85aastase vaheaja järel kõlas vene koorilt Bachi "Mattheuse passioon". J. MacMillani löökpillikontsert "Veni, veni, Emmanuel" on kõlanud enam kui 200 korda 27 riigis tuntud dirigentide juhatusel

Suurtarbijad otsivad Eesti Energiale asendajat / Katre Pilvinski

Index Scriptorium Estoniae

Pilvinski, Katre

2010-01-01

Köögiviljatootja Grüne Fee ei ole enam Eesti Energia klient, sest saab teistelt pakkujatelt osta elektrit soodsamalt. Elektrienergia suurtarbijate liidu esimehe Tiit Kolgi hinnangul võiks valitsus taastuvenergiatasu kolmandiku võrra vähendada. Eelnõu kohaselt väheneks toetus kuni 75%

Karikatuurid vallandasid kultuuride kokkupõrke / Dan Bilefsky ; tõlk. Heiki Suurkask

Index Scriptorium Estoniae

Bilefsky, Dan

2006-01-01

Autori sõnul on Taani kujunenud väheusutavaks tulipunktiks kultuuridesõjas islami ja lääne vahel. Taani muslimikogukonna väitel väljendavad karikatuurid võimenduvat immigrantidevaenulikku õhkkonda. Üha enam noori Taani muslimeid liitub radikaalse rühmitusega Hizb ut-Tahrir

Pärandkultuur - muinsuskaitse reserv / Jüri Kusmin, Vaike Pommer

Index Scriptorium Estoniae

Kusmin, Jüri

2008-01-01

Riigimetsa Majandamise Keskuse initsiatiivil ja Euroopa struktuurifondide toel viidi aastatel 2005-2007 Eesti neljas maakonnas - Läänemaa, Raplamaa, Harjumaal ja Järvamaal - läbi metsandusliku pärandkultuuri inventuur. Kaardistatud on enam kui 6300 objekti. Andmed on kantud Maa-Ameti andmebaasi geoportaali X-GIS.

Aktsiate hinnad languses, tehased kinni, elektrit napib / Kaivo Kopli

Index Scriptorium Estoniae

Kopli, Kaivo

2011-01-01

Jaapani keskpank paiskas rahaturgudele 140 mld. eurot lootuses, et pangad jätkavad laenamist. Esialgsed hinnangud maavärina ja tsunami tekitatud kahju kohta ulatuvad enam kui 100 mld. dollarist 200 mld. dollarini, millele lisanduvad veel ettevõtete kahjumid. Nissan, Toyota ja Honda on peatanud tootmise

Street foods contribute to nutrient intakes among children from rural ...

African Journals Online (AJOL)

The contribution of Street Foods (SF) to the energy and nutrient intakes of young children in rural African communities has been understudied. Under the Enhancing Child Nutrition through Animal Source Food Management (ENAM) project, a microcredit and nutrition education intervention with caregivers of children 2-to ...

Aasia on uus roheline jõud / Fredy-Ewin Esse

Index Scriptorium Estoniae

Esse, Fredy-Edwin

2010-01-01

Investorid on olnud sunnitud hülgama taastuvenergiaga seotud aktsiaid. Langenud on suurte tuulegeneraatoreid tootvate firmade Vestas Wind Systems, Gamesa ja Suzlon Energy aktsia. Taastuvenergia ei pruugi jääda enam kauaks maailma suurimaks roheliseks sektoriks, sest kasvamas on keskkonnasäästlike autode hulk

Poodidele omamärgikraami tegemine säästab kulusid / Ketlin Priilinn

Index Scriptorium Estoniae

Priilinn, Ketlin, 1982-

2008-01-01

Poeketid on üha enam hakanud müüma kaupu oma kaubamärgi all. Vt. samas: Jaemüügiketti omamärgitoode ehk private label. Diagramm: Omamärk teeb Euroopas võidukäiku. Kommenteerivad Kristjan Alaküla ja Ott Licht

"Tänu gaasijuhtmele ujuvad varsti kõik kalad...!" / Külli-Riin Tigasson

Index Scriptorium Estoniae

Tigasson, Külli-Riin, 1975-

2005-01-01

Poliitiliste argumentidega Vene-Saksa gaasijuhtme rajamise vastu enam ei saa, sõnab artikli autor, ainus argument on keskkonnakaitse. Eesti huvides on nõuda, et gaasitrassi keskkonnaekspertiisi ei koostaks Saksamaa ja Venemaa kahekesi, vaid et see koostataks Läänemere-äärsete riikide koostöös

Ettevõtete käive kasvas 20%

Index Scriptorium Estoniae

2006-01-01

Ettevõtete netokäive oli 2006. aasta III kvartalis 142 miljardit krooni, mis on 24 miljardit krooni enam kui eelmise aasta III kvartalis, tööviljakus oli eelmise aasta sama perioodiga võrreldes 15% suurem. Diagramm: Ettevõtete käive kasvab jõudsalt

Inimkonna ainuke võimalus on taastuvate ressursside kasutamine / Taito Mikkonen

Index Scriptorium Estoniae

Mikkonen, Taito

2006-01-01

Enam ei ole aega vaielda, kas tuumajõud või põlevkivi. Energeetika probleemiks pole ainult energia kättesaadavus ja hind, vaid lisaks keskkonnakaitsele terve maailma elukeskkonna säilitamine. Lahendused nõuavad muudatusi mõtlemise alustes ning mõjutavad meie eluviisi, poliitikat ja moraali

Alkohol ja uimastid köidavad teismelisi järjest nooremalt / Airi Ilisson

Index Scriptorium Estoniae

Ilisson, Airi, 1980-

2004-01-01

Eelmisel aastal Eesti koolides korraldatud uuringu kohaselt on noorte seas populaarsed kange alkohol ja kanep. Järjest enam tarvitavad mõnuaineid tütarlapsed. Tallinna Pedagoogikaülikooli rahvusvaheliste ja sotsiaaluuringute instituudi teadur A.-A. Allaste kommenteerib instituudi korraldatud uuringut noorte uimastitarbimisest. Lisaks joonis: Õpilaste uimastitarvitamine

الأخطاء النحويّة والصّرفية فى إنشاء طلاّب شعبة تعليم اللغة العربية بجامعة سلاتيجا الإسلامية الحكومية عام الدراسي ٢٠١١

Directory of Open Access Journals (Sweden)

Muhammad Mas'ud

2013-07-01

Full Text Available Penelitian ini merupakan study analisis terhadap kesalahan tata bahasa “Nahwu dan Shorof” pada mahasiswa program study bahasa Arab semester  enam di Sekolah Tinggi Agama Islam Negeri (STAIN Salatiga. Tulisan ini mereview kembali pentingnya tata bahasa dalam Insya’ dan sebagai bahasa komunikasi tertulis. Penulis juga menganalisis sebab-sebab kesulitan dalam Insya pada mahasiswa PBA semester enam dan menawarkan solusi alternatif dalam pengembangan kriteria penulisan yang baik. Setelah penulis menggunakan tiga metode pengumpulan data yaitu : Tri Anggulasi, Ikhtibar, dan Istifta’. Akhirnya penulis dapat menyimpulkan bahwa kesalahan pada materi nahwu yang tertinggi yaitu “مفعول” dan yang terendah yaitu “خبر كان”. Sedangkan pada materi shorof yang tertinggi adalah “إسناد الفعل المضارع” dan yang terendah yaitu “أوزان الفعل المزيد”

Europarlament ihkab enam tähelepanu / Inga Höglund

Index Scriptorium Estoniae

Höglund, Inga

2010-01-01

Euroopa Parlament korraldas EL-i institutsioonide ja meedia seminari, et leida lahendust probleemile, kuidas suurendada inimeste ja meedia huvi EL-i, Euroopa Parlamendi tegemiste vastu. Parlamendi liikmete Morten Løkkegaardi, Thijs Bermani arvamusi ja ettepanekuid. Parlamendi presidendi Jerzy Buzeki seisukoht

USA leiab maailmas aina enam hukkamõistu / Neeme Raud

Index Scriptorium Estoniae

Raud, Neeme, 1969-

2007-01-01

Ilmunud ka: Postimees : na russkom jazõke, 25. jaan. 2007, lk. 9. 25 maailma riigis korraldatud BBC küsitlusuurimus näitas, et üha suurem osa maailmast mõistab hukka USA praeguse kursi, eriti pälvib kriitikat sõda Iraagis ja terroristide vangilaagri pidamine Kuubal Guantanamo Bays

Enam-vähem otse põrgust / Mari Laaniste

Index Scriptorium Estoniae

Laaniste, Mari, 1977-

2002-01-01

Mängufilm "Põrgust" ("From Hell") : režissöörid Albert ja Allen Hughes : Ameerika Ühendriigid - Tšehhi Vabariik 2001. Analüüsitud filmi lähtekohaks olnud Alan Moore'i 1988. a. ilmunud raamatu, selle varasemate eeskujude ja filmi vahekorda

Briti poliitik : Venemaa käitumine muudab murelikuks / Raimo Poom

Index Scriptorium Estoniae

Poom, Raimo

2007-01-01

IRL-i suurkogul esinenud Briti alamkoja liikme Graham Brady sõnul teadvustab Briti avalik arvamus üha enam Venemaa käitumisest põhjustatud muresid. Ta peab väga ebatõenäoliseks, et Saksamaal õnnestuks meelitada britte oma eesistumise lõpuks alla kirjutama Euroopa põhiseaduslepingule

Eesti on õnnetuste tõttu hukkuvate laste poolest esirinnas / Merje Pors

Index Scriptorium Estoniae

Pors, Merje

2011-01-01

Majandusliku Koostöö ja Arengu Organisatsiooni (OECD) värskest raportist "Doing Better for Families" selgub, et Eestis on aastatel 1997-2008 õnnetuste tagajärjel surma saanud 100 000 kuni 14-aastase lapse kohta enam poisse ja türdukuid kui üheski teises OECD liikmesriigis

Tartu biomeditsiiniettevõtluse võimalused ja riiklikud poliitikad = Über die Möglichkeiten von Biomedizin-Unternehmen in Tartu und die staatliche Politik / Garri Raagmaa

Index Scriptorium Estoniae

Raagmaa, Garri, 1966-

2005-01-01

Teadmistepõhisest majandusest on küll palju räägitud, kuid selle sisu on jätkuvalt segane ja seetõttu ähvardab devalveeruda. Autori hinnangul on vaja enam kommunikatsiooni ning vastastikku arusaamist teadlaste, poliitikute ja ettevõtjate vahel. Vt. ka kommentaare lk. 217-222,467-472

Inimkeskne Talsinki / Kristi Grišakov

Index Scriptorium Estoniae

Grišakov, Kristi

2010-01-01

Talsinki linnaaktivismist. Tallinna ja Helsingi linnaaktivistide laiemast koostööst tulevikus. Autori sõnul võiksid linnaaktivistide kohtumised veelgi enam keskenduda ühiste eesmärkide, ürituste ja tööriistade väljatöötamisele. See oleks alguseks rohujuuretasandi Talsinkile, mis on inimkeskne

Nad teavad meist kõike / Kaivo Kopli

Index Scriptorium Estoniae

Kopli, Kaivo

2006-01-01

USA internetiteenuste pakkuja AOL avaldas täieliku nimekirja oma enam kui 650 000 kliendi kolme kuu jooksul otsingumootorisse sisestatatud küsimustest. Ehkki kliendid ei esinenud andmeis nimeliselt, vaid igaühte neist tähistas number, selgus õige pea, et number ei takista arvutikasutajani jõudmist

Edgar Savisaar : aprill mõjutab meid aastaid / Edgar Savisaar ; interv. Frank Sprenk-Dorn

Index Scriptorium Estoniae

Savisaar, Edgar, 1950-

2007-01-01

Tallinna linnapea hinnangul mõjutasid möödunud aastal Eesti majandust kõige enam aprillisündmused, Schengeni viisaruumiga liitumise mõju on sel aastal tühine. Ta loodab, et järgmisel aastal saab Eesti valitsuse, kelle jaoks on kõik majandusvaldkonnad tähtsad

Estonia no longer a cheap labor stop - Parts / Joel Alas

Index Scriptorium Estoniae

Alas, Joel

2007-01-01

Neli välismaalastest ettevõtte omanikku on sulgenud tehased Eestis, kuna ei leia tööjõudu. Peaminister Juhan Parts tõdes Eesti-Suurbritannia kaubanduskoja konverentsil, et Eestis pole enam odavat tööjõudu. J. Parts on pidanud vajalikuks, et Eesti ostaks tagasi Hansapanga

Banaanikoorimise hooaeg on alanud : mõtiskleb seisundiseikleja / Ingrid Peek

Index Scriptorium Estoniae

Peek, Ingrid

2012-01-01

Raadio 2 enam kui kaks aastat raadiosaadet "Hallo, Kosmos!" juhtinud Ingrid Peek mõtiskleb selle saatesarja jooksul käsitletud teemade infoküllusest, erinevusest ja vasturääkivustest ning võrdleb seda söömise ja erinevates söögikohtades pakutava söögikultuuriga

Saladusliku Sandu Hubani miljonid / Peeter Raidla

Index Scriptorium Estoniae

Raidla, Peeter, 1955-

2005-01-01

Eesti ühe edukaima hokiklubi Välk 494 rahastaja Sandu Hubani alias Aleksandr Gubani tegevusest, ettevõtlusest ja äritegevusest. Lisad: Hubani osalused firmades; Ettevõtted, millega Huban enam seotud ei ole; Välk 494 seob Hubani ja tema äripartnereid. Kommenteerivad Meelis Birk, Enriko Lukecha, Aivo Pärn

President Ilves: Rootsi avas eestlastest paadipõgenikele vabaduse värava / Piret Pert

Index Scriptorium Estoniae

Pert, Piret

2011-01-01

President Toomas Hendrik Ilves külastas Stockholmis mälestusmärki "Vabaduse värav", mis sümboliseerib eestlastest paadipõgenike tänu Rootsile ja rootslastele, kes nad enam kui 65 aastat tagasi vastu võtsid. Riigivisiit Rootsi 17.01.2011 - 20.01.2011

Terroristid, twitter ja Domodedovo / Andrei Hvostov

Index Scriptorium Estoniae

Hvostov, Andrei, 1963-

2011-01-01

Terrorirünnakutest Venemaal, seosest terrorismi ägenemise ja riigivõimu tsentraliseerimise vahel. Avaliku arvamuse uuringud näitavad, et Venemaa kodanike hirm pärast järjekordset terroriakti ei püsi kaua. Venelased ei usu enam oma (riiklikku) massimeediat, info liigub twitteri, blogide jms. kaudu

BLRT : laevaehituses on pidu / Enn Tosso

Index Scriptorium Estoniae

Tosso, Enn, 1976-

2008-01-01

Ilmunud ka: Delovõje Vedomosti 13. aug. lk. 5. BLRT Grupi esimese poolaasta käive oli 2,9 miljardit krooni, mis on 38,4% enam kui mullu samal perioodil. Ettevõtte kommunikatsioonidirektori Anu Halliku kinnitusel on laevaremondi ja -ehituse maailmaturul praegu väga soodne seis. Lisa: Tulemused

Valed otsused lähevad järjest kallimaks / Argo Rannamets

Index Scriptorium Estoniae

Rannamets, Argo

2006-01-01

Valdavalt kulub Eesti ettevõtetel otsuste ettevalmistamise töös Pareto printsiipi rakendades 80% ajast andmete kogumisele ja vaid 20% jääb analüüsile ning järelduste tegemisele. Kommenteerib Alvar Pihlapuu. Vt. samas: Trendid, mis info kogumisele kuluvat aega enam mõjutavad

Gazprom teeb reformi: Ukrainal on aeg gaasipliidid nurka visata / Heiki Suurkask

Index Scriptorium Estoniae

Suurkask, Heiki, 1972-

2009-01-01

Autor leiab, et Ukraina pole 2006. a. kriisist midagi õppinud, maagaasi tarbimine on veelgi suurenenud. Gaasihinna tõusu korral hakatakse Ukrainas ilmselt üha enam loobuma gaasipliitidest ja -boileritest ning niimoodi kaotaks Gazprom ühe oma suurema turu. Gazprom üritab kõrgemat gaasihinda saavutada ka SRÜ maades. Diagrammid

Sexy gene conversions: locating gene conversions on the X-chromosome.

Science.gov (United States)

Lawson, Mark J; Zhang, Liqing

2009-08-01

Gene conversion can have a profound impact on both the short- and long-term evolution of genes and genomes. Here, we examined the gene families that are located on the X-chromosomes of human (Homo sapiens), chimpanzee (Pan troglodytes), mouse (Mus musculus) and rat (Rattus norvegicus) for evidence of gene conversion. We identified seven gene families (WD repeat protein family, Ferritin Heavy Chain family, RAS-related Protein RAB-40 family, Diphosphoinositol polyphosphate phosphohydrolase family, Transcription Elongation Factor A family, LDOC1-related family, Zinc Finger Protein ZIC, and GLI family) that show evidence of gene conversion. Through phylogenetic analyses and synteny evidence, we show that gene conversion has played an important role in the evolution of these gene families and that gene conversion has occurred independently in both primates and rodents. Comparing the results with those of two gene conversion prediction programs (GENECONV and Partimatrix), we found that both GENECONV and Partimatrix have very high false negative rates (i.e. failed to predict gene conversions), which leads to many undetected gene conversions. The combination of phylogenetic analyses with physical synteny evidence exhibits high resolution in the detection of gene conversions.

Evaluation of mechanical and optical behavior of current esthetic dental restorative CAD/CAM composites.

Science.gov (United States)

Stawarczyk, Bogna; Liebermann, Anja; Eichberger, Marlis; Güth, Jan-Frederik

2015-03-01

To determine the mechanical and optical properties of CAD/CAM composites (LAVA Ultimate, Cerasmart, Shofu Block and two exp. CAD/CAM composites), a hybrid material (VITA Enamic), a leucite (IPS Empress CAD) and a lithium disilicate glass-ceramic (IPS e.max CAD). Three-point flexural strength (FS) was investigated according ISO 6872:2008 (N=240/n=30). Two-body wear (TBW) was analyzed in a chewing simulator (1,200,000 cycles, 50N, 5°/55°C) using human teeth as antagonists (N=120/n=15). Quantitative analysis of wear was carried out with a 3D-scanner and associated matching software. Discoloration rate (DR) after 14 days of storage in cress, curry, red wine, and distilled water (N=384/n=12), and translucency (T) (N=384/n=48) of CAD/CAM materials were measured in a spectrophotometer (400-700nm wavelength). Data were analyzed using two-/one-way ANOVA with Scheffé post-hoc test, Kruskal-Wallis-H test, and linear mixed models (α=0.05). IPS e.max CAD showed the highest FS (pCAD/CAM composites (exception: Shofu Block). The lowest FS showed VITA Enamic and IPS Empress CAD (pCAD, VITA Enamic, exp. CAD/CAM composite 2, followed by IPS e.max presented lower material TBW than the remaining CAD/CAM materials (pcurry>cress>distilled water) exerted the highest influence on DR (pCAD/CAM material. Glass-ceramics showed lower DR than CAD/CAM composites (pCAD/CAM composites presented moderate FS, high T and antagonist friendly behavior. Glass-ceramic demonstrated the most favorable DR and lowest TBW on the material side. Copyright © 2015 Elsevier Ltd. All rights reserved.

Optimal Reference Genes for Gene Expression Normalization in Trichomonas vaginalis

Science.gov (United States)

dos Santos, Odelta; de Vargas Rigo, Graziela; Frasson, Amanda Piccoli; Macedo, Alexandre José; Tasca, Tiana

2015-01-01

Trichomonas vaginalis is the etiologic agent of trichomonosis, the most common non-viral sexually transmitted disease worldwide. This infection is associated with several health consequences, including cervical and prostate cancers and HIV acquisition. Gene expression analysis has been facilitated because of available genome sequences and large-scale transcriptomes in T. vaginalis, particularly using quantitative real-time polymerase chain reaction (qRT-PCR), one of the most used methods for molecular studies. Reference genes for normalization are crucial to ensure the accuracy of this method. However, to the best of our knowledge, a systematic validation of reference genes has not been performed for T. vaginalis. In this study, the transcripts of nine candidate reference genes were quantified using qRT-PCR under different cultivation conditions, and the stability of these genes was compared using the geNorm and NormFinder algorithms. The most stable reference genes were α-tubulin, actin and DNATopII, and, conversely, the widely used T. vaginalis reference genes GAPDH and β-tubulin were less stable. The PFOR gene was used to validate the reliability of the use of these candidate reference genes. As expected, the PFOR gene was upregulated when the trophozoites were cultivated with ferrous ammonium sulfate when the DNATopII, α-tubulin and actin genes were used as normalizing gene. By contrast, the PFOR gene was downregulated when the GAPDH gene was used as an internal control, leading to misinterpretation of the data. These results provide an important starting point for reference gene selection and gene expression analysis with qRT-PCR studies of T. vaginalis. PMID:26393928

Patenting human genes: Chinese academic articles' portrayal of gene patents.

Science.gov (United States)

Du, Li

2018-04-24

The patenting of human genes has been the subject of debate for decades. While China has gradually come to play an important role in the global genomics-based testing and treatment market, little is known about Chinese scholars' perspectives on patent protection for human genes. A content analysis of academic literature was conducted to identify Chinese scholars' concerns regarding gene patents, including benefits and risks of patenting human genes, attitudes that researchers hold towards gene patenting, and any legal and policy recommendations offered for the gene patent regime in China. 57.2% of articles were written by law professors, but scholars from health sciences, liberal arts, and ethics also participated in discussions on gene patent issues. While discussions of benefits and risks were relatively balanced in the articles, 63.5% of the articles favored gene patenting in general and, of the articles (n = 41) that explored gene patents in the Chinese context, 90.2% supported patent protections for human genes in China. The patentability of human genes was discussed in 33 articles, and 75.8% of these articles reached the conclusion that human genes are patentable. Chinese scholars view the patent regime as an important legal tool to protect the interests of inventors and inventions as well as the genetic resources of China. As such, many scholars support a gene patent system in China. These attitudes towards gene patents remain unchanged following the court ruling in the Myriad case in 2013, but arguments have been raised about the scope of gene patents, in particular that the increasing numbers of gene patents may negatively impact public health in China.

Research progress in machine learning methods for gene-gene interaction detection.

Science.gov (United States)

Peng, Zhe-Ye; Tang, Zi-Jun; Xie, Min-Zhu

2018-03-20

Complex diseases are results of gene-gene and gene-environment interactions. However, the detection of high-dimensional gene-gene interactions is computationally challenging. In the last two decades, machine-learning approaches have been developed to detect gene-gene interactions with some successes. In this review, we summarize the progress in research on machine learning methods, as applied to gene-gene interaction detection. It systematically examines the principles and limitations of the current machine learning methods used in genome wide association studies (GWAS) to detect gene-gene interactions, such as neural networks (NN), random forest (RF), support vector machines (SVM) and multifactor dimensionality reduction (MDR), and provides some insights on the future research directions in the field.

Comparison of mechanical properties of three machinable ceramics with an experimental fluorophlogopite glass ceramic.

Science.gov (United States)

Leung, Brian T W; Tsoi, James K H; Matinlinna, Jukka P; Pow, Edmond H N

2015-09-01

Fluorophlogopite glass ceramic (FGC) is a biocompatible, etchable, and millable ceramic with fluoride releasing property. However, its mechanical properties and reliability compared with other machinable ceramics remain undetermined. The purpose of this in vitro study was to compare the mechanical properties of 3 commercially available millable ceramic materials, IPS e.max CAD, Vitablocs Mark II, and Vita Enamic, with an experimental FGC. Each type of ceramic block was sectioned into beams (n=15) of standard dimensions of 2×2×15 mm. Before mechanical testing, specimens of the IPS e.max CAD group were further fired for final crystallization. Flexural strength was determined by the 3-point bend test with a universal loading machine at a cross head speed of 1 mm/min. Hardness was determined with a hardness tester with 5 Vickers hardness indentations (n=5) using a 1.96 N load and a dwell time of 15 seconds. Selected surfaces were examined by scanning electron microscopy and energy-dispersive x-ray spectroscopy. Data were analyzed by the 1-way ANOVA test and Weibull analysis (α=.05). Weibull parameters, including the Weibull modulus (m) as well as the characteristic strength at 63.2% (η) and 10.0% (B10), were obtained. A significant difference in flexural strength (PVita Enamic (145.95 ±12.65 MPa)>Vitablocs Mark II (106.67 ±18.50 MPa), and FGC (117.61 ±7.62 MPa). The Weibull modulus ranged from 6.93 to 18.34, with FGC showing the highest Weibull modulus among the 4 materials. The Weibull plot revealed that IPS e.max CAD>Vita Enamic>FGC>Vitablocs Mark II for the characteristic strength at both 63.2% (η) and 10.0% (B10). Significant difference in Vickers hardness among groups (PVitablocs Mark II (594.74 ±25.22 H(V))>Vita Enamic (372.29 ±51.23 H(V))>FGC (153.74 ±23.62 H(V)). The flexural strength and Vickers hardness of IPS e.max CAD were significantly higher than those of the 3 materials tested. The FGC's flexural strength was comparable with Vitablocs Mark II

Gene Circuit Analysis of the Terminal Gap Gene huckebein

Science.gov (United States)

Ashyraliyev, Maksat; Siggens, Ken; Janssens, Hilde; Blom, Joke; Akam, Michael; Jaeger, Johannes

2009-01-01

The early embryo of Drosophila melanogaster provides a powerful model system to study the role of genes in pattern formation. The gap gene network constitutes the first zygotic regulatory tier in the hierarchy of the segmentation genes involved in specifying the position of body segments. Here, we use an integrative, systems-level approach to investigate the regulatory effect of the terminal gap gene huckebein (hkb) on gap gene expression. We present quantitative expression data for the Hkb protein, which enable us to include hkb in gap gene circuit models. Gap gene circuits are mathematical models of gene networks used as computational tools to extract regulatory information from spatial expression data. This is achieved by fitting the model to gap gene expression patterns, in order to obtain estimates for regulatory parameters which predict a specific network topology. We show how considering variability in the data combined with analysis of parameter determinability significantly improves the biological relevance and consistency of the approach. Our models are in agreement with earlier results, which they extend in two important respects: First, we show that Hkb is involved in the regulation of the posterior hunchback (hb) domain, but does not have any other essential function. Specifically, Hkb is required for the anterior shift in the posterior border of this domain, which is now reproduced correctly in our models. Second, gap gene circuits presented here are able to reproduce mutants of terminal gap genes, while previously published models were unable to reproduce any null mutants correctly. As a consequence, our models now capture the expression dynamics of all posterior gap genes and some variational properties of the system correctly. This is an important step towards a better, quantitative understanding of the developmental and evolutionary dynamics of the gap gene network. PMID:19876378

Gene expression

International Nuclear Information System (INIS)

Hildebrand, C.E.; Crawford, B.D.; Walters, R.A.; Enger, M.D.

1983-01-01

We prepared probes for isolating functional pieces of the metallothionein locus. The probes enabled a variety of experiments, eventually revealing two mechanisms for metallothionein gene expression, the order of the DNA coding units at the locus, and the location of the gene site in its chromosome. Once the switch regulating metallothionein synthesis was located, it could be joined by recombinant DNA methods to other, unrelated genes, then reintroduced into cells by gene-transfer techniques. The expression of these recombinant genes could then be induced by exposing the cells to Zn 2+ or Cd 2+ . We would thus take advantage of the clearly defined switching properties of the metallothionein gene to manipulate the expression of other, perhaps normally constitutive, genes. Already, despite an incomplete understanding of how the regulatory switch of the metallothionein locus operates, such experiments have been performed successfully

Mustlaste küüditamine jätkub / Heiki Suurkask

Index Scriptorium Estoniae

Suurkask, Heiki, 1972-

2010-01-01

Prantsusmaa on hakanud mustlasi välja saatma, mis on toonud kaasa kriitika Euroopa Komisjoni justiitsvolinikult Viviane Redingilt. Autor märgib, et Ida-Euroopas levinud sallimatus mustlaste suhtes tõukab neid üha enam vaesusse või otsima paremat elu läänes. Mustlaste kogukondadest Euroopas, nende ajaloost

Nooruslik kaupmeheemand kavatseb äri laiendada / Hille Tänavsuu

Index Scriptorium Estoniae

Tänavsuu, Hille, 1941-2014

2006-01-01

Vt. ka Postimees : na russkom jazõke 23. märts lk. 8. Tallinnas Vana-Kalamaja tänaval paikneva Alma Äri omanik Alma Sooäär avas oma esimese poe enam kui 15 aastat tagasi Nõmmel, praegu plaanib poeomanik majapidamistarvete äri laiendamist. Kaart: Alma Äri

Eesti majanduskriisi dilemma: stimuleerida või lasta kõigil kannatada? / Mikk Salu ; kommenteerinud Ülo Kaasik ja Mart Laar

Index Scriptorium Estoniae

Salu, Mikk, 1975-

2009-01-01

Autor vaatleb, mida teevad praegu maailma riikide keskpangad ja valitsused, et kriisist välja tulla, ning avaldab arvamust, et eelarvepoliitika on enam-vähem ainus vahend, mida Eesti valitsus saab kasutada. Küsimusest, kas Eesti peaks laenama või kasutama reserve. Kommenteerivad Ülo Kaasik ja Mart Laar

Notshnoi Dozor riigikokku? / Edgar Savisaar

Index Scriptorium Estoniae

Savisaar, Edgar, 1950-

2007-01-01

Keskerakonna esimees ja Tallinna linnapea küsib Tallinnas toimunud sündmuste taustal, kuhu jääb Reformierakonna poliitiline vastutus. Tema hinnangul formeerub Eesti poliitiline maastik praegu ümber, valijaskond radikaliseerub ning see toob kaasa muutusi. Tal ei ole enam erilist kahtlust, et Notshnoi Dozori esindajad saavad Riigikogusse

ENPA president jätkas Tallinnaski Eesti-kriitikat / Vahur Koorits

Index Scriptorium Estoniae

Koorits, Vahur, 1981-

2007-01-01

Ilmunud ka: Postimees : na russkom jazõke, 20. sept. 2007, lk. 4. Postimees lüh. Euroopa Nõukogu Parlamentaarse Assamblee president Rene van der Linden külastas Eestit ja kritiseeris Eesti kodakondsuspoliitikat ja soovitas investeerida enam suhetesse Venemaaga. Välisminister Urmas Paeti ja ENPA delegatsiooni juhi Andres Herkeli seisukohad

Nokia ja Sirmens panevad leivad ühte kappi / Lauri Matsulevitsh

Index Scriptorium Estoniae

Matsulevitsh, Lauri

2006-01-01

Nokia ja Siemens ühendavad võrguseadmete tootmise. Lisa: Annika Matson. Eesti võib võita uusi töökohti. Küsimustele vastab Avo Tihamäe. Diagramm: Ühinemisuudis pani aktsiad liikuma. Vt. samas: Sirje Rank. Analüütikud: Siemens võidab tehingust enam; Võrguseadmete tootjatel peal liitumistuhin

Island otsib sõjalisi kaitseingleid / Allan Espenberg

Index Scriptorium Estoniae

Espenberg, Allan

2007-01-01

Islandil toimuvatel parlamendivalimistel peaks arvamusküsitluste kohaselt enam kui 40% valijatest toetama Iseseisvusparteid, teisele kohale jäävad sotsiaaldemokraadid 23,5% ning neile järgnevad rohelised 17,6 ja Progressiivne Partei 10%-ga. Ka Islandi-Norra kahepoolsest lepingust, mis tihendab kaitse- ja julgeolekualast koostööd

Production of Cs and Fr isotopes from a high density UC targets with different grain dimensions

CERN Document Server

Panteleev, V. N; Barzakh, A. E; Fedorov, D. V; Ivanov, V. S; Mezilev, K. A; Moroz, F. V; Molkanov, P. L; Alyakrinskiy, O; Barbui, M; Tonezzer, M; Stroe, L; Orlov, S. Yu; Tecchio, L. B; Lhersonneau, G

A UC target material of 12 g/cm3 density with the grain size of 20 and 5 μm manufactured in a form of pills by the method of powder metallurgy has been tested on-line within the temperature range of (1800-2000) °C. Abstract to ENAM2008

Vaesed kambodzhalased riisuvad muistiseid / Mai Loog

Index Scriptorium Estoniae

Loog, Mai, 1960-

2004-01-01

Siem Riepis asuvast UNESCO maailmapärandina registreeritud Angkor Vati templikompleksist. Ülemaailmse antiigikaubanduse mustal turul ringleb üha enam dzhunglitemplitest pärit iidse khmeeride tsivilisatsiooni muistiseid, mida kambodzhalased müüvad ebaseaduslikele ülesostjaile. Viimasel ajal on eriti hinnas Kambodzha Angkori-eelsest ajastust pärinevad muistised

Riik ostab saastekvoodi eest sadu elektriautosid / Raigo Neudorf

Index Scriptorium Estoniae

Neudorf, Raigo

2011-01-01

Valitsus kiitis heaks 10 miljoni saastekvoodi ühiku ehk AAU müügi Jaapani konglomeraadile Mitshubishi Corporation, vastutasuks saadava raha eest rahastab riik kolmest osast koosnevat kava, mis näeb ette laadimisvõrgustiku rajamise elektriautode tarbeks, elektriautode soetamiseks mõeldud toetusi ja enam kui 500 elekriauto ostmist riigi poolt

Genes from scratch--the evolutionary fate of de novo genes.

Science.gov (United States)

Schlötterer, Christian

2015-04-01

Although considered an extremely unlikely event, many genes emerge from previously noncoding genomic regions. This review covers the entire life cycle of such de novo genes. Two competing hypotheses about the process of de novo gene birth are discussed as well as the high death rate of de novo genes. Despite the high death rate, some de novo genes are retained and remain functional, even in distantly related species, through their integration into gene networks. Further studies combining gene expression with ribosome profiling in multiple populations across different species will be instrumental for an improved understanding of the evolutionary processes operating on de novo genes. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms.

Science.gov (United States)

Li, Zhen; Defoort, Jonas; Tasdighian, Setareh; Maere, Steven; Van de Peer, Yves; De Smet, Riet

2016-02-01

Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes. © 2016 American Society of Plant Biologists. All rights reserved.

Advances in study of reporter gene imaging for monitoring gene therapy

International Nuclear Information System (INIS)

Mu Chuanjie; Zhou Jiwen

2003-01-01

To evaluate the efficiency of gene therapy, it is requisite to monitor localization and expression of the therapeutic gene in vivo. Monitoring expression of reporter gene using radionuclide reporter gene technique is the best method. Adenoviral vectors expressing reporter gene are constructed using gene fusion, bicistronic, double promoter or bidirectional transcriptional recombination techniques, and transferred into target cells and tissues, then injected radiolabeled reporter probes which couple to the reporter genes. The reporter genes can be imaged invasively, repeatedly, quantitatively with γ-camera, PET and SPECT. Recently, several reporter gene and reporter probe systems have been used in studies of gene therapy. The part of them has been used for clinic trials

Down-Regulation of Gene Expression by RNA-Induced Gene Silencing

Science.gov (United States)

Travella, Silvia; Keller, Beat

Down-regulation of endogenous genes via post-transcriptional gene silencing (PTGS) is a key to the characterization of gene function in plants. Many RNA-based silencing mechanisms such as post-transcriptional gene silencing, co-suppression, quelling, and RNA interference (RNAi) have been discovered among species of different kingdoms (plants, fungi, and animals). One of the most interesting discoveries was RNAi, a sequence-specific gene-silencing mechanism initiated by the introduction of double-stranded RNA (dsRNA), homologous in sequence to the silenced gene, which triggers degradation of mRNA. Infection of plants with modified viruses can also induce RNA silencing and is referred to as virus-induced gene silencing (VIGS). In contrast to insertional mutagenesis, these emerging new reverse genetic approaches represent a powerful tool for exploring gene function and for manipulating gene expression experimentally in cereal species such as barley and wheat. We examined how RNAi and VIGS have been used to assess gene function in barley and wheat, including molecular mechanisms involved in the process and available methodological elements, such as vectors, inoculation procedures, and analysis of silenced phenotypes.

Therapeutic genes for anti-HIV/AIDS gene therapy.

Science.gov (United States)

Bovolenta, Chiara; Porcellini, Simona; Alberici, Luca

2013-01-01

The multiple therapeutic approaches developed so far to cope HIV-1 infection, such as anti-retroviral drugs, germicides and several attempts of therapeutic vaccination have provided significant amelioration in terms of life-quality and survival rate of AIDS patients. Nevertheless, no approach has demonstrated efficacy in eradicating this lethal, if untreated, infection. The curative power of gene therapy has been proven for the treatment of monogenic immunodeficiensies, where permanent gene modification of host cells is sufficient to correct the defect for life-time. No doubt, a similar concept is not applicable for gene therapy of infectious immunodeficiensies as AIDS, where there is not a single gene to be corrected; rather engineered cells must gain immunotherapeutic or antiviral features to grant either short- or long-term efficacy mostly by acquisition of antiviral genes or payloads. Anti-HIV/AIDS gene therapy is one of the most promising strategy, although challenging, to eradicate HIV-1 infection. In fact, genetic modification of hematopoietic stem cells with one or multiple therapeutic genes is expected to originate blood cell progenies resistant to viral infection and thereby able to prevail on infected unprotected cells. Ultimately, protected cells will re-establish a functional immune system able to control HIV-1 replication. More than hundred gene therapy clinical trials against AIDS employing different viral vectors and transgenes have been approved or are currently ongoing worldwide. This review will overview anti-HIV-1 infection gene therapy field evaluating strength and weakness of the transgenes and payloads used in the past and of those potentially exploitable in the future.

Discovering implicit entity relation with the gene-citation-gene network.

Directory of Open Access Journals (Sweden)

Min Song

Full Text Available In this paper, we apply the entitymetrics model to our constructed Gene-Citation-Gene (GCG network. Based on the premise there is a hidden, but plausible, relationship between an entity in one article and an entity in its citing article, we constructed a GCG network of gene pairs implicitly connected through citation. We compare the performance of this GCG network to a gene-gene (GG network constructed over the same corpus but which uses gene pairs explicitly connected through traditional co-occurrence. Using 331,411 MEDLINE abstracts collected from 18,323 seed articles and their references, we identify 25 gene pairs. A comparison of these pairs with interactions found in BioGRID reveal that 96% of the gene pairs in the GCG network have known interactions. We measure network performance using degree, weighted degree, closeness, betweenness centrality and PageRank. Combining all measures, we find the GCG network has more gene pairs, but a lower matching rate than the GG network. However, combining top ranked genes in both networks produces a matching rate of 35.53%. By visualizing both the GG and GCG networks, we find that cancer is the most dominant disease associated with the genes in both networks. Overall, the study indicates that the GCG network can be useful for detecting gene interaction in an implicit manner.

Reduced rates of gene loss, gene silencing, and gene mutation in Dnmt1-deficient embryonic stem cells

NARCIS (Netherlands)

Chan, M.F.; van Amerongen, R.; Nijjar, T.; Cuppen, E.; Jones, P.A.; Laird, P.W.

2001-01-01

Tumor suppressor gene inactivation is a crucial event in oncogenesis. Gene inactivation mechanisms include events resulting in loss of heterozygosity (LOH), gene mutation, and transcriptional silencing. The contribution of each of these different pathways varies among tumor suppressor genes and by

A hybrid approach of gene sets and single genes for the prediction of survival risks with gene expression data.

Science.gov (United States)

Seok, Junhee; Davis, Ronald W; Xiao, Wenzhong

2015-01-01

Accumulated biological knowledge is often encoded as gene sets, collections of genes associated with similar biological functions or pathways. The use of gene sets in the analyses of high-throughput gene expression data has been intensively studied and applied in clinical research. However, the main interest remains in finding modules of biological knowledge, or corresponding gene sets, significantly associated with disease conditions. Risk prediction from censored survival times using gene sets hasn't been well studied. In this work, we propose a hybrid method that uses both single gene and gene set information together to predict patient survival risks from gene expression profiles. In the proposed method, gene sets provide context-level information that is poorly reflected by single genes. Complementarily, single genes help to supplement incomplete information of gene sets due to our imperfect biomedical knowledge. Through the tests over multiple data sets of cancer and trauma injury, the proposed method showed robust and improved performance compared with the conventional approaches with only single genes or gene sets solely. Additionally, we examined the prediction result in the trauma injury data, and showed that the modules of biological knowledge used in the prediction by the proposed method were highly interpretable in biology. A wide range of survival prediction problems in clinical genomics is expected to benefit from the use of biological knowledge.

Euroopa uue draama festival "A Est" Napolis / Mari Kolle, Katrin Talts

Index Scriptorium Estoniae

Kolle, Mari

2005-01-01

Festival toimub 9.-11. veebr. Napolis. Eesti näitekirjandusest tõlgiti selleks puhuks itaalia keelde kolm näidendit : J. Tätte "Sild", A. Kivirähki "Eesti matus" ja U. Lennuki "Rongid siin enam ei ..." Sel korral neid avalikult ette ei loeta, kuid nad on kättesaadavad kõigile huvilistele

USA kindral ei soovita sõjalist kohalolekut Iraagis niipea vähendada / Kaivo Kopli

Index Scriptorium Estoniae

Kopli, Kaivo

2007-01-01

USA vägede juhataja Iraagis David Petraeus ja suursaadik Iraagis Ryan Cocker käsitlesid USA Esindajatekoja relvajõudude ja väliskomitee ühisistungil olukorda Iraagis ja USA sõjalist kohalolekut. Nad soovisid Kongressilt USA vägede säilitamist enam-vähem praegusel tasemel kuni 2008. aasta suveni

Inkerinmaalle = Ingerimaale : [luuletus] / Armas Hiiri

Index Scriptorium Estoniae

Hiiri, Armas

2006-01-01

Sisu: Inkerinmaalle = Ingerimaale ; "Koko elinaikani..." = "Kogu eluaja..." ; "Sanovat ettei Inkeriä ole enää olemassa..." = "Öeldakse et pole enam ingerlaste maad..." ; "Unohtuivat miltei kaikki sanat..." = "Paljud sõnad ununenud ; "Niin kauan kuin elän..." = "Kuni jään ma ellu sesse..." ; Ylistystä syksylle = Sügise ülistus

Raamat / Matis Rodin

Index Scriptorium Estoniae

Rodin, Matis

2012-01-01

Tutvustus: Kalm, Mart. Rannalinn, seenrõdu ja viinakapp : Pärnu linnaarhitekt Olev Siinmaa. Eesti Arhitektuurimuuseum : Eesti Kunstiakadeemia, 2012; Olander, Aare. Kadunud vaated : Tallinna muutumine enam kui 400 fotol. Tänapäev, 2012; Mälestiste restaureerimine : enne ja pärast 2005-2011 / koostanud Britta Lainevool ja Ülo Puustak. Muinsuskaitseamet, 2011

CV : [luuletused] / Mari Vallisoo

Index Scriptorium Estoniae

Vallisoo, Mari, 1950-2013

2007-01-01

Sisu: CV ; Sõnaraamat ; Tegijad ; "Kus leemekulp?..." ; "Veel üks viimnepäev mis asja teha sellega..." ; "Ülemise riiuli ääre pääl...", "Alkeemik Alberti elamus...", "Valge pulber veel enam valgega...", "Meie isa, kes sa...", "Ükskord, kui Maa...", "Kevadvesi ja -pori...", "Mõisnik Meeskurat müüs mu vaarisale..."

Maaturism : [2004 Eestis] / Kristine Hindriks

Index Scriptorium Estoniae

Hindriks, Kristine

2005-01-01

Ilmunud ka: Agriculture and the development of rural life : overview 2004/2005. - Tallinn, 2005, lk. 106-109. Tunnustatud maamajutusettevõtteid oli 2004. a. 546 ehk 10% enam kui möödunud aastal, neist kodumajutus ja puhkemajad moodustavad 55%, puhkekülad ning külalistemajad 29%, hostelid, hotellid, motellid kokku 16%. Diagrammid

Hinnatõus otsib pääsu. Siseturu seis pessimistlik / Tea Taruste ; kommenteerinud Kalev Kõnn, Meelis Einstein, Aldo Unga

Index Scriptorium Estoniae

Taruste, Tea

2011-01-01

Ehitusmaterjalide tootjate liidu tegevjuhi Enno Rebase hinnangul on ehitusmaterjalide hinnatõus vältimatu, sest sisendid lähevad kallimaks ja kokkuhoidu pole enam võimalik millegi arvel saavutada, kuid suuremat hinnatõusu võib takistada siseturu väike nõudlus. Vineeri hind on tõusnud 20-30%, OSB tõusis 15%

Time-Course Gene Set Analysis for Longitudinal Gene Expression Data.

Directory of Open Access Journals (Sweden)

Boris P Hejblum

2015-06-01

Full Text Available Gene set analysis methods, which consider predefined groups of genes in the analysis of genomic data, have been successfully applied for analyzing gene expression data in cross-sectional studies. The time-course gene set analysis (TcGSA introduced here is an extension of gene set analysis to longitudinal data. The proposed method relies on random effects modeling with maximum likelihood estimates. It allows to use all available repeated measurements while dealing with unbalanced data due to missing at random (MAR measurements. TcGSA is a hypothesis driven method that identifies a priori defined gene sets with significant expression variations over time, taking into account the potential heterogeneity of expression within gene sets. When biological conditions are compared, the method indicates if the time patterns of gene sets significantly differ according to these conditions. The interest of the method is illustrated by its application to two real life datasets: an HIV therapeutic vaccine trial (DALIA-1 trial, and data from a recent study on influenza and pneumococcal vaccines. In the DALIA-1 trial TcGSA revealed a significant change in gene expression over time within 69 gene sets during vaccination, while a standard univariate individual gene analysis corrected for multiple testing as well as a standard a Gene Set Enrichment Analysis (GSEA for time series both failed to detect any significant pattern change over time. When applied to the second illustrative data set, TcGSA allowed the identification of 4 gene sets finally found to be linked with the influenza vaccine too although they were found to be associated to the pneumococcal vaccine only in previous analyses. In our simulation study TcGSA exhibits good statistical properties, and an increased power compared to other approaches for analyzing time-course expression patterns of gene sets. The method is made available for the community through an R package.

Norrie disease gene is distinct from the monoamine oxidase genes

OpenAIRE

Sims, Katherine B.; Ozelius, Laurie; Corey, Timothy; Rinehart, William B.; Liberfarb, Ruth; Haines, Jonathan; Chen, Wei Jane; Norio, Reijo; Sankila, Eeva; de la Chapelle, Albert; Murphy, Dennis L.; Gusella, James; Breakefield, Xandra O.

1989-01-01

The genes for MAO-A and MAO-B appear to be very close to the Norrie disease gene, on the basis of loss and /or disruption of the MAO genes and activities in atypical Norrie disease patients deleted for the DXS7 locus; linkage among the MAO genes, the Norrie disease gene, and the DXS7 locus; and mapping of all these loci to the chromosomal region Xp11. The present study provides evidence that the MAO genes are not disrupted in “classic” Norrie disease patients. Genomic DNA from these “nondelet...

A genetic ensemble approach for gene-gene interaction identification

Directory of Open Access Journals (Sweden)

Ho Joshua WK

2010-10-01

Full Text Available Abstract Background It has now become clear that gene-gene interactions and gene-environment interactions are ubiquitous and fundamental mechanisms for the development of complex diseases. Though a considerable effort has been put into developing statistical models and algorithmic strategies for identifying such interactions, the accurate identification of those genetic interactions has been proven to be very challenging. Methods In this paper, we propose a new approach for identifying such gene-gene and gene-environment interactions underlying complex diseases. This is a hybrid algorithm and it combines genetic algorithm (GA and an ensemble of classifiers (called genetic ensemble. Using this approach, the original problem of SNP interaction identification is converted into a data mining problem of combinatorial feature selection. By collecting various single nucleotide polymorphisms (SNP subsets as well as environmental factors generated in multiple GA runs, patterns of gene-gene and gene-environment interactions can be extracted using a simple combinatorial ranking method. Also considered in this study is the idea of combining identification results obtained from multiple algorithms. A novel formula based on pairwise double fault is designed to quantify the degree of complementarity. Conclusions Our simulation study demonstrates that the proposed genetic ensemble algorithm has comparable identification power to Multifactor Dimensionality Reduction (MDR and is slightly better than Polymorphism Interaction Analysis (PIA, which are the two most popular methods for gene-gene interaction identification. More importantly, the identification results generated by using our genetic ensemble algorithm are highly complementary to those obtained by PIA and MDR. Experimental results from our simulation studies and real world data application also confirm the effectiveness of the proposed genetic ensemble algorithm, as well as the potential benefits of

The Mycoplasma hominis vaa gene displays a mosaic gene structure

DEFF Research Database (Denmark)

Boesen, Thomas; Emmersen, Jeppe M. G.; Jensen, Lise T.

1998-01-01

Mycoplasma hominis contains a variable adherence-associated (vaa) gene. To classify variants of the vaa genes, we examined 42 M. hominis isolated by PCR, DNA sequencing and immunoblotting. This uncovered the existence of five gene categories. Comparison of the gene types revealed a modular...

Identification of Hematopoietic Stem Cell Engraftment Genes in Gene Therapy Studies.

Science.gov (United States)

Powers, John M; Trobridge, Grant D

2013-09-01

Hematopoietic stem cell (HSC) therapy using replication-incompetent retroviral vectors is a promising approach to provide life-long correction for genetic defects. HSC gene therapy clinical studies have resulted in functional cures for several diseases, but in some studies clonal expansion or leukemia has occurred. This is due to the dyregulation of endogenous host gene expression from vector provirus insertional mutagenesis. Insertional mutagenesis screens using replicating retroviruses have been used extensively to identify genes that influence oncogenesis. However, retroviral mutagenesis screens can also be used to determine the role of genes in biological processes such as stem cell engraftment. The aim of this review is to describe the potential for vector insertion site data from gene therapy studies to provide novel insights into mechanisms of HSC engraftment. In HSC gene therapy studies dysregulation of host genes by replication-incompetent vector proviruses may lead to enrichment of repopulating clones with vector integrants near genes that influence engraftment. Thus, data from HSC gene therapy studies can be used to identify novel candidate engraftment genes. As HSC gene therapy use continues to expand, the vector insertion site data collected will be of great interest to help identify novel engraftment genes and may ultimately lead to new therapies to improve engraftment.

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms[OPEN

Science.gov (United States)

Li, Zhen; Van de Peer, Yves; De Smet, Riet

2016-01-01

Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of “gene duplicability” is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes. PMID:26744215

Kordistamine uue majandus- ja juhtimismudeli tunnus. Kordistamise matemaatiline mudel / Tõnis Mets

Index Scriptorium Estoniae

Mets, Tõnis, 1952-

2003-01-01

Kordistusmehhanismi mudeli kohaselt võib teadmusinvesteeringu rentaablus globaalsesse korporatsioonistruktuuri investeerimisel ületada üksikettevõtte samalaadse investeeringu rentaablust enam kordi kui on globaalses võrgus ettevõtteid. Mudel väärib analüüsi, et leida Eesti ettevõtete võimalusi globaalses konkurentsis ning planeerida vastavat ettevõtluse toetamise ja innovatsioonistrateegiat. Graafikud. Tabel

Uude mängufilmi otsitakse osatäitjaid

Index Scriptorium Estoniae

2006-01-01

Režissöör Veiko Õunpuu järgmine filmi aluseks on Mati Undi romaan "Sügisball". Tegevus toimub Lasnamäel, kõrvalosadesse otsitakse inimesi, kel vanust enam kui 25 aastat. Võttegrupp ja peategelased on suures osas samad, mis režissööri eelmises Mati Undi ekraniseeringus "Tühirand"

Entrepreneurship as a tool of an economic policy : background, factors and possibilities / Raivo Linnas

Index Scriptorium Estoniae

Linnas, Raivo

2006-01-01

Majandusliku arengu ja edu saavutamine majanduspoliitika kujundamise ja elluviimise kaudu ei ole kiiresti muutuvas maailmas enam ainuüksi klassikaliste majandusteooriate mõjuväljas. Lisaks klassikalistele üldtunnustatud majandusteooriatele on oluline arvestada teisi teooriaid ja reaalelu mõjureid ning aspekte. Maailmas toimuvate poliitiliste, sotsiaalsete, majanduslike jt sündmuste mõju majanduspoliitika kujunemisele

Puidu import Venemaalt valmistab raskusi / Ketlin Priilinn

Index Scriptorium Estoniae

Priilinn, Ketlin, 1982-

2007-01-01

Ilmunud ka: Delovõje Vedomosti 21. nov. lk. 16. Eesti puiduettevõtetele valmistab raskusi puidu import Venemaalt, sest raudteed pidi enam vedada ei saa ning maanteetransport on häiritud. Küsimustele vastab Venemaa Stora Enso Foresti logistikajuht Jevgeni Popov. Kommenteerib Kunda sadama direktor Alaksander Nikolajev. Diagrammid: Eesti Raudtee puiduveomaht; Puiduveomahud Kunda sadama kaudu

2008. aastal tõuseb pension 22% / Karin Kalda

Index Scriptorium Estoniae

Kalda, Karin

2007-01-01

Ilmunud ka: Tallinna Teataja : Kesklinn, Lasnamäe, Pirita, okt., 2007, lk. 3; Tallinna Teataja : Haabersti, Kristiine, Põhja-Tallinn, okt., 2007, lk. 3; Tallinnskii Vestnik, okt., 2007, lk. 3. Tallinnskii Vestnik autorita. Valitsusliit on saanud valmis uue pensioniarvestuse süsteemi, mille alusel võetakse aastahinde arvutamisel senisest enam arvesse sotsiaalmaksu laekumist. Kommenteerib Taavi Rõivas

Lahingustress ajab USA sõdurid jooma / Neeme Raud

Index Scriptorium Estoniae

Raud, Neeme, 1969-

2007-01-01

Ilmunud ka: Postimees : na russkom jazõke, 15. märts 2007, lk. 10. USA kaitseministeeriumi siseuurimuse kohaselt kasvas alkoholi kuritarvitamine tegevteenistuses olevate USA sõjaväelaste seas aastatel 2002-2005 enam kui 30%. Alkoholi ja uimastite tarvitamisest Iraagis ja Afganistanis teenivate USA sõdurite hulgas. Vt. samas: USA relvajõududes puhkes uus homoskandaal

Lääne ideaalid Venemaa tõlgenduses : ettevõtjate tootmine siirdeajal / Oksana Shmuljar Green ; tõlk. Kaarel Tarand

Index Scriptorium Estoniae

Shmuljar Green, Oksana

2008-01-01

Venemaal tekkinud uuest majandusühiskonnast, mis ei ole enam allutatud Nõukogude riigile nagu enne 1985. aastat, kuid mis pole ka enamikes lääneriikides tuntud kapitalistlik ühiskond. Lääne tegevuse kolmest mõõtmest Venemaa ümberkujundamisel: siirde diskursus, lääne investeeringud ja eraettevõtluse käivitamine

Renault ja Toyota - mullused turuvõitjad / Andris Feldmanis

Index Scriptorium Estoniae

Feldmanis, Andris, 1982-

2005-01-01

Enam müüdavatest sõiduautodest Eestis aastal 2004. Diagrammid. Tabelid: Toyota edu teiste ees mäe kõrgune; Kõige edukam oli 2004. aasta Renault müüjatele; Saksa ja Jaapani autode müük kasvas enim. Vt. samas: Tõnu Tramm. Euroliit tekitas eelmise aasta kevadel müügibuumi

Oh, for God's Sake! / Karlis Streips

Index Scriptorium Estoniae

Streips, Karlis

2011-01-01

Valdis Zatlersi Reformierakonnast on 6 parlamendiliiget välja astunud, mis tähendab, et koalitsioonil ei ole enam enamust parlamendis. Autor leiab, et koalitsioon võiks alustada läbirääkimisi parlamendivalimised võitnud venemeelse parteiga Üksmeele Keskus ning Valdis Zatlersi parteist välja astunud võiks ka parlamendist lahkuda

Zatlers addresses Harvard audience

Index Scriptorium Estoniae

2010-01-01

Läti presidendi Valdis Zatlersi Harvardi ülikoolis peetud kõnest, milles ta märgib, et üks tema jaoks tähtsamatest küsimustest on, kes võiks Läti uue peaministrina riigi praegust majanduskurssi jätkata, ja leiab, et Läti kuulub oma rahvaarvu arvestades Afganistani enam panustavate riikide hulka

Kõrgest palgast üksi on vähe heade töötajate palkamiseks / Gea Velthut-Sokka

Index Scriptorium Estoniae

Velthut-Sokka, Gea, 1977-

2006-01-01

Palk ei ole heade töötajate värbamisel enam argument, määravaks on kujunenud hoopis kollektiiv ja turvatunne, tõdeti Äripäeva korraldatud tööjõukriisi seminaril. Vt. samas: Üle 45aastased naised on supertöötajad; Eesti Pank langes samuti palgasurve ohvriks

EMI kaob kaubamärgina

Index Scriptorium Estoniae

2002-01-01

Ümberstruktueerimise käigus lõpetab suuruselt maailma kolmas muusikafirma EMI oma nime kasutamise kaubamärgina ega trüki seda enam plaadiümbristele. Plaadid hakkavad ilmuma märkide Capitol ja Virgin all. EMI on lühend nimetusest Electric and Music Industries, see jääb kasutusele firmasiseselt

Osta General Motorsi aktsiaid / Tõnis Oja

Index Scriptorium Estoniae

Oja,Tõnis, 1957-

2008-01-01

General Motorsi aktsia hind langes juuli alguses enam kui 50 aasta madalaimale tasemele, 9,38 dollarini. USA autotööstuse suurimaks probleemiks on võimetus konkureerida Jaapani ja Lõuna-Korea autotootjatega, ka Ford Motors on teatanud ajaloo suurimast kvartalikahjumist. Graafik: Aktsia hind kukkus kümnendike tagusele tasemele. Tabel: Viimaseid aastaid iseloomustavad hiigelkahjumid. Lisa

Tsherez 30 let Jevropu zahvatjat "varvarõ" / Mihhail Ozerov

Index Scriptorium Estoniae

Ozerov, Mihhail

2006-01-01

Briti kontradmiral Chris Parry hoiatab oma ettekandes, et lähema 30 aasta jooksul hõivavad Euroopa immigrandid Kolmandast Maailmast, neil ei midagi ühist Euroopaga, veelgi enam - nad vihkavad seda. Intervjuu Briti parlamendiliikme Boris Johnsoniga. Postindustriaalse ühiskonna uurimise keskuse teaduslik juht Vladislav Inozemtsev on seisukohal, et immigrandid Venemaa julgeolekut ei ohusta. Tabel

Smells Like Teen Spirit / Sandra Jõgeva

Index Scriptorium Estoniae

Jõgeva, Sandra, 1976-

2009-01-01

Kuigi on majanduslik langus, tekib praegu juurde loomelinnakuid ja kultuuriruume (Rotermanni loovala, Baltika loomeinkubaator, Telliskivi loomelinnak jne.). Riia kesklinnas olid septembris projekti Survival Kit raames avatud ajutised kunstigaleriid südalinna äripindadel. Autori sõnul on õhus üheksakümnendate hõngu, vanad jõuvahekorrad enam ei kehti, tekib uusi võimalusi

Effect of the absolute statistic on gene-sampling gene-set analysis methods.

Science.gov (United States)

Nam, Dougu

2017-06-01

Gene-set enrichment analysis and its modified versions have commonly been used for identifying altered functions or pathways in disease from microarray data. In particular, the simple gene-sampling gene-set analysis methods have been heavily used for datasets with only a few sample replicates. The biggest problem with this approach is the highly inflated false-positive rate. In this paper, the effect of absolute gene statistic on gene-sampling gene-set analysis methods is systematically investigated. Thus far, the absolute gene statistic has merely been regarded as a supplementary method for capturing the bidirectional changes in each gene set. Here, it is shown that incorporating the absolute gene statistic in gene-sampling gene-set analysis substantially reduces the false-positive rate and improves the overall discriminatory ability. Its effect was investigated by power, false-positive rate, and receiver operating curve for a number of simulated and real datasets. The performances of gene-set analysis methods in one-tailed (genome-wide association study) and two-tailed (gene expression data) tests were also compared and discussed.

Human Gene Therapy: Genes without Frontiers?

Science.gov (United States)

Simon, Eric J.

2002-01-01

Describes the latest advancements and setbacks in human gene therapy to provide reference material for biology teachers to use in their science classes. Focuses on basic concepts such as recombinant DNA technology, and provides examples of human gene therapy such as severe combined immunodeficiency syndrome, familial hypercholesterolemia, and…

Gene function prediction based on Gene Ontology Hierarchy Preserving Hashing.

Science.gov (United States)

Zhao, Yingwen; Fu, Guangyuan; Wang, Jun; Guo, Maozu; Yu, Guoxian

2018-02-23

Gene Ontology (GO) uses structured vocabularies (or terms) to describe the molecular functions, biological roles, and cellular locations of gene products in a hierarchical ontology. GO annotations associate genes with GO terms and indicate the given gene products carrying out the biological functions described by the relevant terms. However, predicting correct GO annotations for genes from a massive set of GO terms as defined by GO is a difficult challenge. To combat with this challenge, we introduce a Gene Ontology Hierarchy Preserving Hashing (HPHash) based semantic method for gene function prediction. HPHash firstly measures the taxonomic similarity between GO terms. It then uses a hierarchy preserving hashing technique to keep the hierarchical order between GO terms, and to optimize a series of hashing functions to encode massive GO terms via compact binary codes. After that, HPHash utilizes these hashing functions to project the gene-term association matrix into a low-dimensional one and performs semantic similarity based gene function prediction in the low-dimensional space. Experimental results on three model species (Homo sapiens, Mus musculus and Rattus norvegicus) for interspecies gene function prediction show that HPHash performs better than other related approaches and it is robust to the number of hash functions. In addition, we also take HPHash as a plugin for BLAST based gene function prediction. From the experimental results, HPHash again significantly improves the prediction performance. The codes of HPHash are available at: http://mlda.swu.edu.cn/codes.php?name=HPHash. Copyright © 2018 Elsevier Inc. All rights reserved.

A Nonlinear Model for Gene-Based Gene-Environment Interaction

Directory of Open Access Journals (Sweden)

Jian Sa

2016-06-01

Full Text Available A vast amount of literature has confirmed the role of gene-environment (G×E interaction in the etiology of complex human diseases. Traditional methods are predominantly focused on the analysis of interaction between a single nucleotide polymorphism (SNP and an environmental variable. Given that genes are the functional units, it is crucial to understand how gene effects (rather than single SNP effects are influenced by an environmental variable to affect disease risk. Motivated by the increasing awareness of the power of gene-based association analysis over single variant based approach, in this work, we proposed a sparse principle component regression (sPCR model to understand the gene-based G×E interaction effect on complex disease. We first extracted the sparse principal components for SNPs in a gene, then the effect of each principal component was modeled by a varying-coefficient (VC model. The model can jointly model variants in a gene in which their effects are nonlinearly influenced by an environmental variable. In addition, the varying-coefficient sPCR (VC-sPCR model has nice interpretation property since the sparsity on the principal component loadings can tell the relative importance of the corresponding SNPs in each component. We applied our method to a human birth weight dataset in Thai population. We analyzed 12,005 genes across 22 chromosomes and found one significant interaction effect using the Bonferroni correction method and one suggestive interaction. The model performance was further evaluated through simulation studies. Our model provides a system approach to evaluate gene-based G×E interaction.

Vertebrate gene predictions and the problem of large genes

DEFF Research Database (Denmark)

Wang, Jun; Li, ShengTing; Zhang, Yong

2003-01-01

To find unknown protein-coding genes, annotation pipelines use a combination of ab initio gene prediction and similarity to experimentally confirmed genes or proteins. Here, we show that although the ab initio predictions have an intrinsically high false-positive rate, they also have a consistent...

Reranking candidate gene models with cross-species comparison for improved gene prediction

Directory of Open Access Journals (Sweden)

Pereira Fernando CN

2008-10-01

Full Text Available Abstract Background Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc. Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and comparative genomics datasets may help to select among competing models of comparable probability by exploiting features likely to be associated with the correct gene models, such as conserved exon/intron structure or protein sequence features. Results We have investigated the utility of a simple post-processing step for selecting among a set of alternative gene models, using global scoring rules to rerank competing models for more accurate prediction. For each gene locus, we first generate the K best candidate gene models using the gene finder Evigan, and then rerank these models using comparisons with putative orthologous genes from closely-related species. Candidate gene models with lower scores in the original gene finder may be selected if they exhibit strong similarity to probable orthologs in coding sequence, splice site location, or signal peptide occurrence. Experiments on Drosophila melanogaster demonstrate that reranking based on cross-species comparison outperforms the best gene models identified by Evigan alone, and also outperforms the comparative gene finders GeneWise and Augustus+. Conclusion Reranking gene models with cross-species comparison improves gene prediction accuracy. This straightforward method can be readily adapted to incorporate additional lines of evidence, as it requires only a ranked source of candidate gene models.

Evolution of homeobox genes.

Science.gov (United States)

Holland, Peter W H

2013-01-01

Many homeobox genes encode transcription factors with regulatory roles in animal and plant development. Homeobox genes are found in almost all eukaryotes, and have diversified into 11 gene classes and over 100 gene families in animal evolution, and 10 to 14 gene classes in plants. The largest group in animals is the ANTP class which includes the well-known Hox genes, plus other genes implicated in development including ParaHox (Cdx, Xlox, Gsx), Evx, Dlx, En, NK4, NK3, Msx, and Nanog. Genomic data suggest that the ANTP class diversified by extensive tandem duplication to generate a large array of genes, including an NK gene cluster and a hypothetical ProtoHox gene cluster that duplicated to generate Hox and ParaHox genes. Expression and functional data suggest that NK, Hox, and ParaHox gene clusters acquired distinct roles in patterning the mesoderm, nervous system, and gut. The PRD class is also diverse and includes Pax2/5/8, Pax3/7, Pax4/6, Gsc, Hesx, Otx, Otp, and Pitx genes. PRD genes are not generally arranged in ancient genomic clusters, although the Dux, Obox, and Rhox gene clusters arose in mammalian evolution as did several non-clustered PRD genes. Tandem duplication and genome duplication expanded the number of homeobox genes, possibly contributing to the evolution of developmental complexity, but homeobox gene loss must not be ignored. Evolutionary changes to homeobox gene expression have also been documented, including Hox gene expression patterns shifting in concert with segmental diversification in vertebrates and crustaceans, and deletion of a Pitx1 gene enhancer in pelvic-reduced sticklebacks. WIREs Dev Biol 2013, 2:31-45. doi: 10.1002/wdev.78 For further resources related to this article, please visit the WIREs website. The author declares that he has no conflicts of interest. Copyright © 2012 Wiley Periodicals, Inc.

Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes

Science.gov (United States)

2010-01-01

Background Horizontal gene transfer (HGT) is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. Previous results indicate that parasitic plants are often involved as either transfer donors or recipients, suggesting that direct contact between parasite and host facilitates genetic transfer among plants. Results In order to uncover the mechanistic details of plant-to-plant HGT, the extent and evolutionary fate of transfer was investigated between two groups: the parasitic genus Cuscuta and a small clade of Plantago species. A broad polymerase chain reaction (PCR) survey of mitochondrial genes revealed that at least three genes (atp1, atp6 and matR) were recently transferred from Cuscuta to Plantago. Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. Patterns of sequence evolution suggest that these foreign genes degraded into pseudogenes shortly after transfer and reverse transcription (RT)-PCR analyses demonstrate that none are detectably transcribed. Three cases of gene conversion were detected between native and foreign copies of the atp1 gene. The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. However, samplings of multiple individuals from two of the three species in the recipient Plantago clade revealed complex and perplexing phylogenetic discrepancies and patterns of sequence divergence for all three of the foreign genes. Conclusions This study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. The discovery of gene conversion between co-resident foreign and native mitochondrial copies suggests

Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes

Directory of Open Access Journals (Sweden)

Hao Weilong

2010-12-01

Full Text Available Abstract Background Horizontal gene transfer (HGT is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. Previous results indicate that parasitic plants are often involved as either transfer donors or recipients, suggesting that direct contact between parasite and host facilitates genetic transfer among plants. Results In order to uncover the mechanistic details of plant-to-plant HGT, the extent and evolutionary fate of transfer was investigated between two groups: the parasitic genus Cuscuta and a small clade of Plantago species. A broad polymerase chain reaction (PCR survey of mitochondrial genes revealed that at least three genes (atp1, atp6 and matR were recently transferred from Cuscuta to Plantago. Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. Patterns of sequence evolution suggest that these foreign genes degraded into pseudogenes shortly after transfer and reverse transcription (RT-PCR analyses demonstrate that none are detectably transcribed. Three cases of gene conversion were detected between native and foreign copies of the atp1 gene. The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. However, samplings of multiple individuals from two of the three species in the recipient Plantago clade revealed complex and perplexing phylogenetic discrepancies and patterns of sequence divergence for all three of the foreign genes. Conclusions This study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. The discovery of gene conversion between co-resident foreign and native

Gene coexpression network analysis as a source of functional annotation for rice genes.

Directory of Open Access Journals (Sweden)

Kevin L Childs

Full Text Available With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional

The drug target genes show higher evolutionary conservation than non-target genes.

Science.gov (United States)

Lv, Wenhua; Xu, Yongdeng; Guo, Yiying; Yu, Ziqi; Feng, Guanglong; Liu, Panpan; Luan, Meiwei; Zhu, Hongjie; Liu, Guiyou; Zhang, Mingming; Lv, Hongchao; Duan, Lian; Shang, Zhenwei; Li, Jin; Jiang, Yongshuai; Zhang, Ruijie

2016-01-26

Although evidence indicates that drug target genes share some common evolutionary features, there have been few studies analyzing evolutionary features of drug targets from an overall level. Therefore, we conducted an analysis which aimed to investigate the evolutionary characteristics of drug target genes. We compared the evolutionary conservation between human drug target genes and non-target genes by combining both the evolutionary features and network topological properties in human protein-protein interaction network. The evolution rate, conservation score and the percentage of orthologous genes of 21 species were included in our study. Meanwhile, four topological features including the average shortest path length, betweenness centrality, clustering coefficient and degree were considered for comparison analysis. Then we got four results as following: compared with non-drug target genes, 1) drug target genes had lower evolutionary rates; 2) drug target genes had higher conservation scores; 3) drug target genes had higher percentages of orthologous genes and 4) drug target genes had a tighter network structure including higher degrees, betweenness centrality, clustering coefficients and lower average shortest path lengths. These results demonstrate that drug target genes are more evolutionarily conserved than non-drug target genes. We hope that our study will provide valuable information for other researchers who are interested in evolutionary conservation of drug targets.

Identifying potential maternal genes of Bombyx mori using digital gene expression profiling

Science.gov (United States)

Xu, Pingzhen

2018-01-01

Maternal genes present in mature oocytes play a crucial role in the early development of silkworm. Although maternal genes have been widely studied in many other species, there has been limited research in Bombyx mori. High-throughput next generation sequencing provides a practical method for gene discovery on a genome-wide level. Herein, a transcriptome study was used to identify maternal-related genes from silkworm eggs. Unfertilized eggs from five different stages of early development were used to detect the changing situation of gene expression. The expressed genes showed different patterns over time. Seventy-six maternal genes were annotated according to homology analysis with Drosophila melanogaster. More than half of the differentially expressed maternal genes fell into four expression patterns, while the expression patterns showed a downward trend over time. The functional annotation of these material genes was mainly related to transcription factor activity, growth factor activity, nucleic acid binding, RNA binding, ATP binding, and ion binding. Additionally, twenty-two gene clusters including maternal genes were identified from 18 scaffolds. Altogether, we plotted a profile for the maternal genes of Bombyx mori using a digital gene expression profiling method. This will provide the basis for maternal-specific signature research and improve the understanding of the early development of silkworm. PMID:29462160

Novel gene sets improve set-level classification of prokaryotic gene expression data.

Science.gov (United States)

Holec, Matěj; Kuželka, Ondřej; Železný, Filip

2015-10-28

Set-level classification of gene expression data has received significant attention recently. In this setting, high-dimensional vectors of features corresponding to genes are converted into lower-dimensional vectors of features corresponding to biologically interpretable gene sets. The dimensionality reduction brings the promise of a decreased risk of overfitting, potentially resulting in improved accuracy of the learned classifiers. However, recent empirical research has not confirmed this expectation. Here we hypothesize that the reported unfavorable classification results in the set-level framework were due to the adoption of unsuitable gene sets defined typically on the basis of the Gene ontology and the KEGG database of metabolic networks. We explore an alternative approach to defining gene sets, based on regulatory interactions, which we expect to collect genes with more correlated expression. We hypothesize that such more correlated gene sets will enable to learn more accurate classifiers. We define two families of gene sets using information on regulatory interactions, and evaluate them on phenotype-classification tasks using public prokaryotic gene expression data sets. From each of the two gene-set families, we first select the best-performing subtype. The two selected subtypes are then evaluated on independent (testing) data sets against state-of-the-art gene sets and against the conventional gene-level approach. The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. Novel gene sets defined on the basis of regulatory interactions improve set-level classification of gene expression data. The experimental scripts and other material needed to reproduce the experiments are available at http://ida.felk.cvut.cz/novelgenesets.tar.gz.

Outsourcing is the Solution / Janis Berzins

Index Scriptorium Estoniae

Berzins, Janis

2011-01-01

Autor leiab, et Läti poliitikute arusaam neoliberalismist on vale ja et Läti on nõrk riik, kuna ei suuda enam ise majandust ja julgeolekut kontrollida. Autor toob näiteid ja märgib, et riik võiks ka haldusjuhtimise ja juriidilise poolega seotud teenused Rootsi, Saksamaa või EL-i käest sisse osta

Pierre Alechinsky Pariisis

Index Scriptorium Estoniae

1998-01-01

Pariisi näitusemaja Galerie Jeu de Paume tähistab 'Cobra' rühmituse liikme Pierre Alechinsky 71. sünnipäeva ning 50 aasta möödumist kunstniku debüteerimisest Pariisis 22. novembrini avatud ülevaatenäitusega, kus on eksponeeritud enam kui 110 maali ja graafilist lehte ning kunstniku raamatuid

Töölepinguseadus tagab võrdsed õigused / Margi Ein

Index Scriptorium Estoniae

Ein, Margi, 1950-

2006-01-01

Pensioniealiste tööhõivest ning selle seadustamisest töölepinguseaduses. Ilmunud ka Vali Uudised 1. märts 2006, lk. 2 ; Põhjarannik 28. veeb .2006, lk. 9, pealkiri kujul: Vanuse tõttu töötajat enam vallandada ei saa. Valgamaalane 16. märts 2006, lk. 2 ; Vooremaa 16. märts 2006, lk. 4

Braavo, presidendiproua! / Karoliina Vasli

Index Scriptorium Estoniae

Vasli, Karoliina

2008-01-01

Eesti Rulluisuliidu president proua Evelin Ilves tuli Berliini rulluisumaratonil enam kui 6000 osavõtja seas 141. kohale. Kommenteerib treener Jaanus Ritson. Vt. samas: Evelin Ilves näitusel setu kultuuri kaitsmas. Proua E. Ilves avas 25. septembril 2008 Berliinis Eesti suursaatkonna ruumides kunstnik Siiri Taimla näituse "Elu lugu", mille põhiteemaks on setu naised Eestis sajand tagasi

Nõutakse Eesti-Läti-Leedu lastefilme / Jaan Ruus

Index Scriptorium Estoniae

Ruus, Jaan, 1938-2017

2005-01-01

Berliini festivali filmiturul tutvustas Baltic Films kõige edukamalt lastefilme nagu Rene Vilbre "Röövlirahnu Martin". Läti animafilmist räägib festivali lastefilmide konkursil plastiliinanimatsiooniga "Kuule, jänes... papa sõidab Londonisse" esinenud Nils Skapans (s 1969). Lisatud tabelid "Balti riigid ja film 2004" ja "Mida Baltikumis mullu kõige enam vaadati?"

Pengelolaan Logistik Dalam Rantai Pasok Produk Pangan Segar Di Indonesia1

OpenAIRE

Fizzanty, Trina

2012-01-01

Kurangnya pemahaman terhadap lembaga bisnis pedesaan dan lingkungan bisnis telah berpotensimengurangi kapasitas bisnis pedesaan untuk meningkatkan kontribusinya terhadap perekonomian Indonesia.Makalah ini bertujuan untuk mengkaji pengalaman Indonesia dalam membangun rantai pasok pedesaan dalammendukung USAha pertanian dan kinerjanya dengan menggunakan enam prinsip manajemen kunci rantaipasok. Pada beberapa kasus, desain rantai pasok diawali dari bantuan Internasional, instansi pemerintah, ata...

President Putin ähvardas raketid Euroopale sihtida / Krister Paris

Index Scriptorium Estoniae

Paris, Krister, 1977-

2007-01-01

Venemaa president Vladimir Putin süüdistas oma intervjuus lääne ajakirjanikele USA-d uue võidurelvastuse käivitamises ning hoiatas, et kui USA tagasi ei tõmbu, ei lasu vastutus Moskva vastusammude eest enam Kremlil. Kui Tšehhi elanikest üle poole on USA radari paigaldamise vastu, siis Poolas toetatakse baaside rajamist rohkem

Hewlett-Packard tulemas rahva hulka / Tõnis Oja

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Oja, Tõnis, 1957-

2008-01-01

Maailma suurima arvutitootja Hewlett-Packard tegevjuht Mark Hurd on otsustanud printerite läbimüügi suurendamiseks reorganiseerida printerite divisjoni kolmeks üksuseks, senisest enam hakkab ettevõte tähelepanu pöörama eraisikutest tarbijatele. Graafik: Aktsia hind on kolme aastaga kahekordistunud. Tabel: Kasum kasvanud võimsalt: Lisad: Mis on mis; Tasub teada

Põhjakeskuse tehingut ei saa tagasi pöörata / Anne Oja

Index Scriptorium Estoniae

Oja, Anne, 1970-

2008-01-01

Kobe Investmentsi partnerite Veljo Kuuse ja Kaire Kopli sõnul ei saa endine autoärimees Toomas Rüütmann Põhjakeskuse tehingut tagasi pöörata ning T. Rüütmann on keskuse projektist kätte saanud kordades enam raha, kui on sinna investeerinud. Vt. samas: Rüütmann väidab, et ta lasi varad arestida

Zakrõtije bumazhnoi fabriki v Kehra utjanet na dno vsju volost / Kristi Leppik

Index Scriptorium Estoniae

Leppik, Kristi

2008-01-01

Kehra paberivabrikus seiskus ajutiselt tootmine, kuna ettevõte Eesti Gaas lõpetas võlgade tõttu vabriku varustamise maagaasiga. Skeem: Kehra vabriku sulgemine ohustab Jägala jõge. Vt. samas: Eestis on kärbitud enam kui 700 inimese tööd. Paberi tootmine Eestis hääbub. Kommenteerivad Jüri Lillsoo ja Jaan Pikka

Kodus Venus, võõrsil Mars / Priit Simson

Index Scriptorium Estoniae

Simson Priit, 1977-

2007-01-01

Autor leiab, et Eestil ei pole enam vabandusi, miks ta ei peaks hankima rasket sõjatehnikat ja miks peaks keegi teine meie õhuruumi valvama. Autor vaatleb, milline relvastus on mõnedel väikeriikidel, kelle elanike arv ei ületa 6 mln. piiri, ning järeldab, et soovides olla maailma keskmisel tasemel, võiks Eesti muretseda 65 tanki

Briti suursaadik: koostöö sujub / Nigel Haywood ; interv. Holger Roonemaa

Index Scriptorium Estoniae

Haywood, Nigel, 1955-

2007-01-01

Briti suursaadik Eestis vastab küsimustele, mis juhtus, et Eesti luurajad Afganistanis ei saa enam tööd teha, kas suursaadiku meelest on veel võimalik, et Eesti luurajad võiksid töötada välismissioonil Suurbritannia alluvuses, kas segadus Eesti luurajatega ei või jätta vimma Eesti ja Briti kaitseametnike vahele

Evelin Ilvese isa : oleme tütrega ära leppinud / Karoliina Vasli

Index Scriptorium Estoniae

Vasli, Karoliina

2007-01-01

Proua Evelin Ilvese Helsingis elav isa Lembit Int räägib oma suhetest tütre ja väimehega. Vt. samas: Isa: "Evelinil on kahju, et unistus külalistemajast hetkel soiku jääb." Lembit Int väljendab kahetsust, et Ärma talu enam külalistemajana ei tööta

[Gene doping: gene transfer and possible molecular detection].

Science.gov (United States)

Argüelles, Carlos Francisco; Hernández-Zamora, Edgar

2007-01-01

The use of illegal substances in sports to enhance athletic performance during competition has caused international sports organizations such as the COI and WADA to take anti doping measures. A new doping method know as gene doping is defined as "the non-therapeutic use of genes, genetic elements and/or cells that have the capacity to enhance athletic performance". However, gene doping in sports is not easily identified and can cause serious consequences. Molecular biology techniques are needed in order to distinguish the difference between a "normal" and an "altered" genome. Further, we need to develop new analytic methods and biological molecular techniques in anti-doping laboratories, and design programs that avoid the non therapeutic use of genes.

Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets.

Science.gov (United States)

Springer, Mark S; Gatesy, John

2018-02-26

coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including the critical assumption that recombination occurs freely among but not within coalescence genes (c-genes), which are the fundamental units of analysis for these methods. Each c-gene has a single branching history, and large sets of these independent gene histories should be the input for genome-scale coalescence estimates of phylogeny. By contrast, numerous studies have reported the results of coalescence analyses in which complete protein-coding sequences are treated as c-genes even though exons for these loci can span more than a megabase of DNA. Empirical estimates of recombination breakpoints suggest that c-genes may be much shorter, especially when large clades with many species are the focus of analysis. Although this idea has been challenged recently in the literature, the inverse relationship between c-gene size and increased taxon sampling in a dataset-the 'recombination ratchet'-is a fundamental property of c-genes. For taxonomic groups characterized by genes with long intron sequences, complete protein-coding sequences are likely not valid c-genes and are inappropriate units of analysis for summary coalescence methods unless they occur in recombination deserts that are devoid of incomplete lineage sorting (ILS). Finally, it has been argued that coalescence methods are robust when the no-recombination within loci assumption is violated, but recombination must matter at some scale because ILS, a by-product of recombination, is the raison d'etre for coalescence methods. That is, extensive recombination is required to yield the large number of independently segregating c-genes used to infer a species tree. If coalescent methods are powerful

Gene therapy of cancer and development of therapeutic target gene

Energy Technology Data Exchange (ETDEWEB)

Kim, Chang Min; Kwon, Hee Chung

1998-04-01

We applied HSV-tk/GCV strategy to orthotopic rat hepatoma model and showed anticancer effects of hepatoma. The increased expression of Lac Z gene after adenovirus-mediated gene delivery throughout hepatic artery was thought that is increased the possibility of gene therapy for curing hepatoma. With the construction of kGLP-laboratory, it is possible to produce a good quantity and quality of adenovirus in lage-scale production and purification of adenovirus vector. Also, the analysis of hepatoma related genes by PCR-LOH could be used for the diagnosis of patients and the development of therapeutic gene.

Gene therapy of cancer and development of therapeutic target gene

International Nuclear Information System (INIS)

Kim, Chang Min; Kwon, Hee Chung

1998-04-01

We applied HSV-tk/GCV strategy to orthotopic rat hepatoma model and showed anticancer effects of hepatoma. The increased expression of Lac Z gene after adenovirus-mediated gene delivery throughout hepatic artery was thought that is increased the possibility of gene therapy for curing hepatoma. With the construction of kGLP-laboratory, it is possible to produce a good quantity and quality of adenovirus in lage-scale production and purification of adenovirus vector. Also, the analysis of hepatoma related genes by PCR-LOH could be used for the diagnosis of patients and the development of therapeutic gene

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

Directory of Open Access Journals (Sweden)

Baseler Michael W

2007-11-01

Full Text Available Abstract Background Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis. Description The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner. Conclusion The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/.

Evolutionary dynamics of human autoimmune disease genes and malfunctioned immunological genes

Directory of Open Access Journals (Sweden)

Podder Soumita

2012-01-01

Full Text Available Abstract Background One of the main issues of molecular evolution is to divulge the principles in dictating the evolutionary rate differences among various gene classes. Immunological genes have received considerable attention in evolutionary biology as candidates for local adaptation and for studying functionally important polymorphisms. The normal structure and function of immunological genes will be distorted when they experience mutations leading to immunological dysfunctions. Results Here, we examined the fundamental differences between the genes which on mutation give rise to autoimmune or other immune system related diseases and the immunological genes that do not cause any disease phenotypes. Although the disease genes examined are analogous to non-disease genes in product, expression, function, and pathway affiliation, a statistically significant decrease in evolutionary rate has been found in autoimmune disease genes relative to all other immune related diseases and non-disease genes. Possible ways of accumulation of mutation in the three steps of the central dogma (DNA-mRNA-Protein have been studied to trace the mutational effects predisposed to disease consequence and acquiring higher selection pressure. Principal Component Analysis and Multivariate Regression Analysis have established the predominant role of single nucleotide polymorphisms in guiding the evolutionary rate of immunological disease and non-disease genes followed by m-RNA abundance, paralogs number, fraction of phosphorylation residue, alternatively spliced exon, protein residue burial and protein disorder. Conclusions Our study provides an empirical insight into the etiology of autoimmune disease genes and other immunological diseases. The immediate utility of our study is to help in disease gene identification and may also help in medicinal improvement of immune related disease.

Carboxylesterase 1 genes

DEFF Research Database (Denmark)

Rasmussen, Henrik Berg; Madsen, Majbritt Busk

2018-01-01

The carboxylesterase 1 gene (CES1) encodes a hydrolase that metabolizes commonly used drugs. The CES1-related pseudogene, carboxylesterase 1 pseudogene 1 (CES1P1), has been implicated in gene exchange with CES1 and in the formation of hybrid genes including the carboxylesterase 1A2 gene (CES1A2...

Bayesian assignment of gene ontology terms to gene expression experiments

Science.gov (United States)

Sykacek, P.

2012-01-01

Motivation: Gene expression assays allow for genome scale analyses of molecular biological mechanisms. State-of-the-art data analysis provides lists of involved genes, either by calculating significance levels of mRNA abundance or by Bayesian assessments of gene activity. A common problem of such approaches is the difficulty of interpreting the biological implication of the resulting gene lists. This lead to an increased interest in methods for inferring high-level biological information. A common approach for representing high level information is by inferring gene ontology (GO) terms which may be attributed to the expression data experiment. Results: This article proposes a probabilistic model for GO term inference. Modelling assumes that gene annotations to GO terms are available and gene involvement in an experiment is represented by a posterior probabilities over gene-specific indicator variables. Such probability measures result from many Bayesian approaches for expression data analysis. The proposed model combines these indicator probabilities in a probabilistic fashion and provides a probabilistic GO term assignment as a result. Experiments on synthetic and microarray data suggest that advantages of the proposed probabilistic GO term inference over statistical test-based approaches are in particular evident for sparsely annotated GO terms and in situations of large uncertainty about gene activity. Provided that appropriate annotations exist, the proposed approach is easily applied to inferring other high level assignments like pathways. Availability: Source code under GPL license is available from the author. Contact: peter.sykacek@boku.ac.at PMID:22962488

Bayesian assignment of gene ontology terms to gene expression experiments.

Science.gov (United States)

Sykacek, P

2012-09-15

Gene expression assays allow for genome scale analyses of molecular biological mechanisms. State-of-the-art data analysis provides lists of involved genes, either by calculating significance levels of mRNA abundance or by Bayesian assessments of gene activity. A common problem of such approaches is the difficulty of interpreting the biological implication of the resulting gene lists. This lead to an increased interest in methods for inferring high-level biological information. A common approach for representing high level information is by inferring gene ontology (GO) terms which may be attributed to the expression data experiment. This article proposes a probabilistic model for GO term inference. Modelling assumes that gene annotations to GO terms are available and gene involvement in an experiment is represented by a posterior probabilities over gene-specific indicator variables. Such probability measures result from many Bayesian approaches for expression data analysis. The proposed model combines these indicator probabilities in a probabilistic fashion and provides a probabilistic GO term assignment as a result. Experiments on synthetic and microarray data suggest that advantages of the proposed probabilistic GO term inference over statistical test-based approaches are in particular evident for sparsely annotated GO terms and in situations of large uncertainty about gene activity. Provided that appropriate annotations exist, the proposed approach is easily applied to inferring other high level assignments like pathways. Source code under GPL license is available from the author. peter.sykacek@boku.ac.at.

Targeting the human lysozyme gene on bovine αs1- casein gene ...

African Journals Online (AJOL)

Targeting an exogenous gene into a favorable gene locus and for expression under endogenous regulators is an ideal method in mammary gland bioreactor research. For this purpose, a gene targeting vector was constructed to targeting the human lysozyme gene on bovine αs1-casein gene locus. In this case, the ...

A powerful score-based test statistic for detecting gene-gene co-association.

Science.gov (United States)

Xu, Jing; Yuan, Zhongshang; Ji, Jiadong; Zhang, Xiaoshuai; Li, Hongkai; Wu, Xuesen; Xue, Fuzhong; Liu, Yanxun

2016-01-29

The genetic variants identified by Genome-wide association study (GWAS) can only account for a small proportion of the total heritability for complex disease. The existence of gene-gene joint effects which contains the main effects and their co-association is one of the possible explanations for the "missing heritability" problems. Gene-gene co-association refers to the extent to which the joint effects of two genes differ from the main effects, not only due to the traditional interaction under nearly independent condition but the correlation between genes. Generally, genes tend to work collaboratively within specific pathway or network contributing to the disease and the specific disease-associated locus will often be highly correlated (e.g. single nucleotide polymorphisms (SNPs) in linkage disequilibrium). Therefore, we proposed a novel score-based statistic (SBS) as a gene-based method for detecting gene-gene co-association. Various simulations illustrate that, under different sample sizes, marginal effects of causal SNPs and co-association levels, the proposed SBS has the better performance than other existed methods including single SNP-based and principle component analysis (PCA)-based logistic regression model, the statistics based on canonical correlations (CCU), kernel canonical correlation analysis (KCCU), partial least squares path modeling (PLSPM) and delta-square (δ (2)) statistic. The real data analysis of rheumatoid arthritis (RA) further confirmed its advantages in practice. SBS is a powerful and efficient gene-based method for detecting gene-gene co-association.

Prediction of regulatory gene pairs using dynamic time warping and gene ontology.

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Yang, Andy C; Hsu, Hui-Huang; Lu, Ming-Da; Tseng, Vincent S; Shih, Timothy K

2014-01-01

Selecting informative genes is the most important task for data analysis on microarray gene expression data. In this work, we aim at identifying regulatory gene pairs from microarray gene expression data. However, microarray data often contain multiple missing expression values. Missing value imputation is thus needed before further processing for regulatory gene pairs becomes possible. We develop a novel approach to first impute missing values in microarray time series data by combining k-Nearest Neighbour (KNN), Dynamic Time Warping (DTW) and Gene Ontology (GO). After missing values are imputed, we then perform gene regulation prediction based on our proposed DTW-GO distance measurement of gene pairs. Experimental results show that our approach is more accurate when compared with existing missing value imputation methods on real microarray data sets. Furthermore, our approach can also discover more regulatory gene pairs that are known in the literature than other methods.

The Drosophila melanogaster methuselah gene: a novel gene with ancient functions.

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Ana Rita Araújo

Full Text Available The Drosophila melanogaster G protein-coupled receptor gene, methuselah (mth, has been described as a novel gene that is less than 10 million years old. Nevertheless, it shows a highly specific expression pattern in embryos, larvae, and adults, and has been implicated in larval development, stress resistance, and in the setting of adult lifespan, among others. Although mth belongs to a gene subfamily with 16 members in D. melanogaster, there is no evidence for functional redundancy in this subfamily. Therefore, it is surprising that a novel gene influences so many traits. Here, we explore the alternative hypothesis that mth is an old gene. Under this hypothesis, in species distantly related to D. melanogaster, there should be a gene with features similar to those of mth. By performing detailed phylogenetic, synteny, protein structure, and gene expression analyses we show that the D. virilis GJ12490 gene is the orthologous of mth in species distantly related to D. melanogaster. We also show that, in D. americana (a species of the virilis group of Drosophila, a common amino acid polymorphism at the GJ12490 orthologous gene is significantly associated with developmental time, size, and lifespan differences. Our results imply that GJ12490 orthologous genes are candidates for developmental time and lifespan differences in Drosophila in general.

Constructing an integrated gene similarity network for the identification of disease genes.

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Tian, Zhen; Guo, Maozu; Wang, Chunyu; Xing, LinLin; Wang, Lei; Zhang, Yin

2017-09-20

Discovering novel genes that are involved human diseases is a challenging task in biomedical research. In recent years, several computational approaches have been proposed to prioritize candidate disease genes. Most of these methods are mainly based on protein-protein interaction (PPI) networks. However, since these PPI networks contain false positives and only cover less half of known human genes, their reliability and coverage are very low. Therefore, it is highly necessary to fuse multiple genomic data to construct a credible gene similarity network and then infer disease genes on the whole genomic scale. We proposed a novel method, named RWRB, to infer causal genes of interested diseases. First, we construct five individual gene (protein) similarity networks based on multiple genomic data of human genes. Then, an integrated gene similarity network (IGSN) is reconstructed based on similarity network fusion (SNF) method. Finally, we employee the random walk with restart algorithm on the phenotype-gene bilayer network, which combines phenotype similarity network, IGSN as well as phenotype-gene association network, to prioritize candidate disease genes. We investigate the effectiveness of RWRB through leave-one-out cross-validation methods in inferring phenotype-gene relationships. Results show that RWRB is more accurate than state-of-the-art methods on most evaluation metrics. Further analysis shows that the success of RWRB is benefited from IGSN which has a wider coverage and higher reliability comparing with current PPI networks. Moreover, we conduct a comprehensive case study for Alzheimer's disease and predict some novel disease genes that supported by literature. RWRB is an effective and reliable algorithm in prioritizing candidate disease genes on the genomic scale. Software and supplementary information are available at http://nclab.hit.edu.cn/~tianzhen/RWRB/ .

Kotler : teiste inimeste arvamust usutakse enam kui meediat / Philip Kotler

Index Scriptorium Estoniae

Kotler, Philip

2007-01-01

Philip Kotler vastab küsimustele, millised faktorid mõjutasid tänapäevase turunduse kujundamist, millised vahendid on kasulikud tarbijate leidmiseks, meelitamiseks ja hoidmiseks ning milline on tema arvamus selle kohta, et internetti ja sotsiaalseid võrgustikke nähakse kui tuleviku turundusvahendeid

Tudengid tahavad enam ühekohalisi ühikatube / Jüri Saar

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Saar, Jüri, 1973-

2002-01-01

Tartu Ülikooli mitusada ühiselamujärjekorras ootavat tudengit eelistaks ühekohalist ja odavat tuba, ühiselamute remondiprogramm toob aga juurde eelkõige kahekohalisi tube, mille üliõpilased kalli hinna pärast ära põlgavad.

Carter : Iisraelil on 150 või enam tuumapommi / Kaivo Kopli

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Kopli, Kaivo

2008-01-01

USA endine president Jimmy Carter väitis, et Iisraelil on 150 tuumapommi või rohkemgi. Eri hinnangutest Iisraeli tuumapommide arvu kohta, n.-ö. tunnustatud tuumariigid maailmas. Lisa: Tuumakatsetus 1979. aastal?

Oscarite gala pole enam miljoni valge mehe marss / Triin Tael

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Tael, Triin

2007-01-01

79. Oscarite gala oli Martin Scorsese maffiadraama "Kahe tule vahel" ja mustanahaliste näitlejate triumf. Parimaks meesnäitlejaks kuulutati Forest Whitaker ja parimaks naiskõrvalosatäitjaks Jennifer Hudson. Ka varasematest võitjatest

Perang Enam Hari Arab Israel 1967 Menerusi Perspektif Teori Realisme

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MOHD IRWAN SYAZLI SAIDIN

2016-06-01

Full Text Available Realism approach has dominated the studies of world politics and international relations since the last of the World War II and until the start of the Cold War era. The focus of this study is to look into the factors that ignited the war other than identifying the policies or actions taken by the countries involved in the war. The question that arises lies in the extent to which the approach is able to explain the factors and actions taken by the leaders, to the point that it led to the 1967 war, and how this war can serve as guidance for our understanding of the Realism Theory. The objective of this study is to unravel the chains of events that had become the background of the 1967 Arab-Israeli War by concentrating on the root causes of the war and the policies of the countries involved, other than offering justification for the Realism Theory by looking closely into the characteristics, assumptions, and concepts under this approach. The methodology of this work employs document analysis and historical studies to obtain complete data. The analysis was carried out by applying the Arab-Israeli war events to the Realism Theory to prove that there is an association between the causes of the war and the theory through the analysis unit, key assumptions and substantial concepts contained in the Realism approach. The unit of analysis, which places the countries as the main actor in the international system, can be seen through the main role of Egypt, Jordan, Syria and Israel throughout the period of war. Concepts such as power, power balance, national interests, national sovereignty and self-help are also associated with the causes behind this war through a series of facts that have manifested themselves in the event

Laps ja pere vajavad enam tähelepanu / Anne Tiko

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Tiko, Anne, 1949-

2001-01-01

Lääne-Viru Maavalitsuse, Lastekaitse Liidu ja TPÜ sotsiaaltöö osakonna korraldatud kuuenda vabariikliku lastekaitsekonverentsi "Laps ja pere tänases Eestis" pöördumine haridus- ja sotsiaalministeeriumi poole

GAMBARAN FARMASIS YANG MEROKOK DI ENAM KOTA BESAR DI INDONESIA

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Anny Victor Purba

2012-11-01

Full Text Available National Health Survey 2004 reported the prevalence of active smokers aged 10 years and above was 30%. In 2004, among other countries in the world, Indonesia ranked the 5th highest in tobacco consumption. Cigarette smoke produces lung carcinogens, which in America causes 3000 deaths yearly due to lung cancer to adults who are non-smokers. About 300,000 children who are passive smokers inflict a lower respiration infection such as bronchitis and peneumonia, and±1,000,000 asthma sufferers are inflicting an increase in episodes and worsening of symptoms. Damage mucosa of the lungs caused by smoking causes the smokers to easily get infections such as TB. Pharmacists can be as health educators, who are directly in contact with patients, are in unique position to give support and as motivators for patients to stop smoking.This research aimed to provide a description about pharmacists (smoking/non-smoking, their opinions and knowledge about smoking, drugs that help stop smoking and their role in helping patients stop smoking. As an instrument for collecting data, questionnaires were used by pharmacists in 6 (six big cities namely Jakarta, Solo, Surabaya, Medan, and Makassar. Over 711 pharmacists become respondents consisting of 271 (33. 75% men and 440 (66.25%, women. Pharmacists who smoked were 21.7% all were males. And 10.5% tried to seriously quit smoking. Pharmacists who did not smoke in the last 6 months were 12.2% and 9.5% were still smoking. Almost 93% pharmacies did not provide an area for smoking and only 7% provided it. Some reasons why pharmacists did not completely quit smoking were that they did not want to quit, environmental reasons and also it's not a process in which you can just suddenly stop and it needs motivation.Key words: smoking, tobacco. nicotine. lung carcinogen. pharmacists

Enam kui pool eestlastest peab Rüütli otsust õigeks

Index Scriptorium Estoniae

2005-01-01

President Arnold Rüütli otsust mitte sõita 9. mail Moskvasse peab õigeks 61 protsensti eestlastest ja kõigest 6,1 protsensti mitteeestlastest. Kommentaarid Tartu Ülikooli politoloogiaosakonna teadurilt Vello Pettai'lt ja sotsioloog Andrus Saar'elt

On aeg, mil vajame enam leiba kui lilli / Ants Juske

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Juske, Ants, 1956-2016

2009-01-01

Marge Monko isikunäitus "Leib ja lilled" Tallinnas Draakoni Galeriis 21. märtsini. Eksponeeritud fotod ja video "Nora õed". Kunstnik on majanduses ja tööhõives asetleidvaid muutusi uurides aluseks võtnud Narva Kreenholmi Manufaktuuri näited

Evolutionary signatures amongst disease genes permit novel methods for gene prioritization and construction of informative gene-based networks.

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Nolan Priedigkeit

2015-02-01

Full Text Available Genes involved in the same function tend to have similar evolutionary histories, in that their rates of evolution covary over time. This coevolutionary signature, termed Evolutionary Rate Covariation (ERC, is calculated using only gene sequences from a set of closely related species and has demonstrated potential as a computational tool for inferring functional relationships between genes. To further define applications of ERC, we first established that roughly 55% of genetic diseases posses an ERC signature between their contributing genes. At a false discovery rate of 5% we report 40 such diseases including cancers, developmental disorders and mitochondrial diseases. Given these coevolutionary signatures between disease genes, we then assessed ERC's ability to prioritize known disease genes out of a list of unrelated candidates. We found that in the presence of an ERC signature, the true disease gene is effectively prioritized to the top 6% of candidates on average. We then apply this strategy to a melanoma-associated region on chromosome 1 and identify MCL1 as a potential causative gene. Furthermore, to gain global insight into disease mechanisms, we used ERC to predict molecular connections between 310 nominally distinct diseases. The resulting "disease map" network associates several diseases with related pathogenic mechanisms and unveils many novel relationships between clinically distinct diseases, such as between Hirschsprung's disease and melanoma. Taken together, these results demonstrate the utility of molecular evolution as a gene discovery platform and show that evolutionary signatures can be used to build informative gene-based networks.

Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life.

Science.gov (United States)

Kannan, Lavanya; Li, Hua; Rubinstein, Boris; Mushegian, Arcady

2013-12-19

The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their last common ancestor. We have developed a family of models of gene gain and gene loss in evolution, and applied the maximum-likelihood approach that uses phylogenetic tree of prokaryotes and the record of orthologous relationships between their genes to infer the gene content of LUCA, the Last Universal Common Ancestor of all currently living cellular organisms. The crucial parameter, the ratio of gene losses and gene gains, was estimated from the data and was higher in models that take account of the number of in-paralogs in genomes than in models that treat gene presences and absences as a binary trait. While the numbers of genes that are placed confidently into LUCA are similar in the ML methods and in previously published methods that use various parsimony-based approaches, the identities of genes themselves are different. Most of the models of either kind treat the genes found in many existing genomes in a similar way, assigning to them high probabilities of being ancestral ("high ancestrality"). The ML models are more likely than others to assign high ancestrality to the genes that are relatively rare in the present-day genomes.

Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization

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McDonald Karen

2011-08-01

Full Text Available Abstract Background Direct gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications. In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer. Results The software not only provides general functions for gene analysis and optimization along with an interactive user-friendly interface, but also includes unique features such as programming capability, dedicated mRNA secondary structure prediction, artificial neural network modeling, network & multi-threaded computing, and user-accessible programming modules. The software allows a user to analyze and optimize a sequence using main menu functions or specialized module windows. Alternatively, gene optimization can be initiated by designing a gene construct and configuring an optimization strategy. A user can choose several predefined or user-defined algorithms to design a complicated strategy. The software provides expandable functionality as platform software supporting module development using popular script languages such as VBScript and JScript in the software programming environment. Conclusion Visual Gene Developer is useful for both researchers who want to quickly analyze and optimize genes, and those who are interested in developing and testing new algorithms in bioinformatics. The software is available for free download at http://www.visualgenedeveloper.net.

Gene delivery to the lungs: pulmonary gene therapy for cystic fibrosis.

Science.gov (United States)

Villate-Beitia, Ilia; Zarate, Jon; Puras, Gustavo; Pedraz, José Luis

2017-07-01

Cystic fibrosis (CF) is a monogenic autosomal recessive disorder where the defective gene, the cystic fibrosis transmembrane conductance regulator (CFTR), is well identified. Moreover, the respiratory tract can be targeted through noninvasive aerosolized formulations for inhalation. Therefore, gene therapy is considered a plausible strategy to address this disease. Conventional gene therapy strategies rely on the addition of a correct copy of the CFTR gene into affected cells in order to restore the channel activity. In recent years, genome correction strategies have emerged, such as zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats associated to Cas9 nucleases. These gene editing tools aim to repair the mutated gene at its original genomic locus with high specificity. Besides, the success of gene therapy critically depends on the nucleic acids carriers. To date, several clinical studies have been carried out to add corrected copies of the CFTR gene into target cells using viral and non-viral vectors, some of them with encouraging results. Regarding genome editing systems, preliminary in vitro studies have been performed in order to repair the CFTR gene. In this review, after briefly introducing the basis of CF, we discuss the up-to-date gene therapy strategies to address the disease. The review focuses on the main factors to take into consideration when developing gene delivery strategies, such as the design of vectors and plasmid DNA, in vitro/in vivo tests, translation to human use, administration methods, manufacturing conditions and regulatory issues.

Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks.

Science.gov (United States)

Mai, Hans-Jörg; Pateyron, Stéphanie; Bauer, Petra

2016-10-03

FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) is the central regulator of iron uptake in Arabidopsis thaliana roots. We performed transcriptome analyses of six day-old seedlings and roots of six week-old plants using wild type, a fit knock-out mutant and a FIT over-expression line grown under iron-sufficient or iron-deficient conditions. We compared genes regulated in a FIT-dependent manner depending on the developmental stage of the plants. We assembled a high likelihood dataset which we used to perform co-expression and functional analysis of the most stably iron deficiency-induced genes. 448 genes were found FIT-regulated. Out of these, 34 genes were robustly FIT-regulated in root and seedling samples and included 13 novel FIT-dependent genes. Three hundred thirty-one genes showed differential regulation in response to the presence and absence of FIT only in the root samples, while this was the case for 83 genes in the seedling samples. We assembled a virtual dataset of iron-regulated genes based on a total of 14 transcriptomic analyses of iron-deficient and iron-sufficient wild-type plants to pinpoint the best marker genes for iron deficiency and analyzed this dataset in depth. Co-expression analysis of this dataset revealed 13 distinct regulons part of which predominantly contained functionally related genes. We could enlarge the list of FIT-dependent genes and discriminate between genes that are robustly FIT-regulated in roots and seedlings or only in one of those. FIT-regulated genes were mostly induced, few of them were repressed by FIT. With the analysis of a virtual dataset we could filter out and pinpoint new candidates among the most reliable marker genes for iron deficiency. Moreover, co-expression and functional analysis of this virtual dataset revealed iron deficiency-induced and functionally distinct regulons.

Intracellular delivery of potential therapeutic genes: prospects in cancer gene therapy.

Science.gov (United States)

Bakhtiar, Athirah; Sayyad, Mustak; Rosli, Rozita; Maruyama, Atsushi; Chowdhury, Ezharul H

2014-01-01

Conventional therapies for malignant cancer such as chemotherapy and radiotherapy are associated with poor survival rates owing to the development of cellular resistance to cancer drugs and the lack of targetability, resulting in unwanted adverse effects on healthy cells and necessitating the lowering of therapeutic dose with consequential lower efficacy of the treatment. Gene therapy employing different types of viral and non-viral carriers to transport gene(s) of interest and facilitating production of the desirable therapeutic protein(s) has tremendous prospects in cancer treatments due to the high-level of specificity in therapeutic action of the expressed protein(s) with diminished off-target effects, although cancer cell-specific delivery of transgene(s) still poses some challenges to be addressed. Depending on the potential therapeutic target genes, cancer gene therapy could be categorized into tumor suppressor gene replacement therapy, immune gene therapy and enzyme- or prodrug-based therapy. This review would shed light on the current progress of delivery of potentially therapeutic genes into various cancer cells in vitro and animal models utilizing a variety of viral and non-viral vectors.

Divergence of gene body DNA methylation and evolution of plant duplicate genes.

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Jun Wang

Full Text Available It has been shown that gene body DNA methylation is associated with gene expression. However, whether and how deviation of gene body DNA methylation between duplicate genes can influence their divergence remains largely unexplored. Here, we aim to elucidate the potential role of gene body DNA methylation in the fate of duplicate genes. We identified paralogous gene pairs from Arabidopsis and rice (Oryza sativa ssp. japonica genomes and reprocessed their single-base resolution methylome data. We show that methylation in paralogous genes nonlinearly correlates with several gene properties including exon number/gene length, expression level and mutation rate. Further, we demonstrated that divergence of methylation level and pattern in paralogs indeed positively correlate with their sequence and expression divergences. This result held even after controlling for other confounding factors known to influence the divergence of paralogs. We observed that methylation level divergence might be more relevant to the expression divergence of paralogs than methylation pattern divergence. Finally, we explored the mechanisms that might give rise to the divergence of gene body methylation in paralogs. We found that exonic methylation divergence more closely correlates with expression divergence than intronic methylation divergence. We show that genomic environments (e.g., flanked by transposable elements and repetitive sequences of paralogs generated by various duplication mechanisms are associated with the methylation divergence of paralogs. Overall, our results suggest that the changes in gene body DNA methylation could provide another avenue for duplicate genes to develop differential expression patterns and undergo different evolutionary fates in plant genomes.

GeneTopics - interpretation of gene sets via literature-driven topic models

Science.gov (United States)

2013-01-01

Background Annotation of a set of genes is often accomplished through comparison to a library of labelled gene sets such as biological processes or canonical pathways. However, this approach might fail if the employed libraries are not up to date with the latest research, don't capture relevant biological themes or are curated at a different level of granularity than is required to appropriately analyze the input gene set. At the same time, the vast biomedical literature offers an unstructured repository of the latest research findings that can be tapped to provide thematic sub-groupings for any input gene set. Methods Our proposed method relies on a gene-specific text corpus and extracts commonalities between documents in an unsupervised manner using a topic model approach. We automatically determine the number of topics summarizing the corpus and calculate a gene relevancy score for each topic allowing us to eliminate non-specific topics. As a result we obtain a set of literature topics in which each topic is associated with a subset of the input genes providing directly interpretable keywords and corresponding documents for literature research. Results We validate our method based on labelled gene sets from the KEGG metabolic pathway collection and the genetic association database (GAD) and show that the approach is able to detect topics consistent with the labelled annotation. Furthermore, we discuss the results on three different types of experimentally derived gene sets, (1) differentially expressed genes from a cardiac hypertrophy experiment in mice, (2) altered transcript abundance in human pancreatic beta cells, and (3) genes implicated by GWA studies to be associated with metabolite levels in a healthy population. In all three cases, we are able to replicate findings from the original papers in a quick and semi-automated manner. Conclusions Our approach provides a novel way of automatically generating meaningful annotations for gene sets that are directly

Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life

Science.gov (United States)

2013-01-01

Background The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their last common ancestor. Results We have developed a family of models of gene gain and gene loss in evolution, and applied the maximum-likelihood approach that uses phylogenetic tree of prokaryotes and the record of orthologous relationships between their genes to infer the gene content of LUCA, the Last Universal Common Ancestor of all currently living cellular organisms. The crucial parameter, the ratio of gene losses and gene gains, was estimated from the data and was higher in models that take account of the number of in-paralogs in genomes than in models that treat gene presences and absences as a binary trait. Conclusion While the numbers of genes that are placed confidently into LUCA are similar in the ML methods and in previously published methods that use various parsimony-based approaches, the identities of genes themselves are different. Most of the models of either kind treat the genes found in many existing genomes in a similar way, assigning to them high probabilities of being ancestral (“high ancestrality”). The ML models are more likely than others to assign high ancestrality to the genes that are relatively rare in the present-day genomes. Reviewers This article was reviewed by Martijn A Huynen, Toni Gabaldón and Fyodor Kondrashov. PMID:24354654

Gene therapy: An overview

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Sudip Indu

2013-01-01

Full Text Available Gene therapy "the use of genes as medicine" involves the transfer of a therapeutic or working copy of a gene into specific cells of an individual in order to repair a faulty gene copy. The technique may be used to replace a faulty gene, or to introduce a new gene whose function is to cure or to favorably modify the clinical course of a condition. The objective of gene therapy is to introduce new genetic material into target cells while causing no damage to the surrounding healthy cells and tissues, hence the treatment related morbidity is decreased. The delivery system includes a vector that delivers a therapeutic gene into the patient′s target cell. Functional proteins are created from the therapeutic gene causing the cell to return to a normal stage. The vectors used in gene therapy can be viral and non-viral. Gene therapy, an emerging field of biomedicine, is still at infancy and much research remains to be done before this approach to the treatment of condition will realize its full potential.

Gene doping in sports.

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Unal, Mehmet; Ozer Unal, Durisehvar

2004-01-01

Gene or cell doping is defined by the World Anti-Doping Agency (WADA) as "the non-therapeutic use of genes, genetic elements and/or cells that have the capacity to enhance athletic performance". New research in genetics and genomics will be used not only to diagnose and treat disease, but also to attempt to enhance human performance. In recent years, gene therapy has shown progress and positive results that have highlighted the potential misuse of this technology and the debate of 'gene doping'. Gene therapies developed for the treatment of diseases such as anaemia (the gene for erythropoietin), muscular dystrophy (the gene for insulin-like growth factor-1) and peripheral vascular diseases (the gene for vascular endothelial growth factor) are potential doping methods. With progress in gene technology, many other genes with this potential will be discovered. For this reason, it is important to develop timely legal regulations and to research the field of gene doping in order to develop methods of detection. To protect the health of athletes and to ensure equal competitive conditions, the International Olympic Committee, WADA and International Sports Federations have accepted performance-enhancing substances and methods as being doping, and have forbidden them. Nevertheless, the desire to win causes athletes to misuse these drugs and methods. This paper reviews the current status of gene doping and candidate performance enhancement genes, and also the use of gene therapy in sports medicine and ethics of genetic enhancement. Copyright 2004 Adis Data Information BV

Identifying key genes in rheumatoid arthritis by weighted gene co-expression network analysis.

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Ma, Chunhui; Lv, Qi; Teng, Songsong; Yu, Yinxian; Niu, Kerun; Yi, Chengqin

2017-08-01

This study aimed to identify rheumatoid arthritis (RA) related genes based on microarray data using the WGCNA (weighted gene co-expression network analysis) method. Two gene expression profile datasets GSE55235 (10 RA samples and 10 healthy controls) and GSE77298 (16 RA samples and seven healthy controls) were downloaded from Gene Expression Omnibus database. Characteristic genes were identified using metaDE package. WGCNA was used to find disease-related networks based on gene expression correlation coefficients, and module significance was defined as the average gene significance of all genes used to assess the correlation between the module and RA status. Genes in the disease-related gene co-expression network were subject to functional annotation and pathway enrichment analysis using Database for Annotation Visualization and Integrated Discovery. Characteristic genes were also mapped to the Connectivity Map to screen small molecules. A total of 599 characteristic genes were identified. For each dataset, characteristic genes in the green, red and turquoise modules were most closely associated with RA, with gene numbers of 54, 43 and 79, respectively. These genes were enriched in totally enriched in 17 Gene Ontology terms, mainly related to immune response (CD97, FYB, CXCL1, IKBKE, CCR1, etc.), inflammatory response (CD97, CXCL1, C3AR1, CCR1, LYZ, etc.) and homeostasis (C3AR1, CCR1, PLN, CCL19, PPT1, etc.). Two small-molecule drugs sanguinarine and papaverine were predicted to have a therapeutic effect against RA. Genes related to immune response, inflammatory response and homeostasis presumably have critical roles in RA pathogenesis. Sanguinarine and papaverine have a potential therapeutic effect against RA. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

Identification of suitable reference genes for gene expression studies of shoulder instability.

Directory of Open Access Journals (Sweden)

Mariana Ferreira Leal

Full Text Available Shoulder instability is a common shoulder injury, and patients present with plastic deformation of the glenohumeral capsule. Gene expression analysis may be a useful tool for increasing the general understanding of capsule deformation, and reverse-transcription quantitative polymerase chain reaction (RT-qPCR has become an effective method for such studies. Although RT-qPCR is highly sensitive and specific, it requires the use of suitable reference genes for data normalization to guarantee meaningful and reproducible results. In the present study, we evaluated the suitability of a set of reference genes using samples from the glenohumeral capsules of individuals with and without shoulder instability. We analyzed the expression of six commonly used reference genes (ACTB, B2M, GAPDH, HPRT1, TBP and TFRC in the antero-inferior, antero-superior and posterior portions of the glenohumeral capsules of cases and controls. The stability of the candidate reference gene expression was determined using four software packages: NormFinder, geNorm, BestKeeper and DataAssist. Overall, HPRT1 was the best single reference gene, and HPRT1 and B2M composed the best pair of reference genes from different analysis groups, including simultaneous analysis of all tissue samples. GenEx software was used to identify the optimal number of reference genes to be used for normalization and demonstrated that the accumulated standard deviation resulting from the use of 2 reference genes was similar to that resulting from the use of 3 or more reference genes. To identify the optimal combination of reference genes, we evaluated the expression of COL1A1. Although the use of different reference gene combinations yielded variable normalized quantities, the relative quantities within sample groups were similar and confirmed that no obvious differences were observed when using 2, 3 or 4 reference genes. Consequently, the use of 2 stable reference genes for normalization, especially

The Pathway From Genes to Gene Therapy in Glaucoma: A Review of Possibilities for Using Genes as Glaucoma Drugs.

Science.gov (United States)

Borrás, Teresa

2017-01-01

Treatment of diseases with gene therapy is advancing rapidly. The use of gene therapy has expanded from the original concept of re-placing the mutated gene causing the disease to the use of genes to con-trol nonphysiological levels of expression or to modify pathways known to affect the disease. Genes offer numerous advantages over conventional drugs. They have longer duration of action and are more specific. Genes can be delivered to the target site by naked DNA, cells, nonviral, and viral vectors. The enormous progress of the past decade in molecular bi-ology and delivery systems has provided ways for targeting genes to the intended cell/tissue and safe, long-term vectors. The eye is an ideal organ for gene therapy. It is easily accessible and it is an immune-privileged site. Currently, there are clinical trials for diseases affecting practically every tissue of the eye, including those to restore vision in patients with Leber congenital amaurosis. However, the number of eye trials compared with those for systemic diseases is quite low (1.8%). Nevertheless, judg-ing by the vast amount of ongoing preclinical studies, it is expected that such number will increase considerably in the near future. One area of great need for eye gene therapy is glaucoma, where a long-term gene drug would eliminate daily applications and compliance issues. Here, we review the current state of gene therapy for glaucoma and the possibilities for treating the trabecular meshwork to lower intraocular pressure and the retinal ganglion cells to protect them from neurodegeneration. Copyright© 2017 Asia-Pacific Academy of Ophthalmology.

Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity

Energy Technology Data Exchange (ETDEWEB)

Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Tratz, Stephen C.; Gregory, Michelle L.

2006-06-08

With the rising influence of the Gene On-tology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associ-ated with them. So far, these approaches have solely relied on the knowledge en-coded in the Gene Ontology and the gene annotations associated with the Gene On-tology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

UniGene Tabulator: a full parser for the UniGene format.

Science.gov (United States)

Lenzi, Luca; Frabetti, Flavia; Facchin, Federica; Casadei, Raffaella; Vitale, Lorenza; Canaider, Silvia; Carinci, Paolo; Zannotti, Maria; Strippoli, Pierluigi

2006-10-15

UniGene Tabulator 1.0 provides a solution for full parsing of UniGene flat file format; it implements a structured graphical representation of each data field present in UniGene following import into a common database managing system usable in a personal computer. This database includes related tables for sequence, protein similarity, sequence-tagged site (STS) and transcript map interval (TXMAP) data, plus a summary table where each record represents a UniGene cluster. UniGene Tabulator enables full local management of UniGene data, allowing parsing, querying, indexing, retrieving, exporting and analysis of UniGene data in a relational database form, usable on Macintosh (OS X 10.3.9 or later) and Windows (2000, with service pack 4, XP, with service pack 2 or later) operating systems-based computers. The current release, including both the FileMaker runtime applications, is freely available at http://apollo11.isto.unibo.it/software/

Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks.

Directory of Open Access Journals (Sweden)

Vipin Narang

Full Text Available Human gene regulatory networks (GRN can be difficult to interpret due to a tangle of edges interconnecting thousands of genes. We constructed a general human GRN from extensive transcription factor and microRNA target data obtained from public databases. In a subnetwork of this GRN that is active during estrogen stimulation of MCF-7 breast cancer cells, we benchmarked automated algorithms for identifying core regulatory genes (transcription factors and microRNAs. Among these algorithms, we identified K-core decomposition, pagerank and betweenness centrality algorithms as the most effective for discovering core regulatory genes in the network evaluated based on previously known roles of these genes in MCF-7 biology as well as in their ability to explain the up or down expression status of up to 70% of the remaining genes. Finally, we validated the use of K-core algorithm for organizing the GRN in an easier to interpret layered hierarchy where more influential regulatory genes percolate towards the inner layers. The integrated human gene and miRNA network and software used in this study are provided as supplementary materials (S1 Data accompanying this manuscript.

Maximum Gene-Support Tree

Directory of Open Access Journals (Sweden)

Yunfeng Shan

2008-01-01

Full Text Available Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available. In this study, we generated single gene trees of seven yeast species as well as single gene trees of nine baculovirus species using all the orthologous genes among the species compared. Homologous genes among seven known plants were used for validation of the finding. Four algorithms—maximum parsimony (MP, minimum evolution (ME, maximum likelihood (ML, and neighbor-joining (NJ—were used. Trees were reconstructed before and after weighting the DNA and protein sequence lengths among genes. Rarely a gene can always generate the “true tree” by all the four algorithms. However, the most frequent gene tree, termed “maximum gene-support tree” (MGS tree, or WMGS tree for the weighted one, in yeasts, baculoviruses, or plants was consistently found to be the “true tree” among the species. The results provide insights into the overall degree of divergence of orthologous genes of the genomes analyzed and suggest the following: 1 The true tree relationship among the species studied is still maintained by the largest group of orthologous genes; 2 There are usually more orthologous genes with higher similarities between genetically closer species than between genetically more distant ones; and 3 The maximum gene-support tree reflects the phylogenetic relationship among species in comparison.

Interactive visualization of gene regulatory networks with associated gene expression time series data

NARCIS (Netherlands)

Westenberg, M.A.; Hijum, van S.A.F.T.; Lulko, A.T.; Kuipers, O.P.; Roerdink, J.B.T.M.; Linsen, L.; Hagen, H.; Hamann, B.

2008-01-01

We present GENeVis, an application to visualize gene expression time series data in a gene regulatory network context. This is a network of regulator proteins that regulate the expression of their respective target genes. The networks are represented as graphs, in which the nodes represent genes,

Using gene expression noise to understand gene regulation

NARCIS (Netherlands)

Munsky, B.; Neuert, G.; van Oudenaarden, A.

2012-01-01

Phenotypic variation is ubiquitous in biology and is often traceable to underlying genetic and environmental variation. However, even genetically identical cells in identical environments display variable phenotypes. Stochastic gene expression, or gene expression "noise," has been suggested as a

Gene Conversion in Angiosperm Genomes with an Emphasis on Genes Duplicated by Polyploidization

Directory of Open Access Journals (Sweden)

Xi-Yin Wang

2011-01-01

Full Text Available Angiosperm genomes differ from those of mammals by extensive and recursive polyploidizations. The resulting gene duplication provides opportunities both for genetic innovation, and for concerted evolution. Though most genes may escape conversion by their homologs, concerted evolution of duplicated genes can last for millions of years or longer after their origin. Indeed, paralogous genes on two rice chromosomes duplicated an estimated 60–70 million years ago have experienced gene conversion in the past 400,000 years. Gene conversion preserves similarity of paralogous genes, but appears to accelerate their divergence from orthologous genes in other species. The mutagenic nature of recombination coupled with the buffering effect provided by gene redundancy, may facilitate the evolution of novel alleles that confer functional innovations while insulating biological fitness of affected plants. A mixed evolutionary model, characterized by a primary birth-and-death process and occasional homoeologous recombination and gene conversion, may best explain the evolution of multigene families.

Analüütikud soovitavad Eesti Energia börsile viia / Piret Reiljan

Index Scriptorium Estoniae

Reiljan, Piret, 1983-

2008-01-01

Kohalikud analüütikud soovitavad viia Eesti Energia börsile, kuna see elavdaks aktsiaturgu ja tõmbaks ligi välisinvestoreid. Vt. samas: Raivo Vare: raske aeg töötab Eesti Energia börsiletoomise kasuks; Analüüs ootab pääsu valitsuskabinetti; Juhid ei püsi enam Eesti Energias. Diagrammid: Majandusnäitajad; Varade maht

Studi Deskriptif Persepsi Karyawan Hotel Tentang Glass Ceiling Pada Wanita Dalam Pencapaian Jabatan Puncak Manajemen Hotel Di Kota Tanjung Selor

OpenAIRE

Merang, Merycona

2015-01-01

Penelitian ini dilakukan untuk mengetahui persepsi karyawan hotel tentang glass ceiling pada wanita dalam pencapaian jabatan puncak manajemen hotel di kota Tanjung Selor. Glass ceiling memiliki enam variable yaitu diri sendiri, tingkat pendidikan, lingkungan keluarga, kesehatan, lingkungan sosial, dan lingkungan kerja.Teknik analisa yang digunakan adalah kuantitatif deskriptif, crosstab dan chi square. Hasil penelitian menunjukkan bahwa secara keseluruhan, persepsi karyawan tentang glass ceil...

Suhkru hind tõusis ühe müüja luhtunud lepingu tõttu / Ines Kuusik ; kommenteerinud Andres Oopkaup

Index Scriptorium Estoniae

Kuusik, Ines

2011-01-01

Eesti suhkruturu suuremad firmad on AS Antomin, OÜ Montemar (Nordic Sugar) ja AS Haljas. 2010. aastal lõppes AS-i Antomin ja Suedzuckeri vaheline leping ja kuna EL vähendas kõikjal tootjakvoote, siis Suedzuckeril ei jätkunud enam Eesti jaoks suhkrut. AS Antomin müüb praegu Alžeeria suhkrut, millele lisandub EL-i tollimaks. Graafikud, diagrammid

Цена на сахар подскочила из-за неудачного договора продавца / Инес Куузик ; комментировал Андрес Оопкауп

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Куузик, Инес

2011-01-01

Eesti suhkruturu suuremad firmad on AS Antomin, OÜ Montemar (Nordic Sugar) ja AS Haljas. 2010. aastal on lõppenud AS-i Antomin ja Suedzuckeri vaheline leping ja kuna EL vähendas kõikjal tootjakvoote, siis Suedzuckeril ei jätkunud enam Eesti jaoks suhkrut. AS Antomin müüb praegu Alžeeria suhkrut, millele lisandub EL-i tollimaks. Graafikud, diagrammid

Iraani tuumateadlase seiklused päädisid kodumaale naasmisega / Hendrik Vosman

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Vosman, Hendrik

2010-01-01

Iraani tuumateadlane Shahram Amiri jõudis 15. juulil pärast enam kui aastast äraolekut taas kodumaale ja väidab, et CIA oli ta röövinud ja USA-sse viinud. Washington Posti väitel maksis CIA Amirile 5 miljonit dollarit, et ta annaks infot Iraani tuumaprogrammi kohta. Shahram Amiri väidab, et ta ei tea tuumaprogrammist midagi

Euroopa Liit valmistub missiooniks Darfuris / Peter Winkler ; tõlk. Liivi Parrest

Index Scriptorium Estoniae

Winkler, Peter

2007-01-01

Varasemalt Neue Zürcher Zeitungis ilmunud artikkel räägib sellest, kuidas toimib Euroopa Liidu sõjaline element ja millega see praegu kõige enam hõivatud on. Samuti antakse artiklis ülevaade käesolevast Darfuri konfliktistEuroopa Liidu Sõjalise Staabi planeerimismeeskonna (EUMS) tegevusest ja ettevalmistustest Darfuri operatsiooniks Sudaanis. Vt. samas: Tänu taevale Déby eest; Käesolev Darfuri konflikt

SMS-ide hinnad võivad langeda / Lauri Linnamäe

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Linnamäe, Lauri

2007-01-01

Ilmunud ka: Postimees : na russkon jazõke 10. okt. lk. 2. Euroopa Komisjoni määrus langetas välismaal tehtavate mobiilikõnede hindu enam kui poole võrra, sama võib juhtuda ka lühisõnumite ja mobiilse andmeside hindadega. Euroopa Komisjoni infoühiskonna- ja telekomivoliniku Viviane Redingi selgitusi. Eesti telefoniettevõtete hindadest. Lisa: Mobiilikõned välismaal

40 000 riigiteenistuses olijat ootab märgatav töötasu tõus / Kai Kalamees

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Kalamees, Kai

2007-01-01

Ilmunud ka: Postimees : na russkom jazõke, 12. sept. 2007, lk. 3. Riigieelarvekavast, mis näeb ette 2008. aastal keskmiselt enam kui 15%-list palgatõusu õpetajatele, politseinikele, päästjatele ja vangivalvuritele ning kultuuritöötajatele ja lasteaednikele, arst-residentidele ja kiirabiarstidele. TALO juhatuse esimees Ago Tuuling ei lepi alla 20%-lise palgatõusuga. Vt. samas: IRLi ministrid erimeelel

Penjadwalan Perencanaan Produksi Produk Mixed Model Pada Refrigerator Business Unit Di Perusahaan Elektronik Jakarta

OpenAIRE

Rinaldi, Dendi

2011-01-01

Perusahaan elektronik di Jakarta merupakan salah satu perusahaan yang memiliki enam business unit yaitu Refrigerator, Audio, Electric Fan, Air Conditioner, Water Pump, dan Loundry System. Dalam menjalankan produksi khususnya pada Refrigerator Business Unit, perusahaan mengalami permasalahan pada penjadwalan produksinya karena terdapat 30 model yang diproduksi sesuai permintaan menyebabkan perusahaan sulit untuk melakukan penjadwalan. Salah satu penjadwalan yang dipakai dalam sistem produks...

Teadlased: Pere peaks õpetama eakale digiühiskonnas pensionil olemist / Marju Himma

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Himma, Marju

2017-01-01

Iga kahe aasta tagant küsitlevad Tallinna ülikooli rahvastikuteadlased enam kui 6000 üle 50-aastast eesti elanikku. SHARE nime kandev eakateuuring tunneb praegu käimas olevas küsitluslaines huvi inimese lapsepõlve, töö ja lähisuhete vastu. Selgitusi jagavad TLÜ Eesti demograafia keskuse juhataja Luule Sakkeus ja SHARE uuringu projektijuht Tiina Tambaum

Tselluloidi aura ja kaasaegne kunst / Hanno Soans

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Soans, Hanno, 1974-

2004-01-01

Muutustest filmitegemises ja filmiesteetikas. Filmi sarnanemisest tehniliselt üha enam videoga. Kunstnike tegelemisest filmiga. 26. XI näeb kinos "Sõprus" "1+1=1" raames kaasaegsete kunstnike teoseid laiekraanil: Eija-Liisa Ahtila "If 6 was 9" (1995), "Today" (1996-97), "Consolation Service" (1999); Sara Lunden ja Henry Moore Selder (sünd. 1973, Stockholm) "Deadly Boring" (2001), "She is Dead" (2003)

Eesti teadlaste kiip võitleb vähiga

Index Scriptorium Estoniae

2007-01-01

Vt. ka Linnaleht : Tallinn : na russkom jazõke 28. sept., lk. 4. Biotehnoloogiaettevõte Asper Biotech alustas Valgamaal kogutud DNA-proovide analüüsimist kahe kõige enam levinud päriliku vähi - rinnavähi ja jämesoolevähi - suhtes spetsiaalselt selle uuringu jaoks Eesti biokeskuses väljatöötatud ja maailmas unikaalse geenikiibi abil

Sotsiaalsest vastutusest / Mai Treial

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Treial, Mai, 1952-

2006-01-01

Ilmunud ka: Meie Maa, Põhjarannik, Severnoje Poberezhje 1. apr. lk. 2, Hiiu Leht 7. apr. lk. 2, Valgamaalane 11. apr. lk. 2. Autori sõnul on vanuripoliitika nurgakiviks soliidne pension, mis võimaldab igale inimesele väärika vananemise. Enam ei piisa vaesuse leevendamiseks abinõudest, mis taandatud üksnes rahaliste hüvitiste maksmisele, olulisem on paindlik sotsiaalteenuste süsteem

Võrdsus toob edu / Jarno Laur

Index Scriptorium Estoniae

Laur, Jarno, 1975-

2002-01-01

Ilmunud ka: Koit 9. mai lk. 6, Sakala 10. mai lk. 2, Põhjarannik, Severnoje Poberezhje 11. mai lk. 2, Valgamaalane 14. mai lk. 2, Pärnu Postimees 15. mai lk. 2, Hiiu Leht 17. mai lk. 2. Eesti muutub üha enam ükskõiksete ühiskonnaks, kus domineerib edukate egoism ja mahajääjate apaatia. Autor: Rahvaerakond Mõõdukad

Lapsevanemahullus ahistab lapsi / Kate Kelland

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Kelland, Kate

2006-01-01

Brite on haaranud uus tõbi, mida nimetatakse lapsevanemahulluseks, püüdes iga hinna eest teistest paremad olla ja täiuslikkust saavutada, võtavad tavaliselt mõistlikud ja haritud britid üha enam kasutusele haiglasi meetmeid, et oma järeltulijatele tulevases elus eeliseid anda. Sellest on oma raamatus "Tänapäeva perede hullumeelsus" kirjutanud Meg Sanders

RESPON PRIMIPARA SAAT DIPUTUSKAN SECTIO CAESAREA DARURAT

OpenAIRE

Sari, Febria Syafyu

2018-01-01

Primipara yang akan menjalani persalinan secara Sectio Caesarea (SC) dapat mempengaruhi  kesiapan praoperatif saat diputuskan SC. Ketidaksiapan primipara dalam menghadapi praoperatif SC dapat meningkatkan resiko depresi postpartum. Penelitian kualitatif dengan pendekatan desain fenomenologi deskriptif yang bertujuan untuk mengeksplorasi respon pertama kali primipara pada praoperatif SC. Penelitian ini dilaksanakan pada tahun 2016 di ruang Kebidanan, dengan jumlah partisipan sebanyak enam oran...

Linnadisaini lõpp(eesmärgid) / Michael Sorokin

Index Scriptorium Estoniae

Sorokin, Michael

2008-01-01

Autori arvates on linnadisain (urban design) jõudnud tupikusse. Ta on järjest vähem võimeline leidma leidlikke lahendusi linnade ja linnakodanike morfoloogilistele, funktsionaalsetele ja inimlikele vajadustele. Samal ajal kui ülesanded muutuvad keerukamaks ja pakilisemaks, on eriala peavoolustunud, muutudes potensiaalselt laiast ja lootusrikkast kontseptuaalsest kategooriast järjest enam paindumatuks, piiravaks ja igavaks vanade tavade järgimiseks

Loeme veel! / Kristi Pärn-Valdoja, Katrin Pauts

Index Scriptorium Estoniae

Pärn-Valdoja, Kristi, 1970-

2006-01-01

TNS Emor väärtushinnangute uuringu RISC 2006 andmetel on igapäevane lugemisharjumus 29 protsendil Eesti naistest ja 20 protsendil meestest. Tallinna abilinnapea Kaia Jäppinen, investeerimistoodete turundusjuht Piret Reinson, KUMU direktor Sirje Helme, laulja Maarja-Liis Ilus ning näitleja Riina Maide kõige enam nende elu ja tegevust mõjutanud raamatutest. Lisa: Millised on Hollywoodi naiste lemmikraamatud?

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

Directory of Open Access Journals (Sweden)

Lemay Danielle G

2012-09-01

Full Text Available Abstract Background In previous studies, gene neighborhoods—spatial clusters of co-expressed genes in the genome—have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Scoring Tool (G-NEST which combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all possible window sizes simultaneously. Results Using G-NEST on atlases of mouse and human tissue expression data, we found that large neighborhoods of ten or more genes are extremely rare in mammalian genomes. When they do occur, neighborhoods are typically composed of families of related genes. Both the highest scoring and the largest neighborhoods in mammalian genomes are formed by tandem gene duplication. Mammalian gene neighborhoods contain highly and variably expressed genes. Co-localized noisy gene pairs exhibit lower evolutionary conservation of their adjacent genome locations, suggesting that their shared transcriptional background may be disadvantageous. Genes that are essential to mammalian survival and reproduction are less likely to occur in neighborhoods, although neighborhoods are enriched with genes that function in mitosis. We also found that gene orientation and protein-protein interactions are partially responsible for maintenance of gene neighborhoods. Conclusions Our experiments using G-NEST confirm that tandem gene duplication is the primary driver of non-random gene order in mammalian genomes. Non-essentiality, co-functionality, gene orientation, and protein-protein interactions are additional forces that maintain gene neighborhoods, especially those formed by tandem duplicates. We expect G-NEST to be useful for other applications such as the identification of core regulatory modules, common transcriptional backgrounds, and chromatin domains. The

The Cumulative Effect of Gene-Gene and Gene-Environment Interactions on the Risk of Prostate Cancer in Chinese Men

Directory of Open Access Journals (Sweden)

Ming Liu

2016-01-01

Full Text Available Prostate cancer (PCa is a multifactorial disease involving complex genetic and environmental factors interactions. Gene-gene and gene-environment interactions associated with PCa in Chinese men are less studied. We explored the association between 36 SNPs and PCa in 574 subjects from northern China. Body mass index (BMI, smoking, and alcohol consumption were determined through self-administered questionnaires in 134 PCa patients. Then gene-gene and gene-environment interactions among the PCa-associated SNPs were analyzed using the generalized multifactor dimensionality reduction (GMDR and logistic regression methods. Allelic and genotypic association analyses showed that six variants were associated with PCa and the cumulative effect suggested men who carried any combination of 1, 2, or ≥3 risk genotypes had a gradually increased PCa risk (odds ratios (ORs = 1.79–4.41. GMDR analysis identified the best gene-gene interaction model with scores of 10 for both the cross-validation consistency and sign tests. For gene-environment interactions, rs6983561 CC and rs16901966 GG in individuals with a BMI ≥ 28 had ORs of 7.66 (p = 0.032 and 5.33 (p = 0.046, respectively. rs7679673 CC + CA and rs12653946 TT in individuals that smoked had ORs of 2.77 (p = 0.007 and 3.11 (p = 0.024, respectively. rs7679673 CC in individuals that consumed alcohol had an OR of 4.37 (p = 0.041. These results suggest that polymorphisms, either individually or by interacting with other genes or environmental factors, contribute to an increased risk of PCa.

Primetime for Learning Genes.

Science.gov (United States)

Keifer, Joyce

2017-02-11

Learning genes in mature neurons are uniquely suited to respond rapidly to specific environmental stimuli. Expression of individual learning genes, therefore, requires regulatory mechanisms that have the flexibility to respond with transcriptional activation or repression to select appropriate physiological and behavioral responses. Among the mechanisms that equip genes to respond adaptively are bivalent domains. These are specific histone modifications localized to gene promoters that are characteristic of both gene activation and repression, and have been studied primarily for developmental genes in embryonic stem cells. In this review, studies of the epigenetic regulation of learning genes in neurons, particularly the brain-derived neurotrophic factor gene ( BDNF ), by methylation/demethylation and chromatin modifications in the context of learning and memory will be highlighted. Because of the unique function of learning genes in the mature brain, it is proposed that bivalent domains are a characteristic feature of the chromatin landscape surrounding their promoters. This allows them to be "poised" for rapid response to activate or repress gene expression depending on environmental stimuli.

Characterization of Genes for Beef Marbling Based on Applying Gene Coexpression Network

Directory of Open Access Journals (Sweden)

Dajeong Lim

2014-01-01

Full Text Available Marbling is an important trait in characterization beef quality and a major factor for determining the price of beef in the Korean beef market. In particular, marbling is a complex trait and needs a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with marbling, we used a weighted gene coexpression network analysis from the expression value of bovine genes. Hub genes were identified; they were topologically centered with large degree and BC values in the global network. We performed gene expression analysis to detect candidate genes in M. longissimus with divergent marbling phenotype (marbling scores 2 to 7 using qRT-PCR. The results demonstrate that transmembrane protein 60 (TMEM60 and dihydropyrimidine dehydrogenase (DPYD are associated with increasing marbling fat. We suggest that the network-based approach in livestock may be an important method for analyzing the complex effects of candidate genes associated with complex traits like marbling or tenderness.

Simple Comparative Analyses of Differentially Expressed Gene Lists May Overestimate Gene Overlap.

Science.gov (United States)

Lawhorn, Chelsea M; Schomaker, Rachel; Rowell, Jonathan T; Rueppell, Olav

2018-04-16

Comparing the overlap between sets of differentially expressed genes (DEGs) within or between transcriptome studies is regularly used to infer similarities between biological processes. Significant overlap between two sets of DEGs is usually determined by a simple test. The number of potentially overlapping genes is compared to the number of genes that actually occur in both lists, treating every gene as equal. However, gene expression is controlled by transcription factors that bind to a variable number of transcription factor binding sites, leading to variation among genes in general variability of their expression. Neglecting this variability could therefore lead to inflated estimates of significant overlap between DEG lists. With computer simulations, we demonstrate that such biases arise from variation in the control of gene expression. Significant overlap commonly arises between two lists of DEGs that are randomly generated, assuming that the control of gene expression is variable among genes but consistent between corresponding experiments. More overlap is observed when transcription factors are specific to their binding sites and when the number of genes is considerably higher than the number of different transcription factors. In contrast, overlap between two DEG lists is always lower than expected when the genetic architecture of expression is independent between the two experiments. Thus, the current methods for determining significant overlap between DEGs are potentially confounding biologically meaningful overlap with overlap that arises due to variability in control of expression among genes, and more sophisticated approaches are needed.

Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function.

Science.gov (United States)

Di, Chao; Xu, Wenying; Su, Zhen; Yuan, Joshua S

2010-10-07

PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes are ubiquitously present in divergent species from prokaryotes to eukaryotes. Human PHB genes have been found to be associated with various diseases. Recent studies by our group and others have shown diverse function of PHB genes in plants for development, senescence, defence, and others. Despite the importance of the PHB gene family, no comprehensive gene family analysis has been carried to evaluate the relatedness of PHB genes across different species. In order to better guide the gene function analysis and understand the evolution of the PHB gene family, we therefore carried out the comparative genome analysis of the PHB genes across different kingdoms. The relatedness, motif distribution, and intron/exon distribution all indicated that PHB genes is a relatively conserved gene family. The PHB genes can be classified into 5 classes and each class have a very deep evolutionary origin. The PHB genes within the class maintained the same motif patterns during the evolution. With Arabidopsis as the model species, we found that PHB gene intron/exon structure and domains are also conserved during the evolution. Despite being a conserved gene family, various gene duplication events led to the expansion of the PHB genes. Both segmental and tandem gene duplication were involved in Arabidopsis PHB gene family expansion. However, segmental duplication is predominant in Arabidopsis. Moreover, most of the duplicated genes experienced neofunctionalization. The results highlighted that PHB genes might be involved in important functions so that the duplicated genes are under the evolutionary pressure to derive new function. PHB gene family is a conserved gene family and accounts for diverse but important biological functions based on the similar molecular mechanisms. The highly diverse biological function indicated that more research needs to be carried out

Genes and Hearing Loss

Science.gov (United States)

... ENTCareers Marketplace Find an ENT Doctor Near You Genes and Hearing Loss Genes and Hearing Loss Patient ... mutation may only have dystopia canthorum. How Do Genes Work? Genes are a road map for the ...

Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing.

Science.gov (United States)

Seoane-Zonjic, Pedro; Cañas, Rafael A; Bautista, Rocío; Gómez-Maldonado, Josefa; Arrillaga, Isabel; Fernández-Pozo, Noé; Claros, M Gonzalo; Cánovas, Francisco M; Ávila, Concepción

2016-02-27

In the era of DNA throughput sequencing, assembling and understanding gymnosperm mega-genomes remains a challenge. Although drafts of three conifer genomes have recently been published, this number is too low to understand the full complexity of conifer genomes. Using techniques focused on specific genes, gene models can be established that can aid in the assembly of gene-rich regions, and this information can be used to compare genomes and understand functional evolution. In this study, gene capture technology combined with BAC isolation and sequencing was used as an experimental approach to establish de novo gene structures without a reference genome. Probes were designed for 866 maritime pine transcripts to sequence genes captured from genomic DNA. The gene models were constructed using GeneAssembler, a new bioinformatic pipeline, which reconstructed over 82% of the gene structures, and a high proportion (85%) of the captured gene models contained sequences from the promoter regulatory region. In a parallel experiment, the P. pinaster BAC library was screened to isolate clones containing genes whose cDNA sequence were already available. BAC clones containing the asparagine synthetase, sucrose synthase and xyloglucan endotransglycosylase gene sequences were isolated and used in this study. The gene models derived from the gene capture approach were compared with the genomic sequences derived from the BAC clones. This combined approach is a particularly efficient way to capture the genomic structures of gene families with a small number of members. The experimental approach used in this study is a valuable combined technique to study genomic gene structures in species for which a reference genome is unavailable. It can be used to establish exon/intron boundaries in unknown gene structures, to reconstruct incomplete genes and to obtain promoter sequences that can be used for transcriptional studies. A bioinformatics algorithm (GeneAssembler) is also provided as a

Mining tissue specificity, gene connectivity and disease association to reveal a set of genes that modify the action of disease causing genes

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Reverter Antonio

2008-09-01

Full Text Available Abstract Background The tissue specificity of gene expression has been linked to a number of significant outcomes including level of expression, and differential rates of polymorphism, evolution and disease association. Recent studies have also shown the importance of exploring differential gene connectivity and sequence conservation in the identification of disease-associated genes. However, no study relates gene interactions with tissue specificity and disease association. Methods We adopted an a priori approach making as few assumptions as possible to analyse the interplay among gene-gene interactions with tissue specificity and its subsequent likelihood of association with disease. We mined three large datasets comprising expression data drawn from massively parallel signature sequencing across 32 tissues, describing a set of 55,606 true positive interactions for 7,197 genes, and microarray expression results generated during the profiling of systemic inflammation, from which 126,543 interactions among 7,090 genes were reported. Results Amongst the myriad of complex relationships identified between expression, disease, connectivity and tissue specificity, some interesting patterns emerged. These include elevated rates of expression and network connectivity in housekeeping and disease-associated tissue-specific genes. We found that disease-associated genes are more likely to show tissue specific expression and most frequently interact with other disease genes. Using the thresholds defined in these observations, we develop a guilt-by-association algorithm and discover a group of 112 non-disease annotated genes that predominantly interact with disease-associated genes, impacting on disease outcomes. Conclusion We conclude that parameters such as tissue specificity and network connectivity can be used in combination to identify a group of genes, not previously confirmed as disease causing, that are involved in interactions with disease causing

AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data

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Xia Yuannan

2006-12-01

Full Text Available Abstract Background DNA microarrays are a powerful tool for monitoring the expression of tens of thousands of genes simultaneously. With the advance of microarray technology, the challenge issue becomes how to analyze a large amount of microarray data and make biological sense of them. Affymetrix GeneChips are widely used microarrays, where a variety of statistical algorithms have been explored and used for detecting significant genes in the experiment. These methods rely solely on the quantitative data, i.e., signal intensity; however, qualitative data are also important parameters in detecting differentially expressed genes. Results AffyMiner is a tool developed for detecting differentially expressed genes in Affymetrix GeneChip microarray data and for associating gene annotation and gene ontology information with the genes detected. AffyMiner consists of the functional modules, GeneFinder for detecting significant genes in a treatment versus control experiment and GOTree for mapping genes of interest onto the Gene Ontology (GO space; and interfaces to run Cluster, a program for clustering analysis, and GenMAPP, a program for pathway analysis. AffyMiner has been used for analyzing the GeneChip data and the results were presented in several publications. Conclusion AffyMiner fills an important gap in finding differentially expressed genes in Affymetrix GeneChip microarray data. AffyMiner effectively deals with multiple replicates in the experiment and takes into account both quantitative and qualitative data in identifying significant genes. AffyMiner reduces the time and effort needed to compare data from multiple arrays and to interpret the possible biological implications associated with significant changes in a gene's expression.

Gene therapy in periodontics.

Science.gov (United States)

Chatterjee, Anirban; Singh, Nidhi; Saluja, Mini

2013-03-01

GENES are made of DNA - the code of life. They are made up of two types of base pair from different number of hydrogen bonds AT, GC which can be turned into instruction. Everyone inherits genes from their parents and passes them on in turn to their children. Every person's genes are different, and the changes in sequence determine the inherited differences between each of us. Some changes, usually in a single gene, may cause serious diseases. Gene therapy is 'the use of genes as medicine'. It involves the transfer of a therapeutic or working gene copy into specific cells of an individual in order to repair a faulty gene copy. Thus it may be used to replace a faulty gene, or to introduce a new gene whose function is to cure or to favorably modify the clinical course of a condition. It has a promising era in the field of periodontics. Gene therapy has been used as a mode of tissue engineering in periodontics. The tissue engineering approach reconstructs the natural target tissue by combining four elements namely: Scaffold, signaling molecules, cells and blood supply and thus can help in the reconstruction of damaged periodontium including cementum, gingival, periodontal ligament and bone.

Norrie disease gene is distinct from the monoamine oxidase genes.

Science.gov (United States)

Sims, K B; Ozelius, L; Corey, T; Rinehart, W B; Liberfarb, R; Haines, J; Chen, W J; Norio, R; Sankila, E; de la Chapelle, A

1989-09-01

The genes for MAO-A and MAO-B appear to be very close to the Norrie disease gene, on the basis of loss and/or disruption of the MAO genes and activities in atypical Norrie disease patients deleted for the DXS7 locus; linkage among the MAO genes, the Norrie disease gene, and the DXS7 locus; and mapping of all these loci to the chromosomal region Xp11. The present study provides evidence that the MAO genes are not disrupted in "classic" Norrie disease patients. Genomic DNA from these "nondeletion" Norrie disease patients did not show rearrangements at the MAOA or DXS7 loci. Normal levels of MAO-A activities, as well as normal amounts and size of the MAO-A mRNA, were observed in cultured skin fibroblasts from these patients, and MAO-B activity in their platelets was normal. Catecholamine metabolites evaluated in plasma and urine were in the control range. Thus, although some atypical Norrie disease patients lack both MAO-A and MAO-B activities, MAO does not appear to be an etiologic factor in classic Norrie disease.

Gene profile analysis of osteoblast genes differentially regulated by histone deacetylase inhibitors

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Lamblin Anne-Francoise

2007-10-01

Full Text Available Abstract Background Osteoblast differentiation requires the coordinated stepwise expression of multiple genes. Histone deacetylase inhibitors (HDIs accelerate the osteoblast differentiation process by blocking the activity of histone deacetylases (HDACs, which alter gene expression by modifying chromatin structure. We previously demonstrated that HDIs and HDAC3 shRNAs accelerate matrix mineralization and the expression of osteoblast maturation genes (e.g. alkaline phosphatase, osteocalcin. Identifying other genes that are differentially regulated by HDIs might identify new pathways that contribute to osteoblast differentiation. Results To identify other osteoblast genes that are altered early by HDIs, we incubated MC3T3-E1 preosteoblasts with HDIs (trichostatin A, MS-275, or valproic acid for 18 hours in osteogenic conditions. The promotion of osteoblast differentiation by HDIs in this experiment was confirmed by osteogenic assays. Gene expression profiles relative to vehicle-treated cells were assessed by microarray analysis with Affymetrix GeneChip 430 2.0 arrays. The regulation of several genes by HDIs in MC3T3-E1 cells and primary osteoblasts was verified by quantitative real-time PCR. Nine genes were differentially regulated by at least two-fold after exposure to each of the three HDIs and six were verified by PCR in osteoblasts. Four of the verified genes (solute carrier family 9 isoform 3 regulator 1 (Slc9a3r1, sorbitol dehydrogenase 1, a kinase anchor protein, and glutathione S-transferase alpha 4 were induced. Two genes (proteasome subunit, beta type 10 and adaptor-related protein complex AP-4 sigma 1 were suppressed. We also identified eight growth factors and growth factor receptor genes that are significantly altered by each of the HDIs, including Frizzled related proteins 1 and 4, which modulate the Wnt signaling pathway. Conclusion This study identifies osteoblast genes that are regulated early by HDIs and indicates pathways that

Acute Vhl gene inactivation induces cardiac HIF-dependent erythropoietin gene expression.

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Marta Miró-Murillo

Full Text Available Von Hippel Lindau (Vhl gene inactivation results in embryonic lethality. The consequences of its inactivation in adult mice, and of the ensuing activation of the hypoxia-inducible factors (HIFs, have been explored mainly in a tissue-specific manner. This mid-gestation lethality can be also circumvented by using a floxed Vhl allele in combination with an ubiquitous tamoxifen-inducible recombinase Cre-ER(T2. Here, we characterize a widespread reduction in Vhl gene expression in Vhl(floxed-UBC-Cre-ER(T2 adult mice after dietary tamoxifen administration, a convenient route of administration that has yet to be fully characterized for global gene inactivation. Vhl gene inactivation rapidly resulted in a marked splenomegaly and skin erythema, accompanied by renal and hepatic induction of the erythropoietin (Epo gene, indicative of the in vivo activation of the oxygen sensing HIF pathway. We show that acute Vhl gene inactivation also induced Epo gene expression in the heart, revealing cardiac tissue to be an extra-renal source of EPO. Indeed, primary cardiomyocytes and HL-1 cardiac cells both induce Epo gene expression when exposed to low O(2 tension in a HIF-dependent manner. Thus, as well as demonstrating the potential of dietary tamoxifen administration for gene inactivation studies in UBC-Cre-ER(T2 mouse lines, this data provides evidence of a cardiac oxygen-sensing VHL/HIF/EPO pathway in adult mice.

Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data

OpenAIRE

Ezer, Daphne; Moignard, Victoria; G?ttgens, Berthold; Adryan, Boris

2016-01-01

Many genes are expressed in bursts, which can contribute to cell-to-cell heterogeneity. It is now possible to measure this heterogeneity with high throughput single cell gene expression assays (single cell qPCR and RNA-seq). These experimental approaches generate gene expression distributions which can be used to estimate the kinetic parameters of gene expression bursting, namely the rate that genes turn on, the rate that genes turn off, and the rate of transcription. We construct a complete ...

Discovering genes underlying QTL

Energy Technology Data Exchange (ETDEWEB)

Vanavichit, Apichart [Kasetsart University, Kamphaengsaen, Nakorn Pathom (Thailand)

2002-02-01

A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity.

Science.gov (United States)

Kim, Hyunjin; Choi, Sang-Min; Park, Sanghyun

2018-01-01

When a gene shows varying levels of expression among normal people but similar levels in disease patients or shows similar levels of expression among normal people but different levels in disease patients, we can assume that the gene is associated with the disease. By utilizing this gene expression heterogeneity, we can obtain additional information that abets discovery of disease-associated genes. In this study, we used collaborative filtering to calculate the degree of gene expression heterogeneity between classes and then scored the genes on the basis of the degree of gene expression heterogeneity to find "differentially predicted" genes. Through the proposed method, we discovered more prostate cancer-associated genes than 10 comparable methods. The genes prioritized by the proposed method are potentially significant to biological processes of a disease and can provide insight into them.

Validation of reference genes for quantifying changes in gene expression in virus-infected tobacco.

Science.gov (United States)

Baek, Eseul; Yoon, Ju-Yeon; Palukaitis, Peter

2017-10-01

To facilitate quantification of gene expression changes in virus-infected tobacco plants, eight housekeeping genes were evaluated for their stability of expression during infection by one of three systemically-infecting viruses (cucumber mosaic virus, potato virus X, potato virus Y) or a hypersensitive-response-inducing virus (tobacco mosaic virus; TMV) limited to the inoculated leaf. Five reference-gene validation programs were used to establish the order of the most stable genes for the systemically-infecting viruses as ribosomal protein L25 > β-Tubulin > Actin, and the least stable genes Ubiquitin-conjugating enzyme (UCE) genes were EF1α > Cysteine protease > Actin, and the least stable genes were GAPDH genes, three defense responsive genes were examined to compare their relative changes in gene expression caused by each virus. Copyright © 2017 Elsevier Inc. All rights reserved.

Human gene therapy: novel approaches to improve the current gene delivery systems.

Science.gov (United States)

Cucchiarini, Magali

2016-06-01

Even though gene therapy made its way through the clinics to treat a number of human pathologies since the early years of experimental research and despite the recent approval of the first gene-based product (Glybera) in Europe, the safe and effective use of gene transfer vectors remains a challenge in human gene therapy due to the existence of barriers in the host organism. While work is under active investigation to improve the gene transfer systems themselves, the use of controlled release approaches may offer alternative, convenient tools of vector delivery to achieve a performant gene transfer in vivo while overcoming the various physiological barriers that preclude its wide use in patients. This article provides an overview of the most significant contributions showing how the principles of controlled release strategies may be adapted for human gene therapy.

From gene engineering to gene modulation and manipulation: can we prevent or detect gene doping in sports?

Science.gov (United States)

Fischetto, Giuseppe; Bermon, Stéphane

2013-10-01

During the last 2 decades, progress in deciphering the human gene map as well as the discovery of specific defective genes encoding particular proteins in some serious human diseases have resulted in attempts to treat sick patients with gene therapy. There has been considerable focus on human recombinant proteins which were gene-engineered and produced in vitro (insulin, growth hormone, insulin-like growth factor-1, erythropoietin). Unfortunately, these substances and methods also became improper tools for unscrupulous athletes. Biomedical research has focused on the possible direct insertion of gene material into the body, in order to replace some defective genes in vivo and/or to promote long-lasting endogenous synthesis of deficient proteins. Theoretically, diabetes, anaemia, muscular dystrophies, immune deficiency, cardiovascular diseases and numerous other illnesses could benefit from such innovative biomedical research, though much work remains to be done. Considering recent findings linking specific genotypes and physical performance, it is tempting to submit the young athletic population to genetic screening or, alternatively, to artificial gene expression modulation. Much research is already being conducted in order to achieve a safe transfer of genetic material to humans. This is of critical importance since uncontrolled production of the specifically coded protein, with serious secondary adverse effects (polycythaemia, acute cardiovascular problems, cancer, etc.), could occur. Other unpredictable reactions (immunogenicity of vectors or DNA-vector complex, autoimmune anaemia, production of wild genetic material) also remain possible at the individual level. Some new substances (myostatin blockers or anti-myostatin antibodies), although not gene material, might represent a useful and well-tolerated treatment to prevent progression of muscular dystrophies. Similarly, other molecules, in the roles of gene or metabolic activators [5-aminoimidazole-4

A model of gene-gene and gene-environment interactions and its implications for targeting environmental interventions by genotype

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Wallace Helen M

2006-10-01

Full Text Available Abstract Background The potential public health benefits of targeting environmental interventions by genotype depend on the environmental and genetic contributions to the variance of common diseases, and the magnitude of any gene-environment interaction. In the absence of prior knowledge of all risk factors, twin, family and environmental data may help to define the potential limits of these benefits in a given population. However, a general methodology to analyze twin data is required because of the potential importance of gene-gene interactions (epistasis, gene-environment interactions, and conditions that break the 'equal environments' assumption for monozygotic and dizygotic twins. Method A new model for gene-gene and gene-environment interactions is developed that abandons the assumptions of the classical twin study, including Fisher's (1918 assumption that genes act as risk factors for common traits in a manner necessarily dominated by an additive polygenic term. Provided there are no confounders, the model can be used to implement a top-down approach to quantifying the potential utility of genetic prediction and prevention, using twin, family and environmental data. The results describe a solution space for each disease or trait, which may or may not include the classical twin study result. Each point in the solution space corresponds to a different model of genotypic risk and gene-environment interaction. Conclusion The results show that the potential for reducing the incidence of common diseases using environmental interventions targeted by genotype may be limited, except in special cases. The model also confirms that the importance of an individual's genotype in determining their risk of complex diseases tends to be exaggerated by the classical twin studies method, owing to the 'equal environments' assumption and the assumption of no gene-environment interaction. In addition, if phenotypes are genetically robust, because of epistasis

Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes.

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Osato, Naoki

2018-01-19

Transcriptional target genes show functional enrichment of genes. However, how many and how significantly transcriptional target genes include functional enrichments are still unclear. To address these issues, I predicted human transcriptional target genes using open chromatin regions, ChIP-seq data and DNA binding sequences of transcription factors in databases, and examined functional enrichment and gene expression level of putative transcriptional target genes. Gene Ontology annotations showed four times larger numbers of functional enrichments in putative transcriptional target genes than gene expression information alone, independent of transcriptional target genes. To compare the number of functional enrichments of putative transcriptional target genes between cells or search conditions, I normalized the number of functional enrichment by calculating its ratios in the total number of transcriptional target genes. With this analysis, native putative transcriptional target genes showed the largest normalized number of functional enrichments, compared with target genes including 5-60% of randomly selected genes. The normalized number of functional enrichments was changed according to the criteria of enhancer-promoter interactions such as distance from transcriptional start sites and orientation of CTCF-binding sites. Forward-reverse orientation of CTCF-binding sites showed significantly higher normalized number of functional enrichments than the other orientations. Journal papers showed that the top five frequent functional enrichments were related to the cellular functions in the three cell types. The median expression level of transcriptional target genes changed according to the criteria of enhancer-promoter assignments (i.e. interactions) and was correlated with the changes of the normalized number of functional enrichments of transcriptional target genes. Human putative transcriptional target genes showed significant functional enrichments. Functional

Conditional gene expression in the mouse using a Sleeping Beauty gene-trap transposon

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Hackett Perry B

2006-06-01

Full Text Available Abstract Background Insertional mutagenesis techniques with transposable elements have been popular among geneticists studying model organisms from E. coli to Drosophila and, more recently, the mouse. One such element is the Sleeping Beauty (SB transposon that has been shown in several studies to be an effective insertional mutagen in the mouse germline. SB transposon vector studies have employed different functional elements and reporter molecules to disrupt and report the expression of endogenous mouse genes. We sought to generate a transposon system that would be capable of reporting the expression pattern of a mouse gene while allowing for conditional expression of a gene of interest in a tissue- or temporal-specific pattern. Results Here we report the systematic development and testing of a transposon-based gene-trap system incorporating the doxycycline-repressible Tet-Off (tTA system that is capable of activating the expression of genes under control of a Tet response element (TRE promoter. We demonstrate that the gene trap system is fully functional in vitro by introducing the "gene-trap tTA" vector into human cells by transposition and identifying clones that activate expression of a TRE-luciferase transgene in a doxycycline-dependent manner. In transgenic mice, we mobilize gene-trap tTA vectors, discover parameters that can affect germline mobilization rates, and identify candidate gene insertions to demonstrate the in vivo functionality of the vector system. We further demonstrate that the gene-trap can act as a reporter of endogenous gene expression and it can be coupled with bioluminescent imaging to identify genes with tissue-specific expression patterns. Conclusion Akin to the GAL4/UAS system used in the fly, we have made progress developing a tool for mutating and revealing the expression of mouse genes by generating the tTA transactivator in the presence of a secondary TRE-regulated reporter molecule. A vector like the gene

Essential Bacillus subtilis genes

DEFF Research Database (Denmark)

Kobayashi, K.; Ehrlich, S.D.; Albertini, A.

2003-01-01

To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximate to4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were...... predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related...... to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from...

Integrative characterization of germ cell-specific genes from mouse spermatocyte UniGene library

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Eddy Edward M

2007-07-01

Full Text Available Abstract Background The primary regulator of spermatogenesis, a highly ordered and tightly regulated developmental process, is an intrinsic genetic program involving male germ cell-specific genes. Results We analyzed the mouse spermatocyte UniGene library containing 2155 gene-oriented transcript clusters. We predict that 11% of these genes are testis-specific and systematically identified 24 authentic genes specifically and abundantly expressed in the testis via in silico and in vitro approaches. Northern blot analysis disclosed various transcript characteristics, such as expression level, size and the presence of isoform. Expression analysis revealed developmentally regulated and stage-specific expression patterns in all of the genes. We further analyzed the genes at the protein and cellular levels. Transfection assays performed using GC-2 cells provided information on the cellular characteristics of the gene products. In addition, antibodies were generated against proteins encoded by some of the genes to facilitate their identification and characterization in spermatogenic cells and sperm. Our data suggest that a number of the gene products are implicated in transcriptional regulation, nuclear integrity, sperm structure and motility, and fertilization. In particular, we found for the first time that Mm.333010, predicted to contain a trypsin-like serine protease domain, is a sperm acrosomal protein. Conclusion We identify 24 authentic genes with spermatogenic cell-specific expression, and provide comprehensive information about the genes. Our findings establish a new basis for future investigation into molecular mechanisms underlying male reproduction.

Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer.

Science.gov (United States)

Chiu, Yu-Chiao; Wang, Li-Ju; Hsiao, Tzu-Hung; Chuang, Eric Y; Chen, Yidong

2017-10-03

With the advances in high-throughput gene profiling technologies, a large volume of gene interaction maps has been constructed. A higher-level layer of gene-gene interaction, namely modulate gene interaction, is composed of gene pairs of which interaction strengths are modulated by (i.e., dependent on) the expression level of a key modulator gene. Systematic investigations into the modulation by estrogen receptor (ER), the best-known modulator gene, have revealed the functional and prognostic significance in breast cancer. However, a genome-wide identification of key modulator genes that may further unveil the landscape of modulated gene interaction is still lacking. We proposed a systematic workflow to screen for key modulators based on genome-wide gene expression profiles. We designed four modularity parameters to measure the ability of a putative modulator to perturb gene interaction networks. Applying the method to a dataset of 286 breast tumors, we comprehensively characterized the modularity parameters and identified a total of 973 key modulator genes. The modularity of these modulators was verified in three independent breast cancer datasets. ESR1, the encoding gene of ER, appeared in the list, and abundant novel modulators were illuminated. For instance, a prognostic predictor of breast cancer, SFRP1, was found the second modulator. Functional annotation analysis of the 973 modulators revealed involvements in ER-related cellular processes as well as immune- and tumor-associated functions. Here we present, as far as we know, the first comprehensive analysis of key modulator genes on a genome-wide scale. The validity of filtering parameters as well as the conservativity of modulators among cohorts were corroborated. Our data bring new insights into the modulated layer of gene-gene interaction and provide candidates for further biological investigations.

A new type of gene-disruption cassette with a rescue gene for Pichia pastoris.

Science.gov (United States)

Shibui, Tatsuro; Hara, Hiroyoshi

2017-09-01

Pichia pastoris has been used for the production of many recombinant proteins, and many useful mutant strains have been created. However, the efficiency of mutant isolation by gene-targeting is usually low and the procedure is difficult for those inexperienced in yeast genetics. In order to overcome these issues, we developed a new gene-disruption system with a rescue gene using an inducible Cre/mutant-loxP system. With only short homology regions, the gene-disruption cassette of the system replaces its target-gene locus containing a mutation with a compensatory rescue gene. As the cassette contains the AOX1 promoter-driven Cre gene, when targeted strains are grown on media containing methanol, the DNA fragment, i.e., the marker, rescue and Cre genes, between the mutant-loxP sequences in the cassette is excised, leaving only the remaining mutant-loxP sequence in the genome, and consequently a target gene-disrupted mutant can be isolated. The system was initially validated on ADE2 gene disruption, where the disruption can easily be detected by color-change of the colonies. Then, the system was applied for knocking-out URA3 and OCH1 genes, reported to be difficult to accomplish by conventional gene-targeting methods. All three gene-disruption cassettes with their rescue genes replaced their target genes, and the Cre/mutant-loxP system worked well to successfully isolate their knock-out mutants. This study identified a new gene-disruption system that could be used to effectively and strategically knock out genes of interest, especially whose deletion is detrimental to growth, without using special strains, e.g., deficient in nonhomologous end-joining, in P. pastoris. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1201-1208, 2017. © 2017 American Institute of Chemical Engineers.

A recently transferred cluster of bacterial genes in Trichomonas vaginalis - lateral gene transfer and the fate of acquired genes

Science.gov (United States)

2014-01-01

Background Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes. PMID:24898731

PENGUKURAN KUALITAS PERANGKAT LUNAK SISTEM INFORMASI HOTEL BERBASIS STANDARD ISO 9126

Directory of Open Access Journals (Sweden)

Asih Sutanti

2016-02-01

Full Text Available Penelitian ini bertujuan bagaimana mengukur perangkat lunak yang dilihat dari sudut pandang produk, mengukur kualitas perangkat  lunak Sistem Informasi Hotel yang memerlukan  alat bantu untuk mempermudah melakukan pengukuran kualitas software tersebut berdasarkan ISO 9126 yang sesuai dengan enam karakteristik dari model kualitas software/perangkat lunak yaitu Functionability, Reliability, usability, efesiency, maintainability dan portability. Faktor kualitas umum yang paling penting diurutkan dan ditambahkan ke sub-faktor dari ISO 9126. Sehingga pihak manajemen dalam pengukurannya lebih akurat dalam memperoleh informasi untuk menentukan keputusan strategis. Melalui pemrosesan data dari masukan pengguna terhadap tingkat preferensi faktor dan sub-faktor kualitas akan diperoleh bobot faktor kualitas dan bobot relatif sub-faktor kualitas. Perkalian kedua nilai tersebut akan menghasilkan bobot absolut yang kemudian dikalikan dengan penilaian kriteria aplikasi hotel dari pengguna. Hasil akhirnya berupa nilai kualitas total dari aplikasi perangkat lunak Sistem Informasi Hotel. Setelah dilakukan pengukuran dengan enam karakteristik Standart ISO 9126, diperoleh nilai  Sistem Informasi Hotel 13.25 yang merupakan hasil pengukuran kualitas sehingga aplikasi ini tidak masuk kategori standar ISO 9126 karena ada Karakteristik Portability yait u unsur Adaptability, dan Installability tidak terpenuhi.

Gene-based Association Approach Identify Genes Across Stress Traits in Fruit Flies

DEFF Research Database (Denmark)

Rohde, Palle Duun; Edwards, Stefan McKinnon; Sarup, Pernille Merete

Identification of genes explaining variation in quantitative traits or genetic risk factors of human diseases requires both good phenotypic- and genotypic data, but also efficient statistical methods. Genome-wide association studies may reveal association between phenotypic variation and variation...... approach grouping variants accordingly to gene position, thus lowering the number of statistical tests performed and increasing the probability of identifying genes with small to moderate effects. Using this approach we identify numerous genes associated with different types of stresses in Drosophila...... melanogaster, but also identify common genes that affects the stress traits....

Gene doping.

Science.gov (United States)

Haisma, H J; de Hon, O

2006-04-01

Together with the rapidly increasing knowledge on genetic therapies as a promising new branch of regular medicine, the issue has arisen whether these techniques might be abused in the field of sports. Previous experiences have shown that drugs that are still in the experimental phases of research may find their way into the athletic world. Both the World Anti-Doping Agency (WADA) and the International Olympic Committee (IOC) have expressed concerns about this possibility. As a result, the method of gene doping has been included in the list of prohibited classes of substances and prohibited methods. This review addresses the possible ways in which knowledge gained in the field of genetic therapies may be misused in elite sports. Many genes are readily available which may potentially have an effect on athletic performance. The sporting world will eventually be faced with the phenomena of gene doping to improve athletic performance. A combination of developing detection methods based on gene arrays or proteomics and a clear education program on the associated risks seems to be the most promising preventive method to counteract the possible application of gene doping.

Systematic study of association of four GABAergic genes: glutamic acid decarboxylase 1 gene, glutamic acid decarboxylase 2 gene, GABA(B) receptor 1 gene and GABA(A) receptor subunit beta2 gene, with schizophrenia using a universal DNA microarray.

Science.gov (United States)

Zhao, Xu; Qin, Shengying; Shi, Yongyong; Zhang, Aiping; Zhang, Jing; Bian, Li; Wan, Chunling; Feng, Guoyin; Gu, Niufan; Zhang, Guangqi; He, Guang; He, Lin

2007-07-01

Several studies have suggested the dysfunction of the GABAergic system as a risk factor in the pathogenesis of schizophrenia. In the present study, case-control association analysis was conducted in four GABAergic genes: two glutamic acid decarboxylase genes (GAD1 and GAD2), a GABA(A) receptor subunit beta2 gene (GABRB2) and a GABA(B) receptor 1 gene (GABBR1). Using a universal DNA microarray procedure we genotyped a total of 20 SNPs on the above four genes in a study involving 292 patients and 286 controls of Chinese descent. Statistically significant differences were observed in the allelic frequencies of the rs187269C/T polymorphism in the GABRB2 gene (P=0.0450, chi(2)=12.40, OR=1.65) and the -292A/C polymorphism in the GAD1 gene (P=0.0450, chi(2)=14.64 OR=1.77). In addition, using an electrophoretic mobility shift assay (EMSA), we discovered differences in the U251 nuclear protein binding to oligonucleotides representing the -292 SNP on the GAD1 gene, which suggests that the -292C allele has reduced transcription factor binding efficiency compared with the 292A allele. Using the multifactor-dimensionality reduction method (MDR), we found that the interactions among the rs187269C/T polymorphism in the GABRB2 gene, the -243A/G polymorphism in the GAD2 gene and the 27379C/T and 661C/T polymorphisms in the GAD1 gene revealed a significant association with schizophrenia (Pschizophrenia in the Chinese population.

Exploring the key genes and pathways in enchondromas using a gene expression microarray.

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Shi, Zhongju; Zhou, Hengxing; Pan, Bin; Lu, Lu; Kang, Yi; Liu, Lu; Wei, Zhijian; Feng, Shiqing

2017-07-04

Enchondromas are the most common primary benign osseous neoplasms that occur in the medullary bone; they can undergo malignant transformation into chondrosarcoma. However, enchondromas are always undetected in patients, and the molecular mechanism is unclear. To identify key genes and pathways associated with the occurrence and development of enchondromas, we downloaded the gene expression dataset GSE22855 and obtained the differentially expressed genes (DEGs) by analyzing high-throughput gene expression in enchondromas. In total, 635 genes were identified as DEGs. Of these, 225 genes (35.43%) were up-regulated, and the remaining 410 genes (64.57%) were down-regulated. We identified the predominant gene ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were significantly over-represented in the enchondromas samples compared with the control samples. Subsequently the top 10 core genes were identified from the protein-protein interaction (PPI) network. The enrichment analyses of the genes mainly involved in two significant modules showed that the DEGs were principally related to ribosomes, protein digestion and absorption, ECM-receptor interaction, focal adhesion, amoebiasis and the PI3K-Akt signaling pathway.Together, these data elucidate the molecular mechanisms underlying the occurrence and development of enchondromas and provide promising candidates for therapeutic intervention and prognostic evaluation. However, further experimental studies are needed to confirm these results.

Models of gene gain and gene loss for probabilistic reconstruction of gene content in the last universal common ancestor of life

OpenAIRE

Kannan, Lavanya; Li, Hua; Rubinstein, Boris; Mushegian, Arcady

2013-01-01

Background The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes, assign the probability that its ancestral gene was present in the genome of their last common ancestor. Results We have developed a family of models of gene gain and gene loss in evolution, and applied the maximum-likelihood approach that uses phylogenetic tree of prokaryotes...

Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks.

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Saik, Olga V; Demenkov, Pavel S; Ivanisenko, Timofey V; Bragina, Elena Yu; Freidin, Maxim B; Goncharova, Irina A; Dosenko, Victor E; Zolotareva, Olga I; Hofestaedt, Ralf; Lavrik, Inna N; Rogaev, Evgeny I; Ivanisenko, Vladimir A

2018-02-13

Hypertension and bronchial asthma are a major issue for people's health. As of 2014, approximately one billion adults, or ~ 22% of the world population, have had hypertension. As of 2011, 235-330 million people globally have been affected by asthma and approximately 250,000-345,000 people have died each year from the disease. The development of the effective treatment therapies against these diseases is complicated by their comorbidity features. This is often a major problem in diagnosis and their treatment. Hence, in this study the bioinformatical methodology for the analysis of the comorbidity of these two diseases have been developed. As such, the search for candidate genes related to the comorbid conditions of asthma and hypertension can help in elucidating the molecular mechanisms underlying the comorbid condition of these two diseases, and can also be useful for genotyping and identifying new drug targets. Using ANDSystem, the reconstruction and analysis of gene networks associated with asthma and hypertension was carried out. The gene network of asthma included 755 genes/proteins and 62,603 interactions, while the gene network of hypertension - 713 genes/proteins and 45,479 interactions. Two hundred and five genes/proteins and 9638 interactions were shared between asthma and hypertension. An approach for ranking genes implicated in the comorbid condition of two diseases was proposed. The approach is based on nine criteria for ranking genes by their importance, including standard methods of gene prioritization (Endeavor, ToppGene) as well as original criteria that take into account the characteristics of an associative gene network and the presence of known polymorphisms in the analysed genes. According to the proposed approach, the genes IL10, TLR4, and CAT had the highest priority in the development of comorbidity of these two diseases. Additionally, it was revealed that the list of top genes is enriched with apoptotic genes and genes involved in

Tumor targeted gene therapy

International Nuclear Information System (INIS)

Kang, Joo Hyun

2006-01-01

Knowledge of molecular mechanisms governing malignant transformation brings new opportunities for therapeutic intervention against cancer using novel approaches. One of them is gene therapy based on the transfer of genetic material to an organism with the aim of correcting a disease. The application of gene therapy to the cancer treatment had led to the development of new experimental approaches such as suicidal gene therapy, inhibition of oncogenes and restoration of tumor-suppressor genes. Suicidal gene therapy is based on the expression in tumor cells of a gene encoding an enzyme that converts a prodrug into a toxic product. Representative suicidal genes are Herpes simplex virus type 1 thymidine kinase (HSV1-tk) and cytosine deaminase (CD). Especially, physicians and scientists of nuclear medicine field take an interest in suicidal gene therapy because they can monitor the location and magnitude, and duration of expression of HSV1-tk and CD by PET scanner

PCR-based detection of gene transfer vectors: application to gene doping surveillance.

Science.gov (United States)

Perez, Irene C; Le Guiner, Caroline; Ni, Weiyi; Lyles, Jennifer; Moullier, Philippe; Snyder, Richard O

2013-12-01

Athletes who illicitly use drugs to enhance their athletic performance are at risk of being banned from sports competitions. Consequently, some athletes may seek new doping methods that they expect to be capable of circumventing detection. With advances in gene transfer vector design and therapeutic gene transfer, and demonstrations of safety and therapeutic benefit in humans, there is an increased probability of the pursuit of gene doping by athletes. In anticipation of the potential for gene doping, assays have been established to directly detect complementary DNA of genes that are top candidates for use in doping, as well as vector control elements. The development of molecular assays that are capable of exposing gene doping in sports can serve as a deterrent and may also identify athletes who have illicitly used gene transfer for performance enhancement. PCR-based methods to detect foreign DNA with high reliability, sensitivity, and specificity include TaqMan real-time PCR, nested PCR, and internal threshold control PCR.

Evolutionary genomics of plant genes encoding N-terminal-TM-C2 domain proteins and the similar FAM62 genes and synaptotagmin genes of metazoans

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Craxton Molly

2007-07-01

Full Text Available Abstract Background Synaptotagmin genes are found in animal genomes and are known to function in the nervous system. Genes with a similar domain architecture as well as sequence similarity to synaptotagmin C2 domains have also been found in plant genomes. The plant genes share an additional region of sequence similarity with a group of animal genes named FAM62. FAM62 genes also have a similar domain architecture. Little is known about the functions of the plant genes and animal FAM62 genes. Indeed, many members of the large and diverse Syt gene family await functional characterization. Understanding the evolutionary relationships among these genes will help to realize the full implications of functional studies and lead to improved genome annotation. Results I collected and compared plant Syt-like sequences from the primary nucleotide sequence databases at NCBI. The collection comprises six groups of plant genes conserved in embryophytes: NTMC2Type1 to NTMC2Type6. I collected and compared metazoan FAM62 sequences and identified some similar sequences from other eukaryotic lineages. I found evidence of RNA editing and alternative splicing. I compared the intron patterns of Syt genes. I also compared Rabphilin and Doc2 genes. Conclusion Genes encoding proteins with N-terminal-transmembrane-C2 domain architectures resembling synaptotagmins, are widespread in eukaryotes. A collection of these genes is presented here. The collection provides a resource for studies of intron evolution. I have classified the collection into homologous gene families according to distinctive patterns of sequence conservation and intron position. The evolutionary histories of these gene families are traceable through the appearance of family members in different eukaryotic lineages. Assuming an intron-rich eukaryotic ancestor, the conserved intron patterns distinctive of individual gene families, indicate independent origins of Syt, FAM62 and NTMC2 genes. Resemblances

Inferring Gene Regulatory Networks Using Conditional Regulation Pattern to Guide Candidate Genes.

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Fei Xiao

Full Text Available Combining path consistency (PC algorithms with conditional mutual information (CMI are widely used in reconstruction of gene regulatory networks. CMI has many advantages over Pearson correlation coefficient in measuring non-linear dependence to infer gene regulatory networks. It can also discriminate the direct regulations from indirect ones. However, it is still a challenge to select the conditional genes in an optimal way, which affects the performance and computation complexity of the PC algorithm. In this study, we develop a novel conditional mutual information-based algorithm, namely RPNI (Regulation Pattern based Network Inference, to infer gene regulatory networks. For conditional gene selection, we define the co-regulation pattern, indirect-regulation pattern and mixture-regulation pattern as three candidate patterns to guide the selection of candidate genes. To demonstrate the potential of our algorithm, we apply it to gene expression data from DREAM challenge. Experimental results show that RPNI outperforms existing conditional mutual information-based methods in both accuracy and time complexity for different sizes of gene samples. Furthermore, the robustness of our algorithm is demonstrated by noisy interference analysis using different types of noise.

A review for detecting gene-gene interactions using machine learning methods in genetic epidemiology.

Science.gov (United States)

Koo, Ching Lee; Liew, Mei Jing; Mohamad, Mohd Saberi; Salleh, Abdul Hakim Mohamed

2013-01-01

Recently, the greatest statistical computational challenge in genetic epidemiology is to identify and characterize the genes that interact with other genes and environment factors that bring the effect on complex multifactorial disease. These gene-gene interactions are also denoted as epitasis in which this phenomenon cannot be solved by traditional statistical method due to the high dimensionality of the data and the occurrence of multiple polymorphism. Hence, there are several machine learning methods to solve such problems by identifying such susceptibility gene which are neural networks (NNs), support vector machine (SVM), and random forests (RFs) in such common and multifactorial disease. This paper gives an overview on machine learning methods, describing the methodology of each machine learning methods and its application in detecting gene-gene and gene-environment interactions. Lastly, this paper discussed each machine learning method and presents the strengths and weaknesses of each machine learning method in detecting gene-gene interactions in complex human disease.

A Review for Detecting Gene-Gene Interactions Using Machine Learning Methods in Genetic Epidemiology

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Ching Lee Koo

2013-01-01

Full Text Available Recently, the greatest statistical computational challenge in genetic epidemiology is to identify and characterize the genes that interact with other genes and environment factors that bring the effect on complex multifactorial disease. These gene-gene interactions are also denoted as epitasis in which this phenomenon cannot be solved by traditional statistical method due to the high dimensionality of the data and the occurrence of multiple polymorphism. Hence, there are several machine learning methods to solve such problems by identifying such susceptibility gene which are neural networks (NNs, support vector machine (SVM, and random forests (RFs in such common and multifactorial disease. This paper gives an overview on machine learning methods, describing the methodology of each machine learning methods and its application in detecting gene-gene and gene-environment interactions. Lastly, this paper discussed each machine learning method and presents the strengths and weaknesses of each machine learning method in detecting gene-gene interactions in complex human disease.

Reference Gene Screening for Analyzing Gene Expression Across Goat Tissue

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Yu Zhang

2013-12-01

Full Text Available Real-time quantitative PCR (qRT-PCR is one of the important methods for investigating the changes in mRNA expression levels in cells and tissues. Selection of the proper reference genes is very important when calibrating the results of real-time quantitative PCR. Studies on the selection of reference genes in goat tissues are limited, despite the economic importance of their meat and dairy products. We used real-time quantitative PCR to detect the expression levels of eight reference gene candidates (18S, TBP, HMBS, YWHAZ, ACTB, HPRT1, GAPDH and EEF1A2 in ten tissues types sourced from Boer goats. The optimal reference gene combination was selected according to the results determined by geNorm, NormFinder and Bestkeeper software packages. The analyses showed that tissue is an important variability factor in genes expression stability. When all tissues were considered, 18S, TBP and HMBS is the optimal reference combination for calibrating quantitative PCR analysis of gene expression from goat tissues. Dividing data set by tissues, ACTB was the most stable in stomach, small intestine and ovary, 18S in heart and spleen, HMBS in uterus and lung, TBP in liver, HPRT1 in kidney and GAPDH in muscle. Overall, this study provided valuable information about the goat reference genes that can be used in order to perform a proper normalisation when relative quantification by qRT-PCR studies is undertaken.

Refining discordant gene trees.

Science.gov (United States)

Górecki, Pawel; Eulenstein, Oliver

2014-01-01

Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs. While these costs have provided credible results for binary rooted gene trees, corresponding cost definitions for non-binary unrooted gene trees, which are frequently occurring in practice, are challenged by biological realism. We propose a natural extension of the well-established costs for comparing unrooted and non-binary gene trees with rooted binary species trees using a binary refinement model. For the duplication cost we describe an efficient algorithm that is based on a linear time reduction and also computes an optimal rooted binary refinement of the given gene tree. Finally, we show that similar reductions lead to solutions for computing the deep coalescence and the Robinson-Foulds costs. Our binary refinement of Robinson-Foulds, gene duplication, and deep coalescence costs for unrooted and non-binary gene trees together with the linear time reductions provided here for computing these costs significantly extends the range of trees that can be incorporated into approaches dealing with discordance.

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.

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Marion Ouedraogo

Full Text Available BACKGROUND: There has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression of duplicated genes remains sparse. Identifying groups of duplicated genes in different genomes and characterizing their expression and function would therefore be of great interest to the research community. The 'Duplicated Genes Database' (DGD was developed for this purpose. METHODOLOGY: Nine species were included in the DGD. For each species, BLAST analyses were conducted on peptide sequences corresponding to the genes mapped on a same chromosome. Groups of duplicated genes were defined based on these pairwise BLAST comparisons and the genomic location of the genes. For each group, Pearson correlations between gene expression data and semantic similarities between functional GO annotations were also computed when the relevant information was available. CONCLUSIONS: The Duplicated Gene Database provides a list of co-localised and duplicated genes for several species with the available gene co-expression level and semantic similarity value of functional annotation. Adding these data to the groups of duplicated genes provides biological information that can prove useful to gene expression analyses. The Duplicated Gene Database can be freely accessed through the DGD website at http://dgd.genouest.org.

[Key effect genes responding to nerve injury identified by gene ontology and computer pattern recognition].

Science.gov (United States)

Pan, Qian; Peng, Jin; Zhou, Xue; Yang, Hao; Zhang, Wei

2012-07-01

In order to screen out important genes from large gene data of gene microarray after nerve injury, we combine gene ontology (GO) method and computer pattern recognition technology to find key genes responding to nerve injury, and then verify one of these screened-out genes. Data mining and gene ontology analysis of gene chip data GSE26350 was carried out through MATLAB software. Cd44 was selected from screened-out key gene molecular spectrum by comparing genes' different GO terms and positions on score map of principal component. Function interferences were employed to influence the normal binding of Cd44 and one of its ligands, chondroitin sulfate C (CSC), to observe neurite extension. Gene ontology analysis showed that the first genes on score map (marked by red *) mainly distributed in molecular transducer activity, receptor activity, protein binding et al molecular function GO terms. Cd44 is one of six effector protein genes, and attracted us with its function diversity. After adding different reagents into the medium to interfere the normal binding of CSC and Cd44, varying-degree remissions of CSC's inhibition on neurite extension were observed. CSC can inhibit neurite extension through binding Cd44 on the neuron membrane. This verifies that important genes in given physiological processes can be identified by gene ontology analysis of gene chip data.

Radiopharmaceuticals to monitor the expression of transferred genes in gene transfer therapy

International Nuclear Information System (INIS)

Wiebe, L. I.

1997-01-01

The development and application of radiopharmaceuticals has, in many instances, been based on the pharmacological properties of therapeutic agents. The molecular biology-biotechnology revolution has had an important impact on treatment of diseases, in part through the reduced toxicity of 'biologicals', in part because of their specificity for interaction at unique molecular sites and in part because of their selective delivery to the target site. Immunotherapeutic approaches include the use of monoclonal antibodies (MABs), MAB-fragments and chemotactic peptides. Such agents currently form the basis of both diagnostic and immunotherapeutic radiopharmaceuticals. More recently, gene transfer techniques have been advanced to the point that a new molecular approach, gene therapy, has become a reality. Gene therapy offers an opportunity to attack disease at its most fundamental level. The therapeutic mechanism is based on the expression of a specific gene or genes, the product of which will invoke immunological, receptor-based or enzyme-based therapeutic modalities. Several approaches to gene therapy of cancer have been envisioned, the most clinically-advanced concepts involving the introduction of genes that will encode for molecular targets nor normally found in healthy mammalian cells. A number of gene therapy clinical trials are based on the introduction of the Herpes simplex virus type-1 (HSV-1) gene that encodes for viral thymidine kinase (tk+). Once HSV-1 tk+ is expressed in the target (cancer) cell, therapy can be effected by the administration of a highly molecularly-targeted and systemically non-toxic antiviral drug such as ganciclovir. The development of radiodiagnostic imaging in gene therapy will be reviewed, using HSV-1 tk+ and radioiodinated IVFRU as a basis for development of the theme. Molecular targets that could be exploited in gene therapy, other than tk+, will be identified

Radiopharmaceuticals to monitor the expression of transferred genes in gene transfer therapy

Energy Technology Data Exchange (ETDEWEB)

Wiebe, L I [University of Alberta, Edmonton (Canada). Noujaim Institute for Pharmaceutical Oncology Research

1997-10-01

The development and application of radiopharmaceuticals has, in many instances, been based on the pharmacological properties of therapeutic agents. The molecular biology-biotechnology revolution has had an important impact on treatment of diseases, in part through the reduced toxicity of `biologicals`, in part because of their specificity for interaction at unique molecular sites and in part because of their selective delivery to the target site. Immunotherapeutic approaches include the use of monoclonal antibodies (MABs), MAB-fragments and chemotactic peptides. Such agents currently form the basis of both diagnostic and immunotherapeutic radiopharmaceuticals. More recently, gene transfer techniques have been advanced to the point that a new molecular approach, gene therapy, has become a reality. Gene therapy offers an opportunity to attack disease at its most fundamental level. The therapeutic mechanism is based on the expression of a specific gene or genes, the product of which will invoke immunological, receptor-based or enzyme-based therapeutic modalities. Several approaches to gene therapy of cancer have been envisioned, the most clinically-advanced concepts involving the introduction of genes that will encode for molecular targets nor normally found in healthy mammalian cells. A number of gene therapy clinical trials are based on the introduction of the Herpes simplex virus type-1 (HSV-1) gene that encodes for viral thymidine kinase (tk+). Once HSV-1 tk+ is expressed in the target (cancer) cell, therapy can be effected by the administration of a highly molecularly-targeted and systemically non-toxic antiviral drug such as ganciclovir. The development of radiodiagnostic imaging in gene therapy will be reviewed, using HSV-1 tk+ and radioiodinated IVFRU as a basis for development of the theme. Molecular targets that could be exploited in gene therapy, other than tk+, will be identified

Identification of a Transcriptionally Forward α Gene and Two υ Genes within the Pigeon (Columba livia) IgH Gene Locus.

Science.gov (United States)

Huang, Tian; Wang, Xifeng; Si, Run; Chi, Hao; Han, Binyue; Han, Haitang; Cao, Gengsheng; Zhao, Yaofeng

2018-06-01

Compared with mammals, the bird Ig genetic system relies on gene conversion to create an Ab repertoire, with inversion of the IgA-encoding gene and very few cases of Ig subclass diversification. Although gene conversion has been studied intensively, class-switch recombination, a mechanism by which the IgH C region is exchanged, has rarely been investigated in birds. In this study, based on the published genome of pigeon ( Columba livia ) and high-throughput transcriptome sequencing of immune-related tissues, we identified a transcriptionally forward α gene and found that the pigeon IgH gene locus is arranged as μ-α-υ1-υ2. In this article, we show that both DNA deletion and inversion may result from IgA and IgY class switching, and similar junction patterns were observed for both types of class-switch recombination. We also identified two subclasses of υ genes in pigeon, which share low sequence identity. Phylogenetic analysis suggests that divergence of the two pigeon υ genes occurred during the early stage of bird evolution. The data obtained in this study provide new insight into class-switch recombination and Ig gene evolution in birds. Copyright © 2018 by The American Association of Immunologists, Inc.

Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models.

Science.gov (United States)

Mahony, Shaun; McInerney, James O; Smith, Terry J; Golden, Aaron

2004-03-05

Many current gene prediction methods use only one model to represent protein-coding regions in a genome, and so are less likely to predict the location of genes that have an atypical sequence composition. It is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation. This work explores a new approach to gene-prediction, based on the Self-Organizing Map, which has the ability to automatically identify multiple gene models within a genome. The current implementation, named RescueNet, uses relative synonymous codon usage as the indicator of protein-coding potential. While its raw accuracy rate can be less than other methods, RescueNet consistently identifies some genes that other methods do not, and should therefore be of interest to gene-prediction software developers and genome annotation teams alike. RescueNet is recommended for use in conjunction with, or as a complement to, other gene prediction methods.

Evaluation of Appropriate Reference Genes for Gene Expression Normalization during Watermelon Fruit Development.

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Qiusheng Kong

Full Text Available Gene expression analysis in watermelon (Citrullus lanatus fruit has drawn considerable attention with the availability of genome sequences to understand the regulatory mechanism of fruit development and to improve its quality. Real-time quantitative reverse-transcription PCR (qRT-PCR is a routine technique for gene expression analysis. However, appropriate reference genes for transcript normalization in watermelon fruits have not been well characterized. The aim of this study was to evaluate the appropriateness of 12 genes for their potential use as reference genes in watermelon fruits. Expression variations of these genes were measured in 48 samples obtained from 12 successive developmental stages of parthenocarpic and fertilized fruits of two watermelon genotypes by using qRT-PCR analysis. Considering the effects of genotype, fruit setting method, and developmental stage, geNorm determined clathrin adaptor complex subunit (ClCAC, β-actin (ClACT, and alpha tubulin 5 (ClTUA5 as the multiple reference genes in watermelon fruit. Furthermore, ClCAC alone or together with SAND family protein (ClSAND was ranked as the single or two best reference genes by NormFinder. By using the top-ranked reference genes to normalize the transcript abundance of phytoene synthase (ClPSY1, a good correlation between lycopene accumulation and ClPSY1 expression pattern was observed in ripening watermelon fruit. These validated reference genes will facilitate the accurate measurement of gene expression in the studies on watermelon fruit biology.

Evaluation of Appropriate Reference Genes for Gene Expression Normalization during Watermelon Fruit Development.

Science.gov (United States)

Kong, Qiusheng; Yuan, Jingxian; Gao, Lingyun; Zhao, Liqiang; Cheng, Fei; Huang, Yuan; Bie, Zhilong

2015-01-01

Gene expression analysis in watermelon (Citrullus lanatus) fruit has drawn considerable attention with the availability of genome sequences to understand the regulatory mechanism of fruit development and to improve its quality. Real-time quantitative reverse-transcription PCR (qRT-PCR) is a routine technique for gene expression analysis. However, appropriate reference genes for transcript normalization in watermelon fruits have not been well characterized. The aim of this study was to evaluate the appropriateness of 12 genes for their potential use as reference genes in watermelon fruits. Expression variations of these genes were measured in 48 samples obtained from 12 successive developmental stages of parthenocarpic and fertilized fruits of two watermelon genotypes by using qRT-PCR analysis. Considering the effects of genotype, fruit setting method, and developmental stage, geNorm determined clathrin adaptor complex subunit (ClCAC), β-actin (ClACT), and alpha tubulin 5 (ClTUA5) as the multiple reference genes in watermelon fruit. Furthermore, ClCAC alone or together with SAND family protein (ClSAND) was ranked as the single or two best reference genes by NormFinder. By using the top-ranked reference genes to normalize the transcript abundance of phytoene synthase (ClPSY1), a good correlation between lycopene accumulation and ClPSY1 expression pattern was observed in ripening watermelon fruit. These validated reference genes will facilitate the accurate measurement of gene expression in the studies on watermelon fruit biology.

Gene composer: database software for protein construct design, codon engineering, and gene synthesis.

Science.gov (United States)

Lorimer, Don; Raymond, Amy; Walchli, John; Mixon, Mark; Barrow, Adrienne; Wallace, Ellen; Grice, Rena; Burgin, Alex; Stewart, Lance

2009-04-21

To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease

Gene Composer: database software for protein construct design, codon engineering, and gene synthesis

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Mixon Mark

2009-04-01

Full Text Available Abstract Background To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. Results An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. Conclusion We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene

Evaluation of suitable reference genes for gene expression studies in bovine muscular tissue

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Dunner Susana

2008-09-01

Full Text Available Abstract Background Real-time reverse transcriptase quantitative polymerase chain reaction (real-time RTqPCR is a technique used to measure mRNA species copy number as a way to determine key genes involved in different biological processes. However, the expression level of these key genes may vary among tissues or cells not only as a consequence of differential expression but also due to different factors, including choice of reference genes to normalize the expression levels of the target genes; thus the selection of reference genes is critical for expression studies. For this purpose, ten candidate reference genes were investigated in bovine muscular tissue. Results The value of stability of ten candidate reference genes included in three groups was estimated: the so called 'classical housekeeping' genes (18S, GAPDH and ACTB, a second set of genes used in expression studies conducted on other tissues (B2M, RPII, UBC and HMBS and a third set of novel genes (SF3A1, EEF1A2 and CASC3. Three different statistical algorithms were used to rank the genes by their stability measures as produced by geNorm, NormFinder and Bestkeeper. The three methods tend to agree on the most stably expressed genes and the least in muscular tissue. EEF1A2 and HMBS followed by SF3A1, ACTB, and CASC3 can be considered as stable reference genes, and B2M, RPII, UBC and GAPDH would not be appropriate. Although the rRNA-18S stability measure seems to be within the range of acceptance, its use is not recommended because its synthesis regulation is not representative of mRNA levels. Conclusion Based on geNorm algorithm, we propose the use of three genes SF3A1, EEF1A2 and HMBS as references for normalization of real-time RTqPCR in muscle expression studies.

Ageing genes

DEFF Research Database (Denmark)

Rattan, Suresh

2018-01-01

The idea of gerontogenes is in line with the evolutionary explanation of ageing as being an emergent phenomenon as a result of the imperfect maintenance and repair systems. Although evolutionary processes did not select for any specific ageing genes that restrict and determine the lifespan...... of an individual, the term ‘gerontogenes’ primarily refers to any genes that may seem to influence ageing and longevity, without being specifically selected for that role. Such genes can also be called ‘virtual gerontogenes’ by virtue of their indirect influence on the rate and process of ageing. More than 1000...... virtual gerontogenes have been associated with ageing and longevity in model organisms and humans. The ‘real’ genes, which do influence the essential lifespan of a species, and have been selected for in accordance with the evolutionary life history of the species, are known as the longevity assurance...

Correlating Information Contents of Gene Ontology Terms to Infer Semantic Similarity of Gene Products

Directory of Open Access Journals (Sweden)

Mingxin Gan

2014-01-01

Full Text Available Successful applications of the gene ontology to the inference of functional relationships between gene products in recent years have raised the need for computational methods to automatically calculate semantic similarity between gene products based on semantic similarity of gene ontology terms. Nevertheless, existing methods, though having been widely used in a variety of applications, may significantly overestimate semantic similarity between genes that are actually not functionally related, thereby yielding misleading results in applications. To overcome this limitation, we propose to represent a gene product as a vector that is composed of information contents of gene ontology terms annotated for the gene product, and we suggest calculating similarity between two gene products as the relatedness of their corresponding vectors using three measures: Pearson’s correlation coefficient, cosine similarity, and the Jaccard index. We focus on the biological process domain of the gene ontology and annotations of yeast proteins to study the effectiveness of the proposed measures. Results show that semantic similarity scores calculated using the proposed measures are more consistent with known biological knowledge than those derived using a list of existing methods, suggesting the effectiveness of our method in characterizing functional relationships between gene products.

Learning gene regulatory networks from gene expression data using weighted consensus

KAUST Repository

Fujii, Chisato; Kuwahara, Hiroyuki; Yu, Ge; Guo, Lili; Gao, Xin

2016-01-01

An accurate determination of the network structure of gene regulatory systems from high-throughput gene expression data is an essential yet challenging step in studying how the expression of endogenous genes is controlled through a complex interaction of gene products and DNA. While numerous methods have been proposed to infer the structure of gene regulatory networks, none of them seem to work consistently over different data sets with high accuracy. A recent study to compare gene network inference methods showed that an average-ranking-based consensus method consistently performs well under various settings. Here, we propose a linear programming-based consensus method for the inference of gene regulatory networks. Unlike the average-ranking-based one, which treats the contribution of each individual method equally, our new consensus method assigns a weight to each method based on its credibility. As a case study, we applied the proposed consensus method on synthetic and real microarray data sets, and compared its performance to that of the average-ranking-based consensus and individual inference methods. Our results show that our weighted consensus method achieves superior performance over the unweighted one, suggesting that assigning weights to different individual methods rather than giving them equal weights improves the accuracy. © 2016 Elsevier B.V.

Learning gene regulatory networks from gene expression data using weighted consensus

KAUST Repository

Fujii, Chisato

2016-08-25

An accurate determination of the network structure of gene regulatory systems from high-throughput gene expression data is an essential yet challenging step in studying how the expression of endogenous genes is controlled through a complex interaction of gene products and DNA. While numerous methods have been proposed to infer the structure of gene regulatory networks, none of them seem to work consistently over different data sets with high accuracy. A recent study to compare gene network inference methods showed that an average-ranking-based consensus method consistently performs well under various settings. Here, we propose a linear programming-based consensus method for the inference of gene regulatory networks. Unlike the average-ranking-based one, which treats the contribution of each individual method equally, our new consensus method assigns a weight to each method based on its credibility. As a case study, we applied the proposed consensus method on synthetic and real microarray data sets, and compared its performance to that of the average-ranking-based consensus and individual inference methods. Our results show that our weighted consensus method achieves superior performance over the unweighted one, suggesting that assigning weights to different individual methods rather than giving them equal weights improves the accuracy. © 2016 Elsevier B.V.

LINE FUSION GENES: a database of LINE expression in human genes

Directory of Open Access Journals (Sweden)

Park Hong-Seog

2006-06-01

Full Text Available Abstract Background Long Interspersed Nuclear Elements (LINEs are the most abundant retrotransposons in humans. About 79% of human genes are estimated to contain at least one segment of LINE per transcription unit. Recent studies have shown that LINE elements can affect protein sequences, splicing patterns and expression of human genes. Description We have developed a database, LINE FUSION GENES, for elucidating LINE expression throughout the human gene database. We searched the 28,171 genes listed in the NCBI database for LINE elements and analyzed their structures and expression patterns. The results show that the mRNA sequences of 1,329 genes were affected by LINE expression. The LINE expression types were classified on the basis of LINEs in the 5' UTR, exon or 3' UTR sequences of the mRNAs. Our database provides further information, such as the tissue distribution and chromosomal location of the genes, and the domain structure that is changed by LINE integration. We have linked all the accession numbers to the NCBI data bank to provide mRNA sequences for subsequent users. Conclusion We believe that our work will interest genome scientists and might help them to gain insight into the implications of LINE expression for human evolution and disease. Availability http://www.primate.or.kr/line

A Partial Least Square Approach for Modeling Gene-gene and Gene-environment Interactions When Multiple Markers Are Genotyped

Science.gov (United States)

Wang, Tao; Ho, Gloria; Ye, Kenny; Strickler, Howard; Elston, Robert C.

2008-01-01

Genetic association studies achieve an unprecedented level of resolution in mapping disease genes by genotyping dense SNPs in a gene region. Meanwhile, these studies require new powerful statistical tools that can optimally handle a large amount of information provided by genotype data. A question that arises is how to model interactions between two genes. Simply modeling all possible interactions between the SNPs in two gene regions is not desirable because a greatly increased number of degrees of freedom can be involved in the test statistic. We introduce an approach to reduce the genotype dimension in modeling interactions. The genotype compression of this approach is built upon the information on both the trait and the cross-locus gametic disequilibrium between SNPs in two interacting genes, in such a way as to parsimoniously model the interactions without loss of useful information in the process of dimension reduction. As a result, it improves power to detect association in the presence of gene-gene interactions. This approach can be similarly applied for modeling gene-environment interactions. We compare this method with other approaches: the corresponding test without modeling any interaction, that based on a saturated interaction model, that based on principal component analysis, and that based on Tukey’s 1-df model. Our simulations suggest that this new approach has superior power to that of the other methods. In an application to endometrial cancer case-control data from the Women’s Health Initiative (WHI), this approach detected AKT1 and AKT2 as being significantly associated with endometrial cancer susceptibility by taking into account their interactions with BMI. PMID:18615621

A partial least-square approach for modeling gene-gene and gene-environment interactions when multiple markers are genotyped.

Science.gov (United States)

Wang, Tao; Ho, Gloria; Ye, Kenny; Strickler, Howard; Elston, Robert C

2009-01-01

Genetic association studies achieve an unprecedented level of resolution in mapping disease genes by genotyping dense single nucleotype polymorphisms (SNPs) in a gene region. Meanwhile, these studies require new powerful statistical tools that can optimally handle a large amount of information provided by genotype data. A question that arises is how to model interactions between two genes. Simply modeling all possible interactions between the SNPs in two gene regions is not desirable because a greatly increased number of degrees of freedom can be involved in the test statistic. We introduce an approach to reduce the genotype dimension in modeling interactions. The genotype compression of this approach is built upon the information on both the trait and the cross-locus gametic disequilibrium between SNPs in two interacting genes, in such a way as to parsimoniously model the interactions without loss of useful information in the process of dimension reduction. As a result, it improves power to detect association in the presence of gene-gene interactions. This approach can be similarly applied for modeling gene-environment interactions. We compare this method with other approaches, the corresponding test without modeling any interaction, that based on a saturated interaction model, that based on principal component analysis, and that based on Tukey's one-degree-of-freedom model. Our simulations suggest that this new approach has superior power to that of the other methods. In an application to endometrial cancer case-control data from the Women's Health Initiative, this approach detected AKT1 and AKT2 as being significantly associated with endometrial cancer susceptibility by taking into account their interactions with body mass index.

Chuck Jones lahkus, tema kangelased elavad edasi / Neeme Korv

Index Scriptorium Estoniae

Korv, Neeme, 1974-

2002-01-01

Suri Chuck Jones (1912-2002), kuulus USA animafilmirežissöör, kelle animasari "Tom & Jerry" on praegugi Eestis väga populaarne. Ta on loonud enam kui 300 animafilmi, saanud 3 Oscarit ning 1996. aastal ka elutöö Oscari. Eesti lapsed nägid nõukogude ajal esmakordselt Chuck Jones'i loomingut Raivo Järvi lastesaadetes "Laupäeval koos isaga"

Iraak sihikul : veriste rusude kohal kerkib teistsugune riik / Heiki Suurkask

Index Scriptorium Estoniae

Suurkask, Heiki, 1972-

2006-01-01

Iraagis kujunenud olukorrast. Autori väitel ei usu enam peaaegu keegi võimalusse purustada mässulisi Iraagis sõjalise jõuga, vastupanuvõitlus USA okupatsiooni vastu on laienenud kahe kogukonna vaheliseks verevalamiseks. Hukkunute arvust. Vt. samas: Shiiitide sõjakas juht al-Sadri suurendab Iraagis oma võimu; Rahukolle Kurdistan ei rutta iseseisvuma. Lisad: Sunniitide vägivaldne kolmnurk; Iraagi naabrid kaitsevad kiivalt oma huve

Problem Etnisitas India Dalam Cerita Pendek Malaysia

OpenAIRE

M. Shoim Anwar

2015-01-01

Karya sastra adalah dokumen kemanusiaan dan kebudayaan. Kumpulan cerita pendek Menara 7 (1998), terutama enam cerpen yang ditulis oleh pengarang Malaysia beretnis India, memberi gambaran problem kehidupan etnis India di Malaysia. Dengan meminjam teori etnisitas sebagai landasan, tulisan ini bertujuan mengungkap problem etnisitas India di Malaysia. Problem etnis India terkait dengan kemiskinan, pendidikan, gender, religi, budaya, dan persatuan. Keberadaan etnis India di Malaysia secara histori...

Posisi Amerika Serikat dalam Penyelesaian Konflik Palestina-Israel 1

OpenAIRE

Paat, Vera

2013-01-01

Konflik Palestina-Israel boleh jadi merupakan konflik yang memakan waktu panjang setelah Perang Salib yang pernah terjadi antara dunia Timur dan Barat di sekitar abad keduabelas. Konflik yang telah berlangsung enam puluhan tahun ini menjadi konflik cukup akut yang menyita perhatian masyarakat dunia. Penyelesaian konflikPalestina-Israel, semakin menunjukkan bahwa perdamaian Palestina-Israel memang sulit diwujudkan. Pasalnya, akhir 2008 yang diprediksi dunia Internasional (dalam hal ini Amerika...

Visualisasi Luas Daerah Pengurasan Sumur Minyak

OpenAIRE

Sofyan, Herry

2011-01-01

Indonesia merupakan salah satu Negara penghasil minyak dan gas, Pada pertengahan dekade 1980-an, para ahli anggota Ikatan Ahli Geologi Indonesia (IAGI) menyatakan bahwa di wilayah kedaulatan Indonesia terdapat enam puluh cekungan geologi yang secara potensial mengandung sumber daya hidrokarbon. Cekungan geologi yang ternyata mengandung cadangan minyak dan gas yang dapat diproduksikan secara komersial, hingga kini berjumlah 12 cekungan, di antaranya cekungan Sumatera Utara, Sumatera Tengah, Su...

Klasifikasi Atribut Hotel Penentu Kepuasan Di Midtown Hotel Surabaya

OpenAIRE

Prajogo, Liliany; Kusnin, Ronny; Kristanti, Monika

2017-01-01

Penelitian ini dilakukan untuk mengetahui klasifikasi atribut kepuasan di Midtown Hotel Surabaya, yaitu hotel chain domestik yang berkembang di Indonesia. Data penelitian diambil dari komentar TripAdvisor sebanyak 132 komentar. Dengan melakukan teknik content analysis, penulis mengelompokan komentar menjadi 16 atribut hotel penentu kepuasan yang dapat dikategorikan menjadi enam kategori, yaitu location, physical hotel setting, value, food, service, dan room. Teknik analisa kuantitatif yang di...

Kremlis tõstab pead tsaristlik võimuideoloogia / John Hulsman ; interv. Kaarel Kaas

Index Scriptorium Estoniae

Hulsman, John

2004-01-01

USA uurimiskeskuse Heritage Foundation analüütiku hinnangul võtab Venemaa üha enam tsaaririigi näo ning Washington vajab Moskvaga äripartnerlusega sarnanevat suhet. Nn saja kirjast, sellega kaasneda võivatest muutustest, Ameerika varasemast Vene-poliitikast. Vt. samas: "Saja kiri" lööb häirekella Vene pärast; Kommenteerib Strateegiliste ja Rahvusvaheliste uuringute Keskuse vanemanalüütik Simon Serfaty.

Perancangan Buku Biografi Mengenai Kehidupan Piping Irawan Surfer Di Pantai Canggu, Bali

OpenAIRE

Subagio, Veronica Herlina; Negara, I Nengah Sudika; Aryanto, Hendro

2017-01-01

Indonesia merupakan negeri yang memiliki pantai-pantai yang indah, dan memiliki musim yang baik sehingga pantai yang terdapat di Indonesia dapat dipergunakan untuk surfing selama enam bulan. Sehingga Indonesia seharusnya bangga ketika memiliki banyak orang yang berbakat menjadi surfer. Tetapi Kenyataannya surfer yang ada di Indonesia dipandang sebelah mata oleh masyarakat Indonesia ini sendiri. Mereka menganggap bahwa surfer merupakan seorang pengangguran yang hanya menghabisakan waktu di pan...

Peningkatan Kemampuan Memahami Bacaan Bahasa Arab Melalui Teknik Pembelajaran SQ4-R (Penelitian Tindakan pada Mahasiswa Pendidikan Bahasa Arab Jurusan Tarbiyah STAIN Kendari)

OpenAIRE

Batmang, Batmang

2013-01-01

Tujuan dari penelitian ini adalah untuk meningkatkan kemampuan siswa pada semester ke enam Departemen Arab Bahasa Pendidikan Akademik 2012-2013 dalam memahami teks-teks Arab dengan penerapan teknik pembelajaran SQ4-R. Penelitian ini merupakan penelitian tindakan dan pendekatan kualitatif. Metode untuk mengumpulkan data yang: observasi, wawancara, portofolio, membaca tes pemahaman, dan catatan lapangan. Data dianalisis secara kualitatif dengan mengurangi, menyajikan dan dengan menarik kesimpul...

Keragaman Jenis Salak Bangkalan {Salacca Zalacca (Gaertner) Voss} Menggunakan Penanda Morfologi Dan Analisis Isozim

OpenAIRE

Ariestin, Yuliamita; Kuswanto, Kuswanto; Ashari, Sumeru

2015-01-01

Kabupaten Bangkalan merupakan salah satu daerah yang memiliki potensi cukup besar dalam sektor pertanian khususnya salak. Keragaman tanaman salak yang ada di Kabupaten Bangkalan perlu diidentifikasi untuk melihat sifat dan keragaman genetik. Untuk tujuan pemuliaan tanaman salak, telah dilakukan penelitian identifikasi tanaman pada bulan Februari sampai bulan Maret 2014. Berdasarkan hasil survey dan wawancara dengan petani telah ditemukan enam jenis tanaman salak antara lain salak Apel, Bunter...

Perbandingan Efektivitas Sistem Temu Balik Informasi Menggunakan Google Scholar dengan Proquest Medical Library

OpenAIRE

Ajjronisa, Sudia

2012-01-01

Penelitian ini bertujuan untuk membandingkan efektivitas sistem temu balik informasi menggunakan Google Scholar dengan Proquest Medical Library untuk 25 istilah pencarian yang tergabung dari enam subjek Ilmu Kesehatan antara lain (1) Kanker (Cancer); (2) Ilmu Penyakit Dalam (Internal Medicine); (3) Ilmu Penyakit Bayi dan Anak (Pediatrics); (4) Ilmu Kedokteran Jiwa (Psychiatry); (5) Radiologi (Radiology), dan (6) Ilmu Spesialis Bedah (Specialties, Surgical). Metode penelitian yang digunaka...

An intronic microRNA silences genes that are functionally antagonistic to its host gene.

Science.gov (United States)

Barik, Sailen

2008-09-01

MicroRNAs (miRNAs) are short noncoding RNAs that down-regulate gene expression by silencing specific target mRNAs. While many miRNAs are transcribed from their own genes, nearly half map within introns of 'host' genes, the significance of which remains unclear. We report that transcriptional activation of apoptosis-associated tyrosine kinase (AATK), essential for neuronal differentiation, also generates miR-338 from an AATK gene intron that silences a family of mRNAs whose protein products are negative regulators of neuronal differentiation. We conclude that an intronic miRNA, transcribed together with the host gene mRNA, may serve the interest of its host gene by silencing a cohort of genes that are functionally antagonistic to the host gene itself.

Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies.

Science.gov (United States)

Schaid, Daniel J; Sinnwell, Jason P; Jenkins, Gregory D; McDonnell, Shannon K; Ingle, James N; Kubo, Michiaki; Goss, Paul E; Costantino, Joseph P; Wickerham, D Lawrence; Weinshilboum, Richard M

2012-01-01

Gene-set analyses have been widely used in gene expression studies, and some of the developed methods have been extended to genome wide association studies (GWAS). Yet, complications due to linkage disequilibrium (LD) among single nucleotide polymorphisms (SNPs), and variable numbers of SNPs per gene and genes per gene-set, have plagued current approaches, often leading to ad hoc "fixes." To overcome some of the current limitations, we developed a general approach to scan GWAS SNP data for both gene-level and gene-set analyses, building on score statistics for generalized linear models, and taking advantage of the directed acyclic graph structure of the gene ontology when creating gene-sets. However, other types of gene-set structures can be used, such as the popular Kyoto Encyclopedia of Genes and Genomes (KEGG). Our approach combines SNPs into genes, and genes into gene-sets, but assures that positive and negative effects of genes on a trait do not cancel. To control for multiple testing of many gene-sets, we use an efficient computational strategy that accounts for LD and provides accurate step-down adjusted P-values for each gene-set. Application of our methods to two different GWAS provide guidance on the potential strengths and weaknesses of our proposed gene-set analyses. © 2011 Wiley Periodicals, Inc.

With Reference to Reference Genes: A Systematic Review of Endogenous Controls in Gene Expression Studies.

Science.gov (United States)

Chapman, Joanne R; Waldenström, Jonas

2015-01-01

The choice of reference genes that are stably expressed amongst treatment groups is a crucial step in real-time quantitative PCR gene expression studies. Recent guidelines have specified that a minimum of two validated reference genes should be used for normalisation. However, a quantitative review of the literature showed that the average number of reference genes used across all studies was 1.2. Thus, the vast majority of studies continue to use a single gene, with β-actin (ACTB) and/or glyceraldehyde 3-phosphate dehydrogenase (GAPDH) being commonly selected in studies of vertebrate gene expression. Few studies (15%) tested a panel of potential reference genes for stability of expression before using them to normalise data. Amongst studies specifically testing reference gene stability, few found ACTB or GAPDH to be optimal, whereby these genes were significantly less likely to be chosen when larger panels of potential reference genes were screened. Fewer reference genes were tested for stability in non-model organisms, presumably owing to a dearth of available primers in less well characterised species. Furthermore, the experimental conditions under which real-time quantitative PCR analyses were conducted had a large influence on the choice of reference genes, whereby different studies of rat brain tissue showed different reference genes to be the most stable. These results highlight the importance of validating the choice of normalising reference genes before conducting gene expression studies.

Good genes, complementary genes and human mate preferences.

Science.gov (United States)

Roberts, S Craig; Little, Anthony C

2008-09-01

The past decade has witnessed a rapidly growing interest in the biological basis of human mate choice. Here we review recent studies that demonstrate preferences for traits which might reveal genetic quality to prospective mates, with potential but still largely unknown influence on offspring fitness. These include studies assessing visual, olfactory and auditory preferences for potential good-gene indicator traits, such as dominance or bilateral symmetry. Individual differences in these robust preferences mainly arise through within and between individual variation in condition and reproductive status. Another set of studies have revealed preferences for traits indicating complementary genes, focussing on discrimination of dissimilarity at genes in the major histocompatibility complex (MHC). As in animal studies, we are only just beginning to understand how preferences for specific traits vary and inter-relate, how consideration of good and compatible genes can lead to substantial variability in individual mate choice decisions and how preferences expressed in one sensory modality may reflect those in another. Humans may be an ideal model species in which to explore these interesting complexities.

Gene expression studies of reference genes for quantitative real-time PCR: an overview in insects.

Science.gov (United States)

Shakeel, Muhammad; Rodriguez, Alicia; Tahir, Urfa Bin; Jin, Fengliang

2018-02-01

Whenever gene expression is being examined, it is essential that a normalization process is carried out to eliminate non-biological variations. The use of reference genes, such as glyceraldehyde-3-phosphate dehydrogenase, actin, and ribosomal protein genes, is the usual method of choice for normalizing gene expression. Although reference genes are used to normalize target gene expression, a major problem is that the stability of these genes differs among tissues, developmental stages, species, and responses to abiotic factors. Therefore, the use and validation of multiple reference genes are required. This review discusses the reasons that why RT-qPCR has become the preferred method for validating results of gene expression profiles, the use of specific and non-specific dyes and the importance of use of primers and probes for qPCR as well as to discuss several statistical algorithms developed to help the validation of potential reference genes. The conflicts arising in the use of classical reference genes in gene normalization and their replacement with novel references are also discussed by citing the high stability and low stability of classical and novel reference genes under various biotic and abiotic experimental conditions by employing various methods applied for the reference genes amplification.

Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data

Directory of Open Access Journals (Sweden)

Tintle Nathan L

2012-08-01

Full Text Available Abstract Background Statistical analyses of whole genome expression data require functional information about genes in order to yield meaningful biological conclusions. The Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG are common sources of functionally grouped gene sets. For bacteria, the SEED and MicrobesOnline provide alternative, complementary sources of gene sets. To date, no comprehensive evaluation of the data obtained from these resources has been performed. Results We define a series of gene set consistency metrics directly related to the most common classes of statistical analyses for gene expression data, and then perform a comprehensive analysis of 3581 Affymetrix® gene expression arrays across 17 diverse bacteria. We find that gene sets obtained from GO and KEGG demonstrate lower consistency than those obtained from the SEED and MicrobesOnline, regardless of gene set size. Conclusions Despite the widespread use of GO and KEGG gene sets in bacterial gene expression data analysis, the SEED and MicrobesOnline provide more consistent sets for a wide variety of statistical analyses. Increased use of the SEED and MicrobesOnline gene sets in the analysis of bacterial gene expression data may improve statistical power and utility of expression data.

Comprehensive analysis of gene expression patterns of hedgehog-related genes

Directory of Open Access Journals (Sweden)

Baillie David

2006-10-01