ORCID Profile
0000-0001-9417-8894
Current Organisations
Envirola Company
,
American University of Iraq
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Publisher: Springer Science and Business Media LLC
Date: 28-01-1999
Abstract: The yeast gene, GRC5 (growth control), is a member of the highly conserved QM gene family, the human member of which has been associated with the suppression of Wilms' tumor. GRC5 encodes ribosomal protein L10, which is thought to play a regulatory role in the translational control of gene expression. A revertant screen identified four spontaneous revertants of the mutant grc5-1ts allele. Genetic and phenotypic analysis showed that these represent one gene, NMD3, and that the interaction of NMD3 and GRC5 is gene-specific. NMD3 was previously identified as a component of the nonsense-mediated mRNA decay pathway. The point mutations within NMD3 reported here may define a domain important for the functional interaction of Grc5p and Nmd3p.
Publisher: Public Library of Science (PLoS)
Date: 08-10-2012
Publisher: IEEE
Date: 2013
Publisher: Springer Science and Business Media LLC
Date: 28-04-2006
DOI: 10.1038/NG1789
Abstract: Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.
Publisher: Springer Science and Business Media LLC
Date: 20-12-2013
DOI: 10.1007/S10544-013-9832-2
Abstract: 2D imaging of biochips is particularly interesting for multiplex biosensing. Resonant properties allow label-free detection using the change of refractive index at the chip surface. We demonstrate a new principle of Scanning Of Resonance on Chip by Imaging (SORCI) based on spatial profiles of nanopatterns of resonant waveguide gratings (RWGs) and its embodiment in a fluidic chip for real-time biological studies. This scheme allows multiplexing of the resonance itself by providing nanopattern sensing areas in a bioarray format. Through several chip designs we discuss resonance spatial profiles, dispersion and electric field distribution for optimal light-matter interaction with biological species of different sizes. Fluidic integration is carried out with a black anodized aluminum chamber, advantageous in term of mechanical stability, multiple uses of the chip, temperature control and low optical background. Real-time hybridization experiments are illustrated by SNP (Single Nucleotide Polymorphism) detection in gyrase A of E. coli K12, observed in evolution studies of resistance to the antibiotic ciprofloxacin. We choose a 100 base pairs (bp) DNA target (~30 kDa) including the codon of interest and demonstrate the high specificity of our technique for probes and targets with close affinity constants. This work validates the safe applicability of our unique combination of RWGs and simple instrumentation for real-time biosensing with sensitivity in buffer solution of ~10 pg/mm². Paralleling the success of RWGs sensing for cells sensing, our work opens new avenues for a large number of biological studies.
Publisher: Bentham Science Publishers Ltd.
Date: 10-04-2001
Abstract: Phage surface display of cDNA libraries facilitates cloning, expression and rapid selection of functional gene products physically linked to their genetic information through gene product-ligand interactions. Efficient screening technologies based on selective enrichment of clones expressing desired gene products allows, within a short time, the isolation of all ligand-specific clones that are present in a library. Manual identification of clones by restriction analysis and random sequencing is unlike to be successful for the isolation of gene products derived from rare mRNA species resulting from selection of the libraries using polyvalent ligands like serum from patients. Here we describe rapid handling of large numbers of in idual clones selected from molecular libraries displayed on phage surface using the power of robotics-based high throughput screening. The potential of the combination of cDNA-phage surface display, with selection for specific interactions by functional screening and robotic technology is illustrated by the isolation of more sequences potentially encoding IgE-binding proteins than postulated from Western blot analyses using extracts derived from raw material of complex allergenic sources. The subsequent application of functional enrichment and robotics-based screening will facilitate the rapid generation of information about the repertoire of protein structures involved in allergic diseases.
Publisher: MDPI AG
Date: 26-08-2016
DOI: 10.3390/S16091369
Publisher: Bentham Science Publishers Ltd.
Date: 03-2003
Abstract: We describe a high-throughput, quantitative technology for fast identification of all different clones present in selectively enriched phage surface-displayed cDNA libraries. The strategy is based on a combination of phage display and high-density arrays. To demonstrate the utility of the method cDNAs of Aspergillus fumigatus cloned into phagemid pJuFo were expressed on the tip of filamentous M13 phage and affinity-selected on solid phase-immobilized serum IgE from allergic patients. Enriched phagemid libraries were lified in bacteria, plated and arrayed into 384-well microtitre plates by robotic colony picking. cDNA inserts were lified by high-throughput PCR and gridded onto high-density filter membranes. Filters were iteratively probed with randomly-sequenced inserts until all clones were identified. Eighty-one different sequences encoding IgE-binding proteins likely to cover a large part of the allergen repertoire of the mould were found. This approach represents a widely applicable method for rapid high-throughput identification of all in idual cDNAs present in selectively enriched libraries.
Publisher: Springer Science and Business Media LLC
Date: 2006
Publisher: Cold Spring Harbor Laboratory
Date: 02-2008
DOI: 10.1101/PDB.PROT4938
Abstract: In terms of cost per measurement, the use of DNA microarrays for comprehensive and quantitative expression measurements is vastly superior to other methods such as Northern blotting or quantitative reverse transcriptase polymerase chain reaction (QRT-PCR). However, the output values of DNA microarrays are not always highly reliable or accurate compared with other techniques, and the output data sometimes consist of measurements of relative expression (treated s le vs. untreated) rather than absolute expression values as desired. In effect, some measurements from some laboratories do not represent absolute expression values (such as the number of transcripts) and as such are experimentally deficient. To address the problem that some microarray data sets fail to reflect the number of mRNA molecules sufficiently in a given s le (i.e., fail to provide absolute expression levels), additional methods are required. The procedure described here provides a new method for converting microarray data to absolute expression values with the use of external data such as expressed sequence tags (ESTs) and cap analysis of gene expression (CAGE) tags.
Publisher: Elsevier BV
Date: 08-2012
Publisher: Elsevier BV
Date: 06-2012
Publisher: Figshare
Date: 2011
Publisher: Wiley
Date: 15-01-2004
Publisher: Cold Spring Harbor Laboratory
Date: 02-2008
DOI: 10.1101/PDB.PROT4937
Abstract: In terms of cost per measurement, the use of DNA microarrays for comprehensive and quantitative expression measurements is vastly superior to other methods such as Northern blotting or quantitative reverse transcriptase polymerase chain reaction (QRT-PCR). However, the output values of DNA microarrays are not always highly reliable or accurate compared with other techniques, and the output data sometimes consist of measurements of relative expression (treated s le vs. untreated) rather than absolute expression values as desired. In effect, some measurements from some laboratories do not represent absolute expression values (such as the number of transcripts) and as such are experimentally deficient. This protocol addresses one problem in some microarray data: the absence of accurate measurements. Spot reliability evaluation score for DNA microarrays (SRED) offers a reliability value for each spot in the microarray. SRED does not require an entire microarray to assess the reliability, but rather analyzes the reliability of in idual spots of the microarray. The calculation of a reliability index can be used for different microarray systems, which facilitates the analysis of multiple microarray data sets from different experimental platforms.
Publisher: AIP Publishing
Date: 09-2010
DOI: 10.1063/1.3487796
Abstract: We report a simple, low-cost, rapid, and mask-free method to fabricate two-dimensional (2D) and three-dimensional (3D) microfluidic chip for biological analysis researches. In this fabrication process, a laser system is used to cut through paper to form intricate patterns and differently configured channels for specific purposes. Bonded with cyanoacrylate-based resin, the prepared paper sheet is sandwiched between glass slides (hydrophilic) or polymer-based plates (hydrophobic) to obtain a multilayer structure. In order to examine the chip’s biocompatibility and applicability, protein concentration was measured while DNA capillary electrophoresis was carried out, and both of them show positive results. With the utilization of direct laser cutting and one-step gas-sacrificing techniques, the whole fabrication processes for complicated 2D and 3D microfluidic devices are shorten into several minutes which make it a good alternative of poly(dimethylsiloxane) microfluidic chips used in biological analysis researches.
Publisher: Figshare
Date: 2011
Publisher: Figshare
Date: 2011
Publisher: Wiley
Date: 05-2004
Publisher: Elsevier BV
Date: 02-2016
DOI: 10.1016/J.GENE.2015.10.031
Abstract: Environmental studies are primarily done by culturing isolated microorganisms or by lifying and sequencing conserved genes. Difficulties understanding the complexity of large numbers of various microorganisms in an environment led to the development of techniques to enrich specific microorganisms for upstream analysis, ultimately leading to single-cell isolation and analyses. We discuss the significance of single-cell technologies in omics studies with focus on metagenomics and metatranscriptomics. We propose that by reducing s le heterogeneity using single-cell genomics, metaomic studies can be simplified.
Publisher: Figshare
Date: 2011
Publisher: S. Karger AG
Date: 2001
DOI: 10.1159/000053664
Abstract: i Background: /i Complex allergenic sources such as moulds, foods and mites contain complex panels of IgE-binding molecules which need to be cloned, produced and characterized in order to mimic the entire allergenicity of whole extracts reconstituted by mixing single standardized recombinant allergens. i Methods: /i Phage surface display of cDNA libraries selectively enriched for allergen-expressing clones using IgE from allergic patients allows rapid isolation of large panels of allergens. For the characterization of all different clones present in enriched cDNA libraries in a fast and cost-effective way, high-throughput screening technology is required. i Results: /i The combination of selective enrichment of cDNA libraries based on biopanning against serum IgE from sensitized patients and automated robot technology for picking and high-density gridding of clones onto filter membranes, followed by hybridization, enables fast identification of all the different clones present in an enriched library. The consequent application of selective enrichment and robotic-based screening allows, within weeks, cloning and characterization of the whole allergenic repertoire of any organisms. i Conclusions: /i Robotic-based high-throughput screening of clones selected for IgE-binding capacity from phage surface-displayed cDNA libraries of i Aspergillus fumigatus /i , i Cladosporium herbarum /i , i Coprinus comatus, Malassezia furfur /i , peanut and human lung tissue allowed rapid characterization of 81, 28, 37, 27, 8 and 151 different sequences, respectively. All these cDNAs bear a high probability to encode allergens derived from the respective allergenic source.
Publisher: Elsevier BV
Date: 12-2015
DOI: 10.1016/J.MARGEN.2015.07.001
Abstract: This review summarizes usage of genome-editing technologies for metagenomic studies these studies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable s les. The novel genes, pathways and genomes can be deducted. Therefore, metagenomics, particularly genome engineering and system biology, allows for the enhancement of biological and chemical producers and the creation of novel bioresources. With natural resources rapidly depleting, genomics may be an effective way to efficiently produce quantities of known and novel foods, livestock feed, fuels, pharmaceuticals and fine or bulk chemicals.
Publisher: Springer Science and Business Media LLC
Date: 03-2006
Publisher: MDPI AG
Date: 16-02-2018
DOI: 10.3390/GENES9020103
Publisher: MDPI AG
Date: 04-06-2018
DOI: 10.3390/GENES9060281
Publisher: Springer Science and Business Media LLC
Date: 09-2007
DOI: 10.1038/NG0907-1174B
Publisher: MDPI AG
Date: 05-06-2018
DOI: 10.3390/GENES9060283
Publisher: Springer Science and Business Media LLC
Date: 29-12-2011
Publisher: Springer Science and Business Media LLC
Date: 06-10-2011
DOI: 10.1007/S10544-011-9595-6
Abstract: In this paper, we report the construction of a polymerase chain reaction (PCR) device for fast lification and detection of DNA. This device consists of an interchangeable PCR chamber, a temperature control component as well as an optical detection system. The DNA lification happens on an interchangeable chip with the volumes as low as 1.25 μl, while the heating and cooling rate was as fast as 12.7°C/second ensuring that the total time needed of only 25 min to complete the 35 cycle PCR lification. An optimized PCR with two-temperature approach for denaturing and annealing (Td and Ta) of DNA was also formulated with the PCR chip, with which the lification of male-specific sex determining region Y (SRY) gene marker by utilizing raw saliva was successfully achieved and the genetic identification was in-situ detected right after PCR by the optical detection system.
Publisher: MDPI AG
Date: 25-11-2022
Abstract: Polymers are sustainable and renewable materials that are in high demand due to their excellent properties. Natural and synthetic polymers with high flexibility, good biocompatibility, good degradation rate, and stiffness are widely used for various applications, such as tissue engineering, drug delivery, and microfluidic chip fabrication. Indeed, recent advances in microfluidic technology allow the fabrication of polymeric matrix to construct microfluidic scaffolds for tissue engineering and to set up a well-controlled microenvironment for manipulating fluids and particles. In this review, polymers as materials for the fabrication of microfluidic chips have been highlighted. Successful models exploiting polymers in microfluidic devices to generate uniform particles as drug vehicles or artificial cells have been also discussed. Additionally, using polymers as bioink for 3D printing or as a matrix to functionalize the sensing surface in microfluidic devices has also been mentioned. The rapid progress made in the combination of polymers and microfluidics presents a low-cost, reproducible, and scalable approach for a promising future in the manufacturing of biomimetic scaffolds for tissue engineering.
Publisher: MDPI AG
Date: 14-02-2018
DOI: 10.3390/GENES9020089
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/SH13020
Abstract: Background The relationship between pregnancy intentions and contraceptive behaviour is difficult to establish. This study explored the contraceptive histories of teenagers with a recent experience of pregnancy to generate qualitative profiles of pregnancy intentions. Subsequent intentions in relation to birth control were also examined. Methods: A purposive s le of female teenagers aged 14–19 years was recruited from various clinical and community-based antenatal and postnatal services and termination services across the Perth metropolitan area. The current analysis was based on a total of 56 semistructured interviews. A two-staged process of thematic analysis was conducted to identify commonalities emerging from the narrative data. Results: Three pregnancy intention profiles were identified: 1) unplanned, unwanted, unlikely 2) planned, wanted, likely and 3) unplanned, ambivalent, likely. Each profile represents variation in pathways to pregnancy based on teenagers’ accounts of pregnancy desires, personal responsibility over contraceptive use, and perceptions of pregnancy risk. Regardless of the way that pregnancy was resolved (i.e. termination or childbirth), similar postconception intentions surrounding birth control emerged through a shared discourse of pregnancy avoidance across the s le. Conclusions: Exploring adolescents’ understandings of the decisions and behaviours that lead to pregnancy will assist in the development of more accurate assessment tools to identify those at risk of unplanned and unwanted pregnancies. Our research also suggests that the provision of contraceptive counselling immediately after conception, followed by ongoing support, may help to maintain strong intentions to delay further pregnancies as identified in our study.
Publisher: MDPI AG
Date: 05-2018
DOI: 10.20944/PREPRINTS201805.0004.V1
Abstract: The air is not the same as thousands and hundreds of years ago. In the air, suspended particles originate from natural phenomena like dust storms or volcanic activities, as well as anthropogenic pollutants such as fuel engine exhaust and everyday activities at home. The total particles in the air can be classified by sizes, such as PM10, PM2.5 or ultrafine particles. However, there are many other important factors in addition to the particle size, influencing the particle behavior and affecting our health. The surface area, chemical and biological composition, aspect ratio, and the charge are all factors characteristic of particles. OoC microfluidic chips are very useful for the pollutant toxicity measurements on various body tissues. A better understanding of pollutants will help to trace these to the potential sources. The data from the on-the-ground and satellite monitoring can be integrated into models, helping to predict and prevent pollution exposure.
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/C004744A
Abstract: We report a simple, low-cost and detachable microfluidic chip incorporating easily accessible paper, glass slides or other polymer films as the chip materials along with adhesive wax as the recycling bonding material. We use a laser to cut through the paper or film to form patterns and then sandwich the paper and film between glass sheets or polymer membranes. The hot-melt adhesive wax can realize bridge bonding between various materials, for ex le, paper, polymethylmethacrylate (PMMA) film, glass sheets, or metal plate. The bonding process is reversible and the wax is reusable through a melting and cooling process. With this process, a three-dimensional (3D) microfluidic chip is achievable by vacuating and venting the chip in a hot-water bath. To study the biocompatibility and applicability of the wax-based microfluidic chip, we tested the PCR compatibility with the chip materials first. Then we applied the wax-paper based microfluidic chip to HeLa cell electroporation (EP). Subsequently, a prototype of a 5-layer 3D chip was fabricated by multilayer wax bonding. To check the sealing ability and the durability of the chip, green fluorescence protein (GFP) recombinant Escherichia coli (E. coli) bacteria were cultured, with which the chemotaxis of E. coli was studied in order to determine the influence of antibiotic ciprofloxacin concentration on the E. coli migration.
Publisher: Public Library of Science (PLoS)
Date: 15-11-2010
Publisher: Bentham Science Publishers Ltd.
Date: 03-2002
Abstract: Over the past decade, powerful technologies devoted to survey large molecular libraries for the presence of specific clones using the discriminative power of affinity selection have been developed. Phage surface display technology is the most established of these methods and has revolutionised our ability to select agonistic and antagonistic peptides, antibodies with desired specificity and other drug targets. Thereby ligands are expressed as fusions to phage coat proteins and their respective genes are packaged within the phage. The basic concept of linking the phenotype, expressed as gene product displayed on the phage coat, to its genetic information integrated into the phage genome, creates fusion proteins covalently associated with the infectious particle itself. Binding of the phage to the target molecule offers a selective system by which rare phage carrying the desired gene product can be selected from large phage populations carrying inappropriate sequences. Phage selected in this fashion can be used for subsequent rounds of selection because they are able to self-replicate in suitable host cells, yielding target-specific phage populations after several consecutive rounds of affinity selection. Over 1500 publications describe the use of phage display technology highlighting its performance. Phage display possesses certain limitations, including its use for selection of genes from cDNA libraries that has lagged behind, despite the many accomplishments of this technology. Here we discuss recent progress in construction and screening of cDNA libraries displayed on phage surface and emerging concepts allowing fast identification of virtually all different clones present in enriched libraries.
Publisher: MDPI AG
Date: 17-12-2019
DOI: 10.3390/BIOM9120887
Abstract: Recently more consideration has been given to the use of renewable materials and agricultural residues. Wheat production is increasing yearly and correspondingly, the volume of by-products from the wheat process is increasing, as well. It is important to find the use of the residuals for higher value-added products, and not just for the food industry or animal feed purposes as it is happening now. Agricultural residue of the roller milled wheat grain is a wheat bran description. The low-cost of wheat bran and its composition assortment provides a good source of substrate for various enzymes and organic acids production and other biotechnological applications. The main purpose of this review article is to look into recent trends, developments, and applications of wheat bran.
Publisher: S. Karger AG
Date: 2001
DOI: 10.1159/000053679
Publisher: ACM
Date: 20-06-2011
Publisher: Oxford University Press (OUP)
Date: 23-12-2009
Abstract: Stephen (2008) identified 13,736 ultraconserved elements (UCEs) in placental mammals and investigated their evolution in opossum, chicken, frog, and fugu. They found that there was a massive expansion of UCEs during tetrapod evolution and the substitution rate in UCEs showed a significant decline in tetrapods compared with fugu, suggesting they were exapted in tetrapods. They considered it unlikely that these elements are ancient but evolved at a higher rate in teleost fishes. In this study, we investigated the evolution of UCEs in a cartilaginous fish, the elephant shark and show that nearly half the UCEs were present in the jawed vertebrate ancestor. The substitution rate in UCEs is higher in fugu than in elephant shark, and approximately one-third of ancient UCEs have erged beyond recognition in teleost fishes. These data indicate that UCEs have evolved at a higher rate in teleost fishes, which may have implications for their vast ersity and evolutionary success.
Publisher: MDPI AG
Date: 11-10-2017
DOI: 10.3390/GENES8100266
Publisher: MDPI AG
Date: 06-03-2018
DOI: 10.3390/GENES9030144
Publisher: Springer Science and Business Media LLC
Date: 08-04-2014
Publisher: Springer Science and Business Media LLC
Date: 29-03-2014
Location: Saudi Arabia
Location: United States of America
Location: Switzerland
Location: Saudi Arabia
Start Date: 1997
End Date: 1998
Funder: German Academic Exchange Service (DAAD)
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