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Piriyapongsa J.,Genome Institute | Jordan I.K.,Georgia Institute of Technology | Conley A.B.,Georgia Institute of Technology | Ronan T.,University of Illinois at Chicago | Smalheiser N.R.,University of Illinois at Chicago
Biology Direct | Year: 2011

Background: Transcription factors are thought to regulate the transcription of microRNA genes in a manner similar to that of protein-coding genes; that is, by binding to conventional transcription factor binding site DNA sequences located in or near promoter regions that lie upstream of the microRNA genes. However, in the course of analyzing the genomics of human microRNA genes, we noticed that annotated transcription factor binding sites commonly lie within 70- to 110-nt long microRNA small hairpin precursor sequences.Results: We report that about 45% of all human small hairpin microRNA (pre-miR) sequences contain at least one predicted transcription factor binding site motif that is conserved across human, mouse and rat, and this rises to over 75% if one excludes primate-specific pre-miRs. The association is robust and has extremely strong statistical significance; it affects both intergenic and intronic pre-miRs and both isolated and clustered microRNA genes. We also confirmed and extended this finding using a separate analysis that examined all human pre-miR sequences regardless of conservation across species.Conclusions: The transcription factor binding sites localized within small hairpin microRNA precursor sequences may possibly regulate their transcription. Transcription factors may also possibly bind directly to nascent primary microRNA gene transcripts or small hairpin microRNA precursors and regulate their processing.Reviewers: This article was reviewed by Guillaume Bourque (nominated by Jerzy Jurka), Dmitri Pervouchine (nominated by Mikhail Gelfand), and Yuriy Gusev. © 2011 Piriyapongsa et al; licensee BioMed Central Ltd.


Suwannarangsee S.,National Center for Genetic Engineering and Biotechnology | Bunterngsook B.,Kasetsart University | Arnthong J.,National Center for Genetic Engineering and Biotechnology | Paemanee A.,Genome Institute | And 4 more authors.
Bioresource Technology | Year: 2012

Synergistic enzyme system for the hydrolysis of alkali-pretreated rice straw was optimised based on the synergy of crude fungal enzyme extracts with a commercial cellulase (Celluclast™). Among 13 enzyme extracts, the enzyme preparation from Aspergillus aculeatus BCC 199 exhibited the highest level of synergy with Celluclast™. This synergy was based on the complementary cellulolytic and hemicellulolytic activities of the BCC 199 enzyme extract. A mixture design was used to optimise the ternary enzyme complex based on the synergistic enzyme mixture with Bacillus subtilis expansin. Using the full cubic model, the optimal formulation of the enzyme mixture was predicted to the percentage of Celluclast™: BCC 199: expansin = 41.4:37.0:21.6, which produced 769. mg reducing sugar/g. biomass using 2.82. FPU/g enzymes. This work demonstrated the use of a systematic approach for the design and optimisation of a synergistic enzyme mixture of fungal enzymes and expansin for lignocellulosic degradation. © 2012 Elsevier Ltd.


Arpornsuwan T.,Thammasat University | Buasakul B.,STIS | Jaresitthikunchai J.,Genome Institute | Roytrakul S.,Genome Institute
Peptides | Year: 2014

The emergence of multidrug-resistant strains of Neisseria gonorrhoeae constitutes a serious threat to public health and necessitates the discovery of new types of antimicrobial agents. Among the 18 clinical isolates of N. gonorrhoeae with susceptible to spectinomycin, ceftriaxone and cefixime, 14 isolates were resistance to penicillin, tetracycline and ciprofloxacin, while 2 isolates were susceptible to tetracycline and another was penicillin intermediate isolate. Significant differences between laboratory strain and multidrug resistant strains were revealed by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling and bioinformatics examination using the MALDI BioTyper software. However, Maldi Biotyper was not successfully separated ciprofloxacin-penicillin resistance and ciprofloxacin-tetracycline resistance from ciprofloxacin-penicillin-tetracycline resistant N. gonorrhoeae isolates. BmKn2 is a basic, alpha-helical peptide with no disulfide-bridge venom peptides that was first isolated from Buthus martensii Kasch. A panel of BmKn2 scorpion venom peptide and its derivatives of varying length and characteristics were synthesized chemically and evaluated for their ability to inhibit the growth of clinical N. gonorrhoeae isolates. Synthetic BmKn2 displayed potent activity against 18 clinical isolates of N. gonorrhoeae with MIC50 values of 6.9-27.6 μM. BmKn2 exerted its antibacterial activity via a bactericidal mechanism. Cyclic BmKn1 did not show antigonococcal activity. Decreasing the cationicity and helix percentage at the C-terminus of BmKn2 reduced the potency against N. gonorrhoeae. Taken together, the BmKn1 peptide can be developed as a topical therapeutic agent for treating multidrug-resistant strains of N. gonorrhoeae infections. © 2013 Elsevier Inc.


News Article | September 13, 2016
Site: www.chromatographytechniques.com

Researchers in Singapore have developed a new protein that can alter DNA in living cells with much higher precision than current methods. The ability to alter DNA accurately will open more doors in the development of personalized medicine that could help to tackle human diseases that currently have few treatment options. Examples of diseases that have unmet therapeutic needs include neurodegenerative diseases like Huntington's disease, muscular dystrophies and blood disorders like sickle cell anaemia. This new protein, named iCas, can be easily controlled by an external chemical input and thus solves some of the problems with CRISPR-Cas, the existing gold-standard for DNA altering. For example, existing Cas enzymes may sometimes alter places in the DNA that result in dire consequences. With iCas, users now have the ability to control enzyme activity and thus minimize unintended DNA modifications in the cell. Developed by a collaboration between A*STAR's Genome Institute of Singapore (GIS) and Nanyang Technological University, Singapore (NTU Singapore), iCas was published in the peer reviewed scientific journal Nature Chemical Biology this week. Leading the joint research team is Tan Meng How, senior research scientist of stem cell & regenerative  biology at the GIS, and assistant professor at NTU's School of Chemical and Biomedical Engineering. "DNA is like an instruction manual that tells living cells how to behave, so if we can rewrite the instructions in this manual, we will be able to gain control over what the cells are supposed to do," explained Tan. "Our engineered iCas protein is like a light switch that can be readily turned on and off as desired. It also outperforms other existing methods in terms of response time and reliability." To ensure that DNA is precisely altered, which is required in many biomedical and biotechnological applications, the activity of the Cas protein must be tightly regulated. The chemical that switches the iCas protein on or off is tamoxifen, a drug commonly used to treat and prevent breast cancer. In its absence, iCas is switched off with no changes made to the DNA. When switched on with tamoxifen, iCas will then edit the target DNA site. In the study, iCas was found to outperform other chemical-inducible CRISPR-Cas technologies, with a much faster response time and an ability to be switched on and off repeatedly. The higher speed at which iCas reacts will enable tighter control over exactly where and when DNA editing takes place. This is useful in research or applications that demand precise control of DNA editing. For example, in studies of cell signaling pathways or vertebrate development, iCas can precisely target a subset of cells within a tissue (spatial control) or to edit the DNA at a particular developmental stage (temporal control). "The iCas technology developed by Dr Tan is an exciting addition to the growing CRISPR toolbox. It enables genome editing in a precisely controlled manner, thus opening new doors for applications of the CRISPR technology in basic and applied biological research," said Huimin Zhao, the Steven L. Miller Chair Professor of the Chemical and Biomolecular Engineering faculty at the University of Illinois at Urbana-Champaign (UIUC). "This development allows the researchers to have precision control for more accurate DNA editing, and it can help researchers engineer cells with new properties or repair diseased cells with mutated DNA," added Ng Huck Hui, GIS executive director. "DNA editing is an exciting field with many potential uses in the treatment of diseases. NTU has been active in research in the area of gene sequencing and bioengineering over the past years and this work by Dr Tan and his Singapore team will add to the growing body of knowledge in cell engineering for medicine," said Teoh Swee Hin, chair of NTU's School of Chemical and Biomedical Engineering.


News Article | September 13, 2016
Site: www.rdmag.com

Researchers in Singapore have developed a new protein that can alter DNA in living cells with much higher precision than current methods. The ability to alter DNA accurately will open more doors in the development of personalised medicine that could help to tackle human diseases that currently have few treatment options. Examples of diseases that have unmet therapeutic needs include neurodegenerative diseases like Huntington's disease, muscular dystrophies, and blood disorders like sickle cell anaemia. This new protein, named iCas, can be easily controlled by an external chemical input and thus solves some of the problems with CRISPR-Cas*, the existing gold-standard for DNA altering. For example, existing Cas enzymes may sometimes alter places in the DNA that result in dire consequences. With iCas, users now have the ability to control enzyme activity and thus minimize unintended DNA modifications in the cell. Developed by a collaboration between A*STAR's Genome Institute of Singapore (GIS) and Nanyang Technological University, Singapore (NTU Singapore), iCas was published in the peer reviewed scientific journal Nature Chemical Biology this week. Leading the joint research team is Dr Tan Meng How, Senior Research Scientist of Stem Cell & Regenerative Biology at the GIS, and Assistant Professor at NTU's School of Chemical and Biomedical Engineering. "DNA is like an instruction manual that tells living cells how to behave, so if we can rewrite the instructions in this manual, we will be able to gain control over what the cells are supposed to do," explained Dr Tan. "Our engineered iCas protein is like a light switch that can be readily turned on and off as desired. It also outperforms other existing methods in terms of response time and reliability." To ensure that DNA is precisely altered, which is required in many biomedical and biotechnological applications, the activity of the Cas protein must be tightly regulated. The chemical that switches the iCas protein on or off is tamoxifen, a drug commonly used to treat and prevent breast cancer. In its absence, iCas is switched off with no changes made to the DNA. When switched on with tamoxifen, iCas will then edit the target DNA site. In the study, iCas was found to outperform other chemical-inducible CRISPR-Cas technologies, with a much faster response time and an ability to be switched on and off repeatedly. The higher speed at which iCas reacts will enable tighter control over exactly where and when DNA editing takes place. This is useful in research or applications that demand precise control of DNA editing. For example, in studies of cell signalling pathways or vertebrate development, iCas can precisely target a subset of cells within a tissue (spatial control) or to edit the DNA at a particular developmental stage (temporal control). "The iCas technology developed by Dr Tan is an exciting addition to the growing CRISPR toolbox. It enables genome editing in a precisely controlled manner, thus opening new doors for applications of the CRISPR technology in basic and applied biological research," said Dr Huimin Zhao, the Steven L. Miller Chair Professor of the Chemical and Biomolecular Engineering faculty at the University of Illinois at Urbana-Champaign (UIUC). GIS Executive Director Prof Ng Huck Hui added, "This development allows the researchers to have precision control for more accurate DNA editing, and it can help researchers engineer cells with new properties or repair diseased cells with mutated DNA." Prof Teoh Swee Hin, Chair of NTU's School of Chemical and Biomedical Engineering, said, "DNA editing is an exciting field with many potential uses in the treatment of diseases. NTU has been active in research in the area of gene sequencing and bioengineering over the past years and this work by Dr Tan and his Singapore team will add to the growing body of knowledge in cell engineering for medicine."

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