News Article | May 16, 2017
EAST LANSING, Mich. - Electric fish have been a model biology system since the 18th century. Their potential, though, has been mostly isolated to neurological studies. Thanks to the recent availability of electric fish genome sequences, Michigan State University researchers hope to harness the power of CRISPR/Cas9 gene editing in electric fish to make a new type of model for biology. MSU has landed a $1.5 million National Science Foundation grant to develop this cutting-edge technique in electric fish and afford more researchers easy access to this versatile model. Electric fish have already provided deep insights into the very nature of bioelectrogenesis - the ability to produce electric fields outside the body - as well as the molecular structure of the synapse, and granted unprecedented insights into the brain circuitry underlying complex behavior. Jason Gallant, MSU integrative biologist who's leading the grant, believes they could be the model organisms for a new generation of studies that help decode the function of their genomes. He hopes to kick-start research programs that are trying to investigate the connection between genes encoded in the DNA electric fish, and phenotypes, the physical expression of traits encoded by those genes. "Making this connection is an important goal across disciplines of biology, and we want to develop a robust, accessible and easily transferable gene manipulation toolbox to allow the electric fish model to help achieve that goal," Gallant said. "These all-purpose tools then can be applied to a full range of questions under investigation, regardless of a researcher's background." It doesn't matter if scientists are focusing on molecules, cells, organ systems, behaviors or macroevolutionary processes like speciation, Gallant and his team believes these high-tech tools could be used to accelerate their research. A critical step for genetic and medicinal advances is having lines of mutant models, such as mice, zebrafish or fruit flies. Using CRISPR/Cas9 gene editing technologies, Gallant's team will be able to generate mutant lines of transgenic electric fish as well. Gallant's team is composed of researchers from the University of Oklahoma, the University of Texas, Columbia University and the Genome Institute at Washington University in St. Louis. They will work to create large colonies of electric fish at MSU and the University of Oklahoma, and develop new techniques for "knocking down" gene function using morpholinos and introducing foreign genetic material using retroviruses. Gallant's team will rapidly share these new research tools by coordinating workshops and websites to broaden participation in the field and train the next generation of electric fish biologists to harness these powerful new techniques. Gallant's lab and others around the U.S. have already provided a proof-of-concept of the model's strength. Now they're hoping to scale up their efforts, no pun intended. "Currently, our lab is leading efforts in acquiring new genomic data, but there are no techniques to rigorously test hypotheses about the functions of genes that could potentially yield insights in developmental biology, neuroscience, behavior and evolution, just to name a few," Gallant said. "Developing genetic tools for monitoring and manipulating gene activity in electric fish would revolutionize the field and enable a wave of new studies that exploit the unique features of these organisms for addressing central questions in biology at a level of resolution not possible in other vertebrate systems." Michigan State University has been working to advance the common good in uncommon ways for more than 150 years. One of the top research universities in the world, MSU focuses its vast resources on creating solutions to some of the world's most pressing challenges, while providing life-changing opportunities to a diverse and inclusive academic community through more than 200 programs of study in 17 degree-granting colleges. For MSU news on the Web, go to MSUToday. Follow MSU News on Twitter at twitter.com/MSUnews.
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.
Thuzar M.,Kasetsart University |
Vanavichit A.,Kasetsart University |
Tragoonrung S.,Genome Institute |
Jantasuriyarat C.,Kasetsart University
Acta Physiologiae Plantarum | Year: 2011
An efficient and rapid plant regeneration system through somatic embryogenesis was developed using 13-week-old zygotic embryos of oil palm (Elaeis guineensis Jacq.) cv. 'Tenera'. Zygotic embryos were cultured on MS and N6 media supplemented with 2.0 mg L-1 picloram, 2,4-D and dicamba. The highest embryogenic callus formation (32%) was observed on N6 medium with 2,4-D after 3 month culture on callus induction medium. Somatic embryos were continuously formed from nodular calli on embryo maturation medium [N6 + 0.1 mg L-1 2,4-D, 0.16 g L-1 putrescine, 0.5 g L-1 casein amino acids and 2.0 g L-1 activated charcoal(AC)] for 3-5 months. Histological analysis confirmed that embryo development occurred via somatic embryogenesis. For plant regeneration, modified N6 medium (MN6) with AC (0. 5 g L-1) without growth regulators, induced both shoot and root formation simultaneously with the highest regeneration rate of 56%. This combined shoot and root induction protocol shortened the culture time to 9-12 months. Furthermore, after acclimatization, more than 85% of transferred plants from our protocol developed successfully in the soil. © 2010 Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków.
News Article | February 15, 2017
Ömer Ilday was in a buoyant mood on 15 July last year. He was preparing a press release to promote his latest research, which used super-fast laser bursts to cut away at materials with as little wasted energy as possible. He was confident of media interest. His technique had exciting applications for industry and medicine — such as reducing burn damage in certain types of surgery. And the paper describing it had just been published in Nature1 — the first in the journal led by a group from Turkey in nearly 25 years. But that evening Ilday, a materials scientist at Bilkent University in Ankara, started to get alarming text messages from friends: a military coup was under way. In an instant, scientific discovery was swept from the news agenda. The coup was swiftly suppressed. But Turkish President Recep Tayyip Erdoğan declared a state of emergency that is still in force and has thrown the country's science into turmoil. Thousands of academics have been sacked. The national research agency became so depleted of personnel that it stopped functioning entirely for many months. And Erdoğan, fearful of enemies in places of higher learning, took direct charge of appointing university presidents. The country was supposed to have been in the middle of a scientific rebirth. Although it had struggled for decades to stem a brain drain, Turkish research funding had taken off since 2005, when the country started negotiations to join the European Union. Research hotspots emerged. Some optimistic young scientists returned home and set up thriving labs. And in 2014, the government announced serious plans to expand research on many fronts. No one expected progress to be easy. Scientists have long been ill at ease with Turkey's complex politics and its tensions between secular, religious and military forces. But now, faced also with rising rates of terrorism, concerns about Erdoğan's increasing authoritarianism and a currency in free fall, many of the best scientists are wondering whether they should leave the country. “I think worse will come,” says Özgür Akan, a physicist working in neuroscience who decided a few months ago to depart Koç University in Istanbul for the University of Cambridge, UK. “I don't think it will be possible to do high-tech, high-risk research in the next ten years.” Not everyone has abandoned hope — but the mood among scientists is universally nervous. Sitting in his tidy, light-filled office at the Turkish Council of Higher Education (YÖK) in Ankara, Hasan Mandal says he sees something positive in the instability. “These are challenging times, but turbulence gives us opportunities,” says the engineer, who trained and did postdocs in the United Kingdom and Germany. “It is harder to make changes in normal times.” As a deputy president of YÖK, he is one of the architects of the government's research-expansion plans, which include making universities more competitive and creating new research centres and positions (see 'Elevating Turkish science'). The plans emerged from the government's overarching aim for Turkey to become one of the ten largest economies in the world by 2023, the 100th anniversary of the foundation of the Turkish state. (It is now ranked 17th when accounting for purchasing-power parity.) Expanding research capacity on all fronts is integral to that plan, says Hasan. In Turkey's heavily centralized education system, YÖK controls all the significant decisions of state universities, from the distribution of academic positions between departments to salaries and student numbers. The reforms will inject a degree of flexibility for a select few. Inspired by Germany's Excellence Initiative and Russia's Project 5-100, Turkey launched competitions between its universities, with the winners getting more funding and positions. Last year, five provincial institutions were selected as 'regional universities' owing to their close connections with local industries and social programmes. And in January, YÖK opened a second competition for another five to earn the title of 'research university' on the basis of their potential to produce internationally competitive research. On top of other spoils, research universities will win the freedom to open new courses and distribute academic positions without seeking YÖK approval. “The status would make a big difference to us,” says urologist Haluk Özen, president of the research-strong Hacettepe University in Ankara. Outside the university system, the government has established the Health Institutes of Turkey (TÜSEB), which will be headquartered in Istanbul and broadly modelled on the US National Institutes of Health. Its six institutes will emphasize translational research and personalized medicine. TÜSEB is creating 300 research positions this year alone, and will have a generous budget for extramural research. The government is also converting a handful of university institutes into securely funded national research centres, allowing them to manage their own operations and budgets. “I'm particularly happy that we will be able to pay competitive salaries that could be attractive to top scientists from abroad,” says molecular biologist Mehmet Öztürk, director of the International Biomedicine and Genome Institute in İzmir (iBG-izmir), one of the four nominated for this elevated status last December. YÖK has also opened 2,000 new PhD positions to ensure a future generation of scientists. The government hopes that these expansive plans will tantalize Turkey's large scientific diaspora. In fact, many Turkish scientists living abroad had been starting to feel optimistic about their home country. Research spending rose more than tenfold between 2000 and 2011. And some private universities, such as Bilkent and Koç, have developed into havens from the bureaucratic excesses of public universities. For scientists with large international grants to help them establish and equip their labs, the possibility of an excellent research career in their home country seemed real. “With such grants, and a supportive university like mine, you have the right conditions to achieve things,” says molecular biologist Ebru Erbay, who returned from Harvard University in Cambridge, Massachusetts, to Bilkent in 2010. She has since won grants from both the European Research Council (ERC) and the European Molecular Biology Organization (EMBO), and in the past five months has published papers in both Science Translational Medicine2 and Proceedings of the National Academy of Sciences3 on new mechanisms to counter the artery-hardening condition atherosclerosis. A walk through some of Turkey's research hotspots reveals the same energy, enthusiasm and productivity that one sees in top labs anywhere in the world — and they are often as well equipped. But, everywhere, scientists say the political uncertainty is becoming unbearable. They have been shaken by both the coup attempt and the government's response to it. One immediate consequence was the collapse of the national science and technology agency TÜBİTAK, the country's main research funder, which also publishes educational books. Problems had been brewing for a long time: TÜBİTAK had been deeply infiltrated by the religious organization known as the Gülen movement, which is believed to have orchestrated the coup attempt. Over the past few decades, these followers of exiled preacher Fethullah Gülen had established themselves in Turkey's military, judiciary and government offices, as well as in universities. The Gülenists were political allies of Erdoğan's ruling Justice and Development Party until 2013, when the extent of their clandestine power base became clear. Under the state of emergency after the coup attempt, Erdoğan started to purge suspected Gülenists from public organizations. TÜBİTAK's former president, Yücel Altunbaşak, was jailed in October 2016 for his alleged role in supporting the coup attempt; the agency also lost large numbers of employees, and those who remained seemed afraid to make decisions, with scientists receiving no information at all about grant opportunities or meetings. Scientists generally agree that removing Gülenists from the system was necessary, and not just because of the coup attempt. They have long complained that TÜBİTAK's distribution of money had become skewed and that processes were no longer transparent. Some social scientists say their projects seemed to be rejected for political reasons. Ali Çarkoğlu of Koç University studies electoral systems, and has for years contributed data about Turkey to international collaborations such as the International Social Survey Programme and the Comparative Study of Electoral Systems. When TÜBİTAK rejected his proposals to run surveys during the 2015 and 2016 elections in Turkey, he obtained money from external sources, including the Open Society Foundations in New York City, founded by philanthropist George Soros. “But then critics said I was accepting 'big-capital, Jewish money', insinuating I was part of an international conspiracy,” he says. Chemist Engin Umut Akkaya of Bilkent University, an outspoken government critic, was banned for a year from seeking TÜBİTAK funding in November 2014 — ostensibly, for ethical breaches in his reports to the agency, charges that he denied. He took the case to court, which ruled in his favour — two months after the ban was finished. “The situation here makes us feel sad and unfortunate,” he says. One former member of a TÜBİTAK scientific board, who asked not to be named for fear of retribution, told Nature that he resigned in 2015 because the agency had started to replace some of the scientists he had recommended for reviewing panels with people he did not know. “There was a slide over the years towards arbitrary rules and decisions behind closed doors — I felt that the administration was interfering with the choices about grants.” The hobbled agency slowly started to work again last December, although some scientists report that they have heard nothing about applications that they submitted as long ago as spring last year. The long gap in funding has been disruptive, researchers say. And scientists have been unnerved by the purges at state universities, which they say have swept away innocent colleagues — mostly social scientists — along with the Gülenists. In waves of presidential decrees issued under the state of emergency since last September, more than 7,300 academics from across Turkey have been dismissed from universities. Independent analysts confirm that many of them have no association with the coup — but were known critics of Erdoğan and his policies. Many had simply signed a petition calling for peace between government forces and Kurdish separatists. No one knows when the waves of dismissals will stop. One social scientist in Istanbul, who also asked not to be named, was put under official investigation by his university in December, on suspicion of being a sympathizer of the Kurdistan Workers' Party (PKK), which Erdoğan lists as a terrorist organization. His colleagues confirm that he does not support the PKK, and he did not sign the petition. But he did participate in protests against his university's administration a few years ago. He is now nervously waiting to see whether his name is on the next purge list. If convicted, he will lose his job and his pension, and will never be able to work for a public organization again. He may also lose his passport. “I asked them to show me their evidence, but in the state of emergency they do not have to,” he says. “Things are very bleak.” In the reigning confusion, the government further upset scientists by removing evolution from a draft high-school curriculum that it published last month. Evolution has been under pressure from Islamists in Turkey for years. In 2009, TÜBİTAK censored a special issue of its own popular-science magazine dedicated to Charles Darwin's centenary. Since then, it has stopped publication of any books that mention evolution, says evolutionary biologist İsmail Sağlam of Hacettepe University and the University of California, Davis. And last year, the Natural History Museum in Ankara removed its permanent exhibition on evolution. “It adds up to a systematic trend,” says Sağlam. “This is not a matter of politics, but of education.” The atmosphere has frightened off foreign scientists. Nearly all international meetings planned to take place in Turkey in 2017 have been cancelled, and individual researchers have dropped plans to visit. Some Turkish scientists, such as Ilday, are not completely fazed by the political atmosphere — they are watching and waiting to see what happens. “I am not personally affected, and I am happy with the way the country supports science,” he says in his spacious, high-tech labs at Bilkent. His ERC grant allows him to do basic research, which he says is liberating, given that large TÜBİTAK grants are available only for applied science. But even with excellent facilities, Ilday has found that the best students rarely want to stick around. Principal investigators throughout the country routinely report that it is getting ever-harder to recruit PhD students, and almost impossible to hire postdocs. Those who are good enough choose to leave as soon as possible. “I try to concentrate on my science and my students — but we can't help but be distracted by the general news,” says Güneş Özhan, a developmental biologist at the iBG-izmir. “Every day you just don't know what is going to happen.” Still, Özhan, who studies brain regeneration in zebrafish, doesn't regret her return home in 2014, after ten years in Germany. The historic Mediterranean city of İzmir makes for pleasant living, and her EMBO Installation grant, along with funds from other sources, gives her as much money as she needs. It has allowed her to build a state-of-the-art zebrafish facility that is better than the one she enjoyed at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden. She even has a social room where students can sleep when they do overnight experiments. And the iBG-izmir's new status as a national research centre will make things more sustainable, she says. “But it's getting a bit hard to survive,” she admits. Her colleague Yongsoo Park, a South Korean who researches neurotransmission, expresses the same ambivalence. “The research facilities are fine — and, wow, it's so great here that I can go with the kids to the sea every weekend.” But fears linger. His family speaks very little Turkish and he constantly worries about their safety. “The state of emergency has not served science well,” says Gokhan Hotamisligil, a geneticist at Harvard who closely follows developments in science in his homeland and hosts monthly scientific colloquia for the local Turkish diaspora. These meetings regularly attract more than 100 attendees. “The country has made wonderful investments in science — now the government needs to do more to signal that it has not forgotten about it.”
Watthanasurorot A.,Uppsala University |
Saelee N.,Uppsala University |
Saelee N.,Prince of Songkla University |
Phongdara A.,Prince of Songkla University |
And 5 more authors.
PLoS Genetics | Year: 2013
Daily, circadian rhythms influence essentially all living organisms and affect many physiological processes from sleep and nutrition to immunity. This ability to respond to environmental daily rhythms has been conserved along evolution, and it is found among species from bacteria to mammals. The hematopoietic process of the crayfish Pacifastacus leniusculus is under circadian control and is tightly regulated by astakines, a new family of cytokines sharing a prokineticin (PROK) domain. The expression of AST1 and AST2 are light-dependent, and this suggests an evolutionarily conserved function for PROK domain proteins in mediating circadian rhythms. Vertebrate PROKs are transmitters of circadian rhythms of the suprachiasmatic nucleus (SCN) in the brain of mammals, but the mechanism by which they function is unknown. Here we demonstrate that high AST2 expression is induced by melatonin in the brain. We identify RACK1 as a binding protein of AST2 and further provide evidence that a complex between AST2 and RACK1 functions as a negative-feedback regulator of the circadian clock. By DNA mobility shift assay, we showed that the AST2-RACK1 complex will interfere with the binding between BMAL1 and CLK and inhibit the E-box binding activity of the complex BMAL1-CLK. Finally, we demonstrate by gene knockdown that AST2 is necessary for melatonin-induced inhibition of the complex formation between BMAL1 and CLK during the dark period. In summary, we provide evidence that melatonin regulates AST2 expression and thereby affects the core clock of the crustacean brain. This process may be very important in all animals that have AST2 molecules, i.e. spiders, ticks, crustaceans, scorpions, several insect groups such as Hymenoptera, Hemiptera, and Blattodea, but not Diptera and Coleoptera. Our findings further reveal an ancient evolutionary role for the prokineticin superfamily protein that links melatonin to direct regulation of the core clock gene feedback loops. © 2013 Watthanasurorot et al.
Aporntewan C.,Chulalongkorn University |
Phokaew C.,Chulalongkorn University |
Piriyapongsa J.,Genome Institute |
Ngamphiw C.,Genome Institute |
And 3 more authors.
PLoS ONE | Year: 2011
In human cancers, the methylation of long interspersed nuclear element -1 (LINE-1 or L1) retrotransposons is reduced. This occurs within the context of genome wide hypomethylation, and although it is common, its role is poorly understood. L1s are widely distributed both inside and outside of genes, intragenic and intergenic, respectively. Interestingly, the insertion of active full-length L1 sequences into host gene introns disrupts gene expression. Here, we evaluated if intragenic L1 hypomethylation influences their host gene expression in cancer. First, we extracted data from L1base (http://l1base.molgen.mpg.de), a database containing putatively active L1 insertions, and compared intragenic and intergenic L1 characters. We found that intragenic L1 sequences have been conserved across evolutionary time with respect to transcriptional activity and CpG dinucleotide sites for mammalian DNA methylation. Then, we compared regulated mRNA levels of cells from two different experiments available from Gene Expression Omnibus (GEO), a database repository of high throughput gene expression data, (http://www.ncbi.nlm.nih.gov/geo) by chi-square. The odds ratio of down-regulated genes between demethylated normal bronchial epithelium and lung cancer was high (p<1E-27; OR = 3.14; 95% CI = 2.54-3.88), suggesting cancer genome wide hypomethylation down-regulating gene expression. Comprehensive analysis between L1 locations and gene expression showed that expression of genes containing L1s had a significantly higher likelihood to be repressed in cancer and hypomethylated normal cells. In contrast, many mRNAs derived from genes containing L1s are elevated in Argonaute 2 (AGO2 or EIF2C2)-depleted cells. Hypomethylated L1s increase L1 mRNA levels. Finally, we found that AGO2 targets intronic L1 pre-mRNA complexes and represses cancer genes. These findings represent one of the mechanisms of cancer genome wide hypomethylation altering gene expression. Hypomethylated intragenic L1s are a nuclear siRNA mediated cis-regulatory element that can repress genes. This epigenetic regulation of retrotransposons likely influences many aspects of genomic biology. © 2011 Aporntewan et al.
Tangphatsornruang S.,Genome Institute |
Sangsrakru D.,Genome Institute |
Chanprasert J.,Genome Institute |
Uthaipaisanwong P.,Genome Institute |
And 3 more authors.
DNA Research | Year: 2010
Mungbean is an economically important crop which is grown principally for its protein-rich dry seeds. However, genomic research of mungbean has lagged behind other species in the Fabaceae family. Here, we reported the complete chloroplast (cp) genome sequence of mungbean obtained by the 454 pyrosequencing technology. The mungbean cp genome is 151 271 bp in length which includes a pair of inverted repeats (IRs) of 26 474 bp separated by a small single-copy region of 17 427 bp and a large single-copy region of 80 896 bp. The genome contains 108 unique genes and 19 of these genes are duplicated in the IR. Of these, 75 are predicted protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. Relative to other plant cp genomes, we observed two distinct rearrangements: a 50-kb inversion between accD/rps16 and rbcL/trnK-UUU, and a 78-kb rearrangement between trnH/rpl14 and rps19/rps8. We detected sequence length polymorphism in the cp homopolymeric regions at the intra-and inter-specific levels in the Vigna species. Phylogenetic analysis demonstrated a close relationship between Vigna and Phaseolus in the phaseolinae subtribe and provided a strong support for a monophyletic group of the eurosid I. © 2010 The Author.
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.
Piriyapongsa J.,Genome Institute |
Bootchai C.,Genome Institute |
Ngamphiw C.,Genome Institute |
Tongsima S.,Genome Institute
PLoS ONE | Year: 2012
Background: microRNAs are generally understood to regulate gene expression through binding to target sequences within 3′-UTRs of mRNAs. Therefore, computational prediction of target sites is usually restricted to these gene regions. Recent experimental studies though have suggested that microRNAs may alternatively modulate gene expression by interacting with promoters. A database of potential microRNA target sites in promoters would stimulate research in this field leading to more understanding of complex microRNA regulatory mechanism. Methodology: We developed a database hosting predicted microRNA target sites located within human promoter sequences and their associated genomic features, called microPIR (microRNA-Promoter Interaction Resource). microRNA seed sequences were used to identify perfect complementary matching sequences in the human promoters and the potential target sites were predicted using the RNAhybrid program. >15 million target sites were identified which are located within 5000 bp upstream of all human genes, on both sense and antisense strands. The experimentally confirmed argonaute (AGO) binding sites and EST expression data including the sequence conservation across vertebrate species of each predicted target are presented for researchers to appraise the quality of predicted target sites. The microPIR database integrates various annotated genomic sequence databases, e.g. repetitive elements, transcription factor binding sites, CpG islands, and SNPs, offering users the facility to extensively explore relationships among target sites and other genomic features. Furthermore, functional information of target genes including gene ontologies, KEGG pathways, and OMIM associations are provided. The built-in genome browser of microPIR provides a comprehensive view of multidimensional genomic data. Finally, microPIR incorporates a PCR primer design module to facilitate experimental validation. Conclusions: The proposed microPIR database is a useful integrated resource of microRNA-promoter target interactions for experimental microRNA researchers and computational biologists to study the microRNA regulation through gene promoter. The database can be freely accessed from: http://www4a.biotec.or.th/micropir. © 2012 Piriyapongsa et al.
Arpornsuwan T.,Thammasat University |
Buasakul B.,Ministry of Public Health |
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.