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Bokolia NP, Gadepalli R. Identification of consensus hairpin loop structure among the negative sense subgenomic RNAs of SARS-CoV-2. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2023; 47:28. [PMID: 36852284 PMCID: PMC9947893 DOI: 10.1186/s42269-023-01002-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND SARS-CoV-2 is the causative agent of worldwide pandemic disease coronavirus disease 19. SARS-CoV-2 bears positive sense RNA genome that has organized and complex pattern of replication/transcription process including the generation of subgenomic RNAs. Transcription regulatory sequences have important role in the pausing of replication/transcription and generation of subgenomic RNAs. RESULTS In the present bioinformatics analysis, a consensus secondary structure was identified among negative sense subgenomic RNAs of SARS-CoV-2. This consensus region is present at the adjacent of initiation codon. CONCLUSIONS This study proposed that consensus structured domain could involve in mediating the long pausing of replication/transcription complex and responsible for subgenomic RNA production. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s42269-023-01002-3.
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Affiliation(s)
- Naveen Prakash Bokolia
- Viral Research and Diagnostic Laboratory, Microbiology Department, All India Institute of Medical Sciences, Jodhpur, 342001 India
| | - Ravisekhar Gadepalli
- Viral Research and Diagnostic Laboratory, Microbiology Department, All India Institute of Medical Sciences, Jodhpur, 342001 India
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2
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Afshari E, Cohan RA, Sotoodehnejadnematalahi F, Mousavi SF. In-silico design and evaluation of an epitope-based serotype-independent promising vaccine candidate for highly cross-reactive regions of pneumococcal surface protein A. J Transl Med 2023; 21:13. [PMID: 36627666 PMCID: PMC9830136 DOI: 10.1186/s12967-022-03864-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/29/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The pathogenicity of pneumococcus with high morbidity, mortality, and multi-drug resistance patterns has been increasing. The limited coverage of the licensed polysaccharide-based vaccines and the replacement of the non-vaccine serotypes are the main reasons for producing a successful serotype-independent vaccine. Pneumococcal surface protein A (PspA) is an extremely important virulence factor and an interesting candidate for conserved protein-based pneumococcal vaccine classified into two prominent families containing five clades. PspA family-elicited immunity is clade-dependent, and the level of the PspA cross-reactivity is restricted to the same family. METHODS To cover and overcome the clade-dependent immunity of the PspAs in this study, we designed and tested a PspA1-5c+p vaccine candidate composed of the highest immunodominant coverage of B- and T-cell epitope truncated domain of each clade focusing on two cross-reactive B and C regions of the PspAs. The antigenicity, toxicity, physicochemical properties, 3D structure prediction, stability and flexibility of the designed protein using molecular dynamic (MD) simulation, molecular docking of the construct withHLADRB1*(01:01) and human lactoferrin N-lop, and immune simulation were assessed using immunoinformatics tools. In the experimental section, after intraperitoneal immunization of the mice with Alum adjuvanted recombinant PspA1-5c+p, we evaluated the immune response, cross-reactivity, and functionality of the Anti-PspA1-5c+p antibody using ELISA, Opsonophagocytic killing activity, and serum bactericidal assay. RESULTS For the first time, this work suggested a novel PspA-based vaccine candidate using immunoinformatics tools. The designed PspA1-5c+p protein is predicted to be highly antigenic, non-toxic, soluble, stable with low flexibility in MD simulation, and able to stimulate both humoral and cellular immune responses. The designed protein also could interact strongly with HLADRB1*(01:01) and human lactoferrin N-lop in the docking study. Our immunoinformatics predictions were validated using experimental data. Results showed that the anti-PspA1-5c+p IgG not only had a high titer with strong and same cross-reactivity coverage against all pneumococcal serotypes used but also had high and effective bioactivity for pneumococcal clearance using complement system and phagocytic cells. CONCLUSION Our findings elucidated the potential application of the PspA1-5c+p vaccine candidate as a serotype-independent pneumococcal vaccine with a strong cross-reactivity feature. Further in-vitro and in-vivo investigations against other PspA clades should be performed to confirm the full protection of the PspA1-5c+p vaccine candidate.
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Affiliation(s)
- Elnaz Afshari
- grid.411463.50000 0001 0706 2472Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Reza Ahangari Cohan
- grid.420169.80000 0000 9562 2611Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran
| | - Fattah Sotoodehnejadnematalahi
- grid.411463.50000 0001 0706 2472Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Seyed Fazlollah Mousavi
- grid.420169.80000 0000 9562 2611Department of Microbiology, Pasteur Institute of Iran, 69 Pasteur Ave., Tehran, 13164 Iran
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Li Y, Bai Y, Fan TP, Zheng X, Cai Y. Characterization of a putative tropinone reductase from Tarenaya hassleriana with a broad substrate specificity. Biotechnol Appl Biochem 2022; 69:2530-2539. [PMID: 34902878 DOI: 10.1002/bab.2302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022]
Abstract
A novel short-chain alcohol dehydrogenase from Tarenaya hassleriana labeled as putative tropinone reductase was heterologously expressed in Escherichia coli. Purified recombinant protein had molecular weight of approximately 30 kDa on 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis. T. hassleriana tropinone reductase-like enzyme (ThTRL) had not detected oxidative activity. The optimum pH for enzyme activity of ThTRL was weakly acidic (pH 5.0). 50°C was the optimum temperature for ThTRL. The highest catalytic efficiency and substrate affinity for recombinant ThTRL were observed with (+)-camphorquinone (kcat /Km = 814.3 s-1 mM-1 , Km = 44.25 μM). ThTRL exhibited a broad substrate specificity and reduced various carbonyl compounds, including small lipophilic aldehydes and ketones, terpene ketones, and their structural analogs.
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Affiliation(s)
- Yixiang Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, Shanxi, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, Shanxi, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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4
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Leibovich Z, Gronau I. Optimal Design of Synthetic DNA Sequences Without Unwanted Binding Sites. J Comput Biol 2022; 29:974-986. [PMID: 35648072 DOI: 10.1089/cmb.2021.0417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Synthesizing DNA molecules by design has become an essential tool in molecular biology and is expected to become ubiquitous in the coming decade. Successful design of a synthetic DNA molecule often requires satisfying multiple objectives, some of which may conflict with others. One particularly important objective is the elimination of unwanted protein binding sites, which may interfere with the desired function of the synthesized molecule. While most design tools offer this fundamental capability, they do not follow a systematic approach that guarantees elimination of all unwanted sites whenever a feasible solution exists. Furthermore, the algorithms these tools use (when published) are often quite naive and inefficient. We present a formal description of the binding site elimination problem and suggest several efficient algorithms that eliminate unwanted patterns with minimum interference to the desired function of the synthesized sequence. These algorithms are simple, efficient, and flexible and, therefore, can be easily incorporated in all existing DNA design tools, enhancing their design capabilities.
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Affiliation(s)
- Zehavit Leibovich
- Efi Arazi School of Computer Science, Reichman University, Herzliya, Israel
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Reichman University, Herzliya, Israel
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5
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Matsumoto H, Kimura S, Nagai Y, Fukuda Y, Miyazaki K, Imai S, Inenaga T, Kashimura A. Leptin gene contributes to beef marbling standard, meat brightness, meat firmness, and beef fat standard of the Kumamoto sub-breed of Japanese Brown cattle. Anim Sci J 2022; 93:e13698. [PMID: 35247014 DOI: 10.1111/asj.13698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/14/2022] [Accepted: 02/09/2022] [Indexed: 11/29/2022]
Abstract
The Kumamoto sub-breed of Japanese Brown cattle has unique characteristics, such as great growth rate, and their contribution as future breeding materials is expected. To develop a DNA marker for their breeding, we investigated the effects of Leptin gene, controlling energy homeostasis, on carcass traits of the Kumamoto sub-breed. Sequence comparison identified five single nucleotide polymorphisms (SNPs): four linked synonymous mutations and one nonsynonymous mutation. Statistical analysis revealed that c.239C > T (p.A80V) had significant effects on the traits related with quality grade: beef marbling standard (p = 0.0132), meat brightness (p = 0.0383), and meat firmness (p = 0.0115). The C allele showed favorable effects; these scores of the C/C cattle were significantly higher than those of the C/T cattle. On the other hand, the effect of c.399T > C was observed on meat firmness (p = 0.0172) and beef fat standards (BFS) (p = 0.0129). The C/C cattle showed higher values of these traits than the T/T cattle. Our data suggested that these SNPs in Leptin gene could be used as a DNA marker for breeding of the Kumamoto sub-breed.
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Affiliation(s)
- Hirokazu Matsumoto
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Satoshi Kimura
- Course of Agricultural Sciences, Graduate School of Agriculture, Tokai University, Kumamoto, Japan
| | - Yohsuke Nagai
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Yuta Fukuda
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Kunio Miyazaki
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Saki Imai
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Toshiaki Inenaga
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Atsushi Kashimura
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
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Yu TH, Tan SI, Yi YC, Xue C, Ting WW, Chang JJ, Ng IS. New insight into the codon usage and medium optimization toward stable and high-level 5-aminolevulinic acid production in Escherichia coli. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108259] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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7
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Watts A, Sankaranarayanan S, Watts A, Raipuria RK. Optimizing protein expression in heterologous system: Strategies and tools. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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8
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Bayarri-Olmos R, Idorn M, Rosbjerg A, Pérez-Alós L, Hansen CB, Johnsen LB, Helgstrand C, Zosel F, Bjelke JR, Öberg FK, Søgaard M, Paludan SR, Bak-Thomsen T, Jardine JG, Skjoedt MO, Garred P. SARS-CoV-2 Neutralizing Antibody Responses towards Full-Length Spike Protein and the Receptor-Binding Domain. THE JOURNAL OF IMMUNOLOGY 2021; 207:878-887. [PMID: 34301847 DOI: 10.4049/jimmunol.2100272] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023]
Abstract
Tools to monitor SARS-CoV-2 transmission and immune responses are needed. We present a neutralization ELISA to determine the levels of Ab-mediated virus neutralization and a preclinical model of focused immunization strategy. The ELISA is strongly correlated with the elaborate plaque reduction neutralization test (ρ = 0.9231, p < 0.0001). The neutralization potency of convalescent sera strongly correlates to IgG titers against SARS-CoV-2 receptor-binding domain (RBD) and spike (ρ = 0.8291 and 0.8297, respectively; p < 0.0001) and to a lesser extent with the IgG titers against protein N (ρ = 0.6471, p < 0.0001). The preclinical vaccine NMRI mice models using RBD and full-length spike Ag as immunogens show a profound Ab neutralization capacity (IC50 = 1.9 × 104 to 2.6 × 104 and 3.9 × 103 to 5.2 × 103, respectively). Using a panel of novel high-affinity murine mAbs, we also show that a majority of the RBD-raised mAbs have inhibitory properties, whereas only a few of the spike-raised mAbs do. The ELISA-based viral neutralization test offers a time- and cost-effective alternative to the plaque reduction neutralization test. The immunization results indicate that vaccine strategies focused only on the RBD region may have advantages compared with the full spike.
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Affiliation(s)
| | - Manja Idorn
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | | | | | | | | | | | | | | | | | - Max Søgaard
- ExpreS2ion Biotechnologies, Horsholm, Denmark
| | - Søren R Paludan
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | | | - Joseph G Jardine
- Neutralizing Antibody Center, Scripps Research, International AIDS Vaccine Initiative, La Jolla, CA; and
| | | | - Peter Garred
- Copenhagen University Hospital, Copenhagen, Denmark
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Yi S, Jun CP, Jo KN, Lee H, Kim MS, Lee SD, Cao X, Lim J. Asynchronous multi-decadal time-scale series of biotic and abiotic responses to precipitation during the last 1300 years. Sci Rep 2020; 10:17814. [PMID: 33082500 PMCID: PMC7576146 DOI: 10.1038/s41598-020-74994-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/06/2020] [Indexed: 11/30/2022] Open
Abstract
East Asian summer monsoon (EASM)-driven rapid hydroclimatic variation is a crucial factor with major socioeconomic impacts. Nevertheless, decadal- to centennial-scale EASM variability over the last two millennia is still poorly understood. Pollen-based quantitative annual precipitation (PqPann) and annual precipitation reconstructed by artificial neural networks (ANNs) for the period 650-1940 CE were reconstructed from a paleo-reservoir in South Korea. ANNs reconstruction was performed to compensate for a hiatus section. On a decadal timescale, 10 high-precipitation periods were identified, and PqPann and ANNs reconstructions were comparable to local instrumental rainfall and historic drought records. Biotic lags to rapid climatic changes ranging from 25 to 100 years were recognized by asynchronous pollen and speleothem responses to precipitation. We suggest that PqPann-based decadal- to centennial-scale climatic change reconstruction should take biotic lags into account, although the lags can be ignored on the millennial scale. The position of the EASM rainband influenced rainfall magnitude.
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Affiliation(s)
- Sangheon Yi
- Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Korea.
- Korea University of Science and Technology (UST), Daejeon, 34113, Korea.
| | - Chang-Pyo Jun
- Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Korea.
| | - Kyoung-Nam Jo
- Kangwon National University, Chuncheon, 24341, Korea
| | - Hoil Lee
- Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Korea
| | - Min-Seok Kim
- Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Korea
| | - Sang Deuk Lee
- Nakdonggang National Institute of Biological Resources, Sangju, 37242, Korea
| | - Xianyong Cao
- Key Laboratory of Alpine Ecolgoy, Institute of Tibetan Plateau Research, Beijing, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Jaesoo Lim
- Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Korea
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Khezri G, Baghban Kohneh Rouz B, Ofoghi H, Davarpanah SJ. Heterologous expression of biologically active Mambalgin-1 peptide as a new potential anticancer, using a PVX-based viral vector in Nicotiana benthamiana. PLANT CELL, TISSUE AND ORGAN CULTURE 2020; 142:241-251. [PMID: 32836586 PMCID: PMC7323601 DOI: 10.1007/s11240-020-01838-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Mambalgin-1 is a peptide that acts as a potent analgesic through inhibiting acid-sensing ion channels (ASIC) in nerve cells. Research has shown that ASIC channels are involved in the proliferation and growth of cancer cells; therefore, Mambalgin-1 can be a potential anti-cancer by inhibiting these channels. In the present study, the Nicotiana benthamiana codon optimized Mambalgin-1 gene was synthesized and cloned in PVX (potato virus X) viral vector. The two cultures of Agrobacterium containing Mambalgin-1 and P19 silencing suppressor genes were co-agroinfiltrated into N. benthamiana leaves. Five days post infiltration, the production of recombinant Mambalgin-1 was determined by western blotting. For biological activity, MTT (3(4, 5-dimethylthiazole-2-yl)-2, 5-diphenyltetrazolium bromide) was analyzed for the cytotoxicity recombinant Mambalgin-1 from the transformed plants on nervous (SH-SY5Y) and breast (MCF7) cancer cells. The results showed that the plants expressing open reading frame of Mambalgin-1 showed recombinant 7.4 kDa proteins in the entire plant extract. In the MTT test, it was found that Mambalgin-1 had cytotoxic effects on SH-SY5Y cancer cells, yet no effects on MCF7 cancer cells were observed. According to the results, the expression of the biologically active recombinant Mambalgin-1 in the transformed plant leaves was confirmed and Mambalgin-1 can also have anti-cancer (inhibition of ASIC channels) potential along with its already known analgesic effect.
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Affiliation(s)
- Ghaffar Khezri
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran
| | | | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Seyed Javad Davarpanah
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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11
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Cahyadi TA, Syihab Z, Widodo LE, Notosiswoyo S, Widijanto E. Analysis of hydraulic conductivity of fractured groundwater flow media using artificial neural network back propagation. Neural Comput Appl 2020. [DOI: 10.1007/s00521-020-04970-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Şen A, Kargar K, Akgün E, Pınar MÇ. Codon optimization: a mathematical programing approach. Bioinformatics 2020; 36:4012-4020. [DOI: 10.1093/bioinformatics/btaa248] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 11/25/2019] [Accepted: 04/13/2020] [Indexed: 12/11/2022] Open
Abstract
AbstractMotivationSynthesizing proteins in heterologous hosts is an important tool in biotechnology. However, the genetic code is degenerate and the codon usage is biased in many organisms. Synonymous codon changes that are customized for each host organism may have a significant effect on the level of protein expression. This effect can be measured by using metrics, such as codon adaptation index, codon pair bias, relative codon bias and relative codon pair bias. Codon optimization is designing codons that improve one or more of these objectives. Currently available algorithms and software solutions either rely on heuristics without providing optimality guarantees or are very rigid in modeling different objective functions and restrictions.ResultsWe develop an effective mixed integer linear programing (MILP) formulation, which considers multiple objectives. Our numerical study shows that this formulation can be effectively used to generate (Pareto) optimal codon designs even for very long amino acid sequences using a standard commercial solver. We also show that one can obtain designs in the efficient frontier in reasonable solution times and incorporate other complex objectives, such as mRNA secondary structures in codon design using MILP formulations.Availability and implementationhttp://alpersen.bilkent.edu.tr/codonoptimization/CodonOptimization.zip.
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Affiliation(s)
- Alper Şen
- Department of Industrial Engineering, Bilkent University, Ankara 06800, Turkey
| | - Kamyar Kargar
- Department of Industrial Engineering, Bilkent University, Ankara 06800, Turkey
| | - Esma Akgün
- Department of Management Sciences, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Mustafa Ç Pınar
- Department of Industrial Engineering, Bilkent University, Ankara 06800, Turkey
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Antibody signatures in patients with histopathologically defined multiple sclerosis patterns. Acta Neuropathol 2020; 139:547-564. [PMID: 31950335 PMCID: PMC7035238 DOI: 10.1007/s00401-019-02120-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 12/15/2022]
Abstract
Early active multiple sclerosis (MS) lesions can be classified histologically into three main immunopathological patterns of demyelination (patterns I–III), which suggest pathogenic heterogeneity and may predict therapy response. Patterns I and II show signs of immune-mediated demyelination, but only pattern II is associated with antibody/complement deposition. In pattern III lesions, which include Baló’s concentric sclerosis, primary oligodendrocyte damage was proposed. Serum antibody reactivities could reflect disease pathogenesis and thus distinguish histopathologically defined MS patterns. We established a customized microarray with more than 700 peptides that represent human and viral antigens potentially relevant for inflammatory demyelinating CNS diseases, and tested sera from 66 patients (pattern I n = 12; II n = 29; III n = 25, including 8 with Baló’s), healthy controls, patients with Sjögren’s syndrome and stroke patients. Cell-based assays were performed for aquaporin 1 (AQP1) and AQP4 antibody detection. No single peptide showed differential binding among study cohorts. Because antibodies can react with different peptides from one protein, we also analyzed groups of peptides. Patients with pattern II showed significantly higher reactivities to Nogo-A peptides as compared to patterns I (p = 0.02) and III (p = 0.02). Pattern III patients showed higher reactivities to AQP1 (compared to pattern I p = 0.002, pattern II p = 0.001) and varicella zoster virus (VZV, compared to pattern II p = 0.05). In patients with Baló’s, AQP1 reactivity was also significantly higher compared to patients without Baló’s (p = 0.04), and the former revealed distinct antibody signatures. Histologically, Baló’s patients showed loss of AQP1 and AQP4 in demyelinating lesions, but no antibodies binding conformational AQP1 or AQP4 were detected. In summary, higher reactivities to Nogo-A peptides in pattern II patients could be relevant for enhanced axonal repair and remyelination. Higher reactivities to AQP1 peptides in pattern III patients and its subgroup of Baló’s patients possibly reflect astrocytic damage. Finally, latent VZV infection may cause peripheral immune activation.
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14
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Stepwise optimization of recombinant protein production in Escherichia coli utilizing computational and experimental approaches. Appl Microbiol Biotechnol 2020; 104:3253-3266. [DOI: 10.1007/s00253-020-10454-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/28/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022]
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15
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Traubenik S, Reynoso MA, Hobecker K, Lancia M, Hummel M, Rosen B, Town C, Bailey-Serres J, Blanco F, Zanetti ME. Reprogramming of Root Cells during Nitrogen-Fixing Symbiosis Involves Dynamic Polysome Association of Coding and Noncoding RNAs. THE PLANT CELL 2020; 32:352-373. [PMID: 31748328 PMCID: PMC7008484 DOI: 10.1105/tpc.19.00647] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/11/2019] [Accepted: 11/20/2019] [Indexed: 05/04/2023]
Abstract
Translational control is a widespread mechanism that allows the cell to rapidly modulate gene expression in order to provide flexibility and adaptability to eukaryotic organisms. We applied translating ribosome affinity purification combined with RNA sequencing to characterize translational regulation of mRNAs at early stages of the nitrogen-fixing symbiosis established between Medicago truncatula and Sinorhizobium meliloti Our analysis revealed a poor correlation between transcriptional and translational changes and identified hundreds of regulated protein-coding and long noncoding RNAs (lncRNAs), some of which are regulated in specific cell types. We demonstrated that a short variant of the lncRNA Trans-acting small interference RNA3 (TAS3) increased its association to the translational machinery in response to rhizobia. Functional analysis revealed that this short variant of TAS3 might act as a target mimic that captures microRNA390, contributing to reduce trans acting small interference Auxin Response Factor production and modulating nodule formation and rhizobial infection. The analysis of alternative transcript variants identified a translationally upregulated mRNA encoding subunit 3 of the SUPERKILLER complex (SKI3), which participates in mRNA decay. Knockdown of SKI3 decreased nodule initiation and development, as well as the survival of bacteria within nodules. Our results highlight the importance of translational control and mRNA decay pathways for the successful establishment of the nitrogen-fixing symbiosis.
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Affiliation(s)
- Soledad Traubenik
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Mauricio Alberto Reynoso
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Karen Hobecker
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Marcos Lancia
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Maureen Hummel
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521
| | | | | | - Julia Bailey-Serres
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521
| | - Flavio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
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16
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Ren H, Shi C, Zhao H. Computational Tools for Discovering and Engineering Natural Product Biosynthetic Pathways. iScience 2020; 23:100795. [PMID: 31926431 PMCID: PMC6957853 DOI: 10.1016/j.isci.2019.100795] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/24/2019] [Accepted: 12/19/2019] [Indexed: 01/09/2023] Open
Abstract
Natural products (NPs), also known as secondary metabolites, are produced in bacteria, fungi, and plants. NPs represent a rich source of antibacterial, antifungal, and anticancer agents. Recent advances in DNA sequencing technologies and bioinformatics unveiled nature's great potential for synthesizing numerous NPs that may confer unprecedented structural and biological features. However, discovering novel bioactive NPs by genome mining remains a challenge. Moreover, even with interesting bioactivity, the low productivity of many NPs significantly limits their practical applications. Here we discuss the progress in developing bioinformatics tools for efficient discovery of bioactive NPs. In addition, we highlight computational methods for optimizing the productivity of NPs of pharmaceutical importance.
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Affiliation(s)
- Hengqian Ren
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chengyou Shi
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Departments of Chemistry, Biochemistry, and Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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17
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Matsumoto H, Kohara R, Sugi M, Usui A, Oyama K, Mannen H, Sasazaki S. The non-synonymous mutation in bovine SPP1 gene influences carcass weight. Heliyon 2019; 5:e03006. [PMID: 31879711 PMCID: PMC6920195 DOI: 10.1016/j.heliyon.2019.e03006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/12/2019] [Accepted: 12/05/2019] [Indexed: 01/12/2023] Open
Abstract
Meat quality in beef cattle is controlled by genetic factors. SPP1 (secreted phosphoprotein 1) gene, coding a multifunctional cytokine with diverse biological functions, is the candidate gene influencing carcass traits. In this study, we tried to discover DNA polymorphisms associated with beef quality in bovine SPP1 gene, so that two SNPs (single nucleotide polymorphisms) in the promoter region and one SNP in the CDS (coding sequence) region were identified. Although the formers were predicted to alter SPP1 expression, they did not show any effects on the traits. On the contrary, statistical analysis revealed that g.58675C > T, a non-synonymous mutation from threonine to methionine in the conservative region, had a significant effect on carcass weight. Carcass weight of the animals with C/T allele (473.9 ± 6.0 kg) was significantly heavier than that of the C/C homozygotes (459.2 ± 2.8 kg). Because SPP1 gene functions in skeletal muscle cells as a positive regulator, the non-synonymous mutation might influence muscle development and remodeling, resulting in increased carcass weight of the C/T animals. Our results indicate that the SNP can be applied as a DNA marker for the improvement of beef cattle.
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Affiliation(s)
- Hirokazu Matsumoto
- Laboratory of Animal Genetics, Faculty of Agriculture, Tokai University, Kumamoto, 862-8652, Japan
| | - Ryosuke Kohara
- Laboratory of Animal Genetics, Faculty of Agriculture, Tokai University, Kumamoto, 862-8652, Japan
| | - Makoto Sugi
- Laboratory of Animal Genetics, Faculty of Agriculture, Tokai University, Kumamoto, 862-8652, Japan
| | - Azumi Usui
- Laboratory of Animal Genetics, Faculty of Agriculture, Tokai University, Kumamoto, 862-8652, Japan
| | - Kenji Oyama
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai, Hyogo, 675-2103, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
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18
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Kulmala A, Huovinen T, Lamminmäki U. Improvement of Fab expression by screening combinatorial synonymous signal sequence libraries. Microb Cell Fact 2019; 18:157. [PMID: 31526395 PMCID: PMC6745802 DOI: 10.1186/s12934-019-1210-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/06/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Antibody fragments can be expressed in Escherichia coli, where they are commonly directed to the periplasm via Sec pathway to enable disulphide bridge formations and correct folding. In order to transport antibody fragments to the periplasmic space via Sec pathway, they are equipped with N-terminal signal sequence. Periplasmic expression has many benefits but it's also subjected to many hurdles like inefficient translocation across the inner membrane and insufficient capacity of the translocation system. One solution to overcome these hurdles is a modulation of codon usage of signal sequence which has proved to be an efficient way of tuning the translocation process. Modulation of codon usage of signal sequences has been successfully employed also in improving the expression levels of antibody fragments, but unfortunately the effect of codon usage on the expression has not been thoroughly analyzed. RESULTS In the present study we established three synonymous PelB signal sequence libraries by modulating codon usage of light chain and heavy chain PelB signal sequences of a Fab fragment. Each region (n-region, hydrophobic region and c-region) of the PelB signal sequence in the both chains of the Fab fragment in a bicistronic expression vector was mutated separately. We then screened for clones with improved expression profile. The best source for improved clones was the n-region library but in general, improved clones were obtained from all of the three libraries. After screening, we analyzed the effects of codon usage and mRNA secondary structures of chosen clones on the expression levels of the Fab fragment. When it comes to codon usage based factors, it was discovered that especially codon usage of fifth leucine position of the light chain PelB affects the expression levels of Fab fragment. In addition, we observed that mRNA secondary structures in the translation initiation regions of the light and heavy chain have an effect on expression levels as well. CONCLUSIONS In conclusion, the established synonymous signal sequence libraries are good sources for discovering Fab fragments with improved expression profile and obtaining new codon usage related information.
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Affiliation(s)
- Antti Kulmala
- Department of Biochemistry/Biotechnology, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Tuomas Huovinen
- Department of Biochemistry/Biotechnology, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Urpo Lamminmäki
- Department of Biochemistry/Biotechnology, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland.
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19
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In silico analysis of different signal peptides for the secretory production of recombinant human keratinocyte growth factor in Escherichia coli. Comput Biol Chem 2019; 80:225-233. [DOI: 10.1016/j.compbiolchem.2019.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 01/23/2019] [Accepted: 03/11/2019] [Indexed: 12/31/2022]
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20
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Matsumoto H, Kawaguchi F, Itoh S, Yotsu S, Fukuda K, Oyama K, Mannen H, Sasazaki S. The SNPs in bovine MMP14 promoter influence on fat-related traits. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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21
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Dai B, Sargent CJ, Gui X, Liu C, Zhang F. Fibril Self-Assembly of Amyloid–Spider Silk Block Polypeptides. Biomacromolecules 2019; 20:2015-2023. [DOI: 10.1021/acs.biomac.9b00218] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | - Xinrui Gui
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
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22
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Pourseif MM, Yousefpour M, Aminianfar M, Moghaddam G, Nematollahi A. A multi-method and structure-based in silico vaccine designing against Echinococcus granulosus through investigating enolase protein. ACTA ACUST UNITED AC 2019; 9:131-144. [PMID: 31508329 PMCID: PMC6726745 DOI: 10.15171/bi.2019.18] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 12/24/2022]
Abstract
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Introduction: Hydatid disease is a ubiquitous parasitic zoonotic disease, which causes different medical, economic and serious public health problems in some parts of the world. The causal organism is a multi-stage parasite named Echinococcus granulosus whose life cycle is dependent on two types of mammalian hosts viz definitive and intermediate hosts.
Methods: In this study, enolase, as a key functional enzyme in the metabolism of E. granulosus (EgEnolase), was targeted through a comprehensive in silico modeling analysis and designing a host-specific multi-epitope vaccine. Three-dimensional (3D) structure of enolase was modeled using MODELLER v9.18 software. The B-cell epitopes (BEs) were predicted based on the multi-method approach and via some authentic online predictors. ClusPro v2.0 server was used for docking-based T-helper epitope prediction. The 3D structure of the vaccine was modeled using the RaptorX server. The designed vaccine was evaluated for its immunogenicity, physicochemical properties, and allergenicity. The codon optimization of the vaccine sequence was performed based on the codon usage table of E. coli K12. Finally, the energy minimization and molecular docking were implemented for simulating the vaccine binding affinity to the TLR-2 and TLR-4 and the complex stability.
Results: The designed multi-epitope vaccine was found to induce anti-EgEnolase immunity which may have the potential to prevent the survival and proliferation of E. granulosus into the definitive host.
Conclusion: Based on the results, this step-by-step immunoinformatics approach could be considered as a rational platform for designing vaccines against such multi-stage parasites. Furthermore, it is proposed that this multi-epitope vaccine is served as a promising preventive anti-echinococcosis agent.
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Affiliation(s)
- Mohammad Mostafa Pourseif
- Department of Physiology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran.,Infectious Diseases and Tropical Medicine Research Center (IDTMRC), Department of Aerospace and Subaquatic Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Mitra Yousefpour
- Department of Physiology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Mohammad Aminianfar
- Infectious Diseases and Tropical Medicine Research Center (IDTMRC), Department of Aerospace and Subaquatic Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Gholamali Moghaddam
- Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Ahmad Nematollahi
- Department of Pathobiology, Veterinary College, University of Tabriz, Tabriz, Iran
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23
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Torrent M, Chalancon G, de Groot NS, Wuster A, Madan Babu M. Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions. Sci Signal 2018; 11:11/546/eaat6409. [PMID: 30181241 PMCID: PMC6130803 DOI: 10.1126/scisignal.aat6409] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Decoding the information in mRNA during protein synthesis relies on tRNA adaptors, the abundance of which can affect the decoding rate and translation efficiency. To determine whether cells alter tRNA abundance to selectively regulate protein expression, we quantified changes in the abundance of individual tRNAs at different time points in response to diverse stress conditions in Saccharomyces cerevisiae. We found that the tRNA pool was dynamic and rearranged in a manner that facilitated selective translation of stress-related transcripts. Through genomic analysis of multiple data sets, stochastic simulations, and experiments with designed sequences of proteins with identical amino acids but altered codon usage, we showed that changes in tRNA abundance affected protein expression independently of factors such as mRNA abundance. We suggest that cells alter their tRNA abundance to selectively affect the translation rates of specific transcripts to increase the amounts of required proteins under diverse stress conditions.
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Affiliation(s)
- Marc Torrent
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK. .,Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Guilhem Chalancon
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Natalia S de Groot
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Arthur Wuster
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - M Madan Babu
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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24
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Hertz CE, Bayarri-Olmos R, Kirketerp-Møller N, van Putten S, Pilely K, Skjoedt MO, Garred P. Chimeric Proteins Containing MAP-1 and Functional Domains of C4b-Binding Protein Reveal Strong Complement Inhibitory Capacities. Front Immunol 2018; 9:1945. [PMID: 30210498 PMCID: PMC6120983 DOI: 10.3389/fimmu.2018.01945] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/07/2018] [Indexed: 01/23/2023] Open
Abstract
The complement system is a tightly regulated network of proteins involved in defense against pathogens, inflammatory processes, and coordination of the innate and adaptive immune responses. Dysregulation of the complement cascade is associated with many inflammatory disorders. Thus, inhibition of the complement system has emerged as an option for treatment of a range of different inflammatory diseases. MAP-1 is a pattern recognition molecule (PRM)-associated inhibitor of the lectin pathway of the complement system, whereas C4b-binding protein (C4BP) regulates both the classical and lectin pathways. In this study we generated chimeric proteins consisting of MAP-1 and the first five domains of human C4BP (C4BP1−5) in order to develop a targeted inhibitor acting at different levels of the complement cascade. Two different constructs were designed and expressed in CHO cells where MAP-1 was fused with C4BP1−5 in either the C- or N-terminus. The functionality of the chimeric proteins was assessed using different in vitro complement activation assays. Both chimeric proteins displayed the characteristic Ca2+-dependent dimerization and binding to PRMs of native MAP-1, as well as the co-factor activity of native C4BP. In ELISA-based complement activation assays they could effectively inhibit the lectin and classical pathways. Notably, MAP-1:C4BP1−5 was five times more effective than rMAP-1 and rC4BP1−5 applied at the same time, emphasizing the advantage of a single inhibitor containing both functional domains. The MAP-1/C4BP chimeras exert unique complement inhibitory properties and represent a novel therapeutic approach targeting both upstream and central complement activation.
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Affiliation(s)
- Cecilie E Hertz
- Laboratory of Molecular Medicine, Department of Clinical Immunology Section, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rafael Bayarri-Olmos
- Laboratory of Molecular Medicine, Department of Clinical Immunology Section, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nikolaj Kirketerp-Møller
- Laboratory of Molecular Medicine, Department of Clinical Immunology Section, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sander van Putten
- Finsen Laboratory, Rigshospitalet, Biotech Research and Innovation Center (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Katrine Pilely
- Laboratory of Molecular Medicine, Department of Clinical Immunology Section, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel-Ole Skjoedt
- Laboratory of Molecular Medicine, Department of Clinical Immunology Section, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology Section, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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25
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Bowen CH, Dai B, Sargent CJ, Bai W, Ladiwala P, Feng H, Huang W, Kaplan DL, Galazka JM, Zhang F. Recombinant Spidroins Fully Replicate Primary Mechanical Properties of Natural Spider Silk. Biomacromolecules 2018; 19:3853-3860. [DOI: 10.1021/acs.biomac.8b00980] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | | | | | | | | | | | - Wenwen Huang
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Jonathan M. Galazka
- Space Biosciences Division, Ames Research Center, National Aeronautics and Space Administration, Moffett Field, California 94035, United States
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26
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Immanuel SRC, Banerjee D, Rajankar MP, Raghunathan A. Integrated constraints based analysis of an engineered violacein pathway in Escherichia coli. Biosystems 2018; 171:10-19. [PMID: 30008425 DOI: 10.1016/j.biosystems.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/05/2018] [Accepted: 06/15/2018] [Indexed: 12/20/2022]
Abstract
Strategies towards optimal violacein biosynthesis, a potential drug molecule, need systems level coordination of enzymatic activities of individual genes in a multigene operon vioABCDE. Constraints-based flux balance analysis of an extended iAF1260 model (iAF1260vio) with a reconstructed violacein module predicted growth and violacein yields in Escherichia coli accurately. Shadow price (SP) analysis identified tryptophan metabolism and NADPH as limiting. Increased tryptophan levels in Δpgi & ΔpheA were validated using in silico gene deletion analysis. Phenotypic phase plane (PhPP) analysis highlighted sensitivity between tryptophan and NADPH for violacein synthesis at molar growth yields. A synthetic VioABCDE operon (SYNO) sequence was designed to maximize Codon Adaptive Index (CAI: 0.9) and tune translation initiation rates (TIR: 2-50 fold higher) in E. coli. All pSYN E. coli transformants produced higher violacein, with a maximum six-fold increase in yields. The rational design E. coli: ΔpheA SYN: gave the highest violacein titers (33.8 mg/l). Such integrated approaches targeting multiple molecular hierarchies in the cell can be extended further to increase violacein yields.
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Affiliation(s)
| | - Deepanwita Banerjee
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Mayooreshwar P Rajankar
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Anu Raghunathan
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.
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27
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Ty TV, Phat LV, Hiep HV. Groundwater Level Prediction Using Artificial Neural Networks: A Case Study in Tra Noc Industrial Zone, Can Tho City, Vietnam. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/jwarp.2018.109050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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28
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Pourseif MM, Moghaddam G, Daghighkia H, Nematollahi A, Omidi Y. A novel B- and helper T-cell epitopes-based prophylactic vaccine against Echinococcus granulosus. ACTA ACUST UNITED AC 2017; 8:39-52. [PMID: 29713601 PMCID: PMC5915707 DOI: 10.15171/bi.2018.06] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/02/2017] [Accepted: 12/03/2017] [Indexed: 12/17/2022]
Abstract
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Introduction:
In this study, we targeted the worm stage of Echinococcus granulosus to design a novel multi-epitope B- and helper T-cell based vaccine construct for immunization of dogs against this multi-host parasite.
Methods:
The vaccine was designed based on the local Eg14-3-3 antigen (Ag). DNA samples were extracted from the protoscoleces of the infected sheep’s liver, and then subjected to the polymerase chain reaction (PCR) with 14-3-3 specific forward and reverse primers. For the vaccine designing, several in silico steps were undertaken. Three-dimensional (3D) structure of the local Eg14-3-3 Ag was modeled by EasyModeller software. The protein modeling accuracy was then analyzed via various validation assays. Potential transmembrane helix, signal peptide, post-translational modifications and allergenicity of Eg14-3-3 were evaluated as the preliminary measures of B-cell epitopes (BEs ) prediction. Having used many web-servers, a well-designed process was carried out for improved prediction of BEs. High ranked linear and conformational BEs were utilized for engineering the final vaccine construct. Possible T-helper epitopes (TEs) were identified by the molecular docking between 13-mer fragments of the Eg14-3-3 Ag and two high frequent dog class II MHC alleles (i.e., DLA-DRB1*01101 and DRB1*01501). The epitopes coverage was evaluated by Shannon’s variability plot.
Results:
The final designed construct was analyzed based on different physicochemical properties, which was then codon optimized for high-level expression in Escherichia coli k12. This minigene construct is the first dog-specific epitopic vaccine construct that is established based on TEs with high-binding affinity to canine MHC alleles.
Conclusion:
This in silico study is the first part of a multi-antigenic vaccine designing work that represents as a novel dog-specific vaccine against E. granulosus. Here, we present key data on the step-by-step methodologies used for designing this de novo vaccine, which is under comprehensive in vivo investigations.
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Affiliation(s)
- Mohammad M Pourseif
- Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.,Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Gholamali Moghaddam
- Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Hossein Daghighkia
- Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Ahmad Nematollahi
- Department of Pathobiology, Veterinary Collage, University of Tabriz, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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29
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Analysis of codon usage bias of Crimean-Congo hemorrhagic fever virus and its adaptation to hosts. INFECTION GENETICS AND EVOLUTION 2017; 58:1-16. [PMID: 29198972 DOI: 10.1016/j.meegid.2017.11.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 11/02/2017] [Accepted: 11/28/2017] [Indexed: 01/05/2023]
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is a negative-sense, single stranded RNA virus with a three-segmented genome that belongs to the genus Nairovirus within the family Bunyaviridae. CCHFV uses Hyalomma ticks as a vector to infect humans with a wide range of clinical signs, from asymptomatic to Zika-like syndrome. Despite significant progress in genomic analyses, the influences of viral relationships with different hosts on overall viral fitness, survival, and evading the host's immune systems remain unknown. To better understand the evolutionary characteristics of CCHFV, we performed a comprehensive analysis of the codon usage pattern in 179 CCHFV strains by calculating the relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), and other indicators. The results indicate that the codon usage bias of CCHFV is relatively low. Several lines of evidence support the hypothesis that a translation selection factor is shaping codon usage pattern in this virus. A correspondence analysis (CA) showed that other factors, such as base composition, aromaticity, and hydrophobicity may also be involved in shaping the codon usage pattern of CCHFV. Additionally, the results from a comparative analysis of RSCU between CCHFV and its hosts suggest that CCHFV tends to evolve codon usage patterns that are comparable to those of its hosts. Furthermore, the selection pressures from Homo sapiens, Bos taurus, and Ovis aries on the CCHFV RSCU patterns were dominant when compared with selection pressure from Hyalomma spp. vectors. Taken together, both natural selection and mutation pressure are important for shaping the codon usage pattern of CCHFV. We believe that such findings will assist researchers in understanding the evolution of CCHFV and its adaptation to its hosts.
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30
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Goswami AM. Codon usage patterns of 3β-hydroxysteroid dehydrogenase type 2 gene across mammalian species and the influence of mutation and selection pressure. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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31
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Pourseif MM, Moghaddam G, Naghili B, Saeedi N, Parvizpour S, Nematollahi A, Omidi Y. A novel in silico minigene vaccine based on CD4 + T-helper and B-cell epitopes of EG95 isolates for vaccination against cystic echinococcosis. Comput Biol Chem 2017; 72:150-163. [PMID: 29195784 DOI: 10.1016/j.compbiolchem.2017.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 01/03/2023]
Abstract
EG95 oncospheral antigen plays a crucial role in Echinococcus granulosus pathogenicity. Considering the diversity of antigen among different EG95 isolates, it seems to be an ideal antigen for designing a universal multivalent minigene vaccine, so-called multi-epitope vaccine. This is the first in silico study to design a construct for the development of global EG95-based hydatid vaccine against E. granulosus in intermediate hosts. After antigen sequence selection, the three-dimensional structure of EG95 was modeled and multilaterally validated. The preliminary parameters for B-cell epitope prediction were implemented such as the possible transmembrane helix, signal peptide, post-translational modifications and allergenicity. The high ranked linear and conformational B-cell epitopes derived from several online web-servers (e.g., ElliPro, BepiPred v1.0, BcePred, ABCpred, SVMTrip, IEDB algorithms, SEPPA v2.0 and Discotope v2.0) were utilized for multiple sequence alignment and then for engineering the vaccine construct. T-helper based epitopes were predicted by molecular docking between the high frequent ovar class II allele (Ovar-DRB1*1202) and hexadecamer fragments of the EG95 protein. Having used the immune-informatics tools, we formulated the first EG95-based minigene vaccine based on T-helper epitope with high-binding affinity to the ovar MHC allele. This designed construct was analyzed for different physicochemical properties. It was also codon-optimized for high-level expression in Escherichia coli k12. Taken all, we propose the present in silico vaccine constructs as a promising platform for the generation of broadly protective vaccines for species and genus-specific immunization of the natural hosts of the parasite.
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Affiliation(s)
- Mohammad M Pourseif
- Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran; Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Gholamali Moghaddam
- Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
| | - Behrouz Naghili
- Research Center for Infectious and Tropical Diseases, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazli Saeedi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahmad Nematollahi
- Department of Pathobiology, Veterinary College, University of Tabriz, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; School of Advanced Biomedical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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Youshia J, Ali ME, Lamprecht A. Artificial neural network based particle size prediction of polymeric nanoparticles. Eur J Pharm Biopharm 2017; 119:333-342. [DOI: 10.1016/j.ejpb.2017.06.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/29/2017] [Accepted: 06/29/2017] [Indexed: 01/12/2023]
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Rojas Arias AC, Palacio JL, Chaparro-Giraldo A, López-Pazos SA. Patents and genetically modified soybean for glyphosate resistance. WORLD PATENT INFORMATION 2017. [DOI: 10.1016/j.wpi.2017.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Tuan-Anh T, Ly LT, Viet NQ, Bao PT. Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli. BMC Bioinformatics 2017; 18:100. [PMID: 28187713 PMCID: PMC5303253 DOI: 10.1186/s12859-017-1517-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 02/01/2017] [Indexed: 11/18/2022] Open
Abstract
Background Since the recombinant protein was discovered, it has become more popular in many aspects of life science. The value of global pharmaceutical market was $87 billion in 2008 and the sales for industrial enzyme exceeded $4 billion in 2012. This is strong evidence showing the great potential of recombinant protein. However, native genes introduced into a host can cause incompatibility of codon usage bias, GC content, repeat region, Shine-Dalgarno sequence with host’s expression system, so the yields can fall down significantly. Hence, we propose novel methods for gene optimization based on neural network, Bayesian theory, and Euclidian distance. Result The correlation coefficients of our neural network are 0.86, 0.73, and 0.90 in training, validation, and testing process. In addition, genes optimized by our methods seem to associate with highly expressed genes and give reasonable codon adaptation index values. Furthermore, genes optimized by the proposed methods are highly matched with the previous experimental data. Conclusion The proposed methods have high potential for gene optimization and further researches in gene expression. We built a demonstrative program using Matlab R2014a under Mac OS X. The program was published in both standalone executable program and Matlab function files. The developed program can be accessed from http://www.math.hcmus.edu.vn/~ptbao/paper_soft/GeneOptProg/.
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Affiliation(s)
- Tran Tuan-Anh
- Faculty of Mathematics and Computer Science, VNUHCM-University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam
| | - Le Thi Ly
- School of Biotechnology, VNUHCM-International University, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Ngo Quoc Viet
- Faculty of Information Technology, Ho Chi Minh City University of Pedagogy, 280 An Duong Vuong Street, Ward 4, District 5, Ho Chi Minh City, Vietnam
| | - Pham The Bao
- Faculty of Mathematics and Computer Science, VNUHCM-University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam.
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Wang H, Liu S, Zhang B, Wei W. Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts. PLoS One 2016; 11:e0166260. [PMID: 27893824 PMCID: PMC5125587 DOI: 10.1371/journal.pone.0166260] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/25/2016] [Indexed: 11/19/2022] Open
Abstract
Zika virus (ZIKV) is a mosquito-borne virus (arbovirus) in the family Flaviviridae, and the symptoms caused by ZIKV infection in humans include rash, fever, arthralgia, myalgia, asthenia and conjunctivitis. Codon usage bias analysis can reveal much about the molecular evolution and host adaption of ZIKV. To gain insight into the evolutionary characteristics of ZIKV, we performed a comprehensive analysis on the codon usage pattern in 46 ZIKV strains by calculating the effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and other indicators. The results indicate that the codon usage bias of ZIKV is relatively low. Several lines of evidence support the hypothesis that translational selection plays a role in shaping the codon usage pattern of ZIKV. The results from a correspondence analysis (CA) indicate that other factors, such as base composition, aromaticity, and hydrophobicity may also be involved in shaping the codon usage pattern of ZIKV. Additionally, the results from a comparative analysis of RSCU between ZIKV and its hosts suggest that ZIKV tends to evolve codon usage patterns that are comparable to those of its hosts. Moreover, selection pressure from Homo sapiens on the ZIKV RSCU patterns was found to be dominant compared with that from Aedes aegypti and Aedes albopictus. Taken together, both natural translational selection and mutation pressure are important for shaping the codon usage pattern of ZIKV. Our findings contribute to understanding the evolution of ZIKV and its adaption to its hosts.
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Affiliation(s)
- Hongju Wang
- Medical School of Henan University, Kaifeng, China
| | - Siqing Liu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Disease, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Disease, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Wenqiang Wei
- Medical School of Henan University, Kaifeng, China
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Hawari AH, Alnahhal W. Predicting the performance of multi-media filters using artificial neural networks. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 74:2225-2233. [PMID: 27842042 DOI: 10.2166/wst.2016.380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The impact of flow rate and turbidity on the performance of multi-media filtration has been studied using an artificial neural network (ANN) based model. The ANN model was developed and tested based on experimental data collected from a pilot scale multi-media filter system. Several ANN models were tested, and the best results with the lowest errors were achieved with two hidden layers and five neurons per layer. To examine the significance and efficiency of the developed ANN model it was compared with a linear regression model. The R2 values for the actual versus predicted results were 0.9736 and 0.9617 for the ANN model and the linear regression model, respectively. The ANN model showed an R-squared value increase of 1.22% when compared to the linear regression model. In addition, the ANN model gave a significant reduction of 91.5% and 97.9% in the mean absolute error and the root mean square error, respectively when compared to the linear regression model. The proposed model has proven to give plausible results to model complex relationships that can be used in real life water treatment plants.
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Affiliation(s)
- Alaa H Hawari
- Department of Civil and Architectural Engineering, Qatar University, P.O. Box 2713, Doha, Qatar E-mail:
| | - Wael Alnahhal
- Department of Civil and Architectural Engineering, Qatar University, P.O. Box 2713, Doha, Qatar E-mail:
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Zucchelli S, Patrucco L, Persichetti F, Gustincich S, Cotella D. Engineering Translation in Mammalian Cell Factories to Increase Protein Yield: The Unexpected Use of Long Non-Coding SINEUP RNAs. Comput Struct Biotechnol J 2016; 14:404-410. [PMID: 27872686 PMCID: PMC5107644 DOI: 10.1016/j.csbj.2016.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/26/2022] Open
Abstract
Mammalian cells are an indispensable tool for the production of recombinant proteins in contexts where function depends on post-translational modifications. Among them, Chinese Hamster Ovary (CHO) cells are the primary factories for the production of therapeutic proteins, including monoclonal antibodies (MAbs). To improve expression and stability, several methodologies have been adopted, including methods based on media formulation, selective pressure and cell- or vector engineering. This review presents current approaches aimed at improving mammalian cell factories that are based on the enhancement of translation. Among well-established techniques (codon optimization and improvement of mRNA secondary structure), we describe SINEUPs, a family of antisense long non-coding RNAs that are able to increase translation of partially overlapping protein-coding mRNAs. By exploiting their modular structure, SINEUP molecules can be designed to target virtually any mRNA of interest, and thus to increase the production of secreted proteins. Thus, synthetic SINEUPs represent a new versatile tool to improve the production of secreted proteins in biomanufacturing processes.
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Affiliation(s)
- Silvia Zucchelli
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy; Area of Neuroscience, SISSA, Trieste, Italy
| | - Laura Patrucco
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | | | - Stefano Gustincich
- Area of Neuroscience, SISSA, Trieste, Italy; Department of Neuroscience and Brain Technologies, Italian Institute of Technology (IIT), Genova, Italy
| | - Diego Cotella
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
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Karumathil S, Dirisala VR, Srinadh U, Nikhil V, Kumar NSS, Nair RR. Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha. Bioinform Biol Insights 2016; 10:167-84. [PMID: 27688709 PMCID: PMC5034883 DOI: 10.4137/bbi.s38192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/17/2016] [Accepted: 08/28/2016] [Indexed: 11/20/2022] Open
Abstract
Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed. Spearman’s rank correlation analyses of nucleotide contents suggested that mutational pressure and selection were acting in all examined mitogenomes but with varying intensities. The quantification of SCUB using effective number of codons vs. GC composition at the third codon position (GC3) plot suggested that mutational pressure due to GC compositional constraints might be one of the major influencing forces driving the SCUB in all chaetognaths except Sagitta enflata. However, neutrality plots revealed no significant correlation between GC3 and cumulative GC content at first and second codon positions (GC12) in all other species, except in Daphnia pulex. The parity rule 2 bias plot showed that significant compositional differences existed between C and G, as well as between A and T, contents in most of the protein-coding genes (PCGs) and, comparatively, A and T contents were used more proportionally than C and G contents in all chosen mitogenomes. Chi-square analysis revealed the presence of putative optimal codons in all species, except in S. enflata. The correspondence analysis identified that mutational pressure and selection act on the mitogenomes of the selected chaetognaths and other phyla with varying intensities. The cluster analysis based on relative synonymous codon usage (RSCU) values revealed that RSCU variations in the PCGs of mitogenomes of chaetognaths are more comparable with those of protostomes. Apart from mutational pressure and selection, certain unknown selective forces might be acting on the PCGs in the analyzed mitogenomes as the phenomenon of SCUB could not be explained by mutational pressure, by selection, or by both.
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Affiliation(s)
- Sudeesh Karumathil
- Aushmath Biosciences, Administrative office, Devaraj Corner, Vadavalli Post, Coimbatore, Tamil Nadu, India
| | - Vijaya R Dirisala
- Department of Biotechnology, Vignan's University (Vignan's Foundation for Science, Technology and Research University), Guntur, Andhra Pradesh, India
| | - Uthpala Srinadh
- Department of Biotechnology, Vignan's University (Vignan's Foundation for Science, Technology and Research University), Guntur, Andhra Pradesh, India
| | - Valaboju Nikhil
- Department of Biotechnology, Vignan's University (Vignan's Foundation for Science, Technology and Research University), Guntur, Andhra Pradesh, India
| | - N Satya Sampath Kumar
- Department of Biotechnology, Vignan's University (Vignan's Foundation for Science, Technology and Research University), Guntur, Andhra Pradesh, India
| | - Rahul R Nair
- Aushmath Biosciences, Administrative office, Devaraj Corner, Vadavalli Post, Coimbatore, Tamil Nadu, India
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BARUAH VISHWAJYOTI, SATAPATHY SIDDHARTHASANKAR, POWDEL BHESHRAJ, KONWARH ROCKTOTPAL, BURAGOHAIN ALAKKUMAR, RAY SUVENDRAKUMAR. Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins. J Genet 2016; 95:537-49. [PMID: 27659324 DOI: 10.1007/s12041-016-0667-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Jiménez JP, Chaparro Giraldo A. Diseño in silico y evaluación funcional de genes semisintéticos que confieran tolerancia a fosfinotricina. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2016. [DOI: 10.15446/rev.colomb.biote.v18n2.52206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La tolerancia a herbicidas es una de las características más usadas en los cultivos GM, con resultados positivos para los agricultores y el ambiente. El punto de partida, es el desarrollo de casetes de expresión que expresen la característica de interés, inicialmente construidos mediante técnicas de biología molecular convencionales. Actualmente, con herramientas de bioinformática y biología sintética, es posible diseñar y probar el constructo in silico, para luego contratar su síntesis. Esta aproximación, permite optimizar la expresión mediante la modificación del uso codónico. En este trabajo se diseñaron y evaluaron en Nicotiana benthamiana versiones semisintéticas de genes que confieren tolerancia al herbicida fosfinotricina. Se realizó un análisis de libertad de operación, con el fin de asegurar que los constructos diseñados no violen derechos de propiedad intelectual en Colombia. Se obtuvieron dos casetes de expresión con libertad de operación, que expresan versiones del gen bar. Palabras clave: cultivos GM, libertad de operación, tolerancia a herbicidas, uso codónico.
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Critical reflections on synthetic gene design for recombinant protein expression. Curr Opin Struct Biol 2016; 38:155-62. [DOI: 10.1016/j.sbi.2016.07.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/29/2016] [Accepted: 07/06/2016] [Indexed: 11/17/2022]
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Cigliola V, Populaire C, Pierri CL, Deutsch S, Haefliger JA, Fadista J, Lyssenko V, Groop L, Rueedi R, Thorel F, Herrera PL, Meda P. A Variant of GJD2, Encoding for Connexin 36, Alters the Function of Insulin Producing β-Cells. PLoS One 2016; 11:e0150880. [PMID: 26959991 PMCID: PMC4784816 DOI: 10.1371/journal.pone.0150880] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/20/2016] [Indexed: 01/16/2023] Open
Abstract
Signalling through gap junctions contributes to control insulin secretion and, thus, blood glucose levels. Gap junctions of the insulin-producing β-cells are made of connexin 36 (Cx36), which is encoded by the GJD2 gene. Cx36-null mice feature alterations mimicking those observed in type 2 diabetes (T2D). GJD2 is also expressed in neurons, which share a number of common features with pancreatic β-cells. Given that a synonymous exonic single nucleotide polymorphism of human Cx36 (SNP rs3743123) associates with altered function of central neurons in a subset of epileptic patients, we investigated whether this SNP also caused alterations of β-cell function. Transfection of rs3743123 cDNA in connexin-lacking HeLa cells resulted in altered formation of gap junction plaques and cell coupling, as compared to those induced by wild type (WT) GJD2 cDNA. Transgenic mice expressing the very same cDNAs under an insulin promoter revealed that SNP rs3743123 expression consistently lead to a post-natal reduction of islet Cx36 levels and β-cell survival, resulting in hyperglycemia in selected lines. These changes were not observed in sex- and age-matched controls expressing WT hCx36. The variant GJD2 only marginally associated to heterogeneous populations of diabetic patients. The data document that a silent polymorphism of GJD2 is associated with altered β-cell function, presumably contributing to T2D pathogenesis.
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Affiliation(s)
- Valentina Cigliola
- Department of Genetic Medicine and Development, University of Geneva Faculty of Medicine, Geneva, Switzerland
| | - Celine Populaire
- Centre Hospitalier Régional Universitaire Besançon, Besançon, France
| | - Ciro L. Pierri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Samuel Deutsch
- Joint Genome Institute, Walnut Creek, California, United States of America
| | | | - João Fadista
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden
- Steno Diabetes Center A/S, Gentofte, Denmark
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Malmö, Sweden
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Fabrizio Thorel
- Department of Genetic Medicine and Development, University of Geneva Faculty of Medicine, Geneva, Switzerland
| | - Pedro Luis Herrera
- Department of Genetic Medicine and Development, University of Geneva Faculty of Medicine, Geneva, Switzerland
| | - Paolo Meda
- Department of Cell Physiology and Metabolism, University of Geneva Faculty of Medicine, Geneva, Switzerland
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A new strategy to express the extracellular α-amylase from Pyrococcus furiosus in Bacillus amyloliquefaciens. Sci Rep 2016; 6:22229. [PMID: 26916714 PMCID: PMC4768087 DOI: 10.1038/srep22229] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/05/2016] [Indexed: 11/12/2022] Open
Abstract
Extracellular α-amylase from Pyrococcus furiosus (PFA) shows great starch-processing potential for industrial application due to its thermostability, long half-life and optimal activity at low pH; however, it is difficult to produce in large quantities. In contrast, α-amylase from Bacillus amyloliquefaciens (BAA) can be produced in larger quantities, but shows lower stability at high temperatures and low pH. Here, we describe a BAA protein expression pattern-mimicking strategy to express PFA in B. amyloliquefaciens using the expression and secretion elements of BAA, including the codon usage bias and mRNA structure of gene, promoter, signal peptide, host and cultivation conditions. This design was assessed to be successful by comparing the various genes (mpfa and opfa), promoters (PamyA and P43), and strains (F30, F31, F32 and F30-∆amyA). The final production of PFA yielded 2714 U/mL, about 3000- and 14-fold that reportedly produced in B. subtilis or E. coli, respectively. The recombinant PFA was optimally active at ~100 °C and pH 5 and did not require Ca2+ for activity or thermostability, and >80% of the enzyme activity was retained after treatment at 100 °C for 4 h.
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The Art of Gene Redesign and Recombinant Protein Production: Approaches and Perspectives. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Pavani A, Naushad SM, Kumar RM, Srinath M, Malempati AR, Kutala VK. Artificial neural network-based pharmacogenomic algorithm for warfarin dose optimization. Pharmacogenomics 2015; 17:121-31. [PMID: 26666467 DOI: 10.2217/pgs.15.161] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AIM To develop more precise pharmacogenomic algorithm for prediction of safe and effective dose of warfarin. MATERIALS & METHODS An artificial neural network (ANN) algorithm was developed by using age, gender, BMI, plasma vitamin K levels, thyroid status and ten genetic variables as the inputs and therapeutic warfarin dose as the output. Hyperbolic tangent function was used to build an ANN architecture. RESULTS This model explained 93.5% variability in warfarin dosing and predicted warfarin dose accurately in 74.5% patients whose international normalized ratio (INR) was less than 2.0 and in 83.3% patients whose INR was more than 3.5. This algorithm reduced the out-of-range INRs (odds ratio [OR]: 0.49; 95% CI: 0.30-0.79; p = 0.003), the rate of adverse drug reactions (OR: 0.00; 95% CI: 0.00-1.21; p = 0.06) and time to reach first therapeutic INR (OR: 6.73; 95% CI: 2.17-22.31; p < 0.0001). This algorithm was found to be applicable in both euthyroid and hypothyroid status. S-warfarin/7-hydroxywarfarin ratio was found to increase in subjects with CYP2C9*2 and CYP2C9*3 justifying the warfarin sensitivity attributed to these variants. CONCLUSION An application of ANN for warfarin dosing improves predictability and provides safe and effective dosing.
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Affiliation(s)
- Addepalli Pavani
- Department of Clinical Pharmacology & Therapeutics, Nizam's Institute of Medical Sciences, Hyderabad 500082, India
| | | | | | - Murali Srinath
- School of Chemical & Biotechnology, SASTRA University, Thanjavur 613401, India
| | - Amaresh Rao Malempati
- Department of Cardiothoracic Surgery, Nizam's Institute of Medical Sciences, Hyderabad 500082, India
| | - Vijay Kumar Kutala
- Department of Clinical Pharmacology & Therapeutics, Nizam's Institute of Medical Sciences, Hyderabad 500082, India
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Jung SK, McDonald KA, Dandekar AM. Effect of leaf incubation temperature profiles onagrobacterium tumefaciens-mediated transient expression. Biotechnol Prog 2015; 31:783-90. [DOI: 10.1002/btpr.2077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 02/18/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Sang-Kyu Jung
- Dept. of Chemical Engineering and Materials Science; University of California; Davis CA 95616
| | - Karen A. McDonald
- Dept. of Chemical Engineering and Materials Science; University of California; Davis CA 95616
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Jung SK, Lindenmuth BE, McDonald KA, Hwang H, Bui MQN, Falk BW, Uratsu SL, Phu ML, Dandekar AM. Agrobacterium tumefaciens mediated transient expression of plant cell wall-degrading enzymes in detached sunflower leaves. Biotechnol Prog 2015; 30:905-15. [PMID: 25180328 DOI: 10.1002/btpr.1888] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
For biofuel applications, synthetic endoglucanase E1 and xylanase (Xyn10A) derived from Acidothermus cellulolyticus were transiently expressed in detached whole sunflower (Helianthus annuus L.) leaves using vacuum infiltration. Three different expression systems were tested, including the constitutive CaMV 35S-driven, CMVar (Cucumber mosaic virus advanced replicating), and TRBO (Tobacco mosaic virus RNA-Based Overexpression Vector) systems. For 6-day leaf incubations, codon-optimized E1 and xylanase driven by the CaMV 35S promoter were successfully expressed in sunflower leaves. The two viral expression vectors, CMVar and TRBO, were not successful although we found high expression in Nicotiana benthamiana leaves previously for other recombinant proteins. To further enhance transient expression, we demonstrated two novel methods: using the plant hormone methyl jasmonic acid in the agroinfiltration buffer and two-phase optimization of the leaf incubation temperature. When methyl jasmonic acid was added to Agrobacterium tumefaciens cell suspensions and infiltrated into plant leaves, the functional enzyme production increased 4.6-fold. Production also increased up to 4.2-fold when the leaf incubation temperature was elevated above the typical temperature, 20C, to 30C in the late incubation phase, presumably due to enhanced rate of protein synthesis in plant cells. Finally, we demonstrated co-expression of E1 and xylanase in detached sunflower leaves. To our knowledge, this is the first report of (co)expression of heterologous plant cell wall-degrading enzymes in sunflower.
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Gould N, Hendy O, Papamichail D. Computational tools and algorithms for designing customized synthetic genes. Front Bioeng Biotechnol 2014; 2:41. [PMID: 25340050 PMCID: PMC4186344 DOI: 10.3389/fbioe.2014.00041] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/16/2014] [Indexed: 11/13/2022] Open
Abstract
Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein-coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review, we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.
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Affiliation(s)
- Nathan Gould
- Department of Computer Science, The College of New Jersey , Ewing, NJ , USA
| | - Oliver Hendy
- Department of Biology, The College of New Jersey , Ewing, NJ , USA
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Wang X, Wu L, Zhou P, Zhu S, An W, Chen Y, Zhao L. Analysis of synonymous codon usage patterns in the genus Rhizobium. World J Microbiol Biotechnol 2013; 29:2015-24. [PMID: 23653263 DOI: 10.1007/s11274-013-1364-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 04/25/2013] [Indexed: 10/26/2022]
Abstract
The codon usage patterns of rhizobia have received increasing attention. However, little information is available regarding the conserved features of the codon usage patterns in a typical rhizobial genus. The codon usage patterns of six completely sequenced strains belonging to the genus Rhizobium were analysed as model rhizobia in the present study. The relative neutrality plot showed that selection pressure played a role in codon usage in the genus Rhizobium. Spearman's rank correlation analysis combined with correspondence analysis (COA) showed that the codon adaptation index and the effective number of codons (ENC) had strong correlation with the first axis of the COA, which indicated the important role of gene expression level and the ENC in the codon usage patterns in this genus. The relative synonymous codon usage of Cys codons had the strongest correlation with the second axis of the COA. Accordingly, the usage of Cys codons was another important factor that shaped the codon usage patterns in Rhizobium genomes and was a conserved feature of the genus. Moreover, the comparison of codon usage between highly and lowly expressed genes showed that 20 unique preferred codons were shared among Rhizobium genomes, revealing another conserved feature of the genus. This is the first report of the codon usage patterns in the genus Rhizobium.
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Affiliation(s)
- Xinxin Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, People's Republic of China,
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