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A 'bioproduction breadboard': programming, assembling, and actuating cellular networks

Amin Zargar, Gregory F Payne, William E Bentley
2015 Current Opinion in Biotechnology  
With advances in synthetic biology and biofabrication, cellular networks can be functionalized and connected with unprecedented sophistication. We describe a platform for the creation of a 'bioproduction breadboard'. This would consist of physically isolated product-producing cell populations, product capture devices, and other unit operations that function as programmed in place, using unique, orthogonal inputs. For product synthesis, customized cell populations would be connected through
more » ... ardized, generic inputs allowing 'plug and play' functionality and primary, user-mediated regulation. In addition, through autonomous pathway redirection and balancing, the cells themselves would provide secondary, self-directed regulation to optimize bioproduction. By leveraging specialization and division of labor, we envision diverse cell populations linked to create new pathway designs.
doi:10.1016/j.copbio.2015.08.017 pmid:26342587 fatcat:5bwgzmx7gjaz3am3vrd65dvrmu

In VitroAntioxidant and Cytotoxic Activities ofArnebia benthamii(Wall ex. G. Don): A Critically Endangered Medicinal Plant of Kashmir Valley

Showkat Ahmad Ganie, Tanveer Ali Dar, Rabia Hamid, Ovais Zargar, Shayaq Ul Abeer, Akbar Masood, Shajrul Amin, Mohammad Afzal Zargar
2014 Oxidative Medicine and Cellular Longevity  
Arnebia benthamiiis a major ingredient of the commercial drug available under the name Gaozaban, which has antibacterial, antifungal, anti-inflammatory, and wound-healing properties. In the present study,in vitroantioxidant and anticancer activity of different extracts ofArnebia benthamiiwere investigated. Antioxidant potential of plant extracts was evaluated by means of total phenolics, DPPH, reducing power, microsomal lipid peroxidation, and hydroxyl radical scavenging activity. The highest
more » ... enolic content (TPC) of 780 mg GAE/g was observed in ethyl acetate, while the lowest TPC of 462 mg GAE/g was achieved in aqueous extract. At concentration of 700 µg/mL, DPPH radical scavenging activity was found to be highest in ethyl acetate extract (87.99%) and lowest in aqueous extract (73%). The reducing power of extracts increased in a concentration dependent manner. We also observed its inhibition on Fe2+/ascorbic acid-induced lipid peroxidation (LPO) on rat liver microsomesin vitro. In addition,Arnebia benthamiiextracts exhibited antioxidant effects on Calf thymus DNA damage induced by Fenton reaction. Cytotoxicity of the extracts (10–100 µg/mL) was tested on five human cancer cell lines (lung, prostate, leukemia, colon, and pancreatic cell lines) using the Sulphorhodamine B assay.
doi:10.1155/2014/792574 pmid:24734152 pmcid:PMC3964854 fatcat:nlz6df3vdnh6ll2ba6fn7xkmba

A bimodular PKS platform that expands the biological design space [article]

Amin Zargar, Luis Valencia, Jessica Wang, Samantha Chang, Miranda Werts, Andrew Wong, Veronic Benites, Edward Baidoo, Leonard Katz, Jay D Keasling
2020 bioRxiv   pre-print
., 2018b; Zargar et al., 2017 Zargar et al., , 2018 .  ...  They were cloned through Golden Gate assembly into the LipPKS1 module with an inserted RL from NanA2 from Zargar et al (Zargar et al., 2019) .  ... 
doi:10.1101/2020.05.14.096743 fatcat:ebm5zhco4rgotp4taclpfwnwje

Acriflavine enhances the antitumor activity of the chemotherapeutic drug 5‑fluorouracil in colorectal cancer cells

Parisa Zargar, Esmaeel Ghani, Farideh Mashayekhi, Amin Ramezani, Ebrahim Eftekhar
2018 Oncology Letters  
Acknowledgements This study was a part of the dissertation of Parisa Zargar (The effect of acriflavine on HIF-1α expression and 5-fluorouracil chemosensitivity in colorectal cancer cells), submitted to  ... 
doi:10.3892/ol.2018.8569 pmid:29928378 pmcid:PMC6004650 fatcat:mjhdgunvfjdh5jhm337oiavgey

Evaluation of Antibacterial, Antifungal and Phytochemical Screening of Solanum nigrum

Khalid Bashir Dar, Aashiq Hussain Bhat, Shajrul Amin, Mohammad Afzal Zargar, Akbar Masood, Akhtar Hussain Malik, Showkat Ahmad Ganie
2017 Biochemistry & Analytical Biochemistry  
Citation: Dar KB, Bhat AH, Amin S, Zargar MA, Masood A, et al. (2017) Evaluation of Antibacterial, Antifungal and Phytochemical Screening of Solanum nigrum.  ... 
doi:10.4172/2161-1009.1000309 fatcat:tq7gddzzzrhf3odqprz4lomkle

Effects of thread shape on strength and stability of dental mini-screws against orthodontic forces

Fatemeh Motaghi Dastenaei, Amin Hajarian, Omid Zargar, Mahdi Moghimi Zand, Saeed Noorollahian
2019 Procedia Manufacturing  
Orthodontic mini-screws are short-term anchorage implants using widely to assist orthodontic mechano-therapies. Mini-screw loosening from the host bone during the first weeks of treatment is their most frequent problem, which is called weakness in the stability, as well. Applying changes in the macro-design of the mini-screws can considerably solve their problem in the stability. In this study, a 3-D finite element analysis (FEA) is done in order to improve the thread shape aspect in designing
more » ... ini-screws. In this optimized design, a few parameters are considered. First, the upper angle of threads tried to be close to the right angle in order to provide more stability. Second, the sharpness of the threads wanted to be kept because convenience in implantation is helped by sharpness in thread apex, and it is necessary to reduce tissue trauma. Another essential parameter needing to be taken into consideration is the limited stress which bones can tolerate, and it causes to be cautious about stresses amounts. In order to reach this goal, moderate changes in thread angles were done while an axial load was applied to the mini-screw. Finally, the triangular thread shape of the mini-screw was optimized, and one specific shape was considered as the best shape for the given dimensions. These results are valuable to follow the same instruction and steps in order to optimize the design of other miniscrews to ergonomic ones. Also, the obtained relationship between the thread angles facilitates designing a modified thread in order to have less exerted stress on the mini-screw.
doi:10.1016/j.promfg.2019.06.053 fatcat:zezab5r54vbpzbepggil5dmi2i

Leveraging microbial biosynthetic pathways for the generation of 'drop-in' biofuels

Amin Zargar, Constance B Bailey, Robert W Haushalter, Christopher B Eiben, Leonard Katz, Jay D Keasling
2017 Current Opinion in Biotechnology  
Figure 1 FAS 1 Figure 1 Microbial pathways for the production of biofuels Zargar et al. 159 Figure 2 Figure 3 Table 1 1 Microbial pathways for the production of biofuels Zargar et al. 157Maximum  ... 
doi:10.1016/j.copbio.2017.03.004 pmid:28427010 pmcid:PMC6283405 fatcat:ahzxlbmwlveynir33ubfszbvtq

Directed assembly of a bacterial quorum

Matthew D Servinsky, Jessica L Terrell, Chen-Yu Tsao, Hsuan-Chen Wu, David N Quan, Amin Zargar, Patrick C Allen, Christopher M Byrd, Christian J Sund, William E Bentley
2015 The ISME Journal  
Many reports have elucidated the mechanisms and consequences of bacterial quorum sensing (QS), a molecular communication system by which bacterial cells enumerate their cell density and organize collective behavior. In few cases, however, the numbers of bacteria exhibiting this collective behavior have been reported, either as a number concentration or a fraction of the whole. Not all cells in the population, for example, take on the collective phenotype. Thus, the specific attribution of the
more » ... stulated benefit can remain obscure. This is partly due to our inability to independently assemble a defined quorum, for natural and most artificial systems the quorum itself is a consequence of the biological context (niche and signaling mechanisms). Here, we describe the intentional assembly of quantized quorums. These are made possible by independently engineering the autoinducer signal transduction cascade of Escherichia coli (E. coli) and the sensitivity of detector cells so that upon encountering a particular autoinducer level, a discretized sub-population of cells emerges with the desired phenotype. In our case, the emergent cells all express an equivalent amount of marker protein, DsRed, as an indicator of a specific QS-mediated activity. The process is robust, as detector cells are engineered to target both large and small quorums. The process takes about 6 h, irrespective of quorum level. We demonstrate sensitive detection of autoinducer-2 (AI-2) as an application stemming from quantized quorums. We then demonstrate sub-population partitioning in that AI-2-secreting cells can 'call' groups neighboring cells that 'travel' and establish a QS-mediated phenotype upon reaching the new locale.
doi:10.1038/ismej.2015.89 pmid:26046256 pmcid:PMC4681864 fatcat:oti4wcjbvvay3jmkzr235kbkxq

Evaluation of a sulfanilic acid based surfactant in crude oil demulsification: an experimental study

Ghassem Zargar, Reza Ghol Gheysari, Mohammad Ali Takassi, Alireza Rostami, Amin Zadehnazari
2018 Oil & Gas Science and Technology  
Zargar et al.: Oil & Gas Science and Technology -Rev. IFP Energies nouvelles 73, 20 (2018) G. Zargar et al.: Oil & Gas Science and Technology -Rev. IFP Energies nouvelles 73, 20 (2018) 5  ... 
doi:10.2516/ogst/2018016 fatcat:66goat7lvzaeradmy5cwwp2haa


Nasrin Ansari, Reyaz Hassan, Mohd Iqbal Zargar, Wajaht Amin Shah, D P Pathak
2018 International Research Journal of Pharmacy  
Zargar provided invaluable technical assistance also thankful to Prof. D.P. Pathak, Delhi Institute of Pharmaceutical Sciences and Research, Delhi India.  ... 
doi:10.7897/2230-8407.0910240 fatcat:rb3aboketfadtgbxicxpte5x3u

A bimodular PKS platform that expands the biological design space

Amin Zargar, Luis Valencia, Jessica Wang, Ravi Lal, Samantha Chang, Miranda Werts, Andrew R. Wong, Amanda C. Hernández, Veronica Benites, Edward Baidoo, Leonard Katz, Jay D. Keasling
2020 Metabolic Engineering  
., 2018b; Zargar et al., 2017 Zargar et al., , 2018 .  ...  They were cloned through Golden Gate assembly into the LipPKS1 module with an inserted RL from NanA2 from Zargar et al .  ... 
doi:10.1016/j.ymben.2020.07.001 pmid:32771628 fatcat:56vlssuae5e6nnnwg33dfwgcfu

Negotiating Future Uncertainty: Concerns of Mothers of Children with Down Syndrome in Kashmir, India

Bilal Ahmad Khan, Wakar Amin Zargar, Shabir Ahmad Najar
2018 Disability, CBR and Inclusive Development  
Purpose: Down syndrome is developmental disorder that poses unique challenges and implications to families. The present paper is the outcome of a study carried out in Srinagar district of J & K in India, on mothers' apprehensions about the uncertain future for their children with Down syndrome.Method: A phenomenographic approach was followed. Purposive sampling technique was used at selected special schools in Srinagar. Mothers of 8 children with Down syndrome who were enrolled in school,
more » ... ipated in the study. The mothers were between 31 and 67 years of age; their children were between 2 and 30 years of age. In-depth interviews were conducted in Urdu and Kashmiri, the local languages. The recorded information was subsequently transcribed and classified into themes.Results: The key theme that emerged was the participants' worry about the unpredictable future of their child. Once a child is diagnosed with Down syndrome, parents - especially mothers - recognise that their child's future may not include a carefree childhood and, at a later date, higher studies, an independent life and marriage.Conclusion: Mothers of children with Down syndrome experience high levels of stress and often have to make adjustments in their careers, finances and lifestyles. There is a need for training programmes to help parents cope with the problems faced by their children with Down syndrome. Stakeholders in the education sector could help in this regard.
doi:10.5463/dcid.v29i1.703 fatcat:kn7ywvpvdvd2pprlnjsfh3othm

Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B2 Biosynthesis

Jesus F. Barajas, Amin Zargar, Bo Pang, Veronica T. Benites, Jennifer Gin, Edward E. K. Baidoo, Christopher J. Petzold, Nathan J. Hillson, Jay D. Keasling
2018 ChemBioChem  
Naturally occurring lactams, such as the polyketide-derived macrolactams, provide a diverse class of natural products that could enhance existing chemically produced lactams. While β-amino acid loading in the fluvirucin B2 polyketide pathway has been proposed by a previously identified putative biosynthetic gene cluster, biochemical characterization of the complete loading enzymes has not been described. Here we elucidate the complete biosynthetic pathway of the β-amino acid loading pathway in
more » ... luvirucin B2 biosynthesis. We demonstrate the promiscuity of the loading pathway to utilize a range of amino acids and further illustrate the ability to introduce non-native acyl transferases to selectively transfer β-amino acids onto a PKS loading platform. The results presented here provide a detailed biochemical description of β-amino acid selection and will further aid in future efforts to develop engineered lactam-producing PKS platforms.
doi:10.1002/cbic.201800169 pmid:29603548 fatcat:jexb2t2opndwbp7uxu2ayrpesq

Bacterial Secretions of Nonpathogenic Escherichia coli Elicit Inflammatory Pathways: a Closer Investigation of Interkingdom Signaling

Amin Zargar, David N. Quan, Karen K. Carter, Min Guo, Herman O. Sintim, Gregory F. Payne, William E. Bentley
2015 mBio  
Zargar et al. ® March/April 2015 Volume 6 Issue 2 e00025-15 March/April 2015 Volume 6 Issue 2 e00025-15 ® 9  ...  With five biological replicates, we were able to deter- Zargar et al. mine significant differential gene expression between conditions that displayed these small differences (for complete differentialexpression  ... 
doi:10.1128/mbio.00025-15 pmid:25759496 pmcid:PMC4453519 fatcat:nu5q4iqmlrawvfuj3qvoo6hs2y

UGT1A1Gene Mutation due to Crigler-Najjar Syndrome in Iranian Patients: Identification of a Novel Mutation

Javad Mohammadi Asl, Mohammad Amin Tabatabaiefar, Hamid Galehdari, Kourosh Riahi, Mohammad Hosein Masbi, Zohre Zargar Shoshtari, Fakher Rahim
2013 BioMed Research International  
Crigler-Najjar syndrome (CNS) type I and type II are inherited as autosomal recessive conditions that are caused by mutations in theUGT1A1gene. We present the analysis ofUGT1A1gene in 12 individuals from three different families. This analysis allowed us to identify one novel mutation, which was not previously described. In this study, three families with clinically diagnosed CNS referred from Khuzestan province, southwest Iran, were screened. After signing the informed consent, peripheral
more » ... samples from the patients and their parents were collected in EDTA-containing tube followed by DNA extraction using a routine phenol-chloroform method. All five coding exons and the flanking intronic regions of the bilirubin-UGT were amplified by polymerase chain reaction (PCR) followed by DNA sequencing by Sanger method. From the first family, a 9-month-old boy was homozygous for a deletion mutation of two adjacent nucleotides including one adenosine (A) and one glutamine (G) between nucleotides 238 and 239 in exon 1 (c.238_240 del AG). In the second family, there were two affected individuals, an 11-year-old girl and a fetus, found to be homozygous for the same mutation. The third family showed a mutation at nucleotide 479 in exon 1 (Val160Glu) that has been reported previously. Molecular analysis can significantly help confirm the diagnosis of CNS, without any need for the liver biopsy, and may help the therapeutic management by ruling out more harmful causes of hyperbilirubinemia.
doi:10.1155/2013/342371 pmid:24286076 pmcid:PMC3826477 fatcat:d3grzzb62jff7mln4dfrbmt5ha
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