@article{adhikari_olukolu_paudel_pandey_halterman_louws_2024, title={Genotyping-by-Sequencing Reveals Population Differentiation and Linkage Disequilibrium in <i>Alternaria linariae</i> from Tomato}, volume={2}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-07-23-0229-R}, DOI={10.1094/PHYTO-07-23-0229-R}, abstractNote={ Alternaria linariae is an economically important foliar pathogen that causes early blight disease in tomatoes. Understanding genetic diversity, population genetic structure, and evolutionary potential is crucial to contemplating effective disease management strategies. We leveraged genotyping-by-sequencing (GBS) technology to compare genome-wide variation in 124 isolates of Alternaria spp. ( A. alternata, A. linariae, and A. solani) for comparative genome analysis and to test the hypotheses of genetic differentiation and linkage disequilibrium (LD) in A. linariae collected from tomatoes in western North Carolina. We performed a pangenome-aware variant calling and filtering with GBSapp and identified 53,238 variants conserved across the reference genomes of three Alternaria spp. The highest marker density was observed on chromosome 1 (7 Mb). Both discriminant analysis of principal components and Bayesian model-based STRUCTURE analysis of A. linariae isolates revealed three subpopulations with minimal admixture. The genetic differentiation coefficients (FST) within A. linariae subpopulations were similar and high (0.86), indicating that alleles in the subpopulations are fixed and the genetic structure is likely due to restricted recombination. Analysis of molecular variance indicated higher variation among populations (89%) than within the population (11%). We found long-range LD between pairs of loci in A. linariae, supporting the hypothesis of low recombination expected for a fungal pathogen with limited sexual reproduction. Our findings provide evidence of a high level of population genetic differentiation in A. linariae, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. linariae. }, journal={PHYTOPATHOLOGY}, author={Adhikari, Tika B. and Olukolu, Bode A. and Paudel, Rajan and Pandey, Anju and Halterman, Dennis and Louws, Frank J.}, year={2024}, month={Feb} }
 @article{devkota_pandey_yadegari_dumenyo_taheri_2021, title={Amine-Coated Carbon Dots (NH2-FCDs) as Novel Antimicrobial Agent for Gram-Negative Bacteria}, volume={3}, url={http://dx.doi.org/10.3389/fnano.2021.768487}, DOI={10.3389/fnano.2021.768487}, abstractNote={Multidrug resistance (MDR) is a major concern in battling infectious bacterial diseases. The overuse of antibiotics contributes to the emergence of resistance by eradicating the drug-sensitive strains, leaving behind the resistant strains that multiply without any competition. Nanoparticles are becoming popular as novel antimicrobial agents that follow a different mode of action from standard antibiotics and are therefore desirable against MDR bacteria. In this study, we synthesized carbon dots from different precursors including glucosamine HCL (GlcNH2·HCl) and 4,7,10-trioxa-1,13-tridecanediamine (TTDDA, and studied their antimicrobial effects in a diverse list of Gram-negative bacteria including Escherichia coli, Pseudomonas syringae, Salmonella enterica subsp. enterica serovar Typhimurium, Pectobacterium carotovorum, Agrobacterium tumefaciens, and Agrobacterium rhizogenes. We demonstrated the antimicrobial properties of these carbon dots against these bacteria and provided the optimum concentration and incubation times for each bacterial species. Our findings indicated that not all carbon dots carry antimicrobial properties, and there is also a variation between different bacterial species in their resistance against these carbon dots.}, journal={Frontiers in Nanotechnology}, publisher={Frontiers Media SA}, author={Devkota, Asmita and Pandey, Anju and Yadegari, Zeinab and Dumenyo, Korsi and Taheri, Ali}, year={2021}, month={Nov} }
 @article{pandey_devkota_yadegari_dumenyo_taheri_2021, title={Antibacterial Properties of Citric Acid/β-Alanine Carbon Dots against Gram-Negative Bacteria}, volume={11}, url={https://doi.org/10.3390/nano11082012}, DOI={10.3390/nano11082012}, abstractNote={While multi-drug resistance in bacteria is an emerging concern in public health, using carbon dots (CDs) as a new source of antimicrobial activity is gaining popularity due to their antimicrobial and non-toxic properties. Here we prepared carbon dots from citric acid and β-alanine and demonstrated their ability to inhibit the growth of diverse groups of Gram-negative bacteria, including E. coli, Salmonella, Pseudomonas, Agrobacterium, and Pectobacterium species. Carbon dots were prepared using a one-pot, three-minute synthesis process in a commercial microwave oven (700 W). The antibacterial activity of these CDs was studied using the well-diffusion method, and their minimal inhibitory concentration was determined by exposing bacterial cells for 20 h to different concentrations of CDs ranging from 0.5 to 10 mg/mL. Our finding indicates that these CDs can be an effective alternative to commercially available antibiotics. We also demonstrated the minimum incubation time required for complete inhibition of bacterial growth, which varied depending on bacterial species. With 15-min incubation time, A. tumefaciens and P. aeruginosa were the most sensitive strains, whereas E. coli and S. enterica were the most resistant bacterial strains requiring over 20 h incubation with CDs.}, number={8}, journal={Nanomaterials}, publisher={MDPI AG}, author={Pandey, Anju and Devkota, Asmita and Yadegari, Zeinab and Dumenyo, Korsi and Taheri, Ali}, year={2021}, month={Aug}, pages={2012} }
 @article{pandey_devkota_sigdel_yadegari_dumenyo_taheri_2021, title={Citric acid/β-alanine carbon dots as a novel tool for delivery of plasmid DNA into E. coli cells}, volume={11}, url={http://dx.doi.org/10.1038/s41598-021-03437-y}, DOI={10.1038/s41598-021-03437-y}, abstractNote={AbstractSuccessful delivery of plasmid DNA into the microbial cells is fundamental in recombinant DNA technology. Natural bacterial transformation is limited to only certain species due in part to the repulsive forces between negatively charged DNA and bacterial membranes. Most common method of DNA delivery into bacteria is artificial transformation through heat shock and electroporation. These methods require sophisticated instruments and tedious steps in preparation of competent cells. Transformation by conjugation is also not applicable to all plasmids. Nanoparticles have been used successfully in therapeutics for drug delivery into animal cells. They are starting to gain popularity in plant sciences as novel DNA nano carriers. Despite their promise as tool for DNA delivery, their use in microbial cell transformation has not been reported yet. Here we report the synthesis of carbon dots (CDs) from citric acid and β-alanine and their use in DNA delivery into E. coli cells. CDs were fabricated using microwave assisted synthesis. Plasmids carrying RFP reporter and ampicillin resistance genes were transferred to bacterial cells and further confirmed using polymerase chain reaction. Our findings indicate that CDs can be used successfully for delivery of foreign DNA of up to 10 kb into E. coli. We have demonstrated the use of β-alanine/citric acid carbon dots as nanocarriers of DNA into E. coli cells and identified their limitation in terms of the size of plasmid DNA they could carry. Use of these carbon dots is a novel method in foreign DNA delivery into bacterial cells and have a potential for the transformation of resistant organism for which there is still no reliable DNA delivery systems.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Pandey, Anju and Devkota, Asmita and Sigdel, Anil and Yadegari, Zeinab and Dumenyo, Korsi and Taheri, Ali}, year={2021}, month={Dec} }
 @article{devkota_pandey_yadegari_dumenyo_taheri_2021, title={Glucosamine/β-Alanine Carbon Dots Use as DNA Carriers Into E. coli Cells}, volume={3}, url={http://dx.doi.org/10.3389/fnano.2021.777810}, DOI={10.3389/fnano.2021.777810}, abstractNote={Introducing foreign DNA into bacterial cells is essential in functional genomics and molecular research. Currently, heat shock and electroporation are the two major techniques of gene delivery in bacterial cells. However, both the techniques are time and resource consuming and are limited to a few species or strains of bacteria and there is a need to develop new transformation alternatives. Carbon dots with unique features such as facile synthesis, ease of functionalization, nontoxicity, and biocompatibility are considered novel biomolecule nanocarriers. In this study, we synthesized and evaluated DNA delivery potential of four carbon dots including: 1) amine-coated carbon dots (NH2-FCDs); 2) carboxylate carbon dots (COOH-FCDs); 3) L-arginine and glucose carbon dots (N-CDs), and 4) citric acid and polyethyleneimine (PEI) carbon dots into Escherichia. coli cells. We evaluated the minimum incubation time required for the plasmid DNA delivery and the maximum plasmid size that can be delivered into E. coli cells using these CDs. Bacteria were incubated with carbon dots solution for different lengths of time and plated on selection media. Transformed colonies were counted and data were analyzed to identify the optimum incubation time and measure DNA delivery of these CDs with plasmids of different sizes. Our study demonstrated that among all these CDs, only carboxylate carbon dots (COOH-FCDs) prepared from glucosamine and β-alanine were able to deliver plasmid DNA into E. coli cells and the best incubation time was between 30 and 60 min. The maximum plasmid size that could be delivered using these CDs was approximately 10 kb and transformation efficiency decreased with larger plasmids. This study shows the capacity of COOH-CDs to deliver plasmid DNA into bacteria with an immense potential to combine with modern genome-editing tools. However, further studies are needed to evaluate their potential in DNA delivery in other bacterial strains.}, journal={Frontiers in Nanotechnology}, publisher={Frontiers Media SA}, author={Devkota, Asmita and Pandey, Anju and Yadegari, Zeinab and Dumenyo, Korsi and Taheri, Ali}, year={2021}, month={Nov} }
 @article{pandey_ansari_navathe_chand_mishra_joshi_2016, title={Association of lesion mimic trait with spot blotch resistance in wheat}, volume={41}, url={http://dx.doi.org/10.1007/s40858-016-0115-3}, DOI={10.1007/s40858-016-0115-3}, abstractNote={Lesion mimic creates necrosis in the leaf tissue and promotes the growth of necrotrophic/hemibiotrophic pathogens. The presence of lesion mimic locus and their effect on spot blotch disease, days to heading, black point index and thousand kernel weight of wheat were investigated in parents Sujata, Avocet-YRA and their 146 recombinant inbred lines (RILs). The study conducted during two cropping seasons showed that some lines with higher expression of lesion mimic phenotypes exhibited significant increase in AUDPC. Three markers (Xbarc181, Xwmc674 and Xgwm513) were deployed to reveal the presence of lesion mimic locus (lm, lm1 and lm2). Three lesion mimic loci were detected in combinations of lm+lm1+lm2, lm+lm2, lm2 and lm. The three loci combination (lm+lm1+lm2) expressed highest lesion mimic severity and early heading while lowest expression was recorded in the RILs with lm2 locus alone. Lesion mimic grade showed positive and significant correlation with AUDPC and negatively significant association with days to heading. Black point index and thousand kernel weight was not correlated with the lesion mimic grade. These lm loci expression showed differential production of ROS and were characterized by DAB and NBT staining. The combination of the three loci showed increased accumulation of H2O2 and O2 − while genotypes with only lm locus showed reduced accumulation. The microsatellite markers identified in this study may be useful for evaluating whether proposed parents with n.ormal phenotype are carriers of lesion-mimic alleles and could be of interest in breeding wheat for disease resistance.}, number={6}, journal={Tropical Plant Pathology}, publisher={Springer Science and Business Media LLC}, author={Pandey, Anju and Ansari, Shamshul Qumor and Navathe, Sudhir and Chand, Ramesh and Mishra, Vinod Kumar and Joshi, Arun Kumar}, year={2016}, month={Dec}, pages={406–414} }