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1. Impact of an autophagy-inducing peptide on immunogenicity and protection efficacy of an adenovirus-vectored SARS-CoV-2 vaccine

Author

Sayedahmed, Ekramy E., Araújo, Marcelo Valdemir, Silva-Pereira, Taiana Tainá, Chothe, Shubhada K., Elkashif, Ahmed, Alhashimi, Marwa, Wang, Wen-Chien, Santos, Andrea P., Nair, Meera Surendran, Gontu, Abhinay, Nissly, Ruth, Francisco de Souza Filho, Antônio, Tavares, Mariana Silva, Ayupe, Marina Caçador, Salgado, Caio Loureiro, Donizetti de Oliveira Candido, Érika, Leal Oliveira, Danielle Bruna, Durigon, Edison Luiz, Heinemann, Marcos Bryan, Morais da Fonseca, Denise, Jagannath, Chinnaswamy, Sá Guimarães, Ana Marcia, Kuchipudi, Suresh V., and Mittal, Suresh K.

Published
2023
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6. Limited window for donation of convalescent plasma with high live-virus neutralizing antibody titers for COVID-19 immunotherapy

Author

Gontu, Abhinay, Srinivasan, Sreenidhi, Salazar, Eric, Nair, Meera Surendran, Nissly, Ruth H., Greenawalt, Denver, Bird, Ian M., Herzog, Catherine M., Ferrari, Matthew J., Poojary, Indira, Katani, Robab, Lindner, Scott E., Minns, Allen M., Rossi, Randall, Christensen, Paul A., Castillo, Brian, Chen, Jian, Eagar, Todd N., Yi, Xin, Zhao, Picheng, Leveque, Christopher, Olsen, Randall J., Bernard, David W., Gollihar, Jimmy, Kuchipudi, Suresh V., Musser, James M., and Kapur, Vivek

Published
2021
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7. List of contributors

Author

Bartali, R., primary, Brusa, R.S., additional, Bublikov, J.I., additional, Carfagni, Monica, additional, Egger, W., additional, Esteban, Jaime, additional, Furferi, Rocco, additional, Gite, Vikas V., additional, Gottardi, G., additional, Governi, Lapo, additional, Grigoriev, S.N., additional, Hagedorn, Daniel, additional, Hegelbach, Reto, additional, Ishihara, Kazuhiko, additional, Ji, Ruonan, additional, Kaleemulla, Mohamed, additional, Kirillov, A.K., additional, Laidani, N., additional, Liu, Yanyan, additional, Löffler, Frank, additional, Losic, Dusan, additional, Lu, Wei, additional, Luciu, I., additional, Mahato, Manmatha, additional, Marathe, Ravindra J., additional, Mariazzi, S., additional, Markevicius, Tomas, additional, Martínez-Pérez, Marta, additional, Meyer, Helmut, additional, Micheli, V., additional, Mishra, Trilochan, additional, Mudasar Pasha, B.A., additional, Nair, Meera Surendran, additional, Naumov, A.G., additional, Nine, Md Julker, additional, Olsson, Nina, additional, Peremarch, Concepcion Pérez-Jorge, additional, Pylarinos, Dionisios, additional, Raveli, L., additional, Roy, Jagannath, additional, Saborowski, Knud, additional, Safeen, K., additional, Samba Sivudu, K., additional, Schmaljohann, Frank, additional, Seymour, Kate, additional, Siderakis, Kiriakos, additional, Sohn, Daewon, additional, Soma Raju, K.R.C., additional, Sotova, E.S., additional, Subasri, R., additional, Takai, Madoka, additional, Tanasă, Fulga, additional, Tatiya, Piyus, additional, Teacă, Carmen-Alice, additional, Thalassinakis, Emmanuel, additional, Tiwari, Shashi Kant, additional, Upadhyay, Abhinav, additional, Venkitanarayanan, Kumar, additional, Vereschaka, A.A., additional, Volpe, Yary, additional, Wang, Shaowei, additional, Xu, Yan, additional, Yin, Hsinbai, additional, and Zănoagă, Mădălina, additional

Published
2021
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10. SARS-CoV-2 Prevalence and Variant Surveillance among Cats in Pittsburgh, Pennsylvania, USA

Author

Ramasamy, Santhamani, primary, Gontu, Abhinay, additional, Neerukonda, Sabarinath, additional, Ruggiero, Diana, additional, Morrow, Becky, additional, Gupta, Sheweta, additional, Amirthalingam, Saranya, additional, Hardham, John M., additional, Lizer, Joshua T., additional, Yon, Michele, additional, Nissly, Ruth H., additional, Jakka, Padmaja, additional, Chothe, Shubhada K., additional, LaBella, Lindsey C., additional, Tewari, Deepanker, additional, Nair, Meera Surendran, additional, and Kuchipudi, Suresh V., additional

Published
2023
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11. Little Brown Bats (Myotis lucifugus) Support the Binding of SARS-CoV-2 Spike and Are Likely Susceptible to SARS-CoV-2 Infection

Author

Chothe, Shubhada K., primary, Jakka, Padmaja, additional, Boorla, Veda Sheersh, additional, Ramasamy, Santhamani, additional, Gontu, Abhinay, additional, Nissly, Ruth H., additional, Brown, Justin, additional, Turner, Gregory, additional, Sewall, Brent J., additional, Reeder, DeeAnn M., additional, Field, Kenneth A., additional, Engiles, Julie B., additional, Amirthalingam, Saranya, additional, Ravichandran, Abirami, additional, LaBella, Lindsey, additional, Nair, Meera Surendran, additional, Maranas, Costas D., additional, and Kuchipudi, Suresh V., additional

Published
2023
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12. Optimized conditions for Listeria, Salmonella and Escherichia whole genome sequencing using the Illumina iSeq100 platform with point-and-click bioinformatic analysis

Author

Alvarez Narvaez, Sonsiray, primary, Shen, Zhenyu, additional, Yan, Lifang, additional, Stenger, Brianna L. S., additional, Goodman, Laura B., additional, Lim, Ailam, additional, Nissly, Ruth H., additional, Nair, Meera Surendran, additional, Zhang, Shuping, additional, and Sanchez, Susan, additional

Published
2022
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14. List of Contributors

Author

Aehle, Sandra, primary, Barrow, Paul, additional, Bueno, Dante Javier, additional, Byrd, James A., additional, Callaway, Todd R., additional, Chiok, Kim L., additional, Chousalkar, Kapil K., additional, Crandall, Philip G., additional, Curtiss, Roy, additional, Davies, Rob, additional, Dawoud, Turki M., additional, De Cort, Wolfgang, additional, Ducatelle, Richard, additional, Edrington, Tom S., additional, Elder, Jacob R., additional, Foley, Steven L., additional, Gast, Richard K., additional, Godano, Eduardo Ignacio, additional, Kollanoor Johny, Anup, additional, Kaldhone, Pravin R., additional, Kogut, Michael H., additional, Korver, Doug, additional, Kwon, Young Min, additional, Lee, Soo-Kyoung, additional, Martelli, Francesca, additional, McMullen, Lynn, additional, McWhorter, Andrea, additional, Nair, Meera Surendran, additional, Nisbet, David J., additional, O’Bryan, Corliss A., additional, Paul, Narayan C., additional, Procura, Francisco, additional, Ricke, Steven C., additional, Rodriguez, Francisco Isabelino, additional, Seo, Kun-Ho, additional, Shah, Devendra H., additional, Shi, Zhaohao, additional, Soria, María Cecilia, additional, Soria, Mario Alberto, additional, Upadhyaya, Indu, additional, Van Immerseel, Filip, additional, Venkitanarayanan, Kumar, additional, Wales, Andrew, additional, Waltman, Doug, additional, Wigley, Paul, additional, and Yin, Hsin-Bai, additional

Published
2017
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16. Transmission of SARS‐CoV‐2 from humans to a 16‐year‐old domestic cat with comorbidities in Pennsylvania, USA

Author

Tewari, Deepanker, primary, Boger, Lore, additional, Brady, Steven, additional, Livengood, Julia, additional, Killian, Mary Lea, additional, Nair, Meera Surendran, additional, Thirumalapura, Nagaraja, additional, Kuchipudi, Suresh V., additional, Zellers, Corey, additional, Schroder, Betsy, additional, Torchetti, Mia, additional, Carpenter, Ann, additional, Kunkel, Amber, additional, and Brightbill, Kevin, additional

Published
2021
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18. Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike protein and the human ACE2 receptor

Author

Chen, Chen, primary, Boorla, Veda Sheersh, additional, Banerjee, Deepro, additional, Chowdhury, Ratul, additional, Cavener, Victoria S, additional, Nissly, Ruth H, additional, Gontu, Abhinay, additional, Boyle, Nina R, additional, Vandergrift, Kurt, additional, Nair, Meera Surendran, additional, Kuchipudi, Suresh V, additional, and Maranas, Costas D., additional

Published
2021
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19. Inactivation of Escherichia coli O157:H7 in Apple Cider by Resveratrol and Naringenin

Author

Nair, Meera Surendran, Ma, Fulin, Lau, Patrick, Upadhyaya, Indu, Venkitanarayanan, Kumar, Nair, Meera Surendran, Ma, Fulin, Lau, Patrick, Upadhyaya, Indu, and Venkitanarayanan, Kumar

Abstract

The study investigated the efficacy of two GRAS-status phytochemicals, mega-resveratrol (RV) and naringenin (NG) to inactivate Escherichia coli O157:H7 (EHEC) in apple cider. A five-strain mixture of EHEC (∼7 log CFU/ml) was inoculated into cider, followed by the addition of RV (8.7 mM and 13.0 mM) or NG (7.3 mM and 11.0 mM). The cider samples were stored at 4 °C for 14 days and EHEC was enumerated on days 0,1,5,7 and 14. The deleterious effects of RV and NG on EHEC cells were visualized by scanning electron microscopy (SEM), and RT-qPCR was done to determine the effect of phytochemicals on three known acid resistance (AR) systems of EHEC. NG was more effective than RV and reduced EHEC counts by ∼4.5 log CFU/ml by day 14, whereas RV reduced counts by ∼2.5 log CFU/ml compared to controls (P < 0.05). SEM showed that RV and NG resulted in the destruction of EHEC cells, and surviving bacteria appeared ‘lemon shaped’. RT-qPCR results revealed that RV and NG downregulated the transcription of AR associated genes in EHEC (P < 0.05). Results suggest the potential use of RV and NG as natural antimicrobial additives to enhance the microbiological safety of apple cider. However, sensory analysis studies are warranted. © 2019 Elsevier Ltd

Published
2020

20. Transmission of SARS‐CoV‐2 from humans to a 16‐year‐old domestic cat with comorbidities in Pennsylvania, USA.

Author

Tewari, Deepanker, Boger, Lore, Brady, Steven, Livengood, Julia, Killian, Mary Lea, Nair, Meera Surendran, Thirumalapura, Nagaraja, Kuchipudi, Suresh V., Zellers, Corey, Schroder, Betsy, Torchetti, Mia, Carpenter, Ann, Kunkel, Amber, and Brightbill, Kevin

Subjects
TIGERS, SARS-CoV-2, CATS
Abstract

Background and Objectives: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), besides causing human infection, has been shown to naturally infect several susceptible animal species including large cats (tigers, lions, pumas, spotted leopards), dogs, cats, ferrets, gorillas and minks. Cats and minks are continuing to be the most reported species with SARS‐CoV‐2 infections among animals but it needs to be investigated further. Methods and Results: We report the detection of SARS‐CoV‐2 from a domestic cat that exhibited respiratory disease after being exposed to SARS‐CoV‐2 virus from humans in the same household. SARS‐CoV‐2 RNA was detected in two oropharyngeal swabs collected at two time points, 11 days apart; the first, when the cat was reported to be sick and the second, before euthanasia due to poor prognosis. The viral nucleic acid detected at two time points showed no genomic variation and resembled the clade GH circulating in humans in the United States. Clinical and pathological findings noted in this 16‐year‐old cat were consistent with respiratory and cardiac insufficiency. Conclusions: SARS‐CoV‐2 viral infection was likely an incidental clinical finding, as the virus was not detected in fixed lungs, heart, or kidney tissues. Only fresh lung tissue collected at necropsy showed the presence of viral nucleic acid, albeit at a very low level. Further research is needed to clarify the clinical course of SARS‐CoV‐2 in companion animals of advanced age and underlying cardiac disease. [ABSTRACT FROM AUTHOR]

Published
2022
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22. Limited window for donation of convalescent plasma with high live-virus neutralizing antibodies for COVID-19 immunotherapy

Author

Gontu, Abhinay, primary, Srinivasan, Sreenidhi, additional, Salazar, Eric, additional, Nair, Meera Surendran, additional, Nissly, Ruth H., additional, Greenawalt, Denver, additional, Bird, Ian M., additional, Herzog, Catherine, additional, Ferrari, Matthew J., additional, Poojary, Indira, additional, Katani, Robab, additional, Lindner, Scott E., additional, Minns, Allen M., additional, Rossi, Randall, additional, Christensen, Paul A., additional, Castillo, Brian, additional, Chen, Jian, additional, Eagar, Todd N., additional, Yi, Xin, additional, Zhao, Picheng, additional, Leveque, Christopher, additional, Olsen, Randall J., additional, Bernard, David W., additional, Gollihar, Jimmy, additional, Kuchipudi, Suresh V., additional, Musser, James M., additional, and Kapur, Vivek, additional

Published
2020
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23. MOESM3 of Influence of pig gut microbiota on Mycoplasma hyopneumoniae susceptibility

Author

Nair, Meera Surendran, Eucker, Tyson, Martinson, Brian, Neubauer, Axel, Victoria, Joseph, Nicholson, Bryon, and Pieters, Maria

Abstract

Additional file 3. Difference in bacterial composition among different samples. The PERMANOVA results showed that the microbiome composition in samples was influenced by age (p = 0.01). Litters were represented in sequential numbers 0–5. L0 included uninoculated control piglets. Litters 1–5 included all M. hyopneumonaie experimentally inoculated piglets.

Published
2019
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27. Potentiating the Heat Inactivation of Escherichia coli O157:H7 in Ground Beef Patties by Natural Antimicrobials

Author

Nair, Meera Surendran, Lau, Patrick, Belskie, Kaylin, Fancher, Samantha, Chen, Chi-Hung, Karumathil, Deepti Prasad, Yin, Hsin-Bai, Liu, Yanyan, Ma, Fulin, Upadhyaya, Indu, Upadhyay, Abhinav, Mancini, Richard, Venkitanarayanan, Kumar, Nair, Meera Surendran, Lau, Patrick, Belskie, Kaylin, Fancher, Samantha, Chen, Chi-Hung, Karumathil, Deepti Prasad, Yin, Hsin-Bai, Liu, Yanyan, Ma, Fulin, Upadhyaya, Indu, Upadhyay, Abhinav, Mancini, Richard, and Venkitanarayanan, Kumar

Abstract

Escherichia coil O157: H7 (EHEC) is a major foodborne pathogen largely transmitted to humans through the consumption of undercooked ground beef. This study investigated the efficacy of two food-grade, plant derived antimicrobials, namely rutin (RT), and resveratrol (RV) with or without chitosan (CH) in enhancing EHEC inactivation in undercooked hamburger patties. Further, the effect of aforementioned treatments on beef color and lipid oxidation was analyzed. Additionally, the deleterious effects of these antimicrobial treatments on EHEC was determined using scanning electron microscopy (SEM). Ground beef was inoculated with a five-strain mixture of EHEC (7.0 log CFU/g), followed by the addition of RT (0.05%, 0.1% w/w) or RV (0.1, 0.2% w/w) with or without CH (0.01% w/w). The meat was formed into patties (25 g) and stored at 4 degrees C for 5 days. On days 1, 3, and 5, the patties were cooked (65 degrees C, medium rare) and surviving EHEC was enumerated. The effect of these treatments on meat color and lipid oxidation during storage was also determined as per American Meat Science Association guidelines. The study was repeated three times with duplicate samples of each treatment. Both RT and RV enhanced the thermal destruction of EHEC, and reduced the pathogen load by at least 3 log CFU/g compared to control (P < 0.05). The combination of RT or RV with CH was found to be more effective, and reduced EHEC by 5 log CFU/g (P <- 0.05). EHEC counts in uncooked patties did not decline during storage for 5 days (P > 0.05). Moreover, patties treated with RV plus CH were more color stable with higher a{*} values (P < 0.05). SEM results revealed that heat treatment with antimicrobials (CH + RV 0.2%) resulted in complete destruction of EHEC cells and extrusion of intracellular contents. Results suggest that the aforementioned antimicrobials could be used for enhancing the thermal inactivation of EHEC in undercooked patties; however, detailed sensory studies are warranted.

Published
2016

31. Inhibition and Inactivation of Escherichia coliO157:H7 Biofilms by Selenium

Author

Nair, Meera Surendran, Upadhyay, Abhinav, Fancher, Samantha, Upadhyaya, Indu, Dey, Swayandipta, Kollanoor-Johny, Anup, Zhao, Jing, and Venkitanarayanan, Kumar

Abstract

The present study investigated the efficacy of selenium (Se) in reduction of enterohemorrhagic Escherichia coli(EHEC) exopolysaccharide (EPS) synthesis, inhibition of biofilm formation at 25 and 4°C on polystyrene surface, and inactivation of mature EHEC biofilms in combination with hot water. Sterile 96-well polystyrene plates inoculated with EHEC (∼6.0 log CFU per well) were treated with a subinhibitory concentration (SIC) of Se, and biofilms were allowed to mature at 4 and 25°C for 96 h. Biofilm-associated bacterial population was determined by scraping and plating, whereas the extent of EPS production was determined using ruthenium red staining assay. Solid surface assay was used to study the effect of Se on early attachment of EHEC cells to polystyrene. The efficacy of Se in rapid inactivation of preformed, mature EHEC biofilm was investigated by treating biofilms on polystyrene plates with the MBC of Se in combination with hot water at 80°C with a contact time of 0 min, 30 s, 2 min, and 5 min. Furthermore, the effect of Se on EHEC biofilm architecture was visualized using confocal microscopy, whereas the effect of Se on EHEC biofilm genes was determined using real-time quantitative PCR (RT-qPCR). Finally, the potential feasibility of coating stainless steel surfaces with Se nanoparticles to inhibit EHEC biofilm formation was studied. Se reduced early attachment of planktonic cells, biofilm formation, and EPS synthesis in EHEC (P< 0.05). Se in combination with hot water reduced biofilm-associated bacterial counts by 3 to 4 log CFU/mL at 5 min of exposure compared with the control (P< 0.05). However, hot water treatment alone decreased biofilm-associated bacterial counts by only 1.0 log CFU/mL. RT-qPCR results revealed that Se down-regulated the transcription of critical genes associated with biofilm synthesis in EHEC (P< 0.05). The results collectively suggest that Se could potentially be used to control EHEC biofilms in food processing environments, but appropriate applications need to be validated.

Published
2018
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32. Efficacy of Plant-Derived Antimicrobials in Controlling Enterohemorrhagic Escherichia coliVirulence In Vitro

Author

Baskaran, Sangeetha Ananda, Kollanoor-Johny, Anup, Nair, Meera Surendran, and Venkitanarayanan, Kumar

Abstract

Escherichia coliO157:H7 is a major foodborne pathogen that can cause serious human illness characterized by hemorrhagic diarrhea and kidney failure. The pathology of enterohemorrhagic E. coliO157:H7 (EHEC) infection is primarily mediated by verotoxins, which bind to the globotriaosylceramide receptor on host cells. Antibiotics are contraindicated for treating EHEC infection because they lead to increased verotoxin release, thereby increasing the risk of renal failure and death in patients. Thus, alternative strategies are needed for controlling EHEC infections in humans. This study investigated the effect of subinhibitory concentrations of five plant-derived antimicrobial agents (PDAs) that are generally considered as safe, i.e., trans-cinnamaldehyde, eugenol, carvacrol, thymol, and β-resorcylic acid, on EHEC motility, adhesion to human intestinal epithelial cells, verotoxin production, and virulence gene expression. All tested PDAs reduced EHEC motility and attachment to human intestinal epithelial cells (P< 0.05) and decreased verotoxin synthesis by EHEC. The reverse transcription real-time PCR data revealed that PDAs decreased the expression of critical virulence genes in EHEC (P< 0.05). The results collectively suggest that these PDAs could be used to reduce EHEC virulence, but follow-up studies in animal models are necessary to validate these findings.

Published
2016
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33. Lyophilized, thermostable Spike or RBD immunogenic liposomes induce protective immunity against SARS-CoV-2 in mice.

Author

Mabrouk, Moustafa T., Chiem, Kevin, Rujas, Edurne, Wei-Chiao Huang, Jahagirdar, Dushyant, Quinn, Breandan, Nair, Meera Surendran, Nissly, Ruth H., Cavener, Victoria S., Boyle, Nina R., Sornberger, Ty A., Kuchipudi, Suresh V., Ortega, Joaquin, Julien, Jean-Philippe, Martinez-Sobrido, Luis, and Lovell, Jonathan

Subjects
*COVID-19, *LIPOSOMES, *SARS-CoV-2, *MEDICAL sciences, *MOLECULAR biology
Abstract

The article presents a study that explores how lyophilized, thermostable Spike or receptor-binding domain immunogenic liposomes induce protective immunity against SARS-CoV-2 in mice. It mentions about the assessment of low-dose immunization with lyophilized nanoparticles decorated with recombinant SARS-CoV-2 antigens.

Published
2021
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34. A CNN model for predicting binding affinity changes between SARS-CoV-2 spike RBD variants and ACE2 homologues.

Author

Chen C, Boorla VS, Chowdhury R, Nissly RH, Gontu A, Chothe SK, LaBella L, Jakka P, Ramasamy S, Vandegrift KJ, Nair MS, Kuchipudi SV, and Maranas CD

Abstract

The cellular entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) involves the association of its receptor binding domain (RBD) with human angiotensin converting enzyme 2 (hACE2) as the first crucial step. Efficient and reliable prediction of RBD-hACE2 binding affinity changes upon amino acid substitutions can be valuable for public health surveillance and monitoring potential spillover and adaptation into non-human species. Here, we introduce a convolutional neural network (CNN) model trained on protein sequence and structural features to predict experimental RBD-hACE2 binding affinities of 8,440 variants upon single and multiple amino acid substitutions in the RBD or ACE2. The model achieves a classification accuracy of 83.28% and a Pearson correlation coefficient of 0.85 between predicted and experimentally calculated binding affinities in five-fold cross-validation tests and predicts improved binding affinity for most circulating variants. We pro-actively used the CNN model to exhaustively screen for novel RBD variants with combinations of up to four single amino acid substitutions and suggested candidates with the highest improvements in RBD-ACE2 binding affinity for human and animal ACE2 receptors. We found that the binding affinity of RBD variants against animal ACE2s follows similar trends as those against human ACE2. White-tailed deer ACE2 binds to RBD almost as tightly as human ACE2 while cattle, pig, and chicken ACE2s bind weakly. The model allows testing whether adaptation of the virus for increased binding with other animals would cause concomitant increases in binding with hACE2 or decreased fitness due to adaptation to other hosts., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Competing financial interests The authors declare no competing financial interests.

Published
2022
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35. Inhibiting Microbial Toxins Using Plant-Derived Compounds and Plant Extracts.

Author

Upadhyay A, Mooyottu S, Yin H, Nair MS, Bhattaram V, and Venkitanarayanan K

Abstract

Many pathogenic bacteria and fungi produce potentially lethal toxins that cause cytotoxicity or impaired cellular function either at the site of colonization or other locations in the body through receptor-mediated interactions. Various factors, including biotic and abiotic environments, competing microbes, and chemical cues affect toxin expression in these pathogens. Recent work suggests that several natural compounds can modulate toxin production in pathogenic microbes. However, studies explaining the mechanistic basis for their effect are scanty. This review discusses the potential of various plant-derived compounds for reducing toxin production in foodborne and other microbes. In addition, studies highlighting their anti-toxigenic mechanism(s) are discussed.

Published
2015
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