Article
Multidisciplinary Sciences
Elise Richard, Pascale Bourhy, Mathieu Picardeau, Laurent Moulin, Sebastien Wurtzer
Summary: The study introduced a new method, PMAqPCR, which can detect pathogenic and non-pathogenic Leptospira in environmental water while addressing the problem of PCR inhibitors. By testing the killing efficiency of Leptospira to different treatments and comparing PMAqPCR with culture-based enumeration, the research provided insights into the persistence of Leptospira in water treatment processes.
Article
Biotechnology & Applied Microbiology
Minji Kim, Karen Shapiro, Veronica B. Rajal, Andrea Packham, Beatriz Aguilar, Lezlie Rueda, Stefan Wuertz
Summary: The study evaluated the efficacy of RT-qPCR for selective detection of viable protozoan pathogens in spinach. Among the methods tested, RT-qPCR was more effective in discriminating viable from inactivated pathogens. The application of viability methods on leafy greens can be adopted by the produce industry and regulatory agencies for screening purposes.
Article
Engineering, Environmental
A. S. Deshpande, N. L. Fahrenfeld
Summary: Shotgun metagenomic studies have examined antibiotic resistance genes (ARGs) in various environments, and combining this method with viability-based techniques can enhance our understanding of ARG hazards. This study evaluated different methods for separating extracellular DNA (eDNA) and putative non-viable cell DNA to investigate their impact on ARG-host assignments. The results showed significant differences in bacterial community structure and ARG profiles between PMA-DNA and total DNA extracts, indicating the importance of sample preparation methods in assessing the potential hazard of riverine ARGs.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Agriculture, Dairy & Animal Science
Dan Mu, Donggen Zhou, Guoyang Xie, Ju Liu, Zhengzheng Wang, Qin Xiong, Hengyi Xu
Summary: In this study, a method for detecting viable E. coli O157:H7 in food products was established using an enhanced nucleic acid binding dye called improved propidium monoazide (PMAxx) coupled with rRAA assay. The PMAxx-rRAA assay showed high sensitivity and good specificity, and could resist interference from dead bacteria and nontarget bacteria.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Food Science & Technology
Alka Rani, Charles Chinyere Dike, Nitin Mantri, Andrew Ball
Summary: This study developed a rapid and reliable method for the detection of viable Escherichia coli O157:H7 using recombinase polymerase amplification (RPA) combined with propidium monoazide (PMAxx). The assay was able to differentiate between viable/dead bacteria and detect VBNC cells. It showed good performance in terms of detection limit, applicability, and pH stability.
Article
Immunology
Shuo Zhao, Jingyun Zhang, Zhe Li, Yu Han, Biao Kan
Summary: VBNC cells, a survival strategy adopted by bacterial species like Vibrio cholerae under environmental stress, require accurate methods for identification and enumeration. Quantitative PCR methods, particularly ddPCR, show higher accuracy and sensitivity in counting VBNC cells. PMA-ddPCR method presented in this study offers a new tool for quantifying VBNC cells, which can be extended to other bacterial species.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Nutrition & Dietetics
Lisa F. Stinson, Michelle L. Trevenen, Donna T. Geddes
Summary: This study characterized the viable bacterial content and total bacterial DNA content in fresh human milk, finding that the majority of DNA recovered was from non-viable organisms. Samples treated with PMA showed significant differences in bacterial composition compared to untreated samples. These results suggest that the total bacterial DNA content in human milk does not accurately represent the viable human milk microbiome, raising questions about the validity of previous conclusions in this field.
Article
Engineering, Chemical
Ji Yoon Kim, Eun Bi Jeon, Min Gyu Song, Kwang Soo Ha, Sang Hyeon Jeong, Yeoun Joong Jung, Shin Young Park
Summary: This study explored the combined effects of ultrasonic waves and DBD plasma treatment on reducing human norovirus in fresh sea squirt. The results showed that DP treatment alone reduced HNV to a greater extent compared to UW treatment alone. The combined UW 60 min + DP 60 min achieved a significant reduction of viable HNV GII. 4, suggesting a potential nonthermal method for reducing HNV in seafood.
JOURNAL OF FOOD PROCESS ENGINEERING
(2021)
Article
Environmental Sciences
Nury Infante, Refugio Rodriguez, Yaneth Bartolo, Olga Sanchez, Isabel Sanz, Lizeth Bermeo, Jordi Morato
Summary: The study demonstrated the potential of cork biofunctionalized with MoSe extracts in reducing waterborne pathogens. It was found that f-cork effectively reduced the growth of E. coli in the experiment.
Article
Environmental Sciences
B. Reyneke, M. Waso, T. Ndlovu, T. Clements, B. Havenga, S. Khan, W. Khan
Summary: This study compared the effectiveness of EMA and PMA combined with ABS and qPCR assays in detecting viable bacterial species in rainwater. The results showed that both EMA and PMA reduced the detection of nonviable bacteria in rainwater samples, but EMA treatment significantly altered the relative abundance of dominant bacterial families and genera, as well as decreased the detection of unclassified bacteria. Additionally, the use of EMA and PMA increased the detection of less abundant pathogenic bacteria. The combination of viability pre-treatments with ABS and qPCR provides a comprehensive monitoring approach for detecting less abundant bacterial genera and/or pathogens in water sources.
WATER AIR AND SOIL POLLUTION
(2022)
Article
Microbiology
Shuo Zhao, Xin Lu, JingYun Zhang, Biao Kan
Summary: When bacterial pathogens are exposed to adverse conditions, they can enter the viable but nonculturable (VBNC) state. Detecting and quantifying VBNC cells is necessary for microbiological studies and pathogen monitoring. In this study, a droplet digital PCR (ddPCR) method with a chromosomal single-copy gene as an internal reference was developed to accurately enumerate Vibrio cholerae VBNC cells. This method showed greater accuracy and sensitivity than qPCR and has the potential to be extended to other bacterial VBNC cells.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Xiaoling Zheng, Yinhuan Wang, WanZi Gong, Qianru Cai, Jue Li, Jiequn Wu
Summary: A highly sensitive and specific PCR method was established to detect pathogenic bacteria in live Bacillus licheniformis capsules by using PMA-qPCR combined with microporous membrane filtration and centrifugal enrichment, effectively eliminating the interference of excipients and dead bacterial DNA.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Veterinary Sciences
Liu Yang, Yunzhi Long, Qianqian Li, Wenbo Song, Ying Huang, Gong Liang, Daobing Yu, Mingguang Zhou, Gaoyuan Xu, Yao Chen, Chao Huang, Xibiao Tang
Summary: Currently, there is no effective experimental method for detecting the infectivity of suid herpesvirus 1 (SHV-1) in pigs. This study combined propidium monoazide (PMA) with quantitative polymerase chain reaction (qPCR) to determine the infectivity of SHV-1. Heat inactivation proved to be able to differentiate the infective status of the virus, while UV inactivation did not. The method exhibited high stability with a detection rate of 96%.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Wannes Van Holm, Justien Ghesquiere, Nico Boon, Tim Verspecht, Kristel Bernaerts, Naiera Zayed, Ioanna Chatzigiannidou, Wim Teughels
Summary: The use of viability quantitative PCR (v-qPCR) has revolutionized the assessment of microbial viability, but the selection of qPCR amplicon length is crucial for accurate live/dead distinction. Longer amplicon lengths increase the difference in quantification cycle (C-q) between live and dead cells, but decrease qPCR efficiency. The optimal amplicon length for v-qPCR is around 400 bp, balancing efficiency with the ability to distinguish between live and dead bacteria.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Food Science & Technology
Huayou Chen, Lingyu Kang, Keyi Li, Tao Feng, Zhong Ni, Ebin Gao, Zhen Fang
Summary: Real-time monitoring of harmful bacteria in feed fermentation is crucial for enhancing feed quality. This study combined propidium monoazide dyes (PMA) with qPCR technology to investigate microflora changes during artificially contaminated feed fermentation. The results showed that PMA-qPCR had higher Cycle Threshold (Ct) values compared to qPCR, effectively eliminating the influence of dead bacteria. The growth of Escherichia coli O157:H7, Shigella flexneri, and Staphylococcus aureus was inhibited during soybean meal feed fermentation, whereas beneficial bacteria were unaffected. These findings suggest that anaerobically fermented feed can be a promising alternative to antibiotics, and real-time monitoring of harmful bacteria in fermented feed using PMA-qPCR will enhance safety risk assessment.
INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Microbiology
Rehan Deshmukh, Ajay Ghosh Chalasani, Debprasad Chattopadhyay, Utpal Roy
Summary: A novel cyclic peptide-1 (ASP-1) has been isolated from Bacillus subtilis, showing potent activity against methicillin-resistant Staphylococcus aureus (MRSA) by damaging the cell wall, causing membrane lysis, and likely leading to leakage of cytoplasmic contents. Ultrastructure alterations induced by ASP-1 have been compared with oxacillin-treated MRSA cells using scanning electron microscopy.
REVISTA ARGENTINA DE MICROBIOLOGIA
(2021)
Article
Chemistry, Analytical
Rehan Deshmukh, Utpal Roy, Sunil Bhand
Summary: A label-free genosensor for rapid and specific detection of Escherichia coli in water was developed and tested in this study. The genosensor showed a linear range of 1 to 1000 pg/mL for E. coli DNA and demonstrated species-specific detection without cross-reactivity to other bacteria. This genosensor has the potential for practical application in the detection of E. coli in real water samples.
CURRENT ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Pavar Sai Kumar, Sunil Bhand, Ashis Kumar Das, Sanket Goel
Summary: A novel CLSA approach on a 3D printed microfluidic paper-based analytical device was demonstrated, with the working temperature directly influencing the signal intensity and achieving stable CL signal amplification. The method showed strong potential for multiple CL-based detection and monitoring applications.
Article
Multidisciplinary Sciences
Barun Halder, Suranjana Ghosh, Pradosh Basu, Jayanta Bera, Boris Malomed, Utpal Roy
Summary: This article addresses the dynamics of Bose-Einstein condensates loaded into a one-dimensional four-color optical lattice potential. The analysis identifies specific parameter forms of the potential that allow for exact solitary-wave solutions. These solutions offer options for controllable positioning of density maxima and can be used for applications in quantum simulations and quantum information processing.
Article
Entomology
Manish Singh, Estera S. Dey, Sunil Bhand, Cedric Dicko
Summary: The application of nanotechnology in textiles is limited by the difficulties of loading and leakage of nanoparticles. This study used supercritical carbon dioxide as a carrier fluid to successfully impregnate four types of Indian silks with gold nanoparticles. The impregnation caused structural changes in the silk fibers.
Article
Physics, Multidisciplinary
Nilanjan Kundu, Ajay Nath, Jayanta Bera, Suranjana Ghosh, Utpal Roy
Summary: We provide a generic and precise analytical model for achieving negative absolute temperature in ultracold atoms under a quasi-periodic optical lattice and an expulsive trap. By controlling the trap parameters, we explore all the necessary conditions for achieving negative temperature domain and perform a quantitative estimation of the temperature in the negative domain. Numerical stability analysis confirms the stability of the proposed family of solutions and connects it to the merit of negative temperature through mean deviation data with varied trap parameters.
Article
Physics, Multidisciplinary
Jayanta Bera, Barun Halder, Suranjana Ghosh, Ray-Kuang Lee, Utpal Roy
Summary: We report a scheme for quantum sensing in ultracold atoms using an atom-interferometer that creates sub-Planck scale structures. By trapping the condensate in a hybrid potential with atomic beam-splitters, we demonstrate quantum sensing for position, momentum, and temperature. The maximum limit of quantum sensing is identified and our results provide a promising approach for quantum sensing with Bose-Einstein condensate in atomic chips.
Article
Physics, Multidisciplinary
Nilanjan Kundu, Suranjana Ghosh, Utpal Roy
Summary: An exact analytical model is presented to study the phenomenon of rogue waves in Bose-Einstein condensate under a bichromatic optical lattice. The formation mechanism of rogue waves at various trap parameters is qualitatively understood by considering a mixture of bright and dark solitary waves. It is found that lattice parameters can control the spatio-temporal variations of the condensate density, and an Anderson-like localization is identified where the condensate preserves the rogue wave nature at the central frustrated site for larger lattice frustration.
Article
Physics, Condensed Matter
Pradosh Basu, Barun Halder, Sriganapathy Raghav, Utpal Roy
Summary: In this study, various solitary wave excitations for a Bose-Einstein condensate in the presence of two hybrid potentials formed by triple mixtures of optical lattices were explored. The results reveal bright solitary wave, periodic wave, and cnoidal wave excitations. The system also exhibits Anderson localization, bifurcation of condensate at the center, and competition between two different types of localizations upon trap engineering. The obtained solutions are shown to be structurally stable and sufficiently stable for dynamical stability.
Article
Optics
Ajay Nath, Jayanta Bera, Maitri R. Pathak, Utpal Roy
Summary: Using the complex Ginzburg-Landau equation, this study provides an exact analytical model for realizing a cigar-shaped Bose-Einstein condensate trapped in a bi-periodic optical lattice and an exponential periodic trap with cubic and quintic atom-atom interactions. The researchers identify the parameters for controlling localization and illustrate a novel mechanism for transition between bi-chromatic and mono-chromatic lattices.
EUROPEAN PHYSICAL JOURNAL D
(2022)
Review
Biotechnology & Applied Microbiology
Rehan Deshmukh, Utpal Roy
Summary: COVID-19 has changed our way of life and continues to affect people globally. Research has focused on finding effective ways to combat the infection, particularly targeting the cytokine storm phenomenon, which is closely linked to disease severity. Tocilizumab, corticosteroids, TNF-blockers, and JAK inhibitors are potential methods to reduce cytokine-mediated storm in COVID-19 patients.
JOURNAL OF PURE AND APPLIED MICROBIOLOGY
(2023)
Article
Microbiology
Swetha Ramesh, Madhuri Madduri, Shivaprakash M. Rudramurthy, Utpal Roy
Summary: Limited treatment options and drug resistance encourage the search for novel antifungal leads. Antifungal lipopeptides, such as AF(4), have shown broad-spectrum activity and minimal cytotoxicity. AF(4) acts by disrupting the cell membrane and generating reactive oxygen species, making it a potential candidate for alternative antifungal therapies.
MICROBIOLOGY SPECTRUM
(2023)
Article
Multidisciplinary Sciences
Jayanta Bera, Abdul Q. Batin, Suranjana Ghosh, Boris Malomed, Utpal Roy
Summary: This article studies the effects of time-periodic modulation on a quasi-one-dimensional Bose-Einstein condensate with contact and long-range dipolar interactions. The modulation generates a variety of harmonics in the condensate's oscillations, including multiple and combinational harmonics. The results of approximate analytical calculations are confirmed by simulations of the underlying Gross-Pitaevskii equation.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2023)
Article
Optics
Sriganapathy Raghav, Barun Halder, Pradosh Basu, Utpal Roy
Summary: We provide an analytical model to achieve exponential localization of a Bose-Einstein condensate under a bichromatic optical lattice, known as Anderson localization. The degree of localization is investigated using the participation ratio, and the laser parameter domain for Anderson localization is identified. The exponential nature of the localization is proved, and the tunneling and revival phenomenon of Anderson-localized condensate are observed. The study also examines the dynamical and structural stability of the condensate during Anderson localization.
Review
Chemistry, Multidisciplinary
Sruthi Prasood Usha, Hariharan Manoharan, Rehan Deshmukh, Ruslan Alvarez-Diduk, Enric Calucho, V. V. R. Sai, Arben Merkoci
Summary: This review discusses the design and development of high-performance biosensing modalities for detecting ultra-low abundance of analytes in real-life samples. It focuses on Attomolar Analyte Sensing Techniques (AttoSens) that provide relevant sensitivity, selectivity, response time, and sampling efficiency. The summary highlights the technological advances made in the past decade by AttoSens trends for detecting attomolar concentration of analytes.
CHEMICAL SOCIETY REVIEWS
(2021)