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Idrees M, Ali S, Rehman A, Zajif Hussain S, Abbas Bukhari D. Uptake of lead by bacteria isolated from industrial effluents and their potential use in bioremediation of wastewater. Saudi J Biol Sci 2023; 30:103740. [PMID: 37538349 PMCID: PMC10393803 DOI: 10.1016/j.sjbs.2023.103740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/04/2023] [Accepted: 07/08/2023] [Indexed: 08/05/2023] Open
Abstract
Due to rising populations and human activities, heavy metals (HM) toxicity has become a serious problem for all life forms. The present study deals with isolating and identifying lead-resistant bacteria from contaminated wastewater of tanneries effluents. Two isolated strains were identified as Bacillus cereus (ID1), and Bacillus sp. (ID3), and both strains resisted a 25 mM concentration of Lead nitrate (Pb (NO3)2). After four days of treatment, Bacillus cereus (ID1) showed 80% lead uptake, and Bacillus sp. (ID3) showed 88%. Lead uptake was confirmed by Energy dispersive X-Ray (EDX) analysis. Fourier transform infrared spectroscopy (FTIR) showed that structural alterations had occurred in functional groups of the treated samples compared to the controls. Our research indicates that these Bacillus strains may be useful in bioremediating heavy metals from polluted environments. Further investigation into the processes involved in the uptake and homeostasis of heavy metals by these strains is required, as is the identification of the genes and enzymes responsible for Pb-bioremediation.
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Affiliation(s)
- Muhammad Idrees
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Shakir Ali
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Abdul Rehman
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Syed Zajif Hussain
- Department of Chemistry, SBA School of Science and Engineering (SBASSE), Lahore University of Management Sciences (LUMS), DHA, Lahore Cantt 54792, Pakistan
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Pirutin SK, Jia S, Yusipovich AI, Shank MA, Parshina EY, Rubin AB. Vibrational Spectroscopy as a Tool for Bioanalytical and Biomonitoring Studies. Int J Mol Sci 2023; 24:ijms24086947. [PMID: 37108111 PMCID: PMC10138916 DOI: 10.3390/ijms24086947] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
The review briefly describes various types of infrared (IR) and Raman spectroscopy methods. At the beginning of the review, the basic concepts of biological methods of environmental monitoring, namely bioanalytical and biomonitoring methods, are briefly considered. The main part of the review describes the basic principles and concepts of vibration spectroscopy and microspectrophotometry, in particular IR spectroscopy, mid- and near-IR spectroscopy, IR microspectroscopy, Raman spectroscopy, resonance Raman spectroscopy, Surface-enhanced Raman spectroscopy, and Raman microscopy. Examples of the use of various methods of vibration spectroscopy for the study of biological samples, especially in the context of environmental monitoring, are given. Based on the described results, the authors conclude that the near-IR spectroscopy-based methods are the most convenient for environmental studies, and the relevance of the use of IR and Raman spectroscopy in environmental monitoring will increase with time.
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Affiliation(s)
- Sergey K Pirutin
- Faculty of Biology, Shenzhen MSU-BIT University, No. 1, International University Park Road, Dayun New Town, Longgang District, Shenzhen 518172, China
- Faculty of Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia
- Institute of Theoretical and Experimental Biophysics of Russian Academy of Sciences, Institutskaya St. 3, 142290 Pushchino, Russia
| | - Shunchao Jia
- Faculty of Biology, Shenzhen MSU-BIT University, No. 1, International University Park Road, Dayun New Town, Longgang District, Shenzhen 518172, China
| | - Alexander I Yusipovich
- Faculty of Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia
| | - Mikhail A Shank
- Faculty of Biology, Shenzhen MSU-BIT University, No. 1, International University Park Road, Dayun New Town, Longgang District, Shenzhen 518172, China
- Faculty of Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia
| | - Evgeniia Yu Parshina
- Faculty of Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia
| | - Andrey B Rubin
- Faculty of Biology, Shenzhen MSU-BIT University, No. 1, International University Park Road, Dayun New Town, Longgang District, Shenzhen 518172, China
- Faculty of Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia
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Kilicaslan GC, Gurbanov R, Darcan C. Evaluation of copper-induced biomolecular changes in different porin mutants of Escherichia coli W3110 by infrared spectroscopy. J Biol Phys 2023:10.1007/s10867-023-09632-4. [PMID: 37010721 PMCID: PMC10397155 DOI: 10.1007/s10867-023-09632-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 03/12/2023] [Indexed: 04/04/2023] Open
Abstract
Copper (Cu), one of the heavy metals, plays a vital role in many complex biochemical reactions as a trace element. However, it often becomes toxic when its concentration in the cell exceeds a certain level. Homeostasis of metals in the cell is primarily related to regulating metal transport into and out of the cell. Therefore, it is thought that porin proteins, which have a role in membrane permeability, may also play a role in developing Cu resistance. This study identified the differences between the molecular profiles of wild-type Escherichia coli W3110 and its seven different porin mutants exposed to Cu ions using attenuated total reflectance (ATR)-Fourier transform infrared (FTIR) spectroscopy. The results showed that the absence of porin genes elicits global changes in the structure and composition of membrane lipids and proteins, in both the absence and presence of Cu. The lack of porin genes significantly elevated the amounts of fatty acids and phospholipids. When the alterations in protein secondary structures were compared, the quantity of amide I proteins was diminished by the presence of Cu. However, the amount of amide II proteins increased in porin mutant groups independent of Cu presence or absence. The DNAs are transformed from B- and Z-form to A-form due to porin mutations and the presence of Cu ions. The lack of porin genes increased polysaccharide content independent of Cu presence. This study can help characterize Cu detoxification efficiency and guide for obtaining active living cells to be used in bioremediation.
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Affiliation(s)
- Gulcin Cetin Kilicaslan
- Bilecik Şeyh Edebali University, Faculty of Science, Department of Molecular Biology and Genetics TR, Bilecik, TR, 11100, Türkiye
| | - Rafig Gurbanov
- Bilecik Şeyh Edebali University, Faculty of Engineering, Department of Bioengineering, Bilecik, TR, 11100, Türkiye.
- Bilecik Şeyh Edebali University, Central Research Laboratory, Bilecik, TR, 11100, Türkiye.
| | - Cihan Darcan
- Bilecik Şeyh Edebali University, Faculty of Science, Department of Molecular Biology and Genetics TR, Bilecik, TR, 11100, Türkiye
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Changez M, Anwar MF, Al-Ghenaime S, Kapoor S, Balushi RA, Chaudhuri A. Synergic effect of aqueous extracts of Ocimum sanctum and Trigonella foenum-graecum L on the in situ green synthesis of silver nanoparticles and as a preventative agent against antibiotic-resistant food spoiling organisms. RSC Adv 2022; 12:1425-1432. [PMID: 35425194 PMCID: PMC8978925 DOI: 10.1039/d1ra08098a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/15/2021] [Indexed: 11/21/2022] Open
Abstract
The combination of Ocimum sanctum and Trigonella foenum-graecum L leaf water extract synergistically acts as a reducing and capping agent for the synthesis of narrow polydisperse silver nanoparticles (Ag NPs) with controlled sizes depending on the precursor (AgNO3) concentration in the plant extract. The toxicity of 40 nm-sized green synthesized Ag NPs is less than that of 10 nm-sized NPs. The Ag NP solution in Ocimum sanctum and Trigonella foenum-graecum L leaf water extract shows synergic antibacterial effect on Gram-negative bacteria by effecting the ester group of the lipids (hydrolysis) and also breaking the amide bonds of the bacterial chemical constituents, which leads to their rapid death. Combining Ocimum sanctum and Trigonella foenum-graecum L leaf water extracts synergistically act as a reducing and capping agent for the synthesis of narrow polydisperse silver nanoparticles with controlled sizes depending on the precursor (AgNO3) concentration.![]()
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Affiliation(s)
- Mohammad Changez
- College of Applied and Health Sciences, A' Sharqiyah University Ibra 400 Sultanate of Oman
| | | | - Said Al-Ghenaime
- College of Applied and Health Sciences, A' Sharqiyah University Ibra 400 Sultanate of Oman
| | - Sumeet Kapoor
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi (IITD) India
| | - Rayya Al Balushi
- College of Applied and Health Sciences, A' Sharqiyah University Ibra 400 Sultanate of Oman
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Wang Y, Luo H, Peng H, Wang X, Xu F, Xu H. Coprinus comatus endophytic bacteria characteristics and mechanisms for the cadmium resistance. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:584-593. [PMID: 34341927 DOI: 10.1007/s11356-021-15381-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Characteristics and resistant mechanisms of macro-fungus endophytic bacteria to cadmium (Cd) have not been well defined. Strains L1 and L3 with Cd-resistant capacity were isolated from the fruiting body of Coprinus comatus, which were identified as Bacillus sp. Under the stress of Cd, the morphologies of both L1 and L3 changed to reduce the threat of Cd. The results of Fourier Transform Infrared Spectrometry indicated that functional groups such as -OH, -COOH, and -NH2 participated in the Cd adsorption process. The contents of Cd adsorbed on the cell wall of L1 were 83.46-174.51% higher than that of L3. On the contrary, the contents of Cd accumulated in L1 cytoplasm were 38.77-74.77% lower than that of L3. As the level of Cd increased from 10 to 30 mg/L, the percentages of Cd distributed on the cell walls of L1 and L3 increased by 42.43% and 26.78%, respectively. The results also revealed that the contents of Cd absorbed by the sterilized strains L1 and L3 were 47.67-64.94% and 8.65-78.63% higher than that of living ones, respectively. In addition, the proline production of L1 was 23.75-109.68% higher than that of L3, while the malondialdehyde (MDA) production of L1 was 0.96-15.60% lower than that of L3. Thus, through the comparison of endophytic bacterial physiological responses, the possible characteristics and resistant mechanisms of macro-fungus endophytic bacteria under Cd stress were firstly reported.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, People's Republic of China
| | - Huanyan Luo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, People's Republic of China
| | - He Peng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, People's Republic of China
| | - Xitong Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, People's Republic of China
| | - Fei Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, People's Republic of China
| | - Heng Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, People's Republic of China.
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Gupta AD, Gupta A, Reyes-Calderón A, Merupo VI, Kalita G, Herrera-Celis J, Chandra N, Sharma A, Ramirez JT, Arriaga LG, Oza G. Biological Synthesis of PbS, As 3S 4, HgS, CdS Nanoparticles using Pseudomonas aeruginosa and their Structural, Morphological, Photoluminescence as well as Whole Cell Protein Profiling Studies. J Fluoresc 2021; 31:1445-1459. [PMID: 34268653 DOI: 10.1007/s10895-021-02769-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/30/2021] [Indexed: 10/20/2022]
Abstract
Metal sulfide nanoparticles are semi-conductors that possess many applications in optics, optoelectronics and magnetic devices. There are physical and chemical methods for their synthesis but such methods involve toxic precursors as well as many obnoxious by-products. Hence, biological synthesis of metal sulfide nanoparticles are efficient enough to transform toxic metals to non-toxic ones. Pseudomonas aeruginosa, isolated from textile effluent and tolerant of high levels of heavy metals, was used for the green synthesis of metal sulfide (HgS, As3S4, CdS and PbS) nanoparticles. The optical, structural and morphological nature of metal sulfide nanoparticles was also determined. FTIR (Fourier Transform Infra-red) analysis showed spectral changes when P. aeruginosa was grown in medium containing heavy metals viz. Hg, As, Pb and Cd indicating that there are functional groups viz. carboxyl, hydroxyl, phosphate, amino and amide, that exists on the surface of the bacteria, thus facilitating binding of metals on its surface. The bacterial samples which were treated with different metals at different concentrations, were subjected to whole cell protein analysis using SDS-PAGE (Sodium dodecyl Sulphate- Polyacrylamide gel electrophoresis) and protein profiling. The total protein estimation revealed that there was an increase in the protein concentration in the presence of heavy metals and a significant change in the banding pattern was observed which showed induction of a set of proteins under heavy metal stress especially mercury.
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Affiliation(s)
- Annika Durve Gupta
- Department of Biotechnology, Birla College of Arts, Science and Commerce, Thane Dist, Kalyan, MS, India.
| | - Arvind Gupta
- Bioxia, H-7 Rajlakshmi complex khaler Bhiwandi Thane, Bhiwandi, India
| | - Almendra Reyes-Calderón
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio González Fracc. San Pablo, No. 500, 76130, Queretaro, Mexico
| | - Victor Ishrayelu Merupo
- Univ. Lille, CNRS, Centrale Lille, Univ. Artois, UMR 8181 - UCCS - Unité de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - Golap Kalita
- Department of Physical Science and Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Jośe Herrera-Celis
- Laboratorio Nacional de Micro Y Nanofluidica (LABMyN), Centro de Investigación y Desarrollo Tecnológico en Electroquímica (CIDETEQ), Queretaro, 76703, México
| | - Naresh Chandra
- Department of Biotechnology, Birla College of Arts, Science and Commerce, Thane Dist, Kalyan, MS, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio González Fracc. San Pablo, No. 500, 76130, Queretaro, Mexico
| | - Jose Tapia Ramirez
- Department of Genetics and Molecular Biology, Centro de Investigación Y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAVIPN), 0730, Mexico City, Mexico
| | - L G Arriaga
- Laboratorio Nacional de Micro Y Nanofluidica (LABMyN), Centro de Investigación y Desarrollo Tecnológico en Electroquímica (CIDETEQ), Queretaro, 76703, México
| | - Goldie Oza
- Laboratorio Nacional de Micro Y Nanofluidica (LABMyN), Centro de Investigación y Desarrollo Tecnológico en Electroquímica (CIDETEQ), Queretaro, 76703, México.
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Gurbanov R, Karadağ H, Karaçam S, Samgane G. Tapioca Starch Modulates Cellular Events in Oral Probiotic Streptococcus salivarius Strains. Probiotics Antimicrob Proteins 2021; 13:195-207. [PMID: 32601954 DOI: 10.1007/s12602-020-09678-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Considering the implications of microbiota in health, scientists are in search of microbiota-oriented strategies for the effective prevention and/or treatment of a wide variety of serious diseases. A microbiota comprises diverse microorganisms with either probiotic or pathogenic properties. The fermentation of prebiotic carbohydrates by probiotic bacteria can affect host metabolism. Therefore, understanding the prebiotic-mediated metabolic modulations in probiotics is crucial to develop functional foods for the improvement of disturbed microbiota. Studies have emphasized the importance of prebiotics in probiotic therapies for mucosal diseases and highlighted the need for extensive research on oral bacteria. In the present study, the cellular events have been studied in batch cultures of probiotic Streptococcus salivarius exposed to the natural prebiotic, tapioca starch (TS). TS modulated the keystone metabolic events in Streptococcus salivarius in a dose-dependent manner. Besides increasing the live cell counts and altering the colony morphologies, TS affected the protein metabolism in terms of cellular expression and conformational changes in protein secondary structures. After treatment with TS, the nucleic acid synthesis increased and B-DNA was more than A- and Z-DNA, together with the diminished fatty acids and increased polysaccharide synthesis. The study results can be considered for the assessment of functional foods and probiotics in oral health.
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Affiliation(s)
- Rafig Gurbanov
- Department of Molecular Biology and Genetics, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey.
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey.
| | - Hazel Karadağ
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey
| | - Sevinç Karaçam
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey
| | - Gizem Samgane
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey
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8
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Tunçer S, Gurbanov R. A novel approach for the discrimination of culture medium from Vascular Endothelial Growth Factor (VEGF) overexpressing colorectal cancer cells. TURKISH JOURNAL OF BIOCHEMISTRY 2020. [DOI: 10.1515/tjb-2020-0058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Objectives
The expression level of Vascular Endothelial Growth Factor (VEGF) is assumed as a prognostic marker for several tumor types, including colorectal cancer. Therefore, the determination of pre- and post-therapy levels of VEGF appears to have great value in the assessment of tumor prognosis. Enzyme-Linked Immunosorbent Assay (ELISA) is commonly used for the determination of serum or plasma VEGF levels, but the method is costly and time-consuming. In this study, we aimed to describe a rapid and cost-effective analysis method to discriminate VEGF overexpressing colorectal cancer-derived conditioned medium (CM).
Methods
Attenuated Total Reflection (ATR)-Fourier Transform Infrared (FTIR) spectroscopy, combined with Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA), was used to differentiate VEGF overexpressing colorectal cancer cell line CM from CM obtained from the corresponding control cells which express and secrete relatively lower amount of VEGF.
Results
Samples belong to VEGF overexpressing colorectal cancer cells were clearly distinguished from the control group with very high PC scores as PC1 + PC2 = 96%. Besides, a 100% accurate distinction between these two groups was achieved by the LDA analysis.
Conclusions
ATR-FTIR spectroscopy combined with pattern recognition techniques was able to discriminate CM of VEGF overexpressing colorectal cancer cells with high efficiency and accuracy.
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Affiliation(s)
- Sinem Tunçer
- Bilecik Seyh Edebali Universitesi , Vocational School of Health Services Department of Medical Laboratory Techniques , Pelitözü Mah. Fatih Sultan Mehmet Bulvarı No:27, Merkez , Bilecik , Turkey
- Bilecik Seyh Edebali Universitesi , Biotechnology Application and Research Center , Pelitözü Mah. Fatih Sultan Mehmet Bulvarı No:27, Merkez , Bilecik , Turkey
| | - Rafig Gurbanov
- Bilecik Seyh Edebali Universitesi , Department of Molecular Biology and Genetics , Bilecik , Turkey
- Bilecik Seyh Edebali Universitesi , Biotechnology Application and Research Center , Bilecik , Turkey
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9
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Gupta AD, Kavitha E, Singh S, Karthikeyan S. Toxicity mechanism of Cu 2+ ion individually and in combination with Zn 2+ ion in characterizing the molecular changes of Staphylococcus aureus studied using FTIR coupled with chemometric analysis. J Biol Phys 2020; 46:395-414. [PMID: 33237339 DOI: 10.1007/s10867-020-09560-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/08/2020] [Indexed: 10/22/2022] Open
Abstract
Copper and zinc have a high binding affinity with a Staphylococcus aureus bacterial community. This causes a change in the biomolecular composition of S. aureus. Our study aims at understanding the resistance mechanism of Cu and Zn either or in various combinations using FTIR and chemometric techniques. Zn toxicity resulted in a significant change in lipid content (3100-2800 cm-1) compared to Cu. A significant decrease in protein content is observed for Cu treatment in the amide region. The bio-concentration factor shows a higher value for Cu compared to Zn. The increase in band area of carbohydrates moieties 1059 cm-1 shows the secretion of EPS due to Cu toxicity. A significant change in nucleic acid compositions was noted in the region1200-900 cm-1 due to Zn treatment. Secondary structural change in protein shows β sheet formation. The result of the finding shows Cu has greater toxicity than Zn. Further toxicity effects were greatly enhanced for metal mixtures ratio (Cu:2Zn). This shows Zn exhibits synergism effect with Cu. The obtained ROC (receiver operating characteristic) curve area gives good reliability of the experiments. The study attempts to understand the mechanism of toxicity removal of Cu and Zn metal mixtures by bacterial population using FTIR coupled with chemometric techniques. Graphical abstract.
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Affiliation(s)
- Annika Durve Gupta
- Department of Biotechnology, B. K. Birla College, Kalyan, Maharashtra, 421304, India
| | - Esakimuthu Kavitha
- Department of Physics, Dr. MGR Educational and Research Institute, Chennai, Tamil Nadu, 600095, India
| | - Shikha Singh
- Department of Biotechnology, B. K. Birla College, Kalyan, Maharashtra, 421304, India
| | - Sivakumaran Karthikeyan
- Department of Physics, Dr. Ambedkar Government Arts College, Chennai, Tamil Nadu, 600039, India.
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10
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Cell-free supernatant of Streptococcus salivarius M18 impairs the pathogenic properties of Pseudomonas aeruginosa and Klebsiella pneumonia. Arch Microbiol 2020; 202:2825-2840. [PMID: 32747998 DOI: 10.1007/s00203-020-02005-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/15/2020] [Accepted: 07/24/2020] [Indexed: 12/17/2022]
Abstract
M18 strain of Streptococcus salivarius is a bacterial replacement probiotic that has been suggested for use in the oral cavity. Here, we have shown that S. salivarius M18 cell-free supernatant reduced the growth of the two most common human pathogens Pseudomonas aeruginosa and Klebsiella pneumonia and sensitized the pathogenic bacteria to antibiotic. Besides, the supernatant inhibited biofilm formation of P. aeruginosa drastically. For pinpointing the biomolecular changes that occurred in P. aeruginosa incubated with the probiotic supernatant, attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy was used. Unsupervised learning algorithms, principal component analysis (PCA) and hierarchical cluster analysis (HCA), and intensity analyses of individual spectral bands exhibited comprehensive alterations in the polysaccharide and lipid contents and compositions of P. aeruginosa cultivated with S. salivarius M18 cell-free supernatant. These results indicate that S. salivarius M18 has the potential for the prevention or alleviation of different pathogen-induced infections along with the infections of oral pathogens.
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11
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Qi P, Wang Y, Zhang D, Sun Y, Zheng L. Multichannel bacterial discrimination based on recognition and disintegration disparity of short antimicrobial peptides. Anal Biochem 2020; 600:113764. [DOI: 10.1016/j.ab.2020.113764] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/17/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022]
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12
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Ferreira ML, Gerbino E, Cavallero GJ, Casabuono AC, Couto AS, Gomez-Zavaglia A, Ramirez SAM, Vullo DL. Infrared spectroscopy with multivariate analysis to interrogate the interaction of whole cells and secreted soluble exopolimeric substances of Pseudomonas veronii 2E with Cd(II), Cu(II) and Zn(II). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117820. [PMID: 31771908 DOI: 10.1016/j.saa.2019.117820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/23/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
Extracellular polymeric substances (EPS) are bacterial products associated to cell wall or secreted to the liquid media that form the framework of microbial mats. These EPS contain functional groups as carboxyl, amino, hydroxyl, phosphate and sulfhydryl, able to interact with cations. Thus, EPS may be considered natural detoxifying compounds of metal polluted waters and wastewaters. In this work Attenuated Total Reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR) in combination with multivariate analysis (Principal Component Analysis-PCA-) were used to study the interaction of Cd(II), Cu(II) and Zn(II) and Pseudomonas veronii 2E cells, including bound EPS and cell wall, and its different soluble EPS fractions, previously characterized as Cd(II) ligands of moderate strength. Amino groups present in exopolysaccharide fraction were responsible for Zn(II) and Cu(II) complexation, while carboxylates chelated Cd(II). In lipopolysaccharide fraction, phosphoryl and carboxyl sites were involved in Cd(II) and Cu(II) binding, while Zn(II) interacted with amino groups. Similar results were obtained from cells. These studies confirmed that FTIR-PCA is a rapid analytical tool to provide valuable information regarding the functional groups in biomolecules related to metal interaction. Moreover, a discrimination and identification of functional groups present in both EPS and cells that interacted with Cd(II), Zn(II) and Cu(II) was demonstrated.
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Affiliation(s)
- Maria L Ferreira
- Área Química, Instituto de Ciencias, Universidad Nacional de General Sarmiento, J.M. Gutierrez 1150, B1613GSX, Los Polvorines, Buenos Aires, Argentina; CONICET, Godoy Cruz 2290, C1425FQB, Buenos Aires, Argentina.
| | - Esteban Gerbino
- CONICET, Godoy Cruz 2290, C1425FQB, Buenos Aires, Argentina; Centro de Investigación y Desarrollo en Criotecnología de Alimentos CIDCA (CCT-CONICET, La Plata), RA 1900 La Plata, Argentina.
| | - Gustavo J Cavallero
- CONICET, Godoy Cruz 2290, C1425FQB, Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica - Consejo Nacional de Investigaciones Científicas y Técnicas, Centro de Investigación en Hidratos de Carbono (CIHIDECAR), Pab. II, Ciudad Universitaria, 1428, Buenos Aires, Argentina.
| | - Adriana C Casabuono
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica - Consejo Nacional de Investigaciones Científicas y Técnicas, Centro de Investigación en Hidratos de Carbono (CIHIDECAR), Pab. II, Ciudad Universitaria, 1428, Buenos Aires, Argentina.
| | - Alicia S Couto
- CONICET, Godoy Cruz 2290, C1425FQB, Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica - Consejo Nacional de Investigaciones Científicas y Técnicas, Centro de Investigación en Hidratos de Carbono (CIHIDECAR), Pab. II, Ciudad Universitaria, 1428, Buenos Aires, Argentina.
| | - Andrea Gomez-Zavaglia
- CONICET, Godoy Cruz 2290, C1425FQB, Buenos Aires, Argentina; Centro de Investigación y Desarrollo en Criotecnología de Alimentos CIDCA (CCT-CONICET, La Plata), RA 1900 La Plata, Argentina.
| | - Silvana A M Ramirez
- Área Química, Instituto de Ciencias, Universidad Nacional de General Sarmiento, J.M. Gutierrez 1150, B1613GSX, Los Polvorines, Buenos Aires, Argentina.
| | - Diana L Vullo
- Área Química, Instituto de Ciencias, Universidad Nacional de General Sarmiento, J.M. Gutierrez 1150, B1613GSX, Los Polvorines, Buenos Aires, Argentina; CONICET, Godoy Cruz 2290, C1425FQB, Buenos Aires, Argentina.
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13
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Gurbanov R, Tunçer S, Mingu S, Severcan F, Gozen AG. Methylation, sugar puckering and Z-form status of DNA from a heavy metal-acclimated freshwater Gordonia sp. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 198:111580. [DOI: 10.1016/j.jphotobiol.2019.111580] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 07/07/2019] [Accepted: 07/29/2019] [Indexed: 01/27/2023]
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14
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Faghihzadeh F, Anaya NM, Hadjeres H, Boving TB, Oyanedel-Craver V. Pulse UV light effect on microbial biomolecules and organic pollutants degradation in aqueous solutions. CHEMOSPHERE 2019; 216:677-683. [PMID: 30391889 DOI: 10.1016/j.chemosphere.2018.10.176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/13/2018] [Accepted: 10/25/2018] [Indexed: 06/08/2023]
Abstract
This study present assessed the effect of UV pulsed light (PL) on microbial and organic pollutants using two spiral lamps were used, i.e., PL1 and PL2 lamps, with wavelength cut-offs of 190 and 240 nm, respectively. Overall, our study demonstrated that pulsed UV light impacts several microbial biomolecules and degrades polycyclic aromatic hydrocarbons (PAHs) in aqueous solution. In microbial inactivation by PL2, temporary changes of bacterial cellular components, specifically proteins, were observed, but the compositional changes of bacteria that were exposed to PL1 were permanent due to ozonolysis. PL1 irradiation caused greater deactivation of the bacteria than PL2 irradiation due to the generation of ozone. The higher efficacy of PL1 in terms of membrane disruption, reduction of respiration rate, and reduction of growth rate was due to the production of ozone during the irradiation period. The bacteria that were irradiated with both PL lamps regrew due to photoreactivation, such as an enzymatic DNA-repair mechanism. The PAH degradation kinetics indicate that higher molecular weights degraded faster than those with lower molecular weights. For both lamps, the degradation of naphthalene and fluorene was first order, whereas second order for pyrene and anthracene. Any effect of ozonolysis on the PAH degradation rates was not apparent, which indicated that photolysis was the primary degradation pathway. PAH solutions treated with both pulsed UV lamps did not result in a toxicity effect on the bacteria.
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Affiliation(s)
- F Faghihzadeh
- Department of Civil and Environmental Engineering, University of Rhode Island, Kingston, RI, 02881, USA
| | - N M Anaya
- Department of Civil and Environmental Engineering, University of Rhode Island, Kingston, RI, 02881, USA
| | - H Hadjeres
- Department of Geoscience, University of Rhode Island, Kingston, RI, 02881, USA
| | - T B Boving
- Department of Civil and Environmental Engineering, University of Rhode Island, Kingston, RI, 02881, USA; Department of Geoscience, University of Rhode Island, Kingston, RI, 02881, USA
| | - V Oyanedel-Craver
- Department of Civil and Environmental Engineering, University of Rhode Island, Kingston, RI, 02881, USA.
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15
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Tunçer S, Gurbanov R, Sheraj I, Solel E, Esenturk O, Banerjee S. Low dose dimethyl sulfoxide driven gross molecular changes have the potential to interfere with various cellular processes. Sci Rep 2018; 8:14828. [PMID: 30287873 PMCID: PMC6172209 DOI: 10.1038/s41598-018-33234-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/25/2018] [Indexed: 12/18/2022] Open
Abstract
Dimethyl sulfoxide (DMSO) is a small molecule with polar, aprotic and amphiphilic properties. It serves as a solvent for many polar and nonpolar molecules and continues to be one of the most used solvents (vehicle) in medical applications and scientific research. To better understand the cellular effects of DMSO within the concentration range commonly used as a vehicle (0.1-1.5%, v/v) for cellular treatments, we applied Attenuated Total Reflectance (ATR) Fourier Transform Infrared (FT-IR) spectroscopy to DMSO treated and untreated epithelial colon cancer cells. Both unsupervised (Principal Component Analysis-PCA) and supervised (Linear Discriminant Analysis-LDA) pattern recognition/modelling algorithms applied to the IR data revealed total segregation and prominent differences between DMSO treated and untreated cells at whole, lipid and nucleic acid regions. Several of these data were supported by other independent techniques. Further IR data analyses of macromolecular profile indicated comprehensive alterations especially in proteins and nucleic acids. Protein secondary structure analysis showed predominance of β-sheet over α-helix in DMSO treated cells. We also observed for the first time, a reduction in nucleic acid level upon DMSO treatment accompanied by the formation of Z-DNA. Molecular docking and binding free energy studies indicated a stabilization of Z-DNA in the presence of DMSO. This alternate DNA form may be related with the specific actions of DMSO on gene expression, differentiation, and epigenetic alterations. Using analytical tools combined with molecular and cellular biology techniques, our data indicate that even at very low concentrations, DMSO induces a number of changes in all macromolecules, which may affect experimental outcomes where DMSO is used as a solvent.
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Affiliation(s)
- Sinem Tunçer
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
- Vocational School of Health Services, Department of Medical Laboratory Techniques, Bilecik Şeyh Edebali University, Bilecik, 11230, Turkey
| | - Rafig Gurbanov
- Department of Molecular Biology and Genetics, Bilecik Şeyh Edebali University, Bilecik, 11230, Turkey
| | - Ilir Sheraj
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
| | - Ege Solel
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
- Department of Biomedicine, University of Bergen, Postbox 7804, Bergen, N-5020, Norway
| | - Okan Esenturk
- Department of Chemistry, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
| | - Sreeparna Banerjee
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey.
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16
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Gurbanov R, S Ozek N, Tunçer S, Severcan F, Gozen AG. Aspects of silver tolerance in bacteria: infrared spectral changes and epigenetic clues. JOURNAL OF BIOPHOTONICS 2018; 11:e201700252. [PMID: 29243883 DOI: 10.1002/jbio.201700252] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/13/2017] [Indexed: 06/07/2023]
Abstract
In this study, the molecular profile changes leading to the adaptation of bacteria to survive and grow at inhibitory silver concentration were explored. The profile obtained through infrared (IR)-based measurements indicated extensive changes in all biomolecular components, which were supported by chemometric techniques. The changes in biomolecular profile were prominent, including nucleic acids. The changes in nucleic acid region (1350-950 cm-1 ) were encountered as a clue for conformational change in DNA. Further analysis of DNA by IR spectroscopy revealed changes in the backbone and sugar conformations. Moreover, Enzyme-Linked Immunosorbent Assay-based measurements of DNA methylation levels were performed to see if epigenetic mechanisms are in operation during bacterial adaptation to this environmental challenge. The results indicated a notable demethylation in Escherichia coli and methylation in Staphylococcus aureus likely to be associated with their elaborate adaptation process to sustain survival and growth.
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Affiliation(s)
- Rafig Gurbanov
- Department of Molecular Biology and Genetics, Bilecik Şeyh Edebali University, Bilecik, Turkey
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Nihal S Ozek
- Department of Biology, Ataturk University, Erzurum, Turkey
| | - Sinem Tunçer
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Biophysics, Faculty of Medicine, Altinbas University, Istanbul, Turkey
| | - Ayse G Gozen
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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17
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Gurbanov R, Gozen AG, Severcan F. Rapid classification of heavy metal-exposed freshwater bacteria by infrared spectroscopy coupled with chemometrics using supervised method. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 189:282-290. [PMID: 28823969 DOI: 10.1016/j.saa.2017.08.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/08/2017] [Accepted: 08/13/2017] [Indexed: 05/21/2023]
Abstract
Rapid, cost-effective, sensitive and accurate methodologies to classify bacteria are still in the process of development. The major drawbacks of standard microbiological, molecular and immunological techniques call for the possible usage of infrared (IR) spectroscopy based supervised chemometric techniques. Previous applications of IR based chemometric methods have demonstrated outstanding findings in the classification of bacteria. Therefore, we have exploited an IR spectroscopy based chemometrics using supervised method namely Soft Independent Modeling of Class Analogy (SIMCA) technique for the first time to classify heavy metal-exposed bacteria to be used in the selection of suitable bacteria to evaluate their potential for environmental cleanup applications. Herein, we present the powerful differentiation and classification of laboratory strains (Escherichia coli and Staphylococcus aureus) and environmental isolates (Gordonia sp. and Microbacterium oxydans) of bacteria exposed to growth inhibitory concentrations of silver (Ag), cadmium (Cd) and lead (Pb). Our results demonstrated that SIMCA was able to differentiate all heavy metal-exposed and control groups from each other with 95% confidence level. Correct identification of randomly chosen test samples in their corresponding groups and high model distances between the classes were also achieved. We report, for the first time, the success of IR spectroscopy coupled with supervised chemometric technique SIMCA in classification of different bacteria under a given treatment.
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Affiliation(s)
- Rafig Gurbanov
- Department of Molecular Biology and Genetics, Bilecik S.E. University, 11230 Bilecik, Turkey; Department of Biochemistry, Middle East Technical University, 06800 Ankara, Turkey
| | - Ayse Gul Gozen
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey; Department of Biophysics, Faculty of Medicine, Altinbas University, 34217 Istanbul, Turkey.
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18
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Adamus-Białek W, Lechowicz Ł, Kubiak-Szeligowska AB, Wawszczak M, Kamińska E, Chrapek M. A new look at the drug-resistance investigation of uropathogenic E. coli strains. Mol Biol Rep 2017; 44:191-202. [PMID: 28091786 PMCID: PMC5310551 DOI: 10.1007/s11033-017-4099-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 01/02/2017] [Indexed: 11/01/2022]
Abstract
Bacterial drug resistance and uropathogenic tract infections are among the most important issues of current medicine. Uropathogenic Escherichia coli strains are the primary factor of this issue. This article is the continuation of the previous study, where we used Kohonen relations to predict the direction of drug resistance. The characterized collection of uropathogenic E. coli strains was used for microbiological (the disc diffusion method for antimicrobial susceptibility testing), chemical (ATR/FT-IR) and mathematical (artificial neural networks, Ward's hierarchical clustering method, the analysis of distributions of inhibition zone diameters for antibiotics, Cohen's kappa measure of agreement) analysis. This study presents other potential tools for the epidemiological differentiation of E. coli strains. It is noteworthy that ATR/FT-IR technique has turned out to be useful for the quick and simple identification of MDR strains. Also, diameter zones of resistance of this E. coli population were compared to the population of E. coli strains published by EUCAST. We observed the bacterial behaviors toward particular antibiotics in comparison to EUCAST bacterial collections. Additionally, we used Cohen's kappa to show which antibiotics from the same class are closely related to each other and which are not. The presented associations between antibiotics may be helpful in selecting the proper therapy directions. Here we present an adaptation of interdisciplinary studies of drug resistance of E. coli strains for epidemiological and clinical investigations. The obtained results may be some indication in deciding on antibiotic therapy.
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Affiliation(s)
- Wioletta Adamus-Białek
- Institute of Medical Sciences, Jan Kochanowski University, IX Wieków Kielc 19A Av., 25-317, Kielce, Poland.
| | - Łukasz Lechowicz
- Department of Microbiology, Institute of Biology, Jan Kochanowski University, 15 Swietokrzyska St., 25-406, Kielce, Poland
| | | | - Monika Wawszczak
- Department of Microbiology, Institute of Biology, Jan Kochanowski University, 15 Swietokrzyska St., 25-406, Kielce, Poland
| | - Ewelina Kamińska
- Department of Microbiology, Institute of Biology, Jan Kochanowski University, 15 Swietokrzyska St., 25-406, Kielce, Poland
| | - Magdalena Chrapek
- Institute of Mathematics, Jan Kochanowski University, 15 Swietokrzyska St., 25-406, Kielce, Poland
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Gurbanov R, Yıldız F. MOLECULAR PROFILE OF ORAL PROBIOTIC BACTERIA TO BE USED WITH FUNCTIONAL FOODS. ACTA ACUST UNITED AC 2017. [DOI: 10.3153/jfhs17015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Gupta AD, Karthikeyan S. Individual and combined toxic effect of nickel and chromium on biochemical constituents in E. coli using FTIR spectroscopy and Principle component analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 130:289-94. [PMID: 27152659 DOI: 10.1016/j.ecoenv.2016.04.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 04/14/2016] [Accepted: 04/22/2016] [Indexed: 05/28/2023]
Abstract
Ni and Cr are ubiquitous pollutants in the aquatic environments. These heavy metals elicit toxicities to aquatic organisms including microbes. In this study, interaction of the two heavy metals on the toxicity in Escherichia coli (E. coli) was studied using FTIR spectroscopy. The binding of Ni(II) to E. coli was stronger than that for Cr(VI). Cr exhibited antagonistic effects in the presence of Ni in E. coli. FTIR analysis showed a decrease in lipid content in the presence of Ni and not for Cr. Further, a decrease in band area was observed in the region of 3000-2800cm(-1) and at ~1455cm(-1) due to a decrease in fatty acids and lipid molecules. The band area ratio of lipid was used to monitor the changes in fatty acids due to metal toxicity. Principle component method helps to discriminates the results between control and metal toxicities in E. coli from the FTIR data. The study shows the importance of metal interaction and its toxicity on E. coli.
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Affiliation(s)
- Annika Durve Gupta
- Department of Biotechnology, Birla College, Kalyan 421304, Maharashtra, India
| | - Sivakumaran Karthikeyan
- Department of Physics, Dr. Ambedkar Government Arts College, Chennai 600039, Tamil Nadu, India.
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Faghihzadeh F, Anaya NM, Schifman LA, Oyanedel-Craver V. Fourier transform infrared spectroscopy to assess molecular-level changes in microorganisms exposed to nanoparticles. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s41204-016-0001-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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