Review
Biotechnology & Applied Microbiology
Ni Zeng, Yichao Wu, Wenli Chen, Qiaoyun Huang, Peng Cai
Summary: Microbial cell-based bioreporters provide a flexible, rapid, and cost-effective strategy for assessing environmental risks posed by contaminants in soil. This review outlines the recent progress in utilizing bioreporters for soil contamination detection, covering biosensing principles, genetic circuit engineering, and developments in detecting heavy metal and organic contaminants. Future opportunities for using whole-cell bioreporters in soil contamination monitoring are also discussed.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Paulius Matulis, Ingrida Kutraite, Ernesta Augustiniene, Egle Valanciene, Ilona Jonuskiene, Naglis Malys
Summary: Indole is a biologically active compound found in plants and bacteria, with various applications in pharmaceuticals, chemicals, and agriculture. This study focuses on the identification and characterization of the indole-inducible system in Pseudomonas putida KT2440 through genetically encoded biosensors. The results provide a basis for using whole-cell biosensors in screening and characterization of indole metabolism-related bacterial species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
D. B. Kuznetsov, A. Yu. Mironov, V. A. Neschislyaev, I. L. Volkhin, E. V. Orlova, A. D. Shilina
Summary: This article introduces a method to restore the lost indicator properties of whole-cell biosensors using electromagnetic radiation. The study shows that radiation parameters have an impact on biosensor luminescence, and different types of radiation can partially restore the indicator properties of biosensors. The mechanism responsible for the sensitizing effect of radiation is explained, involving changes in solvent dipoles and mobility of acceptor molecules, triggering a cascade of biochemical reactions.
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2022)
Review
Environmental Sciences
Bo Jiang, Yizhi Song, Zengjun Liu, Wei E. Huang, Guanghe Li, Songqiang Deng, Yi Xing, Dayi Zhang
Summary: Whole-cell bioreporters (WCBs) are biological tools that use living microorganisms to sense chemicals by producing quantifiable signals. This paper reviews the concept and recent progress in constructing and applying WCBs for sensing petroleum hydrocarbons, addressing key challenges in improving sensitivity and detection limits. The discussion also highlights factors influencing bioreporter performance in environmental samples and suggests solutions for overcoming these barriers.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2021)
Article
Biochemical Research Methods
Natalia Barger, Ilan Oren, Ximing Li, Mouna Habib, Ramez Daniel
Summary: Early detection of blood in urine is crucial for the treatment of serious diseases, and the development of low-cost portable biosensors for this purpose is necessary. An ultrasensitive whole-cell bacterial biosensor was designed for heme detection in urine, showing promising results for hematuria detection.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Daniela Visaggio, Mattia Pirolo, Emanuela Frangipani, Massimiliano Lucidi, Raffaella Sorrentino, Emma Mitidieri, Francesca Ungaro, Andrea Luraghi, Francesco Peri, Paolo Visca
Summary: A bioluminescent whole cell-based biosensor was constructed for rapid, sensitive, and single-step quantification of the pyochelin siderophore produced by Pseudomonas aeruginosa in biological samples.
Article
Biochemistry & Molecular Biology
Sun-Joo Lim, Miae Choi, Inseop Yun, Seulgi Lee, Ny Chang, Chan-Yong Lee
Summary: The lumazine protein from marine luminescent bacteria binds strongly with the fluorescent chromophore 6,7-dimethyl-8-ribitylumazine. The light emission of bacterial luminescent systems is utilized as a sensitive and rapid assay for various biological systems. Recombinant plasmids were constructed to overproduce lumazine and develop fluorescent bacteria for use as microbial sensors. The expression of the recombinant plasmid in E. coli resulted in significantly increased fluorescence intensity, showcasing the potential of these bacterial systems as biosensors with high sensitivity and rapid analysis times.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Physics, Fluids & Plasmas
Ion Santra, Urna Basu, Sanjib Sabhapandit
Summary: This study investigates four distinct dynamical regimes of active Brownian motion in two dimensions, characterized by the presence of two timescales set by the rotational diffusion constant and the reversal rate. Analytical computation of position distribution and persistence exponents reveals that in regime II, the position distribution orthogonal to the initial orientation can be described using a scaled variable, showing nontrivial scaling behavior with a special scaling function. The exact first-passage time distribution computation demonstrates the emergence of a persistence exponent of 1 due to direction reversal in this regime.
Article
Chemistry, Analytical
Eva Delatour, Christophe Pagnout, Marie L. Zaffino, Jerome F. L. Duval
Summary: This article introduces the applications of whole-cell bacterial sensors in chemical detection and toxicity/stress assessment. The study finds that the functioning principles of specific and non-specific biosensors are not exclusive and both can detect modulations of cell metabolic activity under stressing conditions.
Article
Environmental Sciences
Naifu Jin, Yueqiao Liu, Xinzi Wang, Kai Yang, Dayi Zhang, Aizhong Ding
Summary: This study investigated the in-vitro toxicity of Eucalyptus extracts and found that water-soluble fractions were more toxic than dimethylsulfoxide (DMSO)-soluble fractions. The cytotoxicity of the extracts was mainly caused by programmed cell death (PCD), and water-soluble fractions had a greater contribution to the toxicity. The results imply significant ecotoxicological risks of Eucalyptus extracts.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Biochemical Research Methods
Sang-Min Shin, Ramesh K. Jha, Taraka Dale
Summary: Whole-cell biosensors provide a convenient tool for screening genetically engineered biocatalytic activity, but establishing a biosensor for an anthropogenic molecule requires a custom transporter and a transcription factor. This study overcame this challenge by developing an adipic acid (ADA) sensor and successfully established a highly sensitive biosensor with a wide dynamic range.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Chemistry, Analytical
Chang Hong Voon, Nurida Mohd Yusop, Sook Mei Khor
Summary: This article reviews the advantages, challenges, and limitations of using a whole-cell bioluminescent biosensor technology to measure oil and grease content in wastewater. It attempts to bridge the knowledge gap between conventional laboratory methods and biosensor technology, providing guidance for real-world applications.
Article
Biochemistry & Molecular Biology
Shreya Ghosh, Anam Ejaz, Lucas Repeta, Stewart Shuman
Summary: The study identifies Pseudomonas putida MPE as a novel DNA endonuclease capable of sensing and cutting double-stranded DNA, and hydrolyzing the single-stranded DNA backbone in different orientations to generate distinct cleavage products.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Tae Hyun Kim, Seung-Gyun Woo, Seong Keun Kim, Byeong Hyeon Yoo, Jonghyeok Shin, Eugene Rha, Soo Jung Kim, Kil Koang Kwon, Hyewon Lee, Haseong Kim, Hee-Taek Kim, Bong-Hyun Sung, Seung-Goo Lee, Dae-Hee Lee
Summary: In this study, possible biosynthetic pathways for levulinic acid (LA) production from lignin and poly(ethylene terephthalate) were proposed. A genetically encoded biosensor responsive to LA was also created, which can be used for screening and evolving the LA biosynthesis pathway genes. The biosensor showed a linear correlation between fluorescence intensity and LA concentration in the range of 0.156-10 mM LA when expressed in Pseudomonas putida KT2440.
JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tausif Altamash, Wesam Ahmed, Saad Rasool, Kabir H. Biswas
Summary: Intracellular ionic strength plays a crucial role in cellular processes, and there is a demand for sensitive tools for real-time monitoring of its levels. Here, researchers have developed a bioluminescence-based sensing strategy using Nano Luciferase protein to detect intracellular ionic strength alterations, which holds promise for applications in cellular signaling, ion channel functional genomics, and drug discovery experiments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Ecology
Tingting Xu, Enolia Marr, Haylie Lam, Steven Ripp, Gary Sayler, Dan Close
Article
Ecology
Liyu Du, Kelly Arnholt, Steven Ripp, Gary Sayler, Siqun Wang, Chenghua Liang, Jingkuan Wang, Jie Zhuang
Article
Radiology, Nuclear Medicine & Medical Imaging
Bincy Anu John, Tingting Xu, Steven Ripp, Hwa-Chain Robert Wang
MOLECULAR IMAGING AND BIOLOGY
(2017)
Article
Chemistry, Physical
Gabriela Kuncova, Takayuki Ishizaki, Andrey Solovyev, Josef Trogl, Steven Ripp
Review
Oncology
Tingting Xu, Dan Close, Winode Handagama, Enolia Marr, Gary Sayler, Steven Ripp
FRONTIERS IN ONCOLOGY
(2016)
Article
Chemistry, Analytical
Tingting Xu, Michael Conway, Ashley Frank, Steven Ripp, Gary Sayler, Dan Close
Article
Toxicology
Tingting Xu, Andrew Kirkpatrick, Jody Toperzer, Steven Ripp, Dan Close
TOXICOLOGICAL SCIENCES
(2019)
Article
Biotechnology & Applied Microbiology
G. Din, F. Hasan, M. Conway, B. Denney, S. Ripp, A. A. Shah
JOURNAL OF APPLIED MICROBIOLOGY
(2019)
Article
Microbiology
Liqiong Yang, Xijuan Chen, Xiangfeng Zang, Mark Radosevich, Steven Ripp, Jie Zhuang, Gary S. Sayler
FRONTIERS IN MICROBIOLOGY
(2019)
Article
Environmental Sciences
Ghufranud Din, Abrar Hassan, Muhammad Rafiq, Fariha Hasan, Malik Badshah, Samiullah Khan, Gao Chen, Steven Ripp, Aamer Ali Shah
GEOMICROBIOLOGY JOURNAL
(2020)
Article
Biology
Michael Conway, Tingting Xu, Andrew Kirkpatrick, Steven Ripp, Gary Sayler, Dan Close
Article
Chemistry, Analytical
Jakub Zajic, Steven Ripp, Josef Trogl, Gabriela Kuncova, Marie Pospisilova
Article
Environmental Sciences
G. Din, A. Hassan, J. Dunlap, S. Ripp, A. A. Shah
Summary: A cadmium-tolerant fungus strain FMS2 was isolated from metal-polluted soil in Lahore, Pakistan, and identified as Penicillium chrysogenum. The fungus showed high tolerance to cadmium up to 1000 mg l(-1) and had a cadmium removal capacity of 49% within 15 days. Various analytical methods were used to study the cadmium uptake, distribution, and bioabsorption by the fungal cells.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2022)
Proceedings Paper
Electrochemistry
Jakub Zajic, Steven Ripp, Josef Trogl, Gabriela Kuncova, Marie Pospisilova
2019 IEEE INTERNATIONAL CONFERENCE ON SENSORS AND NANOTECHNOLOGY (SN)
(2019)
Article
Biochemical Research Methods
Tingting Xu, Anna Young, Enolia Marr, Gary Sayler, Steven Ripp, Dan Close
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2018)
Article
Biodiversity Conservation
Yongcui Lan, Jinliang Wang, Qianwei Liu, Fang Liu, Lanfang Liu, Jie Li, Mengjia Luo
Summary: This study focuses on the five major plateau lake basins in central Yunnan, China, and constructs an ecological security pattern using the source-resistance surface-corridor-pinch point framework. The study simulates land use/cover change in the region and identifies early warning regions where future urban expansion poses a threat to current ecological source areas and corridors.
ECOLOGICAL INDICATORS
(2024)
Article
Biodiversity Conservation
Pingping Huang, Feng Zhao, Bailing Zhou, Kuidong Xu
Summary: This study investigates the distribution of benthic microeukaryotes in the China Seas and finds that they can stride over the ecological barrier of 32 degrees N. The study also highlights the significant influence of depth, temperature, and latitude on communities in the China Seas.
ECOLOGICAL INDICATORS
(2024)
Article
Biodiversity Conservation
Federico Morelli, Yanina Benedetti, Jesse Stanford, Leszek Jerzak, Piotr Tryjanowski, Paolo Perna, Riccardo Santolini
Summary: Species distribution models (SDMs) are numerical tools used for predicting species' spatial distribution. This study found that ecological characteristics, such as habitat specialization, play a role in improving the accuracy of SDMs.
ECOLOGICAL INDICATORS
(2024)
Article
Biodiversity Conservation
Xiaoxuan Wu, Hang Liu, Wei Liu
Summary: Global climate change, urbanization, and economic development have increased the need for sustainable human development, urban ecological governance, and low-carbon energy transformation. This study analyzes the green ecological transition in Chengdu based on panel data from 2010 to 2020, exploring its spatiotemporal evolution and key factors. The results show an overall upward trend in Chengdu's green ecological development and positive spatial autocorrelation in certain districts.
ECOLOGICAL INDICATORS
(2024)
Article
Biodiversity Conservation
Castaldi Simona, Formicola Nicola, Mastrocicco Micol, Morales Rodriguez Carmen, Morelli Raffaella, Prodorutti Daniele, Vannini Andrea, Zanzotti Roberto
Summary: Sustainable agricultural practices are increasingly important for global and national environmental policies and economy. This study compared the sustainability of grape production under integrated and organic management using multiple indicators. The results showed that organic management was more beneficial for most environmental aspects of the agroecosystem compared to integrated management, without affecting grape yield.
ECOLOGICAL INDICATORS
(2024)
Article
Biodiversity Conservation
Gaia Vaglio Laurin, Alexander Cotrina-Sanchez, Luca Belelli-Marchesini, Enrico Tomelleri, Giovanna Battipaglia, Claudia Cocozza, Francesco Niccoli, Jerzy Piotr Kabala, Damiano Gianelle, Loris Vescovo, Luca Da Ros, Riccardo Valentini
Summary: Phenology monitoring is important for understanding forest functioning and climate impacts. This research compares the phenological behavior of European beech forests using Tree-Talker (TT+) and Sentinel 2 satellite data. The study finds differences in the information derived by the two sensor types, particularly in terms of season length, phenology changepoints, and leaf period variability. TT+ with its higher temporal resolution demonstrates precision in capturing the phenological changepoints, especially when satellite image availability is limited.
ECOLOGICAL INDICATORS
(2024)
Article
Biodiversity Conservation
Huanhuan Pan, Ziqiang Du, Zhitao Wu, Hong Zhang, Keming Ma
Summary: The land use and cover changes resulting from coal mining activities and ecological restoration have had a significant impact on ecosystem services in mining areas. This study investigates the relationship between ecosystem services and land use intensity in coal mining areas, emphasizing the importance of understanding this interdependence for balanced human-land system development. The research examines the evolving relationship across different reclamation stages in Shanxi, China, using a coupling coordination degree model. The findings suggest the need for timely and judicious reclamation of coalfields, considering the land's bearing capacity.
ECOLOGICAL INDICATORS
(2024)
Article
Biodiversity Conservation
Jingjuan He, Yijun Shi, Lihua Xu, Zhangwei Lu, Mao Feng
Summary: This study examines the spatial interplay between changes in the blue-green spatial distribution and modifications in land surface temperature grades in Shanghai. The findings reveal that the transformation of the blue-green spatial pattern differs between different sectors of the city, and the impact on the thermal environment varies spatially.
ECOLOGICAL INDICATORS
(2024)
Article
Biodiversity Conservation
Yi Xu, Di Zhang, Junqiang Lin, Qidong Peng, Xiaohui Lei, Tiantian Jin, Jia Wang, Ruifang Yuan
Summary: This study analyzed the response relationship between phytoplankton growth and water environmental parameters in the Middle Route of the South-to-North Water Diversion Project in China using long-term monitoring data and machine learning models. The results revealed the differences between monitoring sites and identified the key parameters that affect phytoplankton growth.
ECOLOGICAL INDICATORS
(2024)