In this paper, we present a microfluidic method to observe and analyze the physical elements of nematode navigation in real-time. We use microfluidic devices consisting of T-maze or cylindrical structures with varying geometry to study how nematodes make decisions. We found that the angle of the T-maze intersections affects the decision-making of these microscopic, soil-dwelling worms. Additionally, we were able to passively guide nematodes in a linear direction by adjusting the position and spacing of cylindrical obstacles in their path. To test our method, we conducted experiments on two nematode species (C. elegans and Oesophagostomum dentatum) without the use of chemical or electrical stimulants.
Nematodes are microscopic, soil-dwelling worms that navigate through soil particles in search of food or a suitable host. Most nematode species employ a myriad of physical and chemical cues that define their navigation strategies. Here, we demonstrate a microfluidic method to observe and characterize the physical aspects of nematode navigation at real-time. The microfluidic devices comprise a series of interconnected T-maze or cylindrical structures of varying
geometry. At each physical intersection, nematodes are given the choice to migrate left or right. We found that this decision-making of nematodes is influenced by the angle of intersection of T-maze structures. We further showed that nematodes can be passively directed to move in a linear direction by carefully adjusting the position and spacing of cylindrical obstacles in its path. The experiments were conducted on
two nematodes (non-parasitic C. elegans and pigparasitic Oesophagostomum dentatum) and in the absence of any chemical or electrical stimulants.
We developed a micro-fluidic method to observe the physical aspects of nematode navigation in real-time. This method involves constructing a series of interconnected T-maze or cylindrical structures of varying geometry. Through this, we were able to demonstrate that the decision-making of nematodes is affected by the angle of the T-maze intersections and that they can be directed to move in a linear direction by adjusting the position and spacing of cylindrical obstacles. Our experiments were conducted on two nematodes (C. elegans and Oesophagostomum dentatum) and no chemical or electrical stimulants were employed.
This paper explores how the adaptability of Caenorhabditis elegans locomotion behavior can be assessed through a movement-based assay. This assay is set up with a series of sinusoidal microchannels, featuring a fixed wavelength and modulating amplitude. These channels are comparable to the body diameter of the organism, and worms are allowed to travel from the input port to the output port. In regions that closely fit the worms' natural undulations, progress is quick and steady. As the channel amplitude changes along the device, the worm struggles to generate propulsive force, slows down, and eventually is unable to move forward. An array of locomotion parameters (average forward velocity, number and duration of pauses, range of contact angle, and cut-off region) are generated from the recorded videos to measure how the worm moves in the modulated sinusoidal channels. The device is tested on wild-type (N2) and two mutant (lev-8 and unc-38) C. elegans. We suggest that this passive, movement-based assay can be used to differentiate between nematodes with distinct locomotion phenotypes.
Effect of Static Magnetic Field on Parasitic Worms in MicroChipsIowa State University
This study uses the model organism, C. elegans, to investigate its sensitivity and response to static magnetic fields. Wild-type C. elegans are put into microfluidic channels and exposed to permanent magnets for five cycles of thirty-second time intervals at field strengths ranging from 5 milli Tesla to 120 milli Tesla. Recorded and analyzed with custom software, the results of the worm's movement - the average velocity, turning and curling percentage - were compared to control experiments. Surprisingly, the results did not show any significant difference, indicating that C. elegans may not be able to sense static magnetic fields at the range of field strengths tested.
Njus, Z. , Feldmann, D. , Brien, R. , Kong, T. , Kalwa, U. and Pandey, S. (2015) Characterizing the Effect of Static Magnetic Fields on C. elegans Using Microfluidics. Advances in Bioscience and Biotechnology, 6, 583-591.
doi: 10.4236/abb.2015.69061.
https://www.scirp.org/journal/paperinformation.aspx?paperid=59434
Characterizing the Effect of Static Magnetic Fields on C. elegans Using Micro...Iowa State University
In nature, several organisms possess a magnetic compass to navigate or migrate them to desired locations. It is thought that these organisms may use biogenic magnetic matter or light-sensitive photoreceptors to sense and orient themselves in magnetic fields. To unravel the underlying principles of magnetosensitivity and magnetoreception, previous experiments have been conducted on bacteria, vertebrates, crustaceans, and insects. In this study, the model organism, C. elegans, is used to test their response and sensitivity to static magnetic fields in the range of 5 milli Tesla to 120 milli Tesla. Single wild-type C. elegans are put in microfluidic channels and exposed to permanent magnets for five cycles of thirty-second time intervals. The worm movement is recorded and analyzed with custom software to calculate the average velocity and the percentage of turning and curling. Contrary to some published studies, our results did not show a significant difference compared to control experiments. This suggests that C. elegans may not sense static magnetic fields in the range of field strengths that we tested.
All maze system with video tracking software is useful to study how drugs affects cellular function in the nervous
system and the way by which they influence the behaviour. This review focusses on Elevated plus maze, Y maze, T
maze, Zero maze, Water maze, Multiple unit open field enclosure, Radial arm maze, Tail suspension unit, Light and
dark unit, Novel object recognision test unit, Conditioned Place Preference unit and Barnes maze, which are used in
the evaluation of neuropharmacological and behavioural studies.
Nematodes are microscopic, soil-dwelling worms that navigate through soil particles in search of food or a suitable host. Most nematode species employ a myriad of physical and chemical cues that define their navigation strategies. Here, we demonstrate a microfluidic method to observe and characterize the physical aspects of nematode navigation at real-time. The microfluidic devices comprise a series of interconnected T-maze or cylindrical structures of varying
geometry. At each physical intersection, nematodes are given the choice to migrate left or right. We found that this decision-making of nematodes is influenced by the angle of intersection of T-maze structures. We further showed that nematodes can be passively directed to move in a linear direction by carefully adjusting the position and spacing of cylindrical obstacles in its path. The experiments were conducted on
two nematodes (non-parasitic C. elegans and pigparasitic Oesophagostomum dentatum) and in the absence of any chemical or electrical stimulants.
We developed a micro-fluidic method to observe the physical aspects of nematode navigation in real-time. This method involves constructing a series of interconnected T-maze or cylindrical structures of varying geometry. Through this, we were able to demonstrate that the decision-making of nematodes is affected by the angle of the T-maze intersections and that they can be directed to move in a linear direction by adjusting the position and spacing of cylindrical obstacles. Our experiments were conducted on two nematodes (C. elegans and Oesophagostomum dentatum) and no chemical or electrical stimulants were employed.
This paper explores how the adaptability of Caenorhabditis elegans locomotion behavior can be assessed through a movement-based assay. This assay is set up with a series of sinusoidal microchannels, featuring a fixed wavelength and modulating amplitude. These channels are comparable to the body diameter of the organism, and worms are allowed to travel from the input port to the output port. In regions that closely fit the worms' natural undulations, progress is quick and steady. As the channel amplitude changes along the device, the worm struggles to generate propulsive force, slows down, and eventually is unable to move forward. An array of locomotion parameters (average forward velocity, number and duration of pauses, range of contact angle, and cut-off region) are generated from the recorded videos to measure how the worm moves in the modulated sinusoidal channels. The device is tested on wild-type (N2) and two mutant (lev-8 and unc-38) C. elegans. We suggest that this passive, movement-based assay can be used to differentiate between nematodes with distinct locomotion phenotypes.
Effect of Static Magnetic Field on Parasitic Worms in MicroChipsIowa State University
This study uses the model organism, C. elegans, to investigate its sensitivity and response to static magnetic fields. Wild-type C. elegans are put into microfluidic channels and exposed to permanent magnets for five cycles of thirty-second time intervals at field strengths ranging from 5 milli Tesla to 120 milli Tesla. Recorded and analyzed with custom software, the results of the worm's movement - the average velocity, turning and curling percentage - were compared to control experiments. Surprisingly, the results did not show any significant difference, indicating that C. elegans may not be able to sense static magnetic fields at the range of field strengths tested.
Njus, Z. , Feldmann, D. , Brien, R. , Kong, T. , Kalwa, U. and Pandey, S. (2015) Characterizing the Effect of Static Magnetic Fields on C. elegans Using Microfluidics. Advances in Bioscience and Biotechnology, 6, 583-591.
doi: 10.4236/abb.2015.69061.
https://www.scirp.org/journal/paperinformation.aspx?paperid=59434
Characterizing the Effect of Static Magnetic Fields on C. elegans Using Micro...Iowa State University
In nature, several organisms possess a magnetic compass to navigate or migrate them to desired locations. It is thought that these organisms may use biogenic magnetic matter or light-sensitive photoreceptors to sense and orient themselves in magnetic fields. To unravel the underlying principles of magnetosensitivity and magnetoreception, previous experiments have been conducted on bacteria, vertebrates, crustaceans, and insects. In this study, the model organism, C. elegans, is used to test their response and sensitivity to static magnetic fields in the range of 5 milli Tesla to 120 milli Tesla. Single wild-type C. elegans are put in microfluidic channels and exposed to permanent magnets for five cycles of thirty-second time intervals. The worm movement is recorded and analyzed with custom software to calculate the average velocity and the percentage of turning and curling. Contrary to some published studies, our results did not show a significant difference compared to control experiments. This suggests that C. elegans may not sense static magnetic fields in the range of field strengths that we tested.
All maze system with video tracking software is useful to study how drugs affects cellular function in the nervous
system and the way by which they influence the behaviour. This review focusses on Elevated plus maze, Y maze, T
maze, Zero maze, Water maze, Multiple unit open field enclosure, Radial arm maze, Tail suspension unit, Light and
dark unit, Novel object recognision test unit, Conditioned Place Preference unit and Barnes maze, which are used in
the evaluation of neuropharmacological and behavioural studies.
Indicator role and monitoring of microorganisms in life [autosaved]Maryam Idris
an overview of the role of microbes in determining the health and safety of life support systems including the crew members, rapid diagnostic methods and real time monitoring of enclosed ecosystems using microbes as indicators of the health statues of such systems
Electrical impedance’s effects of flying insects on selectivity of electrica...IJECEIAES
The history of controlling destructive insects in the twentieth century makes
it clear that the difficulties we encounter today in dealing with these types of
insects come from our almost total reliance on one single controlling
method, namely the use of chemical insecticides. These toxic and suspected
carcinogenic products pose a serious threat to agriculture and the
environment. However, the possibility of directing researchers in developing
a new way considered as more efficient, more selective and less toxic has
proved to be possible. The principle of this approach is based on an
attractive effect and an electric effect. Nevertheless, the development of a
bio and selective electrical system requires taking into account certain
parameters involved in the attraction of insects and electrical discharge such
as the electrical impedance. The results showed that the threshold at which
the insect is disturbed depends on its conductivity.
Effects of electric field on histopathological study, electrical properties a...inventy
The present work was undertaken in order to investigate the effects of electric field (EF) of strength 50Hz-3KV/m on the histopathology, dielectric properties and liver function tests in albino rats. Fifty male albino rats were equally divided into three groups namely A, B, and C. Animals of group A used as control group which didn't receive any treatment . Animals of group B was divided into two subgroups namely B1 and B2 which were discretely exposed to 50HZ, 3KV/m electric field for a period of 15 day (8 hours/day, 5day/week). Group B2 animals were left to survive and housed at normal environmental conditions similar to control group A for a period of 15 day post exposed. Animals of group C are divided into two subgroups namely C1 and C2 were discretely exposed to the electric field for a period of 30 day (8 hours/day, 5day/week). Group C2 animals were left to survive and housed at normal environmental conditions similar to control group A for a period of 15 day post exposed. At the end of this period, blood and tissues samples were collected from all groups for experimental investigations. The dielectric constant (έ), electrical conductivity (σ) was measured in frequency range 42Hz-5MHz to investigate any changes in liver structure through studding histopathological examination. Also, the liver function was studied through analysis of glutamic oxaloacetic transaminase (GOT), glutamic pyruvie transaminase (GPT) and total protein (TP) after exposure to electric field this biochemical parameters have been evaluated in the blood serum of rats. The obtained results show high significant changes in the value of έ and σ of liver tissues for all groups exposed to EF as compared with control group. The levels of GOT and GPT were increased up to four times their values during the period of exposure to EF. These variations were recovered during two week after stopping exposure but they did not return to its original control values before exposure. On microscopic level; liver histological observations in liver cells which revealed some alterations including hepatic tissue with two portal tracts showing mild florous expansion and a dilated central vein, also ghosts of hepatocytes denoting necrotic changes also shows hepatic tissue with dilated central veins engorged with blood and splitting out to adjacent hepatocytes.
2017 - Environmental Ordination of Filamentous Bacteria in Activated SludgeWALEBUBLÉ
Reference:
Zornoza, A., Serrano, S. and Alonso, J.L. (2017) Environmental Ordination of Filamentous Bacteria in Activated Sludge. In: Abstracts of the 7th congress of European microbiologists FEMS 2017, Valencia, Spain, 9-13 July 2017.
BIOMINERALISED SILICA-NANOPARTICLES DETECTION FROM MARINE DIATOM CULTURE MEDIAIJSIT Editor
Diatoms are unicellular algae the most spectacular among the microorganisms assemble into a
micro-shell with a distinct 3-D shape and pattern of fine nanoscale features. In this investigation, we present
results; Field Emission Scanning Electron Microscopy images show the presence of ordered arrays of silica
nanoparticles. A number of diatoms with partially opened valves were observed on the surface of the diatom,
which indicates that cell contents inside of diatoms could release the nanoparticles into the culture solution.
We believe that the film forming silica nanoparticles are either released by the diatoms during reproduction
or after cell death due to bacterial action. Further research will investigate whether the silica nanoparticles
are produced intracellular and then released or whether synthesis occurs in cell culture medium. This
approach provides an environmentally friendly means for fabricating silica nanoparticles for drug delivery,
disease diagnostics, artificial opal films, decorative coatings and novel optical materials.
TIE microplastics immersed in Muskegon Lake, Michiganjeanniekane
Toxicity analysis of three different types of microplastics - polyethylene, polypropylene, and polystyrene - immersed in the benthic and pelagic regions of Muskegon Lake, Michigan
The resistance of parasites to existing drugs and the availability of better technology platforms has driven the discovery of new drugs. Microfluidic devices have been used to facilitate faster screening of compounds, controlled sampling/sorting of whole animals, and automated behavioral pattern recognition. In most cases, drug effects on small creatures (e.g., Caenorhabditis elegans) are measuredelegant by a single parameter such as worm velocity or stroke frequency. We present a multi-parameter extraction method to characterize modes of paralysis in C. elegans over a longer duration. This was done using a microfluidic device featuring real-time imaging, exposing worms to four anthelmintic drugs at EC75, where 75% of the worm population is affected. We monitored the worms' behavior with metrics such as curls per second, types of paralyzation, mode frequency, and number/duration of active/immobilization periods. Differences were observed in how the worms paralyzed in the various drug environments at equivalent concentrations. This study highlights the importance of assessing drug effects on small animals with multiple parameters, measured at regular intervals over a prolonged period, to accurately detect resistance and adaptability in chemical environments.
Roy Lycke, Archana Parashar, and Santosh Pandey, "Microfluidics-enabled method to identify modes of Caenorhabditis elegans paralysis in four anthelmintics", Biomicrofluidics 7, 064103 (2013).
https://doi.org/10.1063/1.4829777
https://aip.scitation.org/doi/10.1063/1.4829777
In this review, we focus on the hardware and software technologies used for the purpose of gastrointestinal tract monitoring in a safe and comfortable manner. We review the FDA guidelines for ingestible wireless telemetric medical devices, and the features incorporated in capsule systems such as microrobotics, closed-loop feedback, physiological sensing, nerve stimulation, sampling and delivery, panoramic imaging and rapid reading software. Both experimental and commercialized capsule systems with their sensors, devices, and circuits are discussed. Furthermore, the advances in biocompatible materials and batteries, edible electronics and alternative energy sources for ingestible capsule systems are presented. The clinical studies are reviewed to examine the safety and effectiveness of capsule procedures and the current challenges and outlook are summarized.
Dylan Miley*, Leonardo Bertoncello Machado*, Calvin Condo, Albert E. Jergens, Kyoung-Jin Yoon, Santosh Pandey, “Video Capsule Endoscopy and Ingestible Electronics: Emerging Trends in Sensors, Circuits, Materials, Telemetry, Optics, and Rapid Reading Software“, Advanced Devices & Instrumentation, (Science Partner Journal), Volume 2021, Article ID 9854040, 2021. https://spj.science.org/doi/10.34133/2021/9854040?permanently=true
https://doi.org/10.34133/2021/9854040
Antimicrobial resistance studies in low-cost microfluidic chipsIowa State University
By utilizing a low-cost engineering tool, we have created a microfluidic platform to study bacteria at the single cell level, allowing us to unlock insights into microbial physiology and genetics that would otherwise not be possible. The platform is composed of 3D devices made of adhesive tapes, an agarose membrane as the resting substrate, a temperature-controlled environmental chamber, and an autofocusing module. With this technology, we have been able to observe Escherichia coli morphological changes during ampicillin exposure and measure the minimum inhibitory concentration of the antibiotic. Additionally, we have been able to use CRISPR interference (CRISPRi) to evaluate gene regulation in a concentration gradient. Overall, our microfluidic platform provides a powerful, low-cost tool to uncover new genetic determinants of antibiotic susceptibility and assess the long-term effectiveness of antibiotics in bacterial cultures.
Adhesive Tape Microfluidics with an Autofocusing Module That Incorporates CRISPR Interference: Applications to Long-Term Bacterial Antibiotic Studies, Taejoon Kong, Nicholas Backes, Upender Kalwa, Christopher Legner, Gregory J. Phillips, and Santosh Pandey, ACS Sensors 2019 4 (10), 2638-2645
https://doi.org/10.1021/acssensors.9b01031
https://pubs.acs.org/doi/full/10.1021/acssensors.9b01031
More Related Content
Similar to Decision making ability of Microorganisms in Maze BioChips
Indicator role and monitoring of microorganisms in life [autosaved]Maryam Idris
an overview of the role of microbes in determining the health and safety of life support systems including the crew members, rapid diagnostic methods and real time monitoring of enclosed ecosystems using microbes as indicators of the health statues of such systems
Electrical impedance’s effects of flying insects on selectivity of electrica...IJECEIAES
The history of controlling destructive insects in the twentieth century makes
it clear that the difficulties we encounter today in dealing with these types of
insects come from our almost total reliance on one single controlling
method, namely the use of chemical insecticides. These toxic and suspected
carcinogenic products pose a serious threat to agriculture and the
environment. However, the possibility of directing researchers in developing
a new way considered as more efficient, more selective and less toxic has
proved to be possible. The principle of this approach is based on an
attractive effect and an electric effect. Nevertheless, the development of a
bio and selective electrical system requires taking into account certain
parameters involved in the attraction of insects and electrical discharge such
as the electrical impedance. The results showed that the threshold at which
the insect is disturbed depends on its conductivity.
Effects of electric field on histopathological study, electrical properties a...inventy
The present work was undertaken in order to investigate the effects of electric field (EF) of strength 50Hz-3KV/m on the histopathology, dielectric properties and liver function tests in albino rats. Fifty male albino rats were equally divided into three groups namely A, B, and C. Animals of group A used as control group which didn't receive any treatment . Animals of group B was divided into two subgroups namely B1 and B2 which were discretely exposed to 50HZ, 3KV/m electric field for a period of 15 day (8 hours/day, 5day/week). Group B2 animals were left to survive and housed at normal environmental conditions similar to control group A for a period of 15 day post exposed. Animals of group C are divided into two subgroups namely C1 and C2 were discretely exposed to the electric field for a period of 30 day (8 hours/day, 5day/week). Group C2 animals were left to survive and housed at normal environmental conditions similar to control group A for a period of 15 day post exposed. At the end of this period, blood and tissues samples were collected from all groups for experimental investigations. The dielectric constant (έ), electrical conductivity (σ) was measured in frequency range 42Hz-5MHz to investigate any changes in liver structure through studding histopathological examination. Also, the liver function was studied through analysis of glutamic oxaloacetic transaminase (GOT), glutamic pyruvie transaminase (GPT) and total protein (TP) after exposure to electric field this biochemical parameters have been evaluated in the blood serum of rats. The obtained results show high significant changes in the value of έ and σ of liver tissues for all groups exposed to EF as compared with control group. The levels of GOT and GPT were increased up to four times their values during the period of exposure to EF. These variations were recovered during two week after stopping exposure but they did not return to its original control values before exposure. On microscopic level; liver histological observations in liver cells which revealed some alterations including hepatic tissue with two portal tracts showing mild florous expansion and a dilated central vein, also ghosts of hepatocytes denoting necrotic changes also shows hepatic tissue with dilated central veins engorged with blood and splitting out to adjacent hepatocytes.
2017 - Environmental Ordination of Filamentous Bacteria in Activated SludgeWALEBUBLÉ
Reference:
Zornoza, A., Serrano, S. and Alonso, J.L. (2017) Environmental Ordination of Filamentous Bacteria in Activated Sludge. In: Abstracts of the 7th congress of European microbiologists FEMS 2017, Valencia, Spain, 9-13 July 2017.
BIOMINERALISED SILICA-NANOPARTICLES DETECTION FROM MARINE DIATOM CULTURE MEDIAIJSIT Editor
Diatoms are unicellular algae the most spectacular among the microorganisms assemble into a
micro-shell with a distinct 3-D shape and pattern of fine nanoscale features. In this investigation, we present
results; Field Emission Scanning Electron Microscopy images show the presence of ordered arrays of silica
nanoparticles. A number of diatoms with partially opened valves were observed on the surface of the diatom,
which indicates that cell contents inside of diatoms could release the nanoparticles into the culture solution.
We believe that the film forming silica nanoparticles are either released by the diatoms during reproduction
or after cell death due to bacterial action. Further research will investigate whether the silica nanoparticles
are produced intracellular and then released or whether synthesis occurs in cell culture medium. This
approach provides an environmentally friendly means for fabricating silica nanoparticles for drug delivery,
disease diagnostics, artificial opal films, decorative coatings and novel optical materials.
TIE microplastics immersed in Muskegon Lake, Michiganjeanniekane
Toxicity analysis of three different types of microplastics - polyethylene, polypropylene, and polystyrene - immersed in the benthic and pelagic regions of Muskegon Lake, Michigan
The resistance of parasites to existing drugs and the availability of better technology platforms has driven the discovery of new drugs. Microfluidic devices have been used to facilitate faster screening of compounds, controlled sampling/sorting of whole animals, and automated behavioral pattern recognition. In most cases, drug effects on small creatures (e.g., Caenorhabditis elegans) are measuredelegant by a single parameter such as worm velocity or stroke frequency. We present a multi-parameter extraction method to characterize modes of paralysis in C. elegans over a longer duration. This was done using a microfluidic device featuring real-time imaging, exposing worms to four anthelmintic drugs at EC75, where 75% of the worm population is affected. We monitored the worms' behavior with metrics such as curls per second, types of paralyzation, mode frequency, and number/duration of active/immobilization periods. Differences were observed in how the worms paralyzed in the various drug environments at equivalent concentrations. This study highlights the importance of assessing drug effects on small animals with multiple parameters, measured at regular intervals over a prolonged period, to accurately detect resistance and adaptability in chemical environments.
Roy Lycke, Archana Parashar, and Santosh Pandey, "Microfluidics-enabled method to identify modes of Caenorhabditis elegans paralysis in four anthelmintics", Biomicrofluidics 7, 064103 (2013).
https://doi.org/10.1063/1.4829777
https://aip.scitation.org/doi/10.1063/1.4829777
In this review, we focus on the hardware and software technologies used for the purpose of gastrointestinal tract monitoring in a safe and comfortable manner. We review the FDA guidelines for ingestible wireless telemetric medical devices, and the features incorporated in capsule systems such as microrobotics, closed-loop feedback, physiological sensing, nerve stimulation, sampling and delivery, panoramic imaging and rapid reading software. Both experimental and commercialized capsule systems with their sensors, devices, and circuits are discussed. Furthermore, the advances in biocompatible materials and batteries, edible electronics and alternative energy sources for ingestible capsule systems are presented. The clinical studies are reviewed to examine the safety and effectiveness of capsule procedures and the current challenges and outlook are summarized.
Dylan Miley*, Leonardo Bertoncello Machado*, Calvin Condo, Albert E. Jergens, Kyoung-Jin Yoon, Santosh Pandey, “Video Capsule Endoscopy and Ingestible Electronics: Emerging Trends in Sensors, Circuits, Materials, Telemetry, Optics, and Rapid Reading Software“, Advanced Devices & Instrumentation, (Science Partner Journal), Volume 2021, Article ID 9854040, 2021. https://spj.science.org/doi/10.34133/2021/9854040?permanently=true
https://doi.org/10.34133/2021/9854040
Antimicrobial resistance studies in low-cost microfluidic chipsIowa State University
By utilizing a low-cost engineering tool, we have created a microfluidic platform to study bacteria at the single cell level, allowing us to unlock insights into microbial physiology and genetics that would otherwise not be possible. The platform is composed of 3D devices made of adhesive tapes, an agarose membrane as the resting substrate, a temperature-controlled environmental chamber, and an autofocusing module. With this technology, we have been able to observe Escherichia coli morphological changes during ampicillin exposure and measure the minimum inhibitory concentration of the antibiotic. Additionally, we have been able to use CRISPR interference (CRISPRi) to evaluate gene regulation in a concentration gradient. Overall, our microfluidic platform provides a powerful, low-cost tool to uncover new genetic determinants of antibiotic susceptibility and assess the long-term effectiveness of antibiotics in bacterial cultures.
Adhesive Tape Microfluidics with an Autofocusing Module That Incorporates CRISPR Interference: Applications to Long-Term Bacterial Antibiotic Studies, Taejoon Kong, Nicholas Backes, Upender Kalwa, Christopher Legner, Gregory J. Phillips, and Santosh Pandey, ACS Sensors 2019 4 (10), 2638-2645
https://doi.org/10.1021/acssensors.9b01031
https://pubs.acs.org/doi/full/10.1021/acssensors.9b01031
Flexible chip for long-term antimicrobial resistance experimentsIowa State University
By creating a low-cost, three-dimensional microfluidic platform, we have improved our ability to study bacterial cells at the single cell level. This technology allows for prolonged culturing of bacteria in a controlled environment, as well as high resolution observation and imaging of cells. We have used this platform to examine morphological changes in Escherichia coli exposed to ampicillin and to quantify the minimum inhibitory concentration of the antibiotic. Additionally, we demonstrated the potential for precise gene regulation using CRISPR interference (CRISPRi) in a concentration gradient. Ultimately, this engineering tool should be useful for uncovering new genetic factors that influence antibiotic susceptibility and evaluating the long-term effectiveness of antibiotics.
Adhesive Tape Microfluidics with an Autofocusing Module That Incorporates CRISPR Interference: Applications to Long-Term Bacterial Antibiotic Studies, Taejoon Kong, Nicholas Backes, Upender Kalwa, Christopher Legner, Gregory J. Phillips, and Santosh Pandey, ACS Sensors 2019 4 (10), 2638-2645
https://doi.org/10.1021/acssensors.9b01031
https://pubs.acs.org/doi/full/10.1021/acssensors.9b01031
In this paper, we explore the use of microfluidic paper-based analytical devices (PADs) to study the behavior of Caenorhabditis elegans. We show how these devices can be fabricated on paper and plastic substrates, as well as how to load, visualize, and transfer single and multiple nematodes. We also demonstrate the use of anthelmintic drug, levamisole, to perform chemical testing on C. elegans. Furthermore, we provide a custom program that is able to recognize individual worms on the PADs in real-time and extract their locomotion parameters. This combination of PADs and the nematode tracking program creates a low-cost, easy-to-fabricate imaging and screening assay that is superior to standard agarose plates or polymeric microfluidic devices for non-microfluidic, nematode laboratories.
Zach Njus, Taejoon Kong, Upender Kalwa, Christopher Legner, Matthew Weinstein, Shawn Flanigan, Jenifer Saldanha, and Santosh Pandey, "Flexible and disposable paper- and plastic-based gel micropads for nematode handling, imaging, and chemical testing", APL Bioengineering 1, 016102 (2017)
https://doi.org/10.1063/1.5005829
https://aip.scitation.org/doi/10.1063/1.5005829
Melanoma is a particularly dangerous type of skin cancer and is hard to treat in its later stages. Therefore, early detection is key in reducing mortality rates. In order to assist dermatologists in doing this, computer-aided systems have been designed for desktop computers. However, there is a desire for the development of mobile, at-home diagnostics for melanoma risk assessment. Here, we introduce a smartphone application that captures images and extracts ABCD features to classify skin lesions as either malignant or benign. The algorithms used are adaptive to make the process light and user-friendly, as well as reliable in diagnosis. Images can be taken with the phone's camera or imported from public datasets. The entire process of taking the image, performing preprocessing, segmentation and classification is completed on an Android smartphone in a short time. Our application is evaluated on a dataset of 200 images, and achieved either comparable or better performance metrics than other methods. Additionally, it is easy-to-download and easy-to-navigate for the user, which is important for the widespread use of such diagnostics.
Kalwa, U.; Legner, C.; Kong, T.; Pandey, S. Skin Cancer Diagnostics with an All-Inclusive Smartphone Application. Symmetry 2019, 11, 790. https://doi.org/10.3390/sym11060790
https://www.mdpi.com/2073-8994/11/6/790
A CMOS biosensor with a folded floating-gate is created to detect charged biochemical molecules. It contains a FET, a control-gate and a sensing area. The floating-gate spans the whole device, allowing the sensing area to be placed on top of the FET, resulting in a decrease of the device's total area. The device is sensitive to the polarity and quantity of charged poly amino acids and could be used for electronic recognition of temporal and spatial migration of charges, such as in biological phenomena.
B. Chen, A. Parashar and S. Pandey, "Folded Floating-Gate CMOS Biosensor for the Detection of Charged Biochemical Molecules," IEEE Sensors Journal, vol. 11, no. 11, pp. 2906-2910, Nov. 2011, doi: 10.1109/JSEN.2011.2149514.
https://ieeexplore.ieee.org/document/5762313
We attempt to offer an innovative solution to the issues of long response times, large volumes of actuation fluid, and external control circuitry that have been associated with past approaches in creating switches in paper microfluidics. Our method consists of a device created from chromatography paper and featuring folds which, when selectively wetted with an actuation fluid, will either raise or lower the actuator's tip and thus engage or break the desired fluidic connections. As a result, response time is drastically reduced (2 seconds) and the volume of actuation fluid consumed is extremely small (4 microliters). We have tested this approach with six switch configurations, ranging from single-pole single-throw (normally OFF and normally ON) to single-pole double-throw (with single and double break). We further demonstrate its potential with a colorimetric assay involving six actuators in parallel, which can detect the presence of three analytes (glucose, protein, and nitrite) in artificial saliva. Finally, this work brings in the concept of origami to paper microfluidics, combining multiple-fold geometries for programmable switching of fluidic connections.
"A fast, reconfigurable flow switch for paper
microfluidics based on selective wetting of folded
paper actuator strips",
Lab on Chip, 2017, 17, 3621
A method to create smart and flexible switches for the regulation of liquid flow across multiple channels is essential in paper microfluidics. Prior approaches are hampered by long response times, high actuation fluid volumes, and external control circuitry. To diminish these problems, we designed a distinctive actuator device fashioned entirely from chromatography paper and featuring folds. The fold can be selectively wetted by an actuation fluid at either the crest or trough, resulting in the raising or lowering of the actuator's tip and thus bringing about the connection or severance of fluidic channels. This actuation principle reduces the response time to only two seconds and the amount of fluid used to merely four microliters. We have also added six switch arrangements which can be divided into single-pole single-throw (normally OFF and normally ON) and single-pole double-throw (with single and double break). The utilization of six actuators in a parallel system allowed us to construct an autonomous colorimetric assay for the detection of three analytes - glucose, protein, and nitrite - in artificial saliva. This study has brought the concept of origami to paper microfluidics, allowing the use of multiple-fold geometries for the programmable switching of fluidic connections.
Taejoon Kong et al, "A fast, reconfigurable flow switch for paper
microfluidics based on selective wetting of folded
paper actuator strips", Lab on Chip, 2017, 17, 3621
The transmembrane proteins known as ion channels play a role in controlling and preserving the ionic concentrations across the cell membrane. Modeling the flux of ions in and out of these channels on an atomic level is essential for understanding several neurological diseases and related pharmaceutical discoveries. Recent experimental research has provided information on the channel's physical structure which can be used to create realistic ion transport models. Different trajectories exist for the ions entering the channel, each having its own probability of occurrence. Variables that measure these trajectories are the translocation and return probabilities, average lifetime, and spectral density of the ion number fluctuations. Theoretical analysis of ion transport has been restricted to low-resolution continuum diffusion-based or kinetic-based models which do not consider important factors that have an effect on ionic conduction. This paper extends previous models by an electro-diffusion model which takes into account the effects of electric fields, energy barriers, and rate-limited association/dissociation of ions with surface charges present inside the channel. Derived from the analytical model are the survival probability and spectral density.
:Analytical Modeling of the Ion Number Fluctuations in Biological Ion Channels"
Journal of Nanoscience and Nanotechnology; Vol. 12, 2489–2495, 2012
Ion Channel Fluctuations in Transmemembrane Proteins within Cell MembranesIowa State University
The transmembrane proteins known as ion channels play a role in controlling and preserving the ionic concentrations across the cell membrane. Modeling the flux of ions in and out of these channels on an atomic level is essential for understanding several neurological diseases and related pharmaceutical discoveries. Recent experimental research has provided information on the channel's physical structure which can be used to create realistic ion transport models. Different trajectories exist for the ions entering the channel, each having its own probability of occurrence. Variables that measure these trajectories are the translocation and return probabilities, average lifetime, and spectral density of the ion number fluctuations. Theoretical analysis of ion transport has been restricted to low-resolution continuum diffusion-based or kinetic-based models which do not consider important factors that have an effect on ionic conduction. This paper extends previous models by an electro-diffusion model which takes into account the effects of electric fields, energy barriers, and rate-limited association/dissociation of ions with surface charges present inside the channel. Derived from the analytical model are the survival probability and spectral density.
This paper presents a remote monitoring tool for the objective measurement of behavioral indicators that can help in assessing the health and welfare of pigs in precision swine production. The multiparameter electronic sensor board can measure posture, gait, vocalization, and external temperature, and has been characterized through laboratory measurements and animal tests. Machine learning algorithms and decision support tools can be implemented to detect animal lameness, lethargy, pain, injury, and distress. The adoption of this technology could lead to more efficient management of farm animals, better targeting of sick animals, lower medical costs, and fewer antibiotics being used. Challenges and a road map for technology adoption are discussed, along with suggestions for future improvements.
Animals 2021, 11(9), 2665; https://doi.org/10.3390/ani11092665
We propose a remote monitoring device for measuring behavioral indicators like posture, gait, vocalization, and external temperature which can help in evaluating the health and welfare of pigs. The multiparameter electronic sensor board was tested in a laboratory and on animals. Machine learning algorithms and decision support tools can be used to detect lameness, lethargy, pain, injury, and distress. The roadmap for technology adoption, potential benefits, and further challenges are discussed. This technology could help in efficient management of farm animals, providing targeted attention to sick animals, saving medical costs, and reducing the use of antibiotics.
"Behavioral Monitoring Tool for Pig Farmers: Ear Tag Sensors,
Machine Intelligence, and Technology Adoption Roadmap",
Animals 2021, 11, 2665.
https://doi.org/10.3390/ani11092665
In this study, two sets of experiments were conducted in order to investigate the impact of static magnetic fields on the growth and ethanol production of Saccharomyces cerevisiae. The first experiment ran for 25 hours with a 2% dextrose loading rate, while the second ran for 30 hours with a 6% dextrose loading rate. The magnetic fields used were homogeneous and non-homogeneous, with strengths of 100 mT and 200 mT, respectively. The results showed that the homogenous magnetic field had no significant effect on cell growth, whilst the non-homogeneous field yielded an increase of approximately 8% in peak ethanol concentration compared to the control.
Deutmeyer, A. , Raman, R. , Murphy, P. and Pandey, S. (2011) Effect of magnetic field on the fermentation kinetics of Saccharomyces cerevisiae. Advances in Bioscience and Biotechnology, 2, 207-213.
doi: 10.4236/abb.2011.24031.
https://www.scirp.org/journal/paperinformation.aspx?paperid=6857
Magnetic field to improve fermentation kinetics for ethanol production Iowa State University
Two experiments were conducted to analyze the influence that magnetic fields have on cell growth and ethanol production during fermentation. The first experiment was conducted for 25 hours at a 2% dextrose loading rate with a homogeneous and non-homogeneous static magnetic field of 100 mT and 200 mT, respectively. The second experiment was conducted for 30 hours at a 6% dextrose loading rate with a non-homogeneous static magnetic field of 200 mT. The results indicated that homogeneous magnetic fields did not have a significant effect on the yeast cell growth. However, the non-homogeneous static magnetic field resulted in about 8% more peak ethanol concentration than the control for the 2% dextrose loading rate.
To evaluate the severity of SCN infections in the field, population densities of nematode eggs must be calculated. A method utilizing OptiPrep as a density gradient medium has been shown to provide more effective separation and recovery of extracted eggs compared to sucrose centrifugation. Furthermore, computerized processes have been established to facilitate the discernment and enumeration of eggs from processed samples. A high-resolution scanner was employed to capture static images of eggs and debris on filter papers, and a deep learning network was trained to distinguish and count the eggs from the debris. Additionally, a lensless imaging setup was established using standard components, and the egg samples were allowed to pass through a microfluidic flow chip created from double-sided adhesive tape. Holographic videos were then recorded of the eggs and debris as they moved through, which were reconstructed and processed by a custom software program to obtain the egg counts. The software programs' efficacy for egg counting was validated using soil samples obtained from two farms, and the results were compared to those obtained through manual counting.
Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019) New methods of removing debris and high-throughput counting of cyst nematode eggs extracted from field soil. PLOS ONE 14(10): e0223386.
https://doi.org/10.1371/journal.pone.0223386
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386
To evaluate the level of infestation of the soybean cyst nematode (SCN), Heterodera glycines, in the field, egg population densities are determined from soil samples. Sucrose centrifugation is a common technique for separating debris from the extracted SCN eggs. We have developed a procedure, however, that employs OptiPrep as a density gradient medium, with improved extraction and recovery of the eggs compared to the sucrose centrifugation technique. Also, we have built computerized methods to automate the identification and counting of the nematode eggs from the processed samples. One approach uses a high-resolution scanner to capture static images of the eggs and debris on filter papers and a deep learning network is trained to detect and count the eggs. The second approach utilizes a lensless imaging setup with off-the-shelf components and the egg samples flow through a microfluidic flowchip. Holographic videos are taken of the passing eggs and debris, which are then reconstructed and processed by a custom software program to calculate egg counts. To evaluate the performance of the software programs, SCN-infested soils were collected from two farms and the results were compared with manual counts.
Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019), New methods of removing debris and high-throughput counting of cyst nematode eggs extracted from field soil. PLOS ONE 14(10): e0223386.
https://doi.org/10.1371/journal.pone.0223386
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386
The integration of physical and chemical sensing mechanisms found in nature has been harnessed to enable the development of wearable devices that can track the biochemical and physiological signals of the human body. Numerous consumer electronics have been developed to measure activity, posture, heart rate, respiration rate, and blood oxygen level. Sweat sampling provides a source of biomarkers that is accessible in a continuous, on-the-go, and non-invasive way, allowing for unique developments in wearable sweat sensing. This review focuses on recent trends in material science, device development, sensing mechanisms, power generation, and data management related to these devices. Additionally, exemplary wearable sweat sensors and commercialization efforts in this area are discussed, with an emphasis on the multifunctional sensing platforms that integrate data from both physical and biochemical sweat sensors.
Recent developments in wearable physical sensors have enabled the development of a number of consumer electronics products which measure parameters related to activity, posture, heart rate, respiration rate, and blood oxygen level. However, progress in the development of wearable chemical sensors has been slower due to the inherent challenges in retrieving and processing bodily fluids. Sweat is a valuable source of biomarkers which can be accessed continuously, on-the-go, and non-invasively. This review provides an overview of recent trends in the area of wearable sweat sensing, looking at topics such as material science, device development, sensing mechanisms, power generation, and data management. Examples of wearable sweat sensors published in recent years, as well as commercialization efforts in this field are also presented. The review highlights the trends in multifunctional sensing platforms which incorporate flexible electronics to integrate data from both physical and biochemical sensors.
This paper explores how the adaptability of Caenorhabditis elegans locomotion behavior can be assessed through a movement-based assay. This assay is set up with a series of sinusoidal microchannels, featuring a fixed wavelength and modulating amplitude. These channels are comparable to the body diameter of the organism, and worms are allowed to travel from the input port to the output port. In regions that closely fit the worms' natural undulations, progress is quick and steady. As the channel amplitude changes along the device, the worm struggles to generate propulsive force, slows down, and eventually is unable to move forward. An array of locomotion parameters (average forward velocity, number and duration of pauses, range of contact angle, and cut-off region) are generated from the recorded videos to measure how the worm moves in the modulated sinusoidal channels. The device is tested on wild-type (N2) and two mutant (lev-8 and unc-38) C. elegans. We suggest that this passive, movement-based assay can be used to differentiate between nematodes with distinct locomotion phenotypes.
"Amplitude-modulated sinusoidal microchannels
for observing adaptability in C. elegans locomotion",
Biomicrofluidics 5, 024112 (2011)
https://doi.org/10.1063/1.3604391
Every year, soybean yields are reduced by numerous diseases, especially the soybean cyst nematode (SCN). Identifying the presence of SCN and measuring its population densities in the field is challenging as there are no visible signs of disease. The only sure way to evaluate SCN population levels is to extract the cysts from the soil, extract the eggs from the cysts, and count them. Currently, this extraction process is typically done in commercial soil analysis laboratories and university plant diagnostic clinics and requires multiple steps. To make this process easier, we have created a robotic instrument that can automate the extraction of nematode cysts from soil and the subsequent release of their eggs. This technology is operated using a touchscreen interface and is tested using soil samples from two farms. The results are comparable to the conventional technique. Our robotic instrument makes SCN soil diagnostics more efficient, aiding in the long-term integrated pest management of this harmful soybean pest.
Paper Title: Robotic agricultural instrument
for automated extraction
of nematode cysts and eggs
from soil to improve integrated
pest management,
Scientific Reports (2021) 11:3212.
https://www.nature.com/articles/s41598-021-82261-w
Decision making ability of Microorganisms in Maze BioChips
1. Advances in Bioscience and Biotechnology, 2011, 2, 409-415
doi:10.4236/abb.2011.26060 Published Online December 2011 (http://www.SciRP.org/journal/abb/).
ABB
Decision-making by nematodes in complex microfluidic mazes
Santosh Pandey*
, Andrew Joseph, Roy Lycke, Archana Parashar
Department of Electrical and Computer Engineering, Iowa State University, Ames, USA.
Email: *
pandey@iastate.edu
Received 5 September 2011; revised 9 October 2011; accepted 24 October 2011.
ABSTRACT
Nematodes are microscopic, soil-dwelling worms that
navigate through soil particles in search of food or a
suitable host. Most nematode species employ a my-
riad of physical and chemical cues that define their
navigation strategies. Here, we demonstrate a micro-
fluidic method to observe and characterize the physi-
cal aspects of nematode navigation at real-time. The
microfluidic devices comprise a series of intercon-
nected T-maze or cylindrical structures of varying
geometry. At each physical intersection, nematodes
are given the choice to migrate left or right. We found
that this decision-making of nematodes is influenced
by the angle of intersection of T-maze structures. We
further showed that nematodes can be passively di-
rected to move in a linear direction by carefully ad-
justing the position and spacing of cylindrical obsta-
cles in its path. The experiments were conducted on
two nematodes (non-parasitic C. elegans and pig-
parasitic Oesophagostomum dentatum) and in the ab-
sence of any chemical or electrical stimulants.
Keywords: C. elegans; Navigation; Maze; Microorga-
nism; Microfluidics
1. INTRODUCTION
Nematodes are the most ubiquitous, soil-dwelling micro-
organisms on Earth with over 20,000 known species. Par-
ticularly, the nematode Caenorhabditis elegans (C. ele-
gans) is an important model organism for researchers in
neuroscience, genetics, and behavioral sciences [1-4]. The
primary reasons for choosing C. elegans as a small ani-
mal laboratory model organism are its microscopic size,
transparent body, ease of culture, short lifespan, and a
reasonable genome size [5-11]. Recent advances in vivo
microfluidic testing [12,13] have facilitated the monitor-
ing of several behavioral facets of nematodes such as lo-
comotion, growth, reproduction, and neuronal functioning
[14-16]. In an interesting work by Qin and Wheeler [17], C.
elegans were put in simple T-maze microfluidic channels
and trained to produce a definite chemotactic response.
Other micro-organisms (e.g. bacteria, fungi, and algae)
have also been subjected to complex maze structures and
their attraction/repulsion to chemical gradients or food
reservoirs have been characterized.
Besides chemical cues, nematodes are presented with
a wide range of physical interfaces in their microenvi-
ronment that need to effectively sensed and responded to.
It may be difficult for an experimentalist to visually ob-
serve these physical interfaces or the navigation strate-
gies employed by nematodes in the natural soil habitat.
In this regard, microfluidics has proved to be a boon to
experimental biologists. Microfluidics offers the unique
possibility of creating two-dimensional microstructures,
altering device dimensions in a controlled manner, and
observing the interactions between microorganisms and
artificial chip environment [18-22].
In this work, we demonstrate a microfluidic device
with a range of interconnected T-shaped mazes and cy-
lindrical structures to characterize nematode movement
through a series of physical interfaces. Specifically, we
designed four assays: 1) angled T-maze, 2) sequenced
T-maze, 3) convex intersection maze, and 4) sequenced
pillar array. The tests were conducted on non-parasitic C.
elegans and pig-parasitic Oesophagotomum dentatum (O.
dentatum). No chemical or electrical stimulants were
used in our tests. The experimental results help us deter-
mine a probabilistic impact model based on the geometry
of physical interfaces and the nematodes’ interaction
with hard surfaces. Based on our observations, it is rea-
sonable to assume that, in the absence of any stimulants
or repellents, a nematode navigates essentially blindly
through an agarose gel medium with occasional halts and
turns. Any interactions with physical interfaces in its
path alter its direction of movement, depending on the
angle of the physical interface with respect to its body
line. As we will show in the case of sequenced pillar
array, it is possible to engineer the location, angle, and
interval of physical interfaces for nematodes in order to
modify their natural non-linear direction of motion into a
linear one.
Published Online December 2011 in SciRes. http://www.scirp.org/journal/ABB