Low-cost Imaging of Fluorescent DNA in Agarose Gel Electrophoresis using Raspberry Pi cameras

Abid, Hassan Ali; Ong, Jian Wern; Lin, Eric Shen; Song, Zhixiong; Liew, Oi Wah; Ng, Tuck Wah

doi:10.1007/s10895-021-02884-0

Cited by 8 publications

(4 citation statements)

References 26 publications

(30 reference statements)

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“…In order to achieve high-quality imaging, we selected low-cost but high-performance components. Previous publications have shown that single-board computers combined with matching cameras are a low-cost solution for biological microscopy [22], [36], [37]. For this reason, both versions, the standalone and the plug-in versions use Raspberry Pi 4k cameras.…”

Section: Concept and Methodsmentioning

confidence: 99%

Entomoscope: An Open-Source Photomicroscope for Biodiversity Discovery

Wührl,

Rettenberger,

Meier

et al. 2024

IEEE Access

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Understanding and combatting biodiversity loss are critical tasks facing our planet. They are made especially difficult because much of the earth's biodiversity is concentrated in abundant and speciesrich groups of invertebrates like insects. Traditionally, samples of insects have been analyzed manually by experts using morphology. Not only does this necessitate taxonomic expertise, but it is also error-prone, time-consuming, and often involves commercial microscopes that are too expensive for many countries in the Global South where most species are found. The alternative to expert sorting with morphology is the use of DNA barcoding. However, this requires a well-equipped laboratory and an entirely different skill set. We present an alternative solution: a low-cost, open-source photomicroscope for taking high-resolution, focus-stacked images that can be used for insect classification: the Entomoscope. We describe two different versions of the Entomoscope, a standalone version that can be operated without additional hardware and an even simpler Version, that requires a computer. We show that the optics are of sufficiently high quality to classify specimens with >95% accuracy into 15 different types of insects (mostly 'families' according to the Linnean classification). The classifier can be successively extended or individually trained for specific classification tasks. Here, we provide building instructions, 3D files, and a list of commercially available parts so that everyone can build their own Entomoscope. Open-source DIY hardware like the Entomoscope facilitates affordable, cutting-edge biodiversity research by entomologists around the globe.

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Section: Concept and Methodsmentioning

confidence: 99%

Entomoscope: An Open-Source Photomicroscope for Biodiversity Discovery

Wührl,

Rettenberger,

Meier

et al. 2024

IEEE Access

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“…6X loading dye (Vivantis) was used to track deoxyribonucleic acid (DNA) migration and 0.005% RedSafe™ (iNtRON Biotechnology, Gyeonggi-do, Republic of Korea) was used to stained DNA during electrophoresis. Agarose gel electrophoresis was performed using PowerPac™ Basic Power Supply (BIO-RAD) according to Abid's protocol (25). PCR amplicons were visualized using ImageQuant™ LAS 500, GE Healthcare Bio-Sciences AB (Uppsala, Sweden).…”

Section: Effects Of Cordycepin On Messenger Ribonucleic Acid (Mrna) E...mentioning

confidence: 99%

Cordycepin EnhancesSIRT1Expression and Maintains Stemness of Human Mesenchymal Stem Cells

Chueaphromsri

Kunhorm

Phonchai

et al. 2023

In Vivo

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Background/Aim: Mesenchymal stem cells (MSCs) have been employed for therapeutic applications of various degenerative diseases. However, the major concern is MSC aging during the in vitro cultivation. Thus, the approach to delay MSC aging was examined in this research by focusing on the expression of Sirtuin 1 (SIRT1), a key anti-aging marker. Materials and Methods: Cordycepin, a bioactive compound derived from Cordyceps militaris, was used to up-regulate SIRT1 and maintain stemness of MSCs. Upon treatment with cordycepin, MSCs were investigated for cell viability, doubling time, key gene/protein expression, galactosidase-associated senescence assay, relative telomere length, and telomerase expression. Results: Cordycepin significantly increased the expression of SIRT1 in MSCs by activating the adenosine monophosphate activated protein kinase (AMPK)-SIRT1 signalling pathway. Moreover, cordycepin maintained the stemness of MSCs by deacetylating SRY-box transcription factor 2 (SOX2) via SIRT1, and cordycepin delayed cellular senescence and aging of MSCs by enhancing autophagy, inhibiting the activity of senescence-associated-galactosidase, maintaining proliferation rate, and increasing telomere activity. Conclusion: Cordycepin could be used to increase SIRT1 expression in MSCs for anti-aging applications.Regenerative medicine and cell therapy are modern medical advancements that are gaining a lot of attention as novel methods for treating severe diseases (1). MSCs are used to treat a variety of degenerative diseases, such as cardiovascular diseases, neuro degenerative diseases, bone and cartilage diseases, cancers, liver diseases, kidney diseases, and autoimmune diseases [including: graft versushost diseases, multiple sclerosis, Crohn's disease, type1 diabetes, systemic lupus erythematous, rheumatoid arthritis] (2). MSCs are adult stem cells that can be obtained from the bone marrow, adipose tissue, umbilical cord tissue, and umbilical cord blood (3). MSCs can differentiate into a variety of cells, including adipocytes, osteoblasts, chondrocytes, endothelial cells, and cardiomyocytes (4). MSCs have the capacity for selfrenewal and multipotency (5), and play a significant role in the development of specific organs and tissues with special functions (6). However, MSC aging is a critical problem that contributes to the loss of self-renewal, stemness and differentiation potential (7). MSCs are ineligible to be used in regenerative medicine treatments after prolonged in vitro cultivation because their selfrenewal and multipotency declines (8). Additionally, replicative senescence influences long-term changes in phenotype, differentiation potential, whole-map gene expression patterns, and microRNA profiles, all of which should be taken into consideration as therapeutic targets for MSC rejuvenation (9). Therefore, an appropriate method to maintain the self-renewal and multipotency of MSCs is very important for their use in therapeutic applications.SIRT1 is a nicotinamide adenine dinucleotide (NAD+)dependent lysine deacet...

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“…Furthermore, the required instrumentation employed for fluorometric measurements has evolved in recent years from static designs mainly focused on laboratory assays towards more flexible, portable and handheld devices [10][11][12][13][14][15][16], which can be easily operated for in situ experiments. Thus, the increasing availability of the necessary components to build fluorometric detection devices, such as intense light sources with different excitation wavelengths (LEDs, fiber optic) [17,18] and compact micro-spectrometers for light analysis (C1280 MA) [19], and the existence of numerous computer-programmable microcontrollers (Raspberry Pi, Arduino) [20][21][22][23] allow the building of low-cost equipment [24][25][26] with unique features for in situ sample analysis with spectrofluorometric detection.…”

Section: Introductionmentioning

confidence: 99%

Design of a Portable and Reliable Fluorimeter with High Sensitivity for Molecule Trace Analysis

et al. 2023

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There is a growing need for portable, highly sensitive measuring equipment to analyze samples in situ and in real time. For these reasons, it is becoming increasingly important to research new experimental equipment to carry out this work with advanced, robust and low-cost devices. In this framework, a flexible, portable and low-cost fluorimeter (under EUR 500), based on a C12880 MA MEMS micro-spectrometer with an Arduino compatible breakout board, has been developed for the trace analysis of biological substances. The proposed system can employ two selectable excitation sources for flexibility, one in the visible region at 405 nm (incorporated in the board) and an external LED at 365 nm in the UV region. This additional excitation source can be easily interchanged, varying the LED type for investigating any fluorophore compound of interest. The measurement process is micro-controlled, which allows the precise control of the spectrometer sensitivity by adjusting the integration time of each experiment separately. Data acquisition is easy, reliable and interfaced with a spreadsheet for fast spectra visualization and calculations. For testing the performance of the new device in fluorescence measurements, different fluorophore molecules which can be commonly found in biological samples, such as Fluorescein, Riboflavin, Quinine, Rhodamine b and Ru (II)-bipyridyl, have been employed. A high sensitivity and low quantitation limits (in the ppb range) have been found in all cases for the investigated chemicals. The portable device is also suitable for the study of other interesting phenomena, such as fluorescence quenching induced by chemical agents (such as halide anions or even auto-quenching). In this sense, an application for the quantification of chloride anions in aqueous solutions has been performed obtaining a LOD value of 18 ppm. The obtained results for all chemicals investigated with the proposed fluorimeter are always very similar in quantification figures, or even better than the data reported in literature, when using commercial laboratory equipment.

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Low-cost Imaging of Fluorescent DNA in Agarose Gel Electrophoresis using Raspberry Pi cameras

Cited by 8 publications

References 26 publications

Entomoscope: An Open-Source Photomicroscope for Biodiversity Discovery

Entomoscope: An Open-Source Photomicroscope for Biodiversity Discovery

Cordycepin EnhancesSIRT1Expression and Maintains Stemness of Human Mesenchymal Stem Cells

Design of a Portable and Reliable Fluorimeter with High Sensitivity for Molecule Trace Analysis

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