CRISPR-Microfluidics Nexus: Advancing Biomedical Applications for Understanding and Detection

Sensors and Actuators A Physical, Journal Year: 2024, Volume and Issue: 376, P. 115625 - 115625

Published: June 24, 2024

The integration of CRISPR technology with microfluidic-based biosensors has greatly expanded its applications in medicine and molecular biology. This combination offers enhanced sensitivity selectivity medical diagnostics. CRISPR-powered microfluidics enables the accurate quantification DNA RNA associated diseases such as cancer, viral infections, bacterial diseases. precise targeting capabilities allow for detection specific genetic sequences, aiding early diagnosis, disease monitoring, treatment assessment. improves specificity by leveraging programmable nature coupling it signal readouts. However, challenges assay optimization, standardization, device fabrication need to be addressed. Additionally, complexity presents potential limitations terms off-target effects unintended modifications. Overall, holds tremendous diagnostics, but further research development are required fully exploit benefits clinical settings.

Language: Английский

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ObiWan-Microbi: OMERO-based integrated workflow for annotating microbes in the cloud

SoftwareX, Journal Year: 2024, Volume and Issue: 26, P. 101638 - 101638

Published: Feb. 1, 2024

Automated microscopy techniques combined with high-throughput microfluidic cultivation systems provide unique insights into living microorganisms, enabling hundreds of experiments to be performed in parallel. Such setups generate large data sets rich cellular features that need extracted arrive at quantitative insights. The sheer amount recorded time-lapse images requires reliable automated processing. While recent advances deep learning methods have enabled processing, these rely on large-scale and precisely annotated sets, often not available for new organisms or custom imaging modalities.To overcome the bottleneck, particularly microbial domain, we present open-source ObiWan-Microbi platform providing a fast workflow annotation up hundred thousands segmentation tracking annotations data. focuses easy-to-use semi-automated browser eliminating local installation accelerator hardware, encourages FAIR management using OMERO, provides convenient collaborative cloud deployment simplify creation long-term development sets. public availability such benchmark has potential improve data-driven methods, increase comparability among them, is an essential step towards image processing live-cell microscopy.

Language: Английский

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Advancements in technology for characterizing the tumor immune microenvironment

International Journal of Biological Sciences, Journal Year: 2024, Volume and Issue: 20(6), P. 2151 - 2167

Published: Jan. 1, 2024

Immunotherapy plays a key role in cancer treatment, however, responses are limited to small number of patients.The biological basis for the success immunotherapy is complex interaction between tumor cells and immune microenvironment (TIME).Historically, research on constitution was analysis one or two markers, more novel technologies needed interpret interactions TIME.In recent years, major advances have already been made depicting TIME at considerably elevated degree throughput, dimensionality resolution, allowing dozens markers be labeled simultaneously, analyzing heterogeneity tumour-immune infiltrates detail single cell level, spatial landscape entire microenvironment, as well applying artificial intelligence (AI) large amount data from this review, we summarized emerging that contributions field TIME, provided prospects future research.

Language: Английский

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Integrating microfluidics and synthetic biology: advancements and diverse applications across organisms

Lab on a Chip, Journal Year: 2024, Volume and Issue: 24(11), P. 2834 - 2860

Published: Jan. 1, 2024

Synthetic biology is the design and modification of biological systems for specific functions, integrating several disciplines like engineering, genetics, computer science. The field synthetic to understand processes within host organisms through manipulation regulation their genetic pathways addition biocontrol circuits enhance production capabilities. This pursuit serves address global challenges spanning diverse domains that are difficult tackle conventional routes production. Despite its impact, achieving precise, dynamic, high-throughput still challenging. Microfluidics offers a solution those challenges, enabling controlled fluid handling at microscale, offering lower reagent consumption, faster analysis biochemical reactions, automation, high throughput screening. In this review, we diverge from focus on automating design-build-test-learn cycle, instead, microfluidic platforms role in advancing integration with - bacterial cells, yeast, fungi, animal cells cell-free systems. review illustrates how devices have been instrumental understanding by showcasing microfluidics as an essential tool create circuits, pathways, environments. conclusion, show expedite applications across including but not limited personalized medicine, bioenergy, agriculture.

Language: Английский

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Decoding senescence of aging single cells at the nexus of biomaterials, microfluidics, and spatial omics

npj Aging, Journal Year: 2024, Volume and Issue: 10(1)

Published: Nov. 26, 2024

Aging has profound effects on the body, most notably an increase in prevalence of several diseases. An important aging hallmark is presence senescent cells that no longer multiply nor die off properly. Another characteristic altered immune system fails to properly self-surveil. In this multi-player process, cellular senescence induces a change secretory phenotype, known as senescence-associated phenotype (SASP), many with intention recruiting accelerate clearance these damaged cells. However, SASP results inducing secondary nearby cells, resulting those becoming senescent, and improper activation state chronic inflammation, called inflammaging, Senescence termed immunosenescence, further dysregulation system. interdisciplinary approach needed physiologically assess changes at tissue level. Thus, intersection biomaterials, microfluidics, spatial omics great potential collectively model immunosenescence. Each approaches mimics unique aspects body undergoes part aging. This perspective highlights key how biomaterials provide non-cellular cues cell aging, microfluidics recapitulate flow-induced multi-cellular dynamics, analyses dissect coordination biomarkers function interactions distinct environments. overview play role organ cancer, wound healing, Alzheimer's, osteoporosis included. To illuminate societal impact increasing trend anti-senescence anti-aging interventions, including pharmacological medical procedures, lifestyle discussed, context senescence.

Language: Английский

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Tools and methods for high-throughput single-cell imaging with the mother machine

eLife, Journal Year: 2023, Volume and Issue: 12

Published: July 26, 2023

Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform single-cell time-lapse imaging is the mother machine, which enables long-term tracking microbial cells under precisely controlled growth conditions. While several machine pipelines have been developed in past years, adoption by non-expert audience challenge. To fill this gap, we implemented our own software, MM3, as plugin multidimensional viewer napari. napari-MM3 complete and modular pipeline data, takes advantage high-level interactivity Here, give an overview test it against well-designed widely used pipelines, including BACMMAN DeLTA. Researchers often analyze data with custom scripts using varied methods, but quantitative comparison output different has lacking. end, show that key physiological parameter correlations distributions are robust to choice method. However, also find small changes thresholding parameters can systematically alter extracted from experiments. Moreover, explicitly deep learning-based segmentation, 'what you put what get' (WYPIWYG) - is, pixel-level variation training cell segmentation propagate model bias spatial temporal measurements. Finally, while primary purpose work introduce software over last decade lab, provide information those who want implement machine-based methods their research.

Language: Английский

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Scaling of stochastic growth and division dynamics: A comparative study of individual rod-shaped cells in the Mother Machine and SChemostat platforms

Molecular Biology of the Cell, Journal Year: 2024, Volume and Issue: 35(6)

Published: April 10, 2024

Microfluidic platforms enable long-term quantification of stochastic behaviors individual bacterial cells under precisely controlled growth conditions. Yet, quantitative comparisons physiological parameters and cell different microorganisms in experimental device modalities is not available due to experiment-specific details affecting physiology. To rigorously assess the effects mechanical confinement, we designed, engineered, performed side-by-side experiments otherwise identical conditions Mother Machine (with confinement) SChemostat (without confinement), using latter as ideal comparator. We established a protocol cultivate suitably engineered rod-shaped mutant

Language: Английский

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Exploiting fluctuations in gene expression to detect causal interactions between genes

Published: April 22, 2025

Characterizing and manipulating cellular behaviour requires a mechanistic understanding of the causal interactions between components. We present an approach to detect genes without need perturb physiological state cells. This exploits naturally occurring cell-to-cell variability which is experimentally accessible from static population snapshots genetically identical cells follow over time. Our main contribution simple mathematical relation that constrains propagation gene expression noise through biochemical reaction networks. allows us rigorously interpret fluctuation data even when only small part complex regulatory process can be observed. show how this can, in theory, exploited by synthetically engineering passive reporter expression, akin established “dual as-say”. While focus our theoretical, we also experimental proof-of-principle demonstrate real-world applicability certain circumstances. suggest method specific synthetic circuits E. coli confirming theoretical result narrow set controlled settings. Further work needed practical on large scale, with networks, or organisms other than .

Language: Английский

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Disease modeling and developmental biology through microfluidic channels

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 45 - 59

Published: Jan. 1, 2025

Language: Английский

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PyEcoLib: a python library for simulating stochastic cell size dynamics

Physical Biology, Journal Year: 2023, Volume and Issue: 20(4), P. 045006 - 045006

Published: May 24, 2023

Recently, there has been an increasing need for tools to simulate cell size regulation due important applications in proliferation and gene expression. However, implementing the simulation usually presents some difficulties, as division a cycle-dependent occurrence rate. In this article, we gather recent theoretical framework

Language: Английский

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