Biology subjects

Ranjbaran, M.

Publications and source records attributed to Ranjbaran, M..

4 recordsLinked to original sources

bioRxiv2023

A portable, easy-to-use paper-based biosensor for rapid in-field detection of fecal contamination on fresh produce farms

Laboratory-based nucleic acid amplification tests (NAATs) are highly sensitive and specific, but they require the transportation of samples to centralized testing facilities and have long turnaround times. During the Coronavirus Disease 2019 (COVID-19) pandemic, substantial advancement has been achieved with the development of paper-based point-of-care (POC) NAATs, offering features such as low cost, being easy to use, and providing rapid sample-to-answer times. Although most of the POC NAATs innovations target clinical settings, we have developed a portable, paper-based loop-mediated isothermal amplification (LAMP) testing platform for on-farm applications, capable of detecting Bacteroidales as a fecal contamination biomarker. Our integrated platform includes a drop generator, a heating and imaging unit, and paper-based biosensors, providing sensitive results (limit of detection 3 copies of Bacteroidales per cm2) within an hour of sample collection. We evaluated this integrated platform on a commercial lettuce farm with a concordance of 100% when compared to lab-based tests. Our integrated paper-based LAMP testing platform holds great promise as a reliable and convenient tool for on-site NAATs. We expect that this innovation will encourage the fresh produce industry to adopt NAATs as a complementary tool for decision-making in growing and harvesting. We also hope that our work can stimulate further research in the development of on-farm diagnostic tools for other agricultural applications, leading to improved food safety and technology innovation.

bioengineering↗

bioRxiv2023

Bacteroidales as a Fecal Contamination Indicator in Fresh Produce Industry: A Baseline Measurement

Foodborne outbreaks caused by fecal contamination of fresh produce represent a serious concern to public health and the economy. As the consumption of fresh produce increases, public health officials and organizations have pushed for improvements in food safety procedures and environmental assessments to reduce the risk of contamination. Visual inspections and the establishment of "buffer zones" between animal feeding operations and producing fields are the current best practices for environmental assessments. However, a generalized distance guideline and visual inspections may not be enough to account for all environmental risk variables. Here, we report a baseline measurement surveying the background Bacteroidales concentration, as a quantitative fecal contamination indicator, in Californias Salinas Valley. We collected a total of 1632 samples from two romaine lettuce commercial fields at the time of harvesting through two seasons in a year. The Bacteroidales concentration was very low (0 - 2.00 copies/cm2). Furthermore, we established a practical methodology for evaluating the risk of fecal contamination in a real-world setting, complementing the current environmental assessment practices. This method can identify site-specific risks and offer fresh produce stakeholders a more comprehensive understanding of their fields. We anticipate this work can encourage the use of Bacteroidales in the fresh produce industry to monitor fecal contamination and prevent future foodborne outbreaks.

bioengineering↗

bioRxiv2023

A drop dispenser for simplifying on-farm detection of foodborne pathogens

Rapid nucleic-acid biosensors are useful for on-farm detection of foodborne pathogens on fresh produce during pre-season and pre-harvest stages. Such tools aim to be user-friendly so that a producer could operate them in a few simple steps and detect multiple targets. Currently, an easy-to-use device for on-farm applications does not exist commercially. One of the bottlenecks is the delivery of a prescribed amount of sample to the reaction sites of the biosensor using a simple and precise approach. Here, we developed drop dispensers using 3D printing and a hydrophilic surface chemistry treatment to generate precise drops (DNA/bacterial samples) of a few micro-liters ([~]20 to [~]33 {micro}L). We tested multiple copies of these devices over time of repeated application to estimate their shelf-lives which is about one month. In addition to drop generation tests, we employed these devices in nucleic-acid testing. The tests used loop-mediated isothermal amplification (LAMP) to detect DNA or whole cells of Shiga-toxin-producing Escherichia coli O157:H7. These tests were performed to simulate the on-farm sample collection (using collection flags that we previously designed) and delivery using the drop dispensers. Our results showed that these devices performed similarly to standard commercial pipettors in LAMP assays, providing a limit of detection of 7.8x106 cell/mL for whole-cell detection. This drop dispenser will eventually be part of a user-friendly consumable kit that will enable performing LAMP assays by non-specialist users for a cost of USD 4 per test.

bioengineering↗

bioRxiv2018

Algorithm for Reliable Detection of Beat Onsets in Cerebral Blood Flow Velocity Signals

Transcranial Doppler (TCD) ultrasound has been demonstrated to be a valuable tool for assessing cerebral hemodynamics via measurement of cerebral blood flow velocity (CBFV), with a number of established clinical indications. However, CBFV waveform analysis depends on reliable pulse onset detection, an inherently difficult task for CBFV signals acquired via TCD. We study the application of a new algorithm for CBFV pulse segmentation, which locates pulse onsets in a sequential manner using a moving difference filter and adaptive thresholding. The test data set used in this study consists of 92,012 annotated CBFV pulses, whose quality is representative of real world data. On this test set, the algorithm achieves a true positive rate of 99.998% (2 false negatives), positive predictive value of 99.998% (2 false positives), and mean temporal offset error of 6.10 {+/-} 4.75 ms. We do note that in this context, the way in which true positives, false positives, and false negatives are defined caries some nuance, so care should be taken when drawing comparisons to other algorithms. Additionally, we find that 97.8% and 99.5% of onsets are detected within 10 ms and 30 ms, respectively, of the true onsets. The algorithms performance in spite of the large degree of variation in signal quality and waveform morphology present in the test data suggests that it may serve as a valuable tool for the accurate and reliable identification of CBFV pulse onsets in neurocritical care settings.

bioinformatics↗