Biology subjects

Allen, K. S.

Publications and source records attributed to Allen, K. S..

3 recordsLinked to original sources

bioRxiv2024

Stepwise Isolation of Diverse Metabolic Cell Populations Using Sorting by Interfacial Tension (SIFT)

We present here a passive and label-free droplet microfluidic platform to sort cells stepwise by lactate and proton secretion from glycolysis. A technology developed in our lab, Sorting by Interfacial Tension (SIFT), sorts droplets containing single cells into two populations based on pH by using interfacial tension. Cellular glycolysis lowers the pH of droplets through proton secretion, enabling passive selection based on interfacial tension and hence single-cell glycolysis. The SIFT technique is expanded here by exploiting the dynamic droplet acidification from surfactant adsorption that leads to a concurrent increase in interfacial tension. This allows multiple microfabricated rails at different downstream positions to isolate cells with distinct glycolytic levels. The device is used to correlate sorted cells with three levels of glycolysis with a conventional surface marker for T-cell activation. As glycolysis is associated with both disease and cell state, this technology facilitates the sorting and analysis of crucial cell subpopulations for applications in oncology, immunology and immunotherapy.

bioengineering↗

bioRxiv2023

CUR(E)ating a New Approach to Study Fungal Effectors and Enhance Undergraduate Education through Authentic Research

Course-based Undergraduate Research Experiences (CUREs) integrate active, discovery-based learning into undergraduate curriculums, adding tremendous value to Biochemistry and Molecular Biology (BMB) education. There are multiple challenges in transforming a research project into a CURE, such as the readiness of students, the time commitment of the instructor, and the productivity of the research. In this article, we report a CURE course developed and offered in the University of Massachusetts Amherst BMB Department since 2018 that addresses these challenges. Our CURE focuses on fungal effectors which are proteins secreted by a destructive pathogenic fungus Fusarium oxysporum, one of the top five most devastating plant pathogens. By studying this group of proteins, students are connected to real-world problems and participate in the search for potential solutions. A three-week "standard Bootcamp" is implemented to help students familiarize themselves with all basic techniques and boost their confidence. Next, molecular cloning, a versatile technique with modularity and repeatability, is used as the bedrock of the course. Our past five years of experience have confirmed that we have developed a novel and feasible CURE protocol. Measurable progress documented by students who took this course includes stimulated active learning and increased career trajectory to pursue hypothesis-based research to address societal needs. In addition, data generated through the course advance ongoing lab research. Collectively, we encourage the implementation of CURE among research-intensive faculty to provide a more inclusive research experience to all students, an important element in predicting career success.

scientific communication and education↗

bioRxiv2022

Identification of novel basil downy mildew resistance genes using de novo comparative transcriptomics

O_LISweet basil (Ocimum basilicum L.) production is threatened by the oomycete pathogen Peronospora belbahrii causing basil downy mildew (BDM); BDM resistant cultivar Mrihani (MRI) was identified in a germplasm screen, and fertile progeny were produced through a breeding program with BDM-susceptible Newton (SB22), but the molecular mechanisms conferring resistance in MRI and progeny remained unknown C_LIO_LIComparative transcriptomics was performed to identify candidate resistance genes and potential mechanisms for BDM resistance; RNA samples from BDM-infected MRI and SB22 plants were harvested at 4 time points during the first 3 days of infection to differentiate interactions in resistant and susceptible plants. C_LIO_LIThree categories of genes uniquely induced in resistant MRI upon pathogen challenge were identified: nucleotide-binding leucine rich repeat proteins (NLRs), multi-functional receptor-like kinases (RLKs), and secondary metabolic enzymes; validation of the top resistance candidate NLR gene confirmed its unique presence in MRI as well as in two of four resistant MRIxSB22 F2 progeny. C_LIO_LIIn MRI, pathogen challenge also upregulated transcripts in the salicylic acid synthesis pathway, suggesting its role in BDM resistance, and demonstrating the application of using comparative transcriptomics to identify resistance genes and mechanisms in non-model crops for marker-assisted breeding approaches. C_LI

plant biology↗