Biology subjects

Patel, A. A.

Publications and source records attributed to Patel, A. A..

4 recordsLinked to original sources

bioRxiv2018

Variations in the phagosomal environment of human neutrophils and mononuclear phagocyte subsets.

The phagosomal microenvironment has a major influence on the enzyme activity and biology within these organelles. Here we directly compared the phagosomal pH of human neutrophils, monocytes, dendritic cell (DC) and monocyte-derived cells. An unexpected observation was the striking difference in phagosomal environment between the three monocytes subsets. Classical monocytes and neutrophils had alkaline phagosomes, yet non-classical monocytes had more acid phagosomes. Intermediate monocytes had an intermediate phenotype. We next investigated the differences between primary DCs versus in vitro monocyte-derived DCs and established that both these cells had acidic phagosomal environments. We also confirmed reports of an alkaline phagosome in \"M1\" macrophages, and an acidic one in \"M2\" macrophages. Across all phagocytes, alkalinisation was dependent upon the activity of the NADPH oxidase, as when it was absent in cells from a patient with chronic granulomatous disease (CGD) or was abolished by an inhibitor of the oxidase, diphenyleneiodonium (DPI). An increased alkalinity in the phagosome was associated with more oxidase activity. These data highlight the heterogenous nature of phagocytic vacuoles within the family of mononuclear phagocytes that will dictate the function of these compartments.\n\nKey pointsO_LIPhagosomal function depends upon the action of enzymes released into them from cytoplasmic granules.\nC_LIO_LIThe substantial differences in the phagosomal pH in the different phagocytes will affect their compliment of enzymes and their functions.\nC_LI

immunology↗

bioRxiv2018

Injury-induced cold sensitization in Drosophila larvae involves behavioral shifts that require the TRP channels Pkd2 and Brv1.

Nociceptive sensitization involves an increase in responsiveness of pain sensing neurons to sensory stimuli, typically through the lowering of their nociceptive threshold. Nociceptive sensitization is common following tissue damage, inflammation, and disease and serves to protect the affected area while it heals. Organisms can become sensitized to a range of noxious and innocuous stimuli, including thermal stimuli. The basic mechanisms underlying sensitization to warm or painfully hot stimuli have begun to be elucidated, however, sensitization to cold is not well understood. Here, we develop a Drosophila assay to study cold sensitization after UV-induced epidermal damage in larvae. Larvae respond to acute cold stimuli with a set of unique behaviors that include a contraction of the head and tail (CT) or a raising of the head and tail into a U-Shape (US). Under baseline, non-injured conditions larvae primarily produce a CT response to an acute cold (10 {degrees}C) stimulus, however, we show that cold-evoked responses shift following tissue damage: CT responses decrease, US responses increase and some larvae exhibit a lateral body roll (BR) that is typically only observed in response to high temperature and noxious mechanical stimuli. At the cellular level, class III neurons are required for the decrease in CT, chordotonal neurons are required for the increase in US, and chordotonal and class IV neurons are required for the appearance of BR responses after UV. At the molecular level, we found that the transient receptor potential (TRP) channels Polycystic kidney disease gene 2 (Pkd2) and brivido-1 (brv1) are required for these behavioral shifts. Our Drosophila model will enable a sophisticated molecular genetic dissection of genes and circuits involved in cold nociceptive sensitization.

neuroscience↗

bioRxiv2017

The Drosophila Formin Fhod Nucleates Actin Filaments

Formins are a conserved group of proteins that nucleate and processively elongate actin filaments. Among them, the formin homology domain-containing protein (FHOD) family of formins contributes to contractility of striated muscle and cell motility in several contexts. However, the mechanisms by which they carry out these functions remain poorly understood. Unlike other formins, mammalian FHOD1 and FHOD3 do not accelerate actin assembly in vitro, and have instead been suggested to act as barbed end cappers or bundlers. Here, we show that purified Drosophila Fhod, in contrast with the mammalian homologues, potently accelerates actin assembly by nucleation. We found that Fhod binds tightly to barbed ends, where it slows elongation in the absence of profilin and allows elongation in the presence of profilin. Fhod protects barbed ends from capping protein, but dissociates from barbed ends relatively quickly. Finally, we used cosedimentation assays to determine that Fhod binds the sides of actin filaments and bundles filaments. This work establishes that Fhod shares the capacity of other formins to nucleate and bundle actin filaments, but is notably less effective at processively elongating barbed ends.

cell biology↗

bioRxiv2017

Simple And Multiplexed Enrichment Of Rare DNA Variants Via Sequence-Selective And Temperature-Robust Amplification

Rare DNA sequence variants hold important clinical and biological information, but are chal-lenging for existing methods (e.g. PCR, NGS) to profile in an inexpensive, multiplexed, simple-to-implement, and sequence-general way. Here, we present Blocker Displacement Amplification (BDA), a temperature-robust PCR method that selectively amplifies all sequence variants within a roughly 20 nt window by 1000-fold over wildtype sequences, allowing easy detection and quantitation of hundreds of potentials variants originally at [≤]0.1% allele frequency. BDA employs a rationally designed competitive hybridization reaction to achieve similar enrichment performance across anneal temperatures ranging from 56{degrees}C to 64{degrees}C. This temperature robustness facilitates multiplexed enrichment of many different variants across the genome, and furthermore enables the use of in-expensive and portable thermocycling instruments for rare DNA variant detection. To show the sequence generality of BDA, we demonstrated enrichment on 156 single-nucleotide variants (SNVs). BDA has been validated on multiple different PCR platforms, DNA polymerases, and sample types including clinical cell-free DNA samples collected from the blood plasma of lung cancer patients. BDA quantitation of mutation allele fraction is generally consistent with deep sequencing results.

genomics↗