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Creators/Authors contains: "Abdelgawad, Ahmed"

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  1. ; ; ; ; ; ; ; ; ; ; et al ( , Cell Reports Methods)
    We present an efficient, effective, and economical approach, named E3technology, for proteomics sample preparation. By immobilizing silica microparticles into the polytetrafluoroethylene matrix, we develop a robust membrane medium, which could serve as a reliable platform to generate proteomics-friendly samples in a rapid and low-cost fashion. We benchmark its performance using different formats and demonstrate them with a variety of sample types of varied complexity, quantity, and volume. Our data suggest that E3technology provides proteome-wide identification and quantitation performance equivalent or superior to many existing methods. We further propose an enhanced single-vessel approach, named E4technology, which performs on-filter in-cell digestion with minimal sample loss and high sensitivity, enabling low-input and low-cell proteomics. Lastly, we utilized the above technologies to investigate RNA-binding proteins and profile the intact bacterial cell proteome. 
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    Free, publicly-accessible full text available June 1, 2025
  2. ; ; ; ; ; ; ; ; ( , The Journal of Infectious Diseases)
    Abstract Background

    Brain tissue-derived extracellular vesicles (bdEVs) act locally in the central nervous system (CNS) and may indicate molecular mechanisms in human immunodeficiency virus (HIV) CNS pathology. Using brain homogenate (BH) and bdEVs from a simian immunodeficiency virus (SIV) model of HIV disease, we identified RNA networks in SIV infection and neuroinflammation.

     Methods

    Postmortem occipital cortex samples were obtained from uninfected controls and SIV-infected subjects (acute and chronic phases with or without CNS pathology [SIV encephalitis]). bdEVs were separated and characterized per international consensus guidelines. RNAs from bdEVs and BH were sequenced and quantitative polymerase chain reaction (qPCR)-amplified to detect levels of small RNAs (sRNAs, including microRNAs [miRNAs]) and longer RNAs including messenger RNAs (mRNAs) and circular RNAs (circRNAs).

     Results

    Dysregulated RNAs in BH and bdEVs were identified in acute and chronic infection with pathology groups, including mRNAs, miRNAs, and circRNAs. Most dysregulated mRNAs in bdEVs reflected dysregulation in source BH. These mRNAs are disproportionately involved in inflammation and immune responses. Based on target prediction, several circRNAs that were differentially abundant in source tissue might be responsible for specific differences in sRNA levels in bdEVs during SIV infection.

     Conclusions

    RNA profiling of bdEVs and source tissues reveals potential regulatory networks in SIV infection and SIV-related CNS pathology.

     
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  3. ; ; ; ; ( , Physical Review Applied)
    Full Text Available 
  4. ; ; ; ; ; ; ( , New Phytologist)
    Summary

    In maize, 24‐nt phased, secondary small interfering RNAs (phasiRNAs) are abundant in meiotic stage anthers, but their distribution and functions are not precisely known.

    Using laser capture microdissection, we analyzed tapetal cells, meiocytes and other somatic cells at several stages of anther development to establish the timing of 24‐PHASprecursor transcripts and the 24‐nt phasiRNA products.

    By integrating RNA and small RNA profiling plus single‐molecule and small RNA FISH (smFISH or sRNA‐FISH) spatial detection, we demonstrate that the tapetum is the primary site of 24‐PHASprecursor andDcl5transcripts and the resulting 24‐nt phasiRNAs. Interestingly, 24‐nt phasiRNAs accumulate in all cell types, with the highest levels in meiocytes, followed by tapetum.

    Our data support the conclusion that 24‐nt phasiRNAs are mobile from tapetum to meiocytes and to other somatic cells. We discuss possible roles for 24‐nt phasiRNAs in anther cell types.

     
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