Biology subjects

Haque, M. A.

Publications and source records attributed to Haque, M. A..

3 recordsLinked to original sources

bioRxiv2023

An intact amber-free HIV-1 system for in-virus protein bioorthogonal click labeling that delineates envelope conformational dynamics

The HIV-1 envelope (Env) glycoprotein is conformationally dynamic and mediates membrane fusion required for cell entry. Single-molecule fluorescence resonance energy transfer (smFRET) of Env using peptide tags has provided mechanistic insights into the dynamics of Env conformations. Nevertheless, using peptide tags risks potential effects on structural integrity. Here, we aim to establish minimally invasive smFRET systems of Env on the virus by combining genetic code expansion and bioorthogonal click chemistry. Amber stop-codon suppression allows site-specifically incorporating noncanonical/unnatural amino acids (ncAAs) at introduced amber sites into proteins. However, ncAA incorporation into Env (or other HIV-1 proteins) in the virus context has been challenging due to low copies of Env on virions and incomplete amber suppression in mammalian cells. Here, we developed an intact amber-free virus system that overcomes impediments from preexisting ambers in HIV-1. Using this system, we successfully incorporated dual ncAAs at amber-introduced sites into Env on intact virions. Dual-ncAA incorporated Env retained similar neutralization sensitivities to neutralizing antibodies as wildtype. smFRET of click-labeled Env on intact amber-free virions recapitulated conformational profiles of Env. The amber-free HIV-1 infectious system also permits in-virus protein bioorthogonal labeling, compatible with various advanced microscopic studies of virus entry, trafficking, and egress in living cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/530526v1_ufig1.gif" ALT="Figure 1000"> View larger version (30K): org.highwire.dtl.DTLVardef@10e7728org.highwire.dtl.DTLVardef@b1078aorg.highwire.dtl.DTLVardef@65f874org.highwire.dtl.DTLVardef@9ab0e8_HPS_FORMAT_FIGEXP M_FIG C_FIG Amber-free HIV-1 infectious systems actualized minimal invasive Env tagging for smFRET, versatile for in-virus bioorthogonal click labeling in advanced microscopic studies of virus-host interactions.

microbiology↗

bioRxiv2022

Green synthesis of ZnO nanoparticles using Cocos nucifera leaf extract: Characterization, antimicrobial, antioxidant, and photocatalytic activity

Zinc oxide nanoparticles (ZnO NPs) have been successfully prepared using Cocos nucifera leaf extract and investigated with their antimicrobial, antioxidant, and photocatalytic activity. The structural, compositional, and morphological properties of the NPs were recorded and studied systematically to confirm the synthesis. The aqueous suspension of NPs showed a UV-Vis. absorption maxima of 370 nm indicating primarily its formation. The XRD analysis identified the NPs with hexagonal wurtzite structure with an average particle size of 16.6 nm. The FTIR analysis identified some biomolecules and functional groups in the leaf extract as responsible for the encapsulation and stabilization of ZnO NPs. The EDX analysis showed the desired elemental compositions in the material. A flower-shaped morphology of ZnO NPs was observed by SEM with a grain size of around 15 nm. The optical properties of the NPs were studied by UV-Vis spectroscopy and the band gap was calculated as 3.37 eV. The prepared ZnO NPs have demonstrated antimicrobial activity against T. harzianum and S. aureus with a ZOI (zone of inhibition) of 14 and 10 mm, respectively. The photocatalytic behavior of ZnO NPs showed absorbance degradation at around 640 nm and discolored methylene blue dye after one hour with a degradation maximum of 84.29 %. Thus, the prepared ZnO NPs could be used potentially in antibiotic development, pharmaceutical industries, and as photocatalysts.

biochemistry↗

bioRxiv2022

Evaluating the Phytotoxicity of Methanolic Extracts of Parthenium hysterophorus L. on Selected Crops and Weeds

Herbicides made from natural molecules may be a good environmentally friendly alternative to synthetic chemical herbicides for weed control. As a result, this investigation was carried out to ascertain the phytotoxicity of Parthenium hysterophorus L. as well as to identify its phenolic components. Germination of seeds and development of seedlings of Vigna subterranea (L.) Verdc, Raphanus sativus (L.) Domin, Cucurbita maxima Duchesne., Cucumis sativus L., Solanum lycopersicum L., Capsicum frutescens L., Zea mays L., Abelmoschus esculentus (L.) Moench, Daucus carota L., Digitaria sanguinalis (L.) Scop and Eleusine indica (L.) Gaertn were investigated using P. hysterophorus leaf, stem, and flower methanol extracts. Six concentrations (25, 50, 75, 100, and 150 g L-1) were comparison to the control (distilled water). The concentration of extracts increased, the rate of the seed sprouting and seedling growth decreased. EC50 values showed that the extraction of leaf of P. hysterophorus (811) was phytotoxic in comparison to the stem (1554) and flower (1109) extract. According to PCA analysis, Raphanus sativus, Solanum lycopersicum, Capsicum frutescens, Abelmoschus esculentus, Daucus carota, Digitaria sanguinalis, and Eleusine indica were all very susceptible to allelochemicals. A LC-MS analysis revealed that the P. hysterophorus leaf extract contained 7 phenolic compounds that were responsible for inhibition. These studies also revealed that the leaf of P. hysterophorus is a major source of phytotoxicity, which could be valuable in the future for developing a natural herbicide.

plant biology↗