Biology subjects

Modi, K.

Publications and source records attributed to Modi, K..

3 recordsLinked to original sources

bioRxiv2026

Excessive sample reagent incubation time increases the risk of false rifampin resistance results in Xpert(R) MTB/RIF Ultra tests performed on paucibacillary Mycobacterium tuberculosis sputum.

A high rate of false rifampicin resistance (RIF-R) was recently reported in paucibacillary sputum samples tested with the Xpert(R) MTB/RIF Ultra (Ultra) assay. However, 96% of the studied facilities started the test 8 - 12 hours after addition of sample reagent (SR), exceeding the manufacturers recommended limit of 4 hours. Assessed whether excessive long SR incubation could lead to similar false RIF-R results in paucibacillary samples in a reference laboratory setting. We evaluated the performance of the Ultra assay following incubation of TB-negative sputum spiked with 300 CFU/mL and 100,000 CFU/mL levels of Mycobacterium tuberculosis (Mtb) H37Rv in SR for different durations (15 min to 24hrs.) at different temperatures (-20 to 370C) to determine the effect on RIF result calls. No false RIF-R results were observed in these samples with 105 CFU/mL Mtb at any of the conditions tested, even when they deviated largely from recommended limits. Similarly, freezing the 300 CFU/mL SR treated samples at minus 200C for 18 h also prevented the development of false RIF-R results. However, sputum spiked with 300 CFU/ml Mtb, produced false RIF-R calls at longer incubation times and higher incubation temperatures than are recommended by the manufacturer. Approximately half of the results displayed melt patterns consistent with hetero-resistance, indicating SR-induced mutagenesis in a wild-type background. This study demonstrates that extended off-label SR incubation of paucibacillary specimens beyond the recommended 4-hour limit can generate false RIF-R results. Freezing paucibacillary specimens in SR may mitigate this risk although it is not yet an approved procedure.

microbiology↗

bioRxiv2025

Increased levels of HAPLN2, which anchors dense extracellular matrix, in the hippocampus of APOE4 targeted replacement mice

Hyaluronan and proteoglycan link protein 2 (HAPLN2) / Brain link protein-1 (Bral1) is important for the binding of chondroitin sulfate proteoglycans (CSPGs) to hyaluronan and thus for the formation of specific types of brain extracellular matrix (ECM). It is also significantly increased with aging. Moreover, machine learning has identified it as a brain-derived protein most predictive of Alzheimers disease (AD). HAPLN2 binds to CSPGs that may sequester aggregation-prone proteins and also restrict neuronal plasticity. Because the apolipoprotein 4 (APOE4) allele increases AD risk, in the present study we have examined hippocampal lysates from APOE3 and APOE4 targeted replacement (TR) mice using unbiased proteomics, Western blot and hippocampal immunostaining. With proteomics, we observe that HAPLN2 is among the most significantly upregulated proteins in APOE4 mice. Prior work suggests HAPLN2 is particularly important to the assembly of perinodal matrix, and herein we show that it also co-localizes with Wisteria floribunda agglutinin (WFA) positive perineuronal nets (PNNs). PNNs represent a dense form of ECM that can increase GABAergic neurotransmission to alter overall excitatory/inhibitory (E/I) balance and neuronal oscillations important to mood and memory. Proteomics also detected elevated levels of high temperature requirement peptidase-1 (HTRA1), which accumulates in cerebral blood vessels harboring amyloid, in APOE4 mice. In Western blot studies, lysates from APOE4 mice also showed significantly reduced levels chondroitin-6 sulfated proteoglycans, which makes PNNs more susceptible to proteolysis and less inhibitory. In addition, immunostaining studies showed that levels of the PNN component aggrecan were increased in the hippocampus of APOE4 animals. Overall, these findings contribute to an emerging body of literature suggesting that brain extracellular matrix may be altered with aging and other risk factors for AD, and suggest that future studies should assess PNNs, peri-nodal structure and axonal conduction in the background of APOE4.

neuroscience↗

bioRxiv2019

14-3-3γ prevents centrosome duplication by inhibiting NPM1 function.

14-3-3 proteins bind to ligands via phospho-Serine containing consensus motifs. However, the molecular mechanisms underlying complex formation and dissociation between 14-3-3 proteins and their ligands remain unclear. We identified two conserved acidic residues in the 14-3-3 peptide-binding pocket (D129 and E136) that potentially regulate complex formation and dissociation. Altering these residues to Alanine led to opposing effects on centrosome duplication. D129A inhibited centrosome duplication while E136A stimulated centrosome amplification. These results were due to the differing abilities of these mutant proteins to form a complex with NPM1. Inhibiting complex formation between NPM1 and 14-3-3{gamma} led to an increase in centrosome duplication and overrode the ability of D129A to inhibit centrosome duplication. We identify a novel role of 14-3-3 in regulating centrosome licensing and a novel mechanism underlying the formation and dissociation of 14-3-3 ligand complexes dictated by conserved residues in the 14-3-3 family.

cell biology↗