Biology subjects

Malik, T.

Publications and source records attributed to Malik, T..

4 recordsLinked to original sources

bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗

bioRxiv2026

Autophagy induction mitigates FUS aggregate formation and early synaptic dysfunction at the NMJ in the FUS-ALS model

Mutations in Fused in Sarcoma (FUS), a RNA binding protein, cause Amyotrophic Lateral Sclerosis (ALS). ALS is an aggressive neurodegenerative disease resulting in motor neuron degeneration. Defects in synaptic integrity precede neuronal loss in ALS, but the mechanisms responsible for these early synaptic defects are unclear. To investigate early synaptic defects associated with ALS, we expressed an ALS-linked variant of human FUS in adult motor neurons and assessed synaptic pathology at the neuromuscular junction (NMJ). Here we highlight the accumulation of FUS-positive aggregates at synaptic terminals and subsequent reduction in microtubule stability. We show that inducing autophagy via expression of Rab1 or Fragile-X Mental Retardation Protein 1 (FMR1), or treatment with Rapamycin reduces aggregate formation and restores synaptic structure and function. These findings reveal the utility of inducing autophagy to address early synaptic dysfunction in an ALS model and demonstrate a potential therapeutic target to preventing later stages of disease progression.

neuroscience↗

bioRxiv2024

3D scanning measurement method for seed size research

PremiseTraditionally used seed size and surface area calculation techniques are often inaccurate or destructive. This is especially relevant for organisms with irregular shapes. It is believed that three-dimensional (3D) printing and scanning could also be disruptive technologies. However, these methods hold immense potential for ecology and evolution sciences, which have a longstanding tradition of inventing and creating objects for research, education, and outreach. Methods and ResultsWe describe how to 3D scan seeds reproducible on an inexpensive structured light based commodity 3D scanner. We then compared novel 3D and traditional 2D approaches by reproducibility and timing. ConclusionsThis study demonstrates how 3D scanning methods are easily applicable to the quantification of seed shape and providing an easy entry into it.

ecology↗

bioRxiv2021

Design of the recombinant influenza neuraminidase antigen is crucial for protective efficacy

Supplementing influenza vaccines with recombinant neuraminidase (rNA) remains a promising approach for improving the suboptimal efficacy. However, correlations among rNA designs, properties, and protection have not been systematically investigated. Here, we performed a comparative analysis of several rNAs produced from different construct designs using the baculovirus/insect cell system. The rNAs were designed with different tetramerization motifs and NA domains from a recent H1N1 vaccine strain (A/Brisbane/02/2018) and were analyzed for enzymatic properties, antigenicity, thermal and size stability, and protection in mice. We found that rNAs containing the NA head-domain versus the full-ectodomain possess distinct enzymatic properties and that the molecular size stability is tetramerization domain-dependent, whereas protection is more contingent on the combination of the tetramerization and NA domains. Following single-dose immunizations, a rNA possessing the full-ectodomain, non-native enzymatic activity, and the tetramerization motif from the human vasodilator-stimulated phosphoprotein provided substantially higher protection than a rNA possessing the head-domain, native activity and the same tetramerization motif. In contrast, these two rNAs provided comparable protection when the tetramerization motif was exchanged with the one from the tetrabrachion protein. These findings demonstrate that the rNA design is crucial for the protective efficacy and should be thoroughly evaluated for vaccine development, as the unpredictable nature of the heterologous domain combination can result in rNAs with similar key attributes but vastly differ in protection. IMPORTANCEFor several decades it has been proposed that influenza vaccines could be supplemented with recombinant neuraminidase (rNA) to improve the efficacy. However, some key questions for manufacturing stable and immunogenic rNA remain to be answered. We show here that the tetramerization motifs and NA domains included in the rNA construct design can have a profound impact on the biochemical, immunological and protective properties. We also show that the single-dose immunization regimen is more informative for assessing the rNA immune response and protective efficacy, which is surprisingly more dependent on the specific combination of NA and tetramerization domains than common attributes for evaluating NA. Our findings may help to optimize the design of rNAs that can be used to improve or develop influenza vaccines.

microbiology↗