Biology subjects

Mathew, T.

Publications and source records attributed to Mathew, T..

7 recordsLinked to original sources

bioRxiv2026

Sleeve gastrectomy improves metabolic health, cognition, and Alzheimer's Disease pathology in 3xTG mice

Obesity and diabetes are well-established risk factors for Alzheimers disease (AD), implicating metabolic dysfunction in AD pathogenesis. Sleeve gastrectomy (SG) is among the most effective metabolic interventions available, yet its impact on AD progression remains poorly understood. We hypothesized that SG performed early in life would improve metabolic health, attenuate AD pathology, and preserve cognition in a transgenic AD mouse model. Five-week-old female 3xTg-AD mice were preconditioned on a Western diet (WD) to induce obesity and glucose intolerance, then randomized to SG or sham surgery and maintained on either standard chow or continued WD for 12 months. Metabolic phenotyping, body composition, and cognitive assessments (Novel Object Recognition, Barnes Maze, Fear Conditioning) were performed longitudinally, with histological and molecular analysis of brain tissue at endpoint. Under chow-fed conditions, SG reduced adiposity, improved insulin sensitivity, and decreased cortical A{beta} plaque burden, accompanied by attenuated gliosis (GFAP, IBA1) and region-specific, insulin pathway-dependent modulation of autophagy. Under persistent WD, SG improved metabolic health, frailty, spatial cognition, and A{beta} pathology, again with corresponding perturbations in autophagy pathway activity. Across all groups, food intake did not differ significantly, indicating that these effects were not secondary to caloric restriction. Collectively, these data suggest that SG engages neuroprotective brain insulin signaling pathways, supporting metabolic surgery as a promising disease-modifying intervention for AD prevention in individuals with obesity.

neuroscience↗

bioRxiv2026

Optimization and Parallelization of Sorting by Interfacial Tension (SIFT) for High-Throughput Metabolic Cell Sorting

A systematic optimization of throughput and operational stability in Sorting by Interfacial Tension (SIFT) is presented. Reducing droplet size and enabling a broader distribution of droplet trajectories increased the number of droplets processed per sorting element, resulting in about a four fold improvement in throughput from 30 to 125 droplets per second. Throughput was further enhanced through device parallelization, with devices incorporating two and four independent sorting regions demonstrated. These configurations distributed droplets evenly across sorting elements that exhibited comparable pH sorting thresholds, indicating similar flow conditions and drag forces within each region. Among the designs evaluated, the two-element configuration provided the optimal balance of throughput, robustness, and simplicity, achieving maximum throughputs of about 250 droplets per second. Throughput and pH sorting thresholds were preserved throughout two hours of continuous sorting. The improved platform was applied to examine the relationship between cellular glycolysis and iron homeostasis at the single-cell level for Jurkat cells, revealing a subpopulation of highly glycolytic cells with significantly elevated iron uptake, consistent with prior reports linking iron regulation and T cell metabolism. Collectively, these advances expand the scale, stability, and biological applicability of SIFT, enabling large-scale functional studies while facilitating the capture of rare and metabolically distinct cell populations.

bioengineering↗

bioRxiv2026

Sleeve gastrectomy protects lean mice from future obesity.

BackgroundObesity and metabolic disease drive premature aging and reduced lifespan. While metabolic interventions like calorie restriction, protein restriction, and time restricted feeding have been shown to improved lifespan, they are either not effective or sustainable for most humans. Bariatric surgery is the most efficacious metabolic intervention available and is associated with increased lifespan. However, whether its longevity benefits derive solely from weight reduction or reflect surgery-specific metabolic reprogramming remains unknown. MethodsWe employed a lean mouse model of sleeve gastrectomy (SG) in which young, lean male C57BL/6J mice underwent SG or sham operation while maintained on low-fat chow, then were challenged with high-fat diet (HFD) in midlife. We assessed glucose metabolism, body composition, energy expenditure, hepatic histology, adipose tissue inflammation, and cecal microbiome composition. ResultsDespite identical weight and food intake on low-fat chow, SG mice demonstrated improved glucose tolerance and insulin sensitivity prior to HFD challenge. Upon HFD exposure, SG animals exhibited enhanced metabolic flexibility with greater capacity for fat oxidation, increased energy expenditure, attenuated weight gain, and reduced adiposity compared to sham controls. SG further reduced hepatic lipid accumulation and attenuated visceral adipose tissue inflammation, marked by decreased pro-inflammatory cytokine expression and reduced macrophage infiltration. These metabolic benefits occurred independently of caloric intake. Cecal microbiome profiling revealed surgery-specific remodeling characterized by Lactobacillus enrichment and reductions in Verrucomicrobia and Clostridia -- a pattern distinct from caloric restriction and consistent with prior SG studies. ConclusionsEarly-life SG confers durable, weight-loss-independent protection against midlife metabolic deterioration. Gut microbiome remodeling, particularly enrichment of Lactobacillus species, represents a candidate mediating mechanism and a potential therapeutic target for aging and metabolic disease.

physiology↗

bioRxiv2025

Pre-Sequencing Assessment of RNA-Seq Library Quality Using Real-Time qPCR

RNA sequencing (RNA-Seq) is an essential sequencing assay for studying transcriptome profiling. Ribosomal RNA (rRNA) comprises more than 80 - 90% of total cellular RNA, efficient rRNA removal is essential for accurately capturing the transcriptome, particularly to sequence low-abundance mRNAs. Inefficient rRNA removal during library preparation can result from variations in sample quality, preparation methods and handling. Estimating rRNA content in RNA-Seq libraries pre-sequencing is therefore challenging due to the absence of a reliable and cost-effective assessment method. This study addresses the issue by introducing a scalable qPCR-based assay targeting 18S rRNA to evaluate rRNA depletion efficiency pre-sequencing. qPCR efficiency was optimized using serial dilutions of Universal Human Reference (UHR) control and Ct thresholds were established using pilot data from 644 libraries. Following this optimization, analysis of 1,748 Total RNA-Seq libraries and 445 Poly A+ two widely used RNA-Seq library methods, demonstrated a strong correlation between 18S rRNA qPCR results and post-sequencing rRNA rates. This assay was also used to evaluate the performance of Oligo dT beads from four different vendors to enrich mRNA. This 18S rRNA qPCR assay is a cost-effective, scalable approach for reliably predicting rRNA read percentage in RNA-Seq libraries pre-sequencing. Method SummaryThe 18S rRNA-specific qPCR assay is a cost-effective method for evaluating rRNA depletion efficiency in RNA-Seq libraries prior to sequencing by targeting the 18S ribosomal RNA. qPCR efficiency was optimized, and Ct thresholds were set from pilot data and validated across 1,748 Total RNA and 445 Poly A+ RNA-Seq libraries. A Ct threshold of [≥]16 for Total RNA and Ct 13-14 or greater for Poly A+ libraries demonstrates a strong correlation between qPCR results and post-sequencing rRNA read percentages. The assay enables early identification of poorly depleted samples, reducing unnecessary sequencing costs. Additionally, the method was employed to benchmark oligo-dT beads from four vendors, showing its utility in evaluating RNA-seq library preparation kits. This scalable approach supports quality control in both research and high-throughput sequencing environments.

molecular biology↗

bioRxiv2025

Going green: Recycling transcriptomes to infer evolutionary relationships, gene duplication, gene tree conflict, and patterns of molecular evolution in the Apocynaceae

Background and AimsThe flowering plant family Apocynaceae exhibits diverse adaptations with biological and pharmaceutical significance, many of which have been studied with RNA-seq. However, despite the available transcriptomic data, no focused phylotranscriptomic study has been conducted to characterize the patterns of molecular evolution in this group. In this study, we leverage a dataset composed predominately of publicly available transcriptomes to infer relationships within Apocynaceae and explore the molecular processes that have shaped their divergences. MethodsWe extracted nuclear, chloroplast, and mitochondrial genes from 47 publicly available and one newly sequenced transcriptome to assemble and infer species relationships across Apocynaceae. Leveraging the gene-rich nuclear phylotranscriptomic data, we inferred molecular dates and investigated the complex history of gene tree conflict, molecular rate shifts, and gene duplications. To investigate the genomic basis of adaptations, we analyzed the inferred 14,838 gene duplications at the base of Apocynaceae for shared functional enrichment of genes related to evolutionary innovations. Key ResultsThe Apocynaceae topology inferred from our phylotranscriptomic analysis is highly concordant with the current consensus. Notably, a genome-wide acceleration in molecular rate subtends the Ceropegieae tribe. We observed that a decreased time between divergences is associated with a higher rate of gene tree conflict, a pattern especially prevalent across the Apocynaceaes historically recalcitrant backbone relationships. Furthermore, gene duplications may underlie evolutionary innovations, such as immunity-related gene expansion in the genus Asclepias and duplications associated with trichome modifications in the epiphytic Hoya. Finally, we discuss the contentious history of whole-genome duplication (WGD) within the Apocynaceae and emphasize the need for further investigation into the placement of WGDs. ConclusionsRepurposing transcriptomes is a powerful means of accumulating data for novel insights in plant evolution, especially during uncertain funding and cases where budget restrictions exist. Leveraging this gene-dense dataset, we obtained novel insights into the molecular evolution of Apocynaceae and identified areas for future investigations.

evolutionary biology↗

bioRxiv2024

Stepwise Isolation of Diverse Metabolic Cell Populations Using Sorting by Interfacial Tension (SIFT)

We present here a passive and label-free droplet microfluidic platform to sort cells stepwise by lactate and proton secretion from glycolysis. A technology developed in our lab, Sorting by Interfacial Tension (SIFT), sorts droplets containing single cells into two populations based on pH by using interfacial tension. Cellular glycolysis lowers the pH of droplets through proton secretion, enabling passive selection based on interfacial tension and hence single-cell glycolysis. The SIFT technique is expanded here by exploiting the dynamic droplet acidification from surfactant adsorption that leads to a concurrent increase in interfacial tension. This allows multiple microfabricated rails at different downstream positions to isolate cells with distinct glycolytic levels. The device is used to correlate sorted cells with three levels of glycolysis with a conventional surface marker for T-cell activation. As glycolysis is associated with both disease and cell state, this technology facilitates the sorting and analysis of crucial cell subpopulations for applications in oncology, immunology and immunotherapy.

bioengineering↗

bioRxiv2019

RanBP2/Nup358 enhances RNAi activity by sumoylating and stabilizing Argonaute 1

RanBP2/Nup358 is one of the main components of the cytoplasmic filaments of the nuclear pore complex. It has been speculated that RanBP2, which has an E3 SUMO-ligase domain, may alter the composition of messenger ribonucleoprotein (mRNP) complexes as they emerge from the nuclear pore and thus regulate the ultimate fate of the mRNA in the cytoplasm. Four separate missense mutations in RanBP2 cause Acute Necrotizing Encephalopathy 1 (ANE1), which manifests as a sharp rise in cytokine production after common viral infections such as influenza and parainfluenza. However, how RanBP2 and its ANE1-associated mutations affect cytokine production is not well understood. Here we report that RanBP2 represses the translation of the interleukin-6 (IL6) mRNA, which encodes a cytokine that is aberrantly up-regulated in ANE1. Our data indicates that soon after its production, the IL6 mRNP recruits the RNA-induced silencing complex (RISC) bound to Let7 miRNA. After this mRNP is exported, RanBP2 sumoylates the RISC-component AGO1, thereby stabilizing it and enforcing mRNA silencing. Collectively, these results support a model whereby RanBP2 promotes an mRNP remodelling event that is critical for the miRNA-mediated suppression of clinically relevant mRNAs, such as IL6.

molecular biology↗