Biology subjects

Iyer, H.

Publications and source records attributed to Iyer, H..

6 recordsLinked to original sources

bioRxiv2026

Evolved differences in microglial cell biology between surface and cave populations of Astyanax mexicanus

Microglia govern multiple aspects of brain architecture and function by eliminating dying cells, stimulating neurogenesis, refining neural connections, and orchestrating immune responses. The Mexican tetra, Astyanax mexicanus, is a powerful model system for investigating the evolution of brain function, yet microglia have not been investigated in this system. A. mexicanus exists as surface-dwelling and cave morphotypes with prominent behavioral and physiological differences. Notably, these evolved behavioral and physiological changes in cavefish, including diminished immune response, sleep, circadian rhythms, and sensory processing, are directly linked to known microglial functions. These observations suggest that evolved differences in microglia may shape brain circuitry adaptations in cavefish. Here we develop an experimental toolbox to examine microglial specification, dynamics, and function in A. mexicanus to perform comparative analysis of microglial cell biology between the surface and cave morphotypes. We find that the cave populations show increased numbers of microglia over developmental time relative to their surface counterparts. Microglia in Astyanax rapidly expand in response to inflammatory cues, distinct from microglial responses in the related teleost, zebrafish. Furthermore, lysosomal compartments of microglia in the cave populations exhibit increased enhanced proteolytic activity and reduced pH relative to surface morphotypes. Together, our observations reveal evolved differences in microglial cell biology between surface and cave populations of A. mexicanus and provide a framework to uncover novel neuroimmune mechanisms underlying the remarkable adaptations of A. mexicanus.

evolutionary biology↗

bioRxiv2025

Pathogenic DVL frameshifting variants in Robinow syndrome disrupt WNT signaling and cellular dynamics

Robinow syndrome (RS) is a genetically heterogeneous rare disorder involving six genes in the WNT/planar cell polarity (PCP) signaling pathway. Frameshifting variants in DVL genes that introduce a novel basic C-terminus are a common cause of autosomal dominant RS, accounting for [~]33% of individuals without ROR2 variants. Here, we review ClinVar and literature variants affecting DVL paralogs resulting in RS and investigate the cellular effects of pathogenic DVL frameshift variants with mutant tails replacing at least 82 amino acids. In silico analysis of the new C-termini revealed altered intrinsically disordered regions (IDRs), charge distribution, and predicted protein structures. To explore potential altered biological mechanisms caused by novel C-termini, we generated wild-type (WT), frameshift, and truncated constructs of DVL1-3, and analyzed their behavior in a transfection-based in vitro systems. DVL proteins normally polymerize into cytoplasmic puncta that redistribute upon WNT stimulation. Immunocytochemistry showed that mutant DVL proteins failed to change their localization in response to WNT ligands, in contrast to WT alleles--a consistent observation across all three DVLs. In line with this, TOPFlash reporter assays demonstrated that mutant DVL1 and DVL3 failed to activate canonical WNT signaling, while WT proteins induced strong activation. Additionally, the mutant C-terminal tail interfered with CSNK1E-induced phosphorylation, offering a potential mechanism underlying the impaired WNT response. Our results provide further understanding of the cellular consequences of pathogenic DVL frameshifting variants and offers insights into the effects of such alleles on WNT signaling, and the perturbations thereof, that may lead to developmental phenotypes observed in RS.

genetics↗

bioRxiv2023

Highly localized chemical sampling at sub-second temporal resolution enabled with a silicon nanodialysis platform at exceedingly slow flows.

Microdialysis (MD) is a versatile and powerful technique for chemical profiling of biological tissues and is widely used for quantification of neurotransmitters, neuropeptides, metabolites, biomarkers, and drugs in the central nervous system as well as in dermatology, ophthalmology, and in pain research. However, MD performance is severely limited by fundamental tradeoffs between chemical sensitivity, spatial resolution, and temporal response. Here, by using wafer-scale silicon microfabrication, we develop and demonstrate a nanodialysis (ND) sampling probe that enables highly localized chemical sampling with 100m spatial resolution and sub-second temporal resolution at high recovery rates. These performance metrics, which are 100X-1000X superior to existing MD approaches, are enabled by a 100X reduction of the microfluidic channel cross-section, a corresponding drastic 100X reduction of flow rates to exceedingly slow few nL/min flows, and integration of a nanometer-thin nanoporous membrane with high transport flux into the probe sampling area. Miniaturized ND probes may allow for the minimally invasive and highly localized sampling and chemical profiling in live biological tissues with unprecedented spatio-temporal resolution for clinical, biomedical, and pharmaceutical applications.

bioengineering↗

bioRxiv2021

EXAMINING DISCRIMINATION PERFORMANCE AND LIKELIHOOD RATIO VALUES FOR TWO DIFFERENT LIKELIHOOD RATIO SYSTEMS USING THE PROVEDIT DATASET

The conventional capillary electrophoresis (CE) genotyping workflow used in forensic DNA laboratories is composed of two processes: measurement and interpretation. The outcome of the measurement process is an electropherogram (EPG). The outcome of the interpretation process is a strength of evidence statement often reported in the form of a likelihood ratio (LR) which typically requires probabilistic genotyping software (PGS). An LR system is defined as the entire pipeline of the measurement and interpretation processes where PGS is a piece of the whole LR system. To gain understanding on how two LR systems perform, a total of 154 two-person mixture, 147 three-person mixture, and 127 four-person mixture profiles of varying DNA quality, DNA quantity, and mixture ratios were obtained from the filtered (.CSV) files of the GlobalFiler 29 cycles 15s PROVEDIt dataset and deconvolved in two independently developed fully continuous programs, STRmix v2.6 and EuroForMix v2.1.0. Various parameters were set in each software and LR computations obtained from the two software were based on same/fixed EPG features, same pair of propositions, number of contributors, theta, and population allele frequencies. The ability of each LR system to discriminate between contributor (H1-true) and non-contributor (H2-true) scenarios was evaluated qualitatively and quantitatively. Differences in the numeric LR values and their corresponding verbal classifications between the two LR systems were compared. The magnitude of the differences in the assigned LRs and the potential explanations for the observed differences greater than or equal to 3 on the log10 scale were described. Cases of LR < 1 for H1-true tests and LR > 1 for H2-true tests were also discussed. Our intent is to demonstrate the value of using a publicly available ground truth known mixture dataset to assess discrimination performance of any LR system and show the steps used to investigate and understand similarities and differences between different LR systems. We share our observations with the forensic community and describe how examining more than one PGS with similar discrimination power can be beneficial, help analysts compare interpretation especially with low-template profiles or minor contributor cases, and be a potential additional diagnostic check even if software in use does contain certain diagnostic statistics as part of the output. HighlightsO_LIThe use of two different Likelihood Ratio (LR) systems to assign LRs is discussed. C_LIO_LIH1-true and H2-true tests are performed using STRmix and EuroForMix and a large set of PROVEDIt mixture profiles. C_LIO_LIAssessment of discrimination performance of two LR systems using ROC plots, scatter plots, and relative frequency histograms. C_LIO_LIThe ability of the two LR systems to discriminate between contributors and non-contributors are statistically indistinguishable for the data that we considered. C_LIO_LIPotential reasons for the differences in LR values between the two LR systems that are [≥] 3 on the log10 scale are investigated and discussed. C_LIO_LIContributors with LRs < 1 and non-contributors with LRs > 1 generated from each LR system are discussed. C_LI

genetics↗

bioRxiv2020

Repression of lysosomal transcription factors Tfeb and Tfe3 is essential for the development and function of microglia

As the primary phagocytic cells of the central nervous system, microglia exquisitely regulate their lysosomal activity to facilitate brain development and homeostasis. However, mechanisms that coordinate lysosomal activity with microglia development, migration, and function remain unclear. Here we show that embryonic macrophages require the lysosomal GTPase RagA and the GTPase-activating protein Folliculin to colonize the brain in zebrafish. We demonstrate that embryonic macrophages in rraga mutants show increased expression of lysosomal genes but display significant downregulation of immune and migration-related genes. Furthermore, we find that RagA and Folliculin repress the key lysosomal transcription factor Tfeb, and its homologs Tfe3a and Tfe3b, in the macrophage lineage. Using RNA-Sequencing, we establish that Tfeb and Tfe3 are required for activation of lysosomal target genes under conditions of stress but not for basal expression of lysosomal pathways. Collectively, our data define a lysosomal regulatory circuit essential for macrophage development and function in vivo. TeaserThe degradation machinery of the cell must be carefully controlled for the normal formation and function of key immune cells called microglia.

developmental biology↗

bioRxiv2020

Ebola virus requires phosphatidylserine scrambling activity for efficient budding and optimal infectivity

AbstractEbola virus (EBOV) interacts with cells using two categories of cell surface receptors, C-type lectins and phosphatidylserine (PS) receptors. PS receptors typically bind to apoptotic cell membrane PS and orchestrate the uptake and clearance of apoptotic bodies. Many viruses coated with PS-containing lipid envelopes, acquired during budding from host cells, can also exploit these receptors for internalization. PS is restricted to the inner leaflet of the plasma membrane in homeostatic cells, an orientation that would be unfavorable for PS receptor-mediated uptake if conserved on the viral envelope. Therefore, it is theorized that viral infection induces host cell PS externalization to the outer leaflet during replication. Cells have several membrane scramblase enzymes that enrich outer leaflet PS when activated. Here, we investigate two scramblases, TMEM16F and XKR8, as possible mediators of cellular and viral envelope surface PS levels during recombinant VSV/EBOV-GP replication and EBOV virus-like particle (VLP) production. We found that rVSV/EBOV-GP and EBOV VLPs produced in XKR8 knockout cells contain decreased levels of PS in their outer leaflets. {Delta}XKR8-made rVSV/EBOV-GP is 70% less efficient at infecting cells through apoptotic mimicry compared to viruses made in parental cells. Our data suggest that virion surface PS acquisition requires XKR8 activity, whereas TMEM16F activity is not essential. Unexpectedly, we observed defective rVSV/G, rVSV/EBOV-GP, and EBOV VLP budding in {Delta}XKR8 cells, suggesting that phospholipid scrambling via XKR8 enhances both Ebola infectivity and budding efficiency. Overexpression of XKR8 dramatically increased budding activity, suggesting outer leaflet PS is required for both particle production and increased infectivity. ImportanceThe Democratic Republic of the Congo experienced its deadliest Ebola outbreak from 2018 to 2020, with 3,444 confirmed cases and 2,264 deaths (as of March 12, 2020). Owing to the extensive damage that these outbreaks have caused in Africa, as well as its future epidemic potential, Ebola virus (EBOV) ranks among the top eight priority pathogens outlined by the WHO in 2018. A comprehensive understanding of Ebola entry pathways into target cells is critical for antiviral development and outbreak control. Thus far, host-cell scramblases TMEM16F and XKR8 have each been named as the sole mediator of Ebola envelope surface phosphatidylserine (PS). We assessed the contributions of these proteins using CRISPR knockout cells and two EBOV models: rVSV/EBOV-GP and EBOV VLPs. We observed that XKR8 is required for optimal EBOV envelope PS levels, PS receptor engagement, and particle budding across all viral models, whereas TMEM16F did not play a major role.

microbiology↗