Biology subjects

Kalish, B.

Publications and source records attributed to Kalish, B..

5 recordsLinked to original sources

bioRxiv2026

Spatial dynamics of cellular and molecular plasticity in the maternal and postpartum mouse brain

Pregnancy is a critical window for neuroplasticity and maternal mental health, yet our understanding of the molecular and cellular changes underlying this adaptation remains incomplete. Here we profile the female mouse brain in nulliparous, late-pregnant and postpartum states with three single-cell spatial technologies (Slide-tags, MERFISH and Xenium). Together these assays resolve 1.5 million cells in one coronal plane spanning the cortex, striatum, lateral septum and preoptic area. Pregnancy is associated with changes in gene expression in most cell types, beyond the circuits previously established to govern maternal behavior. These changes resolve into three programs that are reproducible across platforms: synaptic pathways increase in neurons as growth and plasticity pathways decrease; immune and angiogenic pathways increase in glia and vascular cells; and cholesterol synthesis decreases as uptake increases across both neurons and glia. Finally, mapping human depression genetics onto these data, we find risk genes concentrated almost entirely in neurons, and this concentration changes with reproductive state in the preoptic area, basal forebrain and ventral striatum. These results place the neurons carrying depression risk among the circuits remodeled during pregnancy, providing a possible cellular substrate for peripartum vulnerability.

genomics↗

bioRxiv2025

Molecular and Epigenetic Pathways Underlying Epithelial Damage and Repair in Necrotizing Enterocolitis via Multi-omics Approach

IntroductionNeonatal necrotizing enterocolitis (NEC) is a severe gastrointestinal disorder with high mortality, characterized by epithelial cell injury and compromised epithelial repair. The mechanisms underlying defective epithelial regeneration remain poorly understood despite advances in single-cell omics. Addressing these challenges is essential for elucidating the pathogenesis of NEC and identifying therapeutic targets to restore epithelial regeneration and replace the damaged epithelial layer. MethodsMulti-omics approaches were employed to investigate molecular and spatial changes in experimental NEC at epigenetic and transcriptomic levels. These included bulk RNA sequencing, single-nucleus RNA sequencing (snRNA-seq), single-nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq), and multiplexed error-robust fluorescence in situ hybridization (MERFISH) for spatial transcriptomics. Complementary in vitro experiments and in vivo mouse models were utilized to evaluate NEC phenotypes, intestinal tissue morphology, and organoid formation. ResultsChanges in cell type composition, transcriptional network remodeling, and chromatin accessibility were observed in the small intestine of neonatal mice with NEC. Chromatin accessibility significantly changed in epithelial cells, highlighting their pivotal roles in NEC. A marked reduction in intestinal stem cells (ISCs) and transit-amplifying cells, along with an increased proportion of enteroendocrine cells, indicates disrupted epithelial regeneration and functional differentiation. These changes correlated with disrupted WNT signaling and stem cell maintenance genes (e.g., Lgr5, Smoc2, Axin2) and activation of inflammatory and hypoxia-related pathways (e.g., Il6, Tnf). The epigenetic regulator Ezh2 was identified as a critical factor in maintaining LGR5+ ISCs and epithelial homeostasis. Knockdown of Ezh2 reduced stemness and proliferation-related gene expression and exacerbated inflammation. Reactivation of WNT signaling restored Ezh2 and Lgr5 expression, improving intestinal regeneration. ConclusionThis study reveals dynamic transcriptomic, epigenetic, and spatial changes in NEC and highlights Ezh2 as a key regulator of LGR5+ intestinal stem cell function and epithelial regeneration. These findings provide insights into NEC pathogenesis and a basis for therapies targeting Ezh2 and WNT signaling to restore intestinal integrity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/647851v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1ad89eaorg.highwire.dtl.DTLVardef@396282org.highwire.dtl.DTLVardef@172596forg.highwire.dtl.DTLVardef@4daf28_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2024

Rapid colorimetric detection of citrus tristeza virus combining portable sample preparation and reverse transcription-loop mediated isothermal amplification

AbstractsA sensing platform combining semi-automated sample preparation protocol and one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) is reported for rapid colorimetric detection of citrus tristeza virus (CTV) in a greenhouse. An OmniLyse micro-homogenizer and cellulose paper disks were integrated for quick sample preparation of total nucleic acids (<15 min). RT-LAMP assays were optimized in terms of primers concentrations and minimization of false positives for both CTV and cytochrome oxidase (COX) detections. Specifically, the optimal reaction time for lab-based RT-LAMP assays was determined as 40 minutes with the detection limits of CTV and COX as 43 copies/L (equivalent to 86 copies/mg of tissue) and 5 copies/L (equivalent to 10 copies/mg of tissue), respectively. Additionally, an in-greenhouse colorimetric RT-LAMP assay with lyophilized reaction mix for endpoint CTV detection was successfully conducted in 35 minutes without a false response in either colorimetric or fluorometric assays. Overall, this quick sample preparation protocol integrated with the lyophilized RT-LAMP assays showed high efficiency and reliability in plant pathogen detection in a greenhouse. This strategy holds great potential to be integrated into a portable, autonomous system and be universally adopted for in-field diagnosis of different pathogens.

bioengineering↗

bioRxiv2024

A 3D-printed handheld device for quick citrus tissue lysis and nucleic acid extraction

AbstractsA 3D-printed handheld device has been developed for rapid and efficient sample preparation from citrus leaves, aimed at streamlining protocols traditionally reliant on mortar and pestle. With its high-speed motor, knurled lysis chamber for rapid sample lysis, and quick nucleic acid extraction using paper disks, this device can yield ready-to-use extracts in just 12 minutes, significantly reducing the time required for sample preparation. The device was optimized for maximum sample lysis by evaluating operation voltages and chamber features. The results showed that the lysis chamber with internal knurling and the motor operated at 7.5 V was sufficient for effective sample lysis in 1 minute, achieving total RNA concentrations up to 87.6% of those obtained with a mortar and pestle. Furthermore, concerns regarding heat generation and resin release during the lysis process were found to not impact sample quality. To further facilitate in-field diagnosis, the capability of in-device sample preparation was verified with citrus sources infected with citrus tristeza virus and Spiroplasma citri in qPCR-based assays, where low assay variations were demonstrated (< 3.8%). Overall, the in-device sample preparation integrated with the paper disks showed good reliability and compatibility across different pathogens for downstream analysis. An eco-friendly sterilization protocol using household bleach and vitamin C solution was also developed to safely reuse the device for in-field deployment.

bioengineering↗

bioRxiv2022

Administration of amniotic fluid stem cell extracellular vesicles promotes development of fetal hypoplastic lungs by immunomodulating lung macrophages

Congenital diaphragmatic hernia (CDH) is a devastating condition characterized by incomplete closure of the diaphragm and herniation of abdominal organs into the chest. As a result, fetuses have pulmonary hypoplasia, whose severity is the main determinant of poor outcome. The pathogenesis of pulmonary hypoplasia secondary to CDH is at least in part explained by lack or dysregulation of miRNAs that are known to regulate lung developmental processes. Herein, we report that intra-amniotic administration of extracellular vesicles derived from amniotic fluid stem cells (AFSC-EVs) rescues lung growth and maturation in a fetal rat model of CDH. To understand which fetal lung cells and biological pathways are affected by AFSC-EVs, we conducted whole lung single nucleus RNA-sequencing. We discovered that CDH lungs have a multilineage inflammatory signature with macrophage enrichment, and confirmed these findings in autopsy samples of lungs from human fetuses with CDH. Transcriptomic analysis of CDH fetal rat lungs also showed that AFSC-EV treatment reduced macrophage density and inflammation to normal levels. Analyzing the miRNAs contained in the AFSC-EV cargo with validated mRNA targets, we found that the downregulated genes in AFSC-EV treated CDH lungs were involved in inflammatory response and immune system processes. This study reports a single cell atlas of normal and hypoplastic CDH fetal rat lungs and provides evidence that AFSC-EVs restore lung development by addressing multiple pathophysiological aspects of CDH. One Sentence SummaryAmniotic fluid stem cell extracellular vesicle treatment for fetal lung macrophage modulation

developmental biology↗