Biology subjects

Mazur, A.

Publications and source records attributed to Mazur, A..

10 recordsLinked to original sources

bioRxiv2024

Properties of DNA in concentrated aqueous solutions of LiCl suggest transition to C-DNA

C-DNA represents a canonical DNA form related to B-DNA. While C-DNA is known to exist in air-dried fibers, its occurrence in aqueous solutions remains subject to debate. In fibers, the transition from B- to C-DNA is promoted by reduced hydration in the presence of certain monovalent cations (most notably Li+), and this process is generally associated with an increase in the helical twist. To understand if the B-to-C transition can occur in liquid media in principle, we analyzed properties of several circular DNA substrates in aqueous solutions with varying concentrations of LiCl (0.1-8 M). To this end, we estimated changes in the helical twist directly from circular dichroism (CD) spectra of a large supercoiled plasmid and, in parallel, assayed conformational changes in DNA minicircles by atomic force microscopy (AFM). We found that the helical twist increased continuously over the entire range of tested LiCl concentrations, without being subject to saturation even at 8 M LiCl. The overall increase in the helical twist was compatible with the B-to-C transition occurring in solution at a concentration of LiCl of about 8 M, suggesting that C-DNA should be stable above this level.

biophysics↗

bioRxiv2024

Abnormal morphology and synaptogenic signaling in astrocytes following prenatal opioid exposure

In recent decades, there has been a dramatic rise in the rates of children being born after in utero exposure to drugs of abuse, particularly opioids. Opioids have been shown to have detrimental effects on neurons and glia in the central nervous system (CNS), but the impact of prenatal opioid exposure (POE) on still-developing synaptic circuitry is largely unknown. Astrocytes exert a strong influence on synaptic development, secreting factors that both promote and inhibit synapse formation and neuronal maturation in the developing CNS. Here, we investigated the effects of the partial {micro}-opioid receptor agonist, buprenorphine, on astrocyte synaptogenic signaling and morphological development in cortical cell culture. Acute buprenorphine treatment had no effect on excitatory synapse number in astrocyte-free neuron cultures. In conditions where neurons shared culture media with astrocytes, buprenorphine attenuated the synaptogenic capabilities of astrocyte-secreted factors. Neurons cultured from drug-naive mice showed no change in synapses when treated with factors secreted by astrocytes from POE mice. However, this same treatment was synaptogenic when applied to neurons from POE mice, suggestive of a complex neuroadaptive response that maintains synaptogenic pathways in the face of impaired astrocyte signaling. In addition to promoting morphological and connectivity changes in neurons, POE exerted a strong influence on astrocyte development, disrupting their structural maturation and promoting the accumulation of lipid droplets (LD), suggestive of a maladaptive stress response in the developing nervous system.

neuroscience↗

bioRxiv2023

Dynamic molecular mechanism of the nuclear pore complex permeability barrier

Nuclear pore complexes (NPCs) mediate nucleocytoplasmic transport of specific macromolecules while impeding the exchange of unsolicited material. However, key aspects of this gating mechanism remain controversial. To address this issue, we determined the nanoscopic behavior of the permeability barrier directly within yeast S. cerevisiae NPCs at transport-relevant timescales. We show that the large intrinsically disordered domains of phenylalanine-glycine repeat nucleoporins (FG Nups) exhibit highly dynamic fluctuations to create transient voids in the permeability barrier that continuously shape-shift and reseal, resembling a radial polymer brush. Together with cargo-carrying transport factors the FG domains form a feature called the central plug, which is also highly dynamic. Remarkably, NPC mutants with longer FG domains show interweaving meshwork-like behavior that attenuates nucleocytoplasmic transport in vivo. Importantly, the bona fide nanoscale NPC behaviors and morphologies are not recapitulated by in vitro FG domain hydrogels. NPCs also exclude self-assembling FG domain condensates in vivo, thereby indicating that the permeability barrier is not generated by a self-assembling phase condensate, but rather is largely a polymer brush, organized by the NPC scaffold, whose dynamic gating selectivity is strongly enhanced by the presence of transport factors.

biophysics↗

bioRxiv2022

Epigenetic variations are landmarks of freshwater adaptation in threespine sticklebacks

For evolutionary biology, the phenotypic consequences of epigenetic variations and their potential contribution to adaptation and diversification are pressing issues. Marine and freshwater sticklebacks represent an ideal model for studying both genetic and epigenetic components of phenotypic plasticity that allow fish to inhabit water with different salinity. Here, we applied single-cell genomics (scRNA-seq and scATAC-seq) and whole-genome bisulfite sequencing to characterize intercellular variability in transcription, the abundance of open chromatin regions, and CpG methylation level in gills of marine and freshwater stickleback morphs. We found little difference in overall transcriptional variance between the morphs but observed significant changes in chromatin openness variance. In addition, genomic divergence islands (DIs) coincided with regions of increased methylation entropy in freshwater fish. Moreover, analysis of transcription factor binding sites within DIs revealed that [C]TCF motifs around marker SNPs were significantly enriched within the region. Altogether, our data show that increased epigenetic variance accompanies the adaptation of marine sticklebacks to freshwater.

evolutionary biology↗

bioRxiv2021

Astrocyte-derived thrombospondin induces cortical synaptogenesis in a sex-specific manner.

The regulation of synaptic connectivity in the brain is vital to proper functioning and development of the central nervous system (CNS). Formation of neural networks in the CNS has been shown to be heavily influenced by astrocytes, which secrete factors, including thrombospondin (TSP) family proteins, that promote synaptogenesis. However, whether this process is different between males and females has not been thoroughly investigated. In this study, we found that cortical neurons purified from newborn male rats showed a significantly more robust synaptogenic response compared to female-derived cells when exposed to factors secreted from astrocytes. This difference was driven largely by the neuronal response to TSP2, which increased synapses in male neurons while showing no effect on female neurons. Blockade of endogenous 17{beta}-estradiol production with letrozole normalized the TSP response between male and female cells, indicating a level of regulation by estrogen signaling. Our results suggest that TSP-induced synaptogenesis is critical for the development of male but not female cortical synapses, contributing to sex differences in astrocyte-mediated synaptic connectivity.

neuroscience↗

bioRxiv2020

Alterations in excitatory and inhibitory synaptic development within the mesolimbic dopamine pathway in a mouse model of prenatal drug exposure

The rise in rates of opioid abuse in recent years has led to an increase in the incidence of neonatal abstinence syndrome (NAS). Despite having a greater understanding of NAS and its symptoms, there still remains a lack of information surrounding the long-term effects of prenatal exposure to drugs of abuse on neurological development. One potential outcome of prenatal drug exposure that has been increasingly explored is disruption in normal synaptogenesis within the central nervous system. Both opioids and gabapentin, an antiepileptic drug commonly co-abused by opioid abuse disorder patients, have been shown to interfere with the normal functioning of astrocytes, non-neuronal glial cells known to serve many functions, including regulation of synaptic development. The goal of this study was to investigate the effects of prenatal drug exposure on synaptogenesis within brain regions associated with the mesolimbic dopamine pathway, the primary reward pathway within the brain associated with drug abuse and addiction, in a pregnant mouse model. Immunohistochemistry (IHC) and confocal fluorescence microscopy imaging studies on the brains of postnatal day 21 (P21) mouse pups revealed a significant increase in the mean number of excitatory synapses within the anterior cingulate cortex (ACC), nucleus accumbens (NAc), and prefrontal cortex (PFC) in mice that were prenatally exposed to either the opioid drug buprenorphine or gabapentin. These studies also revealed a significant decrease in the mean number of inhibitory synapses within the NAc and PFC of mice treated with buprenorphine. This observed net increase in excitatory signaling capability within the developing mesolimbic dopamine pathway suggests that exposure to drugs of abuse in utero can trigger maladaptive neuronal connectivity that persists beyond the earliest stages of life.

neuroscience↗

bioRxiv2020

Kaiso regulates DNA methylation homeostasis

Gain and loss of DNA methylation in cells is a dynamic process that tends to achieve an equilibrium. Many factors are involved in maintaining the balance between DNA methylation and demethylation. Previously, it was shown that methyl-DNA protein Kaiso may attract NcoR, SMRT repressive complexes affecting histone modifications. On the other hand, the deficiency of Kaiso resulted in slightly reduced methylation of ICR in H19/Igf2 locus and Oct4 promoter in mouse embryonic fibroblasts. However, nothing is known whether Kaiso may attract DNA methyltransferase to influence DNA methylation level. The main idea of this work is that Kaiso may lead to DNA hypermethylation attracting de novo DNA methyltransferases. We demonstrated that Kaiso regulates TRIM25 promoter methylation. It can form a complex with DNMT3b. BTB/POZ domain of Kaiso and ADD domain of DNA methyltransferase are essential for complex formation. Thus, Kaiso can affect DNA methylation.

molecular biology↗

bioRxiv2020

Insights into glycan import by a prominent gut symbiont

In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a "pedal bin" transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the {beta}2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to [~]2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism.

microbiology↗

bioRxiv2019

A draft genome sequence of the miniature parasitoid wasp, Megaphragma amalphitanum

Body size reduction, also known as miniaturization, is an important evolutionary process that affects a number of physiological and phenotypic traits and helps animals to conquer new ecological niches. However, this process is poorly understood at the molecular level. Here, we report genomic and transcriptomic features of arguably the smallest known insect - the parasitoid wasp, Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae). In contrast to expectations, we find that the genome and transcriptome sizes of this parasitoid wasp are comparable to other members of the Chalcidoidea superfamily. Moreover, the gene content of M. amalphitanum compared to other chalcid wasps is remarkably conserved. Among the very rare cases of apparent gene loss is centrosomin, which encodes an important centrosome component; the absence of this protein might be related to the large number of anucleate neurons in M. amalphitanum. Intriguingly, we also observed significant changes in M. amalphitanum transposable element dynamics over time, whereby an initial burst was followed by suppression of activity, possibly due to a recent reinforcement of the genome defense machinery. Thus, while the M. amalphitanum genomic data reveal certain features that may be linked to the unusual biological properties of this organism, miniaturization is not associated with a large decrease in genome complexity.

genomics↗

bioRxiv2018

Enzyme Immunoassays May Be Inaccurate: Familiar Correlates of Male Testosterone (T) Replicate in Britons when T is Measured by Mass Spectrometry but Do Not Replicate in Americans When T is Measured by Enzyme Immunoassay

Several correlations have been reported between mens testosterone (T) and other characteristics, e.g., T declines during the day, declines with obesity, and declines with advancing age. We asked if these relationships hold in older men when T is assayed from saliva. Here seven familiar correlations are tested among older American men, their salivary T measured by enzyme immunoassay (EIA). Some correlations can also be tested among older British men, their salivary T assayed by liquid chromatography-tandem mass spectroscopy (LC-MS/MS), a technique noted for its specificity. Most of our attempts at replication failed in the American data but succeeded in the British data. We conclude that failure to replicate in Americans is likely due to inaccuracy of EIA values for T, and that most T correlations hold true in older men when salivary T is accurately measured by LC-MS/MS.

physiology↗