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Chatterjee, S.

Publications and source records attributed to Chatterjee, S..

At least 91 records · Page 5Linked to original sources

Controllable multi-halogenation of a non-native substrate by SyrB2 iron halogenase

Geminal, multi-halogenated functional groups are widespread in natural products and pharmaceuticals, yet no synthetic methodologies exist that enable selective multi-halogenation of unactivated C-H bonds. Biocatalysts are powerful tools for late-stage C-H functionalization, as they operate with high degrees of regio-, chemo-, and stereoselectivity. 2-oxoglutarate (2OG)-dependent non-heme iron halogenases chlorinate and brominate aliphatic C-H bonds offering a solution for achieving these challenging transformations. Here, we describe the ability of a non-heme iron halogenase, SyrB2, to controllably halogenate non-native substrate alpha-aminobutyric acid (Aba) to yield mono-chlorinated, di-chlorinated, and tri-chlorinated products. These chemoselective outcomes are achieved by controlling the loading of 2OG cofactor and SyrB2 biocatalyst. By using a ferredoxin-based biological reductant for electron transfer to the catalytic center of SyrB2, we demonstrate order-of-magnitude enhancement in the yield of tri-chlorinated product that were previously inaccessible using any single halogenase enzyme. We also apply these strategies to broaden SyrB2s reactivity scope to include multi-bromination and demonstrate chemoenzymatic conversion of the ethyl side chain in Aba to an ethylyne functional group. We show how steric hindrance induced by the successive addition of halogen atoms on Abas C4 carbon dictates the degree of multi-halogenation by hampering C3-C4 bond rotation within SyrB2s catalytic pocket. Overall, our work showcases the synthetic potential of iron halogenases to facilitate multi-C-H functionalization chemistry.

biochemistry↗

Isolation and Characterization of a Halomonas Species for Non-Axenic Growth-Associated Production of Bio-Polyesters from Sustainable Feedstocks

Biodegradable plastics are urgently needed to replace petroleum-derived polymeric materials and prevent their accumulation in the environment. To this end, we isolated and characterized a halophilic and alkaliphilic bacterium from the Great Salt Lake in Utah. The isolate was identified as a Halomonas species and designated "CUBES01". Full-genome sequencing and genomic reconstruction revealed the unique genetic traits and metabolic capabilities of the strain, including the common polyhydroxyalkanoate (PHA) biosynthesis pathway. Fluorescence staining identified intracellular polyester granules that accumulated predominantly during the strains exponential growth, a feature rarely found among natural PHA producers. CUBES01 was found to metabolize a range of renewable carbon-feedstocks, including glucosamine and acetyl-glucosamine, as well as sucrose, glucose, fructose, and further also glycerol, propionate, and acetate. Depending on the substrate, the strain accumulated up to [~]60% of its biomass [dry w/w] in poly(3-hydroxbutyrate), while reaching a doubling time of 1.7 h at 30{whitebullet}C and an optimum osmolarity of 1 M sodium chloride and a pH of 8.8. The physiological preferences of the strain may not only enable long-term aseptic cultivation but can also facilitate the release of intracellular products through osmolysis. Development of a minimal medium also allowed the estimation of maximum PHB production rates, which were projected to exceed 5 gPHB/h. Finally, also the genetic tractability of the strain was assessed in conjugation experiments: two orthogonal plasmid-vectors were stable in the heterologous host, thereby opening the possibility of genetic engineering through the introduction of foreign genes. IMPORTANCEThe urgent need for renewable replacements for synthetic materials may be addressed through microbial biotechnology. To simplify the large-scale implementation of such bio-processes, robust cell factories that can utilize sustainable and widely available feedstocks are pivotal. To this end, non-axenic growth-associated production could reduce operational costs and enhance biomass productivity, thereby improving commercial competitiveness. Another major cost factor is downstream processing. Especially in the case of intracellular products, such as bio-polyesters. Simplified cell-lysis strategies could also further improve economic viability.

microbiology↗

Cross-correlation increases sampling in diffusion-based super-resolution optical fluctuation imaging

Correlation signal processing of optical three-dimensional (x, y, t) data can produce super-resolution images. The second order cross-correlation function XC2 has been documented to produce super-resolution imaging with static and blinking emitters but not for diffusing emitters. Here, we both analytically and numerically demonstrate cross-correlation analysis for diffusing particles. We then expand our fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) analysis to use cross-correlation as a post-processing computational technique to extract both dynamic and structural information of particle diffusion in nanoscale structures simultaneously. We further show how this method increases sampling rates and reduces aliasing for spatial information in both simulated and experimental data. Our work demonstrates how fcsSOFI with cross-correlation can be a powerful signal-processing tool to resolve the nanoscale dynamics and structure in samples relevant to biological and soft materials. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/587586v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@12eb1beorg.highwire.dtl.DTLVardef@975a95org.highwire.dtl.DTLVardef@bc1589org.highwire.dtl.DTLVardef@29d5bf_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

Group Heteroscedasticity - A Silent Saboteur of Power and False Discovery in RNA-Seq Differential Expression

Despite the availability of several high-profile, state-of-the-art methods, analyzing bulk RNA-Seq data continues to face significant challenges. Evidence from recent studies has highlighted that popular differential expression (DE) tools, such as edgeR and DESeq2, are susceptible to an alarmingly high false discovery rate (FDR). These studies suggest that the FDR inflation observed in these models could be attributed to issues such as violations of parametric assumptions or an inability to effectively handle outliers in the data. Here, we argue that group heteroscedasticity can also contribute to this elevated FDR, a phenomenon largely overlooked by the research community. We introduce a novel statistical model, Robseq, designed for effective per-feature modeling in differential analysis, particularly when the assumption of group homoscedasticity is unmet. Robseq utilizes well-established statistical machinery from the robust statistics literature, including M-estimators to robustly estimate gene expression level changes and Huber-Cameron variance estimators to calculate robust standard errors in heteroscedastic settings. Additionally, it incorporates a degrees of freedom adjustment for the Welch t-statistic, based on Bell-McCaffreys recommendation, for inferential purposes, effectively addressing the problem of FDR inflation in RNA-Seq differential expression. Through detailed simulations and comprehensive benchmarking, we show that Robseq successfully maintains the false discovery and type-I error rates at nominal levels while retaining high statistical power compared to well-known DE methods. Analysis of population-level RNA-Seq data further demonstrates that Robseq is capable of identifying biologically significant signals and pathways implicated in complex human diseases that otherwise cannot be revealed by published methods. The implementation of Robseq is publicly available as an R package at https://github.com/schatterjee30/Robseq.

bioinformatics↗

Remodeling Ca2+ dynamics by targeting a promising E-box containing G-quadruplex at ORAI1 promoter in triple-negative breast cancer.

ORAI1 is an intrinsic component of store-operated calcium entry (SOCE) that strictly regulates Ca2+ influx in most non-excitable cells. ORAI1 has been extensively studied to have been overexpressed in various cancer phenotypes, and its signal transduction has been associated with oncotherapy resistance. There is extensive proteomic interaction of ORAI1 with other channels and effectors, resulting in various altered phenotypes. However, the transcription regulation of this gene is not well understood. We have found a putative G-quadruplex (G4) motif, ORAI1-Pu, in the upstream promoter region of the gene, having regulatory functions. High-resolution 3-D NMR structure elucidation suggests that ORAI1-Pu is a stable parallel-stranded G4, having an unusual 8-nt loop imparting dynamics without affecting the structural stability. The protruded loop further houses an E-box motif that provides a docking site for transcription factors like Zeb1. The G4 structure was also endogenously observed using Chromatin Immunoprecipitation (ChIP) with anti-G4 antibody (BG4) in the MDA-MB-231 cell line overexpressing ORAI1. Ligand-mediated stabilization suggested that the stabilized G4 represses transcription in cancer cell line MDA-MB-231. Downregulation of transcription further cascaded down to a decrease in Ca2+ entry by the SOCE pathway, as observed by Fura-2 confocal Ca2+ imaging.

biochemistry↗

Uncovering nick DNA binding by LIG1 at the single-molecule level

DNA ligases repair the strand breaks are made continually and naturally throughout the genome, if left unrepaired and allowed to persist, they can lead to genome instability in the forms of lethal double-strand (ds) breaks, deletions, and duplications. DNA ligase 1 (LIG1) joins Okazaki fragments during the replication machinery and seals nicks at the end of most DNA repair pathways. Yet, how LIG1 recognizes its target substrate is entirely missing. Here, we uncover the dynamics of nick DNA binding by LIG1 at the single-molecule level. Our findings reveal that LIG1 binds to dsDNA both specifically and non-specifically and exhibits diffusive behavior to form a stable complex at the nick. Furthermore, by comparing with the LIG1 C-terminal protein, we demonstrate that the N-terminal non-catalytic region promotes binding enriched at nick sites and facilitates an efficient nick search process by promoting 1D diffusion along the DNA. Our findings provide a novel single-molecule insight into the nick binding by LIG1, which is critical to repair broken phosphodiester bonds in the DNA backbone to maintain genome integrity.

biochemistry↗

Distinct and Asymmetric Neuronal Responses to Pitch- and Roll-Axis Vestibular Stimulation in larval zebrafish

SO_SCPLOWUMMARYC_SCPLOWThe vestibular apparatus plays a pivotal role in maintaining postural equilibrium and processing movement signals, underscoring its importance in studying certain neurological disorders. Here, we present a rotating light-sheet microscope, enabling brain-wide functional recordings during dynamic vestibular stimulation along the pitch axes in addition to the roll axis in head-restrained zebrafish larvae. The system incorporates a double galvanometer mirror configuration, is amenable to 3D printing, and enhances scanning efficiency. Employing this apparatus, we have successfully conducted the first comprehensive mapping of zebrafish brain responses to dynamic pitch-tilt vestibular stimulation. Through Fourier and regression analyses, we report an asymmetry in neuronal recruitment during nose-up versus nose-down pitch tilts within critical regions, including the cerebellum, oculomotor nucleus, caudal hindbrain, and vestibular nucleus, highlighting physiological adaptations to downward motion. We identified specific brain regions, notably the cerebellum and medial-rostral rhombencephalon, that respond to roll-but not pitch-tilt vestibular stimuli. Furthermore, we have identified a transgenic line that closely correlates with our functional mappings and demonstrates a significant response to vestibular stimulation. The elucidation of brain-wide neuronal circuits involved in vestibular processing establishes a foundational framework for subsequent detailed investigations into the molecular and genetic mechanisms underlying postural control and motion perception.

neuroscience↗

Conformational switch of a peptide provides a novel strategy to design peptide loaded porous organic polymer for Pyroptosis pathway mediated cancer therapy

While peptide-based drug development is now extensively explored, this strategy does have limitations, which come from their rapid excretion from the body (or shorter half-life in the body), and vulnerability to protease-mediated degradation. To overcome these limitations, here we introduce a novel strategy for the development of a peptide-based anticancer agent using the conformation switch property of a chameleon sequence stretch, which we derived from a mycobacterium secretory protein, MPT63. Then, we loaded this peptide in a new porous organic polymer (PG-DFC-POP) synthesized using phloroglucinol and acresolderivative via condensation reaction for delivering the peptide selectively to the cancer cells. Employing an ensemble and single molecule approaches, we demonstrate that this peptide undergoes a disordered to alpha-helical conformational transition, which is triggered by a low pH environment inside cancer cells. This adopted alpha-helical conformation results in the formation of proteolysis-resistant oligomers, which show efficient membrane pore-forming activity selectively for negatively charged phospholipid which is accumulated in cancer cell membrane. Our in vitro and in vivo experimental results demonstrate that the peptide-loaded nanomaterial PG-DFC-POP-PEP 1 exhibits significant cytotoxicity in cancer cells, leading to cell death through the Pyroptosis pathway that is confirmed by monitoring numerous associated events starting from lysosome membrane damage to GSDMD-induced cell membrane demolition. We believe that this novel conformational switch-based drug design strategy has great potential in endogenous environment-responsive cancer therapy and the development of future drug candidates to mitigate cancers.

biochemistry↗

Antibiotic Bacteria Interaction: Dataset and Benchmarking.

Withdrawal StatementThe authors have withdrawn their manuscript owing to inability to reproduce the results. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

bioengineering↗

In Silico designed cell-penetrating anti-cancer peptide specifically inhibits VEGF-A expression

Vascular Endothelial Growth Factor-A (VEGF-A), a pluripotent cytokine and angiogenic growth factor mediates the switch to an angiogenic phenotype in cancer cells. The interaction of VEGF-A protein with the VEGF receptors (VEGFR-1and VEGFR-2) starts downstream effect that promotes angiogenesis by mediating migration and increasing the permeability of endothelial cells. A cis-regulatory elements consisting of a polypurine/polypyrimidine (pPu/pPy) tract in the proximal 36-bp region (-85 to -50), can participate in the formation of a stable higher order G-quadruplex structure (G4) which is essential for VEGF promoter activity. During cancer progression the VEGF-A G4 succumbs to cellular pressure and fails to maintain the stable structure. This shifts the balance to form duplex structure thereby increasing the rate of transcription. Earlier research has tried to develop small-molecule ligands to target and stabilize G4, however they either lack specificity or non-toxicity. Peptide on the other hand are very less studied. Here we used bioinformatics in-silico tool to develop peptides which can successfully bind and stabilize the VEGF-A G4 while reducing its gene expression. This further alters the expression fate of the VEGF-A signalling cascade and prevents angiogenesis in cancer cells. We used high resolution Nuclear magnetic resonance and molecular dynamics simulation to map the chemistry of the interaction while the qPCR and western blot allowed us to check the expression pattern of the molecules of VEGF-A signalling cascade. In this investigation, we navigate the complex interplay between peptides and quadruplex structures, unravelling valuable insights that can enhance the crafting of pharmacophores directed at the dynamic quadruplex structure. The outcomes of our study are promising, paving the way for progress in the realms of research, characterization, and optimization of peptides binding to G-quadruplexes, with potential implications for therapeutic applications.

biophysics↗

Pathways in the brain, heart, and lung influenced by SARS-CoV-2 NSP6 and SARS-CoV-2 regulated miRNAs: an in silico study hinting cancer incidence

The influence of SARS-CoV-2 non-structural protein in the hosts tissue-specific complexities remains a mystery and needs more in-depth attention because of COVID-19 recurrence and long COVID. Here we investigated the influence of SARS-CoV-2 transmembrane protein NSP6 (Non-structural protein 6) in three major organs - the brain, heart, and lung in silico. To elucidate the interplay between NSP6 and host proteins, we analyzed the protein-protein interaction network of proteins regulated after SARS-CoV-2 infection and that are interacting with NSP6 interacting proteins. Pathway enrichment analyses provided global insights into biological pathways governed by differentially regulated genes in the three tissues after COVID-19 infection. Many drugs targeting hub genes of tissue-specific protein interactome were found that could be candidates for COVID-19 management. MiRNA-gene network for the tissue-specific regulated proteins was also deduced and comparing gene list targeted by SARS-CoV-2 regulated miRNAs, we found three and two common genes in the brain and lung respectively. Among the five common proteins revealed as potential therapeutic targets across the three tissues, Galectin3 (LGALS3) that was upregulated in the heart and brain after COVID-19 infection is reported to be influencing all the ten hallmarks of cancer positively and is found in multiple cancers. COVID-19 infection also causes myocardial inflammation and heart failure (HF). HF is observed to be increasing cancer incidence. Our bioinformatics and systems study hints probable effect of COVID-19 infection in cancer incidence and warrants in-depth studies in this direction and cancer surveillance especially with the present scenario of long COVID-19 and recurrent COVID-19 infections. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/578752v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@f10223org.highwire.dtl.DTLVardef@c34b64org.highwire.dtl.DTLVardef@18aaf59org.highwire.dtl.DTLVardef@1fe0b35_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules

Changes in the gut microbiome have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a multi-cohort analysis of small molecule biosynthetic gene clusters (BGCs) in 5,306 metagenomic samples of the gut microbiome from 2,033 Inflammatory Bowel Disease (IBD) patients and 833 matched healthy subjects and identified a group of Clostridia-derived BGCs that are significantly associated with IBD. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the IBD-enriched BGCs. Using two mouse models of colitis, we show that the discovered small molecules disrupt gut permeability and exacerbate inflammation in chemically and genetically susceptible mice. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of microbiome-host interactions in the context of microbiome-associated diseases.

microbiology↗

ALTering cancer by triggering telomere replication stress through the stabilization of promoter G-quadruplex in SMARCAL1

Most of the human cancers are dependent on telomerase to extend the telomeres. But [~]10% of all cancers use a telomerase-independent, homologous recombination mediated pathway called alternative lengthening of telomeres (ALT). Due to poor prognosis, the ALT status is not being considered yet in the diagnosis of cancer. No such specific treatment is available till date for ALT cancers. ALT positive cancers are dependent on replication stress to deploy DNA repair pathways to the telomeres to execute homology recombination mediated telomere extension. SMARCAL1 (SWI/SNF related, matrix-associated, actin-dependent regulator of chromatin, subfamily A-like 1) is associated with the ALT telomeres to resolve replication stress thus providing telomere stability. Thus, the dependency on replication stress regulatory factors like SMARCAL1 made it a suitable therapeutic target for the treatment of ALT positive cancers. In this study, we found a significant downregulation of SMARCAL1 expression by stabilizing the G-quadruplex (G4) motif found in the promoter of SMARCAL1 by potent G4 stabilizers, like TMPyP4 and BRACO-19. SMARCAL1 downregulation led towards the increased localization of PML (promyelocytic leukaemia) bodies in ALT telomeres and triggered the formation of APBs (ALT-associated promyelocytic leukaemia bodies) in ALT positive cell lines, thus increasing telomere replication stress and DNA damage at genomic level. Induction of replication stress and hyper recombinogenic phenotype in ALT cells mediated by G4 stabilizing molecules already highlighted their possible application as a new therapeutic window to target ALT-positive tumors. In accordance with this, our study will also provide a valuable insight towards the development of G4 based ALT-therapeutics targeting SMARCAL1.

biochemistry↗

Ribosome Quality Control Mechanism Mitigates the Cytotoxic Impacts of Ribosome Collisions Induced by 5-Fluorouracil

Translation of aberrant or damaged mRNAs results in ribosome stalling and collisions. The Ribosome Quality Control (RQC) mechanism detects collided ribosomes and removes aberrant mRNAs and nascent peptides, thus preventing their cytotoxic effects. Conversely, excessive or unresolved ribosome collisions can induce apoptosis. 5-Fluorouracil (5FU) forms the backbone of standard-of-care chemotherapeutic regimens for several types of cancer. Although best known for its incorporation into DNA and inhibition of thymidylate synthase, a major determinant of 5FUs anticancer activity is its incorporation into RNAs. Nevertheless, the mechanism(s) underlying RNA-dependent 5FU cytotoxicity and the cellular response to its impact on RNA metabolism remain unclear. Here, we report a key role for RQC in mitigating the cytotoxic effects of 5FU-induced dysregulation of mRNA translation. We show that acute 5FU treatment results in the rapid induction of the mTOR signalling pathway, an enhanced rate of mRNA translation initiation, and increased ribosome collisions that trigger RQC. We also found that RQC deficiency, caused by the depletion of ZNF598, results in increased 5FU-induced cell death, a phenotype that is reversed by inhibition of mTOR or repression of mRNA translation initiation. Importantly, 5FU treatment enhances the expression of key RQC factors, including ZNF598 and GIGYF2, via an mTOR-dependent post-translational regulation mechanism. This acute adaptation likely mitigates the cytotoxic consequences of increased ribosome collisions upon 5FU treatment. Overall, our data indicate a heretofore unknown mTOR-dependent mechanism that augments the RQC process, mitigating the cytotoxicity of 5FU and undermining its anticancer efficacy.

cell biology↗

Microscale visualization of cellular features in adult macaque visual cortex

Expansion microscopy and light sheet imaging enable fine-scale resolution of intracellular features that comprise neural circuits. Most current techniques visualize sparsely distributed features across whole brains or densely distributed features within individual brain regions. Here, we visualize dense distributions of immunolabeled proteins across early visual cortical areas in adult macaque monkeys. This process may be combined with multiphoton or magnetic resonance imaging to produce multimodal atlases in large, gyrencephalic brains.

neuroscience↗

Gardenin A improves cognitive and motor function in A53T-α-syn mice

Oxidative stress and neuroinflammation are widespread in the Parkinsons disease (PD) brain and contribute to the synaptic degradation and dopaminergic cell loss that result in cognitive impairment and motor dysfunction. The polymethoxyflavone Gardenin A (GA) has been shown to activate the NRF2-regulated antioxidant pathway and inhibit the NFkB-dependent pro-inflammatory pathway in a Drosophila model of PD. Here, we evaluate the effects of GA on A53T alpha-synuclein overexpressing (A53TSyn) mice. A53TSyn mice were treated orally for 4 weeks with 0, 25, or 100 mg/kg GA. In the fourth week, mice underwent behavioral testing and tissue was harvested for immunohistochemical analysis of tyrosine hydroxylase (TH) and phosphorylated alpha synuclein (pSyn) expression, and quantification of synaptic, antioxidant and inflammatory gene expression. Results were compared to vehicle-treated C57BL6 mice. Treatment with 100 mg/kg GA improved associative memory and decreased abnormalities in mobility and gait in A53TSyn mice. GA treatment also reduced cortical and hippocampal levels of pSyn and attenuated the reduction in TH expression in the striatum. Additionally, GA increased cortical expression of NRF2-regulated antioxidant genes and decreased expression of NFkB-dependent pro-inflammatory genes. GA was readily detectable in the brains of treated mice and modulated the lipid profile in the deep gray brain tissue of those animals. While the beneficial effects of GA on cognitive deficits, motor dysfunction and PD pathology are promising, future studies are needed to further fully elucidate the mechanism of action of GA, optimizing dosing and confirm these effects in other PD models. Significance StatementThe polymethoxyflavone Gardenin A can improve cognitive and motor function and attenuate both increases in phosphorylated alpha synuclein and reductions in tyrosine hydroxylase expression in A53T alpha synuclein overexpressing mice. These effects may be related to activation of the NRF2-regulated antioxidant response and downregulation of NFkB-dependent inflammatory response by Gardenin A in treated animals. The study also showed excellent brain bioavailability of Gardenin A and modifications of the lipid profile, possibly through interactions between Gardenin A with the lipid bilayer, following oral administration. The study confirms neuroprotective activity of Gardenin A previously reported in toxin induced Drosophila model of Parkinsons disease.

neuroscience↗

Extremely oligotrophic and complex organic compounds degrading microaerobic bacteria from Arabian Sea oxygen minimum zone sediments

Sediments underlying marine hypoxic zones are huge sinks of unreacted complex organic matter, where despite acute O2-limitation obligately aerobic bacteria thrive, and steady depletion of organic carbon takes place within a few meters below the seafloor. However, little knowledge exists about the sustenance and complex carbon degradation potentials of aerobic chemoorganotrophs in these sulfidic ecosystems. We isolated and characterized a number of aerobic bacterial chemoorganoheterotrophs from across a [~]3 m sediment horizon underlying the perennial hypoxic zone of the eastern Arabian Sea. High levels of sequence correspondence between the isolates genomes and the habitats metagenomes and metatranscriptomes illustrated that the strains were widespread and active across the sediment-cores explored. The isolates catabolized several complex organic compounds of marine and terrestrial origins in the presence of high or low, but not zero, O2. Some of them could also grow anaerobically on yeast extract or acetate by reducing nitrate and/or nitrite. Fermentation did not support growth, but enabled all the strains to maintain a fraction of their cell populations over prolonged anoxia. Under extreme oligotrophy, limited growth followed by protracted stationary phase was observed for all the isolates at low cell density, amid high or low, but not zero, O2 concentration. While population control and maintenance could be particularly useful for the strains survival in the critically carbon-depleted layers below the explored sediment-depths (core-bottom organic carbon: 0.5-1.0 % w/w), metagenomic data suggested that in situ anoxia could be surmounted via potential supplies of cryptic O2 from previously-reported sources such as Nitrosopumilus species.

microbiology↗

Activity-induced gene expression in the human brain

Direct electrical stimulation (eSTIM) is widely used clinically, from neurosurgical mapping to therapeutic interventions for neurological and neuropsychiatric disorders1-10. Despite over a century of application, its molecular and cellular underpinnings remain unknown. Here, using state-of-the-art single-nuclei multiomic profiling, we map changes in cell-type-specific gene expression and chromatin accessibility in vivo in the human cortex following eSTIM of neurosurgery patients. eSTIM impacts a network of cells that extends beyond excitatory neurons to include inhibitory neurons, astrocytes, oligodendrocytes and microglia. We observed an upregulation of canonical immediate-early genes (IEGs: FOS, NPAS4, EGR4) in excitatory and inhibitory neurons and induction of cytokine-related genes CCL3 and CCL4 in microglia. The cross-species conservation of this gene signature, together with our examination of a cohort of both epilepsy and cancer patients, underscores the fundamental role of these changes in stimulation-driven plasticity while controlling for disease and environmental confounds. Our study of changes in chromatin accessibility reveals a common code that involves a cell-type specific signature of transcription factor binding motifs for members of the EGR family. By addressing these previously unexplored questions about activity-induced gene expression in vivo in the human brain, our findings challenge the long-standing neuron-centric view of eSTIM, highlighting the broader role of non-neuronal cells, including microglia, in mediating the impact of brain stimulation.

neuroscience↗