Biology subjects

Simon, S. A.

Publications and source records attributed to Simon, S. A..

6 recordsLinked to original sources

bioRxiv2024

Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing

Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous approaches can probe the activity of given microbes in enrichment cultures, no single technique can render simultaneous data on both metabolic capacities and mobile genetic elements. Here, we apply long-read sequencing to monitor the incorporation of non-canonical bases in genome-resolved metagenomic datasets and elucidate the replication patterns of both bacteria and phages. This technology enables the simultaneous reconstruction of both prokaryotic and viral genomes (alongside genomics downstream analyses like metabolic predictions), in addition to providing information regarding their replication in enrichment cultures. By spiking the base analog 5-bromo-2-deoxyuridine (BrdU) into activated sludge microcosms, we determined that 114 of the 118 high-quality genomes recovered were actively replicating in enrichment cultures from activated sludge and identified both slow (low BrdU incorporation and change in abundance) and rapidly replicating organisms (high BrdU incorporation and change in abundance). Some of the genomes detected exhibited regions rich in BrdU that were predicted to represent prophages in their lytic cycle. Ultimately, this novel means of monitoring the replication responses of microbes, and deciphering their genomes and active mobile genetic elements will advance and empower strategies aimed at isolating previously uncultivated microbes in pure culture.

microbiology↗

bioRxiv2023

An Alzheimer's disease risk variant in TTC3 modifies the actin cytoskeleton organization and the PI3K-Akt signaling pathway in iPSC-derived forebrain neurons

A missense variant in the tetratricopeptide repeat domain 3 (TTC3) gene (rs377155188, p.S1038C, NM_003316.4:c.3113C>G) was found to segregate with disease in a multigenerational family with late onset Alzheimers disease. This variant was introduced into induced pluripotent stem cells (iPSCs) derived from a cognitively intact individual using CRISPR genome editing and the resulting isogenic pair of iPSC lines were differentiated into cortical neurons. Transcriptome analysis showed an enrichment for genes involved in axon guidance, regulation of actin cytoskeleton, and GABAergic synapse. Functional analysis showed that the TTC3 p.S1038C iPSC-derived neuronal progenitor cells had altered 3D morphology and increased migration, while the corresponding neurons had longer neurites, increased branch points, and altered expression levels of synaptic proteins. Pharmacological treatment with small molecules that target the actin cytoskeleton could revert many of these cellular phenotypes, suggesting a central role for actin in mediating the cellular phenotypes associated with the TTC3 p.S1038C variant. HighlightsO_LIThe AD risk variant TTC3 p.S1038C reduces the expression levels of TTC3 C_LIO_LIThe variant modifies the expression of AD specific genes BACE1, INPP5F, and UNC5C C_LIO_LINeurons with the variant are enriched for genes in the PI3K-Akt pathway C_LIO_LIiPSC-derived neurons with the alteration have increased neurite length and branching C_LIO_LIThe variant interferes with actin cytoskeleton and is ameliorated by Cytochalasin D C_LI

genetics↗

bioRxiv2023

Dancing the Nanopore limbo - Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction

BackgroundWhile genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing has increasingly been used in microbial metagenomics as long reads greatly improve the assembly quality of MAGs, the recommended DNA quantity usually exceeds the recoverable amount of DNA of environmental samples. Here, we evaluated lower-than-recommended DNA quantities for Nanopore library preparation by determining sequencing quality, community composition, assembly quality and recovery of MAGs. ResultsWe generated 27 Nanopore metagenomes using the commercially available ZYMO mock community and varied the amount of input DNA from 1000 ng (the recommended minimum) down to 1 ng in eight steps. The quality of the generated reads remained stable across all input levels. The read mapping accuracy, which reflects how well the reads match a known reference genome, was consistently high across all libraries. The relative abundance of the species in the metagenomes was stable down to input levels of 50 ng. High-quality MAGs (> 95% completeness, [≤] 5% contamination) could be recovered from metagenomes down to 35 ng of input material. When combined with publicly available Illumina reads for the mock community, Nanopore reads from input quantities as low as 1 ng improved the quality of hybrid assemblies. ConclusionOur results show that the recommended DNA amount for Nanopore library preparation can be substantially reduced without any adverse effects to genome recovery and still bolster hybrid assemblies when combined with short-read data. We posit that the results presented herein will enable studies to improve genome recovery from low-biomass environments, enhancing microbiome understanding.

microbiology↗

bioRxiv2023

Virus-host dynamics in archaeal groundwater biofilms and the associated bacterial community composition

Lytic viruses can be prevalent in deep groundwater, yet their spatial and temporal distribution in such an ecosystem remains unexplored. Here, we tackle this gap of knowledge by studying viral infections in individual, archaea-dominated biofilm flocks sampled from deep anoxic groundwater over a period of three years. Using virusFISH whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections between the years 2019 and 2022. Based on various fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the virus-host dynamics of Ca. Altiarchaeum hamiconexum and its abundant virus Altivir_l_MSI described herein represent a suitable model system for studying deep biosphere virus-host interactions in future research endeavors.

microbiology↗

bioRxiv2018

Oral thermosensing by murine trigeminal neurons:modulation by capsaicin, menthol, and mustard oil

When consumed with foods, mint, mustard and chili peppers generate pronounced oral thermosensations. Here we recorded responses in mouse trigeminal ganglion neurons to investigate interactions between thermal sensing and the active ingredients of these plants -- menthol, allyl isothiocyanate (AITC), and capsaicin, respectively -- at concentrations found in foods and commercial hygiene products. We carried out in vivo confocal calcium imaging of trigeminal ganglia in which neurons express GCaMP3 or GCAMP6s and recorded their responses to oral stimulation with thermal and the above chemesthetic stimuli. In the V3 (oral sensory) region of the ganglion, thermoreceptive neurons accounted for [~]10% of imaged neurons. We categorized them into 3 distinct classes: cool-responsive and warm-responsive thermosensors, and nociceptors (responsive only to temperatures [≥]43-45{degrees}). Menthol, AITC, and capsaicin also elicited robust calcium responses that differed markedly in their latencies and durations. Most of the neurons that responded to these chemesthetic stimuli were also thermosensitive. Capsaicin and AITC increased the numbers of warm-responding neurons and shifted the nociceptor threshold to lower temperatures. Menthol attenuated the responses in all classes of thermoreceptors. Our data show that while individual neurons may respond to a narrow temperature range (or even bimodally), taken collectively, the population is able to report on graded changes of temperature. Our findings also substantiate an explanation for the thermal sensations experienced when one consumes pungent spices or mint.\n\nKey points summaryO_LIOrosensory thermal trigeminal afferent neurons respond to cool, warm, and nociceptive hot temperatures with the majority activated in the cool range.\nC_LIO_LIMany of these thermosensitive trigeminal orosensory afferent neurons also respond to capsaicin, menthol and/or mustard oil (allyl isothiocyanate, AITC) at concentrations found in foods and spices.\nC_LIO_LIThere is significant but incomplete overlap between afferent trigeminal neurons that respond to heat and to the above chemesthetic compounds.\nC_LIO_LICapsaicin sensitizes warm trigeminal thermoreceptors and orosensory nociceptors; menthol attenuates cool thermoresponses.\nC_LI

neuroscience↗

bioRxiv2018

Sucrose Intensity coding and decision-making in taste cortices

Sucroses sweet intensity is one attribute contributing to the overconsumption of high-energy palatable foods. However, it is not known how sucrose intensity is encoded and used to make perceptual decisions by neurons in taste-sensitive cortices. We trained rats in a sucrose intensity discrimination task and found that sucrose evoked a widespread response in neurons recorded in posterior-Insula (pIC), anterior-Insula (aIC), and Orbitofrontal cortex (OFC). Remarkably, only a few Intensity-selective neurons conveyed the most information about sucroses intensity, indicating that for sweetness the gustatory system used a compact and distributed code. Sucrose intensity was encoded in both firing-rates and spike-timing. The pIC, aIC, and OFC neurons tracked movement direction, with OFC neurons yielding the most robust response. aIC and OFC neurons encoded the subjects choices, whereas all three regions tracked reward omission. Overall, these multimodal areas provide a neural representation of perceived sucrose intensity, and of task-related information underlying perceptual decision-making.

neuroscience↗