Journal: Frontiers in Microbiology

Article Title: Portable nanopore-sequencing technology: Trends in development and applications

doi: 10.3389/fmicb.2023.1043967

Figure Lengend Snippet:

Article Snippet: BulkVis , An app to visualize raw squiggle data from Oxford Nanopore Technologies (ONT) bulk files , https://github.com/LooseLab/bulkVis.

Techniques: Sequencing, Variant Assay, Selection, Software

Journal: Frontiers in Microbiology

Article Title: Portable nanopore-sequencing technology: Trends in development and applications

doi: 10.3389/fmicb.2023.1043967

Figure Lengend Snippet:

Article Snippet: BulkVis , An app to visualize raw squiggle data from Oxford Nanopore Technologies (ONT) bulk files , https://github.com/LooseLab/bulkVis.

Techniques: Sequencing, Sampling, Illumina Sequencing, Scaffolding, Software, Generated

Journal: Frontiers in Microbiology

Article Title: Portable nanopore-sequencing technology: Trends in development and applications

doi: 10.3389/fmicb.2023.1043967

Figure Lengend Snippet:

Article Snippet: BulkVis , An app to visualize raw squiggle data from Oxford Nanopore Technologies (ONT) bulk files , https://github.com/LooseLab/bulkVis.

Techniques: Nanopore Sequencing, Sequencing, Methylation, Modification, Generated, Extraction

Journal: Frontiers in Microbiology

Article Title: Portable nanopore-sequencing technology: Trends in development and applications

doi: 10.3389/fmicb.2023.1043967

Figure Lengend Snippet:

Article Snippet: BulkVis , An app to visualize raw squiggle data from Oxford Nanopore Technologies (ONT) bulk files , https://github.com/LooseLab/bulkVis.

Techniques: DNA Methylation Assay, Nanopore Sequencing, Modification, Control, RNA Sequencing, Sequencing, Methylation, Bacteria

Journal: Hypertension (Dallas, Tex. : 1979)

Article Title: Neurotransmitter Switching Coupled to β-Adrenergic Signaling in Sympathetic Neurons in Prehypertensive States

doi: 10.1161/HYPERTENSIONAHA.118.10844

Figure Lengend Snippet: Rat sympathetic stellate ganglia express β 1 - and β 2 -adrenergic receptors (ARs). Using RNA sequencing, we identified the presence of β 1 AR ( Adrb1 ), β 2 AR ( Adrb2 ), and α 2A AR ( Adra2a ) mRNA transcripts ( A ) from 16-wk-old male Wistar rats (n=4) and SHR (n=4). Adrb2 expression was significantly lower in SHR ganglia compared with Wistar ( P .adj=0.00945; Salmon-DESeq2 method). There was no significant difference in the levels of mRNA for Adrb1 or Adra2a between strains or between age groups. Data points represent raw counts±SEM for each transcript ( A ). ELISAs confirmed protein expression of β 1 AR and β 2 ARs in 3.5- to 5-wk-old rat neurons (32 stellates, 16 animals/group) and 20-wk-old neurons (20 stellates, 10 animals/group); however, no statistical tests were conducted as stellates were pooled into a single sample to obtain adequate protein concentrations for the ELISA assays. In young rat stellates ( B ), the concentration of β 1 AR protein was calculated as 869.1±50.6 pg/mL (Wistar) and 114.2±23.7 pg/mL (pre-SHR). β 2 AR protein expression was calculated as 363.5±43.6 pg/mL (Wistar) and 82.2±20.0 pg/mL (pre-SHR). In adult rat stellates ( C ), β 1 AR expression was calculated as 674.1±44.6 pg/mL (Wistar) and 489.4±26.3 pg/mL (SHR). β 2 AR protein expression quantified as 353.3±11.2 pg/mL (Wistar) and 147.4±20.7 pg/mL (SHR). Data points depict mean±SEM of 3 to 4 technical replicates. β 1 AR (516±99.17 pg/mL) and β 2 AR (340±104.3 pg/mL) expression was also detected in stellate ganglia from human donors. Data points represent mean±SEM (6 replicates), from 3 pooled stellates obtained from 2 patients ( D ). Immunocytochemistry depicts β 1 AR ( E ) and β 2 AR ( F ) expression on TH (tyrosine hydroxylase)-positive neurons from 4-wk control rats. White arrows demonstrate the localization of β 2 AR on synaptic terminals.

Article Snippet: Our RNA sequencing (RNAseq) raw FastQ files are deposited in the National Center for Biotechnology Information short reads archive under Short Reads Archive number SRP132271, and our quasi-mapped data will be available under Gene Expression Omnibus accession number (GSE110197).

Techniques: RNA Sequencing, Expressing, Enzyme-linked Immunosorbent Assay, Concentration Assay, Immunocytochemistry, Control

Journal: Hypertension (Dallas, Tex. : 1979)

Article Title: Neurotransmitter Switching Coupled to β-Adrenergic Signaling in Sympathetic Neurons in Prehypertensive States

doi: 10.1161/HYPERTENSIONAHA.118.10844

Figure Lengend Snippet: The epinephrine-synthesizing enzyme PNMT (phenylethanolamine-N-methyltransferase) is present in rat and human stellate ganglia. The catecholamine synthesis pathway is outlined ( A ). RNA sequencing (RNAseq) revealed mRNA transcripts that encode the enzymes required for norepinephrine (NE) synthesis: phenylalanine hydroxylase ( Pah ), tyrosine hydroxylase ( Th ), L-DOPA decarboxylase ( Ddc ), dopamine β-hydroxylase ( Dbh ; B ). We also identified the transcript that encodes Pnmt required for the conversion of NE to epinephrine (Epi). Pah and Ddc mRNA expressions as determined by RNAseq were significantly lower in SHR neurons ( P. adj=0.0719, Pah ; 6.64×10 –15 , Ddc ; Salmon-DESeq2). Data depicts raw counts±SEM ( B ). Transcript expression was validated via quantitative real-time polymerase chain reaction (qRT-PCR) using RNA extracted from 4-wk Wistar (n=4) and pre-SHR (n=4) ganglia ( C ). For qRT-PCR analyses, genes were normalized to the housekeeping gene ( B2m ), and SHR counts were normalized to Wistar using the ΔΔC T method. There was a significant (4-fold) decrease in Pah in pre-SHR neurons ( C ; P =0.0098, unpaired 2-tailed Student t test). SHR (red bars) are depicted relative to number of counts calculated from Wistar samples ( x axis). The protein concentration for TH ( D ) was quantified in 4-wk Wistar (460.9±7.979 pg/mL), pre-SHR ganglia (89.12±11.37 pg/mL), 20-wk Wistar (406.6±31.57 pg/mL), and SHR ganglia (277.5±63.03 pg/mL). PNMT protein expression was also quantified ( E ) in 4-wk Wistar (525.7±8.69 pg/mL), pre-SHR ganglia (117±3.73 pg/mL), 20-wk Wistar (466.7±116.2 pg/mL), and SHR ganglia (362.7±70.08 pg/mL). Data represent mean±SEM (2–3 technical replicates). We confirmed the protein expression of TH (163±38.83 pg/mL) and PNMT (108.4±2.386 pg/mL) in human stellates ( F ). Data points represent mean±SEM (2–3 replicates) from 3 pooled stellates obtained from 2 patients. Where stellates were pooled to obtain adequate protein concentrations, no statistical tests were conducted.

Article Snippet: Our RNA sequencing (RNAseq) raw FastQ files are deposited in the National Center for Biotechnology Information short reads archive under Short Reads Archive number SRP132271, and our quasi-mapped data will be available under Gene Expression Omnibus accession number (GSE110197).

Techniques: RNA Sequencing, Expressing, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Protein Concentration