Loren Eiseley and the Dancing Rat: Science as Autobiography

Bushnell, Jack

doi:10.1080/08989575.1998.10815132

Cited by 13 publications

(11 citation statements)

References 27 publications

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“…To challenge RAT with real datasets, we selected relatively unexplored groundwater samples taken 12-64m below surface level from three different monitoring wells in a Dutch agricultural area, which we previously found had high microbial diversity and contain many novel taxa [38]. We performed a metagenomic analysis including quality control [44] assembly [25], and binning [27,28,45], which produced 514 MAGs. We supplied the reads, 2,770,251 contigs, and 423 medium- to high-quality MAGs (>50% completeness, <10% contamination [46]) to RAT to reconstruct taxonomic profiles of the groundwater samples, using nr as a reference database.…”

Section: Resultsmentioning

confidence: 99%

“…For quality-control, assembly, and binning, we used the ATLAS pipeline v2.4 [57]. ATLAS uses BBTools [44] to remove PCR duplicates and adapters and to trim the reads, assembles the reads using SPAdes v3.13.1 in metagenomic mode [25], and bins the contigs using MetaBAT2 v2.14 [27] and maxbin2 v2.2.7 [28], after which DASTool v.1.1.2 [45] is used to optimize MAGs resulting from the two binning approaches. We used MAGs of medium- to high-quality (>50% completeness, <10% contamination [46]) based on CheckM estimates in lineage-wf mode [43].…”

Section: Methodsmentioning

confidence: 99%

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Integration of taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes

Hauptfeld

Pappas

Iwaarden

et al. 2023

Preprint

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Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome. CAT/BAT/RAT is available at https://github.com/MGXlab/CAT. The CAT pack now also supports GTDB annotations.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Integration of taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes

Hauptfeld

Pappas

Iwaarden

et al. 2023

Preprint

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“…Triplicate “bottom” samples from sunrise and sunset were pooled and concentrated (RNA Clean and Concentrator-5, Zymo Research) into two singular samples before ribodepletion and library preparation due to low RNA extraction yields (<10 ng μL –1 ). Metatranscriptomic reads were filtered and trimmed with BBDuk (v38.67) and Sickle (v1.33) and then mapped to our MAG database at 99% identity using BBMap (v38.70) . Mapped read counts were processed in HTSeq (v0.12.4), filtered to retain transcripts with greater than 10 counts per million in at least three samples, and then normalized with trimmed mean of M-values using edgeR (v3.28.1) or a median-of-ratios factor when using DESeq2 (v1.26.0) for differential gene transcription analyses comparing sunrise vs sunset transcripts considering all metatranscriptomes ( n = 20) and also just the surficial ∼0 to 5 mm metatranscriptomes ( n = 6).…”

Section: Methodsmentioning

confidence: 99%

Methane-Oxidizing Activity Enhances Sulfamethoxazole Biotransformation in a Benthic Constructed Wetland Biomat

Vega

Scholes

Brady

et al. 2023

Environ. Sci. Technol.

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Ammonia monooxygenase and analogous oxygenase enzymes contribute to pharmaceutical biotransformation in activated sludge. In this study, we hypothesized that methane monooxygenase can enhance pharmaceutical biotransformation within the benthic, diffuse periphytic sediments (i.e., "biomat") of a shallow, open-water constructed wetland. To test this hypothesis, we combined field-scale metatranscriptomics, porewater geochemistry, and methane gas fluxes to inform microcosms targeting methane monooxygenase activity and its potential role in pharmaceutical biotransformation. In the field, sulfamethoxazole concentrations decreased within surficial biomat layers where genes encoding for the particulate methane monooxygenase (pMMO) were transcribed by a novel methanotroph classified as Methylotetracoccus. Inhibition microcosms provided independent confirmation that methane oxidation was mediated by the pMMO. In these same incubations, sulfamethoxazole biotransformation was stimulated proportional to aerobic methane-oxidizing activity and exhibited negligible removal in the absence of methane, in the presence of methane and pMMO inhibitors, and under anoxia. Nitrate reduction was similarly enhanced under aerobic methaneoxidizing conditions with rates several times faster than for canonical denitrification. Collectively, our results provide convergent in situ and laboratory evidence that methane-oxidizing activity can enhance sulfamethoxazole biotransformation, with possible implications for the combined removal of nitrogen and trace organic contaminants in wetland sediments.

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“…Among the seven EOC tissues, four were platinum-sensitive and three were platinum-resistant. All FASTQ reads were trimmed for quality control and adapters were trimmed using Bbduk (BBMap v36.59) ( 33 ) and FASTQC (v0.11.7) ( 34 ) for sequencing data. Read mapping was performed through the STAR-HTSeq workflow, i.e., STAR (v2.7.3a) ( 35 ) and HTSeq-count (v0.12.4) ( 36 ), where the reference genome (GRCh38) and annotation were aligned with the sequencing reads.…”

Section: Methodsmentioning

confidence: 99%

High ATP6V1B1 expression is associated with poor prognosis and platinum‑based chemotherapy resistance in epithelial ovarian cancer

et al. 2023

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The vacuolar ATPase H+ transporting V1 subunit B1 (ATP6V1B1) belongs to the family of ATP6Vs, which functions to transport hydrogen ions. The expression of ATP6V1B1 and associated clinicopathological features have been linked to various cancers; however, its role in epithelial ovarian cancer (EOC) has remained to be explored. The present study aimed to unveil the function, molecular mechanisms and clinical significance of ATP6V1B1 in EOC. The mRNA levels of ATP6V1 subunits A, B1 and B2 in EOC tissues were determined using data from the Gene Expression Profiling Interactive Analysis database and RNA sequencing. Protein levels of ATP6V1B1 were evaluated through immunohistochemistry staining of EOC, borderline, benign and normal epithelial tissues. The association between ATP6V1B1 expression and clinicopathological features and prognosis of patients with EOC was analyzed. Furthermore, the biological role of ATP6V1B1 in ovarian cancer cell lines was also assessed. RNA sequencing and public dataset analyses revealed elevated ATP6V1B1 mRNA levels in EOCs. High ATP6V1B1 protein levels were also observed in EOC compared with those of borderline and benign tumors and nonadjacent normal epithelial tissues. High ATP6V1B1 expression was associated with the serous cell type, advanced International Federation of Gynecology and Obstetrics stage, high/advanced tumor grade, elevated serum cancer antigen 125 levels and platinum resistance (P<0.001, P<0.001, P=0.035, P=0.029 and P=0.011, respectively). High expression levels of ATP6V1B1 were also associated with poor overall and disease-free survival (P<0.001). Knockdown of ATP6V1B1 decreased cancer cell proliferation and colony-forming abilities (P<0.001) in vitro by inducing cell cycle arrest in G0/G1 phase. Significant upregulation of ATP6V1B1 was observed in EOC and the prognostic significance and association with chemotherapy resistance of ATP6V1B1 in EOC was demonstrated, rendering it an EOC-related biomarker for prognostic evaluation and chemotherapy resistance, as well as a potential therapeutic target for patients with EOC.

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Loren Eiseley and the Dancing Rat: Science as Autobiography

Cited by 13 publications

References 27 publications

Integration of taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes

Integration of taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes

Methane-Oxidizing Activity Enhances Sulfamethoxazole Biotransformation in a Benthic Constructed Wetland Biomat

High ATP6V1B1 expression is associated with poor prognosis and platinum‑based chemotherapy resistance in epithelial ovarian cancer

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