Biology subjects

Fowler, J.

Publications and source records attributed to Fowler, J..

2 recordsLinked to original sources

bioRxiv2019

DNA and RNA-SIP reveal Nitrospira spp. as key drivers of nitrification in groundwater-fed biofilters

Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes and plays a central role in the global nitrogen cycle. Our earlier metagenomics, amoA-amplicon, and amoA-qPCR based investigations of groundwater-fed biofilters indicated a consistently high abundance of comammox Nitrospira, and we hypothesized that these non-classical nitrifiers drive ammonia-N oxidation. Hence, we used DNA and RNA stable isotope probing (SIP) coupled with 16S rRNA amplicon sequencing to identify the active members in the biofilter community when subject to a continuous supply of NH4+ or NO2- in the presence of 13C-HCO3- (labelled) or 12C-HCO3- (unlabelled). Allylthiourea (ATU) and sodium chlorate were added to inhibit autotrophic ammonia- and nitrite-oxidizing bacteria, respectively. Our results confirmed that lineage II Nitrospira dominated ammonium oxidation in the biofilter community. A total of 78 (8 in RNA-SIP and 70 in DNA-SIP) and 96 (25 in RNA-SIP and 71 in DNA-SIP) Nitrospira phylotypes (at 99% 16S rRNA sequence similarity) were identified as complete ammonia- and nitrite-oxidizing, respectively. We also detected significant HCO3- uptake by Acidobacteria subgroup10, Pedomicrobium, Rhizobactera, and Acidovorax under conditions that favoured ammonium oxidation. Canonical Nitrospira alone drove nitrite oxidation in the biofilter community, and activity of archaeal ammonia oxidizing taxa was not detected in the SIP fractions. This study provides the first in-situ evidence of ammonia oxidation by comammox Nitrospira in an ecologically relevant complex microbiome.

physiology↗

bioRxiv2019

Pan cancer patterns of allelic imbalance from chromosomal aberrations in 33 tumor types

Somatic copy number alterations (SCNAs), including deletions and duplications, serve as hallmarks of tumorigenesis. SCNAs may span entire chromosomes and typically result in deviations from an expected one-to-one ratio of alleles at heterozygous loci, leading to allelic imbalance (AI). The Cancer Genome Atlas (TCGA) reports SCNAs identified using a circular binary segmentation (CBS) algorithm, providing segment mean copy number estimates from Affymetrix single-nucleotide polymorphism DNA microarray total (log R ratio) intensities, but not allele-specific (\"B allele\") intensities that inform of AI. Here we seek to provide a TCGA-wide description of AI in tumor genomes, including AI induced by SCNAs and copy-neutral loss-of-heterozygosity (cnLOH), using a powerful haplotype-based method applied to allele-specific intensities. We present AI summaries for all 33 tumor sites and propose an automated adjustment procedure to improve calibration of existing SCNA calls in TCGA for tumors with high levels of aneuploidy where baseline intensities were difficult to establish without annotation of AI. Overall, 94% of tumor samples exhibited AI. Recurrent events included deletions of 17p, 9q, 3p, amplifications of 8q, 1q, 7p as well as mixed event types on 8p and 13q. The AI-based approach identified frequent cnLOH on 17p across multiple tumor sites, with additional site-specific cnLOH patterns. Our findings support the exploration of additional methods for robust automated inference procedures and to aid empirical discoveries across TCGA.

genomics↗