Biology subjects

Gould, T. J.

Publications and source records attributed to Gould, T. J..

6 recordsLinked to original sources

bioRxiv2026

Aviti Sequencing and Marker Gene Data Analysis

Accurate identification of microbial species in complex populations and communities relies on the isolation of representative marker 16S, ITS, and 18S sequences through the use of DNA extraction, PCR, and sequencing. Aviti sequencing has brought an improvement in the read quality and depth of marker gene sequencing technology. Quality scores exceeding Q40 representing highly accurate sequencing allows researchers to ask more questions of their marker gene data. However, this improvement in quality and throughput also brings with it a surprising increase in diversity of amplicon sequencing variants (ASVs) making further analysis and comparisons to previous studies on Illumina platforms challenging. This increased diversity causes downstream processing issues, including an over-reporting of chimeric ASVs. Here we identify this problem and put forward straightforward solutions to retain counts and reduce technically introduced diversity, as well as tying chimeric read identification to minimum parent distance. Through the use of synthetic mock samples, we discovered that erroneous ASVs are systematically substitution errors introduced by the upstream PCR methods. This error can be reduced significantly bioinformatically through clustering of ASVs within 99% similarity. Further we highlight technically introduced variation as a result of variable region length, sample misassignment, and sample biomass. Collectively, these results improve the similarity of Aviti and Illumina datasets for better comparisons of microbial studies from different platforms.

bioinformatics↗

bioRxiv2022

The Transcriptome of Acute Dehydration in Myeloid Leukemia Cells

Live human myeloid leukemia (HL-60/S4) cells exposed to acute hyperosmotic stress with sucrose undergo dehydration and cell shrinkage. Interphase chromatin and mitotic chromosomes congeal, and exhibit altered phase separation (demixing) of chromatin-associated proteins. To investigate concurrent changes in the transcriptome, we exposed exponentially growing HL-60/S4 cells to acute hyperosmotic stress ([~]600 milliOsmolar) for 30 and 60 minutes by addition of sucrose to the culture medium. We employed RNA-Seq of polyA mRNA to identify genes with significantly increased or decreased transcript levels relative to untreated control cells (i.e., differential gene expression). These identified genes were examined for over-representation of Gene Ontology (GO) terms. In hyperosmotically-stressed cells, multiple GO terms associated with transcription, translation, mitochondrial function and proteosome activity, as well as the gene set "replication-dependent histones", were over-represented among genes with increased transcript levels; whereas, genes with decreased transcript levels were over-represented in various GO terms for transcription repressors. The overall transcriptome profiles of these stressed cells suggest a rapid acquisition of cellular rebuilding, a futile homeostatic response, as these cells are ultimately doomed to a dehydrated death. "Do not go gentle into that good night Rage, rage against the dying of the light" Dylan Thomas (1914-1953)

cell biology↗

bioRxiv2022

Pyrfume: A Window to the World's Olfactory Data

Advances in theoretical understanding are frequently unlocked by access to large, diverse experimental datasets. Olfactory neuroscience and psychophysics remain years behind the other senses in part because rich datasets linking olfactory stimuli with their corresponding percepts, behaviors, and neural pathways underlying this transformation, remain scarce. Here we present a concerted effort to unlock and unify dozens of stimulus-linked olfactory datasets across species and modalities under a unified framework called Pyrfume. We present examples of how researchers might use Pyrfume to conduct novel analyses uncovering new principles, introduce trainees to the field, or construct benchmarks for machine olfaction.

neuroscience↗

bioRxiv2021

Synchrony and idiosyncrasy in the gut microbiome of wild primates

Human gut microbial dynamics are highly individualized, making it challenging to link microbiota to health and to design universal microbiome therapies. This individuality is typically attributed to variation in host genetics, diets, environments, and medications, but it could also emerge from fundamental ecological forces that shape microbiota more generally. Here we leverage extensive gut microbial time series from wild baboons--hosts who experience little interindividual dietary and environmental heterogeneity--to test whether gut microbial dynamics are synchronized across hosts or largely idiosyncratic. Despite their shared lifestyles, baboon microbiome dynamics were only weakly synchronized. The strongest synchrony occurred among baboons living in the same social group, likely because group members range over the same habitat and simultaneously encounter the same sources of food and water. However, this synchrony was modest compared to each hosts personalized dynamics. Indeed, host-specific factors, especially host identity, explained 10 times the deviance in longitudinal microbial dynamics, compared to factors shared across hosts. These results contribute to mounting evidence that highly idiosyncratic gut microbiomes are not an artifact of modern human environments, and that synchronizing forces in the gut microbiome (e.g., shared environments, diets, and microbial dispersal) are often not strong enough to overwhelm drivers of microbiome personalization, including host genetics, priority effects, horizontal gene transfer, and functional redundancy.

ecology↗

bioRxiv2020

Spatially organized genomic and physiological heterogeneity of the olfactory bulb mitral cell layer

Sensory inputs to the dorsal vs ventral olfactory bulb derive from distinct receptor families, and drive distinct behaviors. To address whether second-order OB neurons and circuits exhibit matching heterogeneity for input-specific readout, we clustered spatial expression profiles of >2,000 genes from the mitral cell layer (MCL). We observed clear dorsal and ventral clusters, together with dorsoventral differences in mitral cell physiology. Bulbar circuits may therefore be tuned for zone-specific computation.

neuroscience↗

bioRxiv2017

Variation in gut microbiota composition impacts host gene expression

Variation in gut microbiome is associated with wellness and disease in humans, yet the molecular mechanisms by which this variation affects the host are not well understood. A likely mechanism is through changing gene regulation in interfacing host epithelial cells. Here, we treated colonic epithelial cells with live microbiota from five healthy individuals and quantified induced changes in transcriptional regulation and chromatin accessibility in host cells. We identified over 5,000 host genes that change expression, including 588 distinct associations between specific taxa and host genes. The taxa with the strongest influence on gene expression alter the response of genes associated with complex traits. Using ATAC-seq, we show that a subset of these changes in gene expression are likely the result of changes in host chromatin accessibility and transcription factor binding induced by exposure to gut microbiota. We then created a manipulated microbial community with titrated doses of Collinsella, demonstrating that both natural and controlled microbiome composition leads to distinct, and predictable, gene expression profiles in host cells. Together, our results suggest that specific microbes play an important role in regulating expression of individual host genes involved in human complex traits. The ability to fine tune the expression of host genes by manipulating the microbiome suggests future therapeutic routes.

genomics↗