Rob Knight results 34
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Interpretable deep learning reveals spatiotemporal MRI features of brain aging that align with neurodegenerationNARA Subscribed
Cortical thinning and atrophy are hallmarks of brain aging that have been characterized using magnetic resonance imaging (MRI). Brain aging involves many neuroanatomic features whose effects on brain structure remain unexplored. To address this challenge, we trained interpretable deep neural networks (DNNs) to estimate brain age (BA) from T 1 -weighted ( T 1 w) MRI. By identifying MRI features unapparent to humans, DNNs can fi...
Interplay between colorectal cancer-related lifestyles and the gut microbiome: an exploratory analysis of metagenomic dataNARA Subscribed
Purpose The gut microbiome may modify the associations between lifestyle factors and colorectal cancer (CRC) risk, but their complex interplay, including the interactions between lifestyle factors, remain underexplored. We examined associations between CRC-related lifestyle patterns and gut microbiome diversity and composition in Finnish adults. Methods Our data included 1,228 adults aged 25–64 years from the National FINRISK/...
Alzheimer’s disease (AD) disproportionately affects women and carriers of the apolipoprotein E ε4 allele (APOE4), yet little is known about how sex and APOE interact to influence white matter (WM) integrity during disease progression. We integrated diffusion MRI and matched blood transcriptomic data to investigate these interactions and their underlying biological mechanisms. WM microstructure was quantified using diffusion te...
Background Host DNA depletion is a critical tool for accessing the microbiomes of samples that have a small amount of microbial DNA contained in a high host background. Of critical practical importance is the ability to identify microbial DNA sequences in frozen tissue specimens. Here, we compare four existing commercial methods and two newly introduced methods involving chromatin immunoprecipitation (ChIP) on frozen human and...
Predicting the progression of MCI and Alzheimer’s disease on structural brain integrity and other features with machine learningNARA Subscribed
Machine learning (ML) on structural MRI data shows high potential for classifying Alzheimer’s disease (AD) progression, but the specific contribution of brain regions, demographics, and proteinopathy remains unclear. Using Alzheimer’s Disease Neuroimaging Initiative (ADNI) data, we applied an extreme gradient-boosting algorithm and SHAP (SHapley Additive exPlanations) values to classify cognitively normal (CN) older adults, th...
Factors Influencing the Resilience of Created Tidal Marshes in the Fraser River Estuary, British ColumbiaNARA Subscribed
More than 100 tidal marsh creation projects were constructed throughout the Fraser River Estuary, British Columbia, Canada from the 1980s to present. Past studies described and evaluated many of these projects and found varied success, but the underlying factors that determine project outcomes remain uncertain. Combining field sampling, spatial analysis, and statistical modeling of plant communities, we aim to address this kno...
Predicting fungal infection rate and severity with skin‐associated microbial communities on amphibiansNARA Subscribed
Pathogen success (risk and severity) is influenced by host‐associated microbiota, but the degree to which variation in microbial community traits predict future infection presence/absence (risk) and load (severity) for the host is unknown. We conducted a time‐series experiment by sampling the skin‐associated bacterial communities of five amphibian species before and after exposure to the fungal pathogen, Batrachochytrium dendr...
The fish gut microbiome is impacted by a number of biological and environmental factors including fish feed formulations. Unlike mammals, vertical microbiome transmission is largely absent in fish and thus little is known about how the gut microbiome is initially colonized during hatchery rearing nor the stability throughout growout stages. Here we investigate how various microbial-rich surfaces from the built environment “BE”...
Major shifts in gut microbiota during development and its relationship to growth in ostrichesNARA Subscribed
The development of gut microbiota during ontogeny is emerging as an important process influencing physiology, immunity and fitness in vertebrates. However, knowledge of how bacteria colonize the juvenile gut, how this is influenced by changes in the diversity of gut bacteria and to what extent this influences host fitness, particularly in nonmodel organisms, is lacking. Here we used 16S rRNA gene sequencing to describe the suc...
Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopesNARA Subscribed
Summary The marine bacterium Vibrio fischeri is the monospecific symbiont of the Hawaiian bobtail squid, Euprymna scolopes , and the establishment of this association involves a number of signaling pathways and transcriptional responses between both partners. We report here the first full RNA‐Seq dataset representing host‐associated V. fischeri cells from colonized juvenile E. scolopes , as well as comparative transcriptomes u...
Identifying qualitative effects of different grazing types on below‐ground communities and function in a long‐term field experimentNARA Subscribed
Summary Herbivory is an important modulator of plant biodiversity and productivity in grasslands, but our understanding of herbivore‐induced changes on below‐ground processes and communities is limited. Using a long‐term (17 years) experimental site, we evaluated impacts of rabbit and invertebrate grazers on some soil functions involved in carbon cycling, microbial diversity, structure and functional composition. Both rabbit a...
Antifungal isolates database of amphibian skin‐associated bacteria and function against emerging fungal pathogensNARA Subscribed
Microbial symbionts of vertebrate skin have an important function in defense of the host against pathogens. In particular, the emerging chytrid fungus Batrachochytrium dendrobatidis , causes widespread disease in amphibians but can be inhibited via secondary metabolites produced by many different skin‐associated bacteria. Similarly, the fungal pathogens of terrestrial salamander eggs Mariannaea elegans and Rhizomucor variabili...
Major H istocompatibility C omplex class II b polymorphism influences gut microbiota composition and diversityNARA Subscribed
Animals harbour diverse communities of symbiotic bacteria, which differ dramatically among host individuals. This heterogeneity poses an immunological challenge: distinguishing between mutualistic and pathogenic members of diverse and host‐specific microbial communities. We propose that M ajor H istocompatibility class II ( MHC ) genotypes contribute to recognition and regulation of gut microbes, and thus, MHC polymorphism con...
Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)NARA Subscribed
Vertebrates' diets profoundly influence the composition of symbiotic gut microbial communities. Studies documenting diet‐microbiota associations typically focus on univariate or categorical diet variables. However, in nature individuals often consume diverse combinations of foods. If diet components act independently, each providing distinct microbial colonists or nutrients, we expect a positive relationship between diet diver...
The amphibian skin‐associated microbiome across species, space and life history stagesNARA Subscribed
Skin‐associated bacteria of amphibians are increasingly recognized for their role in defence against pathogens, yet we have little understanding of their basic ecology. Here, we use high‐throughput 16 S r RNA gene sequencing to examine the host and environmental influences on the skin microbiota of the cohabiting amphibian species A naxyrus boreas, P seudacris regilla, T aricha torosa and L ithobates catesbeianus from the C en...
Convergence of gut microbiomes in myrmecophagous mammalsNARA Subscribed
Mammals have diversified into many dietary niches. Specialized myrmecophagous (ant‐ and termite‐eating) placental mammals represent a textbook example of evolutionary convergence driven by extreme diet specialization. Armadillos, anteaters, aardvarks, pangolins and aardwolves thus provide a model system for understanding the potential role of gut microbiota in the convergent adaptation to myrmecophagy. Here, we expand upon pre...
Summary Bacteria readily colonize kitchen surfaces, and the exchange of microbes between humans and the kitchen environment can impact human health. However, we have a limited understanding of the overall diversity of these communities, how they differ across surfaces and sources of bacteria to kitchen surfaces. Here we used high‐throughput sequencing of the 16 S rRNA gene to explore biogeographical patterns of bacteria across...
Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan PlateauNARA Subscribed
Summary Continent‐scale biogeography has been extensively studied in soils and marine systems, but little is known about biogeographical patterns in non‐marine sediments. We used barcode pyrosequencing to quantify the effects of local geochemical properties and geographic distance for bacterial community structure and membership, using sediment samples from 15 lakes on the Tibetan Plateau (4–1670 km apart). Bacterial communiti...