D. Scanlan results 23
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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...
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...
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...
2‐Aminoethylphosphonate utilization in Pseudomonas putida BIRD ‐1 is controlled by multiple master regulatorsNARA Subscribed
Summary Bacteria possess various regulatory mechanisms to detect and coordinate a response to elemental nutrient limitation. In pseudomonads, the two‐component system regulators CbrAB, NtrBC and PhoBR, are responsible for regulating cellular response to carbon (C), nitrogen (N) and phosphorus (P) respectively. Phosphonates are reduced organophosphorus compounds produced by a broad range of biota and typified by a direct C‐P bo...
Summary Bacteriophages infecting Escherichia coli (coliphages) have been used as a proxy for faecal matter and water quality from a variety of environments. However, the diversity of coliphages that is present in seawater remains largely unknown, with previous studies largely focusing on morphological diversity. Here, we isolated and characterized coliphages from three coastal locations in the United Kingdom and Poland. Compar...
Thermoacclimation and genome adaptation of the membrane lipidome in marine SynechococcusNARA Subscribed
Summary The marine cyanobacteria of the genus Synechococcus are important primary producers, displaying a wide latitudinal distribution that is underpinned by diversification into temperature ecotypes. The physiological basis underlying these ecotypes is poorly known. In many organisms, regulation of membrane fluidity is crucial for acclimating to variations in temperature. Here, we reveal the detailed composition of the membr...
Parasite genetic distance and local adaptation in co‐evolving bacteria–bacteriophage populationsNARA Subscribed
Antagonistic co‐evolution between hosts and parasites can lead to local adaptation ( LA ) such that parasite fitness is greatest in sympatric hosts (or vice versa). The magnitude of LA typically increases with geographical distance, which is assumed to be because genetic (and hence phenotypic) distance increases with geographical distance. Here, we explicitly test the relationships between parasite genetic and phenotypic dista...
Summary Bacteria that inhabit the rhizosphere of agricultural crops can have a beneficial effect on crop growth. One such mechanism is the microbial‐driven solubilization and remineralization of complex forms of phosphorus (P). It is known that bacteria secrete various phosphatases in response to low P conditions. However, our understanding of their global proteomic response to P stress is limited. Here, exoproteomic analysis...
Summary A caryochloris marina is a symbiotic species of cyanobacteria that is capable of utilizing far‐red light. We report the characterization of the phages A ‐ HIS 1 and A ‐ HIS 2, capable of infecting A caryochloris . Morphological characterization of these phages places them in the family S iphoviridae . However, molecular characterization reveals that they do not show genetic similarity with any known siphoviruses. While...
Shedding new light on viral photosynthesisNARA Subscribed
Methanobactin and MmoD work in concert to act as the ‘copper‐switch’ in methanotrophsNARA Subscribed
Summary Biological oxidation of methane to methanol by aerobic bacteria is catalysed by two different enzymes, the cytoplasmic or soluble methane monooxygenase ( sMMO ) and the membrane‐bound or particulate methane monooxygenase ( pMMO ). Expression of MMOs is controlled by a ‘copper‐switch’, i.e. sMMO is only expressed at very low copper : biomass ratios, while pMMO expression increases as this ratio increases. Methanotrophs...
Genetic basis of infectivity evolution in a bacteriophageNARA Subscribed
Antagonistic coevolution between hosts and parasites is probably ubiquitous. However, very little is known of the genetic changes associated with parasite infectivity evolution during adaptation to a coevolving host. We followed the phenotypic and genetic changes in a lytic virus population (bacteriophage; phage Φ2) that coevolved with its bacterial host, Pseudomonas fluorescens SBW25. First, we show the rapid evolution of num...
From small hosts come big viruses: the complete genome of a second Ostreococcus tauri virus, OtV‐1NARA Subscribed
Summary Ostreococcus tauri virus (OtV‐1) is a large double‐stranded DNA virus and a prospective member of the family Phycodnaviridae , genus Prasinovirus . OtV‐1 infects the unicellular marine green alga O. tauri , the smallest known free‐living eukaryote. Here we present the 191 761 base pair genome sequence of OtV‐1, which has 232 putative protein‐encoding and 4 tRNA‐encoding genes. Approximately 31% of the viral gene produc...
Summary The vast majority of cyanophages isolated to date are cyanomyoviruses, a group related to bacteriophage T4. Comparative genome analysis of five cyanomyoviruses, including a newly sequenced cyanophage S‐RSM4, revealed a ‘core genome’ of 64 genes, the majority of which are also found in other T4‐like phages. Subsequent comparative genomic hybridization analysis using a pilot microarray showed that a number of ‘host’ gene...
Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales ( Alveolata )NARA Subscribed
Summary Syndiniales are a parasitic order within the eukaryotic lineage Dinophyceae ( Alveolata ). Here, we analysed the taxonomy of this group using 43655 18S rRNA gene sequences obtained either from environmental data sets or cultures, including 6874 environmental sequences from this study derived from Atlantic and Mediterranean waters. A total of 5571 out of the 43655 sequences analysed fell within the Dinophyceae . Both ba...
Culture‐independent analysis of the gut microbiota in colorectal cancer and polyposisNARA Subscribed
Summary A role for the intestinal microbiota is routinely cited as a potential aetiological factor in colorectal cancer initiation and progression. As the majority of bacteria in the gut are refractory to culture we investigated this ecosystem in subjects with colorectal cancer and with adenomatous polyposis who are at high risk of developing colorectal cancer, using culture‐independent methods. Twenty colorectal cancer and 20...
Elemental composition of single cells of various strains of marine Prochlorococcus and Synechococcus using X‐ray microanalysisNARA Subscribed
We measured the elemental composition of single cells from six strains of marine Prochlorococcus and two strains of marine Synechococcus by X‐ray microanalysis in the transmission electron microscope (TEM), which allows measurements of all major elements in cells without any fixation or staining. The mean carbon : volume ratios ranged from 136 to 280 fg µm −3 in Prochlorococcus and 138 to 290 fg µm −3 in Synechococcus . Using...
Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440NARA Subscribed
Summary Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomo...
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