David J. Scanlan results 28
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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...
Ecogenomics and limnological dynamics of a new Thiocapsa species blooming in the whole water column of a karstic lakeNARA Subscribed
Purple sulfur bacteria (PSB) of the family Chromatiaceae (Gammaproteobacteria) can perform chemo‐ and photo‐lithoautotrophy (through anoxygenic photosynthesis) in anoxic layers of freshwater stratified (including meromictic) lakes. This group has been extensively studied via physiological and ecological approaches, albeit their genomics has lagged behind. Here, we monitored a small, shallow, karstic lake, Lagunillo de Cardenil...
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...
Membrane lipid renovation in Pseudomonas aeruginosa ‐ implications for phage therapy?NARA Subscribed
Pseudomonas aeruginosa is an important Gram‐negative pathogen with intrinsic resistance to many clinically used antibiotics. It is particularly troublesome in nosocomial infections, immunocompromised patients, and individuals with cystic fibrosis. Antimicrobial resistance (AMR) is a huge threat to global health, with a predicted 10 million people dying from resistant infections by 2050. A promising therapy for combatting AMR i...
Choline and glycine betaine (GBT) are utilized as osmolytes to counteract osmotic stress, but also constitute important nutrient sources for many marine microbes. Bacterial catabolism of these substrates can then lead to the production of climate active trace gases such as methylamine and methane. Using radiotracers, we investigated prokaryotic choline/GBT uptake and determined biotic and abiotic factors driving these processe...
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 The Burkholderia cepacia complex is a group of Burkholderia species that are opportunistic pathogens causing high mortality rates in patients with cystic fibrosis. An environmental stress often encountered by these soil‐dwelling and pathogenic bacteria is phosphorus limitation, an essential element for cellular processes. Here, we describe cellular and extracellular proteins differentially regulated between phosphate‐d...
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...
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...
Comparative genomics and mutagenesis analyses of choline metabolism in the marine R oseobacter cladeNARA Subscribed
Summary Choline is ubiquitous in marine eukaryotes and appears to be widely distributed in surface marine waters; however, its metabolism by marine bacteria is poorly understood. Here, using comparative genomics and molecular genetic approaches, we reveal that the capacity for choline catabolism is widespread in marine heterotrophs of the marine Roseobacter clade ( MRC ). Using the model bacterium R uegeria pomeroyi , we confi...
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
Summary The exported protein fraction of an organism may reflect its life strategy and, ultimately, the way it is perceived by the outside world. Bioinformatic prediction of the exported pan‐proteome of P rochlorococcus and S ynechococcus lineages demonstrated that (i) this fraction of the encoded proteome had a much higher incidence of lineage‐specific proteins than the cytosolic fraction (57% and 73% homologue incidence resp...
Elemental composition of natural populations of key microbial groups in A tlantic watersNARA Subscribed
Summary Intracellular carbon ( C ), nitrogen ( N ) and phosphorus ( P ) content of marine phytoplankton and bacterioplankton can vary according to cell requirements or physiological acclimation to growth under nutrient limited conditions. Although such variation in macronutrient content is well known for cultured organisms, there is a dearth of data from natural populations that reside under a range of environmental conditions...
Multi‐locus sequence analysis, taxonomic resolution and biogeography of marine SynechococcusNARA Subscribed
Summary Conserved markers such as the 16S rRNA gene do not provide sufficient molecular resolution to identify spatially structured populations of marine Synechococcus , or ‘ecotypes’ adapted to distinct ecological niches. Multi‐locus sequence analysis targeting seven ‘core’ genes was employed to taxonomically resolve Synechococcus isolates and correlate previous phylogenetic analyses encompassing a range of markers. Despite t...
Basin‐scale distribution patterns of photosynthetic picoeukaryotes along an Atlantic Meridional TransectNARA Subscribed
Summary Photosynthetic picoeukaryotes (PPEs) of a size
Photosynthetic picoeukaryote community structure in the South East Pacific Ocean encompassing the most oligotrophic waters on EarthNARA Subscribed
Summary Photosynthetic picoeukaryotes (PPEs), comprising organisms
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...
Differential grazing of two heterotrophic nanoflagellates on marine Synechococcus strainsNARA Subscribed
Summary Grazing of heterotrophic nanoflagellates on marine picophytoplankton presents a major mortality factor for this important group of primary producers. However, little is known of the selectivity of the grazing process, often merely being thought of as a general feature of cell size and motility. In this study, we tested grazing of two heterotrophic nanoflagellates, Paraphysomonas imperforata and Pteridomonas danica , on...
Diel rhythmicity in amino acid uptake by ProchlorococcusNARA Subscribed
Summary The marine cyanobacterium Prochlorococcus , the most abundant phototrophic organism on Earth, numerically dominates the phytoplankton in nitrogen (N)‐depleted oceanic gyres. Alongside inorganic N sources such as nitrite and ammonium, natural populations of this genus also acquire organic N, specifically amino acids. Here, we investigated using isotopic tracer and flow cytometric cell sorting techniques whether amino ac...
Microbial control of phosphate in the nutrient‐depleted North Atlantic subtropical gyreNARA Subscribed
Summary Little is known about the dynamics of dissolved phosphate in oligotrophic areas of the world's oceans, where concentrations are typically in the nanomolar range. Here, we have budgeted phosphate uptake by the dominant microbial groups in order to assess the effect of the microbial control of this depleted nutrient in the North Atlantic gyre. Low concentrations (2.2 ± 1.2 nM) and rapid microbial uptake (2.1 ± 2.4 nM day...
We investigated the community structure of Synechococcus and Prochlorococcus along a transect in the Arabian Sea during September 2001. The transect spanned contrasting oceanic conditions, allowing investigation of the effects of both horizontal and vertical environmental gradients over relatively large spatial scales on picocyanobacterial population structure. We applied previously developed oligonucleotide probes specific fo...
Molecular analysis of photosynthetic picoeukaryote community structure along an Arabian Sea transectNARA Subscribed
We developed oligonucleotide probes, based on plastid 16S ribosomal DNA (rDNA) sequences, to target 10 different algal classes (Chlorarachniophyceae, Chrysophyceae, Cryptophyceae, Eustigmatophyceae, Pavlovophyceae, Pelagophyceae, Pinguiophyceae, Prasinophyceae [clade VI], Prymnesiophyceae, and Trebouxiophyceae), for use with dot blot hybridization technology. These class‐specific probes were then used to investigate the commun...