Testing the Optomotor Response in Sepia bandensis

Cephalopods (octopus, squid, and cuttlefish) have commonly been used as models to test visual function and camouflage due to their similarity in eye morphology with humans and because of their readily observable changes in body color in response to visual stimuli. Most studies have used a single species, Sepia officinalis, to make broad conclusions about camouflage and vision. However, these generalizations may not be applicable to all species. Here, I have examined visual function of the dwarf cuttlefish (Sepia bandensis), which differs from S. officinalis in habitat, geographic range, and size. Using the optomotor response, I quantified the minimum separable angle (MSA) of resolution, a behavioral measure of visual acuity, by recording cuttlefish movement in response to rotating black and white stripes of decreasing stripe width. The threshold of visual acuity for these experiments was a stripe width of 5mm and a MSA of 3.76°. These results indicate that S. bandensis has poorer visual acuity than S. officinalis (MSA 0.57°), and therefore, may be less able to resolve fine details in the environment. The ability to perceive these fine details enables animals to navigate, forage, and communicate with conspecifics. Future work should examine the behavioral ecology of S. bandensis to understand the biological and physical environmental context in which visual cues are used by this species

Nitrogen uptake strategies of edaphically specialized Bornean tree species

The association of tree species with particular soil types contributes to high b diversity in forests, but the mechanisms producing such distributions are still debated. Soil nitrogen (N) often limits growth and occurs in differentially available chemical forms. In a Bornean forest where tree species composition changes dramatically along a soil gradient varying in supplies of different N-forms, we investigated whether tree species’ N-uptake and soil specialization strategies covaried. We analyzed foliar 15N natural abundance for a total of 216 tree species on clay or sandy loam (the soils at the gradient’s extremes) and conducted a 15N-tracer experiment with nine specialist and generalist species to test whether species displayed flexible or differential uptake of ammonium and nitrate. Despite variation in ammonium and nitrate supplies and nearly 4 % difference in foliar δ15N between most soil specialists and populations of generalists on these soils, our 15N tracer experiment showed little support for the hypothesis that soil specialists vary in N-form use or the ratios in which they use these forms. Instead, our results indicate that these species possess flexible capacities to take up different inorganic N forms. Variation between soil specialists in uptake of different N forms is thus unlikely to cause the soil associations of tree species and high b diversity characteristic of this Bornean rain forest. Flexible uptake strategies would facilitate N-acquisition when supply rates of N-forms exhibit spatiotemporal variation and suggest that these species may be functionally redundant in their responses to N gradients and influences on ecosystem N-cycles

Adaptive Identification of Cortical and Subcortical Imaging Markers of Early Life Stress and Posttraumatic Stress Disorder

Posttraumatic stress disorder (PTSD) is a heterogeneous condition associated with a range of brain imaging abnormalities. Early life stress (ELS) contributes to this heterogeneity, but we do not know how a history of ELS influences traditionally defined brain signatures of PTSD. Here, we used a novel machine learning method – evolving partitions to improve classification (EPIC) – to identify shared and unique structural neuroimaging markers of ELS and PTSD in 97 combat-exposed military veterans. METHODS: We used EPIC with repeated cross-validation (CV) to determine how combinations of cortical thickness, surface area, and subcortical brain volumes could contribute to classification of PTSD (n = 40) versus controls (n = 57), and classification of ELS within the PTSD (ELS+ n = 16; ELS− n = 24) and control groups (ELS+ n = 16; ELS− n = 41). Additional inputs included intracranial volume, age, sex, adult trauma, and depression. RESULTS: On average, EPIC classified PTSD with 69% accuracy (SD = 5%), and ELS with 64% accuracy in the PTSD group (SD = 10%), and 62% accuracy in controls (SD = 6%). EPIC selected unique sets of individual features that classified each group with 75–85% accuracy in post hoc analyses; combinations of regions marginally improved classification from the individual atlas-defined brain regions. Across analyses, surface area in the right posterior cingulate was the only variable that was repeatedly selected as an important feature for classification of PTSD and ELS. CONCLUSIONS: EPIC revealed unique patterns of features that distinguished PTSD and ELS in this sample of combat-exposed military veterans, which may represent distinct biotypes of stress-related neuropathology

Investigating the physical properties of transiting hot Jupiters with the 1.5-m Kuiper Telescope

We present new photometric data of 11 hot Jupiter transiting exoplanets (CoRoT-12b, HAT-P-5b, HAT-P-12b, HAT-P-33b, HAT-P-37b, WASP-2b, WASP-24b, WASP-60b, WASP-80b, WASP-103b, XO-3b) in order to update their planetary parameters and to constrain information about their atmospheres. These observations of CoRoT-12b, HAT-P-37b and WASP-60b are the first follow-up data since their discovery. Additionally, the first near-UV transits of WASP-80b and WASP-103b are presented. We compare the results of our analysis with previous work to search for transit timing variations (TTVs) and a wavelength dependence in the transit depth. TTVs may be evidence of a third body in the system and variations in planetary radius with wavelength can help constrain the properties of the exoplanet's atmosphere. For WASP-103b and XO-3b, we find a possible variation in the transit depths that may be evidence of scattering in their atmospheres. The B-band transit depth of HAT-P-37b is found to be smaller than its near-IR transit depth and such a variation may indicate TiO/VO absorption. These variations are detected from 2-4.6$\sigma$, so follow-up observations are needed to confirm these results. Additionally, a flat spectrum across optical wavelengths is found for 5 of the planets (HAT-P-5b, HAT-P-12b, WASP-2b, WASP-24b, WASP-80b), suggestive that clouds may be present in their atmospheres. We calculate a refined orbital period and ephemeris for all the targets, which will help with future observations. No TTVs are seen in our analysis with the exception of WASP-80b and follow-up observations are needed to confirm this possible detection.Comment: 18 pages, 7 figures, 9 Tables. Light Curves available online. Accepted to MNRAS (2017 August 25

MRI T2 and T1ρ relaxation in patients at risk for knee osteoarthritis: A systematic review and meta-analysis

© 2019 The Author(s). Background: Magnetic resonance imaging (MRI) T2 and T1ρ relaxation are increasingly being proposed as imaging biomarkers potentially capable of detecting biochemical changes in articular cartilage before structural changes are evident. We aimed to: 1) summarize MRI methods of published studies investigating T2 and T1ρ relaxation time in participants at risk for but without radiographic knee OA; and 2) compare T2 and T1ρ relaxation between participants at-risk for knee OA and healthy controls. Methods: We conducted a systematic review of studies reporting T2 and T1ρ relaxation data that included both participants at risk for knee OA and healthy controls. Participant characteristics, MRI methodology, and T1ρ and T2 relaxation data were extracted. Standardized mean differences (SMDs) were calculated within each study. Pooled effect sizes were then calculated for six commonly segmented knee compartments. Results: 55 articles met eligibility criteria. There was considerable variability between scanners, coils, software, scanning protocols, pulse sequences, and post-processing. Moderate risk of bias due to lack of blinding was common. Pooled effect sizes indicated participants at risk for knee OA had lengthened T2 relaxation time in all compartments (SMDs from 0.33 to 0.74; p \u3c 0.01) and lengthened T1ρ relaxation time in the femoral compartments (SMD from 0.35 to 0.40; p \u3c 0.001). Conclusions: T2 and T1ρ relaxation distinguish participants at risk for knee OA from healthy controls. Greater standardization of MRI methods is both warranted and required for progress towards biomarker validation

ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries

This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of big data (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA\u27s activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors

The [4Fe4S] cluster of human DNA primase functions as a redox switch using DNA charge transport

DNA charge transport chemistry offers a means of long-range, rapid redox signaling. We demonstrate that the [4Fe4S] cluster in human DNA primase can make use of this chemistry to coordinate the first steps of DNA synthesis. Using DNA electrochemistry, we found that a change in oxidation state of the [4Fe4S] cluster acts as a switch for DNA binding. Single-atom mutations that inhibit this charge transfer hinder primase initiation without affecting primase structure or polymerization. Generating a single base mismatch in the growing primer duplex, which attenuates DNA charge transport, inhibits primer truncation. Thus, redox signaling by [4Fe4S] clusters using DNA charge transport regulates primase binding to DNA and illustrates chemistry that may efficiently drive substrate handoff between polymerases during DNA replication

ENIGMA and global neuroscience : a decade of large-scale studies of the brain in health and disease across more than 40 countries

CITATION: Thompson, Paul M. et al. 2020. ENIGMA and global neuroscience : a decade of large-scale studies of the brain in health and disease across more than 40 countries. Translational Psychiatry, 10:100, doi:10.1038/s41398-020-0705-1.The original publication is available at: https://www.nature.comThis review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of “big data” (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attentiondeficit/ hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA’s activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors.Publisher's versio

Response to Comments on “The [4Fe4S] cluster of human DNA primase functions as a redox switch using DNA charge transport”

Baranovskiy et al. and Pellegrini argue that, based on structural data, the path for charge transfer through the [4Fe4S] domain of primase is not feasible. Our manuscript presents electrochemical data directly showing charge transport through DNA to the [4Fe4S] cluster of a primase p58C construct and a reversible switch in the DNA-bound signal with oxidation/reduction, which is inhibited by mutation of three tyrosine residues. Although the dispositions of tyrosines differ in different constructs, all are within range for microsecond electron transfer

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types