Aquatic conditions & bacterial communities as drivers of the decomposition of submerged remains.

Aquatic decomposition, as a forensic discipline, has been largely under-investigated as a consequence of the highly complex and influential variability of the water environment. The limitation to the adaptability of scenario specific results justifies the necessity for experimental research to increase our understanding of the aquatic environment and the development of post-mortem submersion interval (PMSI) methods of estimation. This preliminary research aims to address this contextual gap by assessing the variation in the bacterial composition of aquatic biofilms as explained by water parameter measurements over time, associated with clothed and bare decomposing remains. As part of three field investigations, a total of 9 still-born piglets (n = 3, per trial) were used as human analogues and were submerged bare or clothed in either natural cotton or synthetic nylon. Changes in the bacterial community composition of the water surrounding the submerged remains were assessed at 4 discrete time points post submersion (7, 14, 21 and 28 days) by 16 S rRNA gene Next Generation Sequencing analysis and compared to coinciding water parameter measurements (i.e. conductivity, total dissolved solids (TDS), salinity, pH, and dissolved oxygen (DO)). Bacterial diversity was found to change over time and relative to clothing type, where significant variation was observed between synthetic nylon samples and bare/cotton samples. Seasonality was a major driver of bacterial diversity, where substantial variation was found between samples collected in early winter to those collected in mid - late winter. Water parameter measures of pH, salinity and DO were identified to best explain the global bacterial community composition and their corresponding dynamic trajectory patterns overtime. Further investigation into bacterial community dynamics in accordance with varying environmental conditions could potentially lead to the determination of influential extrinsic factors that may drive bacterial activity in aquatic decomposition. Together with the identification of potential bacterial markers that complement the different stages of decomposition, this may provide a future approach to PMSI estimations.

Sex-Specific Retinal Anomalies Induced by Chronic Social Defeat Stress in Mice.

Major depressive disorder (MDD) is one of the most common consequences of chronic stress. Still, there is currently no reliable biomarker to detect individuals at risk to develop the disease. Recently, the retina emerged as an effective way to investigate psychiatric disorders using the electroretinogram (ERG). In this study, cone and rod ERGs were performed in male and female C57BL/6 mice before and after chronic social defeat stress (CSDS). Mice were then divided as susceptible or resilient to stress. Our results suggest that CSDS reduces the amplitude of both oscillatory potentials and a-waves in the rods of resilient but not susceptible males. Similar effects were revealed following the analysis of the cone b-waves, which were faster after CSDS in resilient mice specifically. In females, rod ERGs revealed age-related changes with no change in cone ERGs. Finally, our analysis suggests that baseline ERG can predict with an efficacy up to 71% the expression of susceptibility and resilience before stress exposition in males and females. Overall, our findings suggest that retinal activity is a valid biomarker of stress response that could potentially serve as a tool to predict whether males and females will become susceptible or resilient when facing CSDS.

Functional Contribution of the Medial Prefrontal Circuitry in Major Depressive Disorder and Stress-Induced Depressive-Like Behaviors.

Despite decades of research on the neurobiology of major depressive disorder (MDD), the mechanisms underlying its expression remain unknown. The medial prefrontal cortex (mPFC), a hub region involved in emotional processing and stress response elaboration, is highly impacted in MDD patients and animal models of chronic stress. Recent advances showed alterations in the morphology and activity of mPFC neurons along with profound changes in their transcriptional programs. Studies at the circuitry level highlighted the relevance of deciphering the contributions of the distinct prefrontal circuits in the elaboration of adapted and maladapted behavioral responses in the context of chronic stress. Interestingly, MDD presents a sexual dimorphism, a feature recognized in the molecular field but understudied on the circuit level. This review examines the recent literature and summarizes the contribution of the mPFC circuitry in the expression of MDD in males and females along with the morphological and functional alterations that change the activity of these neuronal circuits in human MDD and animal models of depressive-like behaviors.

Chronic Stress Induces Sex-Specific Functional and Morphological Alterations in Corticoaccumbal and Corticotegmental Pathways.

BACKGROUND: The medial prefrontal cortex (mPFC) is part of a complex circuit controlling stress responses by sending projections to different limbic structures including the nucleus accumbens (NAc) and ventral tegmental area (VTA). However, the impact of chronic stress on NAc- and VTA-projecting mPFC neurons is still unknown, and the distinct contribution of these pathways to stress responses in males and females is unclear. METHODS: Behavioral stress responses were induced by 21 days of chronic variable stress in male and female C57BL/6NCrl mice. An intersectional viral approach was used to label both pathways and assess the functional, morphological, and transcriptional adaptations in NAc- and VTA-projecting mPFC neurons in stressed males and females. Using chemogenetic approaches, we modified neuronal activity of NAc-projecting mPFC neurons to decipher their contribution to stress phenotypes. RESULTS: Chronic variable stress induced depressive-like behaviors in males and females. NAc- and VTA-projecting mPFC neurons exhibited sex-specific functional, morphological, and transcriptional alterations. The functional changes were more severe in females in NAc-projecting mPFC neurons, while males exhibited more drastic reductions in dendritic complexity in VTA-projecting mPFC neurons after chronic variable stress. Finally, chemogenetic overactivation of the corticoaccumbal pathway triggered anxiety and behavioral despair in both sexes, while its inhibition rescued the phenotype only in females. CONCLUSIONS: Our results suggest that stress responses in males and females result from pathway-specific changes in the activity of transcriptional programs controlling the morphological and synaptic properties of corticoaccumbal and corticotegmental pathways in a sex-specific fashion.

SUMOylation- and GAR1-Dependent Regulation of Dyskerin Nuclear and Subnuclear Localization.

The nuclear and subnuclear compartmentalization of the telomerase-associated protein and H/ACA ribonucleoprotein component dyskerin is an important although incompletely understood aspect of H/ACA ribonucleoprotein function. Four SUMOylation sites were previously identified in the C-terminal nuclear/nucleolar localization signal (N/NoLS) of dyskerin. We found that a cytoplasmic localized C-terminal truncation variant of dyskerin lacking most of the C-terminal N/NoLS represents an under-SUMOylated variant of dyskerin compared to wild-type dyskerin. We demonstrate that mimicking constitutive SUMOylation of dyskerin using a SUMO3 fusion construct can drive nuclear accumulation of this variant and that the SUMO site K467 in this N/NoLS is particularly important for the subnuclear localization of dyskerin to the nucleolus in a mature H/ACA complex assembly- and SUMO-dependent manner. We also characterize a novel SUMO-interacting motif in the mature H/ACA complex component GAR1 that mediates the interaction between dyskerin and GAR1. Mislocalization of dyskerin, either in the cytoplasm or excluded from the nucleolus, disrupts dyskerin function and leads to reduced interaction of dyskerin with the telomerase RNA. These data indicate a role for dyskerin C-terminal N/NoLS SUMOylation in regulating the nuclear and subnuclear localization of dyskerin, which is essential for dyskerin function as both a telomerase-associated protein and as an H/ACA ribonucleoprotein.

Investigating Both Mucosal Immunity and Microbiota in Response to Gut Enteritis in Yellowtail Kingfish.

The mucosal surfaces of fish play numerous roles including, but not limited to, protection against pathogens, nutrient digestion and absorption, excretion of nitrogenous wastes and osmotic regulation. During infection or disease, these surfaces act as the first line of defense, where the mucosal immune system interacts closely with the associated microbiota to maintain homeostasis. This study evaluated microbial changes across the gut and skin mucosal surfaces in yellowtail kingfish displaying signs of gut inflammation, as well as explored the host gene expression in these tissues in order to improve our understanding of the underlying mechanisms that contribute to the emergence of these conditions. For this, we obtained and analyzed 16S rDNA and transcriptomic (RNA-Seq) sequence data from the gut and skin mucosa of fish exhibiting different health states (i.e., healthy fish and fish at the early and late stages of enteritis). Both the gut and skin microbiota were perturbed by the disease. More specifically, the gastrointestinal microbiota of diseased fish was dominated by an uncultured Mycoplasmataceae sp., and fish at the early stage of the disease showed a significant loss of diversity in the skin. Using transcriptomics, we found that only a few genes were significantly differentially expressed in the gut. In contrast, gene expression in the skin differed widely between health states, in particular in the fish at the late stage of the disease. These changes were associated with several metabolic pathways that were differentially expressed and reflected a weakened host. Altogether, this study highlights the sensitivity of the skin mucosal surface in response to gut inflammation.

X-ray phase imaging with the unified modulated pattern analysis of near-field speckles at a laboratory source.

X-ray phase-contrast techniques are powerful methods for discerning features with similar densities, which are normally indistinguishable with conventional absorption contrast. While these techniques are well-established tools at large-scale synchrotron facilities, efforts have increasingly focused on implementations at laboratory sources for widespread use. X-ray speckle-based imaging is one of the phase-contrast techniques with high potential for translation to conventional x-ray systems. It yields phase-contrast, transmission, and dark-field images with high sensitivity using a relatively simple and cost-effective setup tolerant to divergent and polychromatic beams. Recently, we have introduced the unified modulated pattern analysis (UMPA) [Phys. Rev. Lett.118, 203903 (2017)PRLTAO0031-900710.1103/PhysRevLett.118.203903], which further simplifies the translation of x-ray speckle-based imaging to low-brilliance sources. Here, we present the proof-of-principle implementation of UMPA speckle-based imaging at a microfocus liquid-metal-jet x-ray laboratory source.

Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota.

BACKGROUND: The use of antibiotics in aquaculture is a common infection treatment and is increasing in some sectors and jurisdictions. While antibiotic treatment can negatively shift gut bacterial communities, recovery and examination of these communities in fish of commercial importance is not well documented. Examining the impacts of antibiotics on farmed fish microbiota is fundamental for improving our understanding and management of healthy farmed fish. This work assessed yellowtail kingfish (Seriola lalandi) skin and gut bacterial communities after an oral antibiotic combination therapy in poor performing fish that displayed signs of enteritis over an 18-day period. In an attempt to promote improved bacterial re-establishment after antibiotic treatment, faecal microbiota transplantation (FMT) was also administered via gavage or in the surrounding seawater, and its affect was evaluated over 15 days post-delivery. RESULTS: Antibiotic treatment greatly perturbed the global gut bacterial communities of poor-performing fish - an effect that lasted for up to 18 days post treatment. This perturbation was marked by a significant decrease in species diversity and evenness, as well as a concomitant increase in particular taxa like an uncultured Mycoplasmataceae sp., which persisted and dominated antibiotic-treated fish for the entire 18-day period. The skin-associated bacterial communities were also perturbed by the antibiotic treatment, notably within the first 3 days; however, this was unlike the gut, as skin microbiota appeared to shift towards a more 'normal' (though disparate) state after 5 days post antibiotic treatment. FMT was only able to modulate the impacts of antibiotics in some individuals for a short time period, as the magnitude of change varied substantially between individuals. Some fish maintained certain transplanted gut taxa (i.e. present in the FMT inoculum; namely various Aliivibrio related ASVs) at Day 2 post FMT, although these were lost by Day 8 post FMT. CONCLUSION: As we observed notable, prolonged perturbations induced by antibiotics on the gut bacterial assemblages, further work is required to better understand the processes/dynamics of their re-establishment following antibiotic exposure. In this regard, procedures like FMT represent a novel approach for promoting improved microbial recovery, although their efficacy and the factors that support their success requires further investigation.

Rapid detection of Bacillus ionophore cereulide in food products.

Cereulide is a toxic cyclic depsipeptide produced by certain strains of Bacillus cereus found in soil and food products. While some harmless strains of Bacillus are used as probiotic, others can cause nausea and vomiting, and represent an important food safety concern. Current detection methods are time consuming and do not necessarily detect toxic cereulide. Here, we developed a rapid protocol using Matrix Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) mass spectrometry that detects the toxin originating from a colony smear of B. cereus. The distinct molecular feature of the toxin peak at m/z 1,191 was clearly identified from bacterial extracts with a limit of detection (LOD) of 30 ng/mL. Final optimisation of the sample preparation was based on cereulide chelating cations to produce the alkali adduct [M + K]+ without the use of a MALDI matrix, and provided a 1,000-fold improvement of LOD with 30 pg/mL of cereulide. We evaluated the application of this method for the detection of cereulide in rice, milk, and different ready-to-eat meals. The proposed protocol is quick, easy and provides an improvement over conventional methods for the detection of B. cereus toxin.

Corticosterone mediated functional and structural plasticity in corticotropin-releasing hormone neurons.

Corticosteroid stress hormones drive a multitude of adaptations in the brain. Hypothalamic corticotropin-releasing hormone (CRH) neurons control the circulating levels of corticosteroid stress hormones in the body and are themselves highly sensitive to corticosteroids. CRH neurons have been shown to undergo various adaptions in response to acute stress hormone elevations. However, their structural and physiological changes under chronically elevated corticosterone are less clear. To address this, we determined the structural and functional changes in CRH neurons in the paraventricular nucleus of the hypothalamus following 14 days of corticosterone treatment. We find that prolonged corticosterone elevation reduces CRH neuron intrinsic excitability as measured by summation of subthreshold postsynaptic depolarisations and spiking output. We find that under normal conditions, CRH neurons have a relatively compact and simple dendritic arbor, with a low density of somatic and dendritic spines. Interestingly, the axon originated from a proximal dendrite close to the soma in approximately half of the CRH neurons reconstructed. While prolonged elevation in corticosterone levels did not result in any changes to gross dendritic morphology, it induced a significant reduction in both somatic and dendritic spine density. Together these data reveal the morphological features of hypothalamic CRH neurons and highlight their capacity to undergo functional and morphological plasticity in response to chronic corticosterone elevations. This article is part of the Special Issue entitled 'Hypothalamic Control of Homeostasis'.

Expectancies mediate the relationship between perceived injustice and return to work following whiplash injury: A 1-year prospective study.

BACKGROUND: Emerging evidence suggests that perceived injustice is a risk factor for work disability in individuals with whiplash injury. At present, however, little is known about the processes by which perceived injustice impacts on return to work. The purpose of this study was to examine whether expectancies mediated the relationship between perceived injustice and return to work in patients with whiplash injury. METHOD: One hundred and fifty-two individuals (81 men, 71 women) with a primary diagnosis of whiplash injury completed self-report measures of pain intensity, perceived injustice and return-to-work expectancies following admission to a rehabilitation programme. Work status was assessed 1 year after discharge. RESULTS: Consistent with previous research, high scores on a measure of perceived injustice were associated with prolonged work disability. Results indicated that high perceptions of injustice were associated with low return-to-work expectancies. Causal mediation analyses revealed that expectancies fully mediated the relationship between perceived injustice and return to work. CONCLUSION: The findings suggest that intervention techniques designed to target expectancies could improve return-to-work outcomes in patients with whiplash injury. Discussion addresses the processes by which expectancies might impact on return-to-work outcomes and the manner in which negative return-to-work expectancies might be modified through intervention. SIGNIFICANCE: The study confirms that expectancies are the mechanism through which perceived injustice impacts return to work following whiplash injury. The findings suggest that interventions designed to specifically target return-to-work expectancies might improve rehabilitation outcomes in patients with whiplash injury.

The Inner Workings of the Outer Surface: Skin and Gill Microbiota as Indicators of Changing Gut Health in Yellowtail Kingfish.

The mucosal surfaces and associated microbiota of fish are an important primary barrier and provide the first line of defense against potential pathogens. An understanding of the skin and gill microbial assemblages and the factors which drive their composition may provide useful insights into the broad dynamics of fish host-microbial relationships, and may reveal underlying changes in health status. This is particularly pertinent to cultivated systems whereby various stressors may led to conditions (like enteritis) which impinge on productivity. As an economically important species, we assessed whether the outer-surface bacterial communities reflect a change in gut health status of cultivated Yellowtail Kingfish (Seriola lalandi). Active bacterial assemblages were surveyed from RNA extracts from swabs of the skin and gills by constructing Illumina 16S rRNA gene amplicon libraries. Proteobacteria and Bacteroidetes were predominant in both the skin and gills, with enrichment of key ß-proteobacteria in the gills (Nitrosomonadales and Ferrovales). Fish exhibiting early stage chronic lymphocytic enteritis comprised markedly different global bacterial assemblages compared to those deemed healthy and exhibiting late stages of the disease. This corresponded to an overall loss of diversity and enrichment of Proteobacteria and Actinobacteria, particularly in the gills. In contrast, bacterial assemblages of fish with late stage enteritis were generally similar to those of healthy individuals, though with some distinct taxa. In conclusion, gut health status is an important factor which defines the skin and gill bacterial assemblages of fish and likely reflects changes in immune states and barrier systems during the early onset of conditions like enteritis. This study represents the first to investigate the microbiota of the outer mucosal surfaces of fish in response to underlying chronic gut enteritis, revealing potential biomarkers for assessing fish health in commercial aquaculture systems.

Lamb-type waves generated by a cylindrical bubble oscillating between two planar elastic walls.

The volume oscillation of a cylindrical bubble in a microfluidic channel with planar elastic walls is studied. Analytical solutions are found for the bulk scattered wave propagating in the fluid gap and the surface waves of Lamb-type propagating at the fluid-solid interfaces. This type of surface wave has not yet been described theoretically. A dispersion equation for the Lamb-type waves is derived, which allows one to evaluate the wave speed for different values of the channel height h. It is shown that for h<λt, where λt is the wavelength of the transverse wave in the walls, the speed of the Lamb-type waves decreases with decreasing h, while for h on the order of or greater than λt, their speed tends to the Scholte wave speed. The solutions for the wave fields in the elastic walls and in the fluid are derived using the Hankel transforms. Numerical simulations are carried out to study the effect of the surface waves on the dynamics of a bubble confined between two elastic walls. It is shown that its resonance frequency can be up to 50% higher than the resonance frequency of a similar bubble confined between two rigid walls.

Proteogenomic-based discovery of minor histocompatibility antigens with suitable features for immunotherapy of hematologic cancers.

Pre-clinical studies have shown that injection of allogeneic T cells primed against a single minor histocompatibility antigen (MiHA) could cure hematologic cancers (HC) without causing any toxicity to the host. However, translation of this approach in humans has been hampered by the paucity of molecularly defined human MiHAs. Using a novel proteogenomic approach, we have analyzed cells from 13 volunteers and discovered a vast repertoire of MiHAs presented by the most common HLA haplotype in European Americans: HLA-A*02:01;B*44:03. Notably, out of >6000 MiHAs, we have identified a set of 39 MiHAs that share optimal features for immunotherapy of HCs. These 'optimal MiHAs' are coded by common alleles of genes that are preferentially expressed in hematopoietic cells. Bioinformatic modeling based on MiHA allelic frequencies showed that the 39 optimal MiHAs would enable MiHA-targeted immunotherapy of practically all HLA-A*02:01;B*44:03 patients. Further extension of this strategy to a few additional HLA haplotypes would allow treatment of almost all patients.

A computational framework for ptychographic reconstructions.

Ptychography is now a well-established X-ray microscopy tool for synchrotron end-stations equipped with a scanning stage and a pixelated detector. Ptychographic phasing algorithms use information from coherent diffraction to deliver quantitative images of the specimen at a resolution higher than the scanning resolution. These algorithms have traditionally been implemented in software on a per-instrument basis in various degrees of user-friendliness and sophistication. Here, we present Ptypy, a ptychography software written with the intention to serve as a framework across the diverse sets of available instruments and usage cases. A distinctive feature of the software is its formalism, which provides a convenient abstraction of the physical model, thus allowing for concise algorithmic implementations and portability across set-up geometries. We give an overview of the supported usage cases, explain the abstraction layer and design principles, and provide a step-by-step guide describing how an algorithm may be realized in a concise and readable manner. The software capabilities are illustrated with reconstructions from visible light and X-ray data.

Quantitative X-ray phase-contrast microtomography from a compact laser-driven betatron source.

X-ray phase-contrast imaging has recently led to a revolution in resolving power and tissue contrast in biomedical imaging, microscopy and materials science. The necessary high spatial coherence is currently provided by either large-scale synchrotron facilities with limited beamtime access or by microfocus X-ray tubes with rather limited flux. X-rays radiated by relativistic electrons driven by well-controlled high-power lasers offer a promising route to a proliferation of this powerful imaging technology. A laser-driven plasma wave accelerates and wiggles electrons, giving rise to a brilliant keV X-ray emission. This so-called betatron radiation is emitted in a collimated beam with excellent spatial coherence and remarkable spectral stability. Here we present a phase-contrast microtomogram of a biological sample using betatron X-rays. Comprehensive source characterization enables the reconstruction of absolute electron densities. Our results suggest that laser-based X-ray technology offers the potential for filling the large performance gap between synchrotron- and current X-ray tube-based sources.

Ptychographic X-ray nanotomography quantifies mineral distributions in human dentine.

Bones are bio-composites with biologically tunable mechanical properties, where a polymer matrix of nanofibrillar collagen is reinforced by apatite mineral crystals. Some bones, such as antler, form and change rapidly, while other bone tissues, such as human tooth dentine, develop slowly and maintain constant composition and architecture for entire lifetimes. When studying apatite mineral microarchitecture, mineral distributions or mineralization activity of bone-forming cells, representative samples of tissue are best studied at submicrometre resolution while minimizing sample-preparation damage. Here, we demonstrate the power of ptychographic X-ray tomography to map variations in the mineral content distribution in three dimensions and at the nanometre scale. Using this non-destructive method, we observe nanostructures surrounding hollow tracts that exist in human dentine forming dentinal tubules. We reveal unprecedented quantitative details of the ultrastructure clearly revealing the spatially varying mineralization density. Such information is essential for understanding a variety of natural and therapeutic effects for example in bone tissue healing and ageing.

Designs and Tests of Shaking Coils to Reduce Screening Currents Induced in HTS Insert Coils for NMR Magnet.

Two types of shaking coils are focused on reducing screening currents induced in solenoid coils wound with high-temperature superconducting (HTS) tapes. One is a pair of copper shaking coils coaxially located inside and outside the HTS coil to apply an ac magnetic field in the axial direction. The other is an HTS shaking coil with notch located only outside the HTS coil to minimize the radial components of local ac fields applied to windings of the HTS coil as small as possible. It is found that the copper shaking coils yield the allowable amount of power dissipation in liquid helium. The effectiveness of the HTS shaking coil to reduce screening-current-induced fields generated by another magnetized HTS coil is also experimentally validated in liquid nitrogen using a commercially available coated conductor with narrow width.

Objective duplex ultrasound evaluation of the extracranial circulation in multiple sclerosis patients undergoing venoplasty of internal jugular vein stenoses: a pilot study.

OBJECTIVE: Chronic cerebrospinal venous insufficiency (CCSVI) is a condition associated with multiple sclerosis (MS) and manifested by stenoses in the extracranial venous circulation. There is a need for an objective non-invasive assessment of CCSVI that is able to accurately identify the location of stenoses and quantify physiological changes in blood flows following treatment. METHOD: A duplex ultrasound method, extracranial duplex ultrasound (ECDU), is described where the internal jugular veins (IJVs) and vertebral veins (VVs) were examined in the supine and sitting position before and after venoplasty in eight patients with clinically diagnosed MS. High-resolution B-mode imaging was used to detect obvious stenoses, intra-luminal membranes, valve abnormalities and vein wall thickening. ECDU was then used to assess blood flow including reflux. To assess obstruction, venous blood volume flows (BVFs) were taken bilaterally from the proximal (J1), mid (J2) and distal (J3) segments of the IJVs and the mid cervical VVs. To assess cerebral perfusion, bilateral BVF measurements were taken, in the supine position only, from the proximal internal carotid arteries (ICA) and mid cervical vertebral arteries (VA). The global arterial cerebral blood flow (GACBF) was then calculated as the sum of the ICA and VA measurements. RESULTS: Pre-venography ECDU detected IJV stenoses or obstruction in all patients. Venography findings were consistent with those of the pre-treatment ECDU with the exception of the detection of bilateral IJV stenoses in two patients diagnosed with unilateral IJV stenosis by ECDU. A significant improvement in GACBF was evident following venoplasty (p < 0.05). A trend to improvement in the post-treatment BVFs of both the IJVs and the mid cervical VVs was also observed. This improvement was most marked in the left VVs (p = 0.052) and the J2 segment of right IJVs (p < 0.05). CONCLUSION: The ECDU examination described provides a reliable objective assessment of IJV and VV stenoses and, with the use of BVFs, can quantify the degree of obstruction. These results support the use of ECDU as a non-invasive post-operative assessment of the success of venoplasty. The ability of ECDU to measure GACBF provides an additional parameter to monitor vascular pathophysiology in MS patients. The current findings support the view that the early symptomatic benefits observed after venoplasty for stenoses in the extracranial venous circulation may be the result of increased cerebral perfusion.